From 8e255b425a24981be611c27e7a93620255254889 Mon Sep 17 00:00:00 2001 From: Oreoluwa Akinola <101526668+dear-ore@users.noreply.github.com> Date: Tue, 18 Oct 2022 13:33:19 +0100 Subject: [PATCH 001/179] Update command to install graphviz (#307) The command to install graphviz should be "sudo apt-get install graphviz" not "sudo apt get install graphviz". Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com> --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 0646b614..63bdc9d3 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -106,7 +106,7 @@ The `dot` program from Graphviz is needed to render some of the diagrams. * For Debian/Ubuntu users: ```bash -sudo apt get install graphviz +sudo apt-get install graphviz ``` * For non-Debian/Ubuntu users, follow the directions at [the GraphViz download site](https://graphviz.org/download). ```bash From 828f41caaacb47325f35933d8af5cf2a7c2ce351 Mon Sep 17 00:00:00 2001 From: Ngumih Fien <72187339+Fienne@users.noreply.github.com> Date: Tue, 18 Oct 2022 14:12:48 +0100 Subject: [PATCH 002/179] YAML collection require a space after the colon (#301) --- src/topics/yaml-guide.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/topics/yaml-guide.md b/src/topics/yaml-guide.md index 6d05c6ed..6d12538e 100644 --- a/src/topics/yaml-guide.md +++ b/src/topics/yaml-guide.md @@ -25,7 +25,7 @@ You can skip this section if you are already comfortable with YAML. Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, -where whitespace after the `:` is optional. +where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - We use [_camelCase_][camelCase] for multi-word key names that have special meaning in the CWL specification From 2ee768c13c9ad66f626888545db3ea7d7a271c57 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 18 Oct 2022 17:26:32 +0200 Subject: [PATCH 003/179] add attribution for Bamiwo Aluko --- .zenodo.json | 2 +- AUTHORS.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index b36b3818..634d5e79 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -12,7 +12,7 @@ "name": "Andrew Jesaitis" }, { - "name": "bamiwoaluko" + "name": "Bamiwo Aluko" }, { "orcid": "https://orcid.org/0000-0002-6206-4638", diff --git a/AUTHORS.md b/AUTHORS.md index 49ca6978..ed256bfc 100644 --- a/AUTHORS.md +++ b/AUTHORS.md @@ -1,7 +1,7 @@ Thank you to the following contributors (in alphabetical order by user name): * Alain Domissy (@alaindomissy) * Andrew Jesaitis (@andrewjesaitis) -* @bamiwoaluko +* Bamiwo Alukoi (@bamiwoaluko) * Benjamin Carr (@BenjaminHCCarr) * Michele Mastropietro (@elehcim) * Emannuel Fernandes de Oliveira Carvalho (@emannuelOC) From f9e63daf90cb84fb23e5df678592528b451263e0 Mon Sep 17 00:00:00 2001 From: Oreoluwa Akinola <101526668+dear-ore@users.noreply.github.com> Date: Tue, 18 Oct 2022 16:29:25 +0100 Subject: [PATCH 004/179] It should be stated that comments start with # (#300) --- src/introduction/quick-start.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/introduction/quick-start.md b/src/introduction/quick-start.md index 98476fcf..2448de88 100644 --- a/src/introduction/quick-start.md +++ b/src/introduction/quick-start.md @@ -11,7 +11,7 @@ must be comfortable following instructions for the command-line. CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated -with comments: +with comments. Note that comments start with `#`: ```{literalinclude} /_includes/cwl/hello_world.cwl :language: cwl From 864f866dbd21b77acdff6ca8627606c18677717c Mon Sep 17 00:00:00 2001 From: Oreoluwa Akinola <101526668+dear-ore@users.noreply.github.com> Date: Wed, 19 Oct 2022 09:24:25 +0100 Subject: [PATCH 005/179] Changing command to create a virtual environment (#311) `python3 -m venv venv` instead of `python -m venv venv` --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 63bdc9d3..0d38ea9a 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -111,7 +111,7 @@ sudo apt-get install graphviz * For non-Debian/Ubuntu users, follow the directions at [the GraphViz download site](https://graphviz.org/download). ```bash # Create and activate a virtual environment -python -m venv venv +python3 -m venv venv source venv/bin/activate # update the version of pip, setuptools, and wheel (venv) pip install -U pip setuptools wheel From 3b0e1a6502ad0f23b74a7206805d8244e0df21a0 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Wed, 19 Oct 2022 15:32:39 +0200 Subject: [PATCH 006/179] fix typo --- AUTHORS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/AUTHORS.md b/AUTHORS.md index ed256bfc..c5c4d8e6 100644 --- a/AUTHORS.md +++ b/AUTHORS.md @@ -1,7 +1,7 @@ Thank you to the following contributors (in alphabetical order by user name): * Alain Domissy (@alaindomissy) * Andrew Jesaitis (@andrewjesaitis) -* Bamiwo Alukoi (@bamiwoaluko) +* Bamiwo Aluko (@bamiwoaluko) * Benjamin Carr (@BenjaminHCCarr) * Michele Mastropietro (@elehcim) * Emannuel Fernandes de Oliveira Carvalho (@emannuelOC) From 676582f58295fb99786c5804cc18c70a7f049f17 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Levai=20Mackenzie=20=C3=81gb=C3=A0r=C3=A0?= <97461848+Mackenzie-OO7@users.noreply.github.com> Date: Wed, 19 Oct 2022 14:42:02 +0100 Subject: [PATCH 007/179] Made modifications to pages (#299) * modified quick-start.md * Update prerequisites.md * Update basic-concepts.md * Update faq.md * Update yaml-guide.md Co-authored-by: Peter Amstutz --- src/faq.md | 67 +++++++++++++++++++++++++++--- src/introduction/basic-concepts.md | 25 +++++------ src/introduction/prerequisites.md | 41 +++++++++--------- src/topics/yaml-guide.md | 24 +++++------ 4 files changed, 106 insertions(+), 51 deletions(-) diff --git a/src/faq.md b/src/faq.md index 8e7f41a2..1b4419bb 100644 --- a/src/faq.md +++ b/src/faq.md @@ -40,10 +40,10 @@ outputs: ## Rename an input file -This example shows how you can change the name of an input file +This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another -step in a workflow and don't want to work with the default names that these +step in a workflow, and don't want to work with the default names that these files were given when they were created. ```yaml @@ -58,7 +58,7 @@ requirements: ## Rename an output file -This example shows how you can change the name of an output file +This example demonstrates how to change the name of an output file from the default name given to it by a tool: ```yaml @@ -79,6 +79,61 @@ outputs: outputEval: ${self[0].basename=inputs.otu_table_name; return self;} ``` +## Referencing a local script + +There are two ways to reference a local script: + +The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script without using `sh` or `bash` commands. + +Start with adding a _shebang_ at the top of your file: + +```{code-block} +#!/bin/bash +``` + +After that, make the script executable with the command `chmod +x scriptname.sh` + +Finally, modify your `PATH` to add the directory where your script is located. +(It is good practice to use `$HOME/bin` for storing your own scripts). + +```bash +export PATH=$PATH:/appropriate/directory +``` + +Now you can use `baseCommand: scriptname.sh` to run the script directly. + +```cwl +#!/bin/bash +cwlVersion: v1.0 +class: CommandLineTool +baseCommand: scriptname.sh +``` + +When you wish to share your work later, you can place your script in a software container in the Docker format. + +The second method involves including an input of `type: File` in the script itself: + +```cwl +class: CommandLineTool + +inputs: + my_script: + type: File + inputBinding: + position: 0 + + + # other inputs go here + +baseCommand: sh + +outputs: [] +``` + +```{note} +In CWL, everything must be directly stated. +``` + ## Setting `self`-based input bindings for optional inputs Currently, `cwltool` can't cope with missing optional inputs if their @@ -108,8 +163,8 @@ outputs: [] ## Model a "one-or-the-other" parameter -Below is an example of how -you can specify different strings to be added to a command line +Below is an example showing how +to specify different strings to be added to a command line, based on the value given to a Boolean parameter. ```yaml @@ -265,7 +320,7 @@ For command-line flags that are either **mutually exclusive** or **dependent**, ``` ## Setting Mutually Exclusive Parameters -In order to properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline javascript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value. +To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value. ```yaml steps: diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index 30459c8a..1c81fde7 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -1,10 +1,10 @@ # Basic Concepts -This section describes the basic concepts for users to get started working with +This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar -with workflow managers, YAML, and comfortable following instructions for the -command-line. The other sections of the user guide cover the same concepts but -in more detail. If you are already familiar with CWL or looking for more advanced +with workflow managers, YAML, and comfortable with following instructions for the +command-line. The other sections of the user guide cover the same concepts, but +in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section. ## The CWL specification @@ -24,7 +24,7 @@ is the {{ cwl_version }}. The specification version can have up to three numbers separated by `.`'s (dots). The first number is the major release, used for backward-incompatible changes like -the removal of deprecated features. The second is the minor release number, +the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification. @@ -37,7 +37,7 @@ the end of this section to [learn more](#learn-more) about it. ## Implementations An implementation of the CWL specification is any software written following -what is defined in a version of the specification document. Implementations may +what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses. @@ -47,6 +47,7 @@ in parallel across many nodes. % TODO: add a link to the Core Concepts -> Requirements section below? + ```{graphviz} :name: specification-and-implementations-graph :caption: CWL specification, implementations, and other tools. @@ -125,13 +126,13 @@ takes inputs and produces outputs like a command-line tool. The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. -The inputs of a workflow can be passed to any of its steps, and +The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow. Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation -not so commonly used. It is discussed in another section. +not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide. The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. @@ -149,12 +150,12 @@ runners. Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained -in detail in another section. +in detail in the [Requirements](../topics/requirements-and-hints.md) section. ## FAIR workflows > The FAIR principles have laid a foundation for sharing and publishing -> digital assets and, in particular, data. The FAIR principles emphasize +> digital assets, and in particular, data. The FAIR principles emphasize > machine accessibility and that all digital assets should be Findable, > Accessible, Interoperable, and Reusable. Workflows encode the methods > by which the scientific process is conducted and via which data are @@ -164,11 +165,11 @@ in detail in another section. > Workflows Community Initiative. CWL has roots in "make" and many similar tools that determine order of -execution based on dependencies between tasks. However, unlike "make", CWL +execution, based on dependencies between tasks. However, unlike "make", CWL tasks are isolated, and you must be explicit about your inputs and outputs. The benefit of explicitness and isolation are flexibility, portability, and -scalability: tools and workflows described with CWL can transparently leverage +scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors. diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index f739add6..20a654a4 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -1,18 +1,18 @@ # Prerequisites -% This page supersedes the old setup.md. We used that page as reference while +% This page supersedes the old setup page: setup.md. We used that page as a reference while % writing this documentation. The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, -`cwltool`. You can use another CWL compatible runner or workflow systems but the results and +`cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical). ```{admonition} CWL Implementations -There are many implementations of the CWL standards. Some are complete CWL runners, -others are plug-ins or extensions to workflow engines. We have a better +There are many implementations of the CWL standards. Some are complete CWL runners, while +others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section. ``` @@ -26,7 +26,7 @@ of the following options for your operating system: - Windows ```{note} -If you are using Windows, you will have to install the Windows Subsystem for Linux 2. +If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+). @@ -59,7 +59,7 @@ $ (venv) pip install cwltool ``` ```{note} -You can find the `cwl-runner` source code [here](https://github.com/common-workflow-language/cwltool/tree/main/cwlref-runner). +You can find the `cwl-runner` [source code](https://github.com/common-workflow-language/cwltool/tree/main/cwlref-runner) in the `cwltool` repository. Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`. ``` @@ -71,10 +71,10 @@ Let's use a simple CWl tool description `true.cwl` with `cwltool`. :name: true.cwl ``` -The `cwltool` command has an option to validate CWL tool and workflow descriptionss. It will parse the -CWL document, look for syntax errors, and verify that the descriptions are compliant -with the CWL standards, without running it. To validate CWL workflows (or even a -standalone command line tool description like above) pass the `--validate` option +The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the +CWL document, look for syntax errors, and verify that the workflow descriptions are compliant +with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a +standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command: ```{runcmd} cwltool --validate true.cwl @@ -91,7 +91,7 @@ You can run the CWL tool description by omitting the `--validate` option: ### cwl-runner Python module -`cwl-runner` is an implementation-agnostic alias for CWL Runners. +`cwl-runner` is an implementation-agnostic alias for CWL Runners. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` alias command then chooses the correct CWL runner. This is convenient for environments with multiple CWL runners. @@ -106,7 +106,7 @@ an alias for `cwltool` under the name `cwl-runner` $ pip install cwlref-runner ``` -Now you can validate and run your workflow with `cwl-runner` executable, +Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section. @@ -120,9 +120,9 @@ as in the previous section. :caption: Running `true.cwl` with `cwl-runner`. ``` -Another way to execute `cwl-runner` is invoking the file directly. For that, -the first thing you need to copy `true.cwl` workflow into a new file -`true_shebang.cwl` and include a special first line, a *shebang*: +Another way to execute `cwl-runner` is by invoking the file directly. For that, +the first thing you need to do is copy `true.cwl` workflow into a new file: +`true_shebang.cwl`, and include a special first line, a *shebang*: ```{literalinclude} /_includes/cwl/true_shebang.cwl :language: cwl @@ -139,7 +139,7 @@ Now you can make the file `true_shebang.cwl` executable with `chmod u+x`. $ chmod u+x true.cwl ``` -And finally you can execute it directly in the command-line and the program +And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file. @@ -152,9 +152,8 @@ rest of the file. The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is -considered a good practice to use `/usr/bin/env ` since it -looks for the `` program in the system `PATH`, instead of -using a hard-coded location. +considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` +looks for the `` program in the system `PATH`, ``` ## Text Editor @@ -164,7 +163,7 @@ an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs. There are extensions for Visual Studio Code and WebStorm that provide -integration with CWL, with customized syntax highlighting and better +integration with CWL, and features such as customized syntax highlighting and better auto-complete: - Visual Studio Code with the Benten (CWL) plugin - @@ -182,7 +181,7 @@ Follow the instructions in the Docker documentation to install it for your operating system: . You do not need to know how to write and build Docker containers. In the -rest of the user guide we will use existing Docker images for running +rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers. diff --git a/src/topics/yaml-guide.md b/src/topics/yaml-guide.md index 6d12538e..9475f83a 100644 --- a/src/topics/yaml-guide.md +++ b/src/topics/yaml-guide.md @@ -5,7 +5,7 @@ [YAML][yaml] is a file format designed to be readable by both computers and humans. -This guide introduces the features of YAML +This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files. ```{note} @@ -27,7 +27,7 @@ Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - -We use [_camelCase_][camelCase] for multi-word key names +[_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example: @@ -48,7 +48,7 @@ numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below). -Values may be wrapped in quotation marks +Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `"1234"` will be treated as a character string , while `1234` will be treated as an integer. @@ -80,7 +80,7 @@ be sure to add at least one space before the `#`! When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. -Called _maps_, +Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as "children") are written @@ -101,7 +101,7 @@ inputs: # this key has an object value prefix: -f ``` -The YAML above illustrates how you can build up complex nested object +The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, @@ -126,7 +126,7 @@ graph TD ## Arrays -In certain circumstances it is necessary to provide +In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. @@ -166,8 +166,8 @@ exclusive_parameters: ## JSON Style -YAML is based on [JavaScript Object Notation (JSON)][json] -and maps and arrays can also be defined in YAML using the native JSON syntax. +YAML is based on [JavaScript Object Notation (JSON)][json]. +Maps and arrays can also be defined in YAML using the native JSON syntax. For example: ```yaml @@ -182,13 +182,13 @@ inputs: {example_flag: {type: boolean, inputBinding: {position: 1, prefix: -f}}} ``` Native JSON can be useful -to indicate where a field is being left intentionally empty +in indicating where a field is intentionally left empty (such as `[]` for an empty array), -and where it makes more sense +as well as where it makes more sense for the values to be located on the same line -(such as when providing option flags and their values in a shell command). +(For example, when providing option flags and their values in a shell command). However, as the second example above shows, -it can severely affect the readability of a YAML file +it can severely affect the readability of a YAML file, and should be used sparingly. ## Reference From c6daa45ca6e871c73f665d87c98ee8f44d173e10 Mon Sep 17 00:00:00 2001 From: Oreoluwa Akinola <101526668+dear-ore@users.noreply.github.com> Date: Wed, 19 Oct 2022 14:59:50 +0100 Subject: [PATCH 008/179] Update prerequisites.md (#312) --- src/introduction/prerequisites.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index 20a654a4..d4ef8993 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -52,7 +52,7 @@ environment: :name: installing-cwltool-with-pip-and-venv :caption: Installing `cwltool` with `pip` and `venv`. -$ python -m venv venv +$ python3 -m venv venv $ source venv/bin/activate $ (venv) pip install -U pip setuptools wheel $ (venv) pip install cwltool From 8b5809d87c54120ea67799bc1e0f7aa1b76d61dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Levai=20Mackenzie=20=C3=81gb=C3=A0r=C3=A0?= <97461848+Mackenzie-OO7@users.noreply.github.com> Date: Wed, 19 Oct 2022 15:09:09 +0100 Subject: [PATCH 009/179] fixed typos (#314) * fixed typos and punctuation errors * Update best-practices.md * Update best-practices.md Co-authored-by: Peter Amstutz --- src/topics/best-practices.md | 24 ++++++++++++------------ src/topics/operations.md | 6 +++--- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/src/topics/best-practices.md b/src/topics/best-practices.md index fe0d663f..4c2e18ab 100644 --- a/src/topics/best-practices.md +++ b/src/topics/best-practices.md @@ -1,8 +1,8 @@ # Best Practices -Below are a set of recommended good practices to keep in mind when writing a +The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines -are presented for consideration on a scale of usefulness: more is better, not +are presented for consideration on a scale of usefulness: although more is better, not all are required. - No `type: string` parameters for names of input or reference @@ -10,15 +10,15 @@ all are required. - A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this - document. For example if the workflow is shared publicly, licensing terms have to be clear so that - a future user can understand under what conditions they can run the workflow, modify it and/or - combine it with other workflows. For this reason please consider including a license field in the + document. For example, if the workflow is shared publicly, licensing terms must be clear so that + a future user understands under what conditions they can run the workflow, modify it and/or + combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]. If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. - Construct the metadata field for the licence by providing a URL of the form + Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license. @@ -38,7 +38,7 @@ all are required. [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md). - Include [attribution information][license-example] for the author(s) of - the CWL tool or workflow description. Use unambiguous identifiers like + the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]. - In tool descriptions, list dependencies using short name(s) under @@ -60,7 +60,7 @@ all are required. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: "https://www.iana.org/assignments/media-types/" }`. [Full IANA media type list][iana-types] (also known as MIME types). For - non-bioinformatics tools use or build an appropriate ontology/controlled + non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it. - Mark all input and output `File`s that are read from or written to in a @@ -68,15 +68,15 @@ all are required. - Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your - tool descriptions with options that you don't need/use. + tool descriptions with options that you don't need or use. - Custom types should be defined with one external YAML per type definition for re-use. -- Include a top level short `label` summarising the tool/workflow. +- Include a top-level short `label` summarising the tool/workflow. -- If useful, include a top level `doc` as well. This should provide a - longer, more detailed description than was provided in the top level `label` +- If useful, include a top-level `doc` as well. This should provide a + longer, more detailed description than was provided in the top-level `label` (see above). - Use `type: enum` instead of `type: string` for elements with a fixed diff --git a/src/topics/operations.md b/src/topics/operations.md index 19f8c817..b6afca2a 100644 --- a/src/topics/operations.md +++ b/src/topics/operations.md @@ -1,6 +1,6 @@ # Operations -Operation is a type of CWL process just like a workflow, a command line tool, or +An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed. @@ -14,7 +14,7 @@ you are ready to submit the workflow to a CWL runner: ``` The `uppercase` step of the workflow is an operation. It can be used like -use a command line tool or an expression. You can also plot it with the +a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`: ```{runcmd} cwltool --print-dot operations.cwl @@ -52,7 +52,7 @@ style=dashed; } ``` -If you try running it with `cwltool` the command will fail, since `cwltool` +If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it: ```{runcmd} cwltool operations.cwl --message Hello From d269169899cd7dfa6d915494bf9f3417b2861593 Mon Sep 17 00:00:00 2001 From: Smyja Date: Wed, 19 Oct 2022 16:11:59 +0100 Subject: [PATCH 010/179] Docker Clarity (#313) * docker clarity * typo fix Co-authored-by: Peter Amstutz --- src/faq.md | 4 ++-- src/topics/using-containers.md | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/faq.md b/src/faq.md index 1b4419bb..fb50e9ad 100644 --- a/src/faq.md +++ b/src/faq.md @@ -246,7 +246,7 @@ inputs: ## Enum Inputs ⚜️ -For command-line flags that require a specific input as the argument, an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.** +For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.** ```yaml Format: @@ -266,7 +266,7 @@ Format: ## Record Inputs 📀 -For command-line flags that are either **mutually exclusive** or **dependent**, a special record type can be defined. You can also specify null here to create optional inputs. +For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs. ```yaml #Using record inputs to create mutually exclusive inputs diff --git a/src/topics/using-containers.md b/src/topics/using-containers.md index 903e6fdc..90a3f0bb 100644 --- a/src/topics/using-containers.md +++ b/src/topics/using-containers.md @@ -41,7 +41,7 @@ hints: dockerPull: node:slim ``` -`baseCommand: node` tells CWL that we will be running this command in a container. We +`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, @@ -49,7 +49,7 @@ the name of the container image (you can even specify the tag, which is good ide best practices when using containers for reproducible research). In this case we have used a container called `node:slim`. -Provide a "hello.js" and invoke `cwltool` providing the tool description and the +Create a Javascript file named "hello.js" and invoke `cwltool` providing the tool description and the input object on the command line: ```{literalinclude} /_includes/cwl/using-containers/hello.js From e24e362a8662314cca337c1ff7ac28401df899c4 Mon Sep 17 00:00:00 2001 From: Ngumih Fien <72187339+Fienne@users.noreply.github.com> Date: Wed, 19 Oct 2022 18:49:44 +0100 Subject: [PATCH 011/179] format the arrangement of the license terms (#317) Co-authored-by: Peter Amstutz --- LICENSE.md | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/LICENSE.md b/LICENSE.md index d3eb47a0..4345a729 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -28,16 +28,14 @@ Under the following terms: so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. -**No additional restrictions**---You may not apply legal terms or +* **No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that: -Notices: - -* You do not have to comply with the license for elements of the + * You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation. -* No warranties are given. The license may not give you all of the + * No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material. From debd2948da10f9cc9eda88679b22e113910b60fc Mon Sep 17 00:00:00 2001 From: khaiyra <44167602+khaiyra@users.noreply.github.com> Date: Thu, 20 Oct 2022 14:41:17 +0100 Subject: [PATCH 012/179] Update prerequisites.md (#320) --- src/introduction/prerequisites.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index d4ef8993..481caade 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -63,7 +63,7 @@ You can find the `cwl-runner` [source code](https://github.com/common-workflow-l Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`. ``` -Let's use a simple CWl tool description `true.cwl` with `cwltool`. +Let's use a simple CWL tool description `true.cwl` with `cwltool`. ```{literalinclude} /_includes/cwl/true.cwl :language: yaml From aaef4452d3ea296cafd72c9bf79d178a52caeef3 Mon Sep 17 00:00:00 2001 From: Ngumih Fien <72187339+Fienne@users.noreply.github.com> Date: Thu, 20 Oct 2022 20:04:21 +0100 Subject: [PATCH 013/179] edit hd5 to hdf5 and fix broken link (#323) --- src/topics/custom-types.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/topics/custom-types.md b/src/topics/custom-types.md index f0b59caf..e4c47a59 100644 --- a/src/topics/custom-types.md +++ b/src/topics/custom-types.md @@ -7,7 +7,7 @@ customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly. The example below is a CWL description of the [biom convert format][biom] tool for -converting a standard biom table file to hd5 format. +converting a standard biom table file to hdf5 format. ```{literalinclude} /_includes/cwl/custom-types/custom-types.cwl :language: cwl @@ -21,7 +21,7 @@ converting a standard biom table file to hd5 format. :name: custom-types.yml ``` -___Note:___ To follow the example below, you need to [download the example input file](https://raw.githubusercontent.com/common-workflow-language/user_guide/main/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`: +___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`: ```{code-block} console $ wget https://github.com/common-workflow-language/user_guide/raw/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom @@ -48,7 +48,7 @@ the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that -tells the tool to create an OTU table in hd5 format. +tells the tool to create an OTU table in hdf5 format. The contents of the YAML file describing the custom type are given below: From 8b034bb170a0d7424189fb7a3360ce42fadc5e86 Mon Sep 17 00:00:00 2001 From: MARVEBUKA <109809277+MARVEBUKA@users.noreply.github.com> Date: Mon, 24 Oct 2022 18:39:26 +0100 Subject: [PATCH 014/179] updated visualization command (#326) --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 0d38ea9a..3db281a4 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -119,7 +119,7 @@ source venv/bin/activate (venv) pip install ".[all]" # Create the HTML to visualize locally (venv) make html -(venv) open _build/index.html +(venv) open _build/html/index.html # Or you can start a serve that watches for local file changes (venv) make watch # Open in your browser From 8e9dee1316bc5dbf33980b5513791563aa0d810d Mon Sep 17 00:00:00 2001 From: bamiwoaluko <115556244+bamiwoaluko@users.noreply.github.com> Date: Mon, 24 Oct 2022 18:53:00 +0100 Subject: [PATCH 015/179] Update basic-concepts.md (#319) corrected typos, corrected punctuations, rephrased sentences, added a link where required Co-authored-by: Peter Amstutz --- src/introduction/basic-concepts.md | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index 1c81fde7..a7169c43 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -22,7 +22,7 @@ The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}. -The specification version can have up to three numbers separated by `.`'s (dots). +The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number @@ -109,10 +109,10 @@ behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}: -- A command-line tool; -- An expression tool; -- An operation; -- And a workflow. +- A command-line tool. +- An expression tool. +- An operation. +- A workflow. {{ CWL_PROCESSING_UNITS_GRAPH }} @@ -121,7 +121,7 @@ A command-line tool is a wrapper for a command-line utility like `echo`, An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common -parts of a workflow execution into reusable JavaScript code, that +parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool. The workflow is a process that contains steps. Steps can be other @@ -138,9 +138,9 @@ The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance: -- `InlineJavascriptWorkflow`, enables JavaScript in expressions. -- `SubworkflowFeatureRequirement`, enables nested workflows. -- `InitialWorkDirRequirement`, controls staging files in the input directory. +- `InlineJavascriptWorkflow` - enables JavaScript in expressions. +- `SubworkflowFeatureRequirement` - enables nested workflows. +- `InitialWorkDirRequirement` - controls staging files in the input directory. Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the @@ -159,8 +159,8 @@ in detail in the [Requirements](../topics/requirements-and-hints.md) section. > machine accessibility and that all digital assets should be Findable, > Accessible, Interoperable, and Reusable. Workflows encode the methods > by which the scientific process is conducted and via which data are -> created. It is thus important that workflows both support the creation -> of FAIR data and themselves adhere to the FAIR principles. +> created. It is thus important that workflows support the creation +> of FAIR data and adhere to the FAIR principles. > — [FAIR Computational Workflows](https://workflows.community/groups/fair/), > Workflows Community Initiative. From 217d7d8713c633a43da17fc27d0d520164af9dbc Mon Sep 17 00:00:00 2001 From: khaiyra <44167602+khaiyra@users.noreply.github.com> Date: Mon, 24 Oct 2022 19:28:29 +0100 Subject: [PATCH 016/179] Update basic-concepts.md (#324) Co-authored-by: Peter Amstutz --- src/introduction/basic-concepts.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index a7169c43..086f8c11 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -124,16 +124,16 @@ be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool. +Operation is an abstract process that also takes inputs, produces +outputs, and can be used in a workflow. But it is a special operation +not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide. + The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow. -Operation is an abstract process that also takes inputs, produces -outputs, and can be used in a workflow. But it is a special operation -not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide. - The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance: From 0b55dc767ecd8b288d3ffa3e6f24afbf59864f5f Mon Sep 17 00:00:00 2001 From: MARVEBUKA <109809277+MARVEBUKA@users.noreply.github.com> Date: Mon, 24 Oct 2022 21:48:26 +0100 Subject: [PATCH 017/179] Updated titles to use consistent capitalization (#330) Co-authored-by: Peter Amstutz --- CONTRIBUTING.md | 2 +- src/faq.md | 20 ++++++++++---------- src/introduction/basic-concepts.md | 6 +++--- src/introduction/prerequisites.md | 6 +++--- src/introduction/quick-start.md | 4 ++-- src/topics/expressions.md | 2 +- 6 files changed, 20 insertions(+), 20 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 3db281a4..7298c7de 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -148,7 +148,7 @@ are still working after the change. Use “tool description” not “tool wrapper” for describing the first argument given to the `cwl-runner` or `cwltool` commands. -### Code examples +### Code Examples To include code into a Markdown file you have two options. For external files use the following command: diff --git a/src/faq.md b/src/faq.md index fb50e9ad..6da7efa5 100644 --- a/src/faq.md +++ b/src/faq.md @@ -8,7 +8,7 @@ :backlinks: "top" ``` -## Non "`File`" types using `evalFrom` +## Non "`File`" Types Using `evalFrom` ```yaml cwlVersion: v1.0 # or v1.1 @@ -38,7 +38,7 @@ outputs: outputEval: $(self[0].contents) ``` -## Rename an input file +## Rename an Input File This example demonstrates how to change the name of an input file as part of a tool description. @@ -56,7 +56,7 @@ requirements: entryName: $(inputs.src1.basename)_custom_extension ``` -## Rename an output file +## Rename an Output File This example demonstrates how to change the name of an output file from the default name given to it by a tool: @@ -79,7 +79,7 @@ outputs: outputEval: ${self[0].basename=inputs.otu_table_name; return self;} ``` -## Referencing a local script +## Referencing a Local Script There are two ways to reference a local script: @@ -134,7 +134,7 @@ outputs: [] In CWL, everything must be directly stated. ``` -## Setting `self`-based input bindings for optional inputs +## Setting `self`-based Input Bindings for Optional Inputs Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. @@ -161,7 +161,7 @@ baseCommand: echo outputs: [] ``` -## Model a "one-or-the-other" parameter +## Model a "one-or-the-other" Parameter Below is an example showing how to specify different strings to be added to a command line, @@ -184,7 +184,7 @@ baseCommand: echo outputs: [] ``` -## Connect a solo value to an input that expects an array of that type +## Connect a Solo Value to an Input that Expects an Array of that Type Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with @@ -355,7 +355,7 @@ input: My String: $(input.stringvalue) ``` -## `cwltool` errors due to filenames with space characters inside +## `cwltool` Errors due to Filenames with Space Characters Inside `cwltool` does not allow some characters in filenames by default. @@ -369,7 +369,7 @@ Invalid filename: 'a space is here.txt' contains illegal characters If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`. -## CWL Parameter Reference error due to hyphen in input identifier +## CWL Parameter Reference Error due to Hyphen in Input Identifier If `cwltool --validate` returns valid @@ -446,7 +446,7 @@ The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards. -## Debug JavaScript expressions +## Debug JavaScript Expressions You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index 086f8c11..33f1ced7 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -7,7 +7,7 @@ command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section. -## The CWL specification +## The CWL Specification ```{include} /_includes/what-is-cwl.md ``` @@ -152,7 +152,7 @@ Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section. -## FAIR workflows +## FAIR Workflows > The FAIR principles have laid a foundation for sharing and publishing > digital assets, and in particular, data. The FAIR principles emphasize @@ -175,7 +175,7 @@ vendors. `cwltool` also uses the PROV-O standard ontology for data provenance. -## Learn more +## Learn More - Semantic Versioning - - The CWL Specification page in the CWL website: diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index 481caade..94908733 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -32,7 +32,7 @@ for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+). ``` -## CWL runner +## CWL Runner % https://github.com/common-workflow-language/user_guide/issues/166 % https://github.com/common-workflow-language/user_guide/issues/64 @@ -89,7 +89,7 @@ You can run the CWL tool description by omitting the `--validate` option: :caption: Running `true.cwl` with `cwltool`. ``` -### cwl-runner Python module +### Cwl-runner Python Module `cwl-runner` is an implementation-agnostic alias for CWL Runners. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` @@ -191,7 +191,7 @@ Singularity. You can also use alternative container registries for pulling images. ``` -## Learn more +## Learn More - The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts. - The Python `venv` module: diff --git a/src/introduction/quick-start.md b/src/introduction/quick-start.md index 2448de88..84d52dc9 100644 --- a/src/introduction/quick-start.md +++ b/src/introduction/quick-start.md @@ -29,7 +29,7 @@ for the sake of simplicity, we are using the term “workflow” here. You will more about this in the [basic concepts](basic-concepts.md) section. ``` -## Installing a CWL runner +## Installing a CWL Runner `cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the @@ -91,7 +91,7 @@ a requirement. You can choose any name for your workflows and Inputs Object files. ``` -## Learn more +## Learn More Continue reading the next sections of this User Guide! - [List of CWL Implementations](https://www.commonwl.org/implementations). diff --git a/src/topics/expressions.md b/src/topics/expressions.md index eebc027b..4c034a7f 100644 --- a/src/topics/expressions.md +++ b/src/topics/expressions.md @@ -113,7 +113,7 @@ only in certain fields. These are: [file-prop]: https://www.commonwl.org/v1.0/CommandLineTool.html#File -## Using external libraries and inline JavaScript code with `expressionLib` +## Using External Libraries and Inline JavaScript Code with `expressionLib` The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript From 7b71012f6d286fbea44e052a54a1d5977eb9f3ca Mon Sep 17 00:00:00 2001 From: khaiyra <44167602+khaiyra@users.noreply.github.com> Date: Fri, 28 Oct 2022 16:16:00 +0100 Subject: [PATCH 018/179] Network Access documentation (#335) * Update basic-concepts.md * Update command-line-tool.md --- src/topics/command-line-tool.md | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/src/topics/command-line-tool.md b/src/topics/command-line-tool.md index 2977e3a1..1aea6311 100644 --- a/src/topics/command-line-tool.md +++ b/src/topics/command-line-tool.md @@ -63,3 +63,23 @@ and in the [Outputs](../topics/outputs.md) sections. % % - Spaces in commands https://github.com/common-workflow-language/user_guide/issues/39 % - Arguments (tell the reader the different use cases for arguments and inputs, tell them there is a section about inputs) + + +## Network Access +This indicates whether a process requires outgoing IPv4/IPv6 network access. +If a command-line tool is written manually in CWL v1.1+, there is a need to +specify when network access is required. + +```cwl +cwlVersion: v1.2 +class: CommandLineTool + +requirements: + NetworkAccess: + networkAccess: true +``` + +```{note} +CWL v1.0 command-line tools that are upgraded to v1.1 +or v1.2 get Network Access automatically. +``` From ea6ba8e271e85613f4aff849f3c959128dadfdb4 Mon Sep 17 00:00:00 2001 From: "lgtm-com[bot]" <43144390+lgtm-com[bot]@users.noreply.github.com> Date: Wed, 16 Nov 2022 15:20:56 +0100 Subject: [PATCH 019/179] Add CodeQL workflow for GitHub code scanning (#345) Co-authored-by: LGTM Migrator --- .github/workflows/codeql.yml | 42 ++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 .github/workflows/codeql.yml diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml new file mode 100644 index 00000000..c880dca1 --- /dev/null +++ b/.github/workflows/codeql.yml @@ -0,0 +1,42 @@ +name: "CodeQL" + +on: + push: + branches: [ "main", "gh-pages", "release" ] + pull_request: + branches: [ "main" ] + schedule: + - cron: "59 14 * * 5" + +jobs: + analyze: + name: Analyze + runs-on: ubuntu-latest + permissions: + actions: read + contents: read + security-events: write + + strategy: + fail-fast: false + matrix: + language: [ javascript, python ] + + steps: + - name: Checkout + uses: actions/checkout@v3 + + - name: Initialize CodeQL + uses: github/codeql-action/init@v2 + with: + languages: ${{ matrix.language }} + queries: +security-and-quality + + - name: Autobuild + uses: github/codeql-action/autobuild@v2 + if: ${{ matrix.language == 'javascript' || matrix.language == 'python' }} + + - name: Perform CodeQL Analysis + uses: github/codeql-action/analyze@v2 + with: + category: "/language:${{ matrix.language }}" From c90de3221f290b56a7102d94e8851c0cf5cdbf1e Mon Sep 17 00:00:00 2001 From: "Bruno P. Kinoshita" Date: Sun, 13 Nov 2022 09:01:09 +0100 Subject: [PATCH 020/179] Copy fonts style from commonwl.org --- src/_static/css/custom.css | 10 ++++++++++ src/conf.py | 4 ++++ 2 files changed, 14 insertions(+) create mode 100644 src/_static/css/custom.css diff --git a/src/_static/css/custom.css b/src/_static/css/custom.css new file mode 100644 index 00000000..9f53adff --- /dev/null +++ b/src/_static/css/custom.css @@ -0,0 +1,10 @@ +body { + /* + * These settings are copied from the https://commonwl.org website style + * for consistency. + */ + font-family: system-ui, -apple-system, "Segoe UI", Roboto, "Helvetica Neue", Arial, "Noto Sans", "Liberation Sans", sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol", "Noto Color Emoji"; + font-size: 16px; + line-height: 24px; + color: rgb(33, 37, 41); +} diff --git a/src/conf.py b/src/conf.py index c893d8a5..df703367 100644 --- a/src/conf.py +++ b/src/conf.py @@ -157,6 +157,10 @@ # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] +html_css_files = [ + 'css/custom.css', +] + html_logo = '_static/images/logos/cwl/CWL-Logo-HD-cropped2.png' html_favicon = '_static/images/favicons/cwl/favicon.ico' From e5e47e0cc3834e0490aa08fde95ef21204fe32a8 Mon Sep 17 00:00:00 2001 From: "Bruno P. Kinoshita" Date: Sun, 13 Nov 2022 09:07:12 +0100 Subject: [PATCH 021/179] Update template from pydata sphinx theme --- src/_templates/sidebar-nav-bs.html | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/src/_templates/sidebar-nav-bs.html b/src/_templates/sidebar-nav-bs.html index 73c66bee..a559969d 100644 --- a/src/_templates/sidebar-nav-bs.html +++ b/src/_templates/sidebar-nav-bs.html @@ -1,11 +1,8 @@ From 385340e4bc6f586b868e750bf46bd30358acbcd5 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 22 Nov 2022 17:45:53 +0100 Subject: [PATCH 022/179] clarify CWL runner --- src/introduction/prerequisites.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index 94908733..afd26dd1 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -59,7 +59,6 @@ $ (venv) pip install cwltool ``` ```{note} -You can find the `cwl-runner` [source code](https://github.com/common-workflow-language/cwltool/tree/main/cwlref-runner) in the `cwltool` repository. Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`. ``` @@ -91,9 +90,12 @@ You can run the CWL tool description by omitting the `--validate` option: ### Cwl-runner Python Module -`cwl-runner` is an implementation-agnostic alias for CWL Runners. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner. +`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means +that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular +CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` -directly. The `cwl-runner` alias command then chooses the correct CWL runner. +directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred +CWL implementation. This is convenient for environments with multiple CWL runners. The CWL community publishes a Python package with the name `cwlref-runner` that installs @@ -153,7 +155,7 @@ The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` -looks for the `` program in the system `PATH`, +looks for the `` program in the system `PATH`, ``` ## Text Editor From ec5285f8feb1d83eff4a08b498f9406a8e7eae0f Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 22 Nov 2022 17:48:56 +0100 Subject: [PATCH 023/179] clarify local script running --- src/faq.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/faq.md b/src/faq.md index 6da7efa5..50843d6a 100644 --- a/src/faq.md +++ b/src/faq.md @@ -83,7 +83,8 @@ outputs: There are two ways to reference a local script: -The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script without using `sh` or `bash` commands. +The first method involves adding the folder containing your scripts to the `PATH` environment variable. +This allows you to run the shell script directly without using `sh` or `bash` commands. Start with adding a _shebang_ at the top of your file: @@ -97,7 +98,7 @@ Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts). ```bash -export PATH=$PATH:/appropriate/directory +export PATH=$PATH:$HOME/bin ``` Now you can use `baseCommand: scriptname.sh` to run the script directly. From c46b733d36ae7dc1b2f609a78378dc2f039c96a5 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 22 Nov 2022 19:01:18 +0100 Subject: [PATCH 024/179] use CWL version 1.2 everywhere --- CONTRIBUTING.md | 3 +++ .../cwl/additional-arguments-and-parameters/arguments.cwl | 3 +-- src/_includes/cwl/creating-files-at-runtime/createfile.cwl | 3 ++- src/_includes/cwl/custom-types/custom-types.cwl | 2 +- src/_includes/cwl/environment-variables/env.cwl | 3 +-- src/_includes/cwl/expressions/expression.cwl | 3 +-- src/_includes/cwl/file-formats/metadata_example.cwl | 2 +- src/_includes/cwl/inputs/array-inputs.cwl | 3 +-- src/_includes/cwl/inputs/inp.cwl | 3 +-- src/_includes/cwl/inputs/record.cwl | 3 +-- .../cwl/metadata-and-authorship/metadata_example2.cwl | 2 +- .../cwl/metadata-and-authorship/metadata_example3.cwl | 2 +- src/_includes/cwl/outputs/array-outputs.cwl | 3 +-- src/_includes/cwl/outputs/stdout.cwl | 3 +-- src/_includes/cwl/outputs/tar.cwl | 3 +-- src/_includes/cwl/parameter-references/tar-param.cwl | 3 +-- .../cwl/specifying-software-requirements/custom-types.cwl | 3 ++- src/_includes/cwl/staging-input-files/linkfile.cwl | 3 +-- src/_includes/cwl/using-containers/docker.cwl | 3 +-- src/_includes/cwl/workflows/1st-workflow.cwl | 3 +-- src/_includes/cwl/workflows/arguments.cwl | 3 +-- src/_includes/cwl/workflows/hello_world.cwl | 3 +-- src/_includes/cwl/workflows/hello_world_to_stdout.cwl | 3 +-- src/_includes/cwl/workflows/nestedworkflows.cwl | 3 +-- src/_includes/cwl/workflows/scatter-nested-workflow.cwl | 3 +-- src/_includes/cwl/workflows/scatter-two-steps.cwl | 3 +-- src/_includes/cwl/workflows/scatter-workflow.cwl | 3 +-- src/_includes/cwl/workflows/tar-param.cwl | 3 +-- src/_includes/cwl/workflows/wc-tool.cwl | 3 +-- 29 files changed, 33 insertions(+), 50 deletions(-) mode change 100644 => 100755 src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl mode change 100644 => 100755 src/_includes/cwl/creating-files-at-runtime/createfile.cwl mode change 100644 => 100755 src/_includes/cwl/custom-types/custom-types.cwl mode change 100644 => 100755 src/_includes/cwl/expressions/expression.cwl mode change 100644 => 100755 src/_includes/cwl/file-formats/metadata_example.cwl mode change 100644 => 100755 src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl mode change 100644 => 100755 src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl mode change 100644 => 100755 src/_includes/cwl/outputs/tar.cwl mode change 100644 => 100755 src/_includes/cwl/specifying-software-requirements/custom-types.cwl mode change 100644 => 100755 src/_includes/cwl/staging-input-files/linkfile.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/1st-workflow.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/arguments.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/nestedworkflows.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/scatter-nested-workflow.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/scatter-two-steps.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/scatter-workflow.cwl mode change 100644 => 100755 src/_includes/cwl/workflows/tar-param.cwl diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 7298c7de..7b954969 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -148,8 +148,11 @@ are still working after the change. Use “tool description” not “tool wrapper” for describing the first argument given to the `cwl-runner` or `cwltool` commands. + ### Code Examples +All CWL documents should be version 1.2 unless there is a very good reason otherwise. + To include code into a Markdown file you have two options. For external files use the following command: diff --git a/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl b/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl old mode 100644 new mode 100755 index 3a2e4538..a6f7287c --- a/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl +++ b/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: Example trivial wrapper for Java 9 compiler hints: diff --git a/src/_includes/cwl/creating-files-at-runtime/createfile.cwl b/src/_includes/cwl/creating-files-at-runtime/createfile.cwl old mode 100644 new mode 100755 index 5e39a36f..d5694aab --- a/src/_includes/cwl/creating-files-at-runtime/createfile.cwl +++ b/src/_includes/cwl/creating-files-at-runtime/createfile.cwl @@ -1,5 +1,6 @@ +#!/usr/bin/env cwl-runner +cwlVersion: v1.2 class: CommandLineTool -cwlVersion: v1.0 baseCommand: ["sh", "example.sh"] requirements: diff --git a/src/_includes/cwl/custom-types/custom-types.cwl b/src/_includes/cwl/custom-types/custom-types.cwl old mode 100644 new mode 100755 index 707d5c2a..d60e6e92 --- a/src/_includes/cwl/custom-types/custom-types.cwl +++ b/src/_includes/cwl/custom-types/custom-types.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool requirements: diff --git a/src/_includes/cwl/environment-variables/env.cwl b/src/_includes/cwl/environment-variables/env.cwl index 7e4d4087..6162a04c 100755 --- a/src/_includes/cwl/environment-variables/env.cwl +++ b/src/_includes/cwl/environment-variables/env.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: env requirements: diff --git a/src/_includes/cwl/expressions/expression.cwl b/src/_includes/cwl/expressions/expression.cwl old mode 100644 new mode 100755 index da1e75dc..a04695bb --- a/src/_includes/cwl/expressions/expression.cwl +++ b/src/_includes/cwl/expressions/expression.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo diff --git a/src/_includes/cwl/file-formats/metadata_example.cwl b/src/_includes/cwl/file-formats/metadata_example.cwl old mode 100644 new mode 100755 index 9485522b..bcaaff70 --- a/src/_includes/cwl/file-formats/metadata_example.cwl +++ b/src/_includes/cwl/file-formats/metadata_example.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: An example tool demonstrating metadata. diff --git a/src/_includes/cwl/inputs/array-inputs.cwl b/src/_includes/cwl/inputs/array-inputs.cwl index bef63538..0e5d6e44 100755 --- a/src/_includes/cwl/inputs/array-inputs.cwl +++ b/src/_includes/cwl/inputs/array-inputs.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool inputs: filesA: diff --git a/src/_includes/cwl/inputs/inp.cwl b/src/_includes/cwl/inputs/inp.cwl index 576c16da..20ac1d79 100755 --- a/src/_includes/cwl/inputs/inp.cwl +++ b/src/_includes/cwl/inputs/inp.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo inputs: diff --git a/src/_includes/cwl/inputs/record.cwl b/src/_includes/cwl/inputs/record.cwl index e33cb44a..e69a1ac9 100755 --- a/src/_includes/cwl/inputs/record.cwl +++ b/src/_includes/cwl/inputs/record.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool inputs: dependent_parameters: diff --git a/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl b/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl old mode 100644 new mode 100755 index 745c1779..ca2b59bd --- a/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl +++ b/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: An example tool demonstrating metadata. diff --git a/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl b/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl old mode 100644 new mode 100755 index 09d31e4a..e30a3c64 --- a/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl +++ b/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: An example tool demonstrating metadata. diff --git a/src/_includes/cwl/outputs/array-outputs.cwl b/src/_includes/cwl/outputs/array-outputs.cwl index 2d6654ea..9d7d8022 100755 --- a/src/_includes/cwl/outputs/array-outputs.cwl +++ b/src/_includes/cwl/outputs/array-outputs.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: touch inputs: diff --git a/src/_includes/cwl/outputs/stdout.cwl b/src/_includes/cwl/outputs/stdout.cwl index 5908f88f..53e2db0e 100755 --- a/src/_includes/cwl/outputs/stdout.cwl +++ b/src/_includes/cwl/outputs/stdout.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo stdout: output.txt diff --git a/src/_includes/cwl/outputs/tar.cwl b/src/_includes/cwl/outputs/tar.cwl old mode 100644 new mode 100755 index f1b45964..187fe05f --- a/src/_includes/cwl/outputs/tar.cwl +++ b/src/_includes/cwl/outputs/tar.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: [tar, --extract] inputs: diff --git a/src/_includes/cwl/parameter-references/tar-param.cwl b/src/_includes/cwl/parameter-references/tar-param.cwl index 87ad9e0f..913b7fdd 100644 --- a/src/_includes/cwl/parameter-references/tar-param.cwl +++ b/src/_includes/cwl/parameter-references/tar-param.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: [tar, --extract] inputs: diff --git a/src/_includes/cwl/specifying-software-requirements/custom-types.cwl b/src/_includes/cwl/specifying-software-requirements/custom-types.cwl old mode 100644 new mode 100755 index 044db0bf..70cb9dee --- a/src/_includes/cwl/specifying-software-requirements/custom-types.cwl +++ b/src/_includes/cwl/specifying-software-requirements/custom-types.cwl @@ -1,4 +1,5 @@ -cwlVersion: v1.0 +#!/usr/bin/env cwl-runner +cwlVersion: v1.2 class: CommandLineTool label: "InterProScan: protein sequence classifier" diff --git a/src/_includes/cwl/staging-input-files/linkfile.cwl b/src/_includes/cwl/staging-input-files/linkfile.cwl old mode 100644 new mode 100755 index ffeb6996..43cf79bc --- a/src/_includes/cwl/staging-input-files/linkfile.cwl +++ b/src/_includes/cwl/staging-input-files/linkfile.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool hints: DockerRequirement: diff --git a/src/_includes/cwl/using-containers/docker.cwl b/src/_includes/cwl/using-containers/docker.cwl index 9f6090a1..35c5e842 100755 --- a/src/_includes/cwl/using-containers/docker.cwl +++ b/src/_includes/cwl/using-containers/docker.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: node hints: diff --git a/src/_includes/cwl/workflows/1st-workflow.cwl b/src/_includes/cwl/workflows/1st-workflow.cwl old mode 100644 new mode 100755 index 24b19bd2..4da55143 --- a/src/_includes/cwl/workflows/1st-workflow.cwl +++ b/src/_includes/cwl/workflows/1st-workflow.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow inputs: tarball: File diff --git a/src/_includes/cwl/workflows/arguments.cwl b/src/_includes/cwl/workflows/arguments.cwl old mode 100644 new mode 100755 index c26d2642..ff80076a --- a/src/_includes/cwl/workflows/arguments.cwl +++ b/src/_includes/cwl/workflows/arguments.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool label: Example trivial wrapper for Java 9 compiler hints: diff --git a/src/_includes/cwl/workflows/hello_world.cwl b/src/_includes/cwl/workflows/hello_world.cwl index 48e2f792..1c39bca4 100755 --- a/src/_includes/cwl/workflows/hello_world.cwl +++ b/src/_includes/cwl/workflows/hello_world.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo inputs: diff --git a/src/_includes/cwl/workflows/hello_world_to_stdout.cwl b/src/_includes/cwl/workflows/hello_world_to_stdout.cwl index 1d550fc2..39e8e2d4 100755 --- a/src/_includes/cwl/workflows/hello_world_to_stdout.cwl +++ b/src/_includes/cwl/workflows/hello_world_to_stdout.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: echo inputs: diff --git a/src/_includes/cwl/workflows/nestedworkflows.cwl b/src/_includes/cwl/workflows/nestedworkflows.cwl old mode 100644 new mode 100755 index 75a4f00a..c43e5096 --- a/src/_includes/cwl/workflows/nestedworkflows.cwl +++ b/src/_includes/cwl/workflows/nestedworkflows.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow inputs: [] diff --git a/src/_includes/cwl/workflows/scatter-nested-workflow.cwl b/src/_includes/cwl/workflows/scatter-nested-workflow.cwl old mode 100644 new mode 100755 index 9b2f6aa6..7bc6c1d7 --- a/src/_includes/cwl/workflows/scatter-nested-workflow.cwl +++ b/src/_includes/cwl/workflows/scatter-nested-workflow.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/src/_includes/cwl/workflows/scatter-two-steps.cwl b/src/_includes/cwl/workflows/scatter-two-steps.cwl old mode 100644 new mode 100755 index 57b9ca2e..c2963cfc --- a/src/_includes/cwl/workflows/scatter-two-steps.cwl +++ b/src/_includes/cwl/workflows/scatter-two-steps.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/src/_includes/cwl/workflows/scatter-workflow.cwl b/src/_includes/cwl/workflows/scatter-workflow.cwl old mode 100644 new mode 100755 index 80a334f3..954e1660 --- a/src/_includes/cwl/workflows/scatter-workflow.cwl +++ b/src/_includes/cwl/workflows/scatter-workflow.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow requirements: diff --git a/src/_includes/cwl/workflows/tar-param.cwl b/src/_includes/cwl/workflows/tar-param.cwl old mode 100644 new mode 100755 index 87ad9e0f..913b7fdd --- a/src/_includes/cwl/workflows/tar-param.cwl +++ b/src/_includes/cwl/workflows/tar-param.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: [tar, --extract] inputs: diff --git a/src/_includes/cwl/workflows/wc-tool.cwl b/src/_includes/cwl/workflows/wc-tool.cwl index c3064634..397df77e 100755 --- a/src/_includes/cwl/workflows/wc-tool.cwl +++ b/src/_includes/cwl/workflows/wc-tool.cwl @@ -1,6 +1,5 @@ #!/usr/bin/env cwl-runner - -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: wc arguments: ["-c"] From 1e5d8074fad65eb835953d728b1a8c1adf5ac42d Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 22 Nov 2022 19:36:06 +0100 Subject: [PATCH 025/179] rename CWL tests file --- Makefile | 2 +- src/_includes/cwl/{conformance-test.yml => cwl_tests.yml} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename src/_includes/cwl/{conformance-test.yml => cwl_tests.yml} (100%) diff --git a/Makefile b/Makefile index 9f6459ec..81bc3c77 100644 --- a/Makefile +++ b/Makefile @@ -33,7 +33,7 @@ watch: clean ## unittest-examples : unittest-examples: - cd src/_includes/cwl; cwltest --test=conformance-test.yml --tool=${RUNNER} + cd src/_includes/cwl; cwltest --test=cwl_tests.yml --tool=${RUNNER} ## check-json : check-json: diff --git a/src/_includes/cwl/conformance-test.yml b/src/_includes/cwl/cwl_tests.yml similarity index 100% rename from src/_includes/cwl/conformance-test.yml rename to src/_includes/cwl/cwl_tests.yml From 288d912899c6359652cc8544f2186ea4ac3e026d Mon Sep 17 00:00:00 2001 From: XiongJF <624188314@qq.com> Date: Tue, 3 Jan 2023 14:42:19 +0800 Subject: [PATCH 026/179] add exclude_cache_cmd domain for CMDCache --- cwl/sphinx/runcmd.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/cwl/sphinx/runcmd.py b/cwl/sphinx/runcmd.py index ff8bb245..b4ea08de 100644 --- a/cwl/sphinx/runcmd.py +++ b/cwl/sphinx/runcmd.py @@ -40,10 +40,13 @@ class Singleton(_Singleton("SingletonMeta", (object,), {})): class CMDCache(Singleton): cache = {} + exclude_cache_cmd = {hash("cat output.txt")} def get(self, cmd, working_directory): h = hash(cmd) - if h in self.cache: + if h in self.exclude_cache_cmd: + return run_command(cmd, working_directory) + elif h in self.cache: return self.cache[h] else: result = run_command(cmd, working_directory) From a2e4fedd427efcd5c87510c9018093172845597c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Levai=20Mackenzie=20=C3=81gb=C3=A0r=C3=A0?= <97461848+Mackenzie-OO7@users.noreply.github.com> Date: Tue, 3 Jan 2023 17:22:30 +0100 Subject: [PATCH 027/179] add community link to the navbar (#356) --- src/conf.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/conf.py b/src/conf.py index df703367..bcba3134 100644 --- a/src/conf.py +++ b/src/conf.py @@ -171,6 +171,10 @@ ] html_theme_options = { + "external_links": [ + {"name": "Community", "url": "https://www.commonwl.org/community/"}, + ], + "header_links_before_dropdown": 6, "icon_links": [ { "name": "GitHub", From e87eaa2f3927a17b9415c9deaf25a9d337781df3 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Tue, 24 Jan 2023 17:36:11 +0100 Subject: [PATCH 028/179] add PO file for English (#359) --- locales/en/LC_MESSAGES/LICENSE.po | 120 +++++ .../en/LC_MESSAGES/_includes/what-is-cwl.po | 28 + locales/en/LC_MESSAGES/episodes.po | 31 ++ locales/en/LC_MESSAGES/faq.po | 307 +++++++++++ locales/en/LC_MESSAGES/index.po | 68 +++ .../introduction/basic-concepts.po | 270 ++++++++++ locales/en/LC_MESSAGES/introduction/index.po | 31 ++ .../LC_MESSAGES/introduction/prerequisites.po | 298 +++++++++++ .../LC_MESSAGES/introduction/quick-start.po | 191 +++++++ locales/en/LC_MESSAGES/setup.po | 31 ++ locales/en/LC_MESSAGES/sphinx.po | 28 + .../additional-arguments-and-parameters.po | 84 +++ .../en/LC_MESSAGES/topics/best-practices.po | 191 +++++++ .../LC_MESSAGES/topics/command-line-tool.po | 71 +++ .../topics/creating-files-at-runtime.po | 104 ++++ locales/en/LC_MESSAGES/topics/custom-types.po | 99 ++++ .../topics/environment-variables.po | 45 ++ .../en/LC_MESSAGES/topics/expression-tool.po | 53 ++ locales/en/LC_MESSAGES/topics/expressions.po | 383 +++++++++++++ locales/en/LC_MESSAGES/topics/file-formats.po | 93 ++++ locales/en/LC_MESSAGES/topics/index.po | 24 + locales/en/LC_MESSAGES/topics/inputs.po | 313 +++++++++++ .../topics/metadata-and-authorship.po | 70 +++ locales/en/LC_MESSAGES/topics/operations.po | 73 +++ locales/en/LC_MESSAGES/topics/outputs.po | 147 +++++ .../topics/parameter-references.po | 279 ++++++++++ .../topics/requirements-and-hints.po | 24 + .../specifying-software-requirements.po | 68 +++ .../LC_MESSAGES/topics/staging-input-files.po | 48 ++ .../en/LC_MESSAGES/topics/troubleshooting.po | 101 ++++ .../en/LC_MESSAGES/topics/using-containers.po | 106 ++++ locales/en/LC_MESSAGES/topics/workflows.po | 504 ++++++++++++++++++ locales/en/LC_MESSAGES/topics/yaml-guide.po | 193 +++++++ locales/en/LC_MESSAGES/tutorials.po | 58 ++ setup.cfg | 2 + src/conf.py | 4 + 36 files changed, 4540 insertions(+) create mode 100644 locales/en/LC_MESSAGES/LICENSE.po create mode 100644 locales/en/LC_MESSAGES/_includes/what-is-cwl.po create mode 100644 locales/en/LC_MESSAGES/episodes.po create mode 100644 locales/en/LC_MESSAGES/faq.po create mode 100644 locales/en/LC_MESSAGES/index.po create mode 100644 locales/en/LC_MESSAGES/introduction/basic-concepts.po create mode 100644 locales/en/LC_MESSAGES/introduction/index.po create mode 100644 locales/en/LC_MESSAGES/introduction/prerequisites.po create mode 100644 locales/en/LC_MESSAGES/introduction/quick-start.po create mode 100644 locales/en/LC_MESSAGES/setup.po create mode 100644 locales/en/LC_MESSAGES/sphinx.po create mode 100644 locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po create mode 100644 locales/en/LC_MESSAGES/topics/best-practices.po create mode 100644 locales/en/LC_MESSAGES/topics/command-line-tool.po create mode 100644 locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po create mode 100644 locales/en/LC_MESSAGES/topics/custom-types.po create mode 100644 locales/en/LC_MESSAGES/topics/environment-variables.po create mode 100644 locales/en/LC_MESSAGES/topics/expression-tool.po create mode 100644 locales/en/LC_MESSAGES/topics/expressions.po create mode 100644 locales/en/LC_MESSAGES/topics/file-formats.po create mode 100644 locales/en/LC_MESSAGES/topics/index.po create mode 100644 locales/en/LC_MESSAGES/topics/inputs.po create mode 100644 locales/en/LC_MESSAGES/topics/metadata-and-authorship.po create mode 100644 locales/en/LC_MESSAGES/topics/operations.po create mode 100644 locales/en/LC_MESSAGES/topics/outputs.po create mode 100644 locales/en/LC_MESSAGES/topics/parameter-references.po create mode 100644 locales/en/LC_MESSAGES/topics/requirements-and-hints.po create mode 100644 locales/en/LC_MESSAGES/topics/specifying-software-requirements.po create mode 100644 locales/en/LC_MESSAGES/topics/staging-input-files.po create mode 100644 locales/en/LC_MESSAGES/topics/troubleshooting.po create mode 100644 locales/en/LC_MESSAGES/topics/using-containers.po create mode 100644 locales/en/LC_MESSAGES/topics/workflows.po create mode 100644 locales/en/LC_MESSAGES/topics/yaml-guide.po create mode 100644 locales/en/LC_MESSAGES/tutorials.po diff --git a/locales/en/LC_MESSAGES/LICENSE.po b/locales/en/LC_MESSAGES/LICENSE.po new file mode 100644 index 00000000..29b53dd1 --- /dev/null +++ b/locales/en/LC_MESSAGES/LICENSE.po @@ -0,0 +1,120 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../../LICENSE.md:2 f0c9a54a904e42249441ee22e39d6f3a +msgid "Licenses" +msgstr "" + +#: ../../../LICENSE.md:4 6c99230ebe4d48689e09e2da1484abc9 +msgid "Instructional Material" +msgstr "" + +#: ../../../LICENSE.md:6 327a6405608b4df488fc6aee756f94b7 +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." +msgstr "" + +#: ../../../LICENSE.md:12 91d85fe9673942658f5d17e286ac6b69 +msgid "You are free:" +msgstr "" + +#: ../../../LICENSE.md:14 c010a0b9145e4532896b114d4e0c7768 +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../../LICENSE.md:15 8e7d2d9301a8452994e4b33edb3c7ea0 +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../../LICENSE.md:17 0fdc0b2074bc4cfd8cd020d51a3d4f3b +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../../LICENSE.md:19 220eba84dd874fb59ac0d4f7a95695fc +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms." +msgstr "" + +#: ../../../LICENSE.md:22 c21178abaf374ca5ae83fb9b94761e7e +msgid "Under the following terms:" +msgstr "" + +#: ../../../LICENSE.md:24 90e30b28cfdb4c8fb6bf2e2687ac47c3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." +msgstr "" + +#: ../../../LICENSE.md:32 c40a837670f84762bffc0cc8d697d45d +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" +msgstr "" + +#: ../../../LICENSE.md:36 233edb183ff44c7293756df599b2a130 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." +msgstr "" + +#: ../../../LICENSE.md:39 027339c3a92747e8948b11671ace4145 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." +msgstr "" + +#: ../../../LICENSE.md:44 89dcc55f3d5d445b97912648ee5dba03 +msgid "Software" +msgstr "" + +#: ../../../LICENSE.md:46 070952c76313480d92f0b78321a6a1e2 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../../LICENSE.md:51 3279f7573aa44853af83dbf9dd9748a9 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." +msgstr "" + +#: ../../../LICENSE.md:57 979969ab3c3f4080b6c7e879efe9f351 +msgid "Trademark" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/_includes/what-is-cwl.po b/locales/en/LC_MESSAGES/_includes/what-is-cwl.po new file mode 100644 index 00000000..bc854eb9 --- /dev/null +++ b/locales/en/LC_MESSAGES/_includes/what-is-cwl.po @@ -0,0 +1,28 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../_includes/what-is-cwl.md:1 ffc6d3382e944f22a8b13062eb1badc4 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/episodes.po b/locales/en/LC_MESSAGES/episodes.po new file mode 100644 index 00000000..ed5b10aa --- /dev/null +++ b/locales/en/LC_MESSAGES/episodes.po @@ -0,0 +1,31 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../episodes.md:5 0c99dd9365d14d26b9b3bb5e88f33570 +msgid "This page has moved" +msgstr "" + +#: ../../episodes.md:9 2718a75eccf84a1fa22356367d3b772e +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/faq.po b/locales/en/LC_MESSAGES/faq.po new file mode 100644 index 00000000..c74aeb6e --- /dev/null +++ b/locales/en/LC_MESSAGES/faq.po @@ -0,0 +1,307 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../faq.md:1 1479ffe379ea483290f2c16ddc8d6358 +msgid "FAQ" +msgstr "" + +#: ../../faq.md:11 b6cd88863b754a7d8467948ea72063ac +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../faq.md:41 29876633f61f4befa1ba764a8e14909a +msgid "Rename an Input File" +msgstr "" + +#: ../../faq.md:43 c523a45d4fff4ac5b451b8c9e947a0c1 +msgid "" +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." +msgstr "" + +#: ../../faq.md:59 6761f620fae44513ba675bb845dad5af +msgid "Rename an Output File" +msgstr "" + +#: ../../faq.md:61 83312f5876ea492c9a881b8d1d8ec232 +msgid "" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" +msgstr "" + +#: ../../faq.md:82 da3f295db7584f2ab5532fb915c8ada7 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../faq.md:84 e4aec7bca9bf4ef0a3d709fd0771d886 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../faq.md:86 f6fcb55812944ad98053fee5243125fb +msgid "" +"The first method involves adding the folder containing your scripts to " +"the `PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../faq.md:89 7a83b32f4124408ab1f0dc3303d5d640 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../faq.md:95 c59ec88c1d1545699fd0c00f6173dccc +msgid "" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" +msgstr "" + +#: ../../faq.md:97 dbd4fb58d2e34ccbb9544f2106ee56e5 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." +msgstr "" + +#: ../../faq.md:104 9fb24ecdc09b438bb46e8107880e77a0 +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../faq.md:113 b8624be7349d472b9b86409bd5b786cd +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." +msgstr "" + +#: ../../faq.md:115 fdcc23c875974ee58a4e5ae702eaac67 +msgid "" +"The second method involves including an input of `type: File` in the " +"script itself:" +msgstr "" + +#: ../../faq.md:135 da2ee2848dbc4dff8663c1fbf00c863f +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../faq.md:138 782152c8aab84a12bb04375096f492b6 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../faq.md:140 da2600292146447aa527f24c69cfb776 +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." +msgstr "" + +#: ../../faq.md:165 dc07a65c25854ef6b21cb4a43bee4d31 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../faq.md:167 76bfb57ea05647748b60e36712a8b100 +msgid "" +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../faq.md:188 be450f9113f3451691eea5f0d30c3c74 +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../faq.md:190 a328ad7be4e44194b8a1fb5a436d1265 +msgid "" +"Using " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../faq.md:194 d86e24a5d27b418ba29e5439b34a5c13 +msgid "merge_nested" +msgstr "" + +#: ../../faq.md:196 f9b6d21ce7f3405da57fa7443e623b8a +msgid "" +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../faq.md:199 1ac676ef33bb45c4b7fc371e7bd84f07 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../faq.md:201 75cef09a92cc44c397a18f81840743b2 +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." +msgstr "" + +#: ../../faq.md:229 5bd33a98001148e7b8e83b9bb83b62ee +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../faq.md:231 70651f1b65fd4e20b0f1719c3b8ea3f8 +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." +msgstr "" + +#: ../../faq.md:247 cb3f5cae1479448c9669e2751fd34460 +msgid "" +msgstr "" + +#: ../../faq.md:248 74eafea819d6405b8f573da4ec712445 +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../faq.md:250 4955ef4f959143b096125f95ec32c1e2 +msgid "" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" +msgstr "" + +#: ../../faq.md:267 bdf0e5bf3c754f639fbb4ad24076bc4a +msgid "" +msgstr "" + +#: ../../faq.md:268 64c7ae1eaf6b4b0cb4a5fc23feb6349e +msgid "Record Inputs 📀" +msgstr "" + +#: ../../faq.md:270 ad83e44a7f914cfbb46aa191a17d4c85 +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." +msgstr "" + +#: ../../faq.md:322 68e228ecf0be4753832a31ceb933fc19 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../faq.md:324 e2f19825601845b59d5cbeeeb0024622 +msgid "" +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." +msgstr "" + +#: ../../faq.md:342 0824a9e1f5684da481163cd16fed94b9 +msgid "Setting Booleans" +msgstr "" + +#: ../../faq.md:344 192e416a398845838d55bdb71190bb70 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../faq.md:349 eb6a00b2ff3a4ec384a0308f00dd8c4c +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../faq.md:351 9a7df9d0f389421298e6d456822e52a4 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../faq.md:359 9cab760a07114447a817f63ff61ff346 +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../faq.md:361 9ccf1286db084b67a37b2217a9764584 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../faq.md:363 33ea1db2582f4fe78436fb1a8f431b15 +msgid "" +"For example, the filename `a space is here.txt` includes 3 space " +"characters." +msgstr "" + +#: ../../faq.md:371 0f8a3fc6e622464fae1366a053baa78c +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." +msgstr "" + +#: ../../faq.md:373 6a3ba881461642aa8d7654dad772ccd3 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../faq.md:375 253cbea8229743b8a064d4d2fac24f12 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../faq.md:384 63190f04254b4459880b1ee84886bbab +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../faq.md:396 61d3a0026a274eafa31b02220bc4bd0e +msgid "The file is here" +msgstr "" + +#: ../../faq.md:410 2a99b8770636429693ff44563f0ac148 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../faq.md:423 a0d1eff495924aeaaad2ed92010e92f4 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../faq.md:436 a901e5d22e644dcc848d347bcf87d59b +msgid "" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../faq.md:442 5baccb1d1e604c849cce7b27223b1f9f +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../faq.md:445 b8421426848c470db2324fde8ae8f05d +msgid "" +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." +msgstr "" + +#: ../../faq.md:450 1a3fecc9eb7a4dcdaf577983c505ba13 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../faq.md:452 b17460fcb17e40da879383df593f2a93 +msgid "" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/index.po b/locales/en/LC_MESSAGES/index.po new file mode 100644 index 00000000..2437acd8 --- /dev/null +++ b/locales/en/LC_MESSAGES/index.po @@ -0,0 +1,68 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../index.md:1 618bf3fb1f364be791cc5f2bf77667d5 +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../index.md:3 67f4f01edc5b4261a70e4efc3d792f64 +msgid "" +"This guide will introduce you to writing workflows using the [Common " +"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " +"guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../index.md:7 284c0f5ead3142649c3c6d4f04da4851 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../index.md:9 75a3c6a67c2e4593a098c839483ae47f +msgid "" +"If you find that something is missing from this guide, or if you would " +"like to provide other feedback, file an Issue on the [project repository " +"for this guide][repo]. You can also suggest changes directly in a Pull " +"Request by clicking the \"Edit this page\" button at the right sidebar of" +" each page." +msgstr "" + +#: ../../index.md:16 6061795c74ce415eb3e4f1ca3ed91de6 +msgid "Navigating the User Guide" +msgstr "" + +#: ../../index.md:18 c74efbca9bcd4fda9c4e94d774caa91c +msgid "" +"If you are a beginner user get started with the " +"[Introduction](/introduction/index.md) section. For advanced users the " +"subsections of the [Topics](/topics/index.md) have detailed information " +"about the most common topics for CWL." +msgstr "" + +#: ../../index.md:23 f2bc70925dea4573ab177c5d2f2b5dcb +msgid "" +"The Table of Contents is displayed at the top menu and also on the left " +"sidebar. It also appears further down this page but with links to " +"subsections. The right sidebar contains links to the sections of each " +"page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../index.md:28 3e4e62c52c5547c6a4e77131ab1dee39 +msgid "Table of Contents" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/introduction/basic-concepts.po b/locales/en/LC_MESSAGES/introduction/basic-concepts.po new file mode 100644 index 00000000..3fe5662f --- /dev/null +++ b/locales/en/LC_MESSAGES/introduction/basic-concepts.po @@ -0,0 +1,270 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../introduction/basic-concepts.md:1 5f43861a84a2494b8e1bc973ac85b3d0 +msgid "Basic Concepts" +msgstr "" + +#: ../../introduction/basic-concepts.md:3 90cc7b0ef1404f72ae0f5b17f6f2a966 +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." +msgstr "" + +#: ../../introduction/basic-concepts.md:10 1685ddf11a014fe28df75dedb7c39e07 +msgid "The CWL Specification" +msgstr "" + +#: ../../_includes/what-is-cwl.md:2 9cb90a376bfe4058922b1c91ea4ce184 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../introduction/basic-concepts.md:21 cc05f8193ee6403daca03d2d19ccfcd7 +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../introduction/basic-concepts.md:25 f5a0ba9dfc1f49ab937e8122fe4761e0 +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." +msgstr "" + +#: ../../introduction/basic-concepts.md:33 8100683970154870993d19d7a5a6bd22 +msgid "" +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." +msgstr "" + +#: ../../introduction/basic-concepts.md:37 cc5c29f65655465db44dd4eed8f11c7b +msgid "Implementations" +msgstr "" + +#: ../../introduction/basic-concepts.md:39 c07822e70e774ea2bb3da2cfd69aa360 +msgid "" +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." +msgstr "" + +#: ../../introduction/basic-concepts.md:44 6735911046aa466aa2a371ffff22a9fe +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." +msgstr "" + +#: ../../introduction/basic-concepts.md:51 795e23a746c749deacb68a18d9a3333b +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../introduction/basic-concepts.md:105 e7c0b2155a024860b8d3fd7c9ef75f38 +msgid "Processes and Requirements" +msgstr "" + +#: ../../introduction/basic-concepts.md:107 cf57f60e189e40c09e946f56a1fdf0b8 +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" +msgstr "" + +#: ../../introduction/basic-concepts.md:112 6201ed50ccf944c2aaf7795d411e236d +msgid "A command-line tool." +msgstr "" + +#: ../../introduction/basic-concepts.md:113 a6f9f66dec354e09bd1778d2bf71a7ef +msgid "An expression tool." +msgstr "" + +#: ../../introduction/basic-concepts.md:114 43927a824e584c3c8914119bcdfdffbc +msgid "An operation." +msgstr "" + +#: ../../introduction/basic-concepts.md:115 98f30716f9154c51bcf95a9a26613c6e +msgid "A workflow." +msgstr "" + +#: ../../introduction/basic-concepts.md:118 07807b77a0a444568348e8c20e540296 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../introduction/basic-concepts.md:119 f7dd65df72be46e88ad933e85d2cfe32 +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../introduction/basic-concepts.md:122 7c12205b897c4d6ea918fc8b371ba329 +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." +msgstr "" + +#: ../../introduction/basic-concepts.md:127 965bd0c3dedc43d188c9c7b5db33b1f5 +msgid "" +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../introduction/basic-concepts.md:131 7299dcb09d2b4967a9d46d3b433d439e +msgid "" +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." +msgstr "" + +#: ../../introduction/basic-concepts.md:137 ea9d197aab4c41788a4a0e3d48c1c168 +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" +msgstr "" + +#: ../../introduction/basic-concepts.md:141 592f212970f84365a86a69cfb8c26369 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../introduction/basic-concepts.md:142 57e5ad64e68545a788b43e4e921bb23f +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../introduction/basic-concepts.md:143 397171706bf349feb2c9bee5a993ea1e +msgid "" +"`InitialWorkDirRequirement` - controls staging files in the input " +"directory." +msgstr "" + +#: ../../introduction/basic-concepts.md:145 fa9d473ae58b4053981a45a888470655 +msgid "" +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." +msgstr "" + +#: ../../introduction/basic-concepts.md:151 b9cc1fd288764bd78eda4703a2700a02 +msgid "" +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." +msgstr "" + +#: ../../introduction/basic-concepts.md:155 cf12d86b4e7c48c892d6be8233ea2bc9 +msgid "FAIR Workflows" +msgstr "" + +#: ../../introduction/basic-concepts.md:157 a83ecf7c5eaa4af3a676060d12ec7e7e +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows support the creation of FAIR data " +"and adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." +msgstr "" + +#: ../../introduction/basic-concepts.md:167 7451c042271941d6b283bf6d54b76acb +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." +msgstr "" + +#: ../../introduction/basic-concepts.md:171 d356140962c244d78b4a2c888bf03963 +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." +msgstr "" + +#: ../../introduction/basic-concepts.md:176 8fee6b5cd95144e1bced764b112a9d3f +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../introduction/basic-concepts.md:178 38ce1ceb880b4421b9ea2ee52e1153da +msgid "Learn More" +msgstr "" + +#: ../../introduction/basic-concepts.md:180 9a631f69c9504527bcd02a8f40f21c3f +msgid "Semantic Versioning - " +msgstr "" + +#: ../../introduction/basic-concepts.md:181 6141f823850e411691c2ef7047c9ecab +msgid "" +"The CWL Specification page in the CWL website: " +"" +msgstr "" + +#: ../../introduction/basic-concepts.md:182 6a07a8b45dc54851b5b78597891be763 +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../introduction/basic-concepts.md:183 f246c41bb0f946c590736c40713af684 +msgid "" +"The list of Implementations in the CWL website: " +"" +msgstr "" + +#: ../../introduction/basic-concepts.md:184 d9d8d29e5c0e427299f696073dfbfc1b +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../introduction/basic-concepts.md:185 581a427aed9e483489b6123ee1879d80 +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/introduction/index.po b/locales/en/LC_MESSAGES/introduction/index.po new file mode 100644 index 00000000..3b6add35 --- /dev/null +++ b/locales/en/LC_MESSAGES/introduction/index.po @@ -0,0 +1,31 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../introduction/index.md:1 b93db93ee9a24f03805cc032d22ca212 +msgid "Introduction" +msgstr "" + +#: ../../introduction/index.md:3 f77b8595af564c688c37097c43e04c86 +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/introduction/prerequisites.po b/locales/en/LC_MESSAGES/introduction/prerequisites.po new file mode 100644 index 00000000..f8f47a94 --- /dev/null +++ b/locales/en/LC_MESSAGES/introduction/prerequisites.po @@ -0,0 +1,298 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../introduction/prerequisites.md:1 7bbfeec267824100866390bfcfa6cec9 +msgid "Prerequisites" +msgstr "" + +#: ../../introduction/prerequisites.md:6 aa8e8b6a8dfa499f99598f30dca4074f +msgid "" +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../introduction/prerequisites.md:12 cf4757d4aef2456397017d2ff13499ba +msgid "CWL Implementations" +msgstr "" + +#: ../../introduction/prerequisites.md:14 502c3afa077249b98a51051b23698a6d +msgid "" +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." +msgstr "" + +#: ../../introduction/prerequisites.md:19 9a788e46f9d64d30aeff30a86182884c +msgid "Operating System" +msgstr "" + +#: ../../introduction/prerequisites.md:21 cc76660874a944369f69207bb1e0e856 +msgid "" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" +msgstr "" + +#: ../../introduction/prerequisites.md:24 77c62d947e894088afc8520451c79ac1 +msgid "Linux" +msgstr "" + +#: ../../introduction/prerequisites.md:25 32cd53abe1744596b3b33835cd8d1eb1 +msgid "macOS" +msgstr "" + +#: ../../introduction/prerequisites.md:26 1a7b4392aec64e3e9c053288362f342a +msgid "Windows" +msgstr "" + +#: ../../introduction/prerequisites.md:29 dcea6593d35c40bc9c0d39d4a788fbc1 +msgid "" +"If you are using Windows, you will have to install the [Windows Subsystem" +" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " +"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" +"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " +"details on installing WSL2. Your operating system also needs internet " +"access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../introduction/prerequisites.md:35 45bde9e20d0d45eb93427f5b6a3634dd +msgid "CWL Runner" +msgstr "" + +#: ../../introduction/prerequisites.md:41 998f8c45ed8f4075a577d4e6af1eda5b +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../introduction/prerequisites.md:46 813a16e6431744b1aad3bc11a2402e44 +msgid "" +"`cwltool` can be installed with `pip`. We recommend using a virtual " +"environment like `venv` or `conda`. The following commands will create " +"and activate a Python virtual environment using the `venv` module, and " +"install `cwltool` in that environment:" +msgstr "" + +#: ../../introduction/prerequisites.md:51 297d141896a84499a91f312a0016547f +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../introduction/prerequisites.md:62 ad7893d4a87d441c8aedbf168d3ca9ad +msgid "" +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool#install) for other ways to install `cwltool` with `apt` " +"and `conda`." +msgstr "" + +#: ../../introduction/prerequisites.md:65 5dbc4e8a1c544a258d5b2d965db08be2 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../introduction/prerequisites.md:67 380bf05c4a754d008499fa6206e86e90 +msgid "`true.cwl`" +msgstr "" + +#: ../../introduction/prerequisites.md:73 6d772529b43746a9bbb7c3bd2fb033a2 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" +msgstr "" + +#: ../../introduction/prerequisites.md:79 d48c1d5aab4d4b78b610a6a8cecbac3f +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../introduction/prerequisites.md:84 50a41a581e2045fd9fcd7149162d1b43 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../introduction/prerequisites.md:86 35183394d2db4b0797e6a5533cf91eed +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../introduction/prerequisites.md:91 b59575e71904478e8833c13b38d53c91 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../introduction/prerequisites.md:93 c784985a2d3d4d5c9583fe8d76037a90 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../introduction/prerequisites.md:101 1fa903efc96d46c79a00a49b9ed778ee +msgid "" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../introduction/prerequisites.md:104 ebecb9c15b7549c1bf82cbc381721378 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../introduction/prerequisites.md:111 4290343102b746a6987d45a33fb75e8f +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." +msgstr "" + +#: ../../introduction/prerequisites.md:115 95dd822409aa414d848cf74a0882f12d +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../introduction/prerequisites.md:120 be41ce025e294eef8015ac9ffaecd31d +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../introduction/prerequisites.md:125 6ff60669f1ec486e9c80cd32f2f0b8da +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" +msgstr "" + +#: ../../introduction/prerequisites.md:129 284249ed02604c479e8a7f9ae098a936 +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../introduction/prerequisites.md:135 2830ba8ada494febaa3cab175aae5c96 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../introduction/prerequisites.md:137 b4a5c084f47a4524b4bbc783481ddb80 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../introduction/prerequisites.md:144 09daa94a2e764c588ed9bdf05686195c +msgid "" +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." +msgstr "" + +#: ../../introduction/prerequisites.md:148 16b2246ddcde4bd4bab4c9b85a3245cd +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../introduction/prerequisites.md:154 8e5ac54df4264041a8766f683a530806 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env ` rather than" +" using a hard-coded location, since `/usr/bin/env ` looks for" +" the `` program in the system `PATH`," +msgstr "" + +#: ../../introduction/prerequisites.md:161 98043798d4f04488b47f65f6a3d0cbdf +msgid "Text Editor" +msgstr "" + +#: ../../introduction/prerequisites.md:163 dd5138ef1899479eb6a8419834dc94d4 +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../introduction/prerequisites.md:167 2c49302420ca4ef58824a611f6e21631 +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" +msgstr "" + +#: ../../introduction/prerequisites.md:171 121e8e64431f49159424ed4ffad079e0 +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " +"" +msgstr "" + +#: ../../introduction/prerequisites.md:172 786d0c2fb6c44f5c8ddb42ad714b43cc +msgid "" +"cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../introduction/prerequisites.md:174 0a7322840cc64223985de5eaf3f6e5ef +msgid "" +"The CWL community also maintains a list of editors and viewers: " +"" +msgstr "" + +#: ../../introduction/prerequisites.md:177 adf7801f93e54841935427ad5fa76ee1 +msgid "Docker" +msgstr "" + +#: ../../introduction/prerequisites.md:181 2d5c42927e8347efa27e75882e59f27d +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: " +"." +msgstr "" + +#: ../../introduction/prerequisites.md:185 58f717b8eb5546459d0e97cf3f4eef0a +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models " +"with and without containers." +msgstr "" + +#: ../../introduction/prerequisites.md:191 2c0ad9dee73c4e278ef0ad7f731c4931 +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for " +"pulling images." +msgstr "" + +#: ../../introduction/prerequisites.md:196 a80ae1bdfdb04e1598f06d5115d624eb +msgid "Learn More" +msgstr "" + +#: ../../introduction/prerequisites.md:198 baf0ff9fd9314b5884cf6f2110d964b3 +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." +msgstr "" + +#: ../../introduction/prerequisites.md:199 958ac076e60a420b8b8d790cd49f6da8 +msgid "The Python `venv` module: " +msgstr "" + diff --git a/locales/en/LC_MESSAGES/introduction/quick-start.po b/locales/en/LC_MESSAGES/introduction/quick-start.po new file mode 100644 index 00000000..077b542d --- /dev/null +++ b/locales/en/LC_MESSAGES/introduction/quick-start.po @@ -0,0 +1,191 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../introduction/quick-start.md:1 47ace6396c93455bb9b8cb8a70be0679 +msgid "Quick Start" +msgstr "" + +#: ../../introduction/quick-start.md:3 17131fb92d5a46d99b7665d0c2890a46 +msgid "" +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../introduction/quick-start.md:7 ad577f43c1ec4d79b9cbe4cd5125a31a +msgid "“Hello World”" +msgstr "" + +#: ../../_includes/what-is-cwl.md:2 4d26ec28a1fa419bb9a1f536e4168925 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../introduction/quick-start.md:12 12247e5c020e4eabaddc0a62364c45e2 +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../introduction/quick-start.md:16 60c57d9de0e449bbb1ec517663e9047f +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../introduction/quick-start.md:22 0a89aaf525d349349bb23ecf11f00a1e +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../introduction/quick-start.md:27 f33aad86b3194d92b87e51b8551de335 +msgid "" +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." +msgstr "" + +#: ../../introduction/quick-start.md:32 bba033bcce684da99d8561c644a288b9 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../introduction/quick-start.md:34 74c2a60629734132baf21f950f51a2a8 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" +msgstr "" + +#: ../../introduction/quick-start.md:39 688e1f06579d44b8975c3db85d5969f6 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../introduction/quick-start.md:47 77a52c31fce14347bbb47d80f59489e7 +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." +msgstr "" + +#: ../../introduction/quick-start.md:51 235356675f8b492b86a59fe345d67184 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../introduction/quick-start.md:53 4caaccb9352a46678835a5bfb413803b +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../introduction/quick-start.md:57 ccbc60f4811e4a479530094958219224 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../introduction/quick-start.md:62 3b3cd61bd0fe4dddbab7ce4fabc16421 +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../introduction/quick-start.md:65 71f096c461ef47f8a920339e164bf314 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../introduction/quick-start.md:70 cbaa83776dc041dd963ce47a67b3b405 +msgid "" +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" +msgstr "" + +#: ../../introduction/quick-start.md:74 04e272f684be44be911dc6e50ac1660b +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../introduction/quick-start.md:80 5d1ebc06dc2d44439135ee1e75cc714a +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" +msgstr "" + +#: ../../introduction/quick-start.md:82 6ad6b44a644b482382cec3bfda23e4ac +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../introduction/quick-start.md:88 bf7a0bd183f64f6883ecee1dae23607a +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." +msgstr "" + +#: ../../introduction/quick-start.md:94 002680b62d5d4d8fbf8d730e38ef154a +msgid "Learn More" +msgstr "" + +#: ../../introduction/quick-start.md:96 716e6ec03d974ee9ac59a055fcdabe41 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../introduction/quick-start.md:97 a098326c57f34af5972578ebb580d6a2 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../introduction/quick-start.md:98 cba27320bbe844fc8bfbad0ba2aa9c01 +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." +msgstr "" + +#: ../../introduction/quick-start.md:99 e377948d6db94e1aa5c3b28c44a9707c +msgid "" +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../introduction/quick-start.md:100 b554f9e0572e4b02a5cc1cb817c70539 +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../introduction/quick-start.md:101 a2ce57a5a0a24bb0bb858e076df51e6c +msgid "" +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." +msgstr "" + +#: ../../introduction/quick-start.md:102 edb34dacc1674731a7b5fa510c81d38b +msgid "" +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/setup.po b/locales/en/LC_MESSAGES/setup.po new file mode 100644 index 00000000..15bfffe9 --- /dev/null +++ b/locales/en/LC_MESSAGES/setup.po @@ -0,0 +1,31 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../setup.md:5 27e5c491bbd4441d96d85f6d8f66181e +msgid "This page has moved" +msgstr "" + +#: ../../setup.md:9 4b442c302c2d4c84a462c1fa1781b35d +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/sphinx.po b/locales/en/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..d097c6cb --- /dev/null +++ b/locales/en/LC_MESSAGES/sphinx.po @@ -0,0 +1,28 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../_templates/sidebar-nav-bs.html:1 94578a793f824c289114eb8091fcbb83 +msgid "Main navigation" +msgstr "" + +#: ../../_templates/sidebar-nav-bs.html:3 0004714627914a26a46506c14c85806d +msgid "Section Navigation" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po b/locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po new file mode 100644 index 00000000..0adab36c --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po @@ -0,0 +1,84 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/additional-arguments-and-parameters.md:1 +#: 245426859a1e4d2db7facb0504eb028c +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:3 +#: 6be40170e1d14af08a2b49daecae8df7 +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:6 +#: a3f17f29d2ab4ad2993696400f7be61b +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:13 +#: 77443a85f1a14fef94fc4d6d4add43ca +msgid "`arguments.cwl`" +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:19 +#: 42d3138cc25d4570ada1a25ac13fb8bc +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:24 +#: 1a7130850048412fa12f6fcec745e4ee +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:30 +#: f4fcf30ed13c42d3a93817dc29651686 +msgid "" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:36 +#: c470ae16de004280a2bd2b0a99f391b3 +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../topics/additional-arguments-and-parameters.md:43 +#: a31eeefe78ab4442bcfea3e1106cf8a9 +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/best-practices.po b/locales/en/LC_MESSAGES/topics/best-practices.po new file mode 100644 index 00000000..30c7c72e --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/best-practices.po @@ -0,0 +1,191 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/best-practices.md:1 400480770c074343aae662a25b257a31 +msgid "Best Practices" +msgstr "" + +#: ../../topics/best-practices.md:3 fe9e19076d74462cab67b4a3cb340724 +msgid "" +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." +msgstr "" + +#: ../../topics/best-practices.md:8 caab132559d84593ac23530e36ec6c21 +msgid "" +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../topics/best-practices.md:11 e15eb191624846c4b1d3e3e96731a8ff +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." +msgstr "" + +#: ../../topics/best-practices.md:20 d5c2b325d05f4afca4008f4733d92100 +msgid "" +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../topics/best-practices.md:26 99b89f6ce812463093ee0da9255178bb +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" +msgstr "" + +#: ../../topics/best-practices.md:28 56915c2feeb9402fb1210cdf27788c8a +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../topics/best-practices.md:37 4315b219d21742ac88f39415da6807d8 +msgid "" +"For more examples of providing metadata within CWL descriptions, see " +"[the Metadata and Authorship section of this User Guide](../topics" +"/metadata-and-authorship.md)." +msgstr "" + +#: ../../topics/best-practices.md:40 122f553a412d43bd9e55caaafb90b88f +msgid "" +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." +msgstr "" + +#: ../../topics/best-practices.md:44 b5fe5270c8534ad194dbf41bdec90e33 +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"`SoftwareRequirement`." +msgstr "" + +#: ../../topics/best-practices.md:47 889a5c8d24464546a2a1156ef3791b28 +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../topics/best-practices.md:50 7203be6d92a040c2b39f07f0618b7c37 +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../topics/best-practices.md:55 8ea3eee32d8044c5ad0a4caeab435b8b +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../topics/best-practices.md:58 3c033a88a5cd4bf19683add86436a8de +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." +msgstr "" + +#: ../../topics/best-practices.md:66 7731a6bd39a7444e82b96d2a5e8eb44b +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." +msgstr "" + +#: ../../topics/best-practices.md:69 fe8845e0d96f459bbcd69e176e7ff6b1 +msgid "" +"Each `CommandLineTool` description should focus on a single operation " +"only, even if the (sub)command is capable of more. Don't overcomplicate " +"your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../topics/best-practices.md:73 1ffe2266eef94941840c485ca77417b6 +msgid "" +"Custom types should be defined with one external YAML per type definition" +" for re-use." +msgstr "" + +#: ../../topics/best-practices.md:76 e5af104f7c2848c8ac0f97d13a9153a2 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../topics/best-practices.md:78 88c7bfbebad14cf9b39bd3e9488c7dfb +msgid "" +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." +msgstr "" + +#: ../../topics/best-practices.md:82 4f874eee6d884b6c8f2117f61788a4e5 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." +msgstr "" + +#: ../../topics/best-practices.md:85 6c481e56c4ff48fc9854a3c15375f5f7 +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../topics/best-practices.md:90 2e66f35622964ad6bc54faedbfec0eeb +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." +msgstr "" + +#: ../../topics/best-practices.md:93 c5551f6025e445f296d3de936029fab4 +msgid "" +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../topics/best-practices.md:97 eff85713fb344bfb968bda07094485af +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/command-line-tool.po b/locales/en/LC_MESSAGES/topics/command-line-tool.po new file mode 100644 index 00000000..212158b9 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/command-line-tool.po @@ -0,0 +1,71 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/command-line-tool.md:1 48774f562479443fa878218b84edd4f0 +msgid "Command Line Tool" +msgstr "" + +#: ../../topics/command-line-tool.md:3 8cb2bbcf217f4a35acd6fe7aac1b9493 +msgid "" +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." +msgstr "" + +#: ../../topics/command-line-tool.md:8 9d7a6d6def0046c180c951e9ad94afeb +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../topics/command-line-tool.md:19 a6e02298d1fa432d9d6b54b420818901 +msgid "CWL command-line tool." +msgstr "" + +#: ../../topics/command-line-tool.md:50 a6638b2f0c184e95abc23d6207e81802 +msgid "`echo.cwl`" +msgstr "" + +#: ../../topics/command-line-tool.md:57 da7864a3fcf842459475b5b27a693ded +msgid "" +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../topics/command-line-tool.md:68 0a222e61001a4a08bc2e82ca52105a09 +msgid "Network Access" +msgstr "" + +#: ../../topics/command-line-tool.md:69 988c4b4184d0405e9bc26bb7bcb05c8b +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. If a command-line tool is written manually in CWL v1.1+, there is" +" a need to specify when network access is required." +msgstr "" + +#: ../../topics/command-line-tool.md:83 2918cea6f64846c498fdf03b92533d94 +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " +"Network Access automatically." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po b/locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po new file mode 100644 index 00000000..39b54f98 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po @@ -0,0 +1,104 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/creating-files-at-runtime.md:1 2bbf4c0a32054cfebe3b6b1b02ea3558 +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:3 c5010461c4fe4e8fb7c4f7da2653febe +msgid "" +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:7 27879c9542e444dca1a80c1784891bf7 +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:9 61cf19e01c03473aa239bc42394bfcff +msgid "`createfile.cwl`" +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:15 +#: 8d1fb6bc4eed466391ad62fe5be90a13 +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:20 +#: 40e30b78078a4184b4c5bd69c0766cef +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:27 +#: c624145be5a04d65acaaa4bfa086c473 +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:29 +#: 202ff16474a04e29b0e363cb5241b53e +msgid "`echo-job.yml`" +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:35 +#: ea631a00fdd9484486e1ca60a90b6d8a +msgid "" +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:40 +#: 1dea9f63048f40528c904ec2fb4bef69 +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:51 +#: cff49a2cf48c43f0aeaa6241e1bcaabe +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." +msgstr "" + +#: ../../topics/creating-files-at-runtime.md:54 +#: c81ca28ee4d44d82b6cf3bdbf8460642 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/custom-types.po b/locales/en/LC_MESSAGES/topics/custom-types.po new file mode 100644 index 00000000..66cf4c6c --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/custom-types.po @@ -0,0 +1,99 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/custom-types.md:1 ab79908260aa4842b2322e6e4d615f72 +msgid "Custom Types" +msgstr "" + +#: ../../topics/custom-types.md:3 75b9b1f15a744e24b2f7333b6638bcc4 +msgid "" +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." +msgstr "" + +#: ../../topics/custom-types.md:9 7f4a9afccdad41b9892d8424e9fb539d +msgid "" +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../topics/custom-types.md:12 8f03906168eb4bf0a6bf7ae0f6e0ecb1 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../topics/custom-types.md:18 0b8de32a79a14b2a841851ceab22b6b3 +msgid "`custom-types.yml`" +msgstr "" + +#: ../../topics/custom-types.md:24 8ba644c7152247959988abfcd2b4c2be +msgid "" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" +msgstr "" + +#: ../../topics/custom-types.md:30 975bdfc68b1841fa89a055b7f03fb0ec +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../topics/custom-types.md:46 d4efacf670184435a5729e0ba5e16a36 +msgid "" +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." +msgstr "" + +#: ../../topics/custom-types.md:53 ea6ca32a9e6e4f38be19487348cd45f7 +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../topics/custom-types.md:55 5bfed5519bc04c35aa6ad8626201f98f +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../topics/custom-types.md:61 066aef77545f4dc8b11f09caa710be9e +msgid "" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" +msgstr "" + +#: ../../topics/custom-types.md:76 7e35076a9b0347ff967c5271a3ccf881 +msgid "" +"Note also that the author of this CWL description has also included " +"`ResourceRequirement`s, specifying the minimum amount of RAM and number " +"of cores required for the tool to run successfully, as well as details of" +" the version of the software that the description was written for and " +"other useful metadata. These features are discussed further in other " +"chapters of this user guide." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/environment-variables.po b/locales/en/LC_MESSAGES/topics/environment-variables.po new file mode 100644 index 00000000..6ecd617f --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/environment-variables.po @@ -0,0 +1,45 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/environment-variables.md:1 498dbc0db9224aabbc9fd1bef778f8ef +msgid "Environment Variables" +msgstr "" + +#: ../../topics/environment-variables.md:3 9ce0f06bed3649339f666147b45c69e4 +msgid "" +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../topics/environment-variables.md:7 ef471bebcfc94b008c94a2e8056d7af0 +msgid "`env.cwl`" +msgstr "" + +#: ../../topics/environment-variables.md:13 df5ab6417f87475d8d94f2af498cee39 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../topics/environment-variables.md:18 642f1379ebdd4dd381e8f56343547b42 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/expression-tool.po b/locales/en/LC_MESSAGES/topics/expression-tool.po new file mode 100644 index 00000000..8d8ad3dc --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/expression-tool.po @@ -0,0 +1,53 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/expression-tool.md:1 2ed0674b02ee4cd7ac4e169086d02513 +msgid "Expression Tool" +msgstr "" + +#: ../../topics/expression-tool.md:3 95b1b27ad2a84cd9bd1207ff75536502 +msgid "" +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." +msgstr "" + +#: ../../topics/expression-tool.md:8 80caa25305a74efdaed8ada05faaa018 +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../topics/expression-tool.md:17 a664a455f4714071ba0158a4f83a127c +msgid "CWL expression tool." +msgstr "" + +#: ../../topics/expression-tool.md:48 bdfa455a230e4be79031e0777efc7233 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../topics/expression-tool.md:67 0df562c4585e43d1ae4ac8113b50ed71 +msgid "" +"We had to use an `InlineJavascriptRequirement` as our expression contains" +" a JavaScript call in `.toUpperCase()`. This means to tools using the " +"expression tool that JavaScript is a requirement." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/expressions.po b/locales/en/LC_MESSAGES/topics/expressions.po new file mode 100644 index 00000000..f09d91d8 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/expressions.po @@ -0,0 +1,383 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/expressions.md:1 15bf6af8d07d476ea6996a0be17fdca0 +msgid "Expressions" +msgstr "" + +#: ../../topics/expressions.md:3 248bcdddada043abaaf9d53819dd3d01 +msgid "" +"If you need to manipulate input parameters, include the requirement " +"`InlineJavascriptRequirement` and then anywhere a parameter reference is " +"legal you can provide a fragment of Javascript that will be evaluated by " +"the CWL runner." +msgstr "" + +#: ../../topics/expressions.md:9 986c932e94e3496b8ab3ef5c9b1927c5 +msgid "" +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." +msgstr "" + +#: ../../topics/expressions.md:16 a82f11177ce54f7f92b6e5b037a1b6d0 +msgid "`expression.cwl`" +msgstr "" + +#: ../../topics/expressions.md:22 e1c2a91028bc47238421457f323556db +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" +msgstr "" + +#: ../../topics/expressions.md:25 bddb2b6b6507418785bc194340313a39 +msgid "`empty.yml`" +msgstr "" + +#: ../../topics/expressions.md:31 6932ad2e25eb4e3c835bf37557efbf03 +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." +msgstr "" + +#: ../../topics/expressions.md:35 51962babe16e4b8493cafe401f046510 +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../topics/expressions.md:37 f302523bb23049afa0dc534641abba94 +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../topics/expressions.md:47 5e672f895eb94028bb7fbc4ba7646c46 +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" +msgstr "" + +#: ../../topics/expressions.md:54 913d17f1bb474dec91b467db5f45ffab +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." +msgstr "" + +#: ../../topics/expressions.md:62 8f26131c8cc94db88fc88100f0404bff +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../topics/expressions.md:64 ad6af4e35d014ce7bd122b00f99f13dd +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../topics/expressions.md:66 4b2eaee288a4421a91b304a186578361 +msgid "" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../topics/expressions.md:67 032d4eeaeda14354a8b059e4391f3448 +msgid "`arguments`" +msgstr "" + +#: ../../topics/expressions.md:68 ../../topics/expressions.md:76 +#: ../../topics/expressions.md:89 aebe22df1bf6432aa39e402802ce8fcd +#: dcc0d4a9abcb4e35ae4ee341893d757f fca0e4b343c940989ebbf8ce7cf87605 +msgid "`valueFrom`" +msgstr "" + +#: ../../topics/expressions.md:69 0b185807c14741bca2b1ce4252bded44 +msgid "`stdin`" +msgstr "" + +#: ../../topics/expressions.md:70 716a8fad0a5d46bb9d17d35c0866db31 +msgid "`stdout`" +msgstr "" + +#: ../../topics/expressions.md:71 e9d014cdaf794dacb4eee304c1364d1b +msgid "`stderr`" +msgstr "" + +#: ../../topics/expressions.md:72 81333fdf0ac84d4495ec32cd4b58f12e +msgid "" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../topics/expressions.md:73 ../../topics/expressions.md:78 +#: ../../topics/expressions.md:85 ../../topics/expressions.md:93 +#: bf75a275d26345bf86076cea5c44f5d8 c704d979a192458a9315971e6702478a +#: d29995b11d3f4157915f48c52f4eba90 ff462897cd0149c493e50ee87f9d1c0e +msgid "`format`" +msgstr "" + +#: ../../topics/expressions.md:74 ../../topics/expressions.md:79 +#: ../../topics/expressions.md:86 ../../topics/expressions.md:94 +#: 18e86fc5bf684862a30f373766d067eb 195022a4f28f419ea24095350e89c7dd +#: 403516ed7955408fa7a12d34fd1fbe82 dd2932a497104db096a8ecb1986381b6 +msgid "`secondaryFiles`" +msgstr "" + +#: ../../topics/expressions.md:75 49d00678c3d8425db3852e408049e249 +msgid "" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../topics/expressions.md:77 8523d80e16a24adebc3fdad88141e646 +msgid "" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../topics/expressions.md:80 51af437d2c314f18895ae13e58dbd56e +msgid "" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../topics/expressions.md:81 9d9b304dceaa4cb38e01503ff57d726b +msgid "`glob`" +msgstr "" + +#: ../../topics/expressions.md:82 65bceca1c4f7447fa5f3e0c448a02af6 +msgid "`outputEval`" +msgstr "" + +#: ../../topics/expressions.md:83 5bc18fb8fa034c4281b715ab44a5cb75 +msgid "From `Workflow`" +msgstr "" + +#: ../../topics/expressions.md:84 fcfc00ff02d04e61bdc6d5432d04c7da +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../topics/expressions.md:87 e51177ae5daa42429266893d9467cd15 +msgid "From `steps`" +msgstr "" + +#: ../../topics/expressions.md:88 4e6a5b41b2f249b896d7a1e79b2aebbb +msgid "" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../topics/expressions.md:90 9233f867e33d41199e31ed9115442d7e +msgid "" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../topics/expressions.md:91 60fc0bdd44614b61961aa204edae77b9 +msgid "`expression`" +msgstr "" + +#: ../../topics/expressions.md:92 2cf4288d3d594085af2a07026bc71371 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../topics/expressions.md:95 1455be996e7147c99d60cc9f198b78cb +msgid "" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../topics/expressions.md:96 0ac9b337923c4a2793fe198d6bf759f1 +msgid "`coresMin`" +msgstr "" + +#: ../../topics/expressions.md:97 993661b89e4945d0ad4f8a13931eeffb +msgid "`coresMax`" +msgstr "" + +#: ../../topics/expressions.md:98 22d35c6039754b6b96fed696f9a06a71 +msgid "`ramMin`" +msgstr "" + +#: ../../topics/expressions.md:99 53cce3babeac44c98bbfe68d122e5796 +msgid "`ramMax`" +msgstr "" + +#: ../../topics/expressions.md:100 ed43db0eedef4716800239b9c6c5c9f0 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../topics/expressions.md:101 e4e8d9975aa74847a49060459ace3edc +msgid "`tmpdirMax`" +msgstr "" + +#: ../../topics/expressions.md:102 13713c1adb7f4759b1792bbf3e720c29 +msgid "`outdirMin`" +msgstr "" + +#: ../../topics/expressions.md:103 d8c878c467f34807b98c156ad8705445 +msgid "`outdirMax`" +msgstr "" + +#: ../../topics/expressions.md:104 fb119535e57d4a55b6e9a86deaecc100 +msgid "" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../topics/expressions.md:105 dbe84d62840049e7b9ed3498d15847f6 +msgid "`listing`" +msgstr "" + +#: ../../topics/expressions.md:106 6db83a55040447c7903dd5d2d0bb00f8 +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../topics/expressions.md:107 8ff197dd79524f25912ef459fb7b20d1 +msgid "`entry`" +msgstr "" + +#: ../../topics/expressions.md:108 fcea352f4e4246bf8fba2f53665427df +msgid "`entryname`" +msgstr "" + +#: ../../topics/expressions.md:109 120885c8f41e4ad58458699a66b38fc6 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../topics/expressions.md:110 17cea5e071b0430d901810a76ff224d4 +msgid "" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../topics/expressions.md:111 5e6e3c6614d043e596be33cb9aba75c5 +msgid "`envValue`" +msgstr "" + +#: ../../topics/expressions.md:116 54b20c309ca543df81b8221c6d8f9eaa +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../topics/expressions.md:118 54df5f1a63554bf7989dccf12aa205a1 +msgid "" +"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" +" attribute that allows users to load external JavaScript files, or to " +"provide inline JavaScript code." +msgstr "" + +#: ../../topics/expressions.md:122 8e6566d5b3fd424fa95e77df42ae18ed +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." +msgstr "" + +#: ../../topics/expressions.md:128 50f2d063d4864db1b051a41769b3d928 +msgid "" +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." +msgstr "" + +#: ../../topics/expressions.md:135 e2c6c8b5d1b345368e0699a5a2a079cc +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" +msgstr "" + +#: ../../topics/expressions.md:139 1ce74804ca97479fb6bdacbdba2bbc5c +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../topics/expressions.md:146 fbe150d3864e4987ae145a8b7de60151 +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" +msgstr "" + +#: ../../topics/expressions.md:149 7552ea9b4f714fbe8aea6db94fd8894f +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../topics/expressions.md:155 2f3154ec78274b43accde1409c59ec56 +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../topics/expressions.md:158 ee2508f7faf74dd3a2928aebd3dc4314 +msgid "`custom-functions.js`" +msgstr "" + +#: ../../topics/expressions.md:164 9ba72aae0ff546e282aaa2518a5cd237 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../topics/expressions.md:171 e1b9ad0192e44844ab641c883e859510 +msgid "" +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../topics/expressions.md:175 3b40577e79f9432b9bad3fbaf5fc4b78 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../topics/expressions.md:181 6298a4cf813142e09b35c55fd7077cbc +msgid "" +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." +msgstr "" + +#: ../../topics/expressions.md:186 881975804cc246cdb81af6ad04734a19 +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../topics/expressions.md:193 9369098b680540e2b6ea67f861e193ed +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../topics/expressions.md:200 ec09ac813f3142e9b333428a44bb1244 +msgid "" +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/file-formats.po b/locales/en/LC_MESSAGES/topics/file-formats.po new file mode 100644 index 00000000..73be3838 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/file-formats.po @@ -0,0 +1,93 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/file-formats.md:1 24ece5b3bfe646268d48b0339ba10e7b +msgid "File Formats" +msgstr "" + +#: ../../topics/file-formats.md:3 a7520d9841f044f8a33d1acf1f6234bf +msgid "" +"Tools and workflows can take `File` types as input and produce them as " +"output. We also recommend indicating the format for `File` types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." +msgstr "" + +#: ../../topics/file-formats.md:8 544fcf8047db45c3aad991cfdf732309 +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../topics/file-formats.md:14 12d2dc549a684fff9cb46320700143fa +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." +msgstr "" + +#: ../../topics/file-formats.md:17 c362c433ba544d1eaa19781db09aafbd +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../topics/file-formats.md:20 c1007004cc7a4c408a713c38208574c0 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../topics/file-formats.md:26 47ec32f1249f48149068417e431a20f5 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../topics/file-formats.md:32 f99998f5da604c9b827367670cd30879 +msgid "Sample Parameter Files" +msgstr "" + +#: ../../topics/file-formats.md:34 050ec30459884b1581d715038fe2b05a +msgid "" +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." +msgstr "" + +#: ../../topics/file-formats.md:39 dd49f6afbc754b9083888cf822cc369e +msgid "`sample.yml`" +msgstr "" + +#: ../../topics/file-formats.md:45 7e1974e26afc40568d4e483d20c4b86f +msgid "" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../topics/file-formats.md:52 46649847e8d440b9b4f6726be286e067 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/index.po b/locales/en/LC_MESSAGES/topics/index.po new file mode 100644 index 00000000..b90b5d6b --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/index.po @@ -0,0 +1,24 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/index.md:1 55452f6967174ff5a1d8cf776874a90b +msgid "Topics" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/inputs.po b/locales/en/LC_MESSAGES/topics/inputs.po new file mode 100644 index 00000000..03f1b021 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/inputs.po @@ -0,0 +1,313 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/inputs.md:1 03f3a68492ca43bea79742a839864b86 +msgid "Inputs" +msgstr "" + +#: ../../topics/inputs.md:3 9772b8bb0b694b9e9eef5e65b4ffe333 +msgid "Essential Input Parameters" +msgstr "" + +#: ../../topics/inputs.md:5 68cd0cab423c4d10a69989e6a3833e7a +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../topics/inputs.md:9 2a76b22fc015489b81d6c396f4f8ae30 +msgid "" +"Available primitive types are *string*, *int*, *long*, *float*, *double*," +" and *null*; complex types are *array* and *record*; in addition there " +"are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../topics/inputs.md:13 ba487511ecd84b37af0796d5159e50e3 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." +msgstr "" + +#: ../../topics/inputs.md:16 59dd55e707cd49f385f5763aa54bc461 +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../topics/inputs.md:18 0d05676c671a420b87f3808010ccc207 +msgid "`inp.cwl`" +msgstr "" + +#: ../../topics/inputs.md:24 06e169026a20469cb6b04a216045cc87 +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../topics/inputs.md:26 05dd5f7e9edf4c379e66d8b6cfc1f86f +msgid "`inp-job.yml`" +msgstr "" + +#: ../../topics/inputs.md:33 f02466c6a7bf4795892d14963a8ad22e +msgid "" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../topics/inputs.md:40 5e5a2fe06ad04b2d8969d6cbfed213ec +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." +msgstr "" + +#: ../../topics/inputs.md:44 fafabc3b11f14bb68c16e3f497e26e40 +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." +msgstr "" + +#: ../../topics/inputs.md:47 7e3d42ea93dd417195ab6b5559638326 +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." +msgstr "" + +#: ../../topics/inputs.md:53 0bbabcf2be26490dbe920f52f8cbe9b0 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" +msgstr "" + +#: ../../topics/inputs.md:64 c340c8aa7b80488ba6d16329e1ca2149 +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" +msgstr "" + +#: ../../topics/inputs.md:70 5c2e148fdb324017a685f5adefadd74d +msgid "" +"The field `inputBinding` is optional and indicates whether and how the " +"input parameter should appear on the tool's command line. If " +"`inputBinding` is missing, the parameter does not appear on the command " +"line. Let's look at each example in detail." +msgstr "" + +#: ../../topics/inputs.md:83 97d14a1cf8fc4b3687281aa93eb1ceb6 +msgid "" +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." +msgstr "" + +#: ../../topics/inputs.md:95 6c2008aed010466c8e4465c72a4b6d79 +msgid "" +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." +msgstr "" + +#: ../../topics/inputs.md:109 95f2a1493e50455ea6e546f70726fab1 +msgid "" +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../topics/inputs.md:124 3a48173a38904861b9994edddbc2f082 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." +msgstr "" + +#: ../../topics/inputs.md:131 54186920b4a14fbfa059779411b20192 +msgid "" +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../topics/inputs.md:134 920e8b7d7eee4239b327b0386a872492 +msgid "" +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." +msgstr "" + +#: ../../topics/inputs.md:142 690f556fa0854517a4e3e43747178461 +msgid "" +"The `baseCommand` field will always appear in the final command line " +"before the parameters." +msgstr "" + +#: ../../topics/inputs.md:146 65ae530b9da84e7e98bcf5a5cf516c30 +msgid "Array Inputs" +msgstr "" + +#: ../../topics/inputs.md:148 21f30b0db29c4aa4989c39997b1a720c +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." +msgstr "" + +#: ../../topics/inputs.md:154 cefc841cd57c4b19b2be69aa80106c8b +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../topics/inputs.md:160 bae9c79fa8bb42f6922ee937a5c5ff7a +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../topics/inputs.md:166 b756a25aad9e4fcfb68cbe2123cac3c5 +msgid "" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../topics/inputs.md:178 0a930f2019b748858ddc5ca5acbde210 +msgid "" +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." +msgstr "" + +#: ../../topics/inputs.md:185 57551982494e4152b2c2c11f04bae126 +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." +msgstr "" + +#: ../../topics/inputs.md:191 30d6b347401d4304b4dcc1ef2268ded2 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../topics/inputs.md:193 cf8b6d0ed47a4e57a39add29f91f0ec0 +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../topics/inputs.md:198 5aa374f61a2a41e383da4b960e3603d5 +msgid "`record.cwl`" +msgstr "" + +#: ../../topics/inputs.md:204 6557427907d0465695aa88f2f27d5bf1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../topics/inputs.md:215 3f39bfdadeb14b0d8dfb67fe5aad7790 +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." +msgstr "" + +#: ../../topics/inputs.md:217 30829196c2f54dbb9b1c35e462fe4e85 +msgid "`record-job2.yml`" +msgstr "" + +#: ../../topics/inputs.md:233 049396bf53d241cd9d03b9ff81468e0c +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." +msgstr "" + +#: ../../topics/inputs.md:236 a9036f0e32ff418482573d23ed074256 +msgid "`record-job3.yml`" +msgstr "" + +#: ../../topics/inputs.md:252 bc0b43accbf9452ca4b7c2d7d69c2984 +msgid "" +"In the third example, only `itemD` is provided, so it appears on the " +"command line." +msgstr "" + +#: ../../topics/inputs.md:255 6cfc57be54f8458ebc9d784bc9ac2555 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../topics/inputs.md:257 0279c53e41c94ccc9f2de65d057dd903 +msgid "" +"If you use exclusive input parameters combined with expressions, you need" +" to be aware that the `inputs` JavaScript object will contain one of the " +"exclusive input values. This means that you might need to use an **or** " +"boolean operator to check which values are present." +msgstr "" + +#: ../../topics/inputs.md:262 b94737f481d343bfbb6ecf0fd81c9d6f +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." +msgstr "" + +#: ../../topics/inputs.md:265 b5335802dcd148e9bb8f72d75f1ff6cd +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../topics/inputs.md:271 08b50c80fd024f86ba9c6239895385d0 +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as “fasta” (one of the values of the enum), " +"your command should execute successfully:" +msgstr "" + +#: ../../topics/inputs.md:280 77c08d3144b04e58a6733cbd01346102 +msgid "" +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to a `null` value, which does not match the expected type " +"for the output field (a `string`), resulting in failure when running your" +" workflow." +msgstr "" + +#: ../../topics/inputs.md:289 91280fddf3624696b90632ca8466ca59 +msgid "" +"To correct it, you must remember to use an or operator in your JavaScript" +" expression when using exclusive parameters, or any parameter that allows" +" `null`. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value if none was " +"provided in the command line or job input file." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/metadata-and-authorship.po b/locales/en/LC_MESSAGES/topics/metadata-and-authorship.po new file mode 100644 index 00000000..fb846967 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/metadata-and-authorship.po @@ -0,0 +1,70 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/metadata-and-authorship.md:1 e5511fed73914ceeaf73b9ca7020e8d2 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../topics/metadata-and-authorship.md:3 1a4f0cbf7a694f949646c7bfc1d6f5dc +msgid "" +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../topics/metadata-and-authorship.md:13 f1dcef50a880467f82b93f383030501b +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." +msgstr "" + +#: ../../topics/metadata-and-authorship.md:16 1af01d43dfd9408ab58a960b62bf44f0 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../topics/metadata-and-authorship.md:22 ecd7d3e4f19146ef807219add82fff00 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../topics/metadata-and-authorship.md:28 a8b454c10d484726b194de1f8c0775da +msgid "Extended Example" +msgstr "" + +#: ../../topics/metadata-and-authorship.md:30 0e5960b6d60b4a73837d1ea4b36a896d +msgid "" +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." +msgstr "" + +#: ../../topics/metadata-and-authorship.md:35 89713dbe4568459488494cf7f23ee622 +msgid "`metadata_example3.cwl`" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/operations.po b/locales/en/LC_MESSAGES/topics/operations.po new file mode 100644 index 00000000..dd111423 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/operations.po @@ -0,0 +1,73 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/operations.md:1 968848522a1c419e94cdb03a48f7bab8 +msgid "Operations" +msgstr "" + +#: ../../topics/operations.md:3 825f5584a57148e4ba1df435653351a1 +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." +msgstr "" + +#: ../../topics/operations.md:7 1c8a712c12b54c26ac8d2d24270390cf +msgid "" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../topics/operations.md:10 e0e24f86682447ad88bb59f73f4c272f +msgid "`operations.cwl`" +msgstr "" + +#: ../../topics/operations.md:16 a1448ed2695b4b849c0e2879c38640d8 +msgid "" +"The `uppercase` step of the workflow is an operation. It can be used like" +" a command line tool or an expression. You can also plot it with the CWL " +"Viewer or `cwltool`:" +msgstr "" + +#: ../../topics/operations.md:24 0ed9d93f0ead46fea1f3d5f28d22419b +msgid "" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx Graphviz directive (this" +" user guide is built with Sphinx):" +msgstr "" + +#: ../../topics/operations.md:55 4a03e03b140a45b3bfc26d7b0f677cb4 +msgid "" +"If you try running it with `cwltool`, the command will fail since " +"`cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../topics/operations.md:58 7794ec6d263c425bb423135f4025d2f1 +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../topics/operations.md:66 8c8423c44aec4a619ea9bbce986b3b96 +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/outputs.po b/locales/en/LC_MESSAGES/topics/outputs.po new file mode 100644 index 00000000..84287200 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/outputs.po @@ -0,0 +1,147 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/outputs.md:1 8b140307638c4baa9261df35f7372240 +msgid "Outputs" +msgstr "" + +#: ../../topics/outputs.md:3 59a76cb3f5b04cf391310d816bdd4759 +msgid "Returning Output Files" +msgstr "" + +#: ../../topics/outputs.md:5 f1e1c91b796e4c4bbb5c8e234852225d +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." +msgstr "" + +#: ../../topics/outputs.md:10 aa7076aea7e54d489af848f9523794fe +msgid "" +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or come from examining the content of those files." +msgstr "" + +#: ../../topics/outputs.md:16 7ee8d5efbc2d43c297960a3d851628f9 +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." +msgstr "" + +#: ../../topics/outputs.md:19 ba6fcc05fcdd46f6b1f354295bf124de +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../topics/outputs.md:21 7534fb6a5894438f9da2167e08f4e218 +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string we can use an " +"_array of strings_. The first element is the command to run, and any " +"subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../topics/outputs.md:26 3c50004d2d7d4695944015e40bf1f22f +msgid "`tar.cwl`" +msgstr "" + +#: ../../topics/outputs.md:32 cddecc6f8aa640d2b245eef27f5bb87e +msgid "`tar-job.yml`" +msgstr "" + +#: ../../topics/outputs.md:38 3d7918df94094da9b8ecc7ec1c5a1b3b +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../topics/outputs.md:45 7bf5e274a89048838c9fdf28633a5cec +msgid "" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../topics/outputs.md:51 fce348fc9cce4fdaa699b0d0f6f3b542 +msgid "" +"The field `outputBinding` describes how to set the value of each output " +"parameter." +msgstr "" + +#: ../../topics/outputs.md:62 aa92f3f4f14e4025b874ffec26bff141 +msgid "" +"The `glob` field consists of the name of a file in the output directory. " +"If you don't know name of the file in advance, you can use a wildcard " +"pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../topics/outputs.md:65 1a5ab9a9e91640d48a0cb2c13e691cbc +msgid "Capturing Standard Output" +msgstr "" + +#: ../../topics/outputs.md:67 9896a750508f4a57b128f4e30e718814 +msgid "" +"To capture a tool's standard output stream, add the `stdout` field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." +msgstr "" + +#: ../../topics/outputs.md:71 9345911f55b945eab39897e85e648ea4 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../topics/outputs.md:77 cea8fa310b0c471e8f6f6317b9ffcec6 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../topics/outputs.md:82 ../../topics/outputs.md:105 +#: 5e059fc800fa4f9f93e8a5b07e68de36 d62a95decb134c87a4280ce5526e03bd +msgid "" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../topics/outputs.md:89 9d6affcf4fbd4ca2a3f8dbd8d50a5c27 +msgid "Array Outputs" +msgstr "" + +#: ../../topics/outputs.md:91 8c5ad552c70e49b09bdda33cda587fec +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." +msgstr "" + +#: ../../topics/outputs.md:93 0558868e3e554b5890eb69b275a6b14b +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../topics/outputs.md:99 4fae0201b0f64c03a134f0bd9aeae9ba +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../topics/outputs.md:112 9f9c8a4a10d444879c7984a95e40fdb4 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/parameter-references.po b/locales/en/LC_MESSAGES/topics/parameter-references.po new file mode 100644 index 00000000..89399c97 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/parameter-references.po @@ -0,0 +1,279 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/parameter-references.md:1 9f53de1545d2441eaca40a478ab3b2b5 +msgid "Parameter References" +msgstr "" + +#: ../../topics/parameter-references.md:3 86efaeb616844254ac6651e3b312d648 +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../topics/parameter-references.md:13 e19913c8e6bb449aa55959dd82acda2d +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../topics/parameter-references.md:19 7e40643c4a474987aea13be5af260677 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../topics/parameter-references.md:25 46112899f2dd46ba828dc57245680909 +msgid "" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" +msgstr "" + +#: ../../topics/parameter-references.md:36 896da20f29e2465fae5555d1f51cb681 +msgid "" +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../topics/parameter-references.md:47 2e0849d53b6b4491a5d779390ea1319e +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../topics/parameter-references.md:51 3dab2befe3e840738419f1dedaac04d5 +msgid "" +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." +msgstr "" + +#: ../../topics/parameter-references.md:54 f92b2507989f4836bf33c78326bf8bc3 +msgid "" +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." +msgstr "" + +#: ../../topics/parameter-references.md:59 2a7ca85801a841f2acc94431a2accef8 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../topics/parameter-references.md:61 737a086da43644b3979fd3ebb16b2696 +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../topics/parameter-references.md:63 fcf3c4392e48496a8776ba9a49a6e867 +msgid "" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../topics/parameter-references.md:64 1b2a1714c66d4b2398c7fd614b3099c4 +msgid "`arguments`" +msgstr "" + +#: ../../topics/parameter-references.md:65 +#: ../../topics/parameter-references.md:73 +#: ../../topics/parameter-references.md:86 4458fac137854a9499a9afd221c344ac +#: 96f0d31f8d3549689bdfd4908698eed2 b234d82653a44b4ab1f9532e71e5e962 +msgid "`valueFrom`" +msgstr "" + +#: ../../topics/parameter-references.md:66 e6857e57ba424ec1bd86789a27458c8c +msgid "`stdin`" +msgstr "" + +#: ../../topics/parameter-references.md:67 8544dee0d05a492ca7f7727d277001ba +msgid "`stdout`" +msgstr "" + +#: ../../topics/parameter-references.md:68 a73a304246064187a5ef01aa04c528c8 +msgid "`stderr`" +msgstr "" + +#: ../../topics/parameter-references.md:69 8a86bb148ba9488185ac8f7a621aeba9 +msgid "" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../topics/parameter-references.md:70 +#: ../../topics/parameter-references.md:75 +#: ../../topics/parameter-references.md:82 +#: ../../topics/parameter-references.md:90 26f25bcad002476287ac6597033b3a68 +#: 2911d4b287444e159b2a1cfb9880a977 3657033c01b847febc8d6cdae2cf62b6 +#: 65f8db3faadb4fb59f8f26e7084b7a02 +msgid "`format`" +msgstr "" + +#: ../../topics/parameter-references.md:71 +#: ../../topics/parameter-references.md:76 +#: ../../topics/parameter-references.md:83 +#: ../../topics/parameter-references.md:91 3e57f5d7e1934e19a0f5de1bf11516ef +#: 40e34ff2cf47440a87f6548d3fa0ee65 64382062a5d5464fbf679cc774d0b886 +#: 99c94c256ce444a5a7a2ed4f52498c54 +msgid "`secondaryFiles`" +msgstr "" + +#: ../../topics/parameter-references.md:72 9a7a2dc3b4854f998fe36bd55d062abe +msgid "" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../topics/parameter-references.md:74 9f9ebe1562de4739bdf432fa9f51df65 +msgid "" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../topics/parameter-references.md:77 d0ed73eea69a488da98f09b5da9e956a +msgid "" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../topics/parameter-references.md:78 153b0efcb519496b89acf861c4cc0af6 +msgid "`glob`" +msgstr "" + +#: ../../topics/parameter-references.md:79 e3ff712139e640b19b06a9270570ac3d +msgid "`outputEval`" +msgstr "" + +#: ../../topics/parameter-references.md:80 4ab6c83d91eb438a972136acae6c128c +msgid "From `Workflow`" +msgstr "" + +#: ../../topics/parameter-references.md:81 d34255008ec94e0cbbf48381fd81a642 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../topics/parameter-references.md:84 be964cd5acd74de6bf636baa4299eb81 +msgid "From `steps`" +msgstr "" + +#: ../../topics/parameter-references.md:85 038484e05e724c868a2d1d53cfced2c6 +msgid "" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../topics/parameter-references.md:87 1ee43a5c98f6440e95d688afdb6e4822 +msgid "" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../topics/parameter-references.md:88 bf82bae8614f4d3f8e57c20a086ce013 +msgid "`expression`" +msgstr "" + +#: ../../topics/parameter-references.md:89 f708c3a4d3fd404c95285558b8cc6d91 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../topics/parameter-references.md:92 fa914a651d5444ebbcff86b1b6226212 +msgid "" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../topics/parameter-references.md:93 683a5eb1aa8e41adb89b1e7aec649a36 +msgid "`coresMin`" +msgstr "" + +#: ../../topics/parameter-references.md:94 151709a04a0a455481b9458c535a2e54 +msgid "`coresMax`" +msgstr "" + +#: ../../topics/parameter-references.md:95 93ec484b73bd457b9a34b681e62dba55 +msgid "`ramMin`" +msgstr "" + +#: ../../topics/parameter-references.md:96 3e17671a4aca4443b24bca32b1898bbf +msgid "`ramMax`" +msgstr "" + +#: ../../topics/parameter-references.md:97 b9d4ba2a422542609db7c994b9c89971 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../topics/parameter-references.md:98 fdab43c7a8bb420d84154aa70e24d05a +msgid "`tmpdirMax`" +msgstr "" + +#: ../../topics/parameter-references.md:99 fe3f4e63d6014e34a01243d6e1d54b1a +msgid "`outdirMin`" +msgstr "" + +#: ../../topics/parameter-references.md:100 6db5ab1a64ec40e9a6bc16060657b284 +msgid "`outdirMax`" +msgstr "" + +#: ../../topics/parameter-references.md:101 79f66c8ecf60493697c03d90e111f5aa +msgid "" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../topics/parameter-references.md:102 c42fe7e8d1dd4e35a255a5fe1f0dbdd0 +msgid "`listing`" +msgstr "" + +#: ../../topics/parameter-references.md:103 2d14a16d2a354839bcfdbcdd473c59e3 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../topics/parameter-references.md:104 5545855b55f34682b2a4e78dfa401952 +msgid "`entry`" +msgstr "" + +#: ../../topics/parameter-references.md:105 b267ab6613524236b50e698be4381087 +msgid "`entryname`" +msgstr "" + +#: ../../topics/parameter-references.md:106 6eb7f722fe294d2c81bb97e5bb193c0b +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../topics/parameter-references.md:107 43feefec5bc54adf9340f754e3bbe6fd +msgid "" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../topics/parameter-references.md:108 154d6c865631433d89589bd0748c9850 +msgid "`envValue`" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/requirements-and-hints.po b/locales/en/LC_MESSAGES/topics/requirements-and-hints.po new file mode 100644 index 00000000..380aa5be --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/requirements-and-hints.po @@ -0,0 +1,24 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/requirements-and-hints.md:5 1a39722a112b48beb8cf24e0f5e6ad88 +msgid "Requirements and Hints" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/specifying-software-requirements.po b/locales/en/LC_MESSAGES/topics/specifying-software-requirements.po new file mode 100644 index 00000000..c5cd86e9 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/specifying-software-requirements.po @@ -0,0 +1,68 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/specifying-software-requirements.md:1 +#: 206f3f103faf4ac19eccdce6e038ed49 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../topics/specifying-software-requirements.md:3 +#: 4a6f03a974fc4a9e86e260d9bd48b908 +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a `SoftwareRequirement` field in the `hints` section. This may " +"also help to avoid confusion about which version of a tool the " +"description was written for." +msgstr "" + +#: ../../topics/specifying-software-requirements.md:13 +#: 8bd36ba850bc4f04bd886ae39e361dbb +msgid "" +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." +msgstr "" + +#: ../../topics/specifying-software-requirements.md:25 +#: 8a5b0083c986452e82183cdc78d2da87 +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../topics/specifying-software-requirements.md:29 +#: 52df6af7c58b4f099c194b28b0a34de6 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a `SoftwareRequirement`, " +"search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/staging-input-files.po b/locales/en/LC_MESSAGES/topics/staging-input-files.po new file mode 100644 index 00000000..36848e63 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/staging-input-files.po @@ -0,0 +1,48 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/staging-input-files.md:1 da94c2c9fedf40f789a8afe9ff97abe7 +msgid "Staging Input Files" +msgstr "" + +#: ../../topics/staging-input-files.md:3 57675258a9ef4d948e3ebf0edd7779af +msgid "" +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use `InitialWorkDirRequirement` to stage input files into" +" the output directory. In this example, we use a JavaScript expression to" +" extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../topics/staging-input-files.md:9 0cf7fa6cd86c41bf92cd35616a4399e2 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../topics/staging-input-files.md:15 79ff820bc8d34c3ea37d396d98b56688 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../topics/staging-input-files.md:20 5f9403a7426941cb806bb76578d53987 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/troubleshooting.po b/locales/en/LC_MESSAGES/topics/troubleshooting.po new file mode 100644 index 00000000..7658928c --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/troubleshooting.po @@ -0,0 +1,101 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/troubleshooting.md:1 29507aa59aff4e249fcd12240b9fed91 +msgid "Troubleshooting" +msgstr "" + +#: ../../topics/troubleshooting.md:3 fac133f1d79f49599d516794dd45517e +msgid "" +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." +msgstr "" + +#: ../../topics/troubleshooting.md:6 68f47e9e268248af8a07b4b35080a918 +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../topics/troubleshooting.md:8 4ce1b123ee4745a3aa149e0f98ebe310 +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." +msgstr "" + +#: ../../topics/troubleshooting.md:14 afa8d683568747839d41d2e9051d06ec +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." +msgstr "" + +#: ../../topics/troubleshooting.md:20 699bac84262647c7bc091c7cea92a4ba +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../topics/troubleshooting.md:27 c4ce2451329d468a8a5a489eca901262 +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" +msgstr "" + +#: ../../topics/troubleshooting.md:35 31f0242e1c5a4c3bb621ce4414e34add +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" +msgstr "" + +#: ../../topics/troubleshooting.md:44 7294bf3bcfd447bf9b894ffef0b2873a +msgid "" +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." +msgstr "" + +#: ../../topics/troubleshooting.md:48 a18b5467b1c643d987e494d5a9ced7c7 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." +msgstr "" + +#: ../../topics/troubleshooting.md:59 7925dcec83bc48cd88eaf2e6860304fd +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/using-containers.po b/locales/en/LC_MESSAGES/topics/using-containers.po new file mode 100644 index 00000000..6779614b --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/using-containers.po @@ -0,0 +1,106 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/using-containers.md:1 33c3ff349c68416e8968af39e5e588e0 +msgid "Using Containers" +msgstr "" + +#: ../../topics/using-containers.md:3 5c50f28d3926477e965a32d31e5329ee +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../topics/using-containers.md:5 5cb16dd51c1d41aeb34c4aa1fb2e0940 +msgid "" +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." +msgstr "" + +#: ../../topics/using-containers.md:15 e0e83e827b734355aa97b19dc4c7e0d5 +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the " +"container." +msgstr "" + +#: ../../topics/using-containers.md:18 38f82d201fa2455f94afacae2c1c76b2 +msgid "" +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../topics/using-containers.md:21 00459eae5fef4f5f907ceb53eee857dd +msgid "`docker.cwl`" +msgstr "" + +#: ../../topics/using-containers.md:27 7e59171b12eb46e98ffa08a05ccebf16 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../topics/using-containers.md:33 d90442f3550f4e9b84905bb76ecb6fc1 +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that " +"is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../topics/using-containers.md:44 feb03506a2614ea3a0fc97f3154425c2 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." +msgstr "" + +#: ../../topics/using-containers.md:52 fa521c85542c410ba187c69fe5b3aebd +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../topics/using-containers.md:55 f3012553a17a42fca78b210ecec92003 +msgid "`hello.js`" +msgstr "" + +#: ../../topics/using-containers.md:69 fd0ad3c4cd904765ae5b043b44078a1c +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." +msgstr "" + +#: ../../topics/using-containers.md:72 60fa9a28e9bf4a4fa54289516e22f4cd +msgid "" +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/workflows.po b/locales/en/LC_MESSAGES/topics/workflows.po new file mode 100644 index 00000000..9c8321d5 --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/workflows.po @@ -0,0 +1,504 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/workflows.md:1 d6acbcdd75704f7b966a49edb8af28d9 +msgid "Workflows" +msgstr "" + +#: ../../topics/workflows.md:3 4d3032eb6fcc4cf8a2a67958877d7850 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../topics/workflows.md:13 89e89efbb04b47909df04a046169442c +msgid "CWL workflow." +msgstr "" + +#: ../../topics/workflows.md:41 a6e739c210e54652aa8833825f58e36f +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier " +"examples." +msgstr "" + +#: ../../topics/workflows.md:51 5b187be9b5314039a7e16d35fe4672e3 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../topics/workflows.md:81 59c9035c8eb94a4984c2fdf66c1cb787 +msgid "" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../topics/workflows.md:91 0e790b8a77874eeca2efcdf8254226e1 +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../topics/workflows.md:150 176b128d31d549ec947e2112bda59e10 +msgid "" +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../topics/workflows.md:160 058879c518a24859933efd7c62d2b3e4 +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." +msgstr "" + +#: ../../topics/workflows.md:165 9e596d54fc074e3dbb622429244304dc +msgid "Writing Workflows" +msgstr "" + +#: ../../topics/workflows.md:167 14760ea2dd594df4a11af3c2b267e2ee +msgid "" +"This workflow extracts a java source file from a tar file and then " +"compiles it." +msgstr "" + +#: ../../topics/workflows.md:170 73d971cacade4ed4893f03978d930b3b +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../topics/workflows.md:179 ../../topics/workflows.md:180 +#: 54719da53e4043758f29194fda1b0448 652551d8f4cf49fbb785e56b9bccf2ea +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../topics/workflows.md:180 84d558ae6abc432695ccb49d050d92c7 +msgid "" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../topics/workflows.md:183 9ced46957b8b4f20b2315979aecb30b9 +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" +msgstr "" + +#: ../../topics/workflows.md:185 bda955c302b2489fa76f54a08f6a4119 +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../topics/workflows.md:191 e57cce93798d4cb3a2e7a50f88549049 +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." +msgstr "" + +#: ../../topics/workflows.md:198 0270321fc2554e318de95a5684e9b6ea +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + +#: ../../topics/workflows.md:205 e7035e4184a14b1bb2a33b9a22e06df3 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../topics/workflows.md:212 b242d87aa48241c094c78051fd1b4e6d +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a " +"workflow." +msgstr "" + +#: ../../topics/workflows.md:221 fef2e2bdae81488bb23e6a63b8fec415 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." +msgstr "" + +#: ../../topics/workflows.md:233 7e9c2fbfcebf45f0a8c906d32ad4ddb7 +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." +msgstr "" + +#: ../../topics/workflows.md:248 f5dd8d4b1e324d7f81b12657f847c040 +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." +msgstr "" + +#: ../../topics/workflows.md:256 76d103db569b4ec6ab33fbd3d8c11e79 +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." +msgstr "" + +#: ../../topics/workflows.md:261 36ae3b2a1dab47b18b3896d208393e73 +msgid "" +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." +msgstr "" + +#: ../../topics/workflows.md:267 e0e1cf7c5e86443eaf7717b5c683ed89 +msgid "" +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." +msgstr "" + +#: ../../topics/workflows.md:278 91eceaf92e5441ce8b70e57e59fcda75 +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../topics/workflows.md:285 6112278376cb4e84ba05ebe6db7b039f +msgid "Nested Workflows" +msgstr "" + +#: ../../topics/workflows.md:287 19b5cd110ef149819d91c5bb86f56def +msgid "" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../topics/workflows.md:297 5d4aca9586434f40917c3532ae97bb22 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" +msgstr "" + +#: ../../topics/workflows.md:300 a32ab81c1a4a4150a0cf6fc792104a2a +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../topics/workflows.md:309 a28860105216475ab93a1fcd2b740b52 +msgid "" +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../topics/workflows.md:314 b3a4a7cfd77340029137a2cc9462b65c +msgid "" +" \"Visualization" +msgstr "" + +#: ../../topics/workflows.md:322 88aff05f9f3a45b297dd3eda9f52bc91 +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." +msgstr "" + +#: ../../topics/workflows.md:336 d5bc4016a294455baef3fe1e32c5c636 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." +msgstr "" + +#: ../../topics/workflows.md:341 5d59589eef4d44d69d2ef65821aaae45 +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." +msgstr "" + +#: ../../topics/workflows.md:347 d39c9aba4eda4252964711369c0ca9d6 +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../topics/workflows.md:366 dd9b058b571347deb207200501a54651 +msgid "" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../topics/workflows.md:383 c2d3d7b3f62344b3841dadd0c2dd4981 +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../topics/workflows.md:389 847d59018c6940f0b7248bc82abf4818 +msgid "" +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." +msgstr "" + +#: ../../topics/workflows.md:394 f041304d817446d39cd9dd41b00e2e78 +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." +msgstr "" + +#: ../../topics/workflows.md:398 a232c586c24045d7ad0813aabe2c62b7 +msgid "Scattering Steps" +msgstr "" + +#: ../../topics/workflows.md:400 f1d87f16200142318d6ec00d19ae9dcb +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." +msgstr "" + +#: ../../topics/workflows.md:411 884b61d0625a4561a963b381fcff7344 +msgid "" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" +msgstr "" + +#: ../../topics/workflows.md:415 35097a2dfc3c421bab46e81a53c34087 +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../topics/workflows.md:421 44c8319f97b242f197f1311fcb2719b5 +msgid "" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../topics/workflows.md:429 839e0cd993b44899a4049b44eb8aacfa +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." +msgstr "" + +#: ../../topics/workflows.md:441 333b64b5ab4a4078b9189c8bbb5924b9 +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." +msgstr "" + +#: ../../topics/workflows.md:445 73aa0f6708264bc39b0c6398827f1e6e +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../topics/workflows.md:450 5f6a3bf1dc314cb8beb9b336fc2c8f6f +msgid "Using the following input file:" +msgstr "" + +#: ../../topics/workflows.md:452 d5808863a44b4a6695e36ac1ae4a22f2 +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../topics/workflows.md:458 2c642b5be9c94763aee4bdf73d8bc2a1 +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../topics/workflows.md:466 dcf2a0d97e4a4afa842a971b304e23b4 +msgid "" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" +msgstr "" + +#: ../../topics/workflows.md:469 2aea56527429469c8af125414e4f4f00 +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" +msgstr "" + +#: ../../topics/workflows.md:472 a4279d75f660475d82c4bc8f869c17cc +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../topics/workflows.md:480 33ac7f4c0b1040b89811c0445b1f6824 +msgid "" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" +msgstr "" + +#: ../../topics/workflows.md:483 17b1da21293d40f7b246abb4f3a6fcd7 +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../topics/workflows.md:489 5aff13d9cf7841b29e2285ce2fdc90ad +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" +msgstr "" + +#: ../../topics/workflows.md:491 53afeb0f6b4f405782b0eb2e74d3acfe +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../topics/workflows.md:497 fbab18460296443daddb7bc1bcafe4fc +msgid "" +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." +msgstr "" + +#: ../../topics/workflows.md:509 52b2dee5459b4bbdab9f09576ec96f65 +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../topics/workflows.md:513 24185616ce374615a6966a70df77693b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../topics/workflows.md:519 7302c1e575bf4457a04243e9e0ef6f59 +msgid "" +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." +msgstr "" + +#: ../../topics/workflows.md:522 6ac74585b69d4197a26c8230f53f75cb +msgid "Conditional Workflows" +msgstr "" + +#: ../../topics/workflows.md:524 f189ba0d5e7547d1a6540abde5c4da78 +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../topics/workflows.md:527 257301405fda4c6aa98195f4344b496d +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../topics/workflows.md:566 189ea6307a25445ca573ff93cd8c4f1d +msgid "" +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../topics/workflows.md:573 b0701c43575d4dc79c4abe2c932928c3 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." +msgstr "" + +#: ../../topics/workflows.md:587 7de691f8e339422e8b027297e3d16fa6 +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../topics/workflows.md:607 246e5e7c82aa48c9a7f5f2c3b7b4d707 +msgid "" +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../topics/workflows.md:627 b28362ad11bb44c9b7247f411e58caa4 +msgid "" +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/topics/yaml-guide.po b/locales/en/LC_MESSAGES/topics/yaml-guide.po new file mode 100644 index 00000000..4b225c2e --- /dev/null +++ b/locales/en/LC_MESSAGES/topics/yaml-guide.po @@ -0,0 +1,193 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../topics/yaml-guide.md:1 153f05199ec24a5da81da49288e2679a +msgid "YAML Guide" +msgstr "" + +#: ../../topics/yaml-guide.md:6 95951c4a95d943c89be9252a898018d8 +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../topics/yaml-guide.md:13 60a16d7722724500b0a31194b6958cea +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../topics/yaml-guide.md:16 61f0a8fcfa2044ada7761d35e6ee6bbb +msgid "Contents" +msgstr "" + +#: ../../topics/yaml-guide.md:18 3c5dd09c0fbc4079abff7f8ee9c1bd03 +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../topics/yaml-guide.md:19 c7fa245866d0430fb8fcef9392869999 +msgid "[Comments](#comments)" +msgstr "" + +#: ../../topics/yaml-guide.md:20 dde5f9ad058445d1b0131ddf1fd80b74 +msgid "[Maps](#maps)" +msgstr "" + +#: ../../topics/yaml-guide.md:21 fdb88e5dafea4cb0876cea846eccca7d +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../topics/yaml-guide.md:22 f2ae9d617f274c7eb84a2d87c10a4cc5 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../topics/yaml-guide.md:24 47bffc9bb7b64047a25903eb42bde019 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../topics/yaml-guide.md:26 283f64df8dcf4abc8f00ee515d0cc9bb +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" +msgstr "" + +#: ../../topics/yaml-guide.md:42 51a3cd8bd6d2403daadc57d0091e99dc +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." +msgstr "" + +#: ../../topics/yaml-guide.md:51 7d58fe0504534589adfadf74e82de41a +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../topics/yaml-guide.md:61 35e8c97a24344c7d9933f1910d6bd995 +msgid "Comments" +msgstr "" + +#: ../../topics/yaml-guide.md:63 5ba35d4bbb4644949c37993a77a50bf6 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" +msgstr "" + +#: ../../topics/yaml-guide.md:76 e63546bf4b144bfba77767ec7248d63d +msgid "" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" +msgstr "" + +#: ../../topics/yaml-guide.md:79 25ac6edc52bd484cac8eb4fe4d5b6e1c +msgid "Maps" +msgstr "" + +#: ../../topics/yaml-guide.md:81 20e1be6499d9470fa74dde6da33f2120 +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../topics/yaml-guide.md:104 a99731edefb049299d313941156c41a6 +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." +msgstr "" + +#: ../../topics/yaml-guide.md:127 51d8ad7d937540ee88b46fc790319b4a +msgid "Arrays" +msgstr "" + +#: ../../topics/yaml-guide.md:129 bfeee0ef93e44a0ea50e3970e027b2f1 +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" +msgstr "" + +#: ../../topics/yaml-guide.md:146 297035119d42476e8dbebd1ed2241ac3 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../topics/yaml-guide.md:167 563dd83823d745b6aebeb956fca51aa3 +msgid "JSON Style" +msgstr "" + +#: ../../topics/yaml-guide.md:169 7edbeea182fe4043be66f02bc5952114 +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" +msgstr "" + +#: ../../topics/yaml-guide.md:177 37ddb7add5ea4fde94c97ab2bd2c85e7 +msgid "and:" +msgstr "" + +#: ../../topics/yaml-guide.md:184 ed9f6a7d062c43f099b5181e2c930303 +msgid "" +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../topics/yaml-guide.md:194 9cb613e445b5429196ced3d66fe95e45 +msgid "Reference" +msgstr "" + +#: ../../topics/yaml-guide.md:196 030fd9aede23463d981faf746e2b070f +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." +msgstr "" + diff --git a/locales/en/LC_MESSAGES/tutorials.po b/locales/en/LC_MESSAGES/tutorials.po new file mode 100644 index 00000000..5222f765 --- /dev/null +++ b/locales/en/LC_MESSAGES/tutorials.po @@ -0,0 +1,58 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:15+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../tutorials.md:1 99ae22e436b042009833051fac79e2c9 +msgid "Tutorials" +msgstr "" + +#: ../../tutorials.md:5 2ffee614f02343cb94399b8199803149 +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to " +"the list." +msgstr "" + +#: ../../tutorials.md:7 1831288df8f14081b13cf52d587c678a +msgid "Beginner Tutorials" +msgstr "" + +#: ../../tutorials.md:9 bc1fd03f560340d68bdcf39455d25c8d +msgid "" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" +msgstr "" + +#: ../../tutorials.md:11 47d068326ee34835a7a00ce7e24ef711 +msgid "Advanced Tutorials" +msgstr "" + +#: ../../tutorials.md:13 bcee717d8bf740c49c79200b0c660f3e +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../tutorials.md:15 5e55349fd3d749de964e8fcfca5959f3 +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../tutorials.md:17 77245b1c0ebe437f89dc07b45c5fa95e +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" + diff --git a/setup.cfg b/setup.cfg index f4315385..7ccac7d0 100644 --- a/setup.cfg +++ b/setup.cfg @@ -40,6 +40,8 @@ install_requires = sphinx==5.* sphinx-reredirects==0.1.* sphinxcontrib-runcmd==0.2.* + python-Levenshtein + sphinx-intl [options.packages.find] include = cwl* diff --git a/src/conf.py b/src/conf.py index bcba3134..c5000204 100644 --- a/src/conf.py +++ b/src/conf.py @@ -234,3 +234,7 @@ "doc_path": "src", "default_mode": "light" } + +gettext_uuid = True +gettext_compact = False +locale_dirs = ['locales/'] From 712e507c51f778466e22f0fcf2f5a8f80a5fd536 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 24 Jan 2023 17:20:50 +0100 Subject: [PATCH 029/179] include template for new languages --- locales/LICENSE.pot | 102 +++++ locales/_includes/what-is-cwl.pot | 22 ++ locales/episodes.pot | 27 ++ locales/faq.pot | 292 ++++++++++++++ locales/index.pot | 57 +++ locales/introduction/basic-concepts.pot | 217 ++++++++++ locales/introduction/index.pot | 27 ++ locales/introduction/prerequisites.pot | 257 ++++++++++++ locales/introduction/quick-start.pot | 167 ++++++++ locales/setup.pot | 27 ++ locales/sphinx.pot | 27 ++ .../additional-arguments-and-parameters.pot | 62 +++ locales/topics/best-practices.pot | 137 +++++++ locales/topics/command-line-tool.pot | 62 +++ locales/topics/creating-files-at-runtime.pot | 77 ++++ locales/topics/custom-types.pot | 77 ++++ locales/topics/environment-variables.pot | 42 ++ locales/topics/expression-tool.pot | 47 +++ locales/topics/expressions.pot | 373 +++++++++++++++++ locales/topics/file-formats.pot | 77 ++++ locales/topics/index.pot | 22 ++ locales/topics/inputs.pot | 247 ++++++++++++ locales/topics/metadata-and-authorship.pot | 57 +++ locales/topics/operations.pot | 62 +++ locales/topics/outputs.pot | 134 +++++++ locales/topics/parameter-references.pot | 278 +++++++++++++ locales/topics/requirements-and-hints.pot | 22 ++ .../specifying-software-requirements.pot | 42 ++ locales/topics/staging-input-files.pot | 42 ++ locales/topics/troubleshooting.pot | 72 ++++ locales/topics/using-containers.pot | 82 ++++ locales/topics/workflows.pot | 374 ++++++++++++++++++ locales/topics/yaml-guide.pot | 157 ++++++++ locales/tutorials.pot | 57 +++ 34 files changed, 3824 insertions(+) create mode 100644 locales/LICENSE.pot create mode 100644 locales/_includes/what-is-cwl.pot create mode 100644 locales/episodes.pot create mode 100644 locales/faq.pot create mode 100644 locales/index.pot create mode 100644 locales/introduction/basic-concepts.pot create mode 100644 locales/introduction/index.pot create mode 100644 locales/introduction/prerequisites.pot create mode 100644 locales/introduction/quick-start.pot create mode 100644 locales/setup.pot create mode 100644 locales/sphinx.pot create mode 100644 locales/topics/additional-arguments-and-parameters.pot create mode 100644 locales/topics/best-practices.pot create mode 100644 locales/topics/command-line-tool.pot create mode 100644 locales/topics/creating-files-at-runtime.pot create mode 100644 locales/topics/custom-types.pot create mode 100644 locales/topics/environment-variables.pot create mode 100644 locales/topics/expression-tool.pot create mode 100644 locales/topics/expressions.pot create mode 100644 locales/topics/file-formats.pot create mode 100644 locales/topics/index.pot create mode 100644 locales/topics/inputs.pot create mode 100644 locales/topics/metadata-and-authorship.pot create mode 100644 locales/topics/operations.pot create mode 100644 locales/topics/outputs.pot create mode 100644 locales/topics/parameter-references.pot create mode 100644 locales/topics/requirements-and-hints.pot create mode 100644 locales/topics/specifying-software-requirements.pot create mode 100644 locales/topics/staging-input-files.pot create mode 100644 locales/topics/troubleshooting.pot create mode 100644 locales/topics/using-containers.pot create mode 100644 locales/topics/workflows.pot create mode 100644 locales/topics/yaml-guide.pot create mode 100644 locales/tutorials.pot diff --git a/locales/LICENSE.pot b/locales/LICENSE.pot new file mode 100644 index 00000000..0460a73e --- /dev/null +++ b/locales/LICENSE.pot @@ -0,0 +1,102 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../LICENSE.md:2 +#: 3d749a78eb3e47c991d603c2cabd1b91 +msgid "Licenses" +msgstr "" + +#: ../../LICENSE.md:4 +#: 4689ade8475a4c8a9d5e325f072c1392 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 +#: ef8ec0f072d947fbba997c4b2191abc2 +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 +#: 696f3824ca814c9eb314abae51be8202 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 72ebe92edf58434e9d7a4fc6bddf8880 +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 9b403f96d4194ffaab3f309d7d12f360 +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: 10b1befd0f834d79880c8aeb70b595d4 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 9017d0b760bb4370926d511b97a604c6 +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms." +msgstr "" + +#: ../../LICENSE.md:22 +#: 1faadcaead6748dfb34886e5819af9b9 +msgid "Under the following terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 7a49ed3a728349c9b486f3d0b1dbf577 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 57da6294edce46eab00e7d15e6f6d4fa +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 8fc8a30cd63c4a0a9d8ba1b913687029 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 +#: fe59e74a4d024831a6d5cbcfd3e4ee38 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" + +#: ../../LICENSE.md:44 +#: 3ea41d5a14ad46729cabb387a33814b0 +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 +#: 23751e2552ff450c83e3dd255da56dac +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 +#: 13fb5eb48a8a434e95dbbb717ccaef8a +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../LICENSE.md:57 +#: e262fbd0e7de4f148f31afe39d1cb9e9 +msgid "Trademark" +msgstr "" diff --git a/locales/_includes/what-is-cwl.pot b/locales/_includes/what-is-cwl.pot new file mode 100644 index 00000000..22d33219 --- /dev/null +++ b/locales/_includes/what-is-cwl.pot @@ -0,0 +1,22 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_includes/what-is-cwl.md:1 +#: 44a9467c5d3b4a128ceade82a521b6da +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" diff --git a/locales/episodes.pot b/locales/episodes.pot new file mode 100644 index 00000000..8a04d6ae --- /dev/null +++ b/locales/episodes.pot @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/episodes.md:5 +#: 0cbb5e7334a647c3bcae7333ec3ced90 +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 +#: fabb221482cb4ac0a98bbe10943ed025 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" diff --git a/locales/faq.pot b/locales/faq.pot new file mode 100644 index 00000000..7a9282b8 --- /dev/null +++ b/locales/faq.pot @@ -0,0 +1,292 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/faq.md:1 +#: 5daa5afac36f46dd8329e5629056384c +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 40c8efda3caf4c6089bda3027c522f37 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: ee854bcb685941cab45ae7f33b0efe48 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 +#: a4cdd5ab6fe341a3ad3e3055556d96c3 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 +#: d1f359d47f124dfab23a75b196cd5884 +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: d83ced40605e411c92c4ae38761d7ffa +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 +#: bc8997df2e6746cebc2068534f30ee82 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 20b6ae57e1cf4410877a60fb3ef87264 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 +#: 73c66b809e9a4218b624338ccb88a05e +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 +#: 9be72b7d5d604526b125b63148e99320 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: fd96d178901545008a43fa99e3aa6cf3 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 +#: db58a582e66244468f4d31e9213933d1 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" + +#: ../../src/faq.md:104 +#: 3e70f0da5cd7460b90c1690366f40820 +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 +#: db28dc27c82b4b29a7a9a768550bba9b +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 +#: 4474b16fb3fd4cdc85da931159804967 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: 23c9b2e21cec4ee8ade087e6630f62c2 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c01309dcd65c4f1080c396e6a9efb75d +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 0a36801172fd4e24a04b3ba85cf74e29 +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 +#: 433e788ba01141e98ea5a9e73ef71e6f +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 +#: b6de2761ce454992904775a06b7ba326 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 +#: e36c2d53e8ba40f4a602b489a6688e24 +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: a9310166cb514e4e8824bba7fcfcb277 +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: f6144f77152e4284963951abaa30adb2 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 790709dfc2854e4a89fcc4769f84b0f4 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: 438789c8def549d1b4b8a187d5acc48e +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: 23ede7dfd5c84492baee1d5bbb9a91d9 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" + +#: ../../src/faq.md:229 +#: 37c0474e48164160b23c4094d583d2d3 +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 +#: 3b2be0a4a87041b7a5bda20c6df2ffc8 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" + +#: ../../src/faq.md:247 +#: 886300d2dcff4861aae503d34b0bee44 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: fe393ecdff25428da6cbcd30171c7811 +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: ebfd4991d917413b858da8b437a55805 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: 2919ff4f51254e69aea40146e2d911f1 +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 61ed4e87457c41eea31f51740557597e +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 +#: 1e6624104b024eb092682cd0dd0f6a3c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: b741b8333e104feaa6d1f41fd4476304 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 +#: 334673ae870a4dada817857f3a49326e +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: 362f85270df04712b2e2f21c7019e3cb +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: ad6997f24c7c42fe965b5d7bfd1e633e +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99dce9d60b6a4f99bc39899b7c8c10ef +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 6b68fe24cbf64624b49ea56fce2eecad +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: d23326837eb74e7faf1f54e25f8309c4 +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 2e2eabe92670412e95474b25ad9cda4c +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: 81f9308adbee4a3c9e585b8e0f0c4844 +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 +#: a5d3ed6cac28415288e7fc7fbfc6e8a6 +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: 72f9692803304daf9f846e2b90139660 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: a7eb20c817704811b3bcf2f94ec2e51d +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 20fa869849ef4b358a11db46111017de +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: 35032fcd9f23403ca006d62a7d6e7be7 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: f6d6a4e3691446378c8fb01a2d19f8ad +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: 44608fed1048458e999e13b014327e7e +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 96ede8a8f1f34786aabd4004bf2e7acc +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 84634a368e704e8d828678785c784595 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 545c4db9c24f42ee946081254d9ca7a8 +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 1c1e6d583d5646a8a5c9316dcd743d9f +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: cf7d336d444e4f59aa83585b7abb1fe5 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" diff --git a/locales/index.pot b/locales/index.pot new file mode 100644 index 00000000..1d9fcd30 --- /dev/null +++ b/locales/index.pot @@ -0,0 +1,57 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/index.md:1 +#: a58ca61ccefc401588f91699bc98bd32 +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: 6dcf12053f104cb3a8d23ce8d4f90363 +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 1cc90206170d46119c5756f31a9e8799 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: b54801d84a944dadb4e4637551e3f7b9 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 860afd2eda4847e0a0d8834de3af4aa8 +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: d6046316c84b40ffb5478c90b2604911 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: c3c89ac756a74d9688e179b8718c9bf0 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: 0eb795062b484537b090c4d5c361f7f4 +msgid "Table of Contents" +msgstr "" diff --git a/locales/introduction/basic-concepts.pot b/locales/introduction/basic-concepts.pot new file mode 100644 index 00000000..ceeed500 --- /dev/null +++ b/locales/introduction/basic-concepts.pot @@ -0,0 +1,217 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/introduction/basic-concepts.md:1 +#: 570f94ae2d4d4e19a9cf3a9bbceba835 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: 67f2ebceccce441caa8279166f8f901d +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: b7c949f867b8475f8969622abc045729 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:2 +#: 744c9501df5d47dc93962d217838f312 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: 0a0131d9b3be4af484b43fb3d12f804e +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 6c2f26b24ece4319bc9ecbd147f928e0 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: 0305e3bc2de04b15a64a1b1c1188da2a +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: 21d7e31a2abf4d36ba5acef1faa76b97 +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: 1c7e942576304977954be9ddcc9b2927 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: 920cf7f770054d87807273e8901630b4 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: a4c286729d884042aa9f6703ae958896 +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: ea9dc3c2e83246508ee111cbeb5e5379 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: c40f991cf70a4eefbf5b04e4089f809d +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: b3a1d362a96b426992cc37c11e13e09f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 201d5104011e4178adf564f969e45951 +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: d2027b38193f4252908c9f1fa8a1999e +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: df6be4b832ac4bbe9ef1eb5fc8cfc1ec +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 521eb59a379444afa0478b4536923f28 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: b600a21001d24203855b9d972365de5d +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 60b8285020a34af9b8a22688953899e6 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: aac2f76a1da1470cab9ff221c35134a3 +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 1adb2eda9c8a4e2493872e33a13bb77a +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 08847ed6cc8d4b76b23fe54117ecd929 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: d5fa5caa377e4cac9cb9736d54ee312b +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: f1c84c485ad9400aa80dd46eb5c75241 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 500a1a4565f24639ba5e248c382b2c45 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 1b407a21568b4c4da8a90d3eb33611b6 +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: d715b520274949bf9f9e3e7235f6d3f6 +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: 5c18ffe7e7254167a02be50ebab5e285 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: b9cdc830853f45bab2876305373f35b8 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 6d839e88664f41f0b5d01d38053ede18 +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 3e4b846a939a43929c4a45af1a7eafe8 +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: b19094f1044648718b9fdea72eda8994 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: 33191f1525334cc398892bb867135b42 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 6fe0b86d8a3b4bb0ac1f075fbac8988c +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: b206be2c6a5043429a1213b2989a0f53 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: f45e3dc2b0a74948a0977c47aab8db4a +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: afaa1ed8a0b949959992d4f4d7e00356 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: 51073c8b56864cca84600f12048a6036 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: 1215f39220b441a79f56cfe7cd61aa92 +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" diff --git a/locales/introduction/index.pot b/locales/introduction/index.pot new file mode 100644 index 00000000..f4ae1f30 --- /dev/null +++ b/locales/introduction/index.pot @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/introduction/index.md:1 +#: 6c33d560fcc64807a04e7a1536b1032a +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: ad616e9a47d14c5bb4532e5266d61ff5 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" diff --git a/locales/introduction/prerequisites.pot b/locales/introduction/prerequisites.pot new file mode 100644 index 00000000..519e8ca7 --- /dev/null +++ b/locales/introduction/prerequisites.pot @@ -0,0 +1,257 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/introduction/prerequisites.md:1 +#: 789e7b95b23d4bdb8398d691587613ee +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 53432372af8c447cbeb5f05892daee72 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: 36f42adbc26f42a891d996f8b9730589 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: 090df41a03204aac91aa7f663c6a5209 +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: 57ad125f7c2e4f01982acbabb1ff3d80 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: edfd6bf214d042feb6662b1c2d2fa48e +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: a44cd70295f5442fb6651d85794528ba +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: df31f7835d544160be90401bd20993a3 +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: f5e9ef0126f74353bc4c30a6e92bd92a +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: d11b1c901d004a10a7b8cda2e727bae9 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 37e363cb5987436d86e5725a63984e5c +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 1a19bd057d3c48679e2ae844c6b8291a +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 2a18beeff42d4cf8a4315e4a171cdede +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 17f353c8e861492d91e51b78b5da3351 +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: 5f178532a9004163b795c1433248eb77 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: d2ff1f8e720f4bd49912ccd7040f2ccc +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 77e4e1e5b4764d59a990b43ed93a7459 +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 22b4c40f082d4bacac051617b617cbae +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: 7f97cf170a854ce685bae8f30a16572b +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: 11fdbc38c5ed45a4976e16844729a3cd +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: c513823812a5423da694e85a20f86506 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 7be568d02d7e4593a1c0ef719d0f83ac +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 36ee569c74ac4602a51818a92c95f031 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: 06defabc17634ceea15e1f4523164a23 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: ac847d3d1587499ea6e1b3796e16282c +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: a4d5291859bb415b981a7dd6dff3c313 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: d80356bf607b4f7d9572b925c69163f1 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 54ddcf5f932c40c4bbec2f88114e6e20 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: f159836854c14187929cf24f716ccee0 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: 728b24fff1f14726b27168dbf46e4e7b +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 5590cd84de1c4f9382ab37644a5adac7 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: 5a066c4dcd034cfd8902ae01128134c5 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 846f1eaf4f81477c84b885f7c17ab030 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: a972f3ea3b5f41f6b78f682a42616197 +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3165d673bd7341518d2b259932917b53 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: d23de68e21e1429886b3814af9cc3104 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: 9538d8b0944f4e72bceec9ebf1fb5832 +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2e710620d21f44a0a036431453ed5e20 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 25c6c7a87e1847f9aec1c32cbc83cf4c +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: a90b90e926324cd687a29436e82eef38 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 91a2b9d7d7b642c2904bd55d29690254 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: e0cdb48ef04846cd9a39008260b18777 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: ac55bc8b751d440086043c4af6776d10 +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: be04aba59f3c40f1aa90316090792441 +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 2d4790bd46124cd8be789927c25fbbbd +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:196 +#: af2e128598294dee9330002a2f7bfc63 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: f4ffd0d89ef1406f9e957a05a4172c57 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 00fa0dd045054fcbbe3322e10e591430 +msgid "The Python `venv` module: " +msgstr "" diff --git a/locales/introduction/quick-start.pot b/locales/introduction/quick-start.pot new file mode 100644 index 00000000..62c7c9fc --- /dev/null +++ b/locales/introduction/quick-start.pot @@ -0,0 +1,167 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/introduction/quick-start.md:1 +#: 1f7df6c4ef354b4284ffca2f01ba7a40 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: 98a2ea8175314bf5b6fbdd2464402c82 +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 924b8fd198fc487f87a8de4948261bee +msgid "“Hello World”" +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:2 +#: 1d89d9d6798a4e38adc28680ceec1a29 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: ca24ba5ebb324a90b34fb1b28468fbcf +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 7a3bbeb141914c0daee451f2bca9a081 +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: cdd3578d507d41539c38a601701e8854 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 767cf30acc9d4f81b8d34bfc90a8891c +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 8acd83b581f2499fb640153186711660 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: 46d1f843730a4c848a327de9a03c04e2 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 939e54e81c304d21a4eb33f99407ee50 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: 4db304a983cb46fe917563a1884659cd +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: 72d657288bf248b6a53080e6295302e3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: a03263ff919e4777afdca4fc20efc673 +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: 2f6d2f41de974a469babd97d1106608c +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: cef66179a76a432c9b0c1a49b0f6bf69 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 133d0f054f784d7ab5f2fd5f028d80eb +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 454aec8aa868430da0449434df741b21 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 5f7a1d2d705145a58fb37d6b7fe66add +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: 18c580026a2346c8b1e020fa9b2f3f8a +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: 0051eb403e43451390f5775976d11818 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: dbbb23a79b1143a7aa7c91a1277851ce +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:94 +#: f0ad9eabc2c04cde941bf78f0bfcb641 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 0e14c76da55e4501b6fb8ed246a344a7 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 6e813c00aa564fc1a407cc7aae77475a +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 6029a1f35b10455389c63c680a468d3c +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: c1312d1ce89e4a48b31597c5a8b2e603 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: 18cdf73c71574ce9a74c189aeaae971b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: 5488abc1abcd4aa68e7e8a702834c619 +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: 4cf8dc5e58244810866649259ac13f9f +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" diff --git a/locales/setup.pot b/locales/setup.pot new file mode 100644 index 00000000..10900ecf --- /dev/null +++ b/locales/setup.pot @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/setup.md:5 +#: 29bb5c68be6042e5aa4a370e9c4024b3 +msgid "This page has moved" +msgstr "" + +#: ../../src/setup.md:9 +#: 8bcf31398c34491da1a1590422a72cbe +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" diff --git a/locales/sphinx.pot b/locales/sphinx.pot new file mode 100644 index 00000000..0c4554c5 --- /dev/null +++ b/locales/sphinx.pot @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:27+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: b896fd5e11fe4674a7f46ad489476692 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: acede4e78f7e4aefa0ad9425928cbb42 +msgid "Section Navigation" +msgstr "" diff --git a/locales/topics/additional-arguments-and-parameters.pot b/locales/topics/additional-arguments-and-parameters.pot new file mode 100644 index 00000000..c447e7c6 --- /dev/null +++ b/locales/topics/additional-arguments-and-parameters.pot @@ -0,0 +1,62 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 4ad19837b80f40af88edf443c4d4e743 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: a51e98f4fab24b42b225e24b69471869 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: 78e7111611734004b650bdde36fe8079 +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: 0c5cc374383a4f058a6c8d7a3d83c7d4 +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: 67cfc6cc46764b07a6738691bc1cb1f6 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 744b2343db934429b7a04b4ab4f84d15 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: abea839860f447f1b767c3a028ce1ca9 +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 5a44c7cd8feb4593802cdf56254b79d7 +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d5f29eae1af646d5be22c816c5d1a4fd +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" diff --git a/locales/topics/best-practices.pot b/locales/topics/best-practices.pot new file mode 100644 index 00000000..d4460047 --- /dev/null +++ b/locales/topics/best-practices.pot @@ -0,0 +1,137 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/best-practices.md:1 +#: e93667d13f1c481c9ffec6bb3062c073 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 685dedff3cf54c4b95bc56b30a5d7fce +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 2e4c3af1016e4269b6eb3eb7c37b609b +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: ee2f52f0a96449a7b6e49b2c824288d1 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 426fc5489a1a44d2b037f1456b6556c2 +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: ecf6e24373f944a0a3e9453c31e03e8e +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: 0ad7fe10c6584f01991d87544f1d5649 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: b589adbe3f324ecc9670c2355be1e308 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: 50184e2a39fb4a2086afbb236efa603f +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: f000d979ab914d94bbfe988792cf1629 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: a11d2c6e1408411d89cf7d434448a414 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: 3e379d3bd38b40d38a2a448e907918b1 +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: b8eb7c78ffcc4093aea11fa21cef762e +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: ef540052516840638bb7e5bf4dadb945 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: 378f73d8fd864d0bb3ac5d027224ef08 +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: fb1fee0d5583488ea2091dbf9b36eded +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 210127c58cd44557b60d603d8d68725d +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: 6b657c5d109646f5bf7a38cef1b903e3 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: 14951e1b672248f095c31c4c96bf5183 +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: ff9dbfab87a24cfab3734882216d40af +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 444b5580319b4ee69a1439c7ccf703df +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: 9ba7fd2784b2430fb6964b9a16d2d553 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: 0e88ebb9e45c41db83482ccf848ca1ca +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 3b2fe5ca68944df5baf04c7b5705e207 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" diff --git a/locales/topics/command-line-tool.pot b/locales/topics/command-line-tool.pot new file mode 100644 index 00000000..422115ac --- /dev/null +++ b/locales/topics/command-line-tool.pot @@ -0,0 +1,62 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/command-line-tool.md:1 +#: 595e9cc7e0a448f695e27b1cd0427d9e +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: ac9188b4b9dc45589f2173a73dc9d3dc +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: a6dd1084b9b248e08ec2659999f82ac6 +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: 9119bb87ef4b48e7946f5412d197ce0a +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: 312c6373a25b498db63c67abed6c6289 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: 84b6964c9cbb4d67af2794624de86337 +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: c276e21332454452bc814d33f007a670 +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: 1321360b42da4f65975569e2b7314bf0 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: 70739268c7674a99834cf6c166231149 +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" diff --git a/locales/topics/creating-files-at-runtime.pot b/locales/topics/creating-files-at-runtime.pot new file mode 100644 index 00000000..c427c32e --- /dev/null +++ b/locales/topics/creating-files-at-runtime.pot @@ -0,0 +1,77 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: d4e5cee7a82447a696e1e9516ccc2e38 +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 6121650880d4447e9b5a6b66e0f3367c +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: e81edd66cbb2461e905a7adf6bff23fa +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: cb4602ae814b4b47abe61ab3bd88b046 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: f6f5c6dc8ff74db3b1c5aa2403ee12d4 +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 87abe95ca4054b48a8fb76d7916db1d4 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: de2366c1d2d1459ba23fe1410f2b86f4 +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: 28906471c2fb41358706f624e3c8bd8f +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 449fdfe14172498fb80e2f57ca0c05f9 +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 9a9ce102e4ed4dc68eeb161746ab4689 +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 447b2199a76646be8afacb72203e9719 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: aaae789101c742b292ebdcec727b1762 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" diff --git a/locales/topics/custom-types.pot b/locales/topics/custom-types.pot new file mode 100644 index 00000000..f338bd21 --- /dev/null +++ b/locales/topics/custom-types.pot @@ -0,0 +1,77 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/custom-types.md:1 +#: e1169af9b1ed419b80cd7b2ee432c37d +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: e297aa8753564accac64cbad1be99d0b +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: aa76f57cb1eb4a81ba6560ca7b7d47fa +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: 7644b22f9154413cb88f46e9a2a1a9fb +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 1d259a15f1884950953d8536b74d437a +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: db1612c92c3c4d63869aa3d589960ab9 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: 4c7038e3a8d6484e9eecb348e825605a +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: 960610e43cd247dfa5921477558f6a2c +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: cd7d7cb81be74acd81bd3af2ecbeba8c +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: b0b4eb8206f54104a7fe02492cd3c0c5 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: 2d0fc88b5d524b4e814f47a147b7e555 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 8e99e8e00d3340e6bf7025622bdfbf47 +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" diff --git a/locales/topics/environment-variables.pot b/locales/topics/environment-variables.pot new file mode 100644 index 00000000..294a71e7 --- /dev/null +++ b/locales/topics/environment-variables.pot @@ -0,0 +1,42 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/environment-variables.md:1 +#: 201d52b060fb44e3b988d1cf08b32569 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 5438cfdc5df24a2098fc3014731bceb2 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: 295b041049874673b1c4f93e3c8932c8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/environment-variables.md:13 +#: e2076a2e3c4e43228e69f9b4ee535e3a +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/environment-variables.md:18 +#: 74c67839550148b98f8a681f53baae9e +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" diff --git a/locales/topics/expression-tool.pot b/locales/topics/expression-tool.pot new file mode 100644 index 00000000..329b21fd --- /dev/null +++ b/locales/topics/expression-tool.pot @@ -0,0 +1,47 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/expression-tool.md:1 +#: a1a763367700488eaeeeeb6c1d4aaf3f +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: 1baaf7f3bda34cabb4081708f8eb676f +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: cf8f9f21b8bc4cba9e947b631e0452d4 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: 01ad0d7c0c9d4051906424dceb702361 +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: af1958ad56b64631a111aaaa41413a09 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: f50a9dc71c7f4beab2525ce6e6fca385 +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" diff --git a/locales/topics/expressions.pot b/locales/topics/expressions.pot new file mode 100644 index 00000000..012628cd --- /dev/null +++ b/locales/topics/expressions.pot @@ -0,0 +1,373 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/expressions.md:1 +#: 6b0faa9c10ad4da783e2155070095a8d +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 9e44e4e737b545a2b10b97e923027bd9 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: ad6d3dddfda445a5bfce2665cb195605 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: f487ea31d38142839ce5667701b894cd +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: 47d7f42a657a4547af1be1e13662effc +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: c331468453dd4e60a76bc753417b72ce +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: 6b9b7057eb154a95847ec56652de07d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: 6facbcd083f04a60941589da7e21621f +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: a08110192e264a109ee6a568351135e4 +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 1a260934cee04059b4765d154f6388e1 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: ebee54b00af643aba0d53e774b0ac188 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: 02ad120e9a72482780f062ae3cadcce7 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: 8bb623ae7a9646ff992d7a79856aac8a +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: 4437b8ae6fb04a1fa06f494ead97b1c7 +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: 145b4d4cbfaa4c5d914455b0b5b6ef1b +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: b187028dafc040e8ab04d2a69c547874 +#: ecb148c1da01445a8149b500b5ea50f5 +#: 87f7f23e14e54b87b6f1b4f8c148bf8b +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: 9132968dd34f4a9c99ebabcae48a4a3f +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: 34b31b4554b442ab9d9bac1e95cc3029 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: 33e3e471fafb4f609694af59556dedcb +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 941720c894bd45a895e3a8e682b7e884 +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: e2c648a9a5794879b74cf02e489f0c5a +#: 15692bd5c6204aa9b72259e6dae69bec +#: 1a506a3ea7614043a67dd4d93015b19c +#: 166fd96ec8b64db88e1837feaf65df1c +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: 8c65f558109142048b8831f800264bb4 +#: a4e5f9d5354d483392c157f736cd8c20 +#: 9ec2e908459a468b837b572a426bcd8d +#: 2d82125ff94c441ea29b3da5ff5dbb08 +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 6eecf3fa29d9465882a2b6be02504ac0 +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: 92267f3d8f4e4b3fa129e3bec3b16413 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: b9b5551681d046e7a0071eee29987b04 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: b148af79351e4ba49604e24861388496 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: 4c48b367e5494d559484c5395af3a5a4 +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: 5541a07628174dd6a843afa2c37f4973 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: bf6e4a2101654e15bc27ac3db0c6bb6d +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: a295cb00ea034ce7820897606999ae4c +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: 5fd2e9df08404efa9d24d8bfccf91a18 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: 51f8b42f4e7d4c8484133a18f83be491 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: 73fef9b1b2074077a2525f72b2efaf62 +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: cf19b246bc20476899a83e68113dd3d1 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: dfe56b4ea35a440d91f579efcc2c039b +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: 918bc6b265a549f28f027da29368cac4 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: a9182179ebce4c99b4eafe59ba122799 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: 984ceb05b6b24e4986a28436bdca88e7 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: 9a3f6db0d7f64468bbf2f6f861eab96a +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: b7557357360d454dba7ab3c3471b5a23 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: 839ac0ddca374746972ead6d22427edc +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: 89bfd53638504c7aa437c2140afb6035 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: f0af6b4cfc23480aae61f42422ad3afb +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 67ccc10e77d644078b170a28a8ebed3d +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: fcb8b8003fc84ab890ce241e63d43b5d +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 584682d4db424108b89ea8e315838de3 +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: 77439e7f4f214db781edc777a8a03b78 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: 4ba274f6d9c44ad7a05891725299a759 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: 1b751542a9f34fe19ae5f91174e01cb7 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: aca9ad053f5441caa5cd51170e35532d +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: 37c96fdc52c443faa1d1e462ff034425 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: 4bcf5cd130b148f7b3f601902ad0b7b4 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: d6f0074d025742a6b3fe7f91f1dff335 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: c664d4710c404ed0af90dc22c8f273b1 +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: bd8dfef3aa934750bdd790e1de6bced6 +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: 1ae20d38a1574d828ca7cb8e955906da +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: bcda020047784e4191d4de456afc7449 +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: a9ccc2da748644dfb28b590eae974f63 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: aede8f2c722c49f18cd2a86c051bb1d4 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 7d1bd9bfba9c496a90fc45f575505e22 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: 8b906fa3b98c48c68de46f80667d4d2f +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: daa9689f15c746a38dcd22a3f169a4c6 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: d0d8193fbb304f0281db0c6c1147545b +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: e5e1179082c14621bafbd14d887db62a +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 193379258f254ac5a25fcfb61b1c3540 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: ec0d1c972b9942f8a55b7b68fc9cfe07 +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 63ff0565300a493f8c84935139c23552 +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: f8bb29ee047e407ea226599bccd86196 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" diff --git a/locales/topics/file-formats.pot b/locales/topics/file-formats.pot new file mode 100644 index 00000000..86733f1a --- /dev/null +++ b/locales/topics/file-formats.pot @@ -0,0 +1,77 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/file-formats.md:1 +#: f2a1cf1e81e54737af8d81bcef76d88a +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: f81bab33b2ad46d3a852e15d88858879 +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: c1dd91bf59804358be63bcde0614bd31 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 785ed7d362824bb99887694670aac50e +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: c3f54f4d6df44e628c59c1e70124667f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: 6c3942038fd3446db254260530291732 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: db9222078ef04bd29ac45af0cf8a4ebd +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 3b17d233095a40cfae0540e678088860 +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: a7900a2fa76c46e6854d09a7b31df272 +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: ac34d1ad2274499f9ea1413b5648f7dd +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 04198e0858a6415a8e3235c29d15c5f1 +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/file-formats.md:52 +#: 265ff7e37ebd4e9fa85b26a6deb1cd74 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" diff --git a/locales/topics/index.pot b/locales/topics/index.pot new file mode 100644 index 00000000..9f895c55 --- /dev/null +++ b/locales/topics/index.pot @@ -0,0 +1,22 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/index.md:1 +#: 8ecce715c6084f74acf91e896775f6b3 +msgid "Topics" +msgstr "" diff --git a/locales/topics/inputs.pot b/locales/topics/inputs.pot new file mode 100644 index 00000000..6ec07f47 --- /dev/null +++ b/locales/topics/inputs.pot @@ -0,0 +1,247 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/inputs.md:1 +#: 9a97be0420e54706a7c73bc1eb856b96 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: d4b396558d594c84b82369a138358fd6 +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: a3966840a8844e1999e21bcecc96a6f7 +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: ebeb58f7ebd541f581415a43d790811c +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 95cf3ab046b44241ba399c56d4b0c6eb +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: 6e6066facc2141739cac77bf9792572a +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: e257868f6c6646e6a0d1feef62de079d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: 2f2885adf6214b9a8f770097bb02b1e5 +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: 01ec3e60c2f24f9c912d44d3d5dac4c5 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 8c803c9f11414a9f9b92643923a79c65 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: df2b1f41e3e149309ae8b19aaf6034ca +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: df5bd15a6b084bce879270be669f2923 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: e73d20dd91574bcbb7b24932d9ff04e4 +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 56461c62effc487c9e73d1e82ddd3390 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: df42caf04d5f48baa8e5734d6100cdf4 +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: f8db1efc2092415387e4e16dc24775dd +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: 859f5479b2cd4e919e3ba19a3f084b01 +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: d04258dca228411ab16f82585ee53985 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: 760c0af7e36d48d1b1681928ad195eaa +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: 4e5d3fb805f04593b34d5ae88dd6fa83 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: 7b97d452561c4c158a835fd308feafb8 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: c63782e8b8524857a1683578534f8382 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: fe66dc3c9aa743e0a2060a8280e6a59d +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 04993bbb8c7b488d8b1b2517f4333f8d +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: e33e6fd2e8a8472e88c9333c7b44fc2c +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: adc2cd5bd81b459b996ff65de5d25436 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: 67da943c4d6d49cab1931606fb6938d9 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: 0be87de7fd5e41da895dfc9369da7b5a +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: 535a8e26cc3b4e3db43680f030d57879 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 61c26186c1734233bb7d9e5cd3056506 +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 66ec7048099f4720989c8de5be49ea2a +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: efa9d841028c4135a513f3226b37bdfc +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: b3543061283e4bf286ed9fb7127238df +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: afeff005e15d49edbd8222e95b4d6388 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: 0eb5e94bf86a4c84bb112d612c290bce +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 3d1f591442f54f9fa8effb98f4cc4f7f +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 1a8735c689ff4e13bd207eed62d0bc1b +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: f802a2e638764c95bef8889b958f6872 +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 54ffe9e897ff4682aa9d17e9239a5b40 +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: 892a899a9365419c8cdc95e9f05f9e3d +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 2cca4db8543145c0a59da034c82db1fd +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: 1f42c1eba9f44397942d6bf2dd37855f +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: 1c0caf1fd3a4411f83dfc4866edeecfe +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: d0a92fe266614a5db77f32b0fc40ee83 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: e3a608fbb7e14213831c564128421cc2 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: a24cd12cc01b4e23b0ed878a27fcaa46 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" diff --git a/locales/topics/metadata-and-authorship.pot b/locales/topics/metadata-and-authorship.pot new file mode 100644 index 00000000..2d77396e --- /dev/null +++ b/locales/topics/metadata-and-authorship.pot @@ -0,0 +1,57 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: c79f6e6491bb4b6b9f1b2677b79c0ce1 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: 73dd0c3f814b4b77a9fe0ad09be7e00a +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 9dbb204051604ffc8b40ff902f1d6c7e +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: a4bd38b9be374a9da651b4c8a876f57f +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:22 +#: 6d6d2685e0a74c8ab242594fff8885ff +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d8261a4cdde0456db33aa7e6bea9774d +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: 11af70cc279a4cb29135aa440d560999 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 5a3a6d2577544ff1a996b7b7d15693e0 +msgid "`metadata_example3.cwl`" +msgstr "" diff --git a/locales/topics/operations.pot b/locales/topics/operations.pot new file mode 100644 index 00000000..ea3332ce --- /dev/null +++ b/locales/topics/operations.pot @@ -0,0 +1,62 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/operations.md:1 +#: 8766c4065dfa467f9001aa50564f4812 +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: b37c530cac0a4d18b50271b5b5ec4d1b +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 54e76a0465cf40bf8b76896643cc521b +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 9e16b384ac494d07951ad589a0413d2c +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: cfd13e0311104c95b7de0510f0fb54ab +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 468b0b4219a84df49286a95115c5d3fe +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 362bd499ed6b40b8bbf3237a9a08895e +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 24454b17abae4cd9a8a17cfc5bd79e39 +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: f33e158f449e4594b4f0f1c4660e2be2 +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" diff --git a/locales/topics/outputs.pot b/locales/topics/outputs.pot new file mode 100644 index 00000000..eaaa0c37 --- /dev/null +++ b/locales/topics/outputs.pot @@ -0,0 +1,134 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/outputs.md:1 +#: 30d1617ac85d41a0956ef5f7eb30c112 +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: 13aaa50a038f460f829a5554ea950a8b +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: e26db82dbb934d4aac5a7918c39245f4 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: 747f0575223f42cd90157c2ec684ab4e +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: c251eb8f22c54cdbb8683e98d4e527a7 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: e0fc3bde9de84b2ea5e2b9d7d1491ed1 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: cbc068a7d2bc4c1682577ef6b854309a +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: f2923e674d574ea1a52dab96a12e38a7 +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: ebe4a9bec6cd42c089e790108b0ddbff +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: 89c371e54934472e9c09681be5f1ecc3 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 508663424d2f4eb494ca8611cca4073a +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 1ee12d2ed35a414d818127ebaaac2364 +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 0e0fa84bee1042d88386826c22466619 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 9a37679c41eb4287b43d254a8fd823e2 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: 7041b9a7b7034bf881bccccc2b691a44 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 53075db7e4ca436594d4fd3f3e00917d +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:77 +#: 0860836ece81420dba1b2a080e825f6c +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 40d221f9b5b642648b918aa0e6902f1c +#: 7ad8f592f52b4aeeaa703a85e79f6356 +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 6f6a26ee1ade4b4f9ed3a82ed44030f8 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 61a149a84abf40e7ace2248dc0119838 +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: 1322f83871ee49b3a87aa71a0ec5a79f +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: 6f92d0458a924c88aaba9e7336eef87c +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: ce294dbd94ee4624915c398389eaf1f6 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" diff --git a/locales/topics/parameter-references.pot b/locales/topics/parameter-references.pot new file mode 100644 index 00000000..b17a5e7a --- /dev/null +++ b/locales/topics/parameter-references.pot @@ -0,0 +1,278 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/parameter-references.md:1 +#: 0d925f42133646899f4bb3367057e07d +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: 473a89b059e14f649354a76bf882142e +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 4c57e8c446a0441c810493d34311ace7 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 014e74e995bf49eca1c3b09ca011619f +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: 0d475fd8c50c4dc986643c14b82d0576 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: ff886a60af2b49499ef0a0d31386998e +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: d1e080ff809946919ed35e2b1055b6e5 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 52e0d66811bc433b8c21b91e5ac6945d +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: 6252fd49bc814c1c97c2a825a6b1b49f +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: 97abdf2838c444f684629c0578a8ed31 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 3fd741db4c014ea6a53b6bc2fad63e21 +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 986da8d3c56b4227a9481c9e2b0ea0a7 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:64 +#: 1beb8e88637545b8ad365441de547b59 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: 8349b7acc74346e0ac0d18dddafe2205 +#: 9b2e0b712ec146e1a636ed8d1f408c56 +#: eac9f2c8f0c0424ca5e70425fa60f677 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/parameter-references.md:66 +#: cb1036ef7aa449dc8728bf72cf7281e9 +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/parameter-references.md:67 +#: 713a83cfde5e4d4181ec8477f20ac2c4 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/parameter-references.md:68 +#: 8d666991bcc94c83b1259746ced7e43f +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 7ce52aad9f624afeb40e9829ab150651 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: 4207d80deafd4b12a944b4b61e7494bf +#: 0b9493de338a4717bdf643991c72d92c +#: 489bac6cabeb4aeaaf90112969f0bafb +#: 34de0217785146c4ac0130e52319581e +msgid "`format`" +msgstr "" + +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 026108b0d1c344df883689be95db8fad +#: 0b32cdfd79ee469e83a629285223cc0b +#: fbe04046dc744f72b3a88da56f15b483 +#: 9065d837c83d4dd78cd3d664f882300a +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 7f5bdccc51a14535891b13d8e787251b +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: daff49176fca4fd8b12369f4f92eb22d +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: d0208c0307b04cf384c7a9334046bb9b +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:78 +#: b384a85509344ad5bbc3873684a19b9a +msgid "`glob`" +msgstr "" + +#: ../../src/topics/parameter-references.md:79 +#: 83d6911ab8994e55a87871c8a238f4fa +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/parameter-references.md:80 +#: b0298c96113742f6981316ad0e33b018 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: 636f6c50ac274d88a7ca32f7bafbaca4 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:84 +#: d72570d062e54cfb89c82a1ce1a286b8 +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: 5b8e3e7c420c4490ac4a5905189cd166 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:87 +#: 22c6afe7aab84038a74f8478f8d97d64 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:88 +#: 88877e67206e48b3b10e30ddead266fd +msgid "`expression`" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: e763d3be7c3347718bb851b0e601d466 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: d7837cc8e8064348b2698f80e4bf47b5 +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:93 +#: d87be82c3bcb4e1fb33946573d62037c +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/parameter-references.md:94 +#: 2362c7e8e16240e288fbaa49521951a6 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/parameter-references.md:95 +#: f9d381b7bf2c4caeb6a5a3bace39b6a3 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/parameter-references.md:96 +#: f957b015fbb64e448083a5a9b4ff4b0b +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/parameter-references.md:97 +#: be4bb996b5954fb8a90c57e5e6456ec2 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/parameter-references.md:98 +#: 00eb0fff1cc64e41bcbcf63ebb58ee11 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/parameter-references.md:99 +#: 073bb4a51bcf4447bde792e41e876bbd +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/parameter-references.md:100 +#: ed9e837c60a14da0879a309194213033 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 160c7ce007564ee2825517bc29750c65 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:102 +#: 24755cdacd024d949fc6015b43983e22 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 4ad1d82ee80844c581197cb14eab518a +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:104 +#: 6542359022cd4a1ebfb08e8c104620b4 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/parameter-references.md:105 +#: fa4a51155be34b10aa8c1eaecd2cdbbf +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/parameter-references.md:106 +#: c51af125685146dea16c2dcd7f290aef +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: e31fc3370fd948c79e945ab30dacf99e +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/parameter-references.md:108 +#: 7982f559dcff4178b222cdba267d1283 +msgid "`envValue`" +msgstr "" diff --git a/locales/topics/requirements-and-hints.pot b/locales/topics/requirements-and-hints.pot new file mode 100644 index 00000000..a566fb29 --- /dev/null +++ b/locales/topics/requirements-and-hints.pot @@ -0,0 +1,22 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/requirements-and-hints.md:5 +#: 15273fbf009b4036a2574d157740db98 +msgid "Requirements and Hints" +msgstr "" diff --git a/locales/topics/specifying-software-requirements.pot b/locales/topics/specifying-software-requirements.pot new file mode 100644 index 00000000..d65ed83d --- /dev/null +++ b/locales/topics/specifying-software-requirements.pot @@ -0,0 +1,42 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b34314bdb71244f2a263427f22172b5a +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: c8609548e7904e65a5c395bfc07ad808 +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: e4c1c25793884b5aaead1fb15c2e6bbc +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 91586b8767734e0ab01903f2562a7cf2 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: dd7c487024b44a67a26765e59b5bf64b +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" diff --git a/locales/topics/staging-input-files.pot b/locales/topics/staging-input-files.pot new file mode 100644 index 00000000..f9d75eff --- /dev/null +++ b/locales/topics/staging-input-files.pot @@ -0,0 +1,42 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/staging-input-files.md:1 +#: 3064f17a9bae442aaef41b9434cb71fd +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 09bb659a5cbe40948b59208f0fb77ddb +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: a1bcfead8f7f4270945e5512dfa9aea6 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/staging-input-files.md:15 +#: cc0cd8765dac4baab9072a90e82e4f8e +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/staging-input-files.md:20 +#: 77ac403083ff41e0a94b4376d57c4310 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" diff --git a/locales/topics/troubleshooting.pot b/locales/topics/troubleshooting.pot new file mode 100644 index 00000000..cfd4aa74 --- /dev/null +++ b/locales/topics/troubleshooting.pot @@ -0,0 +1,72 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/troubleshooting.md:1 +#: 628f6b4dad6d4b2e87d3c34d99b3bc9a +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: c2f444d8af5b47b389a53f047f42f7fc +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: b4d58509c2874a3a9a4aca8b0eb54b8e +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: cf0d233ea286443d9b4cd7b8e9b03090 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: e742b4b7517a4461ab38cd572fd02412 +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 8d0d5c4374ff4659b0a34f86a106915e +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: 2c4194ab026e41cb807e7cb15bc37e34 +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 0d287a4115ea4e34b239790ceee5d9be +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: b72ee99d9aee4c88bf4ae1a493b40415 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: 6541e0afd1784cdd890cae031fc6b13e +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: 3881a8c9e89c42c3a4a9fb99dffd6de8 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" diff --git a/locales/topics/using-containers.pot b/locales/topics/using-containers.pot new file mode 100644 index 00000000..03e278eb --- /dev/null +++ b/locales/topics/using-containers.pot @@ -0,0 +1,82 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/using-containers.md:1 +#: 3a1cb28acbf64b36b328af24b8ad3896 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: b0788dc4a9694fcface9c2d1122053ee +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: fdb03600e95f43248a8841308892f95f +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: 7e27ca6ce9974ef8a68e4955c377a7cc +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: 7162dac152a344b78a196ab9b304ff96 +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 7ecf64fbdd774b298455e9cdf5be38df +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 7ec954f8c1cd4ba3946ed2b3bd675083 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: b80d058d42c2414299eca96c4edd908b +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: c6ddaf94bc9f49e2b507a3eedaf597ee +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: d0770aeb8b0546ed943d60a3ae3b9f9a +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: d8c679b90ba14cf29280c1f1d271358d +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: c10409c624084be79a3378ae056d50c8 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 28514dd1b76648eb9bcec48290d7b66e +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" diff --git a/locales/topics/workflows.pot b/locales/topics/workflows.pot new file mode 100644 index 00000000..9847836f --- /dev/null +++ b/locales/topics/workflows.pot @@ -0,0 +1,374 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/workflows.md:1 +#: f87317cca4ba43af87f6a19b8fff6751 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: 00756723cfea4c79ab17ae39e400fd4c +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: ee41e057c6be476e9c56ac3c1f4aefad +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: 4e06945e9d794db58ebf5953a7bfc169 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: 3bb6bd3fa9a241b18f725f765f6d8f89 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: bd0042b64ca14e5fa4abe0b696ed8cc0 +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: f640b8cc119544ddb698828751335eef +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: ef0a22597b7b43a09b9d930eb733b181 +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 08e47d409fad4688b3fa893aac699505 +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 979f0abe51a7435991c062b239ab77ce +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 9e7ebb3fd64e4d9b89d10aab7ff6ef5a +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: a8bb6a54010c4563af5dd0e287e19ea9 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 3ca49084a67e48e196a29fce16266ebe +#: 2e5e721e9dcf477aacc5fd7970c8965f +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: cd69af46dab64758a7eeb25b8dd5ada4 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: 1370172b5e4d41dfa0f00268853c4a0c +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: df872d487e3d4e35b68bebcb27948577 +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 5039994944944010990efb63a1423bd2 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:198 +#: ce1bf8dbbe3c448b8d413993b986bee1 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: a72841d1fc594789adca91a6cec6b4c8 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: ab3448be251d454fbaf3e2e40e2a6179 +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: b24bc7e75b5e45a6b40f99122f7a46c6 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: 9eab201c6c314cf682f7623de820f007 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: 7aee0e6910f841eaad08091daaa43819 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: ad9e578cb5154c06b323ed8934f70359 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 6edc6273c5e84842a74b8921875481e9 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: 1d4faf0025bc4fc7bf53b87e4b3477e9 +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: 2185db6e6c9c470abc4e9a4dc95a921d +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: 91c1093736ea45e59fafba7d071bfda4 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 17955d02a70d484f8b2654feffc3f853 +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: 4e9524ce607243b9a6bd749bc436d796 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: 6d24477bbd3245a9be26954768605af8 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: 5525e4fa9a1e4245b5cd3a5465952fa8 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: b9dc7d7eab974749953065c7b7a92077 +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: 268089a26de840e8a01026a3d4ad93c8 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: 1523ed6264e84a0ea3a2c00857a71bb2 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: 125add3880f84620bc124f21096e1d1a +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: 423dd287ac0c4cc4a39b17dcc380fe45 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: d0fb2fada3c74bc2bb81928891b284a3 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 27e720818d69436d8c85931749918ad7 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: efe03781d801470db0950ca5c33e10b7 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: f21f8ee263e043a1b57dc8148a502b85 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: 5c91e32bd51045ec8442b28875e914a9 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: dbef641be8bb4a18ae974357ecb32f78 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: e86d663e2c39446b8c20c5eaf94a8802 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: 19ae2b52a9ab4b6ea4d8d8e57f40c170 +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: b711df1f3b1b4456b015701700c3c818 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: 60fb4221648d40968e1a0965a3b6693c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: c249bd4f52b348faa46918dee778a75d +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: ba039b00b2ea4de693b3358a036fd993 +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: a50560beb0f84c59b52a03b755e4e028 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: b1bde49eb1d6496a8d54094076e9c0f2 +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: 18d238a1bba943778f951b22e777af50 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 1fef76f43e2048718f82b67f66f48197 +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 6c2c8927cadf49858e0e1b3033c22168 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: 7482860af6ec4b519585837fee90289a +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: b9a64729a3c34bb2aaf4d9f780b29022 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: f3ad56146ff3429db2018fcdcef05724 +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: 4050c846b1144a5985b37c76bb24670d +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: fc2512823ca24060992b321fcf0d56db +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: 2eae7d61ffcd485aac22fc1fbbe7093a +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: 39971661faa74b58bf2f64c18a27fa76 +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: b36f484b8f904da58838aac09e7c14ff +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: 0db1e2093f8645df8f13fe394e8bf018 +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: 38a16292b8bb4ec48ae169292db7a2f2 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: 2c07c2968b53407686a8dd3f869b4fc4 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 61f0704412654df781833ffb6d5f33e3 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: d6634b5ec49e4113a90faec6b8de482d +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 9e6488eb6e60434eaf3148208a31a8aa +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: 3fe08f086e374050a89a39fcb3db0b78 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: ec35b97546eb42c28cc9bbdbf2ac2067 +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 22cf017e76d74584991ded94417c19d8 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" diff --git a/locales/topics/yaml-guide.pot b/locales/topics/yaml-guide.pot new file mode 100644 index 00000000..eb8a5519 --- /dev/null +++ b/locales/topics/yaml-guide.pot @@ -0,0 +1,157 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/yaml-guide.md:1 +#: c28a6abcd8334321b7d1c84192b42caa +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: 3e16eeaccec8491dacfde122153d5bd0 +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: 363eb3871f5d4c1288138dbd5f89be62 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: 31d7b17c34e0405b94f95e273bb22ac5 +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 60197a7f2b7c40c48ede3d59626a09d8 +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: 7b76a198bd154da99e38146a74ecec6c +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: 024a6818d1b9492bb6e1f1c11d932953 +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: d0c550b003fa48c8b1b16888c7e9bc5f +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 7c2f8ceba9a141f097767ae8c3688aee +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 5cfa92e1509e41cf9dec646d3a5dad86 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: f76bccaee68c4eec96822d00013395a9 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 5591f710f08a4e8c8d974224cdf018b5 +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: e383736713e243d487b883e669fb7065 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: c50eafc65e8b4b8a81318694098a42e5 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 3d8de32c3f3448e5beb19d395099e27d +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 20edeb5c184f4df2ade328131365d751 +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: 7f436640365249568802a846d4ad896b +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: 7514de6b828f44b1b1d8683d8324a1da +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 01288d81ae2e466d94bbee33751b3bd6 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: 3e6ba9083cdd4ed586110f76cd071896 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: 2c23b44142ba4969bd30c33c97142aed +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: 5956220b3839466aa491e84d2d0a5757 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 0ff275ae871b49449ec789b1bdc814c6 +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: f5215b7de4994cc5890886ac2914be23 +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: 48dec799be364824a5dcbf5329f1f0ce +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: b4d3a3a2823147c9aa7a37ad2fe5ce06 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: 6998b8bd38a944f19c9ca758b14babe8 +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: bcc40a813d344c0abd960add8685e132 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" diff --git a/locales/tutorials.pot b/locales/tutorials.pot new file mode 100644 index 00000000..7864fea7 --- /dev/null +++ b/locales/tutorials.pot @@ -0,0 +1,57 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/tutorials.md:1 +#: d32522e2993f4b48a789f46537fa5ebf +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 63a51dccb29045fd8f78d5e396c6e050 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: cb5f8748a5544be2835467ab07eb7a1c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 685d0cb2faa04703bcef408ecc2b92f4 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 20f45705145d45fc8420c4119b06a49f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 2bccd19d542d4458a1ba8616236f1840 +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: c491c73e4c00476980438ffc79c6e4d3 +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: b8485449206542e097584eca7363c8ce +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" From 0eacbc67346d67fd2ab95f202993f2fd409e0d71 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 24 Jan 2023 18:36:02 +0100 Subject: [PATCH 030/179] don't translate English into English --- locales/en/LC_MESSAGES/LICENSE.po | 120 ----- .../en/LC_MESSAGES/_includes/what-is-cwl.po | 28 - locales/en/LC_MESSAGES/episodes.po | 31 -- locales/en/LC_MESSAGES/faq.po | 307 ----------- locales/en/LC_MESSAGES/index.po | 68 --- .../introduction/basic-concepts.po | 270 ---------- locales/en/LC_MESSAGES/introduction/index.po | 31 -- .../LC_MESSAGES/introduction/prerequisites.po | 298 ----------- .../LC_MESSAGES/introduction/quick-start.po | 191 ------- locales/en/LC_MESSAGES/setup.po | 31 -- locales/en/LC_MESSAGES/sphinx.po | 28 - .../additional-arguments-and-parameters.po | 84 --- .../en/LC_MESSAGES/topics/best-practices.po | 191 ------- .../LC_MESSAGES/topics/command-line-tool.po | 71 --- .../topics/creating-files-at-runtime.po | 104 ---- locales/en/LC_MESSAGES/topics/custom-types.po | 99 ---- .../topics/environment-variables.po | 45 -- .../en/LC_MESSAGES/topics/expression-tool.po | 53 -- locales/en/LC_MESSAGES/topics/expressions.po | 383 ------------- locales/en/LC_MESSAGES/topics/file-formats.po | 93 ---- locales/en/LC_MESSAGES/topics/index.po | 24 - locales/en/LC_MESSAGES/topics/inputs.po | 313 ----------- .../topics/metadata-and-authorship.po | 70 --- locales/en/LC_MESSAGES/topics/operations.po | 73 --- locales/en/LC_MESSAGES/topics/outputs.po | 147 ----- .../topics/parameter-references.po | 279 ---------- .../topics/requirements-and-hints.po | 24 - .../specifying-software-requirements.po | 68 --- .../LC_MESSAGES/topics/staging-input-files.po | 48 -- .../en/LC_MESSAGES/topics/troubleshooting.po | 101 ---- .../en/LC_MESSAGES/topics/using-containers.po | 106 ---- locales/en/LC_MESSAGES/topics/workflows.po | 504 ------------------ locales/en/LC_MESSAGES/topics/yaml-guide.po | 193 ------- locales/en/LC_MESSAGES/tutorials.po | 58 -- 34 files changed, 4534 deletions(-) delete mode 100644 locales/en/LC_MESSAGES/LICENSE.po delete mode 100644 locales/en/LC_MESSAGES/_includes/what-is-cwl.po delete mode 100644 locales/en/LC_MESSAGES/episodes.po delete mode 100644 locales/en/LC_MESSAGES/faq.po delete mode 100644 locales/en/LC_MESSAGES/index.po delete mode 100644 locales/en/LC_MESSAGES/introduction/basic-concepts.po delete mode 100644 locales/en/LC_MESSAGES/introduction/index.po delete mode 100644 locales/en/LC_MESSAGES/introduction/prerequisites.po delete mode 100644 locales/en/LC_MESSAGES/introduction/quick-start.po delete mode 100644 locales/en/LC_MESSAGES/setup.po delete mode 100644 locales/en/LC_MESSAGES/sphinx.po delete mode 100644 locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po delete mode 100644 locales/en/LC_MESSAGES/topics/best-practices.po delete mode 100644 locales/en/LC_MESSAGES/topics/command-line-tool.po delete mode 100644 locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po delete mode 100644 locales/en/LC_MESSAGES/topics/custom-types.po delete mode 100644 locales/en/LC_MESSAGES/topics/environment-variables.po delete mode 100644 locales/en/LC_MESSAGES/topics/expression-tool.po delete mode 100644 locales/en/LC_MESSAGES/topics/expressions.po delete mode 100644 locales/en/LC_MESSAGES/topics/file-formats.po delete mode 100644 locales/en/LC_MESSAGES/topics/index.po delete mode 100644 locales/en/LC_MESSAGES/topics/inputs.po delete mode 100644 locales/en/LC_MESSAGES/topics/metadata-and-authorship.po delete mode 100644 locales/en/LC_MESSAGES/topics/operations.po delete mode 100644 locales/en/LC_MESSAGES/topics/outputs.po delete mode 100644 locales/en/LC_MESSAGES/topics/parameter-references.po delete mode 100644 locales/en/LC_MESSAGES/topics/requirements-and-hints.po delete mode 100644 locales/en/LC_MESSAGES/topics/specifying-software-requirements.po delete mode 100644 locales/en/LC_MESSAGES/topics/staging-input-files.po delete mode 100644 locales/en/LC_MESSAGES/topics/troubleshooting.po delete mode 100644 locales/en/LC_MESSAGES/topics/using-containers.po delete mode 100644 locales/en/LC_MESSAGES/topics/workflows.po delete mode 100644 locales/en/LC_MESSAGES/topics/yaml-guide.po delete mode 100644 locales/en/LC_MESSAGES/tutorials.po diff --git a/locales/en/LC_MESSAGES/LICENSE.po b/locales/en/LC_MESSAGES/LICENSE.po deleted file mode 100644 index 29b53dd1..00000000 --- a/locales/en/LC_MESSAGES/LICENSE.po +++ /dev/null @@ -1,120 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../../LICENSE.md:2 f0c9a54a904e42249441ee22e39d6f3a -msgid "Licenses" -msgstr "" - -#: ../../../LICENSE.md:4 6c99230ebe4d48689e09e2da1484abc9 -msgid "Instructional Material" -msgstr "" - -#: ../../../LICENSE.md:6 327a6405608b4df488fc6aee756f94b7 -msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable " -"summary of (and not a substitute for) the [full legal text of the CC BY " -"4.0 license][cc-by-legal]." -msgstr "" - -#: ../../../LICENSE.md:12 91d85fe9673942658f5d17e286ac6b69 -msgid "You are free:" -msgstr "" - -#: ../../../LICENSE.md:14 c010a0b9145e4532896b114d4e0c7768 -msgid "to **Share**---copy and redistribute the material in any medium or format" -msgstr "" - -#: ../../../LICENSE.md:15 8e7d2d9301a8452994e4b33edb3c7ea0 -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" - -#: ../../../LICENSE.md:17 0fdc0b2074bc4cfd8cd020d51a3d4f3b -msgid "for any purpose, even commercially." -msgstr "" - -#: ../../../LICENSE.md:19 220eba84dd874fb59ac0d4f7a95695fc -msgid "" -"The licensor cannot revoke these freedoms as long as you follow the " -"license terms." -msgstr "" - -#: ../../../LICENSE.md:22 c21178abaf374ca5ae83fb9b94761e7e -msgid "Under the following terms:" -msgstr "" - -#: ../../../LICENSE.md:24 90e30b28cfdb4c8fb6bf2e2687ac47c3 -msgid "" -"**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow " -"Language project, and, where practical, linking to " -"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" -"human], and indicate if changes were made. You may do so in any " -"reasonable manner, but not in any way that suggests the licensor endorses" -" you or your use." -msgstr "" - -#: ../../../LICENSE.md:32 c40a837670f84762bffc0cc8d697d45d -msgid "" -"**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything " -"the license permits. With the understanding that:" -msgstr "" - -#: ../../../LICENSE.md:36 233edb183ff44c7293756df599b2a130 -msgid "" -"You do not have to comply with the license for elements of the material " -"in the public domain or where your use is permitted by an applicable " -"exception or limitation." -msgstr "" - -#: ../../../LICENSE.md:39 027339c3a92747e8948b11671ace4145 -msgid "" -"No warranties are given. The license may not give you all of the " -"permissions necessary for your intended use. For example, other rights " -"such as publicity, privacy, or moral rights may limit how you use the " -"material." -msgstr "" - -#: ../../../LICENSE.md:44 89dcc55f3d5d445b97912648ee5dba03 -msgid "Software" -msgstr "" - -#: ../../../LICENSE.md:46 070952c76313480d92f0b78321a6a1e2 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." -msgstr "" - -#: ../../../LICENSE.md:51 3279f7573aa44853af83dbf9dd9748a9 -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, " -"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " -"See the License for the specific language governing permissions and " -"limitations under the License." -msgstr "" - -#: ../../../LICENSE.md:57 979969ab3c3f4080b6c7e879efe9f351 -msgid "Trademark" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/_includes/what-is-cwl.po b/locales/en/LC_MESSAGES/_includes/what-is-cwl.po deleted file mode 100644 index bc854eb9..00000000 --- a/locales/en/LC_MESSAGES/_includes/what-is-cwl.po +++ /dev/null @@ -1,28 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../_includes/what-is-cwl.md:1 ffc6d3382e944f22a8b13062eb1badc4 -msgid "" -"CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/episodes.po b/locales/en/LC_MESSAGES/episodes.po deleted file mode 100644 index ed5b10aa..00000000 --- a/locales/en/LC_MESSAGES/episodes.po +++ /dev/null @@ -1,31 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../episodes.md:5 0c99dd9365d14d26b9b3bb5e88f33570 -msgid "This page has moved" -msgstr "" - -#: ../../episodes.md:9 2718a75eccf84a1fa22356367d3b772e -msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. Please use the new [Table of Contents](index.md#table-of-" -"contents) to browse the User Guide." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/faq.po b/locales/en/LC_MESSAGES/faq.po deleted file mode 100644 index c74aeb6e..00000000 --- a/locales/en/LC_MESSAGES/faq.po +++ /dev/null @@ -1,307 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../faq.md:1 1479ffe379ea483290f2c16ddc8d6358 -msgid "FAQ" -msgstr "" - -#: ../../faq.md:11 b6cd88863b754a7d8467948ea72063ac -msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "" - -#: ../../faq.md:41 29876633f61f4befa1ba764a8e14909a -msgid "Rename an Input File" -msgstr "" - -#: ../../faq.md:43 c523a45d4fff4ac5b451b8c9e947a0c1 -msgid "" -"This example demonstrates how to change the name of an input file as part" -" of a tool description. This could be useful when you are taking files " -"produced from another step in a workflow, and don't want to work with the" -" default names that these files were given when they were created." -msgstr "" - -#: ../../faq.md:59 6761f620fae44513ba675bb845dad5af -msgid "Rename an Output File" -msgstr "" - -#: ../../faq.md:61 83312f5876ea492c9a881b8d1d8ec232 -msgid "" -"This example demonstrates how to change the name of an output file from " -"the default name given to it by a tool:" -msgstr "" - -#: ../../faq.md:82 da3f295db7584f2ab5532fb915c8ada7 -msgid "Referencing a Local Script" -msgstr "" - -#: ../../faq.md:84 e4aec7bca9bf4ef0a3d709fd0771d886 -msgid "There are two ways to reference a local script:" -msgstr "" - -#: ../../faq.md:86 f6fcb55812944ad98053fee5243125fb -msgid "" -"The first method involves adding the folder containing your scripts to " -"the `PATH` environment variable. This allows you to run the shell script " -"directly without using `sh` or `bash` commands." -msgstr "" - -#: ../../faq.md:89 7a83b32f4124408ab1f0dc3303d5d640 -msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" - -#: ../../faq.md:95 c59ec88c1d1545699fd0c00f6173dccc -msgid "" -"After that, make the script executable with the command `chmod +x " -"scriptname.sh`" -msgstr "" - -#: ../../faq.md:97 dbd4fb58d2e34ccbb9544f2106ee56e5 -msgid "" -"Finally, modify your `PATH` to add the directory where your script is " -"located. (It is good practice to use `$HOME/bin` for storing your own " -"scripts)." -msgstr "" - -#: ../../faq.md:104 9fb24ecdc09b438bb46e8107880e77a0 -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "" - -#: ../../faq.md:113 b8624be7349d472b9b86409bd5b786cd -msgid "" -"When you wish to share your work later, you can place your script in a " -"software container in the Docker format." -msgstr "" - -#: ../../faq.md:115 fdcc23c875974ee58a4e5ae702eaac67 -msgid "" -"The second method involves including an input of `type: File` in the " -"script itself:" -msgstr "" - -#: ../../faq.md:135 da2ee2848dbc4dff8663c1fbf00c863f -msgid "In CWL, everything must be directly stated." -msgstr "" - -#: ../../faq.md:138 782152c8aab84a12bb04375096f492b6 -msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "" - -#: ../../faq.md:140 da2600292146447aa527f24c69cfb776 -msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their " -"input binding makes use of `self`. Below is an example workaround for " -"this, pending a more sophisticated fix." -msgstr "" - -#: ../../faq.md:165 dc07a65c25854ef6b21cb4a43bee4d31 -msgid "Model a \"one-or-the-other\" Parameter" -msgstr "" - -#: ../../faq.md:167 76bfb57ea05647748b60e36712a8b100 -msgid "" -"Below is an example showing how to specify different strings to be added " -"to a command line, based on the value given to a Boolean parameter." -msgstr "" - -#: ../../faq.md:188 be450f9113f3451691eea5f0d30c3c74 -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "" - -#: ../../faq.md:190 a328ad7be4e44194b8a1fb5a436d1265 -msgid "" -"Using " -"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" -" along with [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../faq.md:194 d86e24a5d27b418ba29e5439b34a5c13 -msgid "merge_nested" -msgstr "" - -#: ../../faq.md:196 f9b6d21ce7f3405da57fa7443e623b8a -msgid "" -"The input must be an array consisting of exactly one entry for each input" -" link. If \"merge_nested\" is specified with a single link, the value " -"from the link must be wrapped in a single-item list." -msgstr "" - -#: ../../faq.md:199 1ac676ef33bb45c4b7fc371e7bd84f07 -msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "" - -#: ../../faq.md:201 75cef09a92cc44c397a18f81840743b2 -msgid "" -"Or in other words: if the destination is of type `File[]` (an array of " -"`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " -"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" -" destination step." -msgstr "" - -#: ../../faq.md:229 5bd33a98001148e7b8e83b9bb83b62ee -msgid "Optional Inputs 💯" -msgstr "" - -#: ../../faq.md:231 70651f1b65fd4e20b0f1719c3b8ea3f8 -msgid "" -"To make an input parameter optional, add a question mark to the type " -"declaration." -msgstr "" - -#: ../../faq.md:247 cb3f5cae1479448c9669e2751fd34460 -msgid "" -msgstr "" - -#: ../../faq.md:248 74eafea819d6405b8f573da4ec712445 -msgid "Enum Inputs ⚜️" -msgstr "" - -#: ../../faq.md:250 4955ef4f959143b096125f95ec32c1e2 -msgid "" -"For command line flags that require a specific input as the argument an " -"enum type can be declared in CWL. **Specifying null here is known as long" -" form style. It does the same thing as the question mark on the other " -"inputs.**" -msgstr "" - -#: ../../faq.md:267 bdf0e5bf3c754f639fbb4ad24076bc4a -msgid "" -msgstr "" - -#: ../../faq.md:268 64c7ae1eaf6b4b0cb4a5fc23feb6349e -msgid "Record Inputs 📀" -msgstr "" - -#: ../../faq.md:270 ad83e44a7f914cfbb46aa191a17d4c85 -msgid "" -"For commandline flags that are either **mutually exclusive** or " -"**dependent** a special record type can be defined. You can also specify " -"null here to create optional inputs." -msgstr "" - -#: ../../faq.md:322 68e228ecf0be4753832a31ceb933fc19 -msgid "Setting Mutually Exclusive Parameters" -msgstr "" - -#: ../../faq.md:324 e2f19825601845b59d5cbeeeb0024622 -msgid "" -"To properly set fields in a record input type, you need to pass a " -"dictionary to the input to properly set the parameters. This is done by " -"using inline JavaScript and returning the dictionary with the key of the " -"field you want to set. The source field is set to indicate the input from" -" the workflow to be used as the value." -msgstr "" - -#: ../../faq.md:342 0824a9e1f5684da481163cd16fed94b9 -msgid "Setting Booleans" -msgstr "" - -#: ../../faq.md:344 192e416a398845838d55bdb71190bb70 -msgid "These can be set by using the default field" -msgstr "" - -#: ../../faq.md:349 eb6a00b2ff3a4ec384a0308f00dd8c4c -msgid "Concatenating Strings in Inputs" -msgstr "" - -#: ../../faq.md:351 9a7df9d0f389421298e6d456822e52a4 -msgid "The valueFrom field must be used instead of default." -msgstr "" - -#: ../../faq.md:359 9cab760a07114447a817f63ff61ff346 -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "" - -#: ../../faq.md:361 9ccf1286db084b67a37b2217a9764584 -msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "" - -#: ../../faq.md:363 33ea1db2582f4fe78436fb1a8f431b15 -msgid "" -"For example, the filename `a space is here.txt` includes 3 space " -"characters." -msgstr "" - -#: ../../faq.md:371 0f8a3fc6e622464fae1366a053baa78c -msgid "" -"If you can not avoid these dangerous characters, then pass `--relax-path-" -"checks` to `cwltool`." -msgstr "" - -#: ../../faq.md:373 6a3ba881461642aa8d7654dad772ccd3 -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -msgstr "" - -#: ../../faq.md:375 253cbea8229743b8a064d4d2fac24f12 -msgid "If `cwltool --validate` returns valid" -msgstr "" - -#: ../../faq.md:384 63190f04254b4459880b1ee84886bbab -msgid "But executing it causes an error like:" -msgstr "" - -#: ../../faq.md:396 61d3a0026a274eafa31b02220bc4bd0e -msgid "The file is here" -msgstr "" - -#: ../../faq.md:410 2a99b8770636429693ff44563f0ac148 -msgid "Problem caused by `-` (hyphen character)." -msgstr "" - -#: ../../faq.md:423 a0d1eff495924aeaaad2ed92010e92f4 -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" - -#: ../../faq.md:436 a901e5d22e644dcc848d347bcf87d59b -msgid "" -"If it is not possible to change the input identifier, then you can use an" -" alternative CWL Parameter Reference syntax:" -msgstr "" - -#: ../../faq.md:442 5baccb1d1e604c849cce7b27223b1f9f -msgid "Use CWL and cwltool with Singularity" -msgstr "" - -#: ../../faq.md:445 b8421426848c470db2324fde8ae8f05d -msgid "" -"The CWL standards are built around (optional) Docker format containers. " -"The reference runner and several other CWL implementations support " -"running those Docker format containers using the Singularity engine. " -"Directly specifying a Singularity format container is not part of the CWL" -" standards." -msgstr "" - -#: ../../faq.md:450 1a3fecc9eb7a4dcdaf577983c505ba13 -msgid "Debug JavaScript Expressions" -msgstr "" - -#: ../../faq.md:452 b17460fcb17e40da879383df593f2a93 -msgid "" -"You can use the --js-console option of cwltool," -" or you can try creating a JavaScript or TypeScript project for your " -"code, and load it using expressionLib, e.g.: " -"https://github.com/common-workflow-language/common-workflow-" -"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/index.po b/locales/en/LC_MESSAGES/index.po deleted file mode 100644 index 2437acd8..00000000 --- a/locales/en/LC_MESSAGES/index.po +++ /dev/null @@ -1,68 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../index.md:1 618bf3fb1f364be791cc5f2bf77667d5 -msgid "Common Workflow Language User Guide" -msgstr "" - -#: ../../index.md:3 67f4f01edc5b4261a70e4efc3d792f64 -msgid "" -"This guide will introduce you to writing workflows using the [Common " -"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " -"guide describes the latest specification {{ cwl_version }}." -msgstr "" - -#: ../../index.md:7 284c0f5ead3142649c3c6d4f04da4851 -msgid "Contributions and Feedback are Welcome!" -msgstr "" - -#: ../../index.md:9 75a3c6a67c2e4593a098c839483ae47f -msgid "" -"If you find that something is missing from this guide, or if you would " -"like to provide other feedback, file an Issue on the [project repository " -"for this guide][repo]. You can also suggest changes directly in a Pull " -"Request by clicking the \"Edit this page\" button at the right sidebar of" -" each page." -msgstr "" - -#: ../../index.md:16 6061795c74ce415eb3e4f1ca3ed91de6 -msgid "Navigating the User Guide" -msgstr "" - -#: ../../index.md:18 c74efbca9bcd4fda9c4e94d774caa91c -msgid "" -"If you are a beginner user get started with the " -"[Introduction](/introduction/index.md) section. For advanced users the " -"subsections of the [Topics](/topics/index.md) have detailed information " -"about the most common topics for CWL." -msgstr "" - -#: ../../index.md:23 f2bc70925dea4573ab177c5d2f2b5dcb -msgid "" -"The Table of Contents is displayed at the top menu and also on the left " -"sidebar. It also appears further down this page but with links to " -"subsections. The right sidebar contains links to the sections of each " -"page, and the Search form is on the left sidebar." -msgstr "" - -#: ../../index.md:28 3e4e62c52c5547c6a4e77131ab1dee39 -msgid "Table of Contents" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/introduction/basic-concepts.po b/locales/en/LC_MESSAGES/introduction/basic-concepts.po deleted file mode 100644 index 3fe5662f..00000000 --- a/locales/en/LC_MESSAGES/introduction/basic-concepts.po +++ /dev/null @@ -1,270 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../introduction/basic-concepts.md:1 5f43861a84a2494b8e1bc973ac85b3d0 -msgid "Basic Concepts" -msgstr "" - -#: ../../introduction/basic-concepts.md:3 90cc7b0ef1404f72ae0f5b17f6f2a966 -msgid "" -"This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are " -"expected to be familiar with workflow managers, YAML, and comfortable " -"with following instructions for the command-line. The other sections of " -"the user guide cover the same concepts, but in more detail. If you are " -"already familiar with CWL or you are looking for more advanced content, " -"you may want to skip this section." -msgstr "" - -#: ../../introduction/basic-concepts.md:10 1685ddf11a014fe28df75dedb7c39e07 -msgid "The CWL Specification" -msgstr "" - -#: ../../_includes/what-is-cwl.md:2 9cb90a376bfe4058922b1c91ea4ce184 -msgid "" -"CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../introduction/basic-concepts.md:21 cc05f8193ee6403daca03d2d19ccfcd7 -msgid "" -"The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered " -"in this user guide is the {{ cwl_version }}." -msgstr "" - -#: ../../introduction/basic-concepts.md:25 f5a0ba9dfc1f49ab937e8122fe4761e0 -msgid "" -"The specification version can have up to three numbers separated by `.`s " -"(dots). The first number is the major release, used for backward-" -"incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes " -"that are backward-compatible. The last number is used for bug fixes, like" -" typos and other corrections to the specification." -msgstr "" - -#: ../../introduction/basic-concepts.md:33 8100683970154870993d19d7a5a6bd22 -msgid "" -"The model used for the specification version is called Semantic " -"Versioning. See the end of this section to [learn more](#learn-more) " -"about it." -msgstr "" - -#: ../../introduction/basic-concepts.md:37 cc5c29f65655465db44dd4eed8f11c7b -msgid "Implementations" -msgstr "" - -#: ../../introduction/basic-concepts.md:39 c07822e70e774ea2bb3da2cfd69aa360 -msgid "" -"An implementation of the CWL specification is any software written " -"following what is defined in a version of the specification document. " -"However, implementations may not implement every aspect of the " -"specification. CWL implementations are licensed under both Open Source " -"and commercial licenses." -msgstr "" - -#: ../../introduction/basic-concepts.md:44 6735911046aa466aa2a371ffff22a9fe -msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud" -" and high performance computing environments where tasks are scheduled in" -" parallel across many nodes." -msgstr "" - -#: ../../introduction/basic-concepts.md:51 795e23a746c749deacb68a18d9a3333b -msgid "CWL specification, implementations, and other tools." -msgstr "" - -#: ../../introduction/basic-concepts.md:105 e7c0b2155a024860b8d3fd7c9ef75f38 -msgid "Processes and Requirements" -msgstr "" - -#: ../../introduction/basic-concepts.md:107 cf57f60e189e40c09e946f56a1fdf0b8 -msgid "" -"A process is a computing unit that takes inputs and produces outputs. The" -" behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification" -" {{ cwl_version }}:" -msgstr "" - -#: ../../introduction/basic-concepts.md:112 6201ed50ccf944c2aaf7795d411e236d -msgid "A command-line tool." -msgstr "" - -#: ../../introduction/basic-concepts.md:113 a6f9f66dec354e09bd1778d2bf71a7ef -msgid "An expression tool." -msgstr "" - -#: ../../introduction/basic-concepts.md:114 43927a824e584c3c8914119bcdfdffbc -msgid "An operation." -msgstr "" - -#: ../../introduction/basic-concepts.md:115 98f30716f9154c51bcf95a9a26613c6e -msgid "A workflow." -msgstr "" - -#: ../../introduction/basic-concepts.md:118 07807b77a0a444568348e8c20e540296 -msgid "The processing units available in the CWL objects model." -msgstr "" - -#: ../../introduction/basic-concepts.md:119 f7dd65df72be46e88ad933e85d2cfe32 -msgid "" -"A command-line tool is a wrapper for a command-line utility like `echo`, " -"`ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" - -#: ../../introduction/basic-concepts.md:122 7c12205b897c4d6ea918fc8b371ba329 -msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be " -"used to simplify workflows and command-line tools, moving common parts of" -" a workflow execution into reusable JavaScript code that takes inputs and" -" produces outputs like a command-line tool." -msgstr "" - -#: ../../introduction/basic-concepts.md:127 965bd0c3dedc43d188c9c7b5db33b1f5 -msgid "" -"Operation is an abstract process that also takes inputs, produces " -"outputs, and can be used in a workflow. But it is a special operation not" -" so commonly used. It is discussed in the [Operations " -"section](../topics/operations.md) of this user guide." -msgstr "" - -#: ../../introduction/basic-concepts.md:131 7299dcb09d2b4967a9d46d3b433d439e -msgid "" -"The workflow is a process that contains steps. Steps can be other " -"workflows (nested workflows), command-line tools, or expression tools. " -"The inputs of a workflow can be passed to any of its steps, while the " -"outputs produced by its steps can be used in the final output of the " -"workflow." -msgstr "" - -#: ../../introduction/basic-concepts.md:137 ea9d197aab4c41788a4a0e3d48c1c168 -msgid "" -"The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through " -"*requirements*. There are many requirements defined in the CWL " -"specification, for instance:" -msgstr "" - -#: ../../introduction/basic-concepts.md:141 592f212970f84365a86a69cfb8c26369 -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" - -#: ../../introduction/basic-concepts.md:142 57e5ad64e68545a788b43e4e921bb23f -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" - -#: ../../introduction/basic-concepts.md:143 397171706bf349feb2c9bee5a993ea1e -msgid "" -"`InitialWorkDirRequirement` - controls staging files in the input " -"directory." -msgstr "" - -#: ../../introduction/basic-concepts.md:145 fa9d473ae58b4053981a45a888470655 -msgid "" -"Some CWL runners may provide requirements that are not in the " -"specification. For example, GPU requirements are supported in `cwltool` " -"through the `cwltool:CUDARequirement` requirement, but it is not part of " -"the {{ cwl_version }} specification and may not be supported by other CWL" -" runners." -msgstr "" - -#: ../../introduction/basic-concepts.md:151 b9cc1fd288764bd78eda4703a2700a02 -msgid "" -"Hints are similar to requirements, but while requirements list features " -"that are required, hints list optional features. Requirements are " -"explained in detail in the [Requirements](../topics/requirements-and-" -"hints.md) section." -msgstr "" - -#: ../../introduction/basic-concepts.md:155 cf12d86b4e7c48c892d6be8233ea2bc9 -msgid "FAIR Workflows" -msgstr "" - -#: ../../introduction/basic-concepts.md:157 a83ecf7c5eaa4af3a676060d12ec7e7e -msgid "" -"The FAIR principles have laid a foundation for sharing and publishing " -"digital assets, and in particular, data. The FAIR principles emphasize " -"machine accessibility and that all digital assets should be Findable, " -"Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created." -" It is thus important that workflows support the creation of FAIR data " -"and adhere to the FAIR principles. — [FAIR Computational " -"Workflows](https://workflows.community/groups/fair/), Workflows Community" -" Initiative." -msgstr "" - -#: ../../introduction/basic-concepts.md:167 7451c042271941d6b283bf6d54b76acb -msgid "" -"CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\"," -" CWL tasks are isolated, and you must be explicit about your inputs and " -"outputs." -msgstr "" - -#: ../../introduction/basic-concepts.md:171 d356140962c244d78b4a2c888bf03963 -msgid "" -"The benefit of explicitness and isolation are flexibility, portability, " -"and scalability; tools and workflows described with CWL can transparently" -" leverage technologies such as Docker and be used with CWL " -"implementations from different vendors." -msgstr "" - -#: ../../introduction/basic-concepts.md:176 8fee6b5cd95144e1bced764b112a9d3f -msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" - -#: ../../introduction/basic-concepts.md:178 38ce1ceb880b4421b9ea2ee52e1153da -msgid "Learn More" -msgstr "" - -#: ../../introduction/basic-concepts.md:180 9a631f69c9504527bcd02a8f40f21c3f -msgid "Semantic Versioning - " -msgstr "" - -#: ../../introduction/basic-concepts.md:181 6141f823850e411691c2ef7047c9ecab -msgid "" -"The CWL Specification page in the CWL website: " -"" -msgstr "" - -#: ../../introduction/basic-concepts.md:182 6a07a8b45dc54851b5b78597891be763 -msgid "" -"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" -msgstr "" - -#: ../../introduction/basic-concepts.md:183 f246c41bb0f946c590736c40713af684 -msgid "" -"The list of Implementations in the CWL website: " -"" -msgstr "" - -#: ../../introduction/basic-concepts.md:184 d9d8d29e5c0e427299f696073dfbfc1b -msgid "PROV-O: The PROV Ontology - " -msgstr "" - -#: ../../introduction/basic-concepts.md:185 581a427aed9e483489b6123ee1879d80 -msgid "" -"CWL Operations are covered in the [Operations](../topics/operations.md) " -"section of this user guide." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/introduction/index.po b/locales/en/LC_MESSAGES/introduction/index.po deleted file mode 100644 index 3b6add35..00000000 --- a/locales/en/LC_MESSAGES/introduction/index.po +++ /dev/null @@ -1,31 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../introduction/index.md:1 b93db93ee9a24f03805cc032d22ca212 -msgid "Introduction" -msgstr "" - -#: ../../introduction/index.md:3 f77b8595af564c688c37097c43e04c86 -msgid "" -"This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that" -" are useful to know before reading the rest of the user guide." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/introduction/prerequisites.po b/locales/en/LC_MESSAGES/introduction/prerequisites.po deleted file mode 100644 index f8f47a94..00000000 --- a/locales/en/LC_MESSAGES/introduction/prerequisites.po +++ /dev/null @@ -1,298 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../introduction/prerequisites.md:1 7bbfeec267824100866390bfcfa6cec9 -msgid "Prerequisites" -msgstr "" - -#: ../../introduction/prerequisites.md:6 aa8e8b6a8dfa499f99598f30dca4074f -msgid "" -"The software and configurations listed in this section are prerequisites " -"for following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements " -"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" -"compatible runner or workflow system, but the results and interface may " -"look different (though the exact workflow outputs should be identical)." -msgstr "" - -#: ../../introduction/prerequisites.md:12 cf4757d4aef2456397017d2ff13499ba -msgid "CWL Implementations" -msgstr "" - -#: ../../introduction/prerequisites.md:14 502c3afa077249b98a51051b23698a6d -msgid "" -"There are many implementations of the CWL standards. Some are complete " -"CWL runners, while others could be plug-ins or extensions to workflow " -"engines. We have a better explanation in the [Implementations](basic-" -"concepts.md#implementations) section." -msgstr "" - -#: ../../introduction/prerequisites.md:19 9a788e46f9d64d30aeff30a86182884c -msgid "Operating System" -msgstr "" - -#: ../../introduction/prerequisites.md:21 cc76660874a944369f69207bb1e0e856 -msgid "" -"We recommend using an up-to-date operating system. You can choose any of " -"the following options for your operating system:" -msgstr "" - -#: ../../introduction/prerequisites.md:24 77c62d947e894088afc8520451c79ac1 -msgid "Linux" -msgstr "" - -#: ../../introduction/prerequisites.md:25 32cd53abe1744596b3b33835cd8d1eb1 -msgid "macOS" -msgstr "" - -#: ../../introduction/prerequisites.md:26 1a7b4392aec64e3e9c053288362f342a -msgid "Windows" -msgstr "" - -#: ../../introduction/prerequisites.md:29 dcea6593d35c40bc9c0d39d4a788fbc1 -msgid "" -"If you are using Windows, you will have to install the [Windows Subsystem" -" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " -"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" -"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " -"details on installing WSL2. Your operating system also needs internet " -"access and a recent version of Python (3.6+)." -msgstr "" - -#: ../../introduction/prerequisites.md:35 45bde9e20d0d45eb93427f5b6a3634dd -msgid "CWL Runner" -msgstr "" - -#: ../../introduction/prerequisites.md:41 998f8c45ed8f4075a577d4e6af1eda5b -msgid "" -"The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL " -"community. It is also the CWL reference runner, which means it must " -"support everything in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../introduction/prerequisites.md:46 813a16e6431744b1aad3bc11a2402e44 -msgid "" -"`cwltool` can be installed with `pip`. We recommend using a virtual " -"environment like `venv` or `conda`. The following commands will create " -"and activate a Python virtual environment using the `venv` module, and " -"install `cwltool` in that environment:" -msgstr "" - -#: ../../introduction/prerequisites.md:51 297d141896a84499a91f312a0016547f -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" - -#: ../../introduction/prerequisites.md:62 ad7893d4a87d441c8aedbf168d3ca9ad -msgid "" -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool#install) for other ways to install `cwltool` with `apt` " -"and `conda`." -msgstr "" - -#: ../../introduction/prerequisites.md:65 5dbc4e8a1c544a258d5b2d965db08be2 -msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" - -#: ../../introduction/prerequisites.md:67 380bf05c4a754d008499fa6206e86e90 -msgid "`true.cwl`" -msgstr "" - -#: ../../introduction/prerequisites.md:73 6d772529b43746a9bbb7c3bd2fb033a2 -msgid "" -"The `cwltool` command has an option to validate CWL tool and workflow " -"descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the " -"CWL standards. However, these actions will be performed without running " -"the document. To validate CWL workflows (or even a standalone command " -"line tool description like the above) pass the `--validate` option to the" -" `cwltool` command:" -msgstr "" - -#: ../../introduction/prerequisites.md:79 d48c1d5aab4d4b78b610a6a8cecbac3f -msgid "Validating `true.cwl` with `cwltool`." -msgstr "" - -#: ../../introduction/prerequisites.md:84 50a41a581e2045fd9fcd7149162d1b43 -msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" - -#: ../../introduction/prerequisites.md:86 35183394d2db4b0797e6a5533cf91eed -msgid "Running `true.cwl` with `cwltool`." -msgstr "" - -#: ../../introduction/prerequisites.md:91 b59575e71904478e8833c13b38d53c91 -msgid "Cwl-runner Python Module" -msgstr "" - -#: ../../introduction/prerequisites.md:93 c784985a2d3d4d5c9583fe8d76037a90 -msgid "" -"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be " -"invoked independently, and is not reliant on a particular CWL runner " -"program name. Users can invoke `cwl-runner` instead of invoking a CWL " -"runner like `cwltool` directly. The `cwl-runner` is installed by a system" -" administrator or user to point to the preferred CWL implementation. This" -" is convenient for environments with multiple CWL runners." -msgstr "" - -#: ../../introduction/prerequisites.md:101 1fa903efc96d46c79a00a49b9ed778ee -msgid "" -"The CWL community publishes a Python package with the name `cwlref-" -"runner` that installs an alias for `cwltool` under the name `cwl-runner`" -msgstr "" - -#: ../../introduction/prerequisites.md:104 ebecb9c15b7549c1bf82cbc381721378 -msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" - -#: ../../introduction/prerequisites.md:111 4290343102b746a6987d45a33fb75e8f -msgid "" -"Now you can validate and run your workflow with the `cwl-runner` " -"executable, which will invoke `cwltool`. You should have the same results" -" and output as in the previous section." -msgstr "" - -#: ../../introduction/prerequisites.md:115 95dd822409aa414d848cf74a0882f12d -msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../introduction/prerequisites.md:120 be41ce025e294eef8015ac9ffaecd31d -msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../introduction/prerequisites.md:125 6ff60669f1ec486e9c80cd32f2f0b8da -msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For" -" that, the first thing you need to do is copy `true.cwl` workflow into a " -"new file: `true_shebang.cwl`, and include a special first line, a " -"*shebang*:" -msgstr "" - -#: ../../introduction/prerequisites.md:129 284249ed02604c479e8a7f9ae098a936 -msgid "`true_shebang.cwl`" -msgstr "" - -#: ../../introduction/prerequisites.md:135 2830ba8ada494febaa3cab175aae5c96 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" - -#: ../../introduction/prerequisites.md:137 b4a5c084f47a4524b4bbc783481ddb80 -msgid "Making `true.cwl` executable." -msgstr "" - -#: ../../introduction/prerequisites.md:144 09daa94a2e764c588ed9bdf05686195c -msgid "" -"And finally, you can execute it directly in the command-line. On " -"execution, the program specified in the shebang (`cwl-runner`) will be " -"used to execute the rest of the file." -msgstr "" - -#: ../../introduction/prerequisites.md:148 16b2246ddcde4bd4bab4c9b85a3245cd -msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" - -#: ../../introduction/prerequisites.md:154 8e5ac54df4264041a8766f683a530806 -msgid "" -"The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute " -"the script using the executable specified after the shebang. It is " -"considered a good practice to use `/usr/bin/env ` rather than" -" using a hard-coded location, since `/usr/bin/env ` looks for" -" the `` program in the system `PATH`," -msgstr "" - -#: ../../introduction/prerequisites.md:161 98043798d4f04488b47f65f6a3d0cbdf -msgid "Text Editor" -msgstr "" - -#: ../../introduction/prerequisites.md:163 dd5138ef1899479eb6a8419834dc94d4 -msgid "" -"You can use any text editor with CWL, but for syntax highlighting we " -"recommend an editor with YAML support. Popular editors are Visual Studio " -"Code, Sublime, WebStorm, vim/neovim, and Emacs." -msgstr "" - -#: ../../introduction/prerequisites.md:167 2c49302420ca4ef58824a611f6e21631 -msgid "" -"There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting" -" and better auto-complete:" -msgstr "" - -#: ../../introduction/prerequisites.md:171 121e8e64431f49159424ed4ffad079e0 -msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " -"" -msgstr "" - -#: ../../introduction/prerequisites.md:172 786d0c2fb6c44f5c8ddb42ad714b43cc -msgid "" -"cwl-plugin for IntelliJ - " -msgstr "" - -#: ../../introduction/prerequisites.md:174 0a7322840cc64223985de5eaf3f6e5ef -msgid "" -"The CWL community also maintains a list of editors and viewers: " -"" -msgstr "" - -#: ../../introduction/prerequisites.md:177 adf7801f93e54841935427ad5fa76ee1 -msgid "Docker" -msgstr "" - -#: ../../introduction/prerequisites.md:181 2d5c42927e8347efa27e75882e59f27d -msgid "" -"`cwltool` uses Docker to run tools, workflows, and workflow steps that " -"specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: " -"." -msgstr "" - -#: ../../introduction/prerequisites.md:185 58f717b8eb5546459d0e97cf3f4eef0a -msgid "" -"You do not need to know how to write and build Docker containers. In the " -"rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models " -"with and without containers." -msgstr "" - -#: ../../introduction/prerequisites.md:191 2c0ad9dee73c4e278ef0ad7f731c4931 -msgid "" -"`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for " -"pulling images." -msgstr "" - -#: ../../introduction/prerequisites.md:196 a80ae1bdfdb04e1598f06d5115d624eb -msgid "Learn More" -msgstr "" - -#: ../../introduction/prerequisites.md:198 baf0ff9fd9314b5884cf6f2110d964b3 -msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the " -"next section, Basic Concepts." -msgstr "" - -#: ../../introduction/prerequisites.md:199 958ac076e60a420b8b8d790cd49f6da8 -msgid "The Python `venv` module: " -msgstr "" - diff --git a/locales/en/LC_MESSAGES/introduction/quick-start.po b/locales/en/LC_MESSAGES/introduction/quick-start.po deleted file mode 100644 index 077b542d..00000000 --- a/locales/en/LC_MESSAGES/introduction/quick-start.po +++ /dev/null @@ -1,191 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../introduction/quick-start.md:1 47ace6396c93455bb9b8cb8a70be0679 -msgid "Quick Start" -msgstr "" - -#: ../../introduction/quick-start.md:3 17131fb92d5a46d99b7665d0c2890a46 -msgid "" -"This section will show you a brief overview of what CWL is, and where you" -" can learn more about it. No previous knowledge of CWL is required, but " -"you must be comfortable following instructions for the command-line." -msgstr "" - -#: ../../introduction/quick-start.md:7 ad577f43c1ec4d79b9cbe4cd5125a31a -msgid "“Hello World”" -msgstr "" - -#: ../../_includes/what-is-cwl.md:2 4d26ec28a1fa419bb9a1f536e4168925 -msgid "" -"CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../introduction/quick-start.md:12 12247e5c020e4eabaddc0a62364c45e2 -msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " -"The example below shows a simple CWL “Hello World” workflow annotated " -"with comments. Note that comments start with `#`:" -msgstr "" - -#: ../../introduction/quick-start.md:16 60c57d9de0e449bbb1ec517663e9047f -msgid "`hello_world.cwl`" -msgstr "" - -#: ../../introduction/quick-start.md:22 0a89aaf525d349349bb23ecf11f00a1e -msgid "" -"The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the" -" same result as the command-line `echo \"Hello World\"`." -msgstr "" - -#: ../../introduction/quick-start.md:27 f33aad86b3194d92b87e51b8551de335 -msgid "" -"In CWL, there is a distinction between a command-line tool and a " -"workflow. But for the sake of simplicity, we are using the term " -"“workflow” here. You will learn more about this in the [basic concepts" -"](basic-concepts.md) section." -msgstr "" - -#: ../../introduction/quick-start.md:32 bba033bcce684da99d8561c644a288b9 -msgid "Installing a CWL Runner" -msgstr "" - -#: ../../introduction/quick-start.md:34 74c2a60629734132baf21f950f51a2a8 -msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the " -"CWL *Reference Runner* for the specification, and it is compliant with " -"the latest version of the specification: {{ cwl_version }}. You can " -"install `cwltool` using `pip`:" -msgstr "" - -#: ../../introduction/quick-start.md:39 688e1f06579d44b8975c3db85d5969f6 -msgid "Installing `cwltool` with `pip`." -msgstr "" - -#: ../../introduction/quick-start.md:47 77a52c31fce14347bbb47d80f59489e7 -msgid "" -"If installing the cwltool using the pip command doesn't work for you, the" -" [prerequisites](prerequisites.md) section contains other ways to install" -" `cwltool` and a more detailed list of software and libraries used for " -"following the rest of this user guide." -msgstr "" - -#: ../../introduction/quick-start.md:51 235356675f8b492b86a59fe345d67184 -msgid "Running \"Hello World\"" -msgstr "" - -#: ../../introduction/quick-start.md:53 4caaccb9352a46678835a5bfb413803b -msgid "" -"The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [INPUTS_OBJECT]`. You can run the " -"`hello_world.cwl` workflow without specifying any option:" -msgstr "" - -#: ../../introduction/quick-start.md:57 ccbc60f4811e4a479530094958219224 -msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" - -#: ../../introduction/quick-start.md:62 3b3cd61bd0fe4dddbab7ce4fabc16421 -msgid "" -"Or you can override the default value of the input parameter `message`, " -"similar to how you would change the argument of the `echo` base command:" -msgstr "" - -#: ../../introduction/quick-start.md:65 71f096c461ef47f8a920339e164bf314 -msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" - -#: ../../introduction/quick-start.md:70 cbaa83776dc041dd963ce47a67b3b405 -msgid "" -"Another way of passing values to your workflow input parameters is via an" -" *Inputs Object*. This is a file containing the input fields with their " -"corresponding values. The Inputs Objects file can be written in JSON or " -"YAML. For example:" -msgstr "" - -#: ../../introduction/quick-start.md:74 04e272f684be44be911dc6e50ac1660b -msgid "`hello_world-job.json`" -msgstr "" - -#: ../../introduction/quick-start.md:80 5d1ebc06dc2d44439135ee1e75cc714a -msgid "" -"You can use this Inputs Object file now to execute the “Hello World” " -"workflow:" -msgstr "" - -#: ../../introduction/quick-start.md:82 6ad6b44a644b482382cec3bfda23e4ac -msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" - -#: ../../introduction/quick-start.md:88 bf7a0bd183f64f6883ecee1dae23607a -msgid "" -"We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but " -"it is not a requirement. You can choose any name for your workflows and " -"Inputs Object files." -msgstr "" - -#: ../../introduction/quick-start.md:94 002680b62d5d4d8fbf8d730e38ef154a -msgid "Learn More" -msgstr "" - -#: ../../introduction/quick-start.md:96 716e6ec03d974ee9ac59a055fcdabe41 -msgid "Continue reading the next sections of this User Guide!" -msgstr "" - -#: ../../introduction/quick-start.md:97 a098326c57f34af5972578ebb580d6a2 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" - -#: ../../introduction/quick-start.md:98 cba27320bbe844fc8bfbad0ba2aa9c01 -msgid "" -"The [`common-workflow-language` organization](https://github.com/common-" -"workflow-language) at GitHub." -msgstr "" - -#: ../../introduction/quick-start.md:99 e377948d6db94e1aa5c3b28c44a9707c -msgid "" -"[Common Workflow Language at " -"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -msgstr "" - -#: ../../introduction/quick-start.md:100 b554f9e0572e4b02a5cc1cb817c70539 -msgid "" -"[YAML.org](http://yaml.org/) and [YAML at " -"Wikipedia](https://en.wikipedia.org/wiki/YAML)." -msgstr "" - -#: ../../introduction/quick-start.md:101 a2ce57a5a0a24bb0bb858e076df51e6c -msgid "" -"The {{'[CWL Specification " -"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " -"cwl_version_text) }}." -msgstr "" - -#: ../../introduction/quick-start.md:102 edb34dacc1674731a7b5fa510c81d38b -msgid "" -"[Workflow management system at " -"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/setup.po b/locales/en/LC_MESSAGES/setup.po deleted file mode 100644 index 15bfffe9..00000000 --- a/locales/en/LC_MESSAGES/setup.po +++ /dev/null @@ -1,31 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../setup.md:5 27e5c491bbd4441d96d85f6d8f66181e -msgid "This page has moved" -msgstr "" - -#: ../../setup.md:9 4b442c302c2d4c84a462c1fa1781b35d -msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. The information on this page has been migrated to the " -"[FAQ](/faq.md) section of the new user guide." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/sphinx.po b/locales/en/LC_MESSAGES/sphinx.po deleted file mode 100644 index d097c6cb..00000000 --- a/locales/en/LC_MESSAGES/sphinx.po +++ /dev/null @@ -1,28 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../_templates/sidebar-nav-bs.html:1 94578a793f824c289114eb8091fcbb83 -msgid "Main navigation" -msgstr "" - -#: ../../_templates/sidebar-nav-bs.html:3 0004714627914a26a46506c14c85806d -msgid "Section Navigation" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po b/locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po deleted file mode 100644 index 0adab36c..00000000 --- a/locales/en/LC_MESSAGES/topics/additional-arguments-and-parameters.po +++ /dev/null @@ -1,84 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/additional-arguments-and-parameters.md:1 -#: 245426859a1e4d2db7facb0504eb028c -msgid "Additional Arguments and Parameters" -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:3 -#: 6be40170e1d14af08a2b49daecae8df7 -msgid "" -"Sometimes tools require additional command line options that don't " -"correspond exactly to input parameters." -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:6 -#: a3f17f29d2ab4ad2993696400f7be61b -msgid "" -"In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files " -"in the same directory as the source file. However, CWL input files (and " -"the directories in which they appear) may be read-only, so we need to " -"instruct \"javac\" to write the class file to the designated output " -"directory instead." -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:13 -#: 77443a85f1a14fef94fc4d6d4add43ca -msgid "`arguments.cwl`" -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:19 -#: 42d3138cc25d4570ada1a25ac13fb8bc -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:24 -#: 1a7130850048412fa12f6fcec745e4ee -msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:30 -#: f4fcf30ed13c42d3a93817dc29651686 -msgid "" -"And now invoke `cwltool` providing the tool description and the input " -"object on the command line:" -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:36 -#: c470ae16de004280a2bd2b0a99f391b3 -msgid "" -"Here we use the `arguments` field to add an additional argument to the " -"command line that isn't tied to a specific input parameter." -msgstr "" - -#: ../../topics/additional-arguments-and-parameters.md:43 -#: a31eeefe78ab4442bcfea3e1106cf8a9 -msgid "" -"This example references a runtime parameter. Runtime parameters provide " -"information about the hardware or software environment when the tool is " -"actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include " -"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " -"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " -"Environment][runtime] section of the CWL specification for details." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/best-practices.po b/locales/en/LC_MESSAGES/topics/best-practices.po deleted file mode 100644 index 30c7c72e..00000000 --- a/locales/en/LC_MESSAGES/topics/best-practices.po +++ /dev/null @@ -1,191 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/best-practices.md:1 400480770c074343aae662a25b257a31 -msgid "Best Practices" -msgstr "" - -#: ../../topics/best-practices.md:3 fe9e19076d74462cab67b4a3cb340724 -msgid "" -"The following are a set of recommended good practices to keep in mind " -"when writing a Common Workflow Language description for a tool or " -"workflow. These guidelines are presented for consideration on a scale of " -"usefulness: although more is better, not all are required." -msgstr "" - -#: ../../topics/best-practices.md:8 caab132559d84593ac23530e36ec6c21 -msgid "" -"No `type: string` parameters for names of input or reference " -"files/directories; use `type: File` or `type: Directory` as appropriate." -msgstr "" - -#: ../../topics/best-practices.md:11 e15eb191624846c4b1d3e3e96731a8ff -msgid "" -"A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that" -" the usual rules of software licensing apply to this document. For " -"example, if the workflow is shared publicly, licensing terms must be " -"clear so that a future user understands under what conditions they can " -"run the workflow, modify it and/or combine it with other workflows. For " -"this reason, please consider including a license field in the document. " -"The authors of this guide urge you to choose a pre-existing license " -"rather than trying to write your own (see the link below to learn more " -"about choosing a license), and our recommended practice is to choose a " -"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" -"license]." -msgstr "" - -#: ../../topics/best-practices.md:20 d5c2b325d05f4afca4008f4733d92100 -msgid "" -"If possible, the license should be specified with its corresponding [SPDX" -" identifier][spdx]. Construct the metadata field for the license by " -"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " -"`SPDX-ID` is taken from the list of identifiers linked above. See the " -"example snippet below for guidance. For non-standard licenses without an " -"SPDX identifier, provide a URL to the license." -msgstr "" - -#: ../../topics/best-practices.md:26 99b89f6ce812463093ee0da9255178bb -msgid "" -"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" -"Programmer][sci-license]\"" -msgstr "" - -#: ../../topics/best-practices.md:28 56915c2feeb9402fb1210cdf27788c8a -msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" - -#: ../../topics/best-practices.md:37 4315b219d21742ac88f39415da6807d8 -msgid "" -"For more examples of providing metadata within CWL descriptions, see " -"[the Metadata and Authorship section of this User Guide](../topics" -"/metadata-and-authorship.md)." -msgstr "" - -#: ../../topics/best-practices.md:40 122f553a412d43bd9e55caaafb90b88f -msgid "" -"Include [attribution information][license-example] for the author(s) of " -"the CWL tool or workflow description. Use unambiguous identifiers like " -"[ORCID][orcid]." -msgstr "" - -#: ../../topics/best-practices.md:44 b5fe5270c8534ad194dbf41bdec90e33 -msgid "" -"In tool descriptions, list dependencies using short name(s) under " -"`SoftwareRequirement`." -msgstr "" - -#: ../../topics/best-practices.md:47 889a5c8d24464546a2a1156ef3791b28 -msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in " -"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." -msgstr "" - -#: ../../topics/best-practices.md:50 7203be6d92a040c2b39f07f0618b7c37 -msgid "" -"All `input` and `output` identifiers should reflect their conceptual " -"identity. Use informative names like `unaligned_sequences`, " -"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " -"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." -msgstr "" - -#: ../../topics/best-practices.md:55 8ea3eee32d8044c5ad0a4caeab435b8b -msgid "" -"In tool descriptions, include a list of version(s) of the tool that are " -"known to work with this description under `SoftwareRequirement`." -msgstr "" - -#: ../../topics/best-practices.md:58 3c033a88a5cd4bf19683add86436a8de -msgid "" -"`format` should be specified for all input and output `File`s. " -"Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " -"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" -"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " -"types). For non-bioinformatics tools, use or build an appropriate " -"ontology/controlled vocabulary in the same way. Please edit this page to " -"let us know about it." -msgstr "" - -#: ../../topics/best-practices.md:66 7731a6bd39a7444e82b96d2a5e8eb44b -msgid "" -"Mark all input and output `File`s that are read from or written to in a " -"streaming compatible way (only once, no random-access), as `streamable: " -"true`." -msgstr "" - -#: ../../topics/best-practices.md:69 fe8845e0d96f459bbcd69e176e7ff6b1 -msgid "" -"Each `CommandLineTool` description should focus on a single operation " -"only, even if the (sub)command is capable of more. Don't overcomplicate " -"your tool descriptions with options that you don't need or use." -msgstr "" - -#: ../../topics/best-practices.md:73 1ffe2266eef94941840c485ca77417b6 -msgid "" -"Custom types should be defined with one external YAML per type definition" -" for re-use." -msgstr "" - -#: ../../topics/best-practices.md:76 e5af104f7c2848c8ac0f97d13a9153a2 -msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "" - -#: ../../topics/best-practices.md:78 88c7bfbebad14cf9b39bd3e9488c7dfb -msgid "" -"If useful, include a top-level `doc` as well. This should provide a " -"longer, more detailed description than was provided in the top-level " -"`label` (see above)." -msgstr "" - -#: ../../topics/best-practices.md:82 4f874eee6d884b6c8f2117f61788a4e5 -msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list" -" of valid values." -msgstr "" - -#: ../../topics/best-practices.md:85 6c481e56c4ff48fc9854a3c15375f5f7 -msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. " -"One common example: manipulating `File` names and paths? Consider whether" -" one of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc., could be used instead." -msgstr "" - -#: ../../topics/best-practices.md:90 2e66f35622964ad6bc54faedbfec0eeb -msgid "" -"Give the tool description to a colleague (preferably at a different " -"institution) to test and provide feedback." -msgstr "" - -#: ../../topics/best-practices.md:93 c5551f6025e445f296d3de936029fab4 -msgid "" -"Complex workflows with individual components which can be abstracted " -"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" -" their workflow modular and allow sections of them to be easily reused." -msgstr "" - -#: ../../topics/best-practices.md:97 eff85713fb344bfb968bda07094485af -msgid "" -"Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics" -" software\"][containers] (also useful to other disciplines)." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/command-line-tool.po b/locales/en/LC_MESSAGES/topics/command-line-tool.po deleted file mode 100644 index 212158b9..00000000 --- a/locales/en/LC_MESSAGES/topics/command-line-tool.po +++ /dev/null @@ -1,71 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/command-line-tool.md:1 48774f562479443fa878218b84edd4f0 -msgid "Command Line Tool" -msgstr "" - -#: ../../topics/command-line-tool.md:3 8cb2bbcf217f4a35acd6fe7aac1b9493 -msgid "" -"A command-line tool is a type of Process object that can be run by itself" -" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " -"`tar`, etc. The command-line tool is defined in the `baseCommand` " -"attribute of the command-line tool CWL document." -msgstr "" - -#: ../../topics/command-line-tool.md:8 9d7a6d6def0046c180c951e9ad94afeb -msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The " -"following example contains a minimal example of a CWL command-line tool " -"for the `echo` Linux command, using inputs and outputs." -msgstr "" - -#: ../../topics/command-line-tool.md:19 a6e02298d1fa432d9d6b54b420818901 -msgid "CWL command-line tool." -msgstr "" - -#: ../../topics/command-line-tool.md:50 a6638b2f0c184e95abc23d6207e81802 -msgid "`echo.cwl`" -msgstr "" - -#: ../../topics/command-line-tool.md:57 da7864a3fcf842459475b5b27a693ded -msgid "" -"The example above uses a simplified form to define inputs and outputs. " -"You will learn more about in the [Inputs](../topics/inputs.md) and in the" -" [Outputs](../topics/outputs.md) sections." -msgstr "" - -#: ../../topics/command-line-tool.md:68 0a222e61001a4a08bc2e82ca52105a09 -msgid "Network Access" -msgstr "" - -#: ../../topics/command-line-tool.md:69 988c4b4184d0405e9bc26bb7bcb05c8b -msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network " -"access. If a command-line tool is written manually in CWL v1.1+, there is" -" a need to specify when network access is required." -msgstr "" - -#: ../../topics/command-line-tool.md:83 2918cea6f64846c498fdf03b92533d94 -msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " -"Network Access automatically." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po b/locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po deleted file mode 100644 index 39b54f98..00000000 --- a/locales/en/LC_MESSAGES/topics/creating-files-at-runtime.po +++ /dev/null @@ -1,104 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/creating-files-at-runtime.md:1 2bbf4c0a32054cfebe3b6b1b02ea3558 -msgid "Creating Files at Runtime" -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:3 c5010461c4fe4e8fb7c4f7da2653febe -msgid "" -"Sometimes you need to create a file on the fly from input parameters, " -"such as tools that expect to read their input configuration from a file " -"rather than the command line parameters, or need a small wrapper shell " -"script." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:7 27879c9542e444dca1a80c1784891bf7 -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:9 61cf19e01c03473aa239bc42394bfcff -msgid "`createfile.cwl`" -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:15 -#: 8d1fb6bc4eed466391ad62fe5be90a13 -msgid "" -"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the " -"value at the input `message`." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:20 -#: 40e30b78078a4184b4c5bd69c0766cef -msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later" -" during command line tool invocation. That means that any genuine need " -"for the character `$` must be **escaped** with `\\`. For instance, " -"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " -"be evaluated by the shell script instead of the CWL engine." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:27 -#: c624145be5a04d65acaaa4bfa086c473 -msgid "" -"To test the above CWL tool, use this job to provide the input value " -"`message`:" -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:29 -#: 202ff16474a04e29b0e363cb5241b53e -msgid "`echo-job.yml`" -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:35 -#: ea631a00fdd9484486e1ca60a90b6d8a -msgid "" -"Before we run this, let us look at each step in a little more detail. The" -" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " -"command `sh example.sh`. This will run the file we create in the shell." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:40 -#: 1dea9f63048f40528c904ec2fb4bef69 -msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " -"YAML array, we need a `-` on the first line of each element of the array," -" in this case we have just one element. `entryname:` can have any value, " -"but it must match what was specified in the `baseCommand`. The final part" -" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " -"means that you are using a multiline string (without it, we would need to" -" write the whole script on one line)." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:51 -#: cff49a2cf48c43f0aeaa6241e1bcaabe -msgid "" -"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " -"formatting." -msgstr "" - -#: ../../topics/creating-files-at-runtime.md:54 -#: c81ca28ee4d44d82b6cf3bdbf8460642 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/custom-types.po b/locales/en/LC_MESSAGES/topics/custom-types.po deleted file mode 100644 index 66cf4c6c..00000000 --- a/locales/en/LC_MESSAGES/topics/custom-types.po +++ /dev/null @@ -1,99 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/custom-types.md:1 ab79908260aa4842b2322e6e4d615f72 -msgid "Custom Types" -msgstr "" - -#: ../../topics/custom-types.md:3 75b9b1f15a744e24b2f7333b6638bcc4 -msgid "" -"Sometimes you may want to write your own custom types for use and reuse " -"in CWL descriptions. Use of such custom types can reduce redundancy " -"between multiple descriptions that all use the same type, and also allow " -"for additional customisation/configuration of a tool/analysis without the" -" need to fiddle with the CWL description directly." -msgstr "" - -#: ../../topics/custom-types.md:9 7f4a9afccdad41b9892d8424e9fb539d -msgid "" -"The example below is a CWL description of the [biom convert format][biom]" -" tool for converting a standard biom table file to hdf5 format." -msgstr "" - -#: ../../topics/custom-types.md:12 8f03906168eb4bf0a6bf7ae0f6e0ecb1 -msgid "`custom-types.cwl`" -msgstr "" - -#: ../../topics/custom-types.md:18 0b8de32a79a14b2a841851ceab22b6b3 -msgid "`custom-types.yml`" -msgstr "" - -#: ../../topics/custom-types.md:24 8ba644c7152247959988abfcd2b4c2be -msgid "" -"___Note:___ To follow the example below, you need to [download the " -"example input file](https://github.com/common-workflow-" -"language/user_guide/blob/main/src/_includes/cwl/custom-" -"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " -"`wget`:" -msgstr "" - -#: ../../topics/custom-types.md:30 975bdfc68b1841fa89a055b7f03fb0ec -msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to " -"be used in the table conversion are imported as a custom object:" -msgstr "" - -#: ../../topics/custom-types.md:46 d4efacf670184435a5729e0ba5e16a36 -msgid "" -"The reference to a custom type is a combination of the name of the file " -"in which the object is defined (`biom-convert-table.yaml`) and the name " -"of the object within that file (`table_type`) that defines the custom " -"type. In this case the `symbols` array from the imported `biom-convert-" -"table.yaml` file define the allowable table options. For example, in " -"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" -" to create an OTU table in hdf5 format." -msgstr "" - -#: ../../topics/custom-types.md:53 ea6ca32a9e6e4f38be19487348cd45f7 -msgid "The contents of the YAML file describing the custom type are given below:" -msgstr "" - -#: ../../topics/custom-types.md:55 5bfed5519bc04c35aa6ad8626201f98f -msgid "`biom-convert-table.yaml`" -msgstr "" - -#: ../../topics/custom-types.md:61 066aef77545f4dc8b11f09caa710be9e -msgid "" -"In order for the custom type to be used in the CWL description, it must " -"be imported. Imports are described in " -"`requirements:SchemaDefRequirement`, as below in the example `custom-" -"types.cwl` description:" -msgstr "" - -#: ../../topics/custom-types.md:76 7e35076a9b0347ff967c5271a3ccf881 -msgid "" -"Note also that the author of this CWL description has also included " -"`ResourceRequirement`s, specifying the minimum amount of RAM and number " -"of cores required for the tool to run successfully, as well as details of" -" the version of the software that the description was written for and " -"other useful metadata. These features are discussed further in other " -"chapters of this user guide." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/environment-variables.po b/locales/en/LC_MESSAGES/topics/environment-variables.po deleted file mode 100644 index 6ecd617f..00000000 --- a/locales/en/LC_MESSAGES/topics/environment-variables.po +++ /dev/null @@ -1,45 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/environment-variables.md:1 498dbc0db9224aabbc9fd1bef778f8ef -msgid "Environment Variables" -msgstr "" - -#: ../../topics/environment-variables.md:3 9ce0f06bed3649339f666147b45c69e4 -msgid "" -"Tools run in a restricted environment and do not inherit most environment" -" variables from the parent process. You can set environment variables " -"for the tool using `EnvVarRequirement`." -msgstr "" - -#: ../../topics/environment-variables.md:7 ef471bebcfc94b008c94a2e8056d7af0 -msgid "`env.cwl`" -msgstr "" - -#: ../../topics/environment-variables.md:13 df5ab6417f87475d8d94f2af498cee39 -msgid "`echo-job.yml`" -msgstr "" - -#: ../../topics/environment-variables.md:18 642f1379ebdd4dd381e8f56343547b42 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/expression-tool.po b/locales/en/LC_MESSAGES/topics/expression-tool.po deleted file mode 100644 index 8d8ad3dc..00000000 --- a/locales/en/LC_MESSAGES/topics/expression-tool.po +++ /dev/null @@ -1,53 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/expression-tool.md:1 2ed0674b02ee4cd7ac4e169086d02513 -msgid "Expression Tool" -msgstr "" - -#: ../../topics/expression-tool.md:3 95b1b27ad2a84cd9bd1207ff75536502 -msgid "" -"An expression tool is a type of Process that can be run by itself or as a" -" Workflow step. It executes a pure JavaScript expression. It is meant to " -"be used as a way to isolate complex JavaScript expressions that need to " -"operate on input data and produce some result as output." -msgstr "" - -#: ../../topics/expression-tool.md:8 80caa25305a74efdaed8ada05faaa018 -msgid "" -"Similar to the command-line tool it requires `inputs` and `outputs`. But " -"instead of `baseCommand`, it requires an `expression` attribute." -msgstr "" - -#: ../../topics/expression-tool.md:17 a664a455f4714071ba0158a4f83a127c -msgid "CWL expression tool." -msgstr "" - -#: ../../topics/expression-tool.md:48 bdfa455a230e4be79031e0777efc7233 -msgid "`uppercase.cwl`" -msgstr "" - -#: ../../topics/expression-tool.md:67 0df562c4585e43d1ae4ac8113b50ed71 -msgid "" -"We had to use an `InlineJavascriptRequirement` as our expression contains" -" a JavaScript call in `.toUpperCase()`. This means to tools using the " -"expression tool that JavaScript is a requirement." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/expressions.po b/locales/en/LC_MESSAGES/topics/expressions.po deleted file mode 100644 index f09d91d8..00000000 --- a/locales/en/LC_MESSAGES/topics/expressions.po +++ /dev/null @@ -1,383 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/expressions.md:1 15bf6af8d07d476ea6996a0be17fdca0 -msgid "Expressions" -msgstr "" - -#: ../../topics/expressions.md:3 248bcdddada043abaaf9d53819dd3d01 -msgid "" -"If you need to manipulate input parameters, include the requirement " -"`InlineJavascriptRequirement` and then anywhere a parameter reference is " -"legal you can provide a fragment of Javascript that will be evaluated by " -"the CWL runner." -msgstr "" - -#: ../../topics/expressions.md:9 986c932e94e3496b8ab3ef5c9b1927c5 -msgid "" -"JavaScript expressions should only be used when absolutely necessary. " -"When manipulating file names, extensions, paths etc, consider whether one" -" of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " -"practices](best-practices.md)." -msgstr "" - -#: ../../topics/expressions.md:16 a82f11177ce54f7f92b6e5b037a1b6d0 -msgid "`expression.cwl`" -msgstr "" - -#: ../../topics/expressions.md:22 e1c2a91028bc47238421457f323556db -msgid "" -"As this tool does not require any `inputs` we can run it with an (almost)" -" empty job file:" -msgstr "" - -#: ../../topics/expressions.md:25 bddb2b6b6507418785bc194340313a39 -msgid "`empty.yml`" -msgstr "" - -#: ../../topics/expressions.md:31 6932ad2e25eb4e3c835bf37557efbf03 -msgid "" -"`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object" -" is represented simply by a set of empty brackets." -msgstr "" - -#: ../../topics/expressions.md:35 51962babe16e4b8493cafe401f046510 -msgid "We can then run `expression.cwl`:" -msgstr "" - -#: ../../topics/expressions.md:37 f302523bb23049afa0dc534641abba94 -msgid "Running `expression.cwl`" -msgstr "" - -#: ../../topics/expressions.md:47 5e672f895eb94028bb7fbc4ba7646c46 -msgid "" -"Note that requirements can be provided with the map syntax, as in the " -"example above:" -msgstr "" - -#: ../../topics/expressions.md:54 913d17f1bb474dec91b467db5f45ffab -msgid "" -"Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" -" describe the additional command line arguments." -msgstr "" - -#: ../../topics/expressions.md:62 8f26131c8cc94db88fc88100f0404bff -msgid "Where are JavaScript expressions allowed?" -msgstr "" - -#: ../../topics/expressions.md:64 ad6af4e35d014ce7bd122b00f99f13dd -msgid "" -"Just like [parameter references](parameter-references.md), you can use " -"JavaScript Expressions only in certain fields. These are:" -msgstr "" - -#: ../../topics/expressions.md:66 4b2eaee288a4421a91b304a186578361 -msgid "" -"From " -"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../topics/expressions.md:67 032d4eeaeda14354a8b059e4391f3448 -msgid "`arguments`" -msgstr "" - -#: ../../topics/expressions.md:68 ../../topics/expressions.md:76 -#: ../../topics/expressions.md:89 aebe22df1bf6432aa39e402802ce8fcd -#: dcc0d4a9abcb4e35ae4ee341893d757f fca0e4b343c940989ebbf8ce7cf87605 -msgid "`valueFrom`" -msgstr "" - -#: ../../topics/expressions.md:69 0b185807c14741bca2b1ce4252bded44 -msgid "`stdin`" -msgstr "" - -#: ../../topics/expressions.md:70 716a8fad0a5d46bb9d17d35c0866db31 -msgid "`stdout`" -msgstr "" - -#: ../../topics/expressions.md:71 e9d014cdaf794dacb4eee304c1364d1b -msgid "`stderr`" -msgstr "" - -#: ../../topics/expressions.md:72 81333fdf0ac84d4495ec32cd4b58f12e -msgid "" -"From " -"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../topics/expressions.md:73 ../../topics/expressions.md:78 -#: ../../topics/expressions.md:85 ../../topics/expressions.md:93 -#: bf75a275d26345bf86076cea5c44f5d8 c704d979a192458a9315971e6702478a -#: d29995b11d3f4157915f48c52f4eba90 ff462897cd0149c493e50ee87f9d1c0e -msgid "`format`" -msgstr "" - -#: ../../topics/expressions.md:74 ../../topics/expressions.md:79 -#: ../../topics/expressions.md:86 ../../topics/expressions.md:94 -#: 18e86fc5bf684862a30f373766d067eb 195022a4f28f419ea24095350e89c7dd -#: 403516ed7955408fa7a12d34fd1fbe82 dd2932a497104db096a8ecb1986381b6 -msgid "`secondaryFiles`" -msgstr "" - -#: ../../topics/expressions.md:75 49d00678c3d8425db3852e408049e249 -msgid "" -"From " -"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../topics/expressions.md:77 8523d80e16a24adebc3fdad88141e646 -msgid "" -"From " -"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../topics/expressions.md:80 51af437d2c314f18895ae13e58dbd56e -msgid "" -"From " -"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../topics/expressions.md:81 9d9b304dceaa4cb38e01503ff57d726b -msgid "`glob`" -msgstr "" - -#: ../../topics/expressions.md:82 65bceca1c4f7447fa5f3e0c448a02af6 -msgid "`outputEval`" -msgstr "" - -#: ../../topics/expressions.md:83 5bc18fb8fa034c4281b715ab44a5cb75 -msgid "From `Workflow`" -msgstr "" - -#: ../../topics/expressions.md:84 fcfc00ff02d04e61bdc6d5432d04c7da -msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../topics/expressions.md:87 e51177ae5daa42429266893d9467cd15 -msgid "From `steps`" -msgstr "" - -#: ../../topics/expressions.md:88 4e6a5b41b2f249b896d7a1e79b2aebbb -msgid "" -"From " -"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../topics/expressions.md:90 9233f867e33d41199e31ed9115442d7e -msgid "" -"From " -"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../topics/expressions.md:91 60fc0bdd44614b61961aa204edae77b9 -msgid "`expression`" -msgstr "" - -#: ../../topics/expressions.md:92 2cf4288d3d594085af2a07026bc71371 -msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../topics/expressions.md:95 1455be996e7147c99d60cc9f198b78cb -msgid "" -"From " -"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../topics/expressions.md:96 0ac9b337923c4a2793fe198d6bf759f1 -msgid "`coresMin`" -msgstr "" - -#: ../../topics/expressions.md:97 993661b89e4945d0ad4f8a13931eeffb -msgid "`coresMax`" -msgstr "" - -#: ../../topics/expressions.md:98 22d35c6039754b6b96fed696f9a06a71 -msgid "`ramMin`" -msgstr "" - -#: ../../topics/expressions.md:99 53cce3babeac44c98bbfe68d122e5796 -msgid "`ramMax`" -msgstr "" - -#: ../../topics/expressions.md:100 ed43db0eedef4716800239b9c6c5c9f0 -msgid "`tmpdirMin`" -msgstr "" - -#: ../../topics/expressions.md:101 e4e8d9975aa74847a49060459ace3edc -msgid "`tmpdirMax`" -msgstr "" - -#: ../../topics/expressions.md:102 13713c1adb7f4759b1792bbf3e720c29 -msgid "`outdirMin`" -msgstr "" - -#: ../../topics/expressions.md:103 d8c878c467f34807b98c156ad8705445 -msgid "`outdirMax`" -msgstr "" - -#: ../../topics/expressions.md:104 fb119535e57d4a55b6e9a86deaecc100 -msgid "" -"From " -"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../topics/expressions.md:105 dbe84d62840049e7b9ed3498d15847f6 -msgid "`listing`" -msgstr "" - -#: ../../topics/expressions.md:106 6db83a55040447c7903dd5d2d0bb00f8 -msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../topics/expressions.md:107 8ff197dd79524f25912ef459fb7b20d1 -msgid "`entry`" -msgstr "" - -#: ../../topics/expressions.md:108 fcea352f4e4246bf8fba2f53665427df -msgid "`entryname`" -msgstr "" - -#: ../../topics/expressions.md:109 120885c8f41e4ad58458699a66b38fc6 -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../topics/expressions.md:110 17cea5e071b0430d901810a76ff224d4 -msgid "" -"From " -"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../topics/expressions.md:111 5e6e3c6614d043e596be33cb9aba75c5 -msgid "`envValue`" -msgstr "" - -#: ../../topics/expressions.md:116 54b20c309ca543df81b8221c6d8f9eaa -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" - -#: ../../topics/expressions.md:118 54df5f1a63554bf7989dccf12aa205a1 -msgid "" -"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" -" attribute that allows users to load external JavaScript files, or to " -"provide inline JavaScript code." -msgstr "" - -#: ../../topics/expressions.md:122 8e6566d5b3fd424fa95e77df42ae18ed -msgid "" -"Entries added to the `expressionLib` attribute are parsed with the " -"JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts" -" of the CWL document." -msgstr "" - -#: ../../topics/expressions.md:128 50f2d063d4864db1b051a41769b3d928 -msgid "" -"The CWL standards (versions 1.0 through 1.2) " -"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" -" that the only version of JavaScript valid in CWL expressions is " -"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " -"that any code that you include or write in your CWL Document must be " -"compliant with ECMAScript 5.1." -msgstr "" - -#: ../../topics/expressions.md:135 e2c6c8b5d1b345368e0699a5a2a079cc -msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a " -"JavaScript function inline in `expressionLib`. That function can then be " -"used in other parts of the CWL document:" -msgstr "" - -#: ../../topics/expressions.md:139 1ce74804ca97479fb6bdacbdba2bbc5c -msgid "`hello-world-expressionlib-inline.cwl`" -msgstr "" - -#: ../../topics/expressions.md:146 fbe150d3864e4987ae145a8b7de60151 -msgid "" -"Running this CWL workflow will invoke the JavaScript function and result " -"in the `echo` command printing the input message with capital initial " -"letters:" -msgstr "" - -#: ../../topics/expressions.md:149 7552ea9b4f714fbe8aea6db94fd8894f -msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "" - -#: ../../topics/expressions.md:155 2f3154ec78274b43accde1409c59ec56 -msgid "" -"Let's move the `capitalizeWords` function to an external file, `custom-" -"functions.js`, and import it in our CWL document:" -msgstr "" - -#: ../../topics/expressions.md:158 ee2508f7faf74dd3a2928aebd3dc4314 -msgid "`custom-functions.js`" -msgstr "" - -#: ../../topics/expressions.md:164 9ba72aae0ff546e282aaa2518a5cd237 -msgid "`hello-world-expressionlib-external.cwl`" -msgstr "" - -#: ../../topics/expressions.md:171 e1b9ad0192e44844ab641c883e859510 -msgid "" -"The `custom-functions.js` file is included in the CWL document with the " -"`$include: custom-functions.js` statement. That makes the functions and " -"variables available to be used in other parts of the CWL document." -msgstr "" - -#: ../../topics/expressions.md:175 3b40577e79f9432b9bad3fbaf5fc4b78 -msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "" - -#: ../../topics/expressions.md:181 6298a4cf813142e09b35c55fd7077cbc -msgid "" -"Finally, note that you can have both inline and external JavaScript code " -"in your CWL document. In this final example we have added another entry " -"to the `expressionLib` attribute with the new function " -"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" -" the external file `custom-functions.js`." -msgstr "" - -#: ../../topics/expressions.md:186 881975804cc246cdb81af6ad04734a19 -msgid "`hello-world-expressionlib.cwl`" -msgstr "" - -#: ../../topics/expressions.md:193 9369098b680540e2b6ea67f861e193ed -msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" - -#: ../../topics/expressions.md:200 ec09ac813f3142e9b333428a44bb1244 -msgid "" -"The `$include` statement can be used to include a file from the local " -"disk or from a remote location. It works with both relative and absolute " -"paths. Read the [text about " -"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " -"the CWL specification to learn more about it." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/file-formats.po b/locales/en/LC_MESSAGES/topics/file-formats.po deleted file mode 100644 index 73be3838..00000000 --- a/locales/en/LC_MESSAGES/topics/file-formats.po +++ /dev/null @@ -1,93 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/file-formats.md:1 24ece5b3bfe646268d48b0339ba10e7b -msgid "File Formats" -msgstr "" - -#: ../../topics/file-formats.md:3 a7520d9841f044f8a33d1acf1f6234bf -msgid "" -"Tools and workflows can take `File` types as input and produce them as " -"output. We also recommend indicating the format for `File` types. This " -"helps document for others how to use your tool while allowing you to do " -"some simple type-checking when creating parameter files." -msgstr "" - -#: ../../topics/file-formats.md:8 544fcf8047db45c3aad991cfdf732309 -msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM" -" in our example), reference a local ontology for your institution, or do " -"not add a file format initially for quick development before sharing your" -" tool with others. You can browse existing [IANA file format " -"listings][IANA] and [EDAM file format listings][EDAM] on their websites." -msgstr "" - -#: ../../topics/file-formats.md:14 12d2dc549a684fff9cb46320700143fa -msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` " -"section of the document in greater detail, so don't worry about these for" -" now." -msgstr "" - -#: ../../topics/file-formats.md:17 c362c433ba544d1eaa19781db09aafbd -msgid "" -"Note that for added value `cwltool` can do some basic reasoning based on " -"file formats and warn you if there seem to be some obvious mismatches." -msgstr "" - -#: ../../topics/file-formats.md:20 c1007004cc7a4c408a713c38208574c0 -msgid "`metadata_example.cwl`" -msgstr "" - -#: ../../topics/file-formats.md:26 47ec32f1249f48149068417e431a20f5 -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../topics/file-formats.md:32 f99998f5da604c9b827367670cd30879 -msgid "Sample Parameter Files" -msgstr "" - -#: ../../topics/file-formats.md:34 050ec30459884b1581d715038fe2b05a -msgid "" -"Below is an example of a parameter file for the example above. We " -"encourage checking in working examples of parameter files for your tool. " -"This allows others to quickly work with your tool, starting from a " -"\"known good\" parameterization." -msgstr "" - -#: ../../topics/file-formats.md:39 dd49f6afbc754b9083888cf822cc369e -msgid "`sample.yml`" -msgstr "" - -#: ../../topics/file-formats.md:45 7e1974e26afc40568d4e483d20c4b86f -msgid "" -"___Note:___ To follow the example below, you need to download the example" -" input file, *file-formats.bam*. The file is available from " -" and can be downloaded e.g. via `wget`:" -msgstr "" - -#: ../../topics/file-formats.md:52 46649847e8d440b9b4f6726be286e067 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/index.po b/locales/en/LC_MESSAGES/topics/index.po deleted file mode 100644 index b90b5d6b..00000000 --- a/locales/en/LC_MESSAGES/topics/index.po +++ /dev/null @@ -1,24 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/index.md:1 55452f6967174ff5a1d8cf776874a90b -msgid "Topics" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/inputs.po b/locales/en/LC_MESSAGES/topics/inputs.po deleted file mode 100644 index 03f1b021..00000000 --- a/locales/en/LC_MESSAGES/topics/inputs.po +++ /dev/null @@ -1,313 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/inputs.md:1 03f3a68492ca43bea79742a839864b86 -msgid "Inputs" -msgstr "" - -#: ../../topics/inputs.md:3 9772b8bb0b694b9e9eef5e65b4ffe333 -msgid "Essential Input Parameters" -msgstr "" - -#: ../../topics/inputs.md:5 68cd0cab423c4d10a69989e6a3833e7a -msgid "" -"The `inputs` of a tool is a list of input parameters that control how to " -"run the tool. Each parameter has an `id` for the name of parameter, and " -"`type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../topics/inputs.md:9 2a76b22fc015489b81d6c396f4f8ae30 -msgid "" -"Available primitive types are *string*, *int*, *long*, *float*, *double*," -" and *null*; complex types are *array* and *record*; in addition there " -"are special types *File*, *Directory* and *Any*." -msgstr "" - -#: ../../topics/inputs.md:13 ba487511ecd84b37af0796d5159e50e3 -msgid "" -"The following example demonstrates some input parameters with different " -"types and appearing on the command line in different ways." -msgstr "" - -#: ../../topics/inputs.md:16 59dd55e707cd49f385f5763aa54bc461 -msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "" - -#: ../../topics/inputs.md:18 0d05676c671a420b87f3808010ccc207 -msgid "`inp.cwl`" -msgstr "" - -#: ../../topics/inputs.md:24 06e169026a20469cb6b04a216045cc87 -msgid "Create a file called `inp-job.yml`:" -msgstr "" - -#: ../../topics/inputs.md:26 05dd5f7e9edf4c379e66d8b6cfc1f86f -msgid "`inp-job.yml`" -msgstr "" - -#: ../../topics/inputs.md:33 f02466c6a7bf4795892d14963a8ad22e -msgid "" -"You can use `cwltool` to create a template input object. That saves you " -"from having to type all the input parameters in a input object file:" -msgstr "" - -#: ../../topics/inputs.md:40 5e5a2fe06ad04b2d8969d6cbfed213ec -msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template " -"inp.cwl > inp-job.yml`, and then modify the default values with your " -"desired input values." -msgstr "" - -#: ../../topics/inputs.md:44 fafabc3b11f14bb68c16e3f497e26e40 -msgid "" -"Notice that \"example_file\", as a `File` type, must be provided as an " -"object with the fields `class: File` and `path`." -msgstr "" - -#: ../../topics/inputs.md:47 7e3d42ea93dd417195ab6b5559638326 -msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" -" command line." -msgstr "" - -#: ../../topics/inputs.md:53 0bbabcf2be26490dbe920f52f8cbe9b0 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " -"following boxed text describes these two commands and the expected output" -" from the command line:" -msgstr "" - -#: ../../topics/inputs.md:64 c340c8aa7b80488ba6d16329e1ca2149 -msgid "" -"The CWL reference runner (cwltool) and other runners create temporary " -"directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not " -"explicitly specified" -msgstr "" - -#: ../../topics/inputs.md:70 5c2e148fdb324017a685f5adefadd74d -msgid "" -"The field `inputBinding` is optional and indicates whether and how the " -"input parameter should appear on the tool's command line. If " -"`inputBinding` is missing, the parameter does not appear on the command " -"line. Let's look at each example in detail." -msgstr "" - -#: ../../topics/inputs.md:83 97d14a1cf8fc4b3687281aa93eb1ceb6 -msgid "" -"Boolean types are treated as a flag. If the input parameter " -"\"example_flag\" is \"true\", then `prefix` will be added to the command " -"line. If false, no flag is added." -msgstr "" - -#: ../../topics/inputs.md:95 6c2008aed010466c8e4465c72a4b6d79 -msgid "" -"String types appear on the command line as literal values. The `prefix` " -"is optional, if provided, it appears as a separate argument on the " -"command line before the parameter . In the example above, this is " -"rendered as `--example-string hello`." -msgstr "" - -#: ../../topics/inputs.md:109 95f2a1493e50455ea6e546f70726fab1 -msgid "" -"Integer (and floating point) types appear on the command line with " -"decimal text representation. When the option `separate` is false (the " -"default value is true), the prefix and value are combined into a single " -"argument. In the example above, this is rendered as `-i42`." -msgstr "" - -#: ../../topics/inputs.md:124 3a48173a38904861b9994edddbc2f082 -msgid "" -"File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the " -"parameter is optional. In the example above, this is rendered as " -"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " -"parameter were not provided in the input, nothing would appear on the " -"command line." -msgstr "" - -#: ../../topics/inputs.md:131 54186920b4a14fbfa059779411b20192 -msgid "" -"Input files are read-only. If you wish to update an input file, you must" -" [first copy it to the output directory](staging-input-files.md)." -msgstr "" - -#: ../../topics/inputs.md:134 920e8b7d7eee4239b327b0386a872492 -msgid "" -"The value of `position` is used to determine where parameter should " -"appear on the command line. Positions are relative to one another, not " -"absolute. As a result, positions do not have to be sequential, three " -"parameters with positions 1, 3, 5 will result in the same command line as" -" 1, 2, 3. More than one parameter can have the same position (ties are " -"broken using the parameter name), and the position field itself is " -"optional. The default position is 0." -msgstr "" - -#: ../../topics/inputs.md:142 690f556fa0854517a4e3e43747178461 -msgid "" -"The `baseCommand` field will always appear in the final command line " -"before the parameters." -msgstr "" - -#: ../../topics/inputs.md:146 65ae530b9da84e7e98bcf5a5cf516c30 -msgid "Array Inputs" -msgstr "" - -#: ../../topics/inputs.md:148 21f30b0db29c4aa4989c39997b1a720c -msgid "" -"It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to " -"provide `type` field with `type: array` and `items` defining the valid " -"data types that may appear in the array. Alternatively, brackets `[]` may" -" be added after the type name to indicate that input parameter is array " -"of that type." -msgstr "" - -#: ../../topics/inputs.md:154 cefc841cd57c4b19b2be69aa80106c8b -msgid "`array-inputs.cwl`" -msgstr "" - -#: ../../topics/inputs.md:160 bae9c79fa8bb42f6922ee937a5c5ff7a -msgid "`array-inputs-job.yml`" -msgstr "" - -#: ../../topics/inputs.md:166 b756a25aad9e4fcfb68cbe2123cac3c5 -msgid "" -"Now invoke `cwltool` providing the tool description and the input object " -"on the command line:" -msgstr "" - -#: ../../topics/inputs.md:178 0a930f2019b748858ddc5ca5acbde210 -msgid "" -"The `inputBinding` can appear either on the outer array parameter " -"definition or the inner array element definition, and these produce " -"different behavior when constructing the command line, as shown above. In" -" addition, the `itemSeparator` field, if provided, specifies that array " -"values should be concatenated into a single argument separated by the " -"item separator string." -msgstr "" - -#: ../../topics/inputs.md:185 57551982494e4152b2c2c11f04bae126 -msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` " -"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " -"lines, where array values that are not defined with an associated key are" -" marked by a leading `-`. This will be demonstrated in the next lesson " -"and is discussed in more detail in the [YAML Guide](yaml-" -"guide.md#arrays). You can specify arrays of arrays, arrays of records, " -"and other complex types." -msgstr "" - -#: ../../topics/inputs.md:191 30d6b347401d4304b4dcc1ef2268ded2 -msgid "Inclusive and Exclusive Inputs" -msgstr "" - -#: ../../topics/inputs.md:193 cf8b6d0ed47a4e57a39add29f91f0ec0 -msgid "" -"Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be " -"provided together (they are exclusive). You can use records and type " -"unions to group parameters together to describe these two conditions." -msgstr "" - -#: ../../topics/inputs.md:198 5aa374f61a2a41e383da4b960e3603d5 -msgid "`record.cwl`" -msgstr "" - -#: ../../topics/inputs.md:204 6557427907d0465695aa88f2f27d5bf1 -msgid "`record-job1.yml`" -msgstr "" - -#: ../../topics/inputs.md:215 3f39bfdadeb14b0d8dfb67fe5aad7790 -msgid "" -"In the first example, you can't provide `itemA` without also providing " -"`itemB`." -msgstr "" - -#: ../../topics/inputs.md:217 30829196c2f54dbb9b1c35e462fe4e85 -msgid "`record-job2.yml`" -msgstr "" - -#: ../../topics/inputs.md:233 049396bf53d241cd9d03b9ff81468e0c -msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the " -"first matching item (`itemC`) is added to the command line and remaining " -"item (`itemD`) is ignored." -msgstr "" - -#: ../../topics/inputs.md:236 a9036f0e32ff418482573d23ed074256 -msgid "`record-job3.yml`" -msgstr "" - -#: ../../topics/inputs.md:252 bc0b43accbf9452ca4b7c2d7d69c2984 -msgid "" -"In the third example, only `itemD` is provided, so it appears on the " -"command line." -msgstr "" - -#: ../../topics/inputs.md:255 6cfc57be54f8458ebc9d784bc9ac2555 -msgid "Exclusive Input Parameters with Expressions" -msgstr "" - -#: ../../topics/inputs.md:257 0279c53e41c94ccc9f2de65d057dd903 -msgid "" -"If you use exclusive input parameters combined with expressions, you need" -" to be aware that the `inputs` JavaScript object will contain one of the " -"exclusive input values. This means that you might need to use an **or** " -"boolean operator to check which values are present." -msgstr "" - -#: ../../topics/inputs.md:262 b94737f481d343bfbb6ecf0fd81c9d6f -msgid "" -"Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from" -" an enum." -msgstr "" - -#: ../../topics/inputs.md:265 b5335802dcd148e9bb8f72d75f1ff6cd -msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" - -#: ../../topics/inputs.md:271 08b50c80fd024f86ba9c6239895385d0 -msgid "" -"Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you " -"provide a valid value, such as “fasta” (one of the values of the enum), " -"your command should execute successfully:" -msgstr "" - -#: ../../topics/inputs.md:280 77c08d3144b04e58a6733cbd01346102 -msgid "" -"However, if you do not provide any input value, then `file_format` will " -"be evaluated to a `null` value, which does not match the expected type " -"for the output field (a `string`), resulting in failure when running your" -" workflow." -msgstr "" - -#: ../../topics/inputs.md:289 91280fddf3624696b90632ca8466ca59 -msgid "" -"To correct it, you must remember to use an or operator in your JavaScript" -" expression when using exclusive parameters, or any parameter that allows" -" `null`. For example, the expression could be changed to " -"`$(inputs.file_format || 'auto')`, to have a default value if none was " -"provided in the command line or job input file." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/metadata-and-authorship.po b/locales/en/LC_MESSAGES/topics/metadata-and-authorship.po deleted file mode 100644 index fb846967..00000000 --- a/locales/en/LC_MESSAGES/topics/metadata-and-authorship.po +++ /dev/null @@ -1,70 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/metadata-and-authorship.md:1 e5511fed73914ceeaf73b9ca7020e8d2 -msgid "Metadata and Authorship" -msgstr "" - -#: ../../topics/metadata-and-authorship.md:3 1a4f0cbf7a694f949646c7bfc1d6f5dc -msgid "" -"Implementation extensions not required for correct execution (for " -"example, fields related to GUI presentation) and metadata about the tool " -"or workflow itself (for example, authorship for use in citations) may be " -"provided as additional fields on any object. Such extensions fields (e.g." -" `format: edam:format_2572`) can use a namespace prefix listed in the " -"`$namespaces` section of the document (e.g. edam: " -"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" -"][schema-salad]. Once you add the namespace prefix, you can access it " -"anywhere in the document as shown below. Otherwise, one must use full " -"URLs: `format: http://edamontology.org/format_2572`." -msgstr "" - -#: ../../topics/metadata-and-authorship.md:13 f1dcef50a880467f82b93f383030501b -msgid "" -"For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to " -"cite your tool." -msgstr "" - -#: ../../topics/metadata-and-authorship.md:16 1af01d43dfd9408ab58a960b62bf44f0 -msgid "`metadata_example2.cwl`" -msgstr "" - -#: ../../topics/metadata-and-authorship.md:22 ecd7d3e4f19146ef807219add82fff00 -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../topics/metadata-and-authorship.md:28 a8b454c10d484726b194de1f8c0775da -msgid "Extended Example" -msgstr "" - -#: ../../topics/metadata-and-authorship.md:30 0e5960b6d60b4a73837d1ea4b36a896d -msgid "" -"For those that are highly motivated, it is also possible to annotate your" -" tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints" -" at hardware requirements in order to use the tool, and a few more " -"metadata fields." -msgstr "" - -#: ../../topics/metadata-and-authorship.md:35 89713dbe4568459488494cf7f23ee622 -msgid "`metadata_example3.cwl`" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/operations.po b/locales/en/LC_MESSAGES/topics/operations.po deleted file mode 100644 index dd111423..00000000 --- a/locales/en/LC_MESSAGES/topics/operations.po +++ /dev/null @@ -1,73 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/operations.md:1 968848522a1c419e94cdb03a48f7bab8 -msgid "Operations" -msgstr "" - -#: ../../topics/operations.md:3 825f5584a57148e4ba1df435653351a1 -msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-" -"line tool, or an expression tool. It is a step of a workflow that " -"specifies inputs and outputs, but it does not provide enough information " -"to be executed." -msgstr "" - -#: ../../topics/operations.md:7 1c8a712c12b54c26ac8d2d24270390cf -msgid "" -"You can create operations to visualize a workflow during development, " -"before you are ready to submit the workflow to a CWL runner:" -msgstr "" - -#: ../../topics/operations.md:10 e0e24f86682447ad88bb59f73f4c272f -msgid "`operations.cwl`" -msgstr "" - -#: ../../topics/operations.md:16 a1448ed2695b4b849c0e2879c38640d8 -msgid "" -"The `uppercase` step of the workflow is an operation. It can be used like" -" a command line tool or an expression. You can also plot it with the CWL " -"Viewer or `cwltool`:" -msgstr "" - -#: ../../topics/operations.md:24 0ed9d93f0ead46fea1f3d5f28d22419b -msgid "" -"The output of the command above can be rendered with a Graphviz renderer." -" The following image is rendered with the Sphinx Graphviz directive (this" -" user guide is built with Sphinx):" -msgstr "" - -#: ../../topics/operations.md:55 4a03e03b140a45b3bfc26d7b0f677cb4 -msgid "" -"If you try running it with `cwltool`, the command will fail since " -"`cwltool` does not have enough information to know how to execute it:" -msgstr "" - -#: ../../topics/operations.md:58 7794ec6d263c425bb423135f4025d2f1 -msgid "`cwltool` does not know how to run operations" -msgstr "" - -#: ../../topics/operations.md:66 8c8423c44aec4a619ea9bbce986b3b96 -msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A" -" CWL runner could, for instance, use abstract operations with ID's that " -"correspond to steps executed by a different workflow engine." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/outputs.po b/locales/en/LC_MESSAGES/topics/outputs.po deleted file mode 100644 index 84287200..00000000 --- a/locales/en/LC_MESSAGES/topics/outputs.po +++ /dev/null @@ -1,147 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/outputs.md:1 8b140307638c4baa9261df35f7372240 -msgid "Outputs" -msgstr "" - -#: ../../topics/outputs.md:3 59a76cb3f5b04cf391310d816bdd4759 -msgid "Returning Output Files" -msgstr "" - -#: ../../topics/outputs.md:5 f1e1c91b796e4c4bbb5c8e234852225d -msgid "" -"The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name" -" of parameter, and `type` describing what types of values are valid for " -"that parameter." -msgstr "" - -#: ../../topics/outputs.md:10 aa7076aea7e54d489af848f9523794fe -msgid "" -"When a tool runs under CWL, the starting working directory is the " -"designated output directory. The underlying tool or script must record " -"its results in the form of files created in the output directory. The " -"output parameters returned by the CWL tool are either the output files " -"themselves, or come from examining the content of those files." -msgstr "" - -#: ../../topics/outputs.md:16 7ee8d5efbc2d43c297960a3d851628f9 -msgid "" -"The following example demonstrates how to return a file that has been " -"extracted from a tar file." -msgstr "" - -#: ../../topics/outputs.md:19 ba6fcc05fcdd46f6b1f354295bf124de -msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "" - -#: ../../topics/outputs.md:21 7534fb6a5894438f9da2167e08f4e218 -msgid "" -"In previous examples, the `baseCommand` was just a string, with any " -"arguments passed as CWL inputs. Instead of a single string we can use an " -"_array of strings_. The first element is the command to run, and any " -"subsequent elements are mandatory command line arguments" -msgstr "" - -#: ../../topics/outputs.md:26 3c50004d2d7d4695944015e40bf1f22f -msgid "`tar.cwl`" -msgstr "" - -#: ../../topics/outputs.md:32 cddecc6f8aa640d2b245eef27f5bb87e -msgid "`tar-job.yml`" -msgstr "" - -#: ../../topics/outputs.md:38 3d7918df94094da9b8ecc7ec1c5a1b3b -msgid "Next, create a tar file for the example." -msgstr "" - -#: ../../topics/outputs.md:45 7bf5e274a89048838c9fdf28633a5cec -msgid "" -"And now invoke `cwltool` with the tool description and the input object " -"on the command line:" -msgstr "" - -#: ../../topics/outputs.md:51 fce348fc9cce4fdaa699b0d0f6f3b542 -msgid "" -"The field `outputBinding` describes how to set the value of each output " -"parameter." -msgstr "" - -#: ../../topics/outputs.md:62 aa92f3f4f14e4025b874ffec26bff141 -msgid "" -"The `glob` field consists of the name of a file in the output directory. " -"If you don't know name of the file in advance, you can use a wildcard " -"pattern like `glob: '*.txt'`." -msgstr "" - -#: ../../topics/outputs.md:65 1a5ab9a9e91640d48a0cb2c13e691cbc -msgid "Capturing Standard Output" -msgstr "" - -#: ../../topics/outputs.md:67 9896a750508f4a57b128f4e30e718814 -msgid "" -"To capture a tool's standard output stream, add the `stdout` field with " -"the name of the file where the output stream should go. Then add `type: " -"stdout` on the corresponding output parameter." -msgstr "" - -#: ../../topics/outputs.md:71 9345911f55b945eab39897e85e648ea4 -msgid "`stdout.cwl`" -msgstr "" - -#: ../../topics/outputs.md:77 cea8fa310b0c471e8f6f6317b9ffcec6 -msgid "`echo-job.yml`" -msgstr "" - -#: ../../topics/outputs.md:82 ../../topics/outputs.md:105 -#: 5e059fc800fa4f9f93e8a5b07e68de36 d62a95decb134c87a4280ce5526e03bd -msgid "" -"Now invoke `cwltool` providing the tool description and the input object " -"on the command line:" -msgstr "" - -#: ../../topics/outputs.md:89 9d6affcf4fbd4ca2a3f8dbd8d50a5c27 -msgid "Array Outputs" -msgstr "" - -#: ../../topics/outputs.md:91 8c5ad552c70e49b09bdda33cda587fec -msgid "" -"You can also capture multiple output files into an array of files using " -"`glob`." -msgstr "" - -#: ../../topics/outputs.md:93 0558868e3e554b5890eb69b275a6b14b -msgid "`array-outputs.cwl`" -msgstr "" - -#: ../../topics/outputs.md:99 4fae0201b0f64c03a134f0bd9aeae9ba -msgid "`array-outputs-job.yml`" -msgstr "" - -#: ../../topics/outputs.md:112 9f9c8a4a10d444879c7984a95e40fdb4 -msgid "" -"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " -"expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions" -" to mark entries in arrays, as demonstrated in several of the upcoming " -"sections." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/parameter-references.po b/locales/en/LC_MESSAGES/topics/parameter-references.po deleted file mode 100644 index 89399c97..00000000 --- a/locales/en/LC_MESSAGES/topics/parameter-references.po +++ /dev/null @@ -1,279 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/parameter-references.md:1 9f53de1545d2441eaca40a478ab3b2b5 -msgid "Parameter References" -msgstr "" - -#: ../../topics/parameter-references.md:3 86efaeb616844254ac6651e3b312d648 -msgid "" -"In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file " -"we were interested in was called \"hello.txt\", and this was written into" -" the `.cwl` file. This is not the best way to do this, as the " -"\"hello.txt\" filename may vary or be dependent on the input file(s) " -"used. To avoid this we can specify the name of the file we want in the " -"job parameters file (`.yml`). In this example, you will see how to " -"reference the value of input parameters dynamically from other fields, " -"which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../topics/parameter-references.md:13 e19913c8e6bb449aa55959dd82acda2d -msgid "`tar-param.cwl`" -msgstr "" - -#: ../../topics/parameter-references.md:19 7e40643c4a474987aea13be5af260677 -msgid "`tar-param-job.yml`" -msgstr "" - -#: ../../topics/parameter-references.md:25 46112899f2dd46ba828dc57245680909 -msgid "" -"Create your input files and invoke `cwltool` with the tool description " -"and the input object on the command line:" -msgstr "" - -#: ../../topics/parameter-references.md:36 896da20f29e2465fae5555d1f51cb681 -msgid "" -"Certain fields permit parameter references which are enclosed in " -"`$(...)`. These are evaluated and replaced with value being referenced." -msgstr "" - -#: ../../topics/parameter-references.md:47 2e0849d53b6b4491a5d779390ea1319e -msgid "" -"References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " -"`$(inputs['extractfile'])` are equivalent." -msgstr "" - -#: ../../topics/parameter-references.md:51 3dab2befe3e840738419f1dedaac04d5 -msgid "" -"The value of the \"inputs\" variable is the input object provided when " -"the CWL tool was invoked." -msgstr "" - -#: ../../topics/parameter-references.md:54 f92b2507989f4836bf33c78326bf8bc3 -msgid "" -"Note that because `File` parameters are objects, to get the path to an " -"input file you must reference the path field on a file object; to " -"reference the path to the tar file in the above example you would write " -"`$(inputs.tarfile.path)`." -msgstr "" - -#: ../../topics/parameter-references.md:59 2a7ca85801a841f2acc94431a2accef8 -msgid "Where are parameter references allowed?" -msgstr "" - -#: ../../topics/parameter-references.md:61 737a086da43644b3979fd3ebb16b2696 -msgid "You can only use parameter references in certain fields. These are:" -msgstr "" - -#: ../../topics/parameter-references.md:63 fcf3c4392e48496a8776ba9a49a6e867 -msgid "" -"From " -"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../topics/parameter-references.md:64 1b2a1714c66d4b2398c7fd614b3099c4 -msgid "`arguments`" -msgstr "" - -#: ../../topics/parameter-references.md:65 -#: ../../topics/parameter-references.md:73 -#: ../../topics/parameter-references.md:86 4458fac137854a9499a9afd221c344ac -#: 96f0d31f8d3549689bdfd4908698eed2 b234d82653a44b4ab1f9532e71e5e962 -msgid "`valueFrom`" -msgstr "" - -#: ../../topics/parameter-references.md:66 e6857e57ba424ec1bd86789a27458c8c -msgid "`stdin`" -msgstr "" - -#: ../../topics/parameter-references.md:67 8544dee0d05a492ca7f7727d277001ba -msgid "`stdout`" -msgstr "" - -#: ../../topics/parameter-references.md:68 a73a304246064187a5ef01aa04c528c8 -msgid "`stderr`" -msgstr "" - -#: ../../topics/parameter-references.md:69 8a86bb148ba9488185ac8f7a621aeba9 -msgid "" -"From " -"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../topics/parameter-references.md:70 -#: ../../topics/parameter-references.md:75 -#: ../../topics/parameter-references.md:82 -#: ../../topics/parameter-references.md:90 26f25bcad002476287ac6597033b3a68 -#: 2911d4b287444e159b2a1cfb9880a977 3657033c01b847febc8d6cdae2cf62b6 -#: 65f8db3faadb4fb59f8f26e7084b7a02 -msgid "`format`" -msgstr "" - -#: ../../topics/parameter-references.md:71 -#: ../../topics/parameter-references.md:76 -#: ../../topics/parameter-references.md:83 -#: ../../topics/parameter-references.md:91 3e57f5d7e1934e19a0f5de1bf11516ef -#: 40e34ff2cf47440a87f6548d3fa0ee65 64382062a5d5464fbf679cc774d0b886 -#: 99c94c256ce444a5a7a2ed4f52498c54 -msgid "`secondaryFiles`" -msgstr "" - -#: ../../topics/parameter-references.md:72 9a7a2dc3b4854f998fe36bd55d062abe -msgid "" -"From " -"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../topics/parameter-references.md:74 9f9ebe1562de4739bdf432fa9f51df65 -msgid "" -"From " -"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../topics/parameter-references.md:77 d0ed73eea69a488da98f09b5da9e956a -msgid "" -"From " -"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../topics/parameter-references.md:78 153b0efcb519496b89acf861c4cc0af6 -msgid "`glob`" -msgstr "" - -#: ../../topics/parameter-references.md:79 e3ff712139e640b19b06a9270570ac3d -msgid "`outputEval`" -msgstr "" - -#: ../../topics/parameter-references.md:80 4ab6c83d91eb438a972136acae6c128c -msgid "From `Workflow`" -msgstr "" - -#: ../../topics/parameter-references.md:81 d34255008ec94e0cbbf48381fd81a642 -msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../topics/parameter-references.md:84 be964cd5acd74de6bf636baa4299eb81 -msgid "From `steps`" -msgstr "" - -#: ../../topics/parameter-references.md:85 038484e05e724c868a2d1d53cfced2c6 -msgid "" -"From " -"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../topics/parameter-references.md:87 1ee43a5c98f6440e95d688afdb6e4822 -msgid "" -"From " -"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../topics/parameter-references.md:88 bf82bae8614f4d3f8e57c20a086ce013 -msgid "`expression`" -msgstr "" - -#: ../../topics/parameter-references.md:89 f708c3a4d3fd404c95285558b8cc6d91 -msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../topics/parameter-references.md:92 fa914a651d5444ebbcff86b1b6226212 -msgid "" -"From " -"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../topics/parameter-references.md:93 683a5eb1aa8e41adb89b1e7aec649a36 -msgid "`coresMin`" -msgstr "" - -#: ../../topics/parameter-references.md:94 151709a04a0a455481b9458c535a2e54 -msgid "`coresMax`" -msgstr "" - -#: ../../topics/parameter-references.md:95 93ec484b73bd457b9a34b681e62dba55 -msgid "`ramMin`" -msgstr "" - -#: ../../topics/parameter-references.md:96 3e17671a4aca4443b24bca32b1898bbf -msgid "`ramMax`" -msgstr "" - -#: ../../topics/parameter-references.md:97 b9d4ba2a422542609db7c994b9c89971 -msgid "`tmpdirMin`" -msgstr "" - -#: ../../topics/parameter-references.md:98 fdab43c7a8bb420d84154aa70e24d05a -msgid "`tmpdirMax`" -msgstr "" - -#: ../../topics/parameter-references.md:99 fe3f4e63d6014e34a01243d6e1d54b1a -msgid "`outdirMin`" -msgstr "" - -#: ../../topics/parameter-references.md:100 6db5ab1a64ec40e9a6bc16060657b284 -msgid "`outdirMax`" -msgstr "" - -#: ../../topics/parameter-references.md:101 79f66c8ecf60493697c03d90e111f5aa -msgid "" -"From " -"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../topics/parameter-references.md:102 c42fe7e8d1dd4e35a255a5fe1f0dbdd0 -msgid "`listing`" -msgstr "" - -#: ../../topics/parameter-references.md:103 2d14a16d2a354839bcfdbcdd473c59e3 -msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../topics/parameter-references.md:104 5545855b55f34682b2a4e78dfa401952 -msgid "`entry`" -msgstr "" - -#: ../../topics/parameter-references.md:105 b267ab6613524236b50e698be4381087 -msgid "`entryname`" -msgstr "" - -#: ../../topics/parameter-references.md:106 6eb7f722fe294d2c81bb97e5bb193c0b -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../topics/parameter-references.md:107 43feefec5bc54adf9340f754e3bbe6fd -msgid "" -"From " -"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../topics/parameter-references.md:108 154d6c865631433d89589bd0748c9850 -msgid "`envValue`" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/requirements-and-hints.po b/locales/en/LC_MESSAGES/topics/requirements-and-hints.po deleted file mode 100644 index 380aa5be..00000000 --- a/locales/en/LC_MESSAGES/topics/requirements-and-hints.po +++ /dev/null @@ -1,24 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/requirements-and-hints.md:5 1a39722a112b48beb8cf24e0f5e6ad88 -msgid "Requirements and Hints" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/specifying-software-requirements.po b/locales/en/LC_MESSAGES/topics/specifying-software-requirements.po deleted file mode 100644 index c5cd86e9..00000000 --- a/locales/en/LC_MESSAGES/topics/specifying-software-requirements.po +++ /dev/null @@ -1,68 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/specifying-software-requirements.md:1 -#: 206f3f103faf4ac19eccdce6e038ed49 -msgid "Specifying Software Requirements" -msgstr "" - -#: ../../topics/specifying-software-requirements.md:3 -#: 4a6f03a974fc4a9e86e260d9bd48b908 -msgid "" -"Often, tool descriptions will be written for a specific version of a " -"software. To make it easier for others to use your descriptions, you can " -"include a `SoftwareRequirement` field in the `hints` section. This may " -"also help to avoid confusion about which version of a tool the " -"description was written for." -msgstr "" - -#: ../../topics/specifying-software-requirements.md:13 -#: 8bd36ba850bc4f04bd886ae39e361dbb -msgid "" -"In this example, the software requirement being described is InterProScan" -" version 5.21-60." -msgstr "" - -#: ../../topics/specifying-software-requirements.md:25 -#: 8a5b0083c986452e82183cdc78d2da87 -msgid "" -"Depending on your CWL runner, these hints may be used to check that the " -"required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the " -"[dependency resolvers configuration][dependencies]." -msgstr "" - -#: ../../topics/specifying-software-requirements.md:29 -#: 52df6af7c58b4f099c194b28b0a34de6 -msgid "" -"As well as a version number, a unique resource identifier (URI) for the " -"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" -" looked up in the [SciCrunch][scicrunch] registry, which provides a " -"portal for finding, tracking, and referring to scientific resources " -"consistently. If you want to specify a tool as a `SoftwareRequirement`, " -"search for the tool on SciCrunch and use the RRID that it has been " -"assigned in the registry. (Follow this [Adding a Resource Tutorial" -"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " -"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " -"field of your requirement description. Other good choices, in order of " -"preference, are to include the DOI for the main tool citation and the URL" -" to the tool." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/staging-input-files.po b/locales/en/LC_MESSAGES/topics/staging-input-files.po deleted file mode 100644 index 36848e63..00000000 --- a/locales/en/LC_MESSAGES/topics/staging-input-files.po +++ /dev/null @@ -1,48 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/staging-input-files.md:1 da94c2c9fedf40f789a8afe9ff97abe7 -msgid "Staging Input Files" -msgstr "" - -#: ../../topics/staging-input-files.md:3 57675258a9ef4d948e3ebf0edd7779af -msgid "" -"Normally, input files are located in a read-only directory separate from " -"the output directory. This causes problems if the underlying tool " -"expects to write its output files alongside the input file in the same " -"directory. You use `InitialWorkDirRequirement` to stage input files into" -" the output directory. In this example, we use a JavaScript expression to" -" extract the base name of the input file from its leading directory path." -msgstr "" - -#: ../../topics/staging-input-files.md:9 0cf7fa6cd86c41bf92cd35616a4399e2 -msgid "`linkfile.cwl`" -msgstr "" - -#: ../../topics/staging-input-files.md:15 79ff820bc8d34c3ea37d396d98b56688 -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../topics/staging-input-files.md:20 5f9403a7426941cb806bb76578d53987 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/troubleshooting.po b/locales/en/LC_MESSAGES/topics/troubleshooting.po deleted file mode 100644 index 7658928c..00000000 --- a/locales/en/LC_MESSAGES/topics/troubleshooting.po +++ /dev/null @@ -1,101 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/troubleshooting.md:1 29507aa59aff4e249fcd12240b9fed91 -msgid "Troubleshooting" -msgstr "" - -#: ../../topics/troubleshooting.md:3 fac133f1d79f49599d516794dd45517e -msgid "" -"In this section you will find ways to troubleshoot when you have problems" -" executing CWL. We focus on `cwltool` here but some of these techniques " -"may apply to other CWL Runners." -msgstr "" - -#: ../../topics/troubleshooting.md:6 68f47e9e268248af8a07b4b35080a918 -msgid "Run `cwltool` with `cachedir`" -msgstr "" - -#: ../../topics/troubleshooting.md:8 4ce1b123ee4745a3aa149e0f98ebe310 -msgid "" -"You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor " -"output files, but created while your workflow is running). By default, " -"these files are created in a temporary directory but writing them to a " -"separate directory makes accessing them easier." -msgstr "" - -#: ../../topics/troubleshooting.md:14 afa8d683568747839d41d2e9051d06ec -msgid "" -"In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " -"World\" | rev`, which would print the message \"Hello World\" reversed, " -"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," -" where instead of executing the `rev` command it tries to execute `revv`," -" which fails." -msgstr "" - -#: ../../topics/troubleshooting.md:20 699bac84262647c7bc091c7cea92a4ba -msgid "`troubleshooting-wf1.cwl`" -msgstr "" - -#: ../../topics/troubleshooting.md:27 c4ce2451329d468a8a5a489eca901262 -msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " -"value (`cwltool` will create the directory for you if it does not exist " -"already):" -msgstr "" - -#: ../../topics/troubleshooting.md:35 31f0242e1c5a4c3bb621ce4414e34add -msgid "" -"The workflow is in the `permanentFail` status due to `step_b` failing to " -"execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. " -"You can inspect the intermediate files created:" -msgstr "" - -#: ../../topics/troubleshooting.md:44 7294bf3bcfd447bf9b894ffef0b2873a -msgid "" -"Each workflow step has received a unique ID (the long value that looks " -"like a hash). The `${HASH}.status` files display the status of each step " -"executed by the workflow. And the `step_a` output file `stdout.txt` is " -"visible in the output of the command above." -msgstr "" - -#: ../../topics/troubleshooting.md:48 a18b5467b1c643d987e494d5a9ced7c7 -msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" -" in the `step_b`). After fixing the typo, when you execute `cwltool` with" -" the same arguments as the previous time, note that now `cwltool` output " -"contains information about pre-cached outputs for `step_a`, and about a " -"new cache entry for the output of `step_b`. Also note that the status of " -"`step_b` is now of success." -msgstr "" - -#: ../../topics/troubleshooting.md:59 7925dcec83bc48cd88eaf2e6860304fd -msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had" -" been cached, and there was no change in its execution or output. " -"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for" -" troubleshooting your CWL documents and also as a way to prevent " -"`cwltool` to re-evaluate steps unnecessarily." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/using-containers.po b/locales/en/LC_MESSAGES/topics/using-containers.po deleted file mode 100644 index 6779614b..00000000 --- a/locales/en/LC_MESSAGES/topics/using-containers.po +++ /dev/null @@ -1,106 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/using-containers.md:1 33c3ff349c68416e8968af39e5e588e0 -msgid "Using Containers" -msgstr "" - -#: ../../topics/using-containers.md:3 5c50f28d3926477e965a32d31e5329ee -msgid "Running Tools Inside Docker" -msgstr "" - -#: ../../topics/using-containers.md:5 5cb16dd51c1d41aeb34c4aa1fb2e0940 -msgid "" -"[Docker][docker] containers simplify software installation by providing a" -" complete known-good runtime for software and its dependencies. However," -" containers are also purposefully isolated from the host system, so in " -"order to run a tool inside a Docker container there is additional work to" -" ensure that input files are available inside the container and output " -"files can be recovered from the container. A CWL runner can perform this" -" work automatically, allowing you to use Docker to simplify your software" -" management while avoiding the complexity of invoking and managing Docker" -" containers." -msgstr "" - -#: ../../topics/using-containers.md:15 e0e83e827b734355aa97b19dc4c7e0d5 -msgid "" -"One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the " -"container." -msgstr "" - -#: ../../topics/using-containers.md:18 38f82d201fa2455f94afacae2c1c76b2 -msgid "" -"This example runs a simple Node.js script inside a Docker container which" -" will then print \"Hello World\" to the standard output." -msgstr "" - -#: ../../topics/using-containers.md:21 00459eae5fef4f5f907ceb53eee857dd -msgid "`docker.cwl`" -msgstr "" - -#: ../../topics/using-containers.md:27 7e59171b12eb46e98ffa08a05ccebf16 -msgid "`docker-job.yml`" -msgstr "" - -#: ../../topics/using-containers.md:33 d90442f3550f4e9b84905bb76ecb6fc1 -msgid "" -"Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that " -"is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../topics/using-containers.md:44 feb03506a2614ea3a0fc97f3154425c2 -msgid "" -"`baseCommand: node` tells CWL that we will be running this command using " -"the Node Js runtime that is meant for Javascript files. We then need to " -"specify some `hints` for how to find the container we want. In this case" -" we list just our requirements for the docker container in " -"`DockerRequirements`. The `dockerPull:` parameter takes the same value " -"that you would pass to a `docker pull` command. That is, the name of the " -"container image (you can even specify the tag, which is good idea for " -"best practices when using containers for reproducible research). In this " -"case we have used a container called `node:slim`." -msgstr "" - -#: ../../topics/using-containers.md:52 fa521c85542c410ba187c69fe5b3aebd -msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` " -"providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../topics/using-containers.md:55 f3012553a17a42fca78b210ecec92003 -msgid "`hello.js`" -msgstr "" - -#: ../../topics/using-containers.md:69 fd0ad3c4cd904765ae5b043b44078a1c -msgid "" -"Notice the CWL runner has constructed a Docker command line to run the " -"script." -msgstr "" - -#: ../../topics/using-containers.md:72 60fa9a28e9bf4a4fa54289516e22f4cd -msgid "" -"In this example, the path to the script `hello.js` is " -"`/home/me/cwl/user_guide/hello.js` outside the container but " -"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " -"reflected in the invocation of the `node` command." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/workflows.po b/locales/en/LC_MESSAGES/topics/workflows.po deleted file mode 100644 index 9c8321d5..00000000 --- a/locales/en/LC_MESSAGES/topics/workflows.po +++ /dev/null @@ -1,504 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/workflows.md:1 d6acbcdd75704f7b966a49edb8af28d9 -msgid "Workflows" -msgstr "" - -#: ../../topics/workflows.md:3 4d3032eb6fcc4cf8a2a67958877d7850 -msgid "" -"A workflow is a CWL processing unit that executes command-line tools, " -"expression tools, or workflows (sub-workflows) as steps. It must have " -"`inputs`, `outputs`, and `steps` defined in the CWL document." -msgstr "" - -#: ../../topics/workflows.md:13 89e89efbb04b47909df04a046169442c -msgid "CWL workflow." -msgstr "" - -#: ../../topics/workflows.md:41 a6e739c210e54652aa8833825f58e36f -msgid "" -"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier " -"examples." -msgstr "" - -#: ../../topics/workflows.md:51 5b187be9b5314039a7e16d35fe4672e3 -msgid "`echo-uppercase.cwl`" -msgstr "" - -#: ../../topics/workflows.md:81 59c9035c8eb94a4984c2fdf66c1cb787 -msgid "" -"A command-line tool or expression tool can also be written directly in " -"the same CWL document as the workflow. For example, we can rewrite the " -"`echo-uppercase.cwl` workflow as a single file:" -msgstr "" - -#: ../../topics/workflows.md:91 0e790b8a77874eeca2efcdf8254226e1 -msgid "`echo-uppercase-single-file.cwl`" -msgstr "" - -#: ../../topics/workflows.md:150 176b128d31d549ec947e2112bda59e10 -msgid "" -"Having separate files helps with modularity and code organization. But it" -" can be helpful writing everything in a single file for development. " -"There are other ways to combine multiple files into a single file (e.g. " -"`cwltool --pack`) discussed further in other sections of this user guide." -msgstr "" - -#: ../../topics/workflows.md:160 058879c518a24859933efd7c62d2b3e4 -msgid "" -"For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this" -" user guide in more detail." -msgstr "" - -#: ../../topics/workflows.md:165 9e596d54fc074e3dbb622429244304dc -msgid "Writing Workflows" -msgstr "" - -#: ../../topics/workflows.md:167 14760ea2dd594df4a11af3c2b267e2ee -msgid "" -"This workflow extracts a java source file from a tar file and then " -"compiles it." -msgstr "" - -#: ../../topics/workflows.md:170 73d971cacade4ed4893f03978d930b3b -msgid "`1st-workflow.cwl`" -msgstr "" - -#: ../../topics/workflows.md:179 ../../topics/workflows.md:180 -#: 54719da53e4043758f29194fda1b0448 652551d8f4cf49fbb785e56b9bccf2ea -msgid "Visualization of 1st-workflow.cwl" -msgstr "" - -#: ../../topics/workflows.md:180 84d558ae6abc432695ccb49d050d92c7 -msgid "" -"[![Visualization of 1st-" -"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-" -"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-workflow.cwl)" -msgstr "" - -#: ../../topics/workflows.md:183 9ced46957b8b4f20b2315979aecb30b9 -msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a" -" run:" -msgstr "" - -#: ../../topics/workflows.md:185 bda955c302b2489fa76f54a08f6a4119 -msgid "`1st-workflow-job.yml`" -msgstr "" - -#: ../../topics/workflows.md:191 e57cce93798d4cb3a2e7a50f88549049 -msgid "" -"Next, create a sample Java file and add it to a tar file to use with the " -"command-line tool." -msgstr "" - -#: ../../topics/workflows.md:198 0270321fc2554e318de95a5684e9b6ea -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - -#: ../../topics/workflows.md:205 e7035e4184a14b1bb2a33b9a22e06df3 -msgid "What's going on here? Let's break it down:" -msgstr "" - -#: ../../topics/workflows.md:212 b242d87aa48241c094c78051fd1b4e6d -msgid "" -"The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a " -"workflow." -msgstr "" - -#: ../../topics/workflows.md:221 fef2e2bdae81488bb23e6a63b8fec415 -msgid "" -"The `inputs` section describes the inputs of the workflow. This is a " -"list of input parameters where each parameter consists of an identifier " -"and a data type. These parameters can be used as sources for input to " -"specific workflows steps." -msgstr "" - -#: ../../topics/workflows.md:233 7e9c2fbfcebf45f0a8c906d32ad4ddb7 -msgid "" -"The `outputs` section describes the outputs of the workflow. This is a " -"list of output parameters where each parameter consists of an identifier " -"and a data type. The `outputSource` connects the output parameter " -"`classfile` of the `compile` step to the workflow output parameter " -"`compiled_class`." -msgstr "" - -#: ../../topics/workflows.md:248 f5dd8d4b1e324d7f81b12657f847c040 -msgid "" -"The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second " -"step compiles the file from the first step using the java compiler. " -"Workflow steps are not necessarily run in the order they are listed, " -"instead the order is determined by the dependencies between steps (using " -"`source`). In addition, workflow steps which do not depend on one " -"another may run in parallel." -msgstr "" - -#: ../../topics/workflows.md:256 76d103db569b4ec6ab33fbd3d8c11e79 -msgid "" -"The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input" -" parameters, `tarfile` and `extractfile` and one output parameter " -"`extracted_file`." -msgstr "" - -#: ../../topics/workflows.md:261 36ae3b2a1dab47b18b3896d208393e73 -msgid "" -"The ``in`` section of the workflow step connects these two input " -"parameters to the inputs of the workflow, `tarball` and " -"`name_of_file_to_extract` using `source`. This means that when the " -"workflow step is executed, the values assigned to `tarball` and " -"`name_of_file_to_extract` will be used for the parameters `tarfile` and " -"`extractfile` in order to run the tool." -msgstr "" - -#: ../../topics/workflows.md:267 e0e1cf7c5e86443eaf7717b5c683ed89 -msgid "" -"The `out` section of the workflow step lists the output parameters that " -"are expected from the tool." -msgstr "" - -#: ../../topics/workflows.md:278 91eceaf92e5441ce8b70e57e59fcda75 -msgid "" -"The second step `compile` depends on the results from the first step by " -"connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described " -"previously in [Additional Arguments and Parameters](additional-arguments-" -"and-parameters.md)). The output of this step `classfile` is connected to " -"the `outputs` section for the Workflow, described above." -msgstr "" - -#: ../../topics/workflows.md:285 6112278376cb4e84ba05ebe6db7b039f -msgid "Nested Workflows" -msgstr "" - -#: ../../topics/workflows.md:287 19b5cd110ef149819d91c5bb86f56def -msgid "" -"Workflows are ways to combine multiple tools to perform a larger " -"operations. We can also think of a workflow as being a tool itself; a CWL" -" workflow can be used as a step in another CWL workflow, if the workflow " -"engine supports the `SubworkflowFeatureRequirement`:" -msgstr "" - -#: ../../topics/workflows.md:297 5d4aca9586434f40917c3532ae97bb22 -msgid "" -"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " -"workflow:" -msgstr "" - -#: ../../topics/workflows.md:300 a32ab81c1a4a4150a0cf6fc792104a2a -msgid "`nestedworkflows.cwl`" -msgstr "" - -#: ../../topics/workflows.md:309 a28860105216475ab93a1fcd2b740b52 -msgid "" -"This two-step workflow starts with the `create-tar` step which is " -"connected to the `compile` step in orange; `compile` is another workflow," -" diagrammed on the right. In purple we see the fixed string " -"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../topics/workflows.md:314 b3a4a7cfd77340029137a2cc9462b65c -msgid "" -" \"Visualization" -msgstr "" - -#: ../../topics/workflows.md:322 88aff05f9f3a45b297dd3eda9f52bc91 -msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " -"its CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " -"mapped to become the step's input/outputs." -msgstr "" - -#: ../../topics/workflows.md:336 d5bc4016a294455baef3fe1e32c5c636 -msgid "" -"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and " -"`*.java` filename. This is generally best-practice, as it means it can be" -" reused in multiple parent workflows, or even in multiple steps within " -"the same workflow." -msgstr "" - -#: ../../topics/workflows.md:341 5d59589eef4d44d69d2ef65821aaae45 -msgid "" -"Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar" -" file at `tarball`, which we will prepare in the `create-tar` step. At " -"this point it is probably a good idea to refactor `1st-workflow.cwl` to " -"have more specific input/output names, as those also appear in its usage " -"as a tool." -msgstr "" - -#: ../../topics/workflows.md:347 d39c9aba4eda4252964711369c0ca9d6 -msgid "" -"It is also possible to do a less generic approach and avoid external " -"dependencies in the job file. So in this workflow we can generate a hard-" -"coded `Hello.java` file using the previously mentioned " -"`InitialWorkDirRequirement` requirement, before adding it to a tar file." -msgstr "" - -#: ../../topics/workflows.md:366 dd9b058b571347deb207200501a54651 -msgid "" -"In this case our step can assume `Hello.java` rather than be " -"parameterized, so we can use hardcoded values `hello.tar` and " -"`Hello.java` in a `baseCommand` and the resulting `outputs`:" -msgstr "" - -#: ../../topics/workflows.md:383 c2d3d7b3f62344b3841dadd0c2dd4981 -msgid "" -"Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This " -"is generally not best practice, as the tool then can't be reused. The " -"reason for doing it in this case is because the command line is hard-" -"coded with filenames that only make sense within this workflow." -msgstr "" - -#: ../../topics/workflows.md:389 847d59018c6940f0b7248bc82abf4818 -msgid "" -"In this example we had to prepare a tar file outside, but only because " -"our inner workflow was designed to take that as an input. A better " -"refactoring of the inner workflow would be to take a list of Java files " -"to compile, which would simplify its usage as a tool step in other " -"workflows." -msgstr "" - -#: ../../topics/workflows.md:394 f041304d817446d39cd9dd41b00e2e78 -msgid "" -"Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL" -" Tool description, care must be taken to improve its usability in " -"multiple workflows." -msgstr "" - -#: ../../topics/workflows.md:398 a232c586c24045d7ad0813aabe2c62b7 -msgid "Scattering Steps" -msgstr "" - -#: ../../topics/workflows.md:400 f1d87f16200142318d6ec00d19ae9dcb -msgid "" -"Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish " -"to run a tool or workflow multiple times over a list of inputs. The " -"workflow then takes the input(s) as an array and will run the specified " -"step(s) on each element of the array as if it were a single input. This " -"allows you to run the same workflow on multiple inputs without having to " -"generate many different commands or input yaml files." -msgstr "" - -#: ../../topics/workflows.md:411 884b61d0625a4561a963b381fcff7344 -msgid "" -"The most common reason a new user might want to use scatter is to perform" -" the same analysis on different samples. Let's start with a simple " -"workflow that calls our first example (`hello_world.cwl`) and takes an " -"array of strings as input to the workflow:" -msgstr "" - -#: ../../topics/workflows.md:415 35097a2dfc3c421bab46e81a53c34087 -msgid "`scatter-workflow.cwl`" -msgstr "" - -#: ../../topics/workflows.md:421 44c8319f97b242f197f1311fcb2719b5 -msgid "" -"Aside from the `requirements` section including " -"`ScatterFeatureRequirement`, what is going on here?" -msgstr "" - -#: ../../topics/workflows.md:429 839e0cd993b44899a4049b44eb8aacfa -msgid "" -"First of all, notice that the main workflow level input here requires an " -"array of strings." -msgstr "" - -#: ../../topics/workflows.md:441 333b64b5ab4a4078b9189c8bbb5924b9 -msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This " -"field tells the runner that we'd like to scatter over this input for this" -" particular step. Note that the input name listed after scatter is the " -"one of the step's input, not a workflow level input." -msgstr "" - -#: ../../topics/workflows.md:445 73aa0f6708264bc39b0c6398827f1e6e -msgid "" -"For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if " -"you expect that the final output of your workflow will now have multiple " -"outputs to collect, be sure to update that to an array type as well!" -msgstr "" - -#: ../../topics/workflows.md:450 5f6a3bf1dc314cb8beb9b336fc2c8f6f -msgid "Using the following input file:" -msgstr "" - -#: ../../topics/workflows.md:452 d5808863a44b4a6695e36ac1ae4a22f2 -msgid "`scatter-job.yml`" -msgstr "" - -#: ../../topics/workflows.md:458 2c642b5be9c94763aee4bdf73d8bc2a1 -msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" -" calls the command `echo` on a message. If we invoke `cwltool scatter-" -"workflow.cwl scatter-job.yml` on the command line:" -msgstr "" - -#: ../../topics/workflows.md:466 dcf2a0d97e4a4afa842a971b304e23b4 -msgid "" -"You can see that the workflow calls echo multiple times on each element " -"of our `message_array`. Ok, so how about if we want to scatter over two " -"steps in a workflow?" -msgstr "" - -#: ../../topics/workflows.md:469 2aea56527429469c8af125414e4f4f00 -msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding " -"the following lines instead of `outputs: []`" -msgstr "" - -#: ../../topics/workflows.md:472 a4279d75f660475d82c4bc8f869c17cc -msgid "`hello_world_to_stdout.cwl`" -msgstr "" - -#: ../../topics/workflows.md:480 33ac7f4c0b1040b89811c0445b1f6824 -msgid "" -"And add a second step that uses `wc` to count the characters in each " -"file. See the tool below:" -msgstr "" - -#: ../../topics/workflows.md:483 17b1da21293d40f7b246abb4f3a6fcd7 -msgid "`wc-tool.cwl`" -msgstr "" - -#: ../../topics/workflows.md:489 5aff13d9cf7841b29e2285ce2fdc90ad -msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under " -"each step:" -msgstr "" - -#: ../../topics/workflows.md:491 53afeb0f6b4f405782b0eb2e74d3acfe -msgid "`scatter-two-steps.cwl`" -msgstr "" - -#: ../../topics/workflows.md:497 fbab18460296443daddb7bc1bcafe4fc -msgid "" -"Here we have placed the scatter field under each step. This is fine for " -"this example since it runs quickly, but if you're running many samples " -"for a more complex workflow, you may wish to consider an alternative. " -"Here we are running scatter on each step independently, but since the " -"second step is not dependent on the first step completing all languages, " -"we aren't using the scatter functionality efficiently. The second step " -"expects an array as input from the first step, so it will wait until " -"everything in step one is finished before doing anything. Pretend that " -"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " -"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " -"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " -"could finish in 4 minutes, it will actually finish in 8 minutes because " -"the first step must wait on `echo Hallo welt!`. You can see how this " -"might not scale well." -msgstr "" - -#: ../../topics/workflows.md:509 52b2dee5459b4bbdab9f09576ec96f65 -msgid "" -"Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can" -" make an entire workflow a single step in another workflow! Convert our " -"two-step workflow to a single step subworkflow:" -msgstr "" - -#: ../../topics/workflows.md:513 24185616ce374615a6966a70df77693b -msgid "`scatter-nested-workflow.cwl`" -msgstr "" - -#: ../../topics/workflows.md:519 7302c1e575bf4457a04243e9e0ef6f59 -msgid "" -"Now the scatter acts on a single step, but that step consists of two " -"steps so each step is performed in parallel." -msgstr "" - -#: ../../topics/workflows.md:522 6ac74585b69d4197a26c8230f53f75cb -msgid "Conditional Workflows" -msgstr "" - -#: ../../topics/workflows.md:524 f189ba0d5e7547d1a6540abde5c4da78 -msgid "" -"This workflow contains a conditional step and is executed based on the " -"input. This allows workflows to skip additional steps based on input " -"parameters given at the start of the program or by previous steps." -msgstr "" - -#: ../../topics/workflows.md:527 257301405fda4c6aa98195f4344b496d -msgid "`conditional-workflow.cwl`" -msgstr "" - -#: ../../topics/workflows.md:566 189ea6307a25445ca573ff93cd8c4f1d -msgid "" -"The first thing you'll notice is that this workflow is only compatible " -"for version 1.2 or greater of the CWL standards." -msgstr "" - -#: ../../topics/workflows.md:573 b0701c43575d4dc79c4abe2c932928c3 -msgid "" -"The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when`" -" is where the condition validation takes place. In this case only when " -"`in1` from the workflow contains a value `< 1` this step will be " -"executed." -msgstr "" - -#: ../../topics/workflows.md:587 7de691f8e339422e8b027297e3d16fa6 -msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" -" will pass the first conditional step and will therefore be executed and " -"is shown in the log by `INFO [step step1] start` whereas the second step " -"is skipped as indicated by `INFO [step step2] will be skipped`." -msgstr "" - -#: ../../topics/workflows.md:607 246e5e7c82aa48c9a7f5f2c3b7b4d707 -msgid "" -"When a value of 3 is given the first conditional step will not be " -"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." -msgstr "" - -#: ../../topics/workflows.md:627 b28362ad11bb44c9b7247f411e58caa4 -msgid "" -"If no conditions are met for example when using `--val 2` the workflow " -"will raise a permanentFail." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/topics/yaml-guide.po b/locales/en/LC_MESSAGES/topics/yaml-guide.po deleted file mode 100644 index 4b225c2e..00000000 --- a/locales/en/LC_MESSAGES/topics/yaml-guide.po +++ /dev/null @@ -1,193 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../topics/yaml-guide.md:1 153f05199ec24a5da81da49288e2679a -msgid "YAML Guide" -msgstr "" - -#: ../../topics/yaml-guide.md:6 95951c4a95d943c89be9252a898018d8 -msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers " -"and humans. This guide introduces the features of YAML that are relevant " -"when writing CWL descriptions and input parameter files." -msgstr "" - -#: ../../topics/yaml-guide.md:13 60a16d7722724500b0a31194b6958cea -msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" - -#: ../../topics/yaml-guide.md:16 61f0a8fcfa2044ada7761d35e6ee6bbb -msgid "Contents" -msgstr "" - -#: ../../topics/yaml-guide.md:18 3c5dd09c0fbc4079abff7f8ee9c1bd03 -msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "" - -#: ../../topics/yaml-guide.md:19 c7fa245866d0430fb8fcef9392869999 -msgid "[Comments](#comments)" -msgstr "" - -#: ../../topics/yaml-guide.md:20 dde5f9ad058445d1b0131ddf1fd80b74 -msgid "[Maps](#maps)" -msgstr "" - -#: ../../topics/yaml-guide.md:21 fdb88e5dafea4cb0876cea846eccca7d -msgid "[Arrays](#arrays)" -msgstr "" - -#: ../../topics/yaml-guide.md:22 f2ae9d617f274c7eb84a2d87c10a4cc5 -msgid "[JSON Style](#json-style)" -msgstr "" - -#: ../../topics/yaml-guide.md:24 47bffc9bb7b64047a25903eb42bde019 -msgid "Key-Value Pairs" -msgstr "" - -#: ../../topics/yaml-guide.md:26 283f64df8dcf4abc8f00ee515d0cc9bb -msgid "" -"Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the " -"`:` is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have " -"special meaning in the CWL specification and underscored key names " -"otherwise. For example:" -msgstr "" - -#: ../../topics/yaml-guide.md:42 51a3cd8bd6d2403daadc57d0091e99dc -msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, " -"`age_years`, and `home` - with their four respective values. Values can " -"be character strings, numeric (integer, floating point, or scientific " -"representation), Boolean (`true` or `false`), or more complex nested " -"types (see below)." -msgstr "" - -#: ../../topics/yaml-guide.md:51 7d58fe0504534589adfadf74e82de41a -msgid "" -"Values may be wrapped in quotation marks, but be aware that this may " -"change the way that they are interpreted i.e. `\"1234\"` will be treated " -"as a character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a" -" command: in CWL all parts of `baseCommand` must be strings so, if you " -"want to specify a fixed numeric value to a command, make sure that you " -"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." -msgstr "" - -#: ../../topics/yaml-guide.md:61 35e8c97a24344c7d9933f1910d6bd995 -msgid "Comments" -msgstr "" - -#: ../../topics/yaml-guide.md:63 5ba35d4bbb4644949c37993a77a50bf6 -msgid "" -"You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program " -"interpreting the YAML. For example:" -msgstr "" - -#: ../../topics/yaml-guide.md:76 e63546bf4b144bfba77767ec7248d63d -msgid "" -"If there is anything on the line before the comment, be sure to add at " -"least one space before the `#`!" -msgstr "" - -#: ../../topics/yaml-guide.md:79 25ac6edc52bd484cac8eb4fe4d5b6e1c -msgid "Maps" -msgstr "" - -#: ../../topics/yaml-guide.md:81 20e1be6499d9470fa74dde6da33f2120 -msgid "" -"When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, " -"these hierarchical structures are described in YAML by providing " -"additional key-value pairs as the value of any key. These pairs " -"(sometimes referred to as \"children\") are written on new lines under " -"the key to which they belong (the \"parent\"), and should be indented " -"with two spaces (⇥tab characters are not allowed). For example:" -msgstr "" - -#: ../../topics/yaml-guide.md:104 a99731edefb049299d313941156c41a6 -msgid "" -"The YAML above illustrates how to build up complex nested object " -"descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and " -"`inputBinding`, while one of these children, `inputBinding`, contains a " -"further two key-value pairs (`position` and `prefix`). See the " -"[Arrays](#arrays) section below for more information about providing " -"multiple values/key-value pairs for a single key. For comparison with the" -" example YAML above, here is a graphical representation of the `inputs` " -"object it describes." -msgstr "" - -#: ../../topics/yaml-guide.md:127 51d8ad7d937540ee88b46fc790319b4a -msgid "Arrays" -msgstr "" - -#: ../../topics/yaml-guide.md:129 bfeee0ef93e44a0ea50e3970e027b2f1 -msgid "" -"In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) " -"section above, more than one key-value pair can be mapped to a single " -"key. However, it is also possible to define multiple values for a key " -"without having to provide a unique key for each value. We can achieve " -"this with an _array_, where each value is defined on its own line and " -"preceded by `-`. For example:" -msgstr "" - -#: ../../topics/yaml-guide.md:146 297035119d42476e8dbebd1ed2241ac3 -msgid "and a more complex example combining maps and arrays:" -msgstr "" - -#: ../../topics/yaml-guide.md:167 563dd83823d745b6aebeb956fca51aa3 -msgid "JSON Style" -msgstr "" - -#: ../../topics/yaml-guide.md:169 7edbeea182fe4043be66f02bc5952114 -msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " -"arrays can also be defined in YAML using the native JSON syntax. For " -"example:" -msgstr "" - -#: ../../topics/yaml-guide.md:177 37ddb7add5ea4fde94c97ab2bd2c85e7 -msgid "and:" -msgstr "" - -#: ../../topics/yaml-guide.md:184 ed9f6a7d062c43f099b5181e2c930303 -msgid "" -"Native JSON can be useful in indicating where a field is intentionally " -"left empty (such as `[]` for an empty array), as well as where it makes " -"more sense for the values to be located on the same line (For example, " -"when providing option flags and their values in a shell command). " -"However, as the second example above shows, it can severely affect the " -"readability of a YAML file, and should be used sparingly." -msgstr "" - -#: ../../topics/yaml-guide.md:194 9cb613e445b5429196ced3d66fe95e45 -msgid "Reference" -msgstr "" - -#: ../../topics/yaml-guide.md:196 030fd9aede23463d981faf746e2b070f -msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" -" us while we wrote this guide, though it also covers features that are " -"not valid in CWL." -msgstr "" - diff --git a/locales/en/LC_MESSAGES/tutorials.po b/locales/en/LC_MESSAGES/tutorials.po deleted file mode 100644 index 5222f765..00000000 --- a/locales/en/LC_MESSAGES/tutorials.po +++ /dev/null @@ -1,58 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:15+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../tutorials.md:1 99ae22e436b042009833051fac79e2c9 -msgid "Tutorials" -msgstr "" - -#: ../../tutorials.md:5 2ffee614f02343cb94399b8199803149 -msgid "" -"This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to " -"the list." -msgstr "" - -#: ../../tutorials.md:7 1831288df8f14081b13cf52d587c678a -msgid "Beginner Tutorials" -msgstr "" - -#: ../../tutorials.md:9 bc1fd03f560340d68bdcf39455d25c8d -msgid "" -"[Introduction to Workflows with Common Workflow Language: For " -"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" -"tutorial/)" -msgstr "" - -#: ../../tutorials.md:11 47d068326ee34835a7a00ce7e24ef711 -msgid "Advanced Tutorials" -msgstr "" - -#: ../../tutorials.md:13 bcee717d8bf740c49c79200b0c660f3e -msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" - -#: ../../tutorials.md:15 5e55349fd3d749de964e8fcfca5959f3 -msgid "Bioinformatics Tutorials" -msgstr "" - -#: ../../tutorials.md:17 77245b1c0ebe437f89dc07b45c5fa95e -msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" - From 22702ace6c8a9c71c6bbbb4d83da8a8be4ca6d06 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Tue, 24 Jan 2023 18:59:04 +0100 Subject: [PATCH 031/179] Added translation using Weblate (Spanish) (#360) Co-authored-by: Michael Crusoe --- locales/es/LC_MESSAGES/index.po | 57 +++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 locales/es/LC_MESSAGES/index.po diff --git a/locales/es/LC_MESSAGES/index.po b/locales/es/LC_MESSAGES/index.po new file mode 100644 index 00000000..b87c1d09 --- /dev/null +++ b/locales/es/LC_MESSAGES/index.po @@ -0,0 +1,57 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: es\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/index.md:1 +#: a58ca61ccefc401588f91699bc98bd32 +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: 6dcf12053f104cb3a8d23ce8d4f90363 +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 1cc90206170d46119c5756f31a9e8799 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: b54801d84a944dadb4e4637551e3f7b9 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 860afd2eda4847e0a0d8834de3af4aa8 +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: d6046316c84b40ffb5478c90b2604911 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: c3c89ac756a74d9688e179b8718c9bf0 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: 0eb795062b484537b090c4d5c361f7f4 +msgid "Table of Contents" +msgstr "" From c2115d76e07c5015b508db18c19851f15010ea93 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 24 Jan 2023 19:48:24 +0100 Subject: [PATCH 032/179] collapse the translation references --- locales/LICENSE.pot | 36 +- .../what-is-cwl.pot => _includes.pot} | 4 +- locales/episodes.pot | 6 +- locales/faq.pot | 112 +- locales/index.pot | 18 +- locales/introduction.pot | 607 +++++ locales/introduction/basic-concepts.pot | 217 -- locales/introduction/index.pot | 27 - locales/introduction/prerequisites.pot | 257 -- locales/introduction/quick-start.pot | 167 -- locales/setup.pot | 6 +- locales/sphinx.pot | 6 +- locales/topics.pot | 2083 +++++++++++++++++ .../additional-arguments-and-parameters.pot | 62 - locales/topics/best-practices.pot | 137 -- locales/topics/command-line-tool.pot | 62 - locales/topics/creating-files-at-runtime.pot | 77 - locales/topics/custom-types.pot | 77 - locales/topics/environment-variables.pot | 42 - locales/topics/expression-tool.pot | 47 - locales/topics/expressions.pot | 373 --- locales/topics/file-formats.pot | 77 - locales/topics/index.pot | 22 - locales/topics/inputs.pot | 247 -- locales/topics/metadata-and-authorship.pot | 57 - locales/topics/operations.pot | 62 - locales/topics/outputs.pot | 134 -- locales/topics/parameter-references.pot | 278 --- locales/topics/requirements-and-hints.pot | 22 - .../specifying-software-requirements.pot | 42 - locales/topics/staging-input-files.pot | 42 - locales/topics/troubleshooting.pot | 72 - locales/topics/using-containers.pot | 82 - locales/topics/workflows.pot | 374 --- locales/topics/yaml-guide.pot | 157 -- locales/tutorials.pot | 18 +- src/conf.py | 2 +- 37 files changed, 2794 insertions(+), 3317 deletions(-) rename locales/{_includes/what-is-cwl.pot => _includes.pot} (91%) create mode 100644 locales/introduction.pot delete mode 100644 locales/introduction/basic-concepts.pot delete mode 100644 locales/introduction/index.pot delete mode 100644 locales/introduction/prerequisites.pot delete mode 100644 locales/introduction/quick-start.pot create mode 100644 locales/topics.pot delete mode 100644 locales/topics/additional-arguments-and-parameters.pot delete mode 100644 locales/topics/best-practices.pot delete mode 100644 locales/topics/command-line-tool.pot delete mode 100644 locales/topics/creating-files-at-runtime.pot delete mode 100644 locales/topics/custom-types.pot delete mode 100644 locales/topics/environment-variables.pot delete mode 100644 locales/topics/expression-tool.pot delete mode 100644 locales/topics/expressions.pot delete mode 100644 locales/topics/file-formats.pot delete mode 100644 locales/topics/index.pot delete mode 100644 locales/topics/inputs.pot delete mode 100644 locales/topics/metadata-and-authorship.pot delete mode 100644 locales/topics/operations.pot delete mode 100644 locales/topics/outputs.pot delete mode 100644 locales/topics/parameter-references.pot delete mode 100644 locales/topics/requirements-and-hints.pot delete mode 100644 locales/topics/specifying-software-requirements.pot delete mode 100644 locales/topics/staging-input-files.pot delete mode 100644 locales/topics/troubleshooting.pot delete mode 100644 locales/topics/using-containers.pot delete mode 100644 locales/topics/workflows.pot delete mode 100644 locales/topics/yaml-guide.pot diff --git a/locales/LICENSE.pot b/locales/LICENSE.pot index 0460a73e..67ae058a 100644 --- a/locales/LICENSE.pot +++ b/locales/LICENSE.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,86 +17,86 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../LICENSE.md:2 -#: 3d749a78eb3e47c991d603c2cabd1b91 +#: 087fa59ef53947e683e1b0d1097cfa14 msgid "Licenses" msgstr "" #: ../../LICENSE.md:4 -#: 4689ade8475a4c8a9d5e325f072c1392 +#: e134424e12c14d46a8cfa417dbb39dbf msgid "Instructional Material" msgstr "" #: ../../LICENSE.md:6 -#: ef8ec0f072d947fbba997c4b2191abc2 +#: 44fc3047733e40408793ef3438e4a21c msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." msgstr "" #: ../../LICENSE.md:12 -#: 696f3824ca814c9eb314abae51be8202 +#: b2a65a97826d48aa859843a1dbe646a0 msgid "You are free:" msgstr "" #: ../../LICENSE.md:14 -#: 72ebe92edf58434e9d7a4fc6bddf8880 +#: 922b2a5bc70b49e299d0662622aca1b2 msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" #: ../../LICENSE.md:15 -#: 9b403f96d4194ffaab3f309d7d12f360 +#: 51700e62261a4a20a887c6c5ef4d3f46 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "" #: ../../LICENSE.md:17 -#: 10b1befd0f834d79880c8aeb70b595d4 +#: f84b26c1e38e46d79fa6b5cdcc7c6434 msgid "for any purpose, even commercially." msgstr "" #: ../../LICENSE.md:19 -#: 9017d0b760bb4370926d511b97a604c6 +#: 435cf52ad40643139c4eaec84b263132 msgid "The licensor cannot revoke these freedoms as long as you follow the license terms." msgstr "" #: ../../LICENSE.md:22 -#: 1faadcaead6748dfb34886e5819af9b9 +#: 4eeaef6ed7304ea8ad815fb8b35f374c msgid "Under the following terms:" msgstr "" #: ../../LICENSE.md:24 -#: 7a49ed3a728349c9b486f3d0b1dbf577 +#: 9295c98517134bc0b8b08e088ad630fb msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" #: ../../LICENSE.md:32 -#: 57da6294edce46eab00e7d15e6f6d4fa +#: c07512980b6a4433944edf2e80a88c6c msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" #: ../../LICENSE.md:36 -#: 8fc8a30cd63c4a0a9d8ba1b913687029 +#: 6a4d80c1331c470facd6ccc060a0cd94 msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." msgstr "" #: ../../LICENSE.md:39 -#: fe59e74a4d024831a6d5cbcfd3e4ee38 +#: d00d862c37ef4371bc40ad101c433199 msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" #: ../../LICENSE.md:44 -#: 3ea41d5a14ad46729cabb387a33814b0 +#: 93ba22a55b954a86af163557e05c52a4 msgid "Software" msgstr "" #: ../../LICENSE.md:46 -#: 23751e2552ff450c83e3dd255da56dac +#: 367e01c9a6ad426a83bf5f5374e6a8ab msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" #: ../../LICENSE.md:51 -#: 13fb5eb48a8a434e95dbbb717ccaef8a +#: 565193677802418693fdbc123b34dd2b msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" #: ../../LICENSE.md:57 -#: e262fbd0e7de4f148f31afe39d1cb9e9 +#: a4a99fc7709a49c29482f6e992d9e2bc msgid "Trademark" msgstr "" diff --git a/locales/_includes/what-is-cwl.pot b/locales/_includes.pot similarity index 91% rename from locales/_includes/what-is-cwl.pot rename to locales/_includes.pot index 22d33219..41cc9fb0 100644 --- a/locales/_includes/what-is-cwl.pot +++ b/locales/_includes.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,6 +17,6 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/_includes/what-is-cwl.md:1 -#: 44a9467c5d3b4a128ceade82a521b6da +#: 46f474e1b364495181698bd13ce28a1e msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." msgstr "" diff --git a/locales/episodes.pot b/locales/episodes.pot index 8a04d6ae..ecff4e32 100644 --- a/locales/episodes.pot +++ b/locales/episodes.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,11 +17,11 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/episodes.md:5 -#: 0cbb5e7334a647c3bcae7333ec3ced90 +#: 5b500989fc13480681ecb39954c13fd7 msgid "This page has moved" msgstr "" #: ../../src/episodes.md:9 -#: fabb221482cb4ac0a98bbe10943ed025 +#: ff7a3cc03e2048278bcb9af2429b8dee msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." msgstr "" diff --git a/locales/faq.pot b/locales/faq.pot index 7a9282b8..f4ead324 100644 --- a/locales/faq.pot +++ b/locales/faq.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,276 +17,276 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/faq.md:1 -#: 5daa5afac36f46dd8329e5629056384c +#: 38d96ecb6f4f4835a94fce7389f64290 msgid "FAQ" msgstr "" #: ../../src/faq.md:11 -#: 40c8efda3caf4c6089bda3027c522f37 +#: cf04e2bcede444ec84829b20873bb458 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" #: ../../src/faq.md:41 -#: ee854bcb685941cab45ae7f33b0efe48 +#: 7f5a8ebf64a6457290031a9878fcadb4 msgid "Rename an Input File" msgstr "" #: ../../src/faq.md:43 -#: a4cdd5ab6fe341a3ad3e3055556d96c3 +#: d2da25aa3d4149c6a839e5a9d260d637 msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." msgstr "" #: ../../src/faq.md:59 -#: d1f359d47f124dfab23a75b196cd5884 +#: bb7a7c1994c44fd984a3d6daee56ca77 msgid "Rename an Output File" msgstr "" #: ../../src/faq.md:61 -#: d83ced40605e411c92c4ae38761d7ffa +#: ab649294dceb4701b50840614da498e9 msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" msgstr "" #: ../../src/faq.md:82 -#: bc8997df2e6746cebc2068534f30ee82 +#: 38a2bfda017f48af91062768c29228d6 msgid "Referencing a Local Script" msgstr "" #: ../../src/faq.md:84 -#: 20b6ae57e1cf4410877a60fb3ef87264 +#: 73d6982c5a414307943c5100df766a29 msgid "There are two ways to reference a local script:" msgstr "" #: ../../src/faq.md:86 -#: 73c66b809e9a4218b624338ccb88a05e +#: 81acda6459354bf08b4f1454b3b2dcc4 msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." msgstr "" #: ../../src/faq.md:89 -#: 9be72b7d5d604526b125b63148e99320 +#: c06ed26bc9d54aa2803014ba69e9ac78 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" #: ../../src/faq.md:95 -#: fd96d178901545008a43fa99e3aa6cf3 +#: eb25e79af23e4104b38f6265e677c6a8 msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" msgstr "" #: ../../src/faq.md:97 -#: db58a582e66244468f4d31e9213933d1 +#: b618a3759865456f9ceb02a6a16ccba1 msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." msgstr "" #: ../../src/faq.md:104 -#: 3e70f0da5cd7460b90c1690366f40820 +#: 455b1a1f10044b5c98b7fab451f48ed5 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" #: ../../src/faq.md:113 -#: db28dc27c82b4b29a7a9a768550bba9b +#: 6b44a7665da14b6aa887224b2fe3c15f msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." msgstr "" #: ../../src/faq.md:115 -#: 4474b16fb3fd4cdc85da931159804967 +#: a05b7978ef76413588e211bd9bf9250c msgid "The second method involves including an input of `type: File` in the script itself:" msgstr "" #: ../../src/faq.md:135 -#: 23c9b2e21cec4ee8ade087e6630f62c2 +#: 6caf0ac2ccad4e449dfe5578ff75ec0e msgid "In CWL, everything must be directly stated." msgstr "" #: ../../src/faq.md:138 -#: c01309dcd65c4f1080c396e6a9efb75d +#: ffe1586183ab4a3199639b1f9e8062c1 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" #: ../../src/faq.md:140 -#: 0a36801172fd4e24a04b3ba85cf74e29 +#: a8314e810d564e198e9fad0e32c23117 msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." msgstr "" #: ../../src/faq.md:165 -#: 433e788ba01141e98ea5a9e73ef71e6f +#: 77c15e3d59c74848b3b6ad85f213b30c msgid "Model a \"one-or-the-other\" Parameter" msgstr "" #: ../../src/faq.md:167 -#: b6de2761ce454992904775a06b7ba326 +#: f3d50a6a37494ce9883a4d9cd0ce7870 msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." msgstr "" #: ../../src/faq.md:188 -#: e36c2d53e8ba40f4a602b489a6688e24 +#: 9d7e8ab5d8864376814d12f10b52c6a4 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" #: ../../src/faq.md:190 -#: a9310166cb514e4e8824bba7fcfcb277 +#: 93b78d5afe4541eaba53b6ea29150658 msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/faq.md:194 -#: f6144f77152e4284963951abaa30adb2 +#: 8bfb650cce844e31a30a6e1773d92a48 msgid "merge_nested" msgstr "" #: ../../src/faq.md:196 -#: 790709dfc2854e4a89fcc4769f84b0f4 +#: 0624c44a35e944c2b463146331c9ba4d msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." msgstr "" #: ../../src/faq.md:199 -#: 438789c8def549d1b4b8a187d5acc48e +#: 1f4df1cd685e4bd5a695e7ace5a9159d msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" #: ../../src/faq.md:201 -#: 23ede7dfd5c84492baee1d5bbb9a91d9 +#: 1f057777e7a9430bbbc2036e53a6e4fb msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." msgstr "" #: ../../src/faq.md:229 -#: 37c0474e48164160b23c4094d583d2d3 +#: f64dbbcaac5642cebbd7cbd96d85c40d msgid "Optional Inputs 💯" msgstr "" #: ../../src/faq.md:231 -#: 3b2be0a4a87041b7a5bda20c6df2ffc8 +#: 71f80d93e08342ad8b6db87ec9c837cf msgid "To make an input parameter optional, add a question mark to the type declaration." msgstr "" #: ../../src/faq.md:247 -#: 886300d2dcff4861aae503d34b0bee44 +#: 7dec6a02cc364c8a9723043a3e8b7d79 msgid "" msgstr "" #: ../../src/faq.md:248 -#: fe393ecdff25428da6cbcd30171c7811 +#: 8a06fc5a9f80481888418234671702cd msgid "Enum Inputs ⚜️" msgstr "" #: ../../src/faq.md:250 -#: ebfd4991d917413b858da8b437a55805 +#: 2f3dc891f5b64378abc449947a5117cc msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" msgstr "" #: ../../src/faq.md:267 -#: 2919ff4f51254e69aea40146e2d911f1 +#: b5324b01d6614202b0fac7026a450caa msgid "" msgstr "" #: ../../src/faq.md:268 -#: 61ed4e87457c41eea31f51740557597e +#: 1198ce319b4847f8b74a14d2ec5248d5 msgid "Record Inputs 📀" msgstr "" #: ../../src/faq.md:270 -#: 1e6624104b024eb092682cd0dd0f6a3c +#: d9e2a621f8ae455092120ebb711d1f99 msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." msgstr "" #: ../../src/faq.md:322 -#: b741b8333e104feaa6d1f41fd4476304 +#: 2c4153eb18d94ad7bbad6acab1b5b61a msgid "Setting Mutually Exclusive Parameters" msgstr "" #: ../../src/faq.md:324 -#: 334673ae870a4dada817857f3a49326e +#: 77b90349be254ceb8de2cf58aa410e6d msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." msgstr "" #: ../../src/faq.md:342 -#: 362f85270df04712b2e2f21c7019e3cb +#: 31e2b62687b84efda4924d7108e23cb3 msgid "Setting Booleans" msgstr "" #: ../../src/faq.md:344 -#: ad6997f24c7c42fe965b5d7bfd1e633e +#: 8c72738f5aaa4fcd8457a10e799d0e8d msgid "These can be set by using the default field" msgstr "" #: ../../src/faq.md:349 -#: 99dce9d60b6a4f99bc39899b7c8c10ef +#: 3a83df07178945d4822e3520674d6308 msgid "Concatenating Strings in Inputs" msgstr "" #: ../../src/faq.md:351 -#: 6b68fe24cbf64624b49ea56fce2eecad +#: 2aca2690fdac4922bfdc9e5a9f2741b8 msgid "The valueFrom field must be used instead of default." msgstr "" #: ../../src/faq.md:359 -#: d23326837eb74e7faf1f54e25f8309c4 +#: 3d072aa6b914445ca8326ffe260b4e35 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" #: ../../src/faq.md:361 -#: 2e2eabe92670412e95474b25ad9cda4c +#: fb653b6af6a74231904d2d0f850d1116 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" #: ../../src/faq.md:363 -#: 81f9308adbee4a3c9e585b8e0f0c4844 +#: d3d261dd88a94fa8ae8bf65c39eef6a1 msgid "For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" #: ../../src/faq.md:371 -#: a5d3ed6cac28415288e7fc7fbfc6e8a6 +#: f7125b78a28c4924bdd3fcb37a184ff6 msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." msgstr "" #: ../../src/faq.md:373 -#: 72f9692803304daf9f846e2b90139660 +#: dc28c1a8e15b4499b4af492ac3cd2c1e msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 -#: a7eb20c817704811b3bcf2f94ec2e51d +#: db57566297534dea82c6f66dd9c14b51 msgid "If `cwltool --validate` returns valid" msgstr "" #: ../../src/faq.md:384 -#: 20fa869849ef4b358a11db46111017de +#: 09a115ecb8d2487da88cd31e1bac337f msgid "But executing it causes an error like:" msgstr "" #: ../../src/faq.md:396 -#: 35032fcd9f23403ca006d62a7d6e7be7 +#: 4537ae8ebd5c49f3857b2cbe81032d29 msgid "The file is here" msgstr "" #: ../../src/faq.md:410 -#: f6d6a4e3691446378c8fb01a2d19f8ad +#: d31aa1c1adf343e8b2b71322511bf7f1 msgid "Problem caused by `-` (hyphen character)." msgstr "" #: ../../src/faq.md:423 -#: 44608fed1048458e999e13b014327e7e +#: 096f725de9ee4c558d72695a84c40cbb msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" #: ../../src/faq.md:436 -#: 96ede8a8f1f34786aabd4004bf2e7acc +#: 58316efc7814473383abb738c5c0b5ef msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" msgstr "" #: ../../src/faq.md:442 -#: 84634a368e704e8d828678785c784595 +#: 2ac3f24fd4074acb8e96542b350d5771 msgid "Use CWL and cwltool with Singularity" msgstr "" #: ../../src/faq.md:445 -#: 545c4db9c24f42ee946081254d9ca7a8 +#: ef3c267c3282458f891a76e5d467ec8e msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." msgstr "" #: ../../src/faq.md:450 -#: 1c1e6d583d5646a8a5c9316dcd743d9f +#: aa97ef90186747f7b9d0aaccf17535d1 msgid "Debug JavaScript Expressions" msgstr "" #: ../../src/faq.md:452 -#: cf7d336d444e4f59aa83585b7abb1fe5 +#: bb5bc05d377d441abe02a09e3f1d1a03 msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" diff --git a/locales/index.pot b/locales/index.pot index 1d9fcd30..9000da74 100644 --- a/locales/index.pot +++ b/locales/index.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,41 +17,41 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/index.md:1 -#: a58ca61ccefc401588f91699bc98bd32 +#: 1e479cad716c478689be58d4b4aabd82 msgid "Common Workflow Language User Guide" msgstr "" #: ../../src/index.md:3 -#: 6dcf12053f104cb3a8d23ce8d4f90363 +#: 0afc69049ce0403695a03e30416fd9f9 msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." msgstr "" #: ../../src/index.md:7 -#: 1cc90206170d46119c5756f31a9e8799 +#: 852b4bfd1a374deb803accb90c7fea8c msgid "Contributions and Feedback are Welcome!" msgstr "" #: ../../src/index.md:9 -#: b54801d84a944dadb4e4637551e3f7b9 +#: d702011b81064e65af1fcbd230d9977e msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" #: ../../src/index.md:16 -#: 860afd2eda4847e0a0d8834de3af4aa8 +#: 884f157b64ce4787ab8da8f9e674c233 msgid "Navigating the User Guide" msgstr "" #: ../../src/index.md:18 -#: d6046316c84b40ffb5478c90b2604911 +#: fd0133a1a0214ef49b763ba33e282a9e msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." msgstr "" #: ../../src/index.md:23 -#: c3c89ac756a74d9688e179b8718c9bf0 +#: e699c33ef40045528c31d74b2d797742 msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." msgstr "" #: ../../src/index.md:28 -#: 0eb795062b484537b090c4d5c361f7f4 +#: 21aacf872e7a444c891c41ca3411ee06 msgid "Table of Contents" msgstr "" diff --git a/locales/introduction.pot b/locales/introduction.pot new file mode 100644 index 00000000..32cc94f9 --- /dev/null +++ b/locales/introduction.pot @@ -0,0 +1,607 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/introduction/basic-concepts.md:1 +#: 92c85569d9e746d8a5b7a5e8f9773545 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: 5e501be2f49044c9897f6e8d65186abb +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: a6f5f188f9af4b608b8401996a558e83 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:2 +#: 2ecb1a3a4c7546ba94e560924cfb09a8 +#: 3c0da8bd74824f8b88223c2a9dcc6ec2 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: 7fb9ad094d844047b0d35dc70c295400 +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 303d1a15612846c1b60a4d651f9d1d4a +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: c84c4bde07034846b043c4f281f8e00c +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: d774877d6e4447b7b83d56ebbaf09e96 +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: e8884f39f08c41bab29c4284077fd860 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: 984ac8cee64e4e41957d8c5a4aff0cfd +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 17381e8872414c49b178d91ace2e3e82 +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: c4cdbf2a42644e0eb4eb74512388e9f7 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 7d994284e320413bb8dbb2a42cd16a4e +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: ce92487ca4e3495ebd0693c502773626 +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 0ce512c3cd744652b5feb2d8dcfdb613 +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: dd7d6a1399b04923b25df70abb1becf5 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: ce4c76b46531416bb4006a9c01f45a23 +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 0256a343321447559471d731c86d3546 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: e1235589f24942babe54adaae4f169af +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 81baaa297562452f80afe68657c8099d +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: 0c8bbd88bd8c4c71b19011812e7487c3 +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 3b64da1f14964cea9e5cbf8376578789 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: bf33807babb64befab3385eca4c92131 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: afdb75d374624f4798f358a3dfe7752e +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: bc28744d5fa644218ef55672d726307f +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 24ffb5bfa767424585b6b6c93169de93 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: bd53afe50cc14f2ca428adddb0e60dc9 +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: 35c98c4b352c4f9bb9572c740894dc57 +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: f7fb57fdf9344a7eb0f334aca8d3e85f +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 0dc6a8f19fda4e9eaa80b8e1bd1fc5be +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: ff1224487c35402d8afee6da3803e19b +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 63c2dd9aaec54df088e82febfd7bc49c +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 18f310d11c9b48b4a447b6662446cd3e +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: a3922283fdce4f99832c816626d5f098 +#: 19245373c2e84793a72462b7d2fa1c34 +#: 7c3ea7150c7d41fead10ddf2a6205ec8 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: cf39d3563e344ad9b31d5268c4069972 +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 97b0113a847044b98f79b5e00941f4c3 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 8cf4edbb4b344ac7b3eae86ed52beff8 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: c1dfc170fdf54c9e846539a5170f204f +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: 778babbcfb2648a1ad7a7ad8f80653a8 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: 23abed59f5d44bfb96e8fa13aa213b83 +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: ee93304de4e447c1bd5626e72b99b6fe +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: a79f07e33fc5437c9fa204111d0290d8 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: 3cf08b553a814478b4b2c6c84ebe354e +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 98751950a97f44fdb16e826fece810fb +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: eac153b881fa47ab8bb08074dad8eed2 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: 806ff7b185d74538a9b0e20c6ad84ffe +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: 1f9573b6cd45479bae2481a251132d53 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: c3995fd5588741148e3b2c91ca011ca9 +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: 8a67b172ce524aa09858acd9d1a62762 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: a567e0f952bc46be8b82d0a357f2c209 +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: 21d3bb850bb14fdcb6d4c4a15c9966b6 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 62cbb29459b24e9fa83c7cd7994bdf12 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: aaa319d4446c41ba82bf925f29f7d9dd +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: c49938a0100a4850b67d067a61304d01 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 91e986d0c1f44d7f9c3b32366160da6a +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 301c5a3baaaf46bb81bdc25b53a31f23 +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: 1664589ced314daebfb163e6424f220f +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 1223fecd61f34ad98ebbb7e45eaf4ac7 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 242c496599d84a64959db275ee1e212e +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 9b749d47f48341cb9ac8cd14098e6c47 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: e8ec351d7b79447bb15f4d4518b8de87 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: 58d5613243914dc8bc4ce88676525783 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 731a6c30786f43d88160f9642cbb05d2 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: ca2088eb9565429dbc1ce0b28b2ef1fb +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 5ac9c6bfb50b48878aff52f1194e53c4 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: b8d0c12ff07f4269bba87cd653803345 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 83780c1b43f744b4ae87a917b26293f5 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 2919320c41e94930a0aa9bc6aacb5a87 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b8e799c075214d539aa0a7c04dbc33c0 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: ccbd51a29ca841efb74c5e0a25d1eb87 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 5f3330c1e15a402781c3325f9d3dc779 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: 314fbc9f866a405b86e7bd704781dea1 +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 9434e3680aa9487fab9ddb782c6ff3d0 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: 2ce0bda38d814b248a2c23ebc26bf462 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 105c3be6f5f34f4388b9999603275bb5 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: bd378c8483a14c93b5fe00d76e5b0a06 +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 5ace5416560247c7a3304c41caa000c6 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: 5d7a175b3c5a4f888daf037672211d61 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: 4e0c0c345527412eaf70e8efe67fab8f +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 6dd8379682824d1397c48ac10db4b894 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 57691f7bd87741d68f4e1a963da91654 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: 13a4d71f127b4bd09c12a37752d27c8b +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: a574ed30000541b2816fbfe66b32c314 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 9bb9c9052ad14c7c9fc0275c8f1b651b +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 5afcf2e79ceb424ea0a570797a712321 +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: cc5b91b8c5b14a40bdd09d3bd45fe9bb +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: d5e36c7827334fc69498459db5137d30 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 39d3eff64d004a0f8257d61f2a90b186 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 19946d0d9a6f42d487537273225b91cd +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: 66048204601a439d8245455c48b08826 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: dcc41d0ce48e42a0ba209ca1fa37220a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: e2ebe32f12b74608b35217cea30cd0e0 +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: 37a4f461b82f4e48948c5eab400b14a5 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 371c6801e92448f9875fff60a509f509 +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: e3fb51cd196542008cb16458fdef7c1f +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: d00cd96d47c6450a8c0955765eff9ac1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: e06fdf0744344d0193b99791b9b94c7d +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: 6e2191fbb8794f83a51897028a2e50f7 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 931b6b49a46d4d5581a05446ac2e9a7d +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: 5cb281f4d0ea4163af0f7203c150345e +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: 4e6c4c2b6bae49a2b2d93bc95538c7b9 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: b37ba76e0dd940559e13543ea241376e +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: 22d7ac26f2ca41b2aa141fd4774b6f5c +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 15033ad0574d46b2951bb2121c80c462 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 2b2fc79461674b9ebdef49750f7fb319 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 8b11c9920b97427aa2d29498664e24bb +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: d11de6ee015f46c991fbc8b48cd1fb60 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: 71adfebd042a4820ac533a2e6e07c0ca +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: 8f199e6778a84ba68d385b42169f6b26 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: 28ec66afdad24dfd871ef1a2686f9976 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: cccb84844ce0453cb77ce3db65ffbc1b +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 0c5a431846f241829975552ef8dd9c32 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 8e383a7ea5b54c56adb9cb0c6ed6c179 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 98473d00529345d4989f0f5d2101da1b +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: d105326cb76b455d907c283a509f038c +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d4d00a573e36474f9c915563d4ea8709 +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: aa8195d109974f9da3b9da97479525cb +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" diff --git a/locales/introduction/basic-concepts.pot b/locales/introduction/basic-concepts.pot deleted file mode 100644 index ceeed500..00000000 --- a/locales/introduction/basic-concepts.pot +++ /dev/null @@ -1,217 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/introduction/basic-concepts.md:1 -#: 570f94ae2d4d4e19a9cf3a9bbceba835 -msgid "Basic Concepts" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:3 -#: 67f2ebceccce441caa8279166f8f901d -msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:10 -#: b7c949f867b8475f8969622abc045729 -msgid "The CWL Specification" -msgstr "" - -#: ../../src/_includes/what-is-cwl.md:2 -#: 744c9501df5d47dc93962d217838f312 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:21 -#: 0a0131d9b3be4af484b43fb3d12f804e -msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:25 -#: 6c2f26b24ece4319bc9ecbd147f928e0 -msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:33 -#: 0305e3bc2de04b15a64a1b1c1188da2a -msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:37 -#: 21d7e31a2abf4d36ba5acef1faa76b97 -msgid "Implementations" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:39 -#: 1c7e942576304977954be9ddcc9b2927 -msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:44 -#: 920cf7f770054d87807273e8901630b4 -msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:51 -#: a4c286729d884042aa9f6703ae958896 -msgid "CWL specification, implementations, and other tools." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:105 -#: ea9dc3c2e83246508ee111cbeb5e5379 -msgid "Processes and Requirements" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:107 -#: c40f991cf70a4eefbf5b04e4089f809d -msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:112 -#: b3a1d362a96b426992cc37c11e13e09f -msgid "A command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:113 -#: 201d5104011e4178adf564f969e45951 -msgid "An expression tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:114 -#: d2027b38193f4252908c9f1fa8a1999e -msgid "An operation." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:115 -#: df6be4b832ac4bbe9ef1eb5fc8cfc1ec -msgid "A workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:118 -#: 521eb59a379444afa0478b4536923f28 -msgid "The processing units available in the CWL objects model." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:119 -#: b600a21001d24203855b9d972365de5d -msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:122 -#: 60b8285020a34af9b8a22688953899e6 -msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:127 -#: aac2f76a1da1470cab9ff221c35134a3 -msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:131 -#: 1adb2eda9c8a4e2493872e33a13bb77a -msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:137 -#: 08847ed6cc8d4b76b23fe54117ecd929 -msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:141 -#: d5fa5caa377e4cac9cb9736d54ee312b -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:142 -#: f1c84c485ad9400aa80dd46eb5c75241 -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:143 -#: 500a1a4565f24639ba5e248c382b2c45 -msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:145 -#: 1b407a21568b4c4da8a90d3eb33611b6 -msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:151 -#: d715b520274949bf9f9e3e7235f6d3f6 -msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:155 -#: 5c18ffe7e7254167a02be50ebab5e285 -msgid "FAIR Workflows" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:157 -#: b9cdc830853f45bab2876305373f35b8 -msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:167 -#: 6d839e88664f41f0b5d01d38053ede18 -msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:171 -#: 3e4b846a939a43929c4a45af1a7eafe8 -msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:176 -#: b19094f1044648718b9fdea72eda8994 -msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:178 -#: 33191f1525334cc398892bb867135b42 -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:180 -#: 6fe0b86d8a3b4bb0ac1f075fbac8988c -msgid "Semantic Versioning - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:181 -#: b206be2c6a5043429a1213b2989a0f53 -msgid "The CWL Specification page in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:182 -#: f45e3dc2b0a74948a0977c47aab8db4a -msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:183 -#: afaa1ed8a0b949959992d4f4d7e00356 -msgid "The list of Implementations in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:184 -#: 51073c8b56864cca84600f12048a6036 -msgid "PROV-O: The PROV Ontology - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:185 -#: 1215f39220b441a79f56cfe7cd61aa92 -msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." -msgstr "" diff --git a/locales/introduction/index.pot b/locales/introduction/index.pot deleted file mode 100644 index f4ae1f30..00000000 --- a/locales/introduction/index.pot +++ /dev/null @@ -1,27 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/introduction/index.md:1 -#: 6c33d560fcc64807a04e7a1536b1032a -msgid "Introduction" -msgstr "" - -#: ../../src/introduction/index.md:3 -#: ad616e9a47d14c5bb4532e5266d61ff5 -msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." -msgstr "" diff --git a/locales/introduction/prerequisites.pot b/locales/introduction/prerequisites.pot deleted file mode 100644 index 519e8ca7..00000000 --- a/locales/introduction/prerequisites.pot +++ /dev/null @@ -1,257 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/introduction/prerequisites.md:1 -#: 789e7b95b23d4bdb8398d691587613ee -msgid "Prerequisites" -msgstr "" - -#: ../../src/introduction/prerequisites.md:6 -#: 53432372af8c447cbeb5f05892daee72 -msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:12 -#: 36f42adbc26f42a891d996f8b9730589 -msgid "CWL Implementations" -msgstr "" - -#: ../../src/introduction/prerequisites.md:14 -#: 090df41a03204aac91aa7f663c6a5209 -msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:19 -#: 57ad125f7c2e4f01982acbabb1ff3d80 -msgid "Operating System" -msgstr "" - -#: ../../src/introduction/prerequisites.md:21 -#: edfd6bf214d042feb6662b1c2d2fa48e -msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:24 -#: a44cd70295f5442fb6651d85794528ba -msgid "Linux" -msgstr "" - -#: ../../src/introduction/prerequisites.md:25 -#: df31f7835d544160be90401bd20993a3 -msgid "macOS" -msgstr "" - -#: ../../src/introduction/prerequisites.md:26 -#: f5e9ef0126f74353bc4c30a6e92bd92a -msgid "Windows" -msgstr "" - -#: ../../src/introduction/prerequisites.md:29 -#: d11b1c901d004a10a7b8cda2e727bae9 -msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:35 -#: 37e363cb5987436d86e5725a63984e5c -msgid "CWL Runner" -msgstr "" - -#: ../../src/introduction/prerequisites.md:41 -#: 1a19bd057d3c48679e2ae844c6b8291a -msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/prerequisites.md:46 -#: 2a18beeff42d4cf8a4315e4a171cdede -msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:51 -#: 17f353c8e861492d91e51b78b5da3351 -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:62 -#: 5f178532a9004163b795c1433248eb77 -msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:65 -#: d2ff1f8e720f4bd49912ccd7040f2ccc -msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:67 -#: 77e4e1e5b4764d59a990b43ed93a7459 -msgid "`true.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:73 -#: 22b4c40f082d4bacac051617b617cbae -msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:79 -#: 7f97cf170a854ce685bae8f30a16572b -msgid "Validating `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:84 -#: 11fdbc38c5ed45a4976e16844729a3cd -msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:86 -#: c513823812a5423da694e85a20f86506 -msgid "Running `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:91 -#: 7be568d02d7e4593a1c0ef719d0f83ac -msgid "Cwl-runner Python Module" -msgstr "" - -#: ../../src/introduction/prerequisites.md:93 -#: 36ee569c74ac4602a51818a92c95f031 -msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." -msgstr "" - -#: ../../src/introduction/prerequisites.md:101 -#: 06defabc17634ceea15e1f4523164a23 -msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:104 -#: ac847d3d1587499ea6e1b3796e16282c -msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:111 -#: a4d5291859bb415b981a7dd6dff3c313 -msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:115 -#: d80356bf607b4f7d9572b925c69163f1 -msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:120 -#: 54ddcf5f932c40c4bbec2f88114e6e20 -msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:125 -#: f159836854c14187929cf24f716ccee0 -msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:129 -#: 728b24fff1f14726b27168dbf46e4e7b -msgid "`true_shebang.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:135 -#: 5590cd84de1c4f9382ab37644a5adac7 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:137 -#: 5a066c4dcd034cfd8902ae01128134c5 -msgid "Making `true.cwl` executable." -msgstr "" - -#: ../../src/introduction/prerequisites.md:144 -#: 846f1eaf4f81477c84b885f7c17ab030 -msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." -msgstr "" - -#: ../../src/introduction/prerequisites.md:148 -#: a972f3ea3b5f41f6b78f682a42616197 -msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" - -#: ../../src/introduction/prerequisites.md:154 -#: 3165d673bd7341518d2b259932917b53 -msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," -msgstr "" - -#: ../../src/introduction/prerequisites.md:161 -#: d23de68e21e1429886b3814af9cc3104 -msgid "Text Editor" -msgstr "" - -#: ../../src/introduction/prerequisites.md:163 -#: 9538d8b0944f4e72bceec9ebf1fb5832 -msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." -msgstr "" - -#: ../../src/introduction/prerequisites.md:167 -#: 2e710620d21f44a0a036431453ed5e20 -msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:171 -#: 25c6c7a87e1847f9aec1c32cbc83cf4c -msgid "Visual Studio Code with the Benten (CWL) plugin - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:172 -#: a90b90e926324cd687a29436e82eef38 -msgid "cwl-plugin for IntelliJ - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:174 -#: 91a2b9d7d7b642c2904bd55d29690254 -msgid "The CWL community also maintains a list of editors and viewers: " -msgstr "" - -#: ../../src/introduction/prerequisites.md:177 -#: e0cdb48ef04846cd9a39008260b18777 -msgid "Docker" -msgstr "" - -#: ../../src/introduction/prerequisites.md:181 -#: ac55bc8b751d440086043c4af6776d10 -msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." -msgstr "" - -#: ../../src/introduction/prerequisites.md:185 -#: be04aba59f3c40f1aa90316090792441 -msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." -msgstr "" - -#: ../../src/introduction/prerequisites.md:191 -#: 2d4790bd46124cd8be789927c25fbbbd -msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." -msgstr "" - -#: ../../src/introduction/prerequisites.md:196 -#: af2e128598294dee9330002a2f7bfc63 -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/prerequisites.md:198 -#: f4ffd0d89ef1406f9e957a05a4172c57 -msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." -msgstr "" - -#: ../../src/introduction/prerequisites.md:199 -#: 00fa0dd045054fcbbe3322e10e591430 -msgid "The Python `venv` module: " -msgstr "" diff --git a/locales/introduction/quick-start.pot b/locales/introduction/quick-start.pot deleted file mode 100644 index 62c7c9fc..00000000 --- a/locales/introduction/quick-start.pot +++ /dev/null @@ -1,167 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/introduction/quick-start.md:1 -#: 1f7df6c4ef354b4284ffca2f01ba7a40 -msgid "Quick Start" -msgstr "" - -#: ../../src/introduction/quick-start.md:3 -#: 98a2ea8175314bf5b6fbdd2464402c82 -msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." -msgstr "" - -#: ../../src/introduction/quick-start.md:7 -#: 924b8fd198fc487f87a8de4948261bee -msgid "“Hello World”" -msgstr "" - -#: ../../src/_includes/what-is-cwl.md:2 -#: 1d89d9d6798a4e38adc28680ceec1a29 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../src/introduction/quick-start.md:12 -#: ca24ba5ebb324a90b34fb1b28468fbcf -msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:16 -#: 7a3bbeb141914c0daee451f2bca9a081 -msgid "`hello_world.cwl`" -msgstr "" - -#: ../../src/introduction/quick-start.md:22 -#: cdd3578d507d41539c38a601701e8854 -msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." -msgstr "" - -#: ../../src/introduction/quick-start.md:27 -#: 767cf30acc9d4f81b8d34bfc90a8891c -msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." -msgstr "" - -#: ../../src/introduction/quick-start.md:32 -#: 8acd83b581f2499fb640153186711660 -msgid "Installing a CWL Runner" -msgstr "" - -#: ../../src/introduction/quick-start.md:34 -#: 46d1f843730a4c848a327de9a03c04e2 -msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:39 -#: 939e54e81c304d21a4eb33f99407ee50 -msgid "Installing `cwltool` with `pip`." -msgstr "" - -#: ../../src/introduction/quick-start.md:47 -#: 4db304a983cb46fe917563a1884659cd -msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." -msgstr "" - -#: ../../src/introduction/quick-start.md:51 -#: 72d657288bf248b6a53080e6295302e3 -msgid "Running \"Hello World\"" -msgstr "" - -#: ../../src/introduction/quick-start.md:53 -#: a03263ff919e4777afdca4fc20efc673 -msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" -msgstr "" - -#: ../../src/introduction/quick-start.md:57 -#: 2f6d2f41de974a469babd97d1106608c -msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:62 -#: cef66179a76a432c9b0c1a49b0f6bf69 -msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" -msgstr "" - -#: ../../src/introduction/quick-start.md:65 -#: 133d0f054f784d7ab5f2fd5f028d80eb -msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" - -#: ../../src/introduction/quick-start.md:70 -#: 454aec8aa868430da0449434df741b21 -msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" -msgstr "" - -#: ../../src/introduction/quick-start.md:74 -#: 5f7a1d2d705145a58fb37d6b7fe66add -msgid "`hello_world-job.json`" -msgstr "" - -#: ../../src/introduction/quick-start.md:80 -#: 18c580026a2346c8b1e020fa9b2f3f8a -msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" -msgstr "" - -#: ../../src/introduction/quick-start.md:82 -#: 0051eb403e43451390f5775976d11818 -msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:88 -#: dbbb23a79b1143a7aa7c91a1277851ce -msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." -msgstr "" - -#: ../../src/introduction/quick-start.md:94 -#: f0ad9eabc2c04cde941bf78f0bfcb641 -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/quick-start.md:96 -#: 0e14c76da55e4501b6fb8ed246a344a7 -msgid "Continue reading the next sections of this User Guide!" -msgstr "" - -#: ../../src/introduction/quick-start.md:97 -#: 6e813c00aa564fc1a407cc7aae77475a -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" - -#: ../../src/introduction/quick-start.md:98 -#: 6029a1f35b10455389c63c680a468d3c -msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." -msgstr "" - -#: ../../src/introduction/quick-start.md:99 -#: c1312d1ce89e4a48b31597c5a8b2e603 -msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -msgstr "" - -#: ../../src/introduction/quick-start.md:100 -#: 18cdf73c71574ce9a74c189aeaae971b -msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." -msgstr "" - -#: ../../src/introduction/quick-start.md:101 -#: 5488abc1abcd4aa68e7e8a702834c619 -msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." -msgstr "" - -#: ../../src/introduction/quick-start.md:102 -#: 4cf8dc5e58244810866649259ac13f9f -msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -msgstr "" diff --git a/locales/setup.pot b/locales/setup.pot index 10900ecf..961f7927 100644 --- a/locales/setup.pot +++ b/locales/setup.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,11 +17,11 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/setup.md:5 -#: 29bb5c68be6042e5aa4a370e9c4024b3 +#: 8395100e210f4ac5a87cc2aeb3d7067c msgid "This page has moved" msgstr "" #: ../../src/setup.md:9 -#: 8bcf31398c34491da1a1590422a72cbe +#: 1e47ac8e393541d19b9499e307fe69e7 msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." msgstr "" diff --git a/locales/sphinx.pot b/locales/sphinx.pot index 0c4554c5..f8448bb7 100644 --- a/locales/sphinx.pot +++ b/locales/sphinx.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:27+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,11 +17,11 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/_templates/sidebar-nav-bs.html:1 -#: b896fd5e11fe4674a7f46ad489476692 +#: 1c343f1abfaa4e14b7f1b645c77c595c msgid "Main navigation" msgstr "" #: ../../src/_templates/sidebar-nav-bs.html:3 -#: acede4e78f7e4aefa0ad9425928cbb42 +#: 3c55f014feb3477889c4df5a158a8804 msgid "Section Navigation" msgstr "" diff --git a/locales/topics.pot b/locales/topics.pot new file mode 100644 index 00000000..1f40bff2 --- /dev/null +++ b/locales/topics.pot @@ -0,0 +1,2083 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 1a006f1604c0405aaa4b93e41edc5184 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: b61b4d7ed53a436486c1429987a2a21b +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: 1bf9e65f1cc249ee93656a53ddd354ca +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: 3329dc69c32f4b9092b196d79ae5d0c1 +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: a003a3d1de0e4dfe8c777905e55fb9fe +#: e2dc24c683054cd785326de2c3f3f136 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: aca6a0cd24a2411c8cfb1ad392f6d315 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: bcf37e403eb041269e351d7f98a19587 +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: c5f68f8a9f34445ebcbd5783f96cb046 +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: 4eca90c659ba43158db373d36ee681df +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 7474eeb128624dc4b1e980dbd0f04ca4 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 0c520e5add334609a1afddc559abe19a +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 125a69207077425fa54f346abc45342d +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 6ca38a04844c403b836942b2f2f1e1e2 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 1da05be0d97d429a84085459ebae54cf +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: fb1b2a8c54f34d78ac61dd4b5ffd9063 +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: a8b1b5caf9904fc5b9eef8c110474b84 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 42a5a8cb3b284549aabb817b73ce5810 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: eddd878eb0324851997de2a69bcbb43f +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: b05c8ff667174f6798feb811cdd3c41d +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: 9dc16d1a6b0546cead6967f5e9b1526a +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: b8bf85e8523a4553a58face698aa863b +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: 6fb9a1a2ffe14f39b01af8736a9698eb +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 0a935aa93e554c0987af7349f94ccd3a +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: cadb5982a13e4621807ad976cf9b1524 +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: bd7ab2cc6234458181e9b99938eba824 +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 7beb72d7dd5a405f9be8b6fb6a310f10 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: e5942c4d4b4d4e1a8c0e9ed3da80960e +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: 5a5dbc9b9d2242ba8d15ecf39123694b +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: dd3016d33b7d4340a09a7c8e5aec4f0b +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 45d110a660b348f58a1107476df18cee +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: 97a5b141592e4415aa4acef4f6228045 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: 85f624f8879348e8bb368ec2749925bf +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 20a851dae87941c7975173ed9cd1e360 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: bb19e1b689564a11bb9e72d5f82cf3d9 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: b14199173add4585be62c4e8278b49f4 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: 9e883f18843a41d7b10102bc11655839 +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: fe3a1468aa864742b92c6e8f4ff1a38f +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: e9dbf14538404cceb02507962a173ee8 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a650a7dacbb547db97158a8ac2c9d0dc +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 501217b98c424a319e70ef963de506f6 +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: 7143809471454e00880ad8faaf43f141 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: 7ad86e42708a465980a56f735644de9f +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a8f29712337b4d1daf3190cc8973b8f7 +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 534843389795437991fad0b5a702b483 +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2052170aa2624feeb2253477895aa838 +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d5ed098a33ae4c1ab2a30eba483ecc6f +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: 2b55c028602f41babb6e535b425ba5dc +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 47408669ae8b4432a43d763dba12a466 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: b2e5e925971849a09a8d54d9c649a32d +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 9a39f53bdcc94904a90effb507767645 +#: f296149bf19947528b134b01a4d7ce81 +#: 965fa9769dea4ac9b3dd252e0a3bc603 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 79d8ea95f0c34585a3dec4f83453de60 +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 4afab699247b4f619702c4086eb1b6f3 +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 693b91423f004118b806bb8ee7952eaf +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: e4a25f04a6fa4001bb1e58cb775cdd84 +#: c771cbc64607412a9164c28934e9e0f5 +#: bdd5a3eac1e3436496e05a13c4f06073 +#: 1e62b28ef0184081b4d6e53f34b753e1 +#: 33edd6deb38740ed98466b6e023b0393 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: a3a8bcdfadc4484ea5e4c13a25b2da85 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 7800570badf149b3bb1f81d470dbf4be +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 496313f8ec67403ca78ba66130df261e +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: f7cc0d1ac5dd47658093cd0360f90329 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 0d563f15c1cc4484b6b2955bdc70e1a9 +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: 06425b6cdaf244b198fdde312e864190 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: 26c3762a637a4492a6c12588544cb0a7 +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: 221433aa39104642af8afb70ebd08576 +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: 197bf36a5d7741b3a9ac56c19d4a7686 +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: d9249cf936d24ab3b3fc508d17d94745 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: 2ff7ce81cd3a492a8549484ba8d1f135 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 2bb45c56e2fc49e094be2cf742222e67 +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: e2a4a531c6164f15bc711618db058f52 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 90f7960bd24d4481bd05da1d61ef146b +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: a51814548e44467c841ca65b2ac63b2c +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: fa13573d9c174ca1accf20a449e5984f +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: f2912b17e3be47b0b7186efdb4c4010f +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 4d9c95d18c1a4880845e7194a99aed3c +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: c656a020978f465b85b8754346ea5b6d +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: ff4d0b6bc0264650a21adc811b8caf4c +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: 77e00be2c0984465af5bf501b4031f32 +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: 3d7b7238be974c0487f219cb5c030149 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 03a62f421c8241779c0e79f4dbad96cc +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 31a85893835748339b6c84fb98fde14b +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 08d9ecd7d3294c5b9dd4db228a1d8d5b +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: d94d6c69aaa64edd9c75624286713c2e +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: 020019b8aedb494fad022d19b7106f83 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: a6b66e0fc0de442e8f72f0d0c37c7e8c +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: 48b7d9ddac2940c0815e5c855bfca6d9 +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 894b843f9c064d56913e1a8c48093314 +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 2319e845caee41a3bc5888c3f1fc28d1 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 9ea661d749db428eacd2207dc7a01e36 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: 4ff76250f28144a4a9d8807a9d4ed3b4 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: 7f9f2df357a740feb89bfbcc44ff4d61 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: 12633ed841dd447a8753faeb4f9e5096 +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 4db64481d38c4896a85a8f6038a9931c +#: 1b4ff3eeddde4a9a8018235b9d706567 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: 50547062ee404e2ebeae7eeb54b9de4b +#: 88933bc02fa84412944673c3463af1ad +#: 4fde39d8a50e49f09bd28a8598760682 +#: b933cbf847d94c5fb8471918ce8cb4ad +#: 0145c520b85a4bc29302bb654f08f23b +#: a3e322ac8a0d4e2ba9bfbece6b5ae64b +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: d9b166225120432f9a2bf2cc7b6ffdfe +#: 28f8ec2fc5c0436aaba19e9d479aa466 +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: b866a0e5897e44329714f4c55eb20d2e +#: e64b5027878346d79f9ab52b3d3b916e +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: ed38ec582fbb48ff9f9cffa7962ef515 +#: 6cc0788250624fd69fa4e3881191ab7f +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 17eefb5f38534c1b87116c3a061ea1bb +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: ce0572fc81b343e6991c88ca0195149a +#: f8b77ad06ebe43d7b03b2135737902e2 +#: c7953486c99d4c7898c0155a6085dfd5 +#: 46d99b1f7f0747479bd58486cf7941d2 +#: cd0a797b3619404f964ba9efb33756bd +#: 528cd5e0d3994230b719fbfb39b1f13e +#: 324241aae8ff4505ab0467f2a7f27fe2 +#: f4086b1ad2e44c2b9de2636f8bc1eb90 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 764d7cf3fb5444d58dc9e0eb6b8fc649 +#: 0450a4b8de3046998d30ce1f09c10daf +#: fd6bf79cbb694dbb89e8731aed733e6c +#: e6048a64e09d46099132fee40a2e0644 +#: 9512391eb96440bd8e48c3754821e3d0 +#: 3e8669bf4a6741f9aba170864b251dac +#: a02ede726d3f4eec9602f72054c0d963 +#: 4ed593dfc39246789f1e4ecdc742323b +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 304de40206cb43d7b651245586cfa55b +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: 7855471c93bc44aabb1a2b9beb52b56a +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: f0452f324bfa451f9f3264f9a55e0e5d +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 6dc476cf8689465ea3993f49a9eead75 +#: 4dfc0be21065471d91def850bc2528fb +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: 09d69778a89044099b3e5d7cf02471bb +#: e3077bdff0dc4dfdae60eb60f3d66d8b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: b28843f7b57745db9cb3648ef23fda0f +#: 6a745fa266dd42849c95410775b690e0 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: be00ed49197f48ecb7cb244ecc214369 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: 90ad2b27f97b4ca089cf23a073cdf17b +#: 38d062892cb04bc7bbf0b56f263079e1 +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: c2d2756d617743b886c67160c2face21 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: 8681600183d1429cbd1b15639e1a222f +#: 1d49cd7337004fc38f4e8e9aa4270481 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: 24b7f85116cc4d2f904600555aa19b8b +#: c401a68b4f384d3eb13ab3e89a4a7195 +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: 0e1f9d22d0714bc5b80e420f63b34cff +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: 5fed95f16aaf42d4b41c569d9546b7f0 +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: b539a931f31d4cfe9d72aa5800115fb2 +#: 48e497c024bc4c38a86dd027aaa4fd2d +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: be638c80121948c99cc9fdb67a5d291e +#: 1fd8fe769ba8497eb8a9520af91ea33e +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: b5f3ad78a233411c97520c1fffdec18f +#: 7854e46c7fd24afd9c1942808521bee1 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 211bd57896494fca9ea8aa2fc142eea2 +#: 28ec0718d3114bfdaae4524c009da944 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: c6a421f7a0214d89958d4c258b58aac8 +#: 07bd0bc74ad74187bdc24c26041467ca +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 3afc146cde2e47d5b52e62fbd1f37426 +#: 2225f5acb44a4ce0ad16be5c4f6cba48 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 9acd61d4d67a4d2c82171a79462fb458 +#: cd7e7fea3b8346268618c31b70581326 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 140e449e46a84e3ca1a604176e583f44 +#: 3d8b717d4568458eb53b0b91695b3de8 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 76f35653e34b433d8e9fedc6d12ce856 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 1a2edf61fda8404689e3c0a7389d7d02 +#: 3bced6d84fa6453195be82dbc6d7ec83 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 0b5aceb6c9d24bd9bfe95cc04fdc61ad +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: 3523cc46c6324fca9053d6b1dd8c7495 +#: 21eee2c1cb6b430486446d223dcca0eb +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: b4f126415048402ca388c4c63f34ebe5 +#: fdf588cf8cd34d60bfb6cece3ef859e0 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 1b494245c14e4e22918c43ad9f26cc8d +#: df4d781178f2465b8a421651bdd2f66f +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: a88008a23ede4ea49ffcaccba7029d31 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: a256b51f1e944b7d9659b945d8ab05c9 +#: 23bbd631e73147e3af561eb4a14d2d6c +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: a446842e26e44781ad10cdaad73bc49d +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 3cc10263ab2f4dbfb6ccb12612b89cf1 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 995f6af5fc244293b34f5d840f01ce1c +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: b556a1d134764505aa25003d79a53e88 +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: ad23da5452bd46248606f6799ce93db0 +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: c63036ac68344465af6c7756be00b60b +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 2f7f270b0ac24f2f8df506f5dde72cf7 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: f49272e5e4c1491eb59c79d2dfb88a86 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 8b50c892d36d4d178ec4268c7c13887d +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: 9d22117a6f5a434593d5144bf824999f +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 4fbc454a144a466b9dd7ff74903fc5fb +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 281b129a76a24b0a818092acd1038757 +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 4dda6ca233d54c12b6ddceabae198495 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 59d87fecfd7f4438b68e0bcdecdcfb46 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: 0f7e33673ad349e5ad41a078032e5806 +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 77a7141f897048139ef3785b5f870b43 +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: 14ed183bc7e346598921445c0dea11e0 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 9406d05bf0ed4774af50fd66d24aa299 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: f5a9048ef9e047528c291505ef9a2c12 +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: 51e8c5a231eb45fb8c15be49b37a7bff +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 860a6f01ebac45938abd220758fd1109 +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 32155f96d47f4d76998a401aa9e9591f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: a62bbb9251794560ace0e52be3d9ebd3 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: e301af8f675444c69cfb6b578c02fdc7 +#: 3da1dec243994409bd764b133d4fc243 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 82c6efcfb5d5410eb316399b7c4f638e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: 29c3d25c657340a1bab7123a166b78c2 +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: ef8e7bd7e944429da78474d2fc5e0348 +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 08dd50bc6a5942ec8f3b6c201fc4497f +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 78c51215a68f40b280cc21d0e412eacf +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: bb8e2203374a4ae7b833c543ecc563b0 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: f34aa1e4d08944c497602b2a35f38a50 +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 2932972efc94447987b02a7707c62656 +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: 968f4e83c511425d8faf4c8d0f18097e +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 2eb89bdbaee04a899a961a7b87f0aef1 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: 3781fc7cd22d48bdb5aa4abc0c93b06f +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: f4af4a85efb243728d2ee783393dce14 +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: dbf8350f003a46b984b7432160e6def5 +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: db2993fe83814747a52f9db0b2fcc81e +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 39fe18bf5d4b4539b2f98e3bf0feea2a +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 58e7b0e7d0a149498e846dd2790c0eee +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: 4b78c5437904492ea3e692372d2fc163 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: f2626686125d4ec29fb2338373b54c93 +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 46327aca33cb49d1ba61149e94884991 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 43f2e7020da94f77bce4e1f852ab11f1 +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 8342aa3f84624325aff8f7f4de788187 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: 2d54f11f99b245e5b2802b984bc024a5 +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: 83a357dc06b343549876035b03b8c5d1 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: 0461538fa12a44c5a9d230a928ae930d +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: 2b2552958f404447b711d09650d22395 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: 82c97e60f8634bd6b4d3e88524722412 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 0ae1393a80e94b899023c29f4af6084b +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 74339f624bba49d6b68e1dfc4724f673 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 3a4473864ec04d2e9a0d550b2051f717 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: 575661b36a2040699956f897bd6cc614 +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 3d18a704f5a94e2889e847c32a78aaab +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: fceca2b53d0646b2ae9f1cf9dbefe2fc +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: cba49054785b4ec2a7acd3aaa2e165d8 +#: 647c0e302af841d7b1789447281d7344 +#: d23de44d5d5b4bc7b32f3726afa97500 +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: dd867685663f4728b9fbe446a9b14a3d +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 67bf2c2cbbc44f6eb870af3a3a852676 +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 94d66455bfd04697814495e116176ffe +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: 39a9d3583f29451d8035158c54266ed6 +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: eba6af5cf8224d198fc04f090362307c +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: b48377cceff342e793e982c9fa2095d3 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: b64ef70d944c461b8ec7219e14e47795 +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 73cd08a2226f4cbe99fcde2d3636d640 +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 3c33bffa2c574ef888b041c1e6735b8e +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: 23bd067b32724dad9daba1e924757d86 +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 1be92fc3d0b44ea089273cfcd47318ef +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: 3d08125883b74f49bba042ed58d34648 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 7636c7e8b6e04d7089ba1cb10c4c475d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: e1c95ce96db043eb86ff9b3ae595017b +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: e6588c4b8fa64959b2dcac52403a6415 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: e7f85cb69a5342889525fbb81b44c86c +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: 71756719e0274300a839b38c8b4ea986 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: 88bf75fce3064eaf823b5d88be0ce053 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: 60374713dea84fff92b89b4ebaa8d7ac +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: 7616d5ea746f47ac972183150b97e8b0 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 0ca022c095334ec4a9fe41cb732e11a1 +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 1c807f8fd1c540ae8802092fbcec7159 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: c51956eb3ece432ea0ed5b676b2f037a +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: 45e6ab3a53b94f5b90136d68c1c0e479 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 7e05dc23d6be4428b4a414b3a65c4727 +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 96e7266ef25b429da42337c3582cc201 +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 9cb6959a877f4590bccb977416753410 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 7b54a3cd870d4b038dff685064bbca1a +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 0d661c96ac2d41ee94641a397aa3bdf7 +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: 94d39b79923a4a65b1a6ce5c464528c6 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 56801121f70b4cb2ab6207e254ec8bbf +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 42418ff882d44c1b9584fb9f7887f744 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 1118de96d202444d9bb4db74ebe4792d +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: aca51d371db84aa79418c79a18310055 +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: 3473e6d2942e4546a2c1590edeb502f8 +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: c210ad12f61047b68302e67da9b5dae0 +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: 1c15cff5a4614d88a62c8d2df97029fc +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: 4beae917368545688c01a4a929685cae +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 4f4f63b7107e4dc194760802c4581c2a +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: d942035c4c914ccb9de75836af9761c7 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 0e9064cf55fe43588053d37100634538 +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: aa1dcfc618e74a53b3c579380e5e1558 +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: 3ec3f4a2d1c547b18780db17fbff060c +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: 21e598983ce94d22b9d40a77577a6608 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 62f79a2c055b455d9626ca5a18d1bd72 +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 19c2b9b13bcc480aa7474301422faab3 +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 17bb520489a74f64b76ddbe2ffedcb5e +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 9e2b97aa3bfe4eae8524b325bf2ea3f1 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: 028c844ef208450f994b3949210ca996 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 2b758e44e4be4fdf89a5897385db6c59 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 16395173b7ee468f85ee8450493504de +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 51e2e929dadc41a78cea98f779e2e2a3 +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b757d4b151ef46fa96897bf00a0d9ab4 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: 2f2f46a81e8946bf8a9b48a5956c82f8 +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: 75177c797c704385bfa5ce86e03266c9 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: 4d05d16c3cb74eb291da7586fa859b90 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: c115b7ed044346d6a9c4c06306ee82d8 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 8f83261e3e91424b9a3c38280c643f02 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 269af269348e4da5b93cb25dcd10374a +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: c376ab464fec4ee78a33d42dfed5dc1c +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 53d468d14703494699478e6847d82e34 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: 32bd7abe387e4999a0864f6e6a48e435 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 0712e952fe2442daa9ceb0cee79a3ebf +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: ef2b8db0c8d64e41b839b47aae34d0ec +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: f9f45dcc2bcb4fd1a1021d2843137fa3 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 4ffbc016a5344e6e9272793d921e4900 +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7118718b98c5488c9d9a54e5ec84c055 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 20fe8fa105a84171972722158bafbc0d +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 836fa2a818854cf9af13d674f5bb859c +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: 5d56e1ac063d48c2b140a72db9f78540 +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: 0166655553ac4d8fb868138936176986 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: e43fe4a9340b458786c51499c75b5556 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: 0ba13966a1364d4e9992b5cfeb6871d1 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: feb8bce610be4a3a92053f2e2e5aab76 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: 0f5fd76c57e7412097b4ebdeb074f2fd +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: b645dd17256543b0a42d231171140c95 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: c8d5743769bd4fee93f77a52ba318883 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: af6cbb89b7a84bf78b7443b6746484fe +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: ad9394b163a94340975a66ea2bba7094 +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: 677bce1f24f449beb2bac5ed8469f624 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 4c0d14a24b354feabf4b6ad4852f9543 +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: d407e5c9aa9043b0b6ab234348467db0 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: f06b60c926204ca88b4355803f1b7b11 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 0a7c19b054d2400abd327736b6829670 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: cd1773f336544b3688bc76c28e9d1f79 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 6b7bbca601f04f7183bc75988bd6db13 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: 069d1dd1f03f4cd79e44f2dcd890b531 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 4924b1a69a5f48b0aa6af943b40ffc68 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: e100d8d8f23c4d6996ac59c5ad68acf0 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: a87dfd0dc0274ff4b34354678f2d49d2 +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 772078ff701a477cae9acb8dda16ef1f +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: d2d67048e93e40c4820b805f1ba28cc9 +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 580477152be041a8ae5c5f546ecbf21d +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: 05f8faea082b4fb9b9c22b8eff7eb356 +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 4c107fb18fb34c2dba7743118c51e8c8 +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: 729ea19aa03b49bdadccc6e6f0d2e7d9 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: e849cda9fb1d4a48b5b1f9a4e44213a1 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: bfc20f529d2d4797b87c63c7b2c05e91 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: 761a900275a044f28ddcebe509a4637a +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 59af21cf1ee848e993563ad47f7bb248 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: d711ce1ccdcf427aba25a2ab3d11165d +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: eaaaa01fe0894f479a42a9c3ce199819 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: 92489f186e3f449295b0dc864ebf17f7 +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 1360c3a2d43b48f3b3e1153bb26b3f30 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 2e993e21a3624910b4282bd088694fec +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: df5b4b041dc944be8580e43012339168 +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: 92ac2766d118428ea148094c022a8b0d +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: e4ddaca03eb449eabbf2d2fce752c367 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 0bc50411a4b748d8864305070d11a304 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 74453227279a46cea3644f3ca7df61b9 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 75ce3269886645eda46a6575fca186eb +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 1e7e5b46017a476a80d57ab7eb614758 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: 1ee41e983ca14a959caa199b1ce12700 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: 070e6a00d09e4675b89afec5d066aec1 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: fd37ebe3aad9473891cc764a47363f8e +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: 85176099018c4ae19bed1261e92e6e92 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 952e9a347f444ef496fa0cdf00160ffd +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 2b5ad46ca3024ce1b37e1c92a820aabf +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: ea17d17cd08b4c40a842598c8521af56 +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 6e5f1266974d4a32995aaa69fbbfd648 +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 20be823f70c348bbaad6bfc8b88201a9 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 02311e5310cb49d19bf2998513f73124 +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: ca6e4a3fe04145a9a21cc43cc53a07bc +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 75452467551a46a2b2b3685f1a4aae0d +#: 93efa8e941a7427f949afc794ed16e75 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: 39beed65cb114bd78c79aa4a5d6f4398 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: dd880d0589fe45dbaf9b7d799402f158 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 671d0bd54bb147518c35f0844a76c61d +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 66de58a51b034f6a8d5dbe742046f817 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 564e68d58e364715aa72183cb16b3d72 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: 558739ceb3fe40de8ea87ff1e7d3fe9d +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: fdc601ee1aa54e1f84cd00eed2e44e52 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: e4f4a76cee96473d9da3bc1c9e35324a +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: d524ed5f1e964688af9d74eef8e46e04 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: c646e4714d78437fb450127b119fbd70 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 8351ddfd726c40159d81c017ef221606 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: 456794c7274f4654b54aae8d4073a2df +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: 6485e8d6814144d1bcbe66bfe4fcbdb9 +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: a2b9e47cc923466f8bd2fbc4b33fc4fa +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 698cc640807247fd8d512c59ce32ee48 +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: dd658e10da624918b7dec1ea18bbf432 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: f6bd95a4fbc44ffdbfec7fcac90f6bb6 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: ac7b02a71d3544848d4fb539b2a4f115 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: 4380dbd066a44102a71c7e42ca7de8d8 +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: da946c9d59f44fb995daa6aadc44031d +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: 7c73bc555f604afd8491c1619d6905eb +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: e79ce424410e4682881fe14326955a14 +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: be8d2b89052e4f9d96ff2bf15526e229 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 967b064ec4284d0aaf374509915497e1 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 02d667b922264f8e8021844df0085578 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: db8734e07541495188d9ee97eaaaeff3 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: 22542da60ac24403827e2e2a14595770 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: d10f35716f9c4b878da0f2b4ff3d44aa +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 1fd555d1f8ca499ead8d5601eb62266a +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: f5fc85accf8c4bb9bc701ba0b4ee2e21 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: e69cb5e87f4b4670abbc1606197d804c +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: 15d763c45a2749a8926b1f965db9d97f +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: c2aac63fc0c347d9833d253039000fa3 +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: 06a23beb753c4a97b302943f59128d78 +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 45985434cfe9438cb558075e1fd73809 +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: e92da36d865142289b11d245221ff8d4 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 3ed7a2b9f77b4eadae3bf6e4a98d14b9 +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: fd66c4fb9c2a4beea0ed5ed8874fcd61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 65944dc8b32a46a4beb73dbdebb7b01a +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 6250fe161ab0421b8799040b79ce695a +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: cc40c0f1ade34ab3b400a02b59b7ba01 +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 29f53a5d64fa498bad0dbe94b238fd97 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: 037fccb419bc4e9f839c665ae31e28ee +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: fdd4bec90c484a618ed8e4d1199deff8 +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 11afb584f37947358963f6510935c5d5 +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: a77e0bfb589c40b6a61a9ca559961a7c +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: 3f4aa12588204fe5b33db590a9446283 +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 640c67f3bcd740c59f90c361024acbcc +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: 8c4d30cbbea146a584731d164d4ad9ef +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: 5d0fd4f8b58e4a8e8f46902e64e6556b +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: e98ab273645340f9a1446183a642e79e +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 37a83ed92d9e44689cfd3a31c2785418 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 7cebef0a9e1444149b1dc58d30f6c10e +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 0cd2bd98918b4622bc586d50f1ce1fa4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: 92458de979564d19a634bb8d3bf6f586 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: d4ee6cc8903f4e6992439ca2586246ed +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 62b438c4ed8a409f96974f3d59cc5854 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: f0f288aeae4f4649ba3615437b531e97 +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: f35023cb05504d1db0cbee41c4e5f371 +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: 01564f1d2038489685160f03db92085f +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: ad662dce1e4149728b8e17f74d8f975f +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 4f6a57f34f094418b7c13aa07eef95c7 +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: 373a6c24de9144e69f37418d6ce8857d +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: f804a8493c8e40178772d94bdc45b43e +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: b3c504b8ab1a42788ef4e3339d27b0dc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 2c2681fe72e24a5d8d98f0aa8e8c56a2 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 571e5c13552c4381bb6de53c02fe5f43 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: fd789f444d9a4061b4fc61bac70353bb +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 2cef838551994b078e460c63214517f9 +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: 2a3a8a553d3c455e9288f63b9a02898d +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: b0b8def4623a4018b1ac913a9256c0a2 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 3f0d4346f0104cc08c059eed9ab4b3a9 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 22e0ac963278414d8141ce5ce4031029 +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: 49cad54646d04adc8e5ac9f0f3c8f895 +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: c8776a4511b24f46bbe0a34d52cf3c8b +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 401b053bd08a4286b9059cb6ebf8d679 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: 8d48a277f37f458f88c54f362534d7b5 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: de90253a11f24f29a4a57348b4f60941 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: 1e20968f957441c58cabfbc46c21e8ca +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 4cf2e158afb348d7b3fd6274fe888129 +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 44c5c010c97a40068a6b930949dcd8cf +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: c6277b2a7a934f81a91e406ef317a1fb +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: 8b3ece04170c447e9b5a8f76374c4c23 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: 6b952b7369b447bdb0bf1e9ff8540194 +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: a6024fb7ce664896a6858d5ea3562fb7 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" diff --git a/locales/topics/additional-arguments-and-parameters.pot b/locales/topics/additional-arguments-and-parameters.pot deleted file mode 100644 index c447e7c6..00000000 --- a/locales/topics/additional-arguments-and-parameters.pot +++ /dev/null @@ -1,62 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 4ad19837b80f40af88edf443c4d4e743 -msgid "Additional Arguments and Parameters" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:3 -#: a51e98f4fab24b42b225e24b69471869 -msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 78e7111611734004b650bdde36fe8079 -msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 0c5cc374383a4f058a6c8d7a3d83c7d4 -msgid "`arguments.cwl`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:19 -#: 67cfc6cc46764b07a6738691bc1cb1f6 -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 744b2343db934429b7a04b4ab4f84d15 -msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:30 -#: abea839860f447f1b767c3a028ce1ca9 -msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 5a44c7cd8feb4593802cdf56254b79d7 -msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d5f29eae1af646d5be22c816c5d1a4fd -msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." -msgstr "" diff --git a/locales/topics/best-practices.pot b/locales/topics/best-practices.pot deleted file mode 100644 index d4460047..00000000 --- a/locales/topics/best-practices.pot +++ /dev/null @@ -1,137 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/best-practices.md:1 -#: e93667d13f1c481c9ffec6bb3062c073 -msgid "Best Practices" -msgstr "" - -#: ../../src/topics/best-practices.md:3 -#: 685dedff3cf54c4b95bc56b30a5d7fce -msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." -msgstr "" - -#: ../../src/topics/best-practices.md:8 -#: 2e4c3af1016e4269b6eb3eb7c37b609b -msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." -msgstr "" - -#: ../../src/topics/best-practices.md:11 -#: ee2f52f0a96449a7b6e49b2c824288d1 -msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." -msgstr "" - -#: ../../src/topics/best-practices.md:20 -#: 426fc5489a1a44d2b037f1456b6556c2 -msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." -msgstr "" - -#: ../../src/topics/best-practices.md:26 -#: ecf6e24373f944a0a3e9453c31e03e8e -msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" -msgstr "" - -#: ../../src/topics/best-practices.md:28 -#: 0ad7fe10c6584f01991d87544f1d5649 -msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" - -#: ../../src/topics/best-practices.md:37 -#: b589adbe3f324ecc9670c2355be1e308 -msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." -msgstr "" - -#: ../../src/topics/best-practices.md:40 -#: 50184e2a39fb4a2086afbb236efa603f -msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." -msgstr "" - -#: ../../src/topics/best-practices.md:44 -#: f000d979ab914d94bbfe988792cf1629 -msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:47 -#: a11d2c6e1408411d89cf7d434448a414 -msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." -msgstr "" - -#: ../../src/topics/best-practices.md:50 -#: 3e379d3bd38b40d38a2a448e907918b1 -msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." -msgstr "" - -#: ../../src/topics/best-practices.md:55 -#: b8eb7c78ffcc4093aea11fa21cef762e -msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:58 -#: ef540052516840638bb7e5bf4dadb945 -msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." -msgstr "" - -#: ../../src/topics/best-practices.md:66 -#: 378f73d8fd864d0bb3ac5d027224ef08 -msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." -msgstr "" - -#: ../../src/topics/best-practices.md:69 -#: fb1fee0d5583488ea2091dbf9b36eded -msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." -msgstr "" - -#: ../../src/topics/best-practices.md:73 -#: 210127c58cd44557b60d603d8d68725d -msgid "Custom types should be defined with one external YAML per type definition for re-use." -msgstr "" - -#: ../../src/topics/best-practices.md:76 -#: 6b657c5d109646f5bf7a38cef1b903e3 -msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "" - -#: ../../src/topics/best-practices.md:78 -#: 14951e1b672248f095c31c4c96bf5183 -msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." -msgstr "" - -#: ../../src/topics/best-practices.md:82 -#: ff9dbfab87a24cfab3734882216d40af -msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." -msgstr "" - -#: ../../src/topics/best-practices.md:85 -#: 444b5580319b4ee69a1439c7ccf703df -msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." -msgstr "" - -#: ../../src/topics/best-practices.md:90 -#: 9ba7fd2784b2430fb6964b9a16d2d553 -msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." -msgstr "" - -#: ../../src/topics/best-practices.md:93 -#: 0e88ebb9e45c41db83482ccf848ca1ca -msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." -msgstr "" - -#: ../../src/topics/best-practices.md:97 -#: 3b2fe5ca68944df5baf04c7b5705e207 -msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." -msgstr "" diff --git a/locales/topics/command-line-tool.pot b/locales/topics/command-line-tool.pot deleted file mode 100644 index 422115ac..00000000 --- a/locales/topics/command-line-tool.pot +++ /dev/null @@ -1,62 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/command-line-tool.md:1 -#: 595e9cc7e0a448f695e27b1cd0427d9e -msgid "Command Line Tool" -msgstr "" - -#: ../../src/topics/command-line-tool.md:3 -#: ac9188b4b9dc45589f2173a73dc9d3dc -msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." -msgstr "" - -#: ../../src/topics/command-line-tool.md:8 -#: a6dd1084b9b248e08ec2659999f82ac6 -msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." -msgstr "" - -#: ../../src/topics/command-line-tool.md:19 -#: 9119bb87ef4b48e7946f5412d197ce0a -msgid "CWL command-line tool." -msgstr "" - -#: ../../src/topics/command-line-tool.md:50 -#: 312c6373a25b498db63c67abed6c6289 -msgid "`echo.cwl`" -msgstr "" - -#: ../../src/topics/command-line-tool.md:57 -#: 84b6964c9cbb4d67af2794624de86337 -msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." -msgstr "" - -#: ../../src/topics/command-line-tool.md:68 -#: c276e21332454452bc814d33f007a670 -msgid "Network Access" -msgstr "" - -#: ../../src/topics/command-line-tool.md:69 -#: 1321360b42da4f65975569e2b7314bf0 -msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." -msgstr "" - -#: ../../src/topics/command-line-tool.md:83 -#: 70739268c7674a99834cf6c166231149 -msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." -msgstr "" diff --git a/locales/topics/creating-files-at-runtime.pot b/locales/topics/creating-files-at-runtime.pot deleted file mode 100644 index c427c32e..00000000 --- a/locales/topics/creating-files-at-runtime.pot +++ /dev/null @@ -1,77 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/creating-files-at-runtime.md:1 -#: d4e5cee7a82447a696e1e9516ccc2e38 -msgid "Creating Files at Runtime" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:3 -#: 6121650880d4447e9b5a6b66e0f3367c -msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:7 -#: e81edd66cbb2461e905a7adf6bff23fa -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:9 -#: cb4602ae814b4b47abe61ab3bd88b046 -msgid "`createfile.cwl`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:15 -#: f6f5c6dc8ff74db3b1c5aa2403ee12d4 -msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:20 -#: 87abe95ca4054b48a8fb76d7916db1d4 -msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:27 -#: de2366c1d2d1459ba23fe1410f2b86f4 -msgid "To test the above CWL tool, use this job to provide the input value `message`:" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:29 -#: 28906471c2fb41358706f624e3c8bd8f -msgid "`echo-job.yml`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:35 -#: 449fdfe14172498fb80e2f57ca0c05f9 -msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:40 -#: 9a9ce102e4ed4dc68eeb161746ab4689 -msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:51 -#: 447b2199a76646be8afacb72203e9719 -msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:54 -#: aaae789101c742b292ebdcec727b1762 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" diff --git a/locales/topics/custom-types.pot b/locales/topics/custom-types.pot deleted file mode 100644 index f338bd21..00000000 --- a/locales/topics/custom-types.pot +++ /dev/null @@ -1,77 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/custom-types.md:1 -#: e1169af9b1ed419b80cd7b2ee432c37d -msgid "Custom Types" -msgstr "" - -#: ../../src/topics/custom-types.md:3 -#: e297aa8753564accac64cbad1be99d0b -msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." -msgstr "" - -#: ../../src/topics/custom-types.md:9 -#: aa76f57cb1eb4a81ba6560ca7b7d47fa -msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:12 -#: 7644b22f9154413cb88f46e9a2a1a9fb -msgid "`custom-types.cwl`" -msgstr "" - -#: ../../src/topics/custom-types.md:18 -#: 1d259a15f1884950953d8536b74d437a -msgid "`custom-types.yml`" -msgstr "" - -#: ../../src/topics/custom-types.md:24 -#: db1612c92c3c4d63869aa3d589960ab9 -msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/custom-types.md:30 -#: 4c7038e3a8d6484e9eecb348e825605a -msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" -msgstr "" - -#: ../../src/topics/custom-types.md:46 -#: 960610e43cd247dfa5921477558f6a2c -msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:53 -#: cd7d7cb81be74acd81bd3af2ecbeba8c -msgid "The contents of the YAML file describing the custom type are given below:" -msgstr "" - -#: ../../src/topics/custom-types.md:55 -#: b0b4eb8206f54104a7fe02492cd3c0c5 -msgid "`biom-convert-table.yaml`" -msgstr "" - -#: ../../src/topics/custom-types.md:61 -#: 2d0fc88b5d524b4e814f47a147b7e555 -msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" -msgstr "" - -#: ../../src/topics/custom-types.md:76 -#: 8e99e8e00d3340e6bf7025622bdfbf47 -msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." -msgstr "" diff --git a/locales/topics/environment-variables.pot b/locales/topics/environment-variables.pot deleted file mode 100644 index 294a71e7..00000000 --- a/locales/topics/environment-variables.pot +++ /dev/null @@ -1,42 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/environment-variables.md:1 -#: 201d52b060fb44e3b988d1cf08b32569 -msgid "Environment Variables" -msgstr "" - -#: ../../src/topics/environment-variables.md:3 -#: 5438cfdc5df24a2098fc3014731bceb2 -msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." -msgstr "" - -#: ../../src/topics/environment-variables.md:7 -#: 295b041049874673b1c4f93e3c8932c8 -msgid "`env.cwl`" -msgstr "" - -#: ../../src/topics/environment-variables.md:13 -#: e2076a2e3c4e43228e69f9b4ee535e3a -msgid "`echo-job.yml`" -msgstr "" - -#: ../../src/topics/environment-variables.md:18 -#: 74c67839550148b98f8a681f53baae9e -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" diff --git a/locales/topics/expression-tool.pot b/locales/topics/expression-tool.pot deleted file mode 100644 index 329b21fd..00000000 --- a/locales/topics/expression-tool.pot +++ /dev/null @@ -1,47 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/expression-tool.md:1 -#: a1a763367700488eaeeeeb6c1d4aaf3f -msgid "Expression Tool" -msgstr "" - -#: ../../src/topics/expression-tool.md:3 -#: 1baaf7f3bda34cabb4081708f8eb676f -msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." -msgstr "" - -#: ../../src/topics/expression-tool.md:8 -#: cf8f9f21b8bc4cba9e947b631e0452d4 -msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." -msgstr "" - -#: ../../src/topics/expression-tool.md:17 -#: 01ad0d7c0c9d4051906424dceb702361 -msgid "CWL expression tool." -msgstr "" - -#: ../../src/topics/expression-tool.md:48 -#: af1958ad56b64631a111aaaa41413a09 -msgid "`uppercase.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:67 -#: f50a9dc71c7f4beab2525ce6e6fca385 -msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." -msgstr "" diff --git a/locales/topics/expressions.pot b/locales/topics/expressions.pot deleted file mode 100644 index 012628cd..00000000 --- a/locales/topics/expressions.pot +++ /dev/null @@ -1,373 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/expressions.md:1 -#: 6b0faa9c10ad4da783e2155070095a8d -msgid "Expressions" -msgstr "" - -#: ../../src/topics/expressions.md:3 -#: 9e44e4e737b545a2b10b97e923027bd9 -msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." -msgstr "" - -#: ../../src/topics/expressions.md:9 -#: ad6d3dddfda445a5bfce2665cb195605 -msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." -msgstr "" - -#: ../../src/topics/expressions.md:16 -#: f487ea31d38142839ce5667701b894cd -msgid "`expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:22 -#: 47d7f42a657a4547af1be1e13662effc -msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" -msgstr "" - -#: ../../src/topics/expressions.md:25 -#: c331468453dd4e60a76bc753417b72ce -msgid "`empty.yml`" -msgstr "" - -#: ../../src/topics/expressions.md:31 -#: 6b9b7057eb154a95847ec56652de07d9 -msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." -msgstr "" - -#: ../../src/topics/expressions.md:35 -#: 6facbcd083f04a60941589da7e21621f -msgid "We can then run `expression.cwl`:" -msgstr "" - -#: ../../src/topics/expressions.md:37 -#: a08110192e264a109ee6a568351135e4 -msgid "Running `expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:47 -#: 1a260934cee04059b4765d154f6388e1 -msgid "Note that requirements can be provided with the map syntax, as in the example above:" -msgstr "" - -#: ../../src/topics/expressions.md:54 -#: ebee54b00af643aba0d53e774b0ac188 -msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." -msgstr "" - -#: ../../src/topics/expressions.md:62 -#: 02ad120e9a72482780f062ae3cadcce7 -msgid "Where are JavaScript expressions allowed?" -msgstr "" - -#: ../../src/topics/expressions.md:64 -#: 8bb623ae7a9646ff992d7a79856aac8a -msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" -msgstr "" - -#: ../../src/topics/expressions.md:66 -#: 4437b8ae6fb04a1fa06f494ead97b1c7 -msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/expressions.md:67 -#: 145b4d4cbfaa4c5d914455b0b5b6ef1b -msgid "`arguments`" -msgstr "" - -#: ../../src/topics/expressions.md:68 -#: ../../src/topics/expressions.md:76 -#: ../../src/topics/expressions.md:89 -#: b187028dafc040e8ab04d2a69c547874 -#: ecb148c1da01445a8149b500b5ea50f5 -#: 87f7f23e14e54b87b6f1b4f8c148bf8b -msgid "`valueFrom`" -msgstr "" - -#: ../../src/topics/expressions.md:69 -#: 9132968dd34f4a9c99ebabcae48a4a3f -msgid "`stdin`" -msgstr "" - -#: ../../src/topics/expressions.md:70 -#: 34b31b4554b442ab9d9bac1e95cc3029 -msgid "`stdout`" -msgstr "" - -#: ../../src/topics/expressions.md:71 -#: 33e3e471fafb4f609694af59556dedcb -msgid "`stderr`" -msgstr "" - -#: ../../src/topics/expressions.md:72 -#: 941720c894bd45a895e3a8e682b7e884 -msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:73 -#: ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 -#: ../../src/topics/expressions.md:93 -#: e2c648a9a5794879b74cf02e489f0c5a -#: 15692bd5c6204aa9b72259e6dae69bec -#: 1a506a3ea7614043a67dd4d93015b19c -#: 166fd96ec8b64db88e1837feaf65df1c -msgid "`format`" -msgstr "" - -#: ../../src/topics/expressions.md:74 -#: ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 -#: ../../src/topics/expressions.md:94 -#: 8c65f558109142048b8831f800264bb4 -#: a4e5f9d5354d483392c157f736cd8c20 -#: 9ec2e908459a468b837b572a426bcd8d -#: 2d82125ff94c441ea29b3da5ff5dbb08 -msgid "`secondaryFiles`" -msgstr "" - -#: ../../src/topics/expressions.md:75 -#: 6eecf3fa29d9465882a2b6be02504ac0 -msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:77 -#: 92267f3d8f4e4b3fa129e3bec3b16413 -msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:80 -#: b9b5551681d046e7a0071eee29987b04 -msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:81 -#: b148af79351e4ba49604e24861388496 -msgid "`glob`" -msgstr "" - -#: ../../src/topics/expressions.md:82 -#: 4c48b367e5494d559484c5395af3a5a4 -msgid "`outputEval`" -msgstr "" - -#: ../../src/topics/expressions.md:83 -#: 5541a07628174dd6a843afa2c37f4973 -msgid "From `Workflow`" -msgstr "" - -#: ../../src/topics/expressions.md:84 -#: bf6e4a2101654e15bc27ac3db0c6bb6d -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:87 -#: a295cb00ea034ce7820897606999ae4c -msgid "From `steps`" -msgstr "" - -#: ../../src/topics/expressions.md:88 -#: 5fd2e9df08404efa9d24d8bfccf91a18 -msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/expressions.md:90 -#: 51f8b42f4e7d4c8484133a18f83be491 -msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../src/topics/expressions.md:91 -#: 73fef9b1b2074077a2525f72b2efaf62 -msgid "`expression`" -msgstr "" - -#: ../../src/topics/expressions.md:92 -#: cf19b246bc20476899a83e68113dd3d1 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:95 -#: dfe56b4ea35a440d91f579efcc2c039b -msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:96 -#: 918bc6b265a549f28f027da29368cac4 -msgid "`coresMin`" -msgstr "" - -#: ../../src/topics/expressions.md:97 -#: a9182179ebce4c99b4eafe59ba122799 -msgid "`coresMax`" -msgstr "" - -#: ../../src/topics/expressions.md:98 -#: 984ceb05b6b24e4986a28436bdca88e7 -msgid "`ramMin`" -msgstr "" - -#: ../../src/topics/expressions.md:99 -#: 9a3f6db0d7f64468bbf2f6f861eab96a -msgid "`ramMax`" -msgstr "" - -#: ../../src/topics/expressions.md:100 -#: b7557357360d454dba7ab3c3471b5a23 -msgid "`tmpdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:101 -#: 839ac0ddca374746972ead6d22427edc -msgid "`tmpdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:102 -#: 89bfd53638504c7aa437c2140afb6035 -msgid "`outdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:103 -#: f0af6b4cfc23480aae61f42422ad3afb -msgid "`outdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:104 -#: 67ccc10e77d644078b170a28a8ebed3d -msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:105 -#: fcb8b8003fc84ab890ce241e63d43b5d -msgid "`listing`" -msgstr "" - -#: ../../src/topics/expressions.md:106 -#: 584682d4db424108b89ea8e315838de3 -msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/expressions.md:107 -#: 77439e7f4f214db781edc777a8a03b78 -msgid "`entry`" -msgstr "" - -#: ../../src/topics/expressions.md:108 -#: 4ba274f6d9c44ad7a05891725299a759 -msgid "`entryname`" -msgstr "" - -#: ../../src/topics/expressions.md:109 -#: 1b751542a9f34fe19ae5f91174e01cb7 -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../src/topics/expressions.md:110 -#: aca9ad053f5441caa5cd51170e35532d -msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/expressions.md:111 -#: 37c96fdc52c443faa1d1e462ff034425 -msgid "`envValue`" -msgstr "" - -#: ../../src/topics/expressions.md:116 -#: 4bcf5cd130b148f7b3f601902ad0b7b4 -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" - -#: ../../src/topics/expressions.md:118 -#: d6f0074d025742a6b3fe7f91f1dff335 -msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." -msgstr "" - -#: ../../src/topics/expressions.md:122 -#: c664d4710c404ed0af90dc22c8f273b1 -msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:128 -#: bd8dfef3aa934750bdd790e1de6bced6 -msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." -msgstr "" - -#: ../../src/topics/expressions.md:135 -#: 1ae20d38a1574d828ca7cb8e955906da -msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:139 -#: bcda020047784e4191d4de456afc7449 -msgid "`hello-world-expressionlib-inline.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:146 -#: a9ccc2da748644dfb28b590eae974f63 -msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" -msgstr "" - -#: ../../src/topics/expressions.md:149 -#: aede8f2c722c49f18cd2a86c051bb1d4 -msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:155 -#: 7d1bd9bfba9c496a90fc45f575505e22 -msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:158 -#: 8b906fa3b98c48c68de46f80667d4d2f -msgid "`custom-functions.js`" -msgstr "" - -#: ../../src/topics/expressions.md:164 -#: daa9689f15c746a38dcd22a3f169a4c6 -msgid "`hello-world-expressionlib-external.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:171 -#: d0d8193fbb304f0281db0c6c1147545b -msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:175 -#: e5e1179082c14621bafbd14d887db62a -msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:181 -#: 193379258f254ac5a25fcfb61b1c3540 -msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." -msgstr "" - -#: ../../src/topics/expressions.md:186 -#: ec0d1c972b9942f8a55b7b68fc9cfe07 -msgid "`hello-world-expressionlib.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:193 -#: 63ff0565300a493f8c84935139c23552 -msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:200 -#: f8bb29ee047e407ea226599bccd86196 -msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." -msgstr "" diff --git a/locales/topics/file-formats.pot b/locales/topics/file-formats.pot deleted file mode 100644 index 86733f1a..00000000 --- a/locales/topics/file-formats.pot +++ /dev/null @@ -1,77 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/file-formats.md:1 -#: f2a1cf1e81e54737af8d81bcef76d88a -msgid "File Formats" -msgstr "" - -#: ../../src/topics/file-formats.md:3 -#: f81bab33b2ad46d3a852e15d88858879 -msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." -msgstr "" - -#: ../../src/topics/file-formats.md:8 -#: c1dd91bf59804358be63bcde0614bd31 -msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." -msgstr "" - -#: ../../src/topics/file-formats.md:14 -#: 785ed7d362824bb99887694670aac50e -msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." -msgstr "" - -#: ../../src/topics/file-formats.md:17 -#: c3f54f4d6df44e628c59c1e70124667f -msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." -msgstr "" - -#: ../../src/topics/file-formats.md:20 -#: 6c3942038fd3446db254260530291732 -msgid "`metadata_example.cwl`" -msgstr "" - -#: ../../src/topics/file-formats.md:26 -#: db9222078ef04bd29ac45af0cf8a4ebd -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../src/topics/file-formats.md:32 -#: 3b17d233095a40cfae0540e678088860 -msgid "Sample Parameter Files" -msgstr "" - -#: ../../src/topics/file-formats.md:34 -#: a7900a2fa76c46e6854d09a7b31df272 -msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." -msgstr "" - -#: ../../src/topics/file-formats.md:39 -#: ac34d1ad2274499f9ea1413b5648f7dd -msgid "`sample.yml`" -msgstr "" - -#: ../../src/topics/file-formats.md:45 -#: 04198e0858a6415a8e3235c29d15c5f1 -msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/file-formats.md:52 -#: 265ff7e37ebd4e9fa85b26a6deb1cd74 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" diff --git a/locales/topics/index.pot b/locales/topics/index.pot deleted file mode 100644 index 9f895c55..00000000 --- a/locales/topics/index.pot +++ /dev/null @@ -1,22 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/index.md:1 -#: 8ecce715c6084f74acf91e896775f6b3 -msgid "Topics" -msgstr "" diff --git a/locales/topics/inputs.pot b/locales/topics/inputs.pot deleted file mode 100644 index 6ec07f47..00000000 --- a/locales/topics/inputs.pot +++ /dev/null @@ -1,247 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/inputs.md:1 -#: 9a97be0420e54706a7c73bc1eb856b96 -msgid "Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:3 -#: d4b396558d594c84b82369a138358fd6 -msgid "Essential Input Parameters" -msgstr "" - -#: ../../src/topics/inputs.md:5 -#: a3966840a8844e1999e21bcecc96a6f7 -msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/inputs.md:9 -#: ebeb58f7ebd541f581415a43d790811c -msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." -msgstr "" - -#: ../../src/topics/inputs.md:13 -#: 95cf3ab046b44241ba399c56d4b0c6eb -msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." -msgstr "" - -#: ../../src/topics/inputs.md:16 -#: 6e6066facc2141739cac77bf9792572a -msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "" - -#: ../../src/topics/inputs.md:18 -#: e257868f6c6646e6a0d1feef62de079d -msgid "`inp.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:24 -#: 2f2885adf6214b9a8f770097bb02b1e5 -msgid "Create a file called `inp-job.yml`:" -msgstr "" - -#: ../../src/topics/inputs.md:26 -#: 01ec3e60c2f24f9c912d44d3d5dac4c5 -msgid "`inp-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:33 -#: 8c803c9f11414a9f9b92643923a79c65 -msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" -msgstr "" - -#: ../../src/topics/inputs.md:40 -#: df2b1f41e3e149309ae8b19aaf6034ca -msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." -msgstr "" - -#: ../../src/topics/inputs.md:44 -#: df5bd15a6b084bce879270be669f2923 -msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." -msgstr "" - -#: ../../src/topics/inputs.md:47 -#: e73d20dd91574bcbb7b24932d9ff04e4 -msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:53 -#: 56461c62effc487c9e73d1e82ddd3390 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:64 -#: df42caf04d5f48baa8e5734d6100cdf4 -msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" -msgstr "" - -#: ../../src/topics/inputs.md:70 -#: f8db1efc2092415387e4e16dc24775dd -msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." -msgstr "" - -#: ../../src/topics/inputs.md:83 -#: 859f5479b2cd4e919e3ba19a3f084b01 -msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." -msgstr "" - -#: ../../src/topics/inputs.md:95 -#: d04258dca228411ab16f82585ee53985 -msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." -msgstr "" - -#: ../../src/topics/inputs.md:109 -#: 760c0af7e36d48d1b1681928ad195eaa -msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." -msgstr "" - -#: ../../src/topics/inputs.md:124 -#: 4e5d3fb805f04593b34d5ae88dd6fa83 -msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:131 -#: 7b97d452561c4c158a835fd308feafb8 -msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." -msgstr "" - -#: ../../src/topics/inputs.md:134 -#: c63782e8b8524857a1683578534f8382 -msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." -msgstr "" - -#: ../../src/topics/inputs.md:142 -#: fe66dc3c9aa743e0a2060a8280e6a59d -msgid "The `baseCommand` field will always appear in the final command line before the parameters." -msgstr "" - -#: ../../src/topics/inputs.md:146 -#: 04993bbb8c7b488d8b1b2517f4333f8d -msgid "Array Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:148 -#: e33e6fd2e8a8472e88c9333c7b44fc2c -msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." -msgstr "" - -#: ../../src/topics/inputs.md:154 -#: adc2cd5bd81b459b996ff65de5d25436 -msgid "`array-inputs.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:160 -#: 67da943c4d6d49cab1931606fb6938d9 -msgid "`array-inputs-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:166 -#: 0be87de7fd5e41da895dfc9369da7b5a -msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:178 -#: 535a8e26cc3b4e3db43680f030d57879 -msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." -msgstr "" - -#: ../../src/topics/inputs.md:185 -#: 61c26186c1734233bb7d9e5cd3056506 -msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." -msgstr "" - -#: ../../src/topics/inputs.md:191 -#: 66ec7048099f4720989c8de5be49ea2a -msgid "Inclusive and Exclusive Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:193 -#: efa9d841028c4135a513f3226b37bdfc -msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." -msgstr "" - -#: ../../src/topics/inputs.md:198 -#: b3543061283e4bf286ed9fb7127238df -msgid "`record.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:204 -#: afeff005e15d49edbd8222e95b4d6388 -msgid "`record-job1.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:215 -#: 0eb5e94bf86a4c84bb112d612c290bce -msgid "In the first example, you can't provide `itemA` without also providing `itemB`." -msgstr "" - -#: ../../src/topics/inputs.md:217 -#: 3d1f591442f54f9fa8effb98f4cc4f7f -msgid "`record-job2.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:233 -#: 1a8735c689ff4e13bd207eed62d0bc1b -msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." -msgstr "" - -#: ../../src/topics/inputs.md:236 -#: f802a2e638764c95bef8889b958f6872 -msgid "`record-job3.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:252 -#: 54ffe9e897ff4682aa9d17e9239a5b40 -msgid "In the third example, only `itemD` is provided, so it appears on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:255 -#: 892a899a9365419c8cdc95e9f05f9e3d -msgid "Exclusive Input Parameters with Expressions" -msgstr "" - -#: ../../src/topics/inputs.md:257 -#: 2cca4db8543145c0a59da034c82db1fd -msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." -msgstr "" - -#: ../../src/topics/inputs.md:262 -#: 1f42c1eba9f44397942d6bf2dd37855f -msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." -msgstr "" - -#: ../../src/topics/inputs.md:265 -#: 1c0caf1fd3a4411f83dfc4866edeecfe -msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:271 -#: d0a92fe266614a5db77f32b0fc40ee83 -msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" -msgstr "" - -#: ../../src/topics/inputs.md:280 -#: e3a608fbb7e14213831c564128421cc2 -msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." -msgstr "" - -#: ../../src/topics/inputs.md:289 -#: a24cd12cc01b4e23b0ed878a27fcaa46 -msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." -msgstr "" diff --git a/locales/topics/metadata-and-authorship.pot b/locales/topics/metadata-and-authorship.pot deleted file mode 100644 index 2d77396e..00000000 --- a/locales/topics/metadata-and-authorship.pot +++ /dev/null @@ -1,57 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/metadata-and-authorship.md:1 -#: c79f6e6491bb4b6b9f1b2677b79c0ce1 -msgid "Metadata and Authorship" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:3 -#: 73dd0c3f814b4b77a9fe0ad09be7e00a -msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:13 -#: 9dbb204051604ffc8b40ff902f1d6c7e -msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:16 -#: a4bd38b9be374a9da651b4c8a876f57f -msgid "`metadata_example2.cwl`" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:22 -#: 6d6d2685e0a74c8ab242594fff8885ff -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:28 -#: d8261a4cdde0456db33aa7e6bea9774d -msgid "Extended Example" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:30 -#: 11af70cc279a4cb29135aa440d560999 -msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:35 -#: 5a3a6d2577544ff1a996b7b7d15693e0 -msgid "`metadata_example3.cwl`" -msgstr "" diff --git a/locales/topics/operations.pot b/locales/topics/operations.pot deleted file mode 100644 index ea3332ce..00000000 --- a/locales/topics/operations.pot +++ /dev/null @@ -1,62 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/operations.md:1 -#: 8766c4065dfa467f9001aa50564f4812 -msgid "Operations" -msgstr "" - -#: ../../src/topics/operations.md:3 -#: b37c530cac0a4d18b50271b5b5ec4d1b -msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." -msgstr "" - -#: ../../src/topics/operations.md:7 -#: 54e76a0465cf40bf8b76896643cc521b -msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" -msgstr "" - -#: ../../src/topics/operations.md:10 -#: 9e16b384ac494d07951ad589a0413d2c -msgid "`operations.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:16 -#: cfd13e0311104c95b7de0510f0fb54ab -msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" -msgstr "" - -#: ../../src/topics/operations.md:24 -#: 468b0b4219a84df49286a95115c5d3fe -msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" -msgstr "" - -#: ../../src/topics/operations.md:55 -#: 362bd499ed6b40b8bbf3237a9a08895e -msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" -msgstr "" - -#: ../../src/topics/operations.md:58 -#: 24454b17abae4cd9a8a17cfc5bd79e39 -msgid "`cwltool` does not know how to run operations" -msgstr "" - -#: ../../src/topics/operations.md:66 -#: f33e158f449e4594b4f0f1c4660e2be2 -msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." -msgstr "" diff --git a/locales/topics/outputs.pot b/locales/topics/outputs.pot deleted file mode 100644 index eaaa0c37..00000000 --- a/locales/topics/outputs.pot +++ /dev/null @@ -1,134 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/outputs.md:1 -#: 30d1617ac85d41a0956ef5f7eb30c112 -msgid "Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:3 -#: 13aaa50a038f460f829a5554ea950a8b -msgid "Returning Output Files" -msgstr "" - -#: ../../src/topics/outputs.md:5 -#: e26db82dbb934d4aac5a7918c39245f4 -msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/outputs.md:10 -#: 747f0575223f42cd90157c2ec684ab4e -msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." -msgstr "" - -#: ../../src/topics/outputs.md:16 -#: c251eb8f22c54cdbb8683e98d4e527a7 -msgid "The following example demonstrates how to return a file that has been extracted from a tar file." -msgstr "" - -#: ../../src/topics/outputs.md:19 -#: e0fc3bde9de84b2ea5e2b9d7d1491ed1 -msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "" - -#: ../../src/topics/outputs.md:21 -#: cbc068a7d2bc4c1682577ef6b854309a -msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" -msgstr "" - -#: ../../src/topics/outputs.md:26 -#: f2923e674d574ea1a52dab96a12e38a7 -msgid "`tar.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:32 -#: ebe4a9bec6cd42c089e790108b0ddbff -msgid "`tar-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:38 -#: 89c371e54934472e9c09681be5f1ecc3 -msgid "Next, create a tar file for the example." -msgstr "" - -#: ../../src/topics/outputs.md:45 -#: 508663424d2f4eb494ca8611cca4073a -msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/outputs.md:51 -#: 1ee12d2ed35a414d818127ebaaac2364 -msgid "The field `outputBinding` describes how to set the value of each output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:62 -#: 0e0fa84bee1042d88386826c22466619 -msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." -msgstr "" - -#: ../../src/topics/outputs.md:65 -#: 9a37679c41eb4287b43d254a8fd823e2 -msgid "Capturing Standard Output" -msgstr "" - -#: ../../src/topics/outputs.md:67 -#: 7041b9a7b7034bf881bccccc2b691a44 -msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:71 -#: 53075db7e4ca436594d4fd3f3e00917d -msgid "`stdout.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:77 -#: 0860836ece81420dba1b2a080e825f6c -msgid "`echo-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 -#: 40d221f9b5b642648b918aa0e6902f1c -#: 7ad8f592f52b4aeeaa703a85e79f6356 -msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/outputs.md:89 -#: 6f6a26ee1ade4b4f9ed3a82ed44030f8 -msgid "Array Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:91 -#: 61a149a84abf40e7ace2248dc0119838 -msgid "You can also capture multiple output files into an array of files using `glob`." -msgstr "" - -#: ../../src/topics/outputs.md:93 -#: 1322f83871ee49b3a87aa71a0ec5a79f -msgid "`array-outputs.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:99 -#: 6f92d0458a924c88aaba9e7336eef87c -msgid "`array-outputs-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:112 -#: ce294dbd94ee4624915c398389eaf1f6 -msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." -msgstr "" diff --git a/locales/topics/parameter-references.pot b/locales/topics/parameter-references.pot deleted file mode 100644 index b17a5e7a..00000000 --- a/locales/topics/parameter-references.pot +++ /dev/null @@ -1,278 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/parameter-references.md:1 -#: 0d925f42133646899f4bb3367057e07d -msgid "Parameter References" -msgstr "" - -#: ../../src/topics/parameter-references.md:3 -#: 473a89b059e14f649354a76bf882142e -msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../src/topics/parameter-references.md:13 -#: 4c57e8c446a0441c810493d34311ace7 -msgid "`tar-param.cwl`" -msgstr "" - -#: ../../src/topics/parameter-references.md:19 -#: 014e74e995bf49eca1c3b09ca011619f -msgid "`tar-param-job.yml`" -msgstr "" - -#: ../../src/topics/parameter-references.md:25 -#: 0d475fd8c50c4dc986643c14b82d0576 -msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/parameter-references.md:36 -#: ff886a60af2b49499ef0a0d31386998e -msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." -msgstr "" - -#: ../../src/topics/parameter-references.md:47 -#: d1e080ff809946919ed35e2b1055b6e5 -msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." -msgstr "" - -#: ../../src/topics/parameter-references.md:51 -#: 52e0d66811bc433b8c21b91e5ac6945d -msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." -msgstr "" - -#: ../../src/topics/parameter-references.md:54 -#: 6252fd49bc814c1c97c2a825a6b1b49f -msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." -msgstr "" - -#: ../../src/topics/parameter-references.md:59 -#: 97abdf2838c444f684629c0578a8ed31 -msgid "Where are parameter references allowed?" -msgstr "" - -#: ../../src/topics/parameter-references.md:61 -#: 3fd741db4c014ea6a53b6bc2fad63e21 -msgid "You can only use parameter references in certain fields. These are:" -msgstr "" - -#: ../../src/topics/parameter-references.md:63 -#: 986da8d3c56b4227a9481c9e2b0ea0a7 -msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/parameter-references.md:64 -#: 1beb8e88637545b8ad365441de547b59 -msgid "`arguments`" -msgstr "" - -#: ../../src/topics/parameter-references.md:65 -#: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 -#: 8349b7acc74346e0ac0d18dddafe2205 -#: 9b2e0b712ec146e1a636ed8d1f408c56 -#: eac9f2c8f0c0424ca5e70425fa60f677 -msgid "`valueFrom`" -msgstr "" - -#: ../../src/topics/parameter-references.md:66 -#: cb1036ef7aa449dc8728bf72cf7281e9 -msgid "`stdin`" -msgstr "" - -#: ../../src/topics/parameter-references.md:67 -#: 713a83cfde5e4d4181ec8477f20ac2c4 -msgid "`stdout`" -msgstr "" - -#: ../../src/topics/parameter-references.md:68 -#: 8d666991bcc94c83b1259746ced7e43f -msgid "`stderr`" -msgstr "" - -#: ../../src/topics/parameter-references.md:69 -#: 7ce52aad9f624afeb40e9829ab150651 -msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:70 -#: ../../src/topics/parameter-references.md:75 -#: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 -#: 4207d80deafd4b12a944b4b61e7494bf -#: 0b9493de338a4717bdf643991c72d92c -#: 489bac6cabeb4aeaaf90112969f0bafb -#: 34de0217785146c4ac0130e52319581e -msgid "`format`" -msgstr "" - -#: ../../src/topics/parameter-references.md:71 -#: ../../src/topics/parameter-references.md:76 -#: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 -#: 026108b0d1c344df883689be95db8fad -#: 0b32cdfd79ee469e83a629285223cc0b -#: fbe04046dc744f72b3a88da56f15b483 -#: 9065d837c83d4dd78cd3d664f882300a -msgid "`secondaryFiles`" -msgstr "" - -#: ../../src/topics/parameter-references.md:72 -#: 7f5bdccc51a14535891b13d8e787251b -msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:74 -#: daff49176fca4fd8b12369f4f92eb22d -msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:77 -#: d0208c0307b04cf384c7a9334046bb9b -msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:78 -#: b384a85509344ad5bbc3873684a19b9a -msgid "`glob`" -msgstr "" - -#: ../../src/topics/parameter-references.md:79 -#: 83d6911ab8994e55a87871c8a238f4fa -msgid "`outputEval`" -msgstr "" - -#: ../../src/topics/parameter-references.md:80 -#: b0298c96113742f6981316ad0e33b018 -msgid "From `Workflow`" -msgstr "" - -#: ../../src/topics/parameter-references.md:81 -#: 636f6c50ac274d88a7ca32f7bafbaca4 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:84 -#: d72570d062e54cfb89c82a1ce1a286b8 -msgid "From `steps`" -msgstr "" - -#: ../../src/topics/parameter-references.md:85 -#: 5b8e3e7c420c4490ac4a5905189cd166 -msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/parameter-references.md:87 -#: 22c6afe7aab84038a74f8478f8d97d64 -msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../src/topics/parameter-references.md:88 -#: 88877e67206e48b3b10e30ddead266fd -msgid "`expression`" -msgstr "" - -#: ../../src/topics/parameter-references.md:89 -#: e763d3be7c3347718bb851b0e601d466 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:92 -#: d7837cc8e8064348b2698f80e4bf47b5 -msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:93 -#: d87be82c3bcb4e1fb33946573d62037c -msgid "`coresMin`" -msgstr "" - -#: ../../src/topics/parameter-references.md:94 -#: 2362c7e8e16240e288fbaa49521951a6 -msgid "`coresMax`" -msgstr "" - -#: ../../src/topics/parameter-references.md:95 -#: f9d381b7bf2c4caeb6a5a3bace39b6a3 -msgid "`ramMin`" -msgstr "" - -#: ../../src/topics/parameter-references.md:96 -#: f957b015fbb64e448083a5a9b4ff4b0b -msgid "`ramMax`" -msgstr "" - -#: ../../src/topics/parameter-references.md:97 -#: be4bb996b5954fb8a90c57e5e6456ec2 -msgid "`tmpdirMin`" -msgstr "" - -#: ../../src/topics/parameter-references.md:98 -#: 00eb0fff1cc64e41bcbcf63ebb58ee11 -msgid "`tmpdirMax`" -msgstr "" - -#: ../../src/topics/parameter-references.md:99 -#: 073bb4a51bcf4447bde792e41e876bbd -msgid "`outdirMin`" -msgstr "" - -#: ../../src/topics/parameter-references.md:100 -#: ed9e837c60a14da0879a309194213033 -msgid "`outdirMax`" -msgstr "" - -#: ../../src/topics/parameter-references.md:101 -#: 160c7ce007564ee2825517bc29750c65 -msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:102 -#: 24755cdacd024d949fc6015b43983e22 -msgid "`listing`" -msgstr "" - -#: ../../src/topics/parameter-references.md:103 -#: 4ad1d82ee80844c581197cb14eab518a -msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/parameter-references.md:104 -#: 6542359022cd4a1ebfb08e8c104620b4 -msgid "`entry`" -msgstr "" - -#: ../../src/topics/parameter-references.md:105 -#: fa4a51155be34b10aa8c1eaecd2cdbbf -msgid "`entryname`" -msgstr "" - -#: ../../src/topics/parameter-references.md:106 -#: c51af125685146dea16c2dcd7f290aef -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../src/topics/parameter-references.md:107 -#: e31fc3370fd948c79e945ab30dacf99e -msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/parameter-references.md:108 -#: 7982f559dcff4178b222cdba267d1283 -msgid "`envValue`" -msgstr "" diff --git a/locales/topics/requirements-and-hints.pot b/locales/topics/requirements-and-hints.pot deleted file mode 100644 index a566fb29..00000000 --- a/locales/topics/requirements-and-hints.pot +++ /dev/null @@ -1,22 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/requirements-and-hints.md:5 -#: 15273fbf009b4036a2574d157740db98 -msgid "Requirements and Hints" -msgstr "" diff --git a/locales/topics/specifying-software-requirements.pot b/locales/topics/specifying-software-requirements.pot deleted file mode 100644 index d65ed83d..00000000 --- a/locales/topics/specifying-software-requirements.pot +++ /dev/null @@ -1,42 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/specifying-software-requirements.md:1 -#: b34314bdb71244f2a263427f22172b5a -msgid "Specifying Software Requirements" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:3 -#: c8609548e7904e65a5c395bfc07ad808 -msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:13 -#: e4c1c25793884b5aaead1fb15c2e6bbc -msgid "In this example, the software requirement being described is InterProScan version 5.21-60." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:25 -#: 91586b8767734e0ab01903f2562a7cf2 -msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:29 -#: dd7c487024b44a67a26765e59b5bf64b -msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." -msgstr "" diff --git a/locales/topics/staging-input-files.pot b/locales/topics/staging-input-files.pot deleted file mode 100644 index f9d75eff..00000000 --- a/locales/topics/staging-input-files.pot +++ /dev/null @@ -1,42 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/staging-input-files.md:1 -#: 3064f17a9bae442aaef41b9434cb71fd -msgid "Staging Input Files" -msgstr "" - -#: ../../src/topics/staging-input-files.md:3 -#: 09bb659a5cbe40948b59208f0fb77ddb -msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." -msgstr "" - -#: ../../src/topics/staging-input-files.md:9 -#: a1bcfead8f7f4270945e5512dfa9aea6 -msgid "`linkfile.cwl`" -msgstr "" - -#: ../../src/topics/staging-input-files.md:15 -#: cc0cd8765dac4baab9072a90e82e4f8e -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../src/topics/staging-input-files.md:20 -#: 77ac403083ff41e0a94b4376d57c4310 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" diff --git a/locales/topics/troubleshooting.pot b/locales/topics/troubleshooting.pot deleted file mode 100644 index cfd4aa74..00000000 --- a/locales/topics/troubleshooting.pot +++ /dev/null @@ -1,72 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/troubleshooting.md:1 -#: 628f6b4dad6d4b2e87d3c34d99b3bc9a -msgid "Troubleshooting" -msgstr "" - -#: ../../src/topics/troubleshooting.md:3 -#: c2f444d8af5b47b389a53f047f42f7fc -msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." -msgstr "" - -#: ../../src/topics/troubleshooting.md:6 -#: b4d58509c2874a3a9a4aca8b0eb54b8e -msgid "Run `cwltool` with `cachedir`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:8 -#: cf0d233ea286443d9b4cd7b8e9b03090 -msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." -msgstr "" - -#: ../../src/topics/troubleshooting.md:14 -#: e742b4b7517a4461ab38cd572fd02412 -msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." -msgstr "" - -#: ../../src/topics/troubleshooting.md:20 -#: 8d0d5c4374ff4659b0a34f86a106915e -msgid "`troubleshooting-wf1.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:27 -#: 2c4194ab026e41cb807e7cb15bc37e34 -msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" -msgstr "" - -#: ../../src/topics/troubleshooting.md:35 -#: 0d287a4115ea4e34b239790ceee5d9be -msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" -msgstr "" - -#: ../../src/topics/troubleshooting.md:44 -#: b72ee99d9aee4c88bf4ae1a493b40415 -msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." -msgstr "" - -#: ../../src/topics/troubleshooting.md:48 -#: 6541e0afd1784cdd890cae031fc6b13e -msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." -msgstr "" - -#: ../../src/topics/troubleshooting.md:59 -#: 3881a8c9e89c42c3a4a9fb99dffd6de8 -msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." -msgstr "" diff --git a/locales/topics/using-containers.pot b/locales/topics/using-containers.pot deleted file mode 100644 index 03e278eb..00000000 --- a/locales/topics/using-containers.pot +++ /dev/null @@ -1,82 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/using-containers.md:1 -#: 3a1cb28acbf64b36b328af24b8ad3896 -msgid "Using Containers" -msgstr "" - -#: ../../src/topics/using-containers.md:3 -#: b0788dc4a9694fcface9c2d1122053ee -msgid "Running Tools Inside Docker" -msgstr "" - -#: ../../src/topics/using-containers.md:5 -#: fdb03600e95f43248a8841308892f95f -msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 -#: 7e27ca6ce9974ef8a68e4955c377a7cc -msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." -msgstr "" - -#: ../../src/topics/using-containers.md:18 -#: 7162dac152a344b78a196ab9b304ff96 -msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." -msgstr "" - -#: ../../src/topics/using-containers.md:21 -#: 7ecf64fbdd774b298455e9cdf5be38df -msgid "`docker.cwl`" -msgstr "" - -#: ../../src/topics/using-containers.md:27 -#: 7ec954f8c1cd4ba3946ed2b3bd675083 -msgid "`docker-job.yml`" -msgstr "" - -#: ../../src/topics/using-containers.md:33 -#: b80d058d42c2414299eca96c4edd908b -msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 -#: c6ddaf94bc9f49e2b507a3eedaf597ee -msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." -msgstr "" - -#: ../../src/topics/using-containers.md:52 -#: d0770aeb8b0546ed943d60a3ae3b9f9a -msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/using-containers.md:55 -#: d8c679b90ba14cf29280c1f1d271358d -msgid "`hello.js`" -msgstr "" - -#: ../../src/topics/using-containers.md:69 -#: c10409c624084be79a3378ae056d50c8 -msgid "Notice the CWL runner has constructed a Docker command line to run the script." -msgstr "" - -#: ../../src/topics/using-containers.md:72 -#: 28514dd1b76648eb9bcec48290d7b66e -msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." -msgstr "" diff --git a/locales/topics/workflows.pot b/locales/topics/workflows.pot deleted file mode 100644 index 9847836f..00000000 --- a/locales/topics/workflows.pot +++ /dev/null @@ -1,374 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/workflows.md:1 -#: f87317cca4ba43af87f6a19b8fff6751 -msgid "Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:3 -#: 00756723cfea4c79ab17ae39e400fd4c -msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." -msgstr "" - -#: ../../src/topics/workflows.md:13 -#: ee41e057c6be476e9c56ac3c1f4aefad -msgid "CWL workflow." -msgstr "" - -#: ../../src/topics/workflows.md:41 -#: 4e06945e9d794db58ebf5953a7bfc169 -msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." -msgstr "" - -#: ../../src/topics/workflows.md:51 -#: 3bb6bd3fa9a241b18f725f765f6d8f89 -msgid "`echo-uppercase.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:81 -#: bd0042b64ca14e5fa4abe0b696ed8cc0 -msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" -msgstr "" - -#: ../../src/topics/workflows.md:91 -#: f640b8cc119544ddb698828751335eef -msgid "`echo-uppercase-single-file.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:150 -#: ef0a22597b7b43a09b9d930eb733b181 -msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." -msgstr "" - -#: ../../src/topics/workflows.md:160 -#: 08e47d409fad4688b3fa893aac699505 -msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." -msgstr "" - -#: ../../src/topics/workflows.md:165 -#: 979f0abe51a7435991c062b239ab77ce -msgid "Writing Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:167 -#: 9e7ebb3fd64e4d9b89d10aab7ff6ef5a -msgid "This workflow extracts a java source file from a tar file and then compiles it." -msgstr "" - -#: ../../src/topics/workflows.md:170 -#: a8bb6a54010c4563af5dd0e287e19ea9 -msgid "`1st-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:179 -#: ../../src/topics/workflows.md:180 -#: 3ca49084a67e48e196a29fce16266ebe -#: 2e5e721e9dcf477aacc5fd7970c8965f -msgid "Visualization of 1st-workflow.cwl" -msgstr "" - -#: ../../src/topics/workflows.md:180 -#: cd69af46dab64758a7eeb25b8dd5ada4 -msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" -msgstr "" - -#: ../../src/topics/workflows.md:183 -#: 1370172b5e4d41dfa0f00268853c4a0c -msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" -msgstr "" - -#: ../../src/topics/workflows.md:185 -#: df872d487e3d4e35b68bebcb27948577 -msgid "`1st-workflow-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:191 -#: 5039994944944010990efb63a1423bd2 -msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." -msgstr "" - -#: ../../src/topics/workflows.md:198 -#: ce1bf8dbbe3c448b8d413993b986bee1 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/workflows.md:205 -#: a72841d1fc594789adca91a6cec6b4c8 -msgid "What's going on here? Let's break it down:" -msgstr "" - -#: ../../src/topics/workflows.md:212 -#: ab3448be251d454fbaf3e2e40e2a6179 -msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." -msgstr "" - -#: ../../src/topics/workflows.md:221 -#: b24bc7e75b5e45a6b40f99122f7a46c6 -msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." -msgstr "" - -#: ../../src/topics/workflows.md:233 -#: 9eab201c6c314cf682f7623de820f007 -msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." -msgstr "" - -#: ../../src/topics/workflows.md:248 -#: 7aee0e6910f841eaad08091daaa43819 -msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:256 -#: ad9e578cb5154c06b323ed8934f70359 -msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." -msgstr "" - -#: ../../src/topics/workflows.md:261 -#: 6edc6273c5e84842a74b8921875481e9 -msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." -msgstr "" - -#: ../../src/topics/workflows.md:267 -#: 1d4faf0025bc4fc7bf53b87e4b3477e9 -msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." -msgstr "" - -#: ../../src/topics/workflows.md:278 -#: 2185db6e6c9c470abc4e9a4dc95a921d -msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." -msgstr "" - -#: ../../src/topics/workflows.md:285 -#: 91c1093736ea45e59fafba7d071bfda4 -msgid "Nested Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:287 -#: 17955d02a70d484f8b2654feffc3f853 -msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" -msgstr "" - -#: ../../src/topics/workflows.md:297 -#: 4e9524ce607243b9a6bd749bc436d796 -msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:300 -#: 6d24477bbd3245a9be26954768605af8 -msgid "`nestedworkflows.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:309 -#: 5525e4fa9a1e4245b5cd3a5465952fa8 -msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 -#: b9dc7d7eab974749953065c7b7a92077 -msgid "\"Visualization \"Visualization" -msgstr "" - -#: ../../src/topics/workflows.md:322 -#: 268089a26de840e8a01026a3d4ad93c8 -msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." -msgstr "" - -#: ../../src/topics/workflows.md:336 -#: 1523ed6264e84a0ea3a2c00857a71bb2 -msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." -msgstr "" - -#: ../../src/topics/workflows.md:341 -#: 125add3880f84620bc124f21096e1d1a -msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." -msgstr "" - -#: ../../src/topics/workflows.md:347 -#: 423dd287ac0c4cc4a39b17dcc380fe45 -msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." -msgstr "" - -#: ../../src/topics/workflows.md:366 -#: d0fb2fada3c74bc2bb81928891b284a3 -msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" -msgstr "" - -#: ../../src/topics/workflows.md:383 -#: 27e720818d69436d8c85931749918ad7 -msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." -msgstr "" - -#: ../../src/topics/workflows.md:389 -#: efe03781d801470db0950ca5c33e10b7 -msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." -msgstr "" - -#: ../../src/topics/workflows.md:394 -#: f21f8ee263e043a1b57dc8148a502b85 -msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." -msgstr "" - -#: ../../src/topics/workflows.md:398 -#: 5c91e32bd51045ec8442b28875e914a9 -msgid "Scattering Steps" -msgstr "" - -#: ../../src/topics/workflows.md:400 -#: dbef641be8bb4a18ae974357ecb32f78 -msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." -msgstr "" - -#: ../../src/topics/workflows.md:411 -#: e86d663e2c39446b8c20c5eaf94a8802 -msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:415 -#: 19ae2b52a9ab4b6ea4d8d8e57f40c170 -msgid "`scatter-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:421 -#: b711df1f3b1b4456b015701700c3c818 -msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" -msgstr "" - -#: ../../src/topics/workflows.md:429 -#: 60fb4221648d40968e1a0965a3b6693c -msgid "First of all, notice that the main workflow level input here requires an array of strings." -msgstr "" - -#: ../../src/topics/workflows.md:441 -#: c249bd4f52b348faa46918dee778a75d -msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." -msgstr "" - -#: ../../src/topics/workflows.md:445 -#: ba039b00b2ea4de693b3358a036fd993 -msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" -msgstr "" - -#: ../../src/topics/workflows.md:450 -#: a50560beb0f84c59b52a03b755e4e028 -msgid "Using the following input file:" -msgstr "" - -#: ../../src/topics/workflows.md:452 -#: b1bde49eb1d6496a8d54094076e9c0f2 -msgid "`scatter-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:458 -#: 18d238a1bba943778f951b22e777af50 -msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" -msgstr "" - -#: ../../src/topics/workflows.md:466 -#: 1fef76f43e2048718f82b67f66f48197 -msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" -msgstr "" - -#: ../../src/topics/workflows.md:469 -#: 6c2c8927cadf49858e0e1b3033c22168 -msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" -msgstr "" - -#: ../../src/topics/workflows.md:472 -#: 7482860af6ec4b519585837fee90289a -msgid "`hello_world_to_stdout.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:480 -#: b9a64729a3c34bb2aaf4d9f780b29022 -msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" -msgstr "" - -#: ../../src/topics/workflows.md:483 -#: f3ad56146ff3429db2018fcdcef05724 -msgid "`wc-tool.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:489 -#: 4050c846b1144a5985b37c76bb24670d -msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" -msgstr "" - -#: ../../src/topics/workflows.md:491 -#: fc2512823ca24060992b321fcf0d56db -msgid "`scatter-two-steps.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:497 -#: 2eae7d61ffcd485aac22fc1fbbe7093a -msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 -#: 39971661faa74b58bf2f64c18a27fa76 -msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" -msgstr "" - -#: ../../src/topics/workflows.md:513 -#: b36f484b8f904da58838aac09e7c14ff -msgid "`scatter-nested-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:519 -#: 0db1e2093f8645df8f13fe394e8bf018 -msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:522 -#: 38a16292b8bb4ec48ae169292db7a2f2 -msgid "Conditional Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:524 -#: 2c07c2968b53407686a8dd3f869b4fc4 -msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." -msgstr "" - -#: ../../src/topics/workflows.md:527 -#: 61f0704412654df781833ffb6d5f33e3 -msgid "`conditional-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:566 -#: d6634b5ec49e4113a90faec6b8de482d -msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." -msgstr "" - -#: ../../src/topics/workflows.md:573 -#: 9e6488eb6e60434eaf3148208a31a8aa -msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." -msgstr "" - -#: ../../src/topics/workflows.md:587 -#: 3fe08f086e374050a89a39fcb3db0b78 -msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." -msgstr "" - -#: ../../src/topics/workflows.md:607 -#: ec35b97546eb42c28cc9bbdbf2ac2067 -msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." -msgstr "" - -#: ../../src/topics/workflows.md:627 -#: 22cf017e76d74584991ded94417c19d8 -msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." -msgstr "" diff --git a/locales/topics/yaml-guide.pot b/locales/topics/yaml-guide.pot deleted file mode 100644 index eb8a5519..00000000 --- a/locales/topics/yaml-guide.pot +++ /dev/null @@ -1,157 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/yaml-guide.md:1 -#: c28a6abcd8334321b7d1c84192b42caa -msgid "YAML Guide" -msgstr "" - -#: ../../src/topics/yaml-guide.md:6 -#: 3e16eeaccec8491dacfde122153d5bd0 -msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." -msgstr "" - -#: ../../src/topics/yaml-guide.md:13 -#: 363eb3871f5d4c1288138dbd5f89be62 -msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" - -#: ../../src/topics/yaml-guide.md:16 -#: 31d7b17c34e0405b94f95e273bb22ac5 -msgid "Contents" -msgstr "" - -#: ../../src/topics/yaml-guide.md:18 -#: 60197a7f2b7c40c48ede3d59626a09d8 -msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:19 -#: 7b76a198bd154da99e38146a74ecec6c -msgid "[Comments](#comments)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:20 -#: 024a6818d1b9492bb6e1f1c11d932953 -msgid "[Maps](#maps)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:21 -#: d0c550b003fa48c8b1b16888c7e9bc5f -msgid "[Arrays](#arrays)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:22 -#: 7c2f8ceba9a141f097767ae8c3688aee -msgid "[JSON Style](#json-style)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:24 -#: 5cfa92e1509e41cf9dec646d3a5dad86 -msgid "Key-Value Pairs" -msgstr "" - -#: ../../src/topics/yaml-guide.md:26 -#: f76bccaee68c4eec96822d00013395a9 -msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:42 -#: 5591f710f08a4e8c8d974224cdf018b5 -msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." -msgstr "" - -#: ../../src/topics/yaml-guide.md:51 -#: e383736713e243d487b883e669fb7065 -msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." -msgstr "" - -#: ../../src/topics/yaml-guide.md:61 -#: c50eafc65e8b4b8a81318694098a42e5 -msgid "Comments" -msgstr "" - -#: ../../src/topics/yaml-guide.md:63 -#: 3d8de32c3f3448e5beb19d395099e27d -msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:76 -#: 20edeb5c184f4df2ade328131365d751 -msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" -msgstr "" - -#: ../../src/topics/yaml-guide.md:79 -#: 7f436640365249568802a846d4ad896b -msgid "Maps" -msgstr "" - -#: ../../src/topics/yaml-guide.md:81 -#: 7514de6b828f44b1b1d8683d8324a1da -msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:104 -#: 01288d81ae2e466d94bbee33751b3bd6 -msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." -msgstr "" - -#: ../../src/topics/yaml-guide.md:127 -#: 3e6ba9083cdd4ed586110f76cd071896 -msgid "Arrays" -msgstr "" - -#: ../../src/topics/yaml-guide.md:129 -#: 2c23b44142ba4969bd30c33c97142aed -msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:146 -#: 5956220b3839466aa491e84d2d0a5757 -msgid "and a more complex example combining maps and arrays:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:167 -#: 0ff275ae871b49449ec789b1bdc814c6 -msgid "JSON Style" -msgstr "" - -#: ../../src/topics/yaml-guide.md:169 -#: f5215b7de4994cc5890886ac2914be23 -msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:177 -#: 48dec799be364824a5dcbf5329f1f0ce -msgid "and:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:184 -#: b4d3a3a2823147c9aa7a37ad2fe5ce06 -msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." -msgstr "" - -#: ../../src/topics/yaml-guide.md:194 -#: 6998b8bd38a944f19c9ca758b14babe8 -msgid "Reference" -msgstr "" - -#: ../../src/topics/yaml-guide.md:196 -#: bcc40a813d344c0abd960add8685e132 -msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." -msgstr "" diff --git a/locales/tutorials.pot b/locales/tutorials.pot index 7864fea7..f989fb64 100644 --- a/locales/tutorials.pot +++ b/locales/tutorials.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,41 +17,41 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/tutorials.md:1 -#: d32522e2993f4b48a789f46537fa5ebf +#: b963a4be60544dec9a0c34e04aa43371 msgid "Tutorials" msgstr "" #: ../../src/tutorials.md:5 -#: 63a51dccb29045fd8f78d5e396c6e050 +#: f9246ba9313948f7b8547822aae2305d msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." msgstr "" #: ../../src/tutorials.md:7 -#: cb5f8748a5544be2835467ab07eb7a1c +#: 9a3d1f4c2d0b438188e84b692f831dc5 msgid "Beginner Tutorials" msgstr "" #: ../../src/tutorials.md:9 -#: 685d0cb2faa04703bcef408ecc2b92f4 +#: 3c4d6087706b4c90ac69005cebed9adc msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" #: ../../src/tutorials.md:11 -#: 20f45705145d45fc8420c4119b06a49f +#: 585908b83f854dd7a28715a4a0f6b1c4 msgid "Advanced Tutorials" msgstr "" #: ../../src/tutorials.md:13 -#: 2bccd19d542d4458a1ba8616236f1840 +#: 8934504b3c924a7d812014c344d58dce msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" #: ../../src/tutorials.md:15 -#: c491c73e4c00476980438ffc79c6e4d3 +#: 0c6b1dbd9f464c698322783bd55d6d6c msgid "Bioinformatics Tutorials" msgstr "" #: ../../src/tutorials.md:17 -#: b8485449206542e097584eca7363c8ce +#: 9a767964b3cb4f619f0b7a7d5d08a97d msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" diff --git a/src/conf.py b/src/conf.py index c5000204..60ece96c 100644 --- a/src/conf.py +++ b/src/conf.py @@ -236,5 +236,5 @@ } gettext_uuid = True -gettext_compact = False +gettext_compact = True locale_dirs = ['locales/'] From 230d934d45eeed062b6c02c94b5c9011db4d8fd7 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Tue, 24 Jan 2023 19:58:36 +0100 Subject: [PATCH 033/179] refresh ES --- locales/es/LC_MESSAGES/LICENSE.po | 120 ++ locales/es/LC_MESSAGES/_includes.po | 28 + locales/es/LC_MESSAGES/episodes.po | 31 + locales/es/LC_MESSAGES/faq.po | 307 +++ locales/es/LC_MESSAGES/introduction.po | 746 +++++++ locales/es/LC_MESSAGES/setup.po | 31 + locales/es/LC_MESSAGES/sphinx.po | 28 + locales/es/LC_MESSAGES/topics.po | 2577 ++++++++++++++++++++++++ locales/es/LC_MESSAGES/tutorials.po | 58 + 9 files changed, 3926 insertions(+) create mode 100644 locales/es/LC_MESSAGES/LICENSE.po create mode 100644 locales/es/LC_MESSAGES/_includes.po create mode 100644 locales/es/LC_MESSAGES/episodes.po create mode 100644 locales/es/LC_MESSAGES/faq.po create mode 100644 locales/es/LC_MESSAGES/introduction.po create mode 100644 locales/es/LC_MESSAGES/setup.po create mode 100644 locales/es/LC_MESSAGES/sphinx.po create mode 100644 locales/es/LC_MESSAGES/topics.po create mode 100644 locales/es/LC_MESSAGES/tutorials.po diff --git a/locales/es/LC_MESSAGES/LICENSE.po b/locales/es/LC_MESSAGES/LICENSE.po new file mode 100644 index 00000000..a9655e9f --- /dev/null +++ b/locales/es/LC_MESSAGES/LICENSE.po @@ -0,0 +1,120 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../LICENSE.md:2 385524707375429989b7b4fc7e4c7aa5 +msgid "Licenses" +msgstr "" + +#: ../../LICENSE.md:4 7682a147e3f74921948bde67ac684338 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 7273f384601c4f18a4cc33c833f05e56 +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 2cd9327d0e2e43aaa963633db1320b96 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 793123b1e0ba4603a0c54c952ea4a590 +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 151178e4c9a9444fb65dbf926edad28d +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 e44aed84ff0d48b3aea3946b3a7c85fc +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 d8bb44ca55b642d6bb4a88eaa8292204 +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms." +msgstr "" + +#: ../../LICENSE.md:22 6859f286e52c417096b072c923b9f235 +msgid "Under the following terms:" +msgstr "" + +#: ../../LICENSE.md:24 ee4ea8e1fd044924b34b2d96ca158257 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." +msgstr "" + +#: ../../LICENSE.md:32 7598558aee3244b6b7892b06df94a393 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 a83123e7ae79486c80107d176ea951c7 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 0cc05e8ed5274019998b1dfd6ab76824 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." +msgstr "" + +#: ../../LICENSE.md:44 d70e680300524c8583f1e7fd361ad2ba +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 d17e76d478354904b679b4f5ebde418d +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 015fba86005946eebc5959cc3b0493d0 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." +msgstr "" + +#: ../../LICENSE.md:57 524088befae04f5485dc731d505c769b +msgid "Trademark" +msgstr "" + diff --git a/locales/es/LC_MESSAGES/_includes.po b/locales/es/LC_MESSAGES/_includes.po new file mode 100644 index 00000000..ed23c04f --- /dev/null +++ b/locales/es/LC_MESSAGES/_includes.po @@ -0,0 +1,28 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/_includes/what-is-cwl.md:1 66189f9a18df470791d7e6ab690b3475 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + diff --git a/locales/es/LC_MESSAGES/episodes.po b/locales/es/LC_MESSAGES/episodes.po new file mode 100644 index 00000000..1dbd9f7b --- /dev/null +++ b/locales/es/LC_MESSAGES/episodes.po @@ -0,0 +1,31 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/episodes.md:5 49382fe02e4f4aae96ce4d1b666d649a +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 ebd3b75bc9a347029e9e164e94b43374 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." +msgstr "" + diff --git a/locales/es/LC_MESSAGES/faq.po b/locales/es/LC_MESSAGES/faq.po new file mode 100644 index 00000000..ba1f01be --- /dev/null +++ b/locales/es/LC_MESSAGES/faq.po @@ -0,0 +1,307 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/faq.md:1 e53c79b325b749a691434bf2f7825a5a +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 d95bfefa6344474d9820a266922831f8 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 991a77ca372d4324843ed340ffbfbae7 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 4654eac499464be4845a59bc281ec242 +msgid "" +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 4fcb9907771940d8857fab5b8211d337 +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 9f3ed67bcb13459d9e7196e9d82cb58f +msgid "" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 af6d80606de6412a8fe63ee379702eac +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 fc7c21e08e8e45adb8f1265af494160e +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 e37343ad3edd412f981397b995e6c841 +msgid "" +"The first method involves adding the folder containing your scripts to " +"the `PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 2b7e94e816fa46f4a221b5ce6b2214b2 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 0fd0fd13672d48cda0f3ef7f2b0701da +msgid "" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 a21be18c313d430a8986760ee3725198 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." +msgstr "" + +#: ../../src/faq.md:104 404295b5792747c8a87306181d078cbc +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 92582f3845b446d08ca9cbc4ad76a0a7 +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 2d62b6e5d7944818acd0f43b7d37ce67 +msgid "" +"The second method involves including an input of `type: File` in the " +"script itself:" +msgstr "" + +#: ../../src/faq.md:135 c72fa80f79594d479cb99dc6bfcb207d +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 5f2b7881a7c64cf29b05b4d78158e176 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 eb11641ac17e496384a60e4aacc5209b +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 c0aee2cf9ee046128002b09a8aa397d8 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 34a04d6d09e94fd796a5ee13c6b9856a +msgid "" +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 b1ee951a6e6e4f4c8e88de4dc93bd616 +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 1664807c6b264fc3b58e9f2c40a9543c +msgid "" +"Using " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 a7ab83c7f31e4e8d83fbfba1abadef2b +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 908451dc6990489e88edc1012899c440 +msgid "" +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 30947198b46d4151a5d92076c30659c0 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 0b320fb2e40442608137ed9d6f2a74cd +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." +msgstr "" + +#: ../../src/faq.md:229 a143590b23384ed79fc37b17a0abd46e +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 6b36effcb80040c79396a1df241f635e +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." +msgstr "" + +#: ../../src/faq.md:247 2873af63ee324fab948d16a9e14db5a7 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 a11f170a082a4df2b4a0c068dd0573ed +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 bd2ccba5ac7e486c9af1d906ad96b07a +msgid "" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" +msgstr "" + +#: ../../src/faq.md:267 3f1d8cf3390c43f8b78ce33fc020f1a0 +msgid "" +msgstr "" + +#: ../../src/faq.md:268 89626d59c2164bb99d0b123def33f701 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 028c6179803b4dc8a718669312804101 +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 23d9d603d4d44880aea5ebfd86e02d8d +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 06ae9317c6af481bbf4fd70236ca10a9 +msgid "" +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 0c6c0af33a274a8cb64ae3111c014338 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 1139a2f4e58046f9aac4c64b7d5a2e4d +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 ca97418a37bb4ae99bce1b44eebefbad +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 7a5d2d6c6474492fa65ffd8a5048c733 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 2549c8887b204ddabe4221978dce7e57 +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 d15ae28e932446b48bfc1dbdc34d8eab +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 925a0bb31c5f428b93232e42d96bddeb +msgid "" +"For example, the filename `a space is here.txt` includes 3 space " +"characters." +msgstr "" + +#: ../../src/faq.md:371 591dd97f12ca4b8ca263b17abe674fd6 +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 3ccdf1a970c14cbe8e1d269dc4ae77b3 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 4cefff22947f4d9eb2f66d1b6bca2a8f +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 bfcbe4003ccb4e59baeed0b631871970 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 d729277d8bc0488eadddf507ba63202f +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 ca99353cf8f94d11add95ba36408ee46 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 deb9ae92120d4e30aebd6e4d0374a0a2 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 7f4054de28a243c89bd3aca1e2764b93 +msgid "" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 29658fd7b5724addb5074891942f79fe +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 2dd0d8092e5640e3a930478497b78efd +msgid "" +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." +msgstr "" + +#: ../../src/faq.md:450 0d385ebff8c14cbfa418fa45c9b42e51 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 67d82ee82a184ed3921da6fd1928e83e +msgid "" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + diff --git a/locales/es/LC_MESSAGES/introduction.po b/locales/es/LC_MESSAGES/introduction.po new file mode 100644 index 00000000..3452a5bc --- /dev/null +++ b/locales/es/LC_MESSAGES/introduction.po @@ -0,0 +1,746 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/introduction/basic-concepts.md:1 7d238c155d6a40df8c8471ebb448a41e +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 4af76ab7bd674e6ab73765ddcc81d5bf +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 4fafbbbfec734215872f455f1c7e62e9 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:2 7250962d9fcc4338a7c9e64e0c2b3868 +#: f8759274ac67447ab61551060918d9bc +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 106e3e4dd19b42beaa90908e17529869 +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 eb85aefcc6824c028479e299f3477c5a +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 59a0083e4e594253b5eb0a6d2756f271 +msgid "" +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 19dbee8336704859b5bd9f232879e81e +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 947d98768fef4c3cb5b87208303b5712 +msgid "" +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 de6edc23dc9b4759b2aaa0954050b6be +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 ccee7288b79745d9a6a4bb32e9249594 +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: 10b787163c2e418291616a7bc1caf0bd +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 0176badcaff14e79ba00f1f26c40f42d +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 36e1e02745a44b4ab7f80f593eb3c408 +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: c3e19102cf7d44c795dbd57897e4ad8a +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: 288483391ca742e18ed19cd89666c4a1 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 5f5df951ffd6414eb054ca3af83a1abe +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 430425889a4c4f0a9f774d1b2e67debb +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: 9e42047299834ec6b41edf6c1b6d6513 +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: f6d4657261e042fd8bd9782047d19ea9 +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: fb8fa26ade2e4555bc5904a680d4de23 +msgid "" +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 1eb86d0cb6c74685829e7f978b177212 +msgid "" +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: dda24aff00964493ae997f36dff74c04 +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: e696bf67d6d04416b3f9c43f12376a10 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: b9746c3e3e554c2684be3917a31c7d10 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 8605fc09a1a04ab7ad271ac2bea9a17b +msgid "" +"`InitialWorkDirRequirement` - controls staging files in the input " +"directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: a1fb5f8dd8964b6fb8990f7e877f8e3f +msgid "" +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: 8fe3e01579524ef2badf284092ce00de +msgid "" +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c0ca689a49334564baf49359b582c491 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: fa9a58da83a04493bee1d1e6c1cba8e1 +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows support the creation of FAIR data " +"and adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 93e390de3c1445e5afa0a8bc8ee99480 +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 4b5b1dfad3aa4fee9a41463d5feeb8ea +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 6c0621375a704ed0a79d4ae65538bb31 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 357ae9a25a644caab49ddb3c9ead1028 +#: 646006005df94092ac1134bc194d5fe7 e495fae55ee1480c88438ec4dcc1fc5c +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: ab4a78d72dfa43b180615e565080d07a +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: ba8d7155363b4ed59912fc426b207ffc +msgid "" +"The CWL Specification page in the CWL website: " +"" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 37fc683fd3564bd698e3a8843ed7e401 +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: e6af1cb1c3484a1db8fa8577dd5684c6 +msgid "" +"The list of Implementations in the CWL website: " +"" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: fe7682c04d344a71a2d1de3586f83f38 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: caf02d5ff6c04255a2144ff453884b0b +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 a22112574264441eb4b775ce72f7ee62 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 fe9e792085024abb95180662bf0657a9 +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 23849325192045f5aa48c9f3d9a2080a +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 c7c0e1cd18d54dcca7062d7d053dcc35 +msgid "" +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 5d7a4a2cccbb47bbaa9ba2ca2de1eff2 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 a0ebb398fd1944858fde855a37938446 +msgid "" +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 83d90d246db24c07a73bcd73a3c6bfb6 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 c2fd09dd72af46ca8e3284d0c1c7dffb +msgid "" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 00694f21c8bd435f9de10785d2a829dc +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 3cd6a5a0a9754a678ec4eb5a9569a2ab +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 2b0d2a5dc85c4216840c2ce406e10413 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 0f8ab0f07c9f4e92b6907685a21e0d09 +msgid "" +"If you are using Windows, you will have to install the [Windows Subsystem" +" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " +"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" +"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " +"details on installing WSL2. Your operating system also needs internet " +"access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 eb1b97c2f64c43c78cf620f0b3197707 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 b0fff1b3d67e4e01b7140def8004924a +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 dfad9ccfdc5949adb5785e57a3f0a345 +msgid "" +"`cwltool` can be installed with `pip`. We recommend using a virtual " +"environment like `venv` or `conda`. The following commands will create " +"and activate a Python virtual environment using the `venv` module, and " +"install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 229d3b94015c46f89a7fcf3035a06e38 +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 bede33df513b4ff0bf31a1c4a1b76304 +msgid "" +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool#install) for other ways to install `cwltool` with `apt` " +"and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 f20e6ae025fc48cf82b490aa1e45d978 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 10c729f31bd94b2580a494a07e8c8c06 +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 55571e0099af459bb38ef2cbb5ce3720 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 436d10464d0540da9227bff0e7721928 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 db76c196cff7476c9f0059410071109e +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 5c34965d08704905af72df2d02f399ea +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 c4b1c6f7a6214a2a8cda037dfd1ce5e7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 22b70a1995e24ae1a5e688b08d69be78 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 2b078afe85c9496ebe7c4fd5fa849506 +msgid "" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 edb107bbbef94363a531344862b0646b +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 c92da002f02148e485fccabfb80f78c6 +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 5ff5383fffc646cf860b9e6adffe0d4a +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 3fb6539b1da24c6d8cab103ebaa728e9 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 56f8f92a8e4e46de9def7d33926a9354 +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 f024c312097941cc838f6e4684709e2d +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 27eb4624fa6a4fbca5c842bc69e277ff +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 a086a591e5034a768d6ed9f95ccffb41 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 dacb4f334ee64afa9da1418b806fbb8a +msgid "" +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 64cb2e80ed554f75aa64bc856c011e74 +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 7c008d7286b242c4989809773075e369 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env ` rather than" +" using a hard-coded location, since `/usr/bin/env ` looks for" +" the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 3d0c3d9473b64745aaadd1c97f86e6bd +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 f87429becda74bdab6e9e8956da16786 +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 40faebbbe3974365adbf4190ac9571af +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 24ce76cffa4c4dc3b1471c932ce34d28 +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " +"" +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 1a14a5c5c15941ff8f957be9b7e346fd +msgid "" +"cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 6fccaea992b74740b91aa4dea1e9b6f6 +msgid "" +"The CWL community also maintains a list of editors and viewers: " +"" +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 ff2d02dada844e349ce39147eaec02a0 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 756d50a22d9944989e83fd49691b7dc1 +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: " +"." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 208ae40269d64a95922c3b6b88fa7af0 +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models " +"with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 676cbeed9ecf468587f88adf03f088f2 +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for " +"pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 97048cb2351f4408946828ff46cd513e +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 28810c389a8f480d8af7af37580fba6e +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 6eba770f0a494294ada23cdfe563ada6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 bc84e8e2bd7b4e2eadf8e09b64f8b11e +msgid "" +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 244007c12d0e4c11b5bc5a50fbb7b263 +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 1b7f68f5a3214f4da4f1887d14ced464 +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 aab574ceba8348b7a62c1c645c7ae300 +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 e3e88da22e65425292b19d8159e6bcdc +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 fbdbaead418f4246b4216acce9c6a51f +msgid "" +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 008fc4481f1c4c7bb215fa3b6096048f +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 31d3ab3f31c44729989ee72a756c7242 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 069fa8bae74d4c24b680c4199d714277 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 62cacbc189d0440ebe4a8dde4878450c +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 f208e50c0089409aa7463c915be80092 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 6c551e9af341475496b7b6b104330183 +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 da2c9a63648342aab3f3b8a34660a4bc +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 1217d999216f47aa8f1903e2417fc57a +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 3559a76a1fc64f3eb61a503bf7c77757 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 21386999503341408b798efa9fc4f262 +msgid "" +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 215e425a5ae64cd0ac5e8d34d7f47b58 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 963c003c4a334dbe874edc0ab38ea92f +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 83921375eed44fc695cbc172d9317032 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 9795092d234e4fa5a2bdfc4c9c02460f +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 8846a5ff35b64859b8ec7b16be9f8f6b +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 785c9e2330b045b39bf02f77ab6513f6 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 b6d05398bca648b8ac25755fbaab91c0 +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 2ccf7e847e0b476493ae514381ca3612 +msgid "" +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 d7168eb1f7384733be6316fe72f486eb +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 14bbd3ce1f2a488ca919d4f26c8f1e5a +msgid "" +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 86f1fc65d2d14a41ac282eb63fd9de86 +msgid "" +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + diff --git a/locales/es/LC_MESSAGES/setup.po b/locales/es/LC_MESSAGES/setup.po new file mode 100644 index 00000000..68494d21 --- /dev/null +++ b/locales/es/LC_MESSAGES/setup.po @@ -0,0 +1,31 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/setup.md:5 715f40c8e3f544e4805ae2b456b9d699 +msgid "This page has moved" +msgstr "" + +#: ../../src/setup.md:9 c9641546c55a44eab9ae40ec272d5df8 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." +msgstr "" + diff --git a/locales/es/LC_MESSAGES/sphinx.po b/locales/es/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..1c2687a9 --- /dev/null +++ b/locales/es/LC_MESSAGES/sphinx.po @@ -0,0 +1,28 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 ada5c93414a84374b3eaea93dc11ae74 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 a3cc1c498bad434ebadd4a2e92dbf5f0 +msgid "Section Navigation" +msgstr "" + diff --git a/locales/es/LC_MESSAGES/topics.po b/locales/es/LC_MESSAGES/topics.po new file mode 100644 index 00000000..80ee8dd9 --- /dev/null +++ b/locales/es/LC_MESSAGES/topics.po @@ -0,0 +1,2577 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: be1d17fdb27345ffb7fe0cbe92002434 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: 82ff1f5ebb0647e886d131f7a8c4f5c3 +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: 4dbbc91d876746b59f53d3ba49df43f8 +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: 82f4844017ec4f609c8f0f5bf9812f75 +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 afb24d50c0a94693ab9ef9271068e58d +#: ca7a2bce1de34dd2ad8f77095854037b +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 23f9dcf2c7344a40aa2d512f1349135a +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 3d26cfb6a1204ba89ac812bc4fe3df4f +msgid "" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 317f82f2a0d54af29baaf5e3fca1558e +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: c5f85db684c842a5a2d55afb8ea44e94 +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 92154668e72240e48268a3dc593f65c5 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 df0c80b10cde412c901b9bfa235b4521 +msgid "" +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 93e66f6c1c9643a3944ad3c7651464a1 +msgid "" +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 7b54e111b9a2485d912b9c1dde0e6816 +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 c58100a01b034441b247e761df1f6a12 +msgid "" +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 53c3357a75df4704a96848aebc093327 +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 a9ae73ef4d3447038d1180032b41255c +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 a2a654e113d64f37bb3bfcb8828301ce +msgid "" +"For more examples of providing metadata within CWL descriptions, see " +"[the Metadata and Authorship section of this User Guide](../topics" +"/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 66ad30cdce23481d90042b63c3bf8d16 +msgid "" +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 f3c0be3d1a3249288a8cd3053bc1cdcf +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"`SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 07ad1cf2508d4cb780a6e703c07d5a5b +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 f0931e33e50a495aabd1c58daca72c3e +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 3da4c1e61c53469e8e313553130a5b28 +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 8d3930c2039347beb1383b0dab7ea1d5 +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 275a541a634345d2b88a7e982d3a84cb +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 23e3e58d1b5245919d1be053b0c53ddc +msgid "" +"Each `CommandLineTool` description should focus on a single operation " +"only, even if the (sub)command is capable of more. Don't overcomplicate " +"your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 0a7b19343ab34220a615f9d5735f62f3 +msgid "" +"Custom types should be defined with one external YAML per type definition" +" for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 fbb538cc258a445a938333315248a4f8 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 dee070dbc0c54210a3b276dcd1e3b151 +msgid "" +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 0d5c1c5e50de42809afdf4bcddeb86e0 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 63a5664bb6f043529e753fa27faa9104 +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 e3832fa90bc540dd9c92dc606c8a3d1f +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 8a2e36ed7ae0486b9a569b8a7c336fe9 +msgid "" +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 00dd50adbb734f0ab7e08d005cf30487 +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 eb2ea54b83304757ba4b835d4ae45642 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 ad6f136a690e4c4d9320cbff4b1a3469 +msgid "" +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 3018247f156c470ca7b9c7801a6f59bd +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 7c07c9401a3d424089828def1d272842 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 d5300fa60ee942cc961594a504b0d08d +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 f56c8f69d71f4f4da40fbb007008500e +msgid "" +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 4621ef6fe81a4048944814aff22f508f +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 1d3f1abb81ff4186843df880dc732ee2 +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. If a command-line tool is written manually in CWL v1.1+, there is" +" a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 93f0719b3b2c4c5297bf925801c93b45 +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " +"Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: 46b4df81014846aea9e0fe7c5caade0d +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 722ed10f0fed4ff59852fa09c45a92f1 +msgid "" +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 20b151c8c270433ab74288011f2ad47d +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: 0625cac27fdc4127b50bd7f195117189 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: 2035501f61434c339a5abdf693696c84 +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: f6e00a5502ef4bb386ee5f88b0085527 +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 4fbbc941c4f7412b936446fbf9115363 +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 +#: 9f546d2c6a454542a860ead319642479 e6c179499aee4824a5c02babbf26a869 +#: eb2052144d844cdaa0e9e4b3bc487628 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: d9ea213b07e64d04b53cdb32a3650322 +msgid "" +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: fcc7a6d59f8a4e13bf821d488fa17db7 +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: f7c967a182734c8ca47f873a0cb28093 +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 +#: 20f1807303474b5c8c18cede5df322a3 2c41b94f3196446ea483c630af9eea67 +#: 5735865bd655415a9a136f441eebafaf 7364d5ebf81e4949b3212b06788e2381 +#: f1195863b1b345f9a718776763466533 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 d2e58b004bfb4c6cae7c69658de21321 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 484ff45699964c2996a0cdfea0fdb329 +msgid "" +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 c30f12911bb649c6b71e7ad73edd0b4c +msgid "" +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 c8ecf2ef21fa4b8ba562625355ba8a65 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 3f328356740644a582ca21d5fa60b2f6 +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 b9569867a46745268f37ff47c18079fb +msgid "" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 636449effdeb481da9ada5d283db2ab9 +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 d6d41dc3bbd746bab0a5905a8611a356 +msgid "" +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 e742d68f3a994b9595bae07ee2099831 +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 f338008e7fb646038a7dcec456d9dce6 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 e69fcaf1f01049d6824058969e87e0f0 +msgid "" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 31abe821b66643d098ecdb4e207ed064 +msgid "" +"Note also that the author of this CWL description has also included " +"`ResourceRequirement`s, specifying the minimum amount of RAM and number " +"of cores required for the tool to run successfully, as well as details of" +" the version of the software that the description was written for and " +"other useful metadata. These features are discussed further in other " +"chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 b2a8bdbc4e4347389dc9e2c34e7c71ca +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 8de1ffb0a81547f7a616d5ea912998c3 +msgid "" +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 9596b81e881549fba7910947a202ba5e +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 8473228fc0104b4c940a967294276542 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 75f469063959433a8ed459c2b09cd61f +msgid "" +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 6676f841711d43f682e18d954438fc65 +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 d6d043d8ce9a41c59ad0d3239f8f306e +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 f3378c740b854b9695ea6ccfb0ab434a +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 c9d5c0dd3eeb4617891f90d1a081a3e7 +msgid "" +"We had to use an `InlineJavascriptRequirement` as our expression contains" +" a JavaScript call in `.toUpperCase()`. This means to tools using the " +"expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 08240053421545288788e84dec6d6614 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 cf3ebc8d28d2443ca0e67b5974a963ab +msgid "" +"If you need to manipulate input parameters, include the requirement " +"`InlineJavascriptRequirement` and then anywhere a parameter reference is " +"legal you can provide a fragment of Javascript that will be evaluated by " +"the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 767a6dc8370b4f9aad42e07a657e3e1f +msgid "" +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 f38d9e8192614ba689d17c1cc48ac848 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 ce88970e57f2427a905e1bc66c20ffe8 +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 e7238751e3604a34a15fff753136eada +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 ff81d45c3f124c738871b40e5b717d7b +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 f92515a70adc4366bc46e2eacf49e47b +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 dcefffb5ecdc4ec3bcc216c21df896ec +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 bdb0a61e53cf4521bc0f16593eaa5fdd +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 80c3b1fb37aa40038f0bc98905604c47 +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 22a6a66f05c94b988789edfc7acb7951 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 f09db29f329141e6b3dc3bf348e62b92 +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 ae0f7e0009944da58df73fbc70600fc4 +msgid "" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 3c17c559cfbb4fbcabd0dd57afd0f710 +#: b2c2a86928eb40a18e72586ca43ac3f3 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 0042cbd326484bc985f48f469bedff14 +#: 447dcc99dc59453ca560d6c54bf8d7bb 996a1497269345569208c861d8bcba6b +#: ab62eac4484146cb83f26c5bc74a92e7 ac9c83c8605d47818cd2eceaa107e44a +#: ee13a1bcafb0428abc6f97816476b8a5 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 2054a8bc6ed643129482f73bd0b53823 +#: 4bcda5432fe74135ae0d31b4eb0d5d7b +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 4e5551d884b74e5caa0cad273883fa11 +#: c37ea64ad4f54949b17e442698e25a49 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 28453a745d8f468b94157409007415de +#: 7b476f5cb3f64cafadbd962d465eacee +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 12c9aeec38514f7193d41be7d2b81976 +msgid "" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 280eea3ba89e4d84a5a8bbb14c74e36c +#: 447f71c801564eefa5b04659c834ea23 69f163066cc04c30a34d7b97ac7a4bc2 +#: 6a5d8d98b190442f9aadc2c074227835 89fba2d03ddd4cdc943e9175bd0ece33 +#: 9a9fa9f67e434ddeb38b339d004aec53 c533a40746e44835a82b1cc6461576b4 +#: cca5748633ab4899beddd115e0178db6 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 05182018082a474384e29c2ff90cb060 +#: 30217d1193e142729205e28e4cde49d7 308e0245ba0b48fc8f665d12ce5fa0c0 +#: 64bef9a598ed4adab4b517bb8f23fb25 7f7bbf1a07684e54b97ca1950c34930b +#: c3ae98ea21e244e3a76d06b87aa8bfae d4f067c6c06c4059b133c18affdac280 +#: dae8990502254aa99cc1ba44bd42bc89 +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 88c61f4dc48f457b828143b1f0e86168 +msgid "" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 2473f34317664da3888f6696f1bce0e7 +msgid "" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 ced207b70446434bbe64d228a34c825d +msgid "" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 9b6ddcbbd00c4f5fa4088674586b8b60 +#: d02b26eba3b44df5bcc65436f66248f9 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 38ebe3bb55484f61be01dbd31274b05c +#: c6018e429f30454cb30a33a92c39bda6 +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 a13cf40c0af743dea7589c4186465d1f +#: f51dc811ec154fd6a0b60d637ae42f06 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 a115dab301e34a958a9acea03c2b76a8 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 1540eea771934469b6b092c7eba2c223 +#: 6876d25a0d324dcabc7ae2e6202378a1 +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 927df10417db4669916e08b9e4e37641 +msgid "" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 75ec03ffd3e64fabab680a2fcc66e0a4 +#: fa2635bff88c49b38401e2c87035d023 +msgid "" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 cbe310d7612e4f68b4832692cc0d145e +#: fa897f1a899141fc9e6be1b6af9c01ce +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 ba5b5e8410df4acab9ad6459df2ff061 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 935d707d1e31415e806b2bbcb851e322 +msgid "" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 89f051a47b99491b9ce17ded769ad1a3 +#: 9d59f22a9e734f8982b89830b4e7e6fc +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 182e1b73426e4367bf8fe430a415a9c6 +#: 5b5d3f05e6c647a38af612c10b2b8b71 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 3fa480e44ffe473abb3af953f2d000f9 +#: 6375ee37a7fd4fa19be33c6f0ae75196 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 b6d5c6ff972a4607873daa53817a6860 +#: d0a0be70585842d8b17a8ddc7fabfc3e +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 0d558c8e126f427ca9862d7dae8a2cb7 +#: 293d592f29e34a5aa4f7420368d2f24b +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 43f37d9ec9b5429ab811039d1e8211d0 +#: b3a9149a14d346fbbc844d4de2cb3acb +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 5dbe9152fa2b4554a4ceae0b5163a7f8 +#: e137a1254667427f816aa6b5219e7f26 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 7af83d9455a944c180349d9f3123901c e8219f72a0854febb800511e2897cea1 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 f3f205c655eb4a2fb8c34407ee02fe76 +msgid "" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 0f3325af2b674d07aba8d1b254b7bb67 92c818fc42b64e94b8a3bae737df6ac6 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 a8bc743f7dc648889ce51d8a787597dd +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: 04b9cd485e1342d0870c341321089d15 a07dc02fe7bd416994f9755934e6a524 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: 69d9c547532644408b14655f50175684 df87b2c504dc4ae8865a0f4c94a84dff +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: d248acde95024c94b3921e290276a2d1 f77892ff017d48fa833343150cdad6ca +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 c0909df1820f40d599151a7b45db2f04 +msgid "" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 2d62117b8b824035916716cc818348d4 9f0237a087b5445eb0a8fe474d3e3869 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 bdbae4965a344e778ed0e80a8e23845d +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 1af8bb96001e43d9b649044d9631f360 +msgid "" +"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" +" attribute that allows users to load external JavaScript files, or to " +"provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 303ce6bcd17d4a219d2c3f4079e9b332 +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 d4e0acefb25d458982b37167431c8364 +msgid "" +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 b43add5b2d72451db8eee00a03b347a2 +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 0908315609f1413392b2ed9b5769a62b +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 d8aac17a8a9c4c209695ce760fc4cffb +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 2deae9db0d394245bf21ba3e469fb64f +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 6849411091ab422f8ebffc27e68c3286 +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 a74d3576acbc4694bbf75d371c57c4b0 +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 330e32b4188141c083465fd77ac0d962 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 61fae30939644f2e830107bb6815659a +msgid "" +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 8e057a368eae43f892cdfcf1492fefae +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 108a176667a74331a9c634537c6073be +msgid "" +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 dc1a23ba61fe417aab857a2cf3b87d09 +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 683b69656c23424d9a171f72cc1ee355 +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 a2d926603ed24b13a77a64606b72f7db +msgid "" +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 f00b6549fb2b40c7a0930fa2d70f78e9 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 02364803949047ddbad575b3f7ed27a3 +msgid "" +"Tools and workflows can take `File` types as input and produce them as " +"output. We also recommend indicating the format for `File` types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 8f25e0b9d6564f089bc07050eecd2cbe +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 051d96f1784a44478c888a692a43020e +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 c0b16138c24243f7882de4ea02ef14e4 +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 05c4a830b7084575bfd35263d9226104 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: 1af1e2ed821a435088471aa1d28c039c 441a574563f246118f24fc1ab8324b2e +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 241dfed53c39469d9e340a2494f97572 +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 c377cf86598d4ca4bf5311a47978e302 +msgid "" +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 53ff3c58049a4096ae894c4b0214d5cb +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 6c6c380437634412900e3f8dff4558f6 +msgid "" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 4ca0f8c05d9e451387a1eda0e6a04dad +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 339cc31ba40c4d2cba0ff21d668701b6 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 802f62184fd545eabc2afb78d90930c1 +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 9b641ae58d834dcc8a79fc547ead64a0 +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 8886c014968d4e32b0ce1cc44a9068a0 +msgid "" +"Available primitive types are *string*, *int*, *long*, *float*, *double*," +" and *null*; complex types are *array* and *record*; in addition there " +"are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 f40f938f5ac140cea72a4146a3329579 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 415298524e35434ea19a25c31e9ae649 +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 e8b631d0d4e64779aa7333b8e756fcbe +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 c5f3fddee0734d2da9207d64e268463f +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 fed45d1ab5574bd889af14787ac2cd20 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 1654a2e9bca0443c8fb46f7191beb81a +msgid "" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 b22b453eb5d0497e88243bcfc4d3cb1b +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 c136e4badbf3429b8c9c9efbc91d7f65 +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 31ddeb567d744c21bbfa76e8cdf95e6d +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 b19099fa3f3a4b5491e094f1ababc4a2 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 685e49311ba547f697fc90073168041b +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 d31fc4e804a34097ab506fa3aa469b1d +msgid "" +"The field `inputBinding` is optional and indicates whether and how the " +"input parameter should appear on the tool's command line. If " +"`inputBinding` is missing, the parameter does not appear on the command " +"line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 26ca8366924a442d9a3fb26f7223b028 +msgid "" +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 e9ba36f7d5ff4776aad272c9a0a7a81b +msgid "" +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 bde0dfcb13ea4ac8bab41a8c3fa024ec +msgid "" +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 0a38fa331eaa41ad9d61c869e5b73574 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 afe9f6fca7314610b25aa519d145f1c8 +msgid "" +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 e976913dca354fd1b027ceba53e279fd +msgid "" +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 3f5437225c06473ca6d99f256b735771 +msgid "" +"The `baseCommand` field will always appear in the final command line " +"before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 e0a6c25648394dc4a06c1a1ab11656d1 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 895ca55530674398af4f3ab0a2ff8295 +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 2c9f27b7c4534f5087194653288fc473 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 2f54898bb89b4f24abcbb9e032b14fac +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 07e7e4b0f9d047aba2b860033e9c939c +#: 12a54ad82e994ce485e2996d4e804373 5fb5d18d006242c2ad4cd143c6e6b5c4 +msgid "" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 36d386d92a7a47099dff930b89063d26 +msgid "" +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 eb22abf9766e441f835aaad0d12fe198 +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 dad1426793764a71ab0a71c8f6872da4 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 22c9fdaebc8c4e0f9e1e8b72ef87003a +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 c1e21b305da34c6b8960ebe5ca0d60bc +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 5f3e64b47249408c9a1e006d27826a48 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 76984af8223c45688a49ca7082b24cc3 +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 ff1dff0c91ac4324acc01188f2ef2bab +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 951aff2f38bc43c8bd1086a9e62243fe +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 ac93b8f5dd1646b8bbb7f5edc86ad2c7 +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 baa943e150554186ace37f310442a8a0 +msgid "" +"In the third example, only `itemD` is provided, so it appears on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 53f7e15ad5dc472faf409f30d902d4ce +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 1c455770202547a0bc3c62c063a0b3ed +msgid "" +"If you use exclusive input parameters combined with expressions, you need" +" to be aware that the `inputs` JavaScript object will contain one of the " +"exclusive input values. This means that you might need to use an **or** " +"boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 918873fedf60421f9e3713f82ac0c207 +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 4999688d5c954eb48fc42524e7a33176 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 294545640c6148dc8043027d4e4ea7d4 +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as “fasta” (one of the values of the enum), " +"your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 258d3d9ec6bb410eb012f89b44bf4072 +msgid "" +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to a `null` value, which does not match the expected type " +"for the output field (a `string`), resulting in failure when running your" +" workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 6470c55fcf5e45b09534705df1fb4e7b +msgid "" +"To correct it, you must remember to use an or operator in your JavaScript" +" expression when using exclusive parameters, or any parameter that allows" +" `null`. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value if none was " +"provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: 0bf3128f26ef41f7b31418f506dc83d4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: ef7ddf8716214cfbb8a411a13967198a +msgid "" +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 913df947afb7420097be3f15caede947 +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 4c773c6b1db9460ba58d5d276781d6e7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: c593b5d1f7e1469da7e97ca737632bc2 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: 28f6bc9a1465450ead788703b8329902 +msgid "" +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 84b37f20f8cb4136b274ecef284039fa +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 391ca127d3594bf0bd12a3ed29a85fc7 +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 e58e02c974ca451ca7e52d4a7e14ad99 +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 b725956dd0ff4906b54a002afacafd09 +msgid "" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 42e684d404aa4715a538bc209e84b469 +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 3bc2f8d60cce460788cff24274fee913 +msgid "" +"The `uppercase` step of the workflow is an operation. It can be used like" +" a command line tool or an expression. You can also plot it with the CWL " +"Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 910029acb5864b919b452e62a365c789 +msgid "" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx Graphviz directive (this" +" user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 edcbb0fc660840f29309e24a1f934d25 +msgid "" +"If you try running it with `cwltool`, the command will fail since " +"`cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 14bf9940996647ac91ea2de9e95dbe13 +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 71459c6b3efa47a1856c8f22f1b529da +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 77937377da354c46afb8c7d4988cf964 +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 7dbd814741e4452e95af2bddbbd41c73 +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 10965b18de5841eda0658840d0e726c4 +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 d1ebab8483744101b29a095067495897 +msgid "" +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 030b920fe9ee445f9f996aef68087129 +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 81f1b2d425f244728504cab01a06dfeb +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 d23514327fbd476d87e9a3308cac38e4 +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string we can use an " +"_array of strings_. The first element is the command to run, and any " +"subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 ebae564b85824cd1818837689b134af5 +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 94a88afd7acc4576b8cc22780991d629 +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 a4dc894fe82e4b779771b512424ce70c +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 dfd9feebfc7049498f807dfeb91e70e3 +msgid "" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 343cba8708a14ff9bd281fdff790bf39 +msgid "" +"The field `outputBinding` describes how to set the value of each output " +"parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 485a5a4cba354640a53832e4c7460fcb +msgid "" +"The `glob` field consists of the name of a file in the output directory. " +"If you don't know name of the file in advance, you can use a wildcard " +"pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 bafc8ef1a46b4f97af05a146a8903e2f +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 3fafdc8d21344bceb8262e8534e34afe +msgid "" +"To capture a tool's standard output stream, add the `stdout` field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 14fff0b709774a4cbb9213dc97ae9d42 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 ae07eb32467f40189765939c2fb4f6ae +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 98aa9d49f5b14429b5fb9e38ab9c594d +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 ddb1cc7a7f6f44cd96748c88753b5bdf +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 af69c5bbfac241809fd6e882dc1cafdd +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 7910b5ce6997467096db8d432cfb2088 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 11452076e78d4ccd9773b301d831d350 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 f8227a94ae9544a189886f90e9a3433c +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 38a045a2b8614cbba3a02d4f27b50127 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 13529a4cc80a4070b85bf29829c762b1 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 da5a588a3155445098b7ad81b78f1fa4 +msgid "" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 9e91e38ca0e4473384498c6e28b1f116 +msgid "" +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 a0e0270144df4b6aa3bf0ad261938b17 +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 a4a0147041724445b7ab3459cbc786b0 +msgid "" +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 ea5153744a3d41dc883c4bb7df4e16de +msgid "" +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 84270504a1c445d2917825b8e854a80d +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 9616d24145e74d17ac76cbe80ee4972a +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 fe869638aa4a4cd3a43bc071ed66cb37 +msgid "" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 1e3f77c12d1c48a7b2df7cdccfe92d41 +msgid "" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 2b86b2eb9a2e4310923aa3e3c16fac1a +msgid "" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 6ad56ee119684a83b42821f3b366cc73 +msgid "" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 11b45dd3f4a644b2b6175fb9bf4219ad +msgid "" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 c5446e59a6bd4a3cbfc0ed2cd21783f4 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 3fefaf0fbde94a85be6db02643d0a5ec +msgid "" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 3911b95f4a72415f968ed640f445bd00 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 841837a2edca4aff8231a0b955def3a4 +msgid "" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 665c8d7b622441cda2c1f6b20da5d664 +msgid "" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: cb71700c69694a53a62a43ef11a62595 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 6be0e1471d164c5099c0ccc2824cf038 +msgid "" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: 5984d3f30ab14197bcc03ce556bad3ab +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: 5357d8f77e504324a2904e7dc327e46a +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 1bbff970e33144148c394d7f18ebfd96 +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a `SoftwareRequirement` field in the `hints` section. This may " +"also help to avoid confusion about which version of a tool the " +"description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 0774b6bc9c8f4ab0acf943ed07f4b0d4 +msgid "" +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 5cadc31694ee45d99ffa369983971756 +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: a8a0b7191ce9404292df0699b96c51d6 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a `SoftwareRequirement`, " +"search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 86c81fb6d34b4b36ac8778c79cbc0306 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 4bd8293be25d401a868df24fabfc6538 +msgid "" +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use `InitialWorkDirRequirement` to stage input files into" +" the output directory. In this example, we use a JavaScript expression to" +" extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 05c39f514e234bd88895716c99eabcda +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 83fa50745b7e486db93f4d7883a778cc +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 d8d67e5238d049479e9c1a1c4b9b62c3 +msgid "" +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 60e89aea0d634296a9753910a55a4493 +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 7ff74ba8fd9443cc9e1cdda32e38ca7c +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 1c8afaa3ef0c41b2a1ebc57d329d6ed4 +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 b540a4f7a25148098a369350e22c247a +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 1cda8c6f9ed6421bafb39554bdc9b5f7 +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 93b8b99518474d709a90f5442c0d2b65 +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 059deec3f12448b8a673e1d957595d7d +msgid "" +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 9c40b03256274b43a484b2a1108186c5 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 45314aa766a5479f9855cbc054ad17b9 +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 8289b75b054040e5bfa71f482554eb4e +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 333b0ee71bde4ce8aacf4ff8946dfbfe +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 54ef32fbf91a4edfa0006f62b51bcbb9 +msgid "" +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 de34c8de4fda441d80abb9990e75b494 +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the " +"container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 fbd75c368e6444d89978f010a235709c +msgid "" +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 88ba9fb9da1d493ca8a4e37982ff27dd +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 76dc921551ac44de9f07583d304bde3a +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 20b169511e734f0fb8b047b06e442146 +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that " +"is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 bb3199ee47b746529f088a323a72a434 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 562109bed3cc4da896d8307f74244552 +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 417e5bfea2ac485b880ee544984996ea +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 ecd67cff285a43b5b66777032c7f690c +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 e5b8c1e93fda4043839ef0dc204f2ec1 +msgid "" +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 d09c4c6d692548d4b317e5c74445795f +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 9e3bc00a91f948eeb26624078dce6823 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 177aaf8abaf940d1ac006423998974fa +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 28308117076d4adcaf0f923c3f52d666 +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier " +"examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 c851029a3fa542b6ac21e00675661ca1 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 30cb988a8f814823a5dfb2f6ca3928fc +msgid "" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 a7c8734f60664e619c63b98e5d3399b9 +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 f4bb9b7b6ada46a4a1701daaac993798 +msgid "" +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 f4da934d636f4455a63f5ecbda2cfdea +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 529d327e58f64544aa02b075976aee32 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 a4207261aa314fd98cbfdc368d96c1b6 +msgid "" +"This workflow extracts a java source file from a tar file and then " +"compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 7571eba01bc44d0a97d8f283f19a8b49 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 +#: 8e58b0c4e12e4a1183fe7b33e8ee39e6 c8833b0a5dc04e35a48575713bed3f24 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 6a0e9118c6ee49fbb9111504dcebe190 +msgid "" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 87e0059d86b64212a1cceee185fe264d +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 77943b217ba34d409ed4a18fd262388f +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 aceb3bee46034a94bdb6784a8c1a484c +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 916621f2ca5d47c4935d68d20c5ea616 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 4a0ceee7f9ac4e80994ac8a750d77855 +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a " +"workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 3408935eb4f945349e00486a8df27c39 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 c0790bc2b8a34016b2eb3d64f0b8903e +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 5ad0adb359db4652a4b7ebd98369190e +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 753f0dc2fa3a45358dfc66e7a86fb65a +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 7eb328b2d93d4ee3b47ec26340bd3e98 +msgid "" +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 9b2cdf146f3d4906931ec9be50a194e8 +msgid "" +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 b48d08c1caa241e68a758934f6d934f9 +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 cac7f881e9984afcae77afd99b049334 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 2a60f236d6194b2daebed0fa094edc30 +msgid "" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 6cc53ff3acef4bbc87a5124a4f473b52 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 635696160b8d4b2b9607986a761a0fa0 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 4511d99ea12f4389a18f9fd061e207ce +msgid "" +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 dbd710aa7bd049018af5a693a16f93c6 +msgid "" +" \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 f9f192f956eb47d7a4fa47c80f1b56c0 +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 711bc01e2e5c47f293abe478f43c1b92 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 68509d8627a14073aabfe2071faf5214 +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 0744ac6efec34b61a4a7c3d1060bdb42 +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 2f6f5592fb5d44eb8c9998d8d9e9b9f1 +msgid "" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 af8995565822455388c9e32b59f7319b +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 a71808fbee3349079bb3a4fd4382662c +msgid "" +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 3684b45ee2b146c2a1470712375b8fb0 +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 882cda0615624d7e94c1a8708c35733b +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 3f5af7cf008446f3ad18a7ea5e8aab5b +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 d927b215d2e3400c941e490f1a102c97 +msgid "" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 52466df4530640d8bf65fa8f8dac87b1 +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 15488985c612469d80d9c20b00f1569b +msgid "" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 ccc00c4b29134214ac79fc6815ba15e0 +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 93cf2c2587394b00828a7f944d201c84 +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 5151bd4448314e7c9aac6d4841539613 +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 9154dd4987ad44e3bcb227324179a854 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 636ad7e5c8ec4b8b9f9ea1e70f166695 +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 c3f371626c2f49da9092cd5aabc8e075 +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 5b186b36c71d42d19b8ef294384a0365 +msgid "" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 67f8b32d49284698ad5248f7960cb95b +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 e49cbede4a4942e99b6f90e878898362 +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 168b8b8983f84a49ab94c09be99753b4 +msgid "" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 9d2f8b5fc572494e8e1ff54be1ba146e +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 0448518b8c514ec18fea6b32676528ce +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 315b8d60537c4e1b98136ffed099df1e +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 fc4d347151574b95907c3db531b3467d +msgid "" +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 235259da671547188634a55a5616b32c +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 8621d777883f41dead6ec6de0bb01094 +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 87f8702d0b88446ca01018b08b42e5d7 +msgid "" +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 c5dacc8526fa4341a13ce9872c1fcba1 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 9dfd2c7d475245d68052fc30d44b90d3 +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 c48070836d1a4e53a9256f4e40716f3c +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 88fc7b9654734d838aaf202083a6dcd1 +msgid "" +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 2fc5956dbad1411f86aeefe5b8655b07 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 e8a7a80a070148e4958af6b4d70250a1 +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 6c2980f728e44c82bfad95316f405be8 +msgid "" +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 8d0fbfb49a3a4aefa3ec7d71e782dbab +msgid "" +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 b847adf4f9b343518c45eec4b5fb881b +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 51d36eca415b4040ae7cd2dea438b829 +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 12816605aedd40e5babe852973366a9d +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 9a5c688b2c584362b78fe3041832ee6d +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 b9c062f153ae40f8ae59164f6096a0fa +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 2bd3b6f3998a461f9b4f5babe423242e +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 6a7a52d67e954928b57731d64f9962d5 +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 c0fe4464296e448d89fba9adae04ab71 +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 c5f7a9a163884b18a7dfd3cccbf6bfae +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 5ebef4a028ef4f0dabd3caae4a0b0bfe +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 08f3b7b52d0d48499445fd30cd71640c +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 888ae81b155f41a6860428e200948950 +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 4aa3831e2b9f4fb5b4161c198b9f6419 +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 952c18ae0fb24c3ab42ae3f7b7db0844 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 bd5835e2b35349679b1e69a50b958ee6 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 2d36d90d86c3484c9f767e3fcdb29b25 +msgid "" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 48ca1f4243e343c2a3da3c9b5596097d +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 5d15caab19694c58a78d566b2897f6cc +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 42cb06c103784fb087a44e55f570cc79 +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 90b1474dba5442a48f9fdd07b07ed9fd +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 76a1a131ac7648f9aa14ce14b09d17fe +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 f04cae70233848f7bd051fd553a89b9b +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 b6b1ad435b13428cb56c22fc135b303f +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 4a45ba50729c42ec949780bbcf495ef7 +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 57fa577b531645ae890c634c6549d680 +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 0cef0765d01e4525878389bb5ae8f6c5 +msgid "" +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 1730e578bf2f4a7b8836d0a41e059de8 +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 f5e7fb0d74924c9e9b4ca1434f724ff0 +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." +msgstr "" + diff --git a/locales/es/LC_MESSAGES/tutorials.po b/locales/es/LC_MESSAGES/tutorials.po new file mode 100644 index 00000000..9aee982a --- /dev/null +++ b/locales/es/LC_MESSAGES/tutorials.po @@ -0,0 +1,58 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide \n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../src/tutorials.md:1 cba829ebca95427ca72b0c259e199cc1 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 413874a8cfb84860b7bce0ee5f4e6022 +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to " +"the list." +msgstr "" + +#: ../../src/tutorials.md:7 5242c591a9814c9793856f432d06adc1 +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 4a3e41ee134d491eafc9a7b07776b926 +msgid "" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 207a4a90ec2f406b8541f687540a71a5 +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 ead7b80dc37647289f83036eef8ca959 +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 95a0dd8e5c354219a3eb3140565aa853 +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 82e0cb6989494cef91c464d45cc64728 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" + From 76b24797c7b78de3304f5e3baeed90c9513325e1 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Tue, 24 Jan 2023 20:20:37 +0100 Subject: [PATCH 034/179] Translations update from Hosted Weblate (#361) Co-authored-by: Sarah Wait Zaranek --- locales/es/LC_MESSAGES/LICENSE.po | 75 ++++--- locales/es/LC_MESSAGES/episodes.po | 7 +- locales/es/LC_MESSAGES/faq.po | 157 ++++++++++----- locales/es/LC_MESSAGES/setup.po | 9 +- locales/es/LC_MESSAGES/sphinx.po | 3 +- locales/es/LC_MESSAGES/tutorials.po | 18 +- locales/pt/LC_MESSAGES/LICENSE.po | 102 ++++++++++ locales/pt/LC_MESSAGES/episodes.po | 27 +++ locales/pt/LC_MESSAGES/faq.po | 292 ++++++++++++++++++++++++++++ locales/pt/LC_MESSAGES/index.po | 57 ++++++ locales/pt/LC_MESSAGES/setup.po | 27 +++ locales/pt/LC_MESSAGES/sphinx.po | 27 +++ locales/pt/LC_MESSAGES/tutorials.po | 57 ++++++ 13 files changed, 761 insertions(+), 97 deletions(-) create mode 100644 locales/pt/LC_MESSAGES/LICENSE.po create mode 100644 locales/pt/LC_MESSAGES/episodes.po create mode 100644 locales/pt/LC_MESSAGES/faq.po create mode 100644 locales/pt/LC_MESSAGES/index.po create mode 100644 locales/pt/LC_MESSAGES/setup.po create mode 100644 locales/pt/LC_MESSAGES/sphinx.po create mode 100644 locales/pt/LC_MESSAGES/tutorials.po diff --git a/locales/es/LC_MESSAGES/LICENSE.po b/locales/es/LC_MESSAGES/LICENSE.po index a9655e9f..87af7480 100644 --- a/locales/es/LC_MESSAGES/LICENSE.po +++ b/locales/es/LC_MESSAGES/LICENSE.po @@ -19,102 +19,117 @@ msgstr "" "Generated-By: Babel 2.10.3\n" #: ../../LICENSE.md:2 385524707375429989b7b4fc7e4c7aa5 +#: 3d749a78eb3e47c991d603c2cabd1b91 msgid "Licenses" msgstr "" #: ../../LICENSE.md:4 7682a147e3f74921948bde67ac684338 +#: 4689ade8475a4c8a9d5e325f072c1392 msgid "Instructional Material" msgstr "" #: ../../LICENSE.md:6 7273f384601c4f18a4cc33c833f05e56 +#: ef8ec0f072d947fbba997c4b2191abc2 msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable " -"summary of (and not a substitute for) the [full legal text of the CC BY " -"4.0 license][cc-by-legal]." +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable summary " +"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" +"[cc-by-legal]." msgstr "" #: ../../LICENSE.md:12 2cd9327d0e2e43aaa963633db1320b96 +#: 696f3824ca814c9eb314abae51be8202 msgid "You are free:" msgstr "" #: ../../LICENSE.md:14 793123b1e0ba4603a0c54c952ea4a590 -msgid "to **Share**---copy and redistribute the material in any medium or format" +#: 72ebe92edf58434e9d7a4fc6bddf8880 +msgid "" +"to **Share**---copy and redistribute the material in any medium or format" msgstr "" #: ../../LICENSE.md:15 151178e4c9a9444fb65dbf926edad28d +#: 9b403f96d4194ffaab3f309d7d12f360 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "" #: ../../LICENSE.md:17 e44aed84ff0d48b3aea3946b3a7c85fc +#: 10b1befd0f834d79880c8aeb70b595d4 msgid "for any purpose, even commercially." msgstr "" #: ../../LICENSE.md:19 d8bb44ca55b642d6bb4a88eaa8292204 +#: 9017d0b760bb4370926d511b97a604c6 msgid "" -"The licensor cannot revoke these freedoms as long as you follow the " -"license terms." +"The licensor cannot revoke these freedoms as long as you follow the license " +"terms." msgstr "" #: ../../LICENSE.md:22 6859f286e52c417096b072c923b9f235 +#: 1faadcaead6748dfb34886e5819af9b9 msgid "Under the following terms:" msgstr "" #: ../../LICENSE.md:24 ee4ea8e1fd044924b34b2d96ca158257 +#: 7a49ed3a728349c9b486f3d0b1dbf577 msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow " -"Language project, and, where practical, linking to " -"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" -"human], and indicate if changes were made. You may do so in any " -"reasonable manner, but not in any way that suggests the licensor endorses" -" you or your use." +"work is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a [link to the license][cc-by-human], and indicate if changes were " +"made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." msgstr "" #: ../../LICENSE.md:32 7598558aee3244b6b7892b06df94a393 +#: 57da6294edce46eab00e7d15e6f6d4fa msgid "" "**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything " -"the license permits. With the understanding that:" +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" msgstr "" #: ../../LICENSE.md:36 a83123e7ae79486c80107d176ea951c7 +#: 8fc8a30cd63c4a0a9d8ba1b913687029 msgid "" -"You do not have to comply with the license for elements of the material " -"in the public domain or where your use is permitted by an applicable " -"exception or limitation." +"You do not have to comply with the license for elements of the material in " +"the public domain or where your use is permitted by an applicable exception " +"or limitation." msgstr "" #: ../../LICENSE.md:39 0cc05e8ed5274019998b1dfd6ab76824 +#: fe59e74a4d024831a6d5cbcfd3e4ee38 msgid "" -"No warranties are given. The license may not give you all of the " -"permissions necessary for your intended use. For example, other rights " -"such as publicity, privacy, or moral rights may limit how you use the " -"material." +"No warranties are given. The license may not give you all of the permissions " +"necessary for your intended use. For example, other rights such as " +"publicity, privacy, or moral rights may limit how you use the material." msgstr "" #: ../../LICENSE.md:44 d70e680300524c8583f1e7fd361ad2ba +#: 3ea41d5a14ad46729cabb387a33814b0 msgid "Software" msgstr "" #: ../../LICENSE.md:46 d17e76d478354904b679b4f5ebde418d +#: 23751e2552ff450c83e3dd255da56dac msgid "" "Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +"provided by Common Workflow Language project are made available under the " +"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" #: ../../LICENSE.md:51 015fba86005946eebc5959cc3b0493d0 +#: 13fb5eb48a8a434e95dbbb717ccaef8a msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, " -"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " -"See the License for the specific language governing permissions and " -"limitations under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." msgstr "" #: ../../LICENSE.md:57 524088befae04f5485dc731d505c769b +#: e262fbd0e7de4f148f31afe39d1cb9e9 msgid "Trademark" msgstr "" - diff --git a/locales/es/LC_MESSAGES/episodes.po b/locales/es/LC_MESSAGES/episodes.po index 1dbd9f7b..897540f7 100644 --- a/locales/es/LC_MESSAGES/episodes.po +++ b/locales/es/LC_MESSAGES/episodes.po @@ -19,13 +19,14 @@ msgstr "" "Generated-By: Babel 2.10.3\n" #: ../../src/episodes.md:5 49382fe02e4f4aae96ce4d1b666d649a +#: 0cbb5e7334a647c3bcae7333ec3ced90 msgid "This page has moved" msgstr "" #: ../../src/episodes.md:9 ebd3b75bc9a347029e9e164e94b43374 +#: fabb221482cb4ac0a98bbe10943ed025 msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" - diff --git a/locales/es/LC_MESSAGES/faq.po b/locales/es/LC_MESSAGES/faq.po index ba1f01be..4b38c453 100644 --- a/locales/es/LC_MESSAGES/faq.po +++ b/locales/es/LC_MESSAGES/faq.po @@ -19,61 +19,73 @@ msgstr "" "Generated-By: Babel 2.10.3\n" #: ../../src/faq.md:1 e53c79b325b749a691434bf2f7825a5a +#: 5daa5afac36f46dd8329e5629056384c msgid "FAQ" msgstr "" #: ../../src/faq.md:11 d95bfefa6344474d9820a266922831f8 +#: 40c8efda3caf4c6089bda3027c522f37 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" #: ../../src/faq.md:41 991a77ca372d4324843ed340ffbfbae7 +#: ee854bcb685941cab45ae7f33b0efe48 msgid "Rename an Input File" msgstr "" #: ../../src/faq.md:43 4654eac499464be4845a59bc281ec242 +#: a4cdd5ab6fe341a3ad3e3055556d96c3 msgid "" -"This example demonstrates how to change the name of an input file as part" -" of a tool description. This could be useful when you are taking files " -"produced from another step in a workflow, and don't want to work with the" -" default names that these files were given when they were created." +"This example demonstrates how to change the name of an input file as part of " +"a tool description. This could be useful when you are taking files produced " +"from another step in a workflow, and don't want to work with the default " +"names that these files were given when they were created." msgstr "" #: ../../src/faq.md:59 4fcb9907771940d8857fab5b8211d337 +#: d1f359d47f124dfab23a75b196cd5884 msgid "Rename an Output File" msgstr "" #: ../../src/faq.md:61 9f3ed67bcb13459d9e7196e9d82cb58f +#: d83ced40605e411c92c4ae38761d7ffa msgid "" -"This example demonstrates how to change the name of an output file from " -"the default name given to it by a tool:" +"This example demonstrates how to change the name of an output file from the " +"default name given to it by a tool:" msgstr "" #: ../../src/faq.md:82 af6d80606de6412a8fe63ee379702eac +#: bc8997df2e6746cebc2068534f30ee82 msgid "Referencing a Local Script" msgstr "" #: ../../src/faq.md:84 fc7c21e08e8e45adb8f1265af494160e +#: 20b6ae57e1cf4410877a60fb3ef87264 msgid "There are two ways to reference a local script:" msgstr "" #: ../../src/faq.md:86 e37343ad3edd412f981397b995e6c841 +#: 73c66b809e9a4218b624338ccb88a05e msgid "" -"The first method involves adding the folder containing your scripts to " -"the `PATH` environment variable. This allows you to run the shell script " +"The first method involves adding the folder containing your scripts to the " +"`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" #: ../../src/faq.md:89 2b7e94e816fa46f4a221b5ce6b2214b2 +#: 9be72b7d5d604526b125b63148e99320 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" #: ../../src/faq.md:95 0fd0fd13672d48cda0f3ef7f2b0701da +#: fd96d178901545008a43fa99e3aa6cf3 msgid "" -"After that, make the script executable with the command `chmod +x " -"scriptname.sh`" +"After that, make the script executable with the command `chmod +x scriptname." +"sh`" msgstr "" #: ../../src/faq.md:97 a21be18c313d430a8986760ee3725198 +#: db58a582e66244468f4d31e9213933d1 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " @@ -81,117 +93,138 @@ msgid "" msgstr "" #: ../../src/faq.md:104 404295b5792747c8a87306181d078cbc -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +#: 3e70f0da5cd7460b90c1690366f40820 +msgid "" +"Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" #: ../../src/faq.md:113 92582f3845b446d08ca9cbc4ad76a0a7 +#: db28dc27c82b4b29a7a9a768550bba9b msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" #: ../../src/faq.md:115 2d62b6e5d7944818acd0f43b7d37ce67 +#: 4474b16fb3fd4cdc85da931159804967 msgid "" -"The second method involves including an input of `type: File` in the " -"script itself:" +"The second method involves including an input of `type: File` in the script " +"itself:" msgstr "" #: ../../src/faq.md:135 c72fa80f79594d479cb99dc6bfcb207d +#: 23c9b2e21cec4ee8ade087e6630f62c2 msgid "In CWL, everything must be directly stated." msgstr "" #: ../../src/faq.md:138 5f2b7881a7c64cf29b05b4d78158e176 +#: c01309dcd65c4f1080c396e6a9efb75d msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" #: ../../src/faq.md:140 eb11641ac17e496384a60e4aacc5209b +#: 0a36801172fd4e24a04b3ba85cf74e29 msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their " -"input binding makes use of `self`. Below is an example workaround for " -"this, pending a more sophisticated fix." +"Currently, `cwltool` can't cope with missing optional inputs if their input " +"binding makes use of `self`. Below is an example workaround for this, " +"pending a more sophisticated fix." msgstr "" #: ../../src/faq.md:165 c0aee2cf9ee046128002b09a8aa397d8 +#: 433e788ba01141e98ea5a9e73ef71e6f msgid "Model a \"one-or-the-other\" Parameter" msgstr "" #: ../../src/faq.md:167 34a04d6d09e94fd796a5ee13c6b9856a +#: b6de2761ce454992904775a06b7ba326 msgid "" -"Below is an example showing how to specify different strings to be added " -"to a command line, based on the value given to a Boolean parameter." +"Below is an example showing how to specify different strings to be added to " +"a command line, based on the value given to a Boolean parameter." msgstr "" #: ../../src/faq.md:188 b1ee951a6e6e4f4c8e88de4dc93bd616 +#: e36c2d53e8ba40f4a602b489a6688e24 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" #: ../../src/faq.md:190 1664807c6b264fc3b58e9f2c40a9543c +#: a9310166cb514e4e8824bba7fcfcb277 msgid "" -"Using " -"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" -" along with [`linkMerge: " +"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/faq.md:194 a7ab83c7f31e4e8d83fbfba1abadef2b +#: f6144f77152e4284963951abaa30adb2 msgid "merge_nested" msgstr "" #: ../../src/faq.md:196 908451dc6990489e88edc1012899c440 +#: 790709dfc2854e4a89fcc4769f84b0f4 msgid "" -"The input must be an array consisting of exactly one entry for each input" -" link. If \"merge_nested\" is specified with a single link, the value " -"from the link must be wrapped in a single-item list." +"The input must be an array consisting of exactly one entry for each input " +"link. If \"merge_nested\" is specified with a single link, the value from " +"the link must be wrapped in a single-item list." msgstr "" #: ../../src/faq.md:199 30947198b46d4151a5d92076c30659c0 +#: 438789c8def549d1b4b8a187d5acc48e msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" #: ../../src/faq.md:201 0b320fb2e40442608137ed9d6f2a74cd +#: 23ede7dfd5c84492baee1d5bbb9a91d9 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " -"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" -" destination step." +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " +"add `linkMerge: merge_nested` under the appropriate `in` entry of the " +"destination step." msgstr "" #: ../../src/faq.md:229 a143590b23384ed79fc37b17a0abd46e +#: 37c0474e48164160b23c4094d583d2d3 msgid "Optional Inputs 💯" msgstr "" #: ../../src/faq.md:231 6b36effcb80040c79396a1df241f635e +#: 3b2be0a4a87041b7a5bda20c6df2ffc8 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" #: ../../src/faq.md:247 2873af63ee324fab948d16a9e14db5a7 +#: 886300d2dcff4861aae503d34b0bee44 msgid "" msgstr "" #: ../../src/faq.md:248 a11f170a082a4df2b4a0c068dd0573ed +#: fe393ecdff25428da6cbcd30171c7811 msgid "Enum Inputs ⚜️" msgstr "" #: ../../src/faq.md:250 bd2ccba5ac7e486c9af1d906ad96b07a +#: ebfd4991d917413b858da8b437a55805 msgid "" -"For command line flags that require a specific input as the argument an " -"enum type can be declared in CWL. **Specifying null here is known as long" -" form style. It does the same thing as the question mark on the other " -"inputs.**" +"For command line flags that require a specific input as the argument an enum " +"type can be declared in CWL. **Specifying null here is known as long form " +"style. It does the same thing as the question mark on the other inputs.**" msgstr "" #: ../../src/faq.md:267 3f1d8cf3390c43f8b78ce33fc020f1a0 +#: 2919ff4f51254e69aea40146e2d911f1 msgid "" msgstr "" #: ../../src/faq.md:268 89626d59c2164bb99d0b123def33f701 +#: 61ed4e87457c41eea31f51740557597e msgid "Record Inputs 📀" msgstr "" #: ../../src/faq.md:270 028c6179803b4dc8a718669312804101 +#: 1e6624104b024eb092682cd0dd0f6a3c msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " @@ -199,109 +232,127 @@ msgid "" msgstr "" #: ../../src/faq.md:322 23d9d603d4d44880aea5ebfd86e02d8d +#: b741b8333e104feaa6d1f41fd4476304 msgid "Setting Mutually Exclusive Parameters" msgstr "" #: ../../src/faq.md:324 06ae9317c6af481bbf4fd70236ca10a9 +#: 334673ae870a4dada817857f3a49326e msgid "" -"To properly set fields in a record input type, you need to pass a " -"dictionary to the input to properly set the parameters. This is done by " -"using inline JavaScript and returning the dictionary with the key of the " -"field you want to set. The source field is set to indicate the input from" -" the workflow to be used as the value." +"To properly set fields in a record input type, you need to pass a dictionary " +"to the input to properly set the parameters. This is done by using inline " +"JavaScript and returning the dictionary with the key of the field you want " +"to set. The source field is set to indicate the input from the workflow to " +"be used as the value." msgstr "" #: ../../src/faq.md:342 0c6c0af33a274a8cb64ae3111c014338 +#: 362f85270df04712b2e2f21c7019e3cb msgid "Setting Booleans" msgstr "" #: ../../src/faq.md:344 1139a2f4e58046f9aac4c64b7d5a2e4d +#: ad6997f24c7c42fe965b5d7bfd1e633e msgid "These can be set by using the default field" msgstr "" #: ../../src/faq.md:349 ca97418a37bb4ae99bce1b44eebefbad +#: 99dce9d60b6a4f99bc39899b7c8c10ef msgid "Concatenating Strings in Inputs" msgstr "" #: ../../src/faq.md:351 7a5d2d6c6474492fa65ffd8a5048c733 +#: 6b68fe24cbf64624b49ea56fce2eecad msgid "The valueFrom field must be used instead of default." msgstr "" #: ../../src/faq.md:359 2549c8887b204ddabe4221978dce7e57 +#: d23326837eb74e7faf1f54e25f8309c4 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" #: ../../src/faq.md:361 d15ae28e932446b48bfc1dbdc34d8eab +#: 2e2eabe92670412e95474b25ad9cda4c msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" #: ../../src/faq.md:363 925a0bb31c5f428b93232e42d96bddeb +#: 81f9308adbee4a3c9e585b8e0f0c4844 msgid "" -"For example, the filename `a space is here.txt` includes 3 space " -"characters." +"For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" #: ../../src/faq.md:371 591dd97f12ca4b8ca263b17abe674fd6 +#: a5d3ed6cac28415288e7fc7fbfc6e8a6 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" #: ../../src/faq.md:373 3ccdf1a970c14cbe8e1d269dc4ae77b3 +#: 72f9692803304daf9f846e2b90139660 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 4cefff22947f4d9eb2f66d1b6bca2a8f +#: a7eb20c817704811b3bcf2f94ec2e51d msgid "If `cwltool --validate` returns valid" msgstr "" #: ../../src/faq.md:384 bfcbe4003ccb4e59baeed0b631871970 +#: 20fa869849ef4b358a11db46111017de msgid "But executing it causes an error like:" msgstr "" #: ../../src/faq.md:396 d729277d8bc0488eadddf507ba63202f +#: 35032fcd9f23403ca006d62a7d6e7be7 msgid "The file is here" msgstr "" #: ../../src/faq.md:410 ca99353cf8f94d11add95ba36408ee46 +#: f6d6a4e3691446378c8fb01a2d19f8ad msgid "Problem caused by `-` (hyphen character)." msgstr "" #: ../../src/faq.md:423 deb9ae92120d4e30aebd6e4d0374a0a2 +#: 44608fed1048458e999e13b014327e7e msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" #: ../../src/faq.md:436 7f4054de28a243c89bd3aca1e2764b93 +#: 96ede8a8f1f34786aabd4004bf2e7acc msgid "" -"If it is not possible to change the input identifier, then you can use an" -" alternative CWL Parameter Reference syntax:" +"If it is not possible to change the input identifier, then you can use an " +"alternative CWL Parameter Reference syntax:" msgstr "" #: ../../src/faq.md:442 29658fd7b5724addb5074891942f79fe +#: 84634a368e704e8d828678785c784595 msgid "Use CWL and cwltool with Singularity" msgstr "" #: ../../src/faq.md:445 2dd0d8092e5640e3a930478497b78efd +#: 545c4db9c24f42ee946081254d9ca7a8 msgid "" -"The CWL standards are built around (optional) Docker format containers. " -"The reference runner and several other CWL implementations support " -"running those Docker format containers using the Singularity engine. " -"Directly specifying a Singularity format container is not part of the CWL" -" standards." +"The CWL standards are built around (optional) Docker format containers. The " +"reference runner and several other CWL implementations support running those " +"Docker format containers using the Singularity engine. Directly specifying a " +"Singularity format container is not part of the CWL standards." msgstr "" #: ../../src/faq.md:450 0d385ebff8c14cbfa418fa45c9b42e51 +#: 1c1e6d583d5646a8a5c9316dcd743d9f msgid "Debug JavaScript Expressions" msgstr "" #: ../../src/faq.md:452 67d82ee82a184ed3921da6fd1928e83e +#: cf7d336d444e4f59aa83585b7abb1fe5 msgid "" -"You can use the --js-console option of cwltool," -" or you can try creating a JavaScript or TypeScript project for your " -"code, and load it using expressionLib, e.g.: " -"https://github.com/common-workflow-language/common-workflow-" -"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +"You can use the --js-console option of cwltool, or " +"you can try creating a JavaScript or TypeScript project for your code, and " +"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" - diff --git a/locales/es/LC_MESSAGES/setup.po b/locales/es/LC_MESSAGES/setup.po index 68494d21..6b6fd9db 100644 --- a/locales/es/LC_MESSAGES/setup.po +++ b/locales/es/LC_MESSAGES/setup.po @@ -19,13 +19,14 @@ msgstr "" "Generated-By: Babel 2.10.3\n" #: ../../src/setup.md:5 715f40c8e3f544e4805ae2b456b9d699 +#: 29bb5c68be6042e5aa4a370e9c4024b3 msgid "This page has moved" msgstr "" #: ../../src/setup.md:9 c9641546c55a44eab9ae40ec272d5df8 +#: 8bcf31398c34491da1a1590422a72cbe msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. The information on this page has been migrated to the " -"[FAQ](/faq.md) section of the new user guide." +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. The information on this page has been migrated to the [FAQ](/faq." +"md) section of the new user guide." msgstr "" - diff --git a/locales/es/LC_MESSAGES/sphinx.po b/locales/es/LC_MESSAGES/sphinx.po index 1c2687a9..27d21259 100644 --- a/locales/es/LC_MESSAGES/sphinx.po +++ b/locales/es/LC_MESSAGES/sphinx.po @@ -19,10 +19,11 @@ msgstr "" "Generated-By: Babel 2.10.3\n" #: ../../src/_templates/sidebar-nav-bs.html:1 ada5c93414a84374b3eaea93dc11ae74 +#: b896fd5e11fe4674a7f46ad489476692 msgid "Main navigation" msgstr "" #: ../../src/_templates/sidebar-nav-bs.html:3 a3cc1c498bad434ebadd4a2e92dbf5f0 +#: acede4e78f7e4aefa0ad9425928cbb42 msgid "Section Navigation" msgstr "" - diff --git a/locales/es/LC_MESSAGES/tutorials.po b/locales/es/LC_MESSAGES/tutorials.po index 9aee982a..0c412e90 100644 --- a/locales/es/LC_MESSAGES/tutorials.po +++ b/locales/es/LC_MESSAGES/tutorials.po @@ -19,40 +19,46 @@ msgstr "" "Generated-By: Babel 2.10.3\n" #: ../../src/tutorials.md:1 cba829ebca95427ca72b0c259e199cc1 +#: d32522e2993f4b48a789f46537fa5ebf msgid "Tutorials" msgstr "" #: ../../src/tutorials.md:5 413874a8cfb84860b7bce0ee5f4e6022 +#: 63a51dccb29045fd8f78d5e396c6e050 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to " -"the list." +"this page` link in the menu if you would like to add another tutorial to the " +"list." msgstr "" #: ../../src/tutorials.md:7 5242c591a9814c9793856f432d06adc1 +#: cb5f8748a5544be2835467ab07eb7a1c msgid "Beginner Tutorials" msgstr "" #: ../../src/tutorials.md:9 4a3e41ee134d491eafc9a7b07776b926 +#: 685d0cb2faa04703bcef408ecc2b92f4 msgid "" -"[Introduction to Workflows with Common Workflow Language: For " -"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" -"tutorial/)" +"[Introduction to Workflows with Common Workflow Language: For Contributors.]" +"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" #: ../../src/tutorials.md:11 207a4a90ec2f406b8541f687540a71a5 +#: 20f45705145d45fc8420c4119b06a49f msgid "Advanced Tutorials" msgstr "" #: ../../src/tutorials.md:13 ead7b80dc37647289f83036eef8ca959 +#: 2bccd19d542d4458a1ba8616236f1840 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" #: ../../src/tutorials.md:15 95a0dd8e5c354219a3eb3140565aa853 +#: c491c73e4c00476980438ffc79c6e4d3 msgid "Bioinformatics Tutorials" msgstr "" #: ../../src/tutorials.md:17 82e0cb6989494cef91c464d45cc64728 +#: b8485449206542e097584eca7363c8ce msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" - diff --git a/locales/pt/LC_MESSAGES/LICENSE.po b/locales/pt/LC_MESSAGES/LICENSE.po new file mode 100644 index 00000000..c3591ece --- /dev/null +++ b/locales/pt/LC_MESSAGES/LICENSE.po @@ -0,0 +1,102 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../LICENSE.md:2 +#: 3d749a78eb3e47c991d603c2cabd1b91 +msgid "Licenses" +msgstr "" + +#: ../../LICENSE.md:4 +#: 4689ade8475a4c8a9d5e325f072c1392 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 +#: ef8ec0f072d947fbba997c4b2191abc2 +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 +#: 696f3824ca814c9eb314abae51be8202 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 72ebe92edf58434e9d7a4fc6bddf8880 +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 9b403f96d4194ffaab3f309d7d12f360 +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: 10b1befd0f834d79880c8aeb70b595d4 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 9017d0b760bb4370926d511b97a604c6 +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms." +msgstr "" + +#: ../../LICENSE.md:22 +#: 1faadcaead6748dfb34886e5819af9b9 +msgid "Under the following terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 7a49ed3a728349c9b486f3d0b1dbf577 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 57da6294edce46eab00e7d15e6f6d4fa +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 8fc8a30cd63c4a0a9d8ba1b913687029 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 +#: fe59e74a4d024831a6d5cbcfd3e4ee38 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" + +#: ../../LICENSE.md:44 +#: 3ea41d5a14ad46729cabb387a33814b0 +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 +#: 23751e2552ff450c83e3dd255da56dac +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 +#: 13fb5eb48a8a434e95dbbb717ccaef8a +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../LICENSE.md:57 +#: e262fbd0e7de4f148f31afe39d1cb9e9 +msgid "Trademark" +msgstr "" diff --git a/locales/pt/LC_MESSAGES/episodes.po b/locales/pt/LC_MESSAGES/episodes.po new file mode 100644 index 00000000..94101eb0 --- /dev/null +++ b/locales/pt/LC_MESSAGES/episodes.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/episodes.md:5 +#: 0cbb5e7334a647c3bcae7333ec3ced90 +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 +#: fabb221482cb4ac0a98bbe10943ed025 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" diff --git a/locales/pt/LC_MESSAGES/faq.po b/locales/pt/LC_MESSAGES/faq.po new file mode 100644 index 00000000..ce416d3d --- /dev/null +++ b/locales/pt/LC_MESSAGES/faq.po @@ -0,0 +1,292 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/faq.md:1 +#: 5daa5afac36f46dd8329e5629056384c +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 40c8efda3caf4c6089bda3027c522f37 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: ee854bcb685941cab45ae7f33b0efe48 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 +#: a4cdd5ab6fe341a3ad3e3055556d96c3 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 +#: d1f359d47f124dfab23a75b196cd5884 +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: d83ced40605e411c92c4ae38761d7ffa +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 +#: bc8997df2e6746cebc2068534f30ee82 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 20b6ae57e1cf4410877a60fb3ef87264 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 +#: 73c66b809e9a4218b624338ccb88a05e +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 +#: 9be72b7d5d604526b125b63148e99320 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: fd96d178901545008a43fa99e3aa6cf3 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 +#: db58a582e66244468f4d31e9213933d1 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" + +#: ../../src/faq.md:104 +#: 3e70f0da5cd7460b90c1690366f40820 +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 +#: db28dc27c82b4b29a7a9a768550bba9b +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 +#: 4474b16fb3fd4cdc85da931159804967 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: 23c9b2e21cec4ee8ade087e6630f62c2 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c01309dcd65c4f1080c396e6a9efb75d +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 0a36801172fd4e24a04b3ba85cf74e29 +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 +#: 433e788ba01141e98ea5a9e73ef71e6f +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 +#: b6de2761ce454992904775a06b7ba326 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 +#: e36c2d53e8ba40f4a602b489a6688e24 +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: a9310166cb514e4e8824bba7fcfcb277 +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: f6144f77152e4284963951abaa30adb2 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 790709dfc2854e4a89fcc4769f84b0f4 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: 438789c8def549d1b4b8a187d5acc48e +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: 23ede7dfd5c84492baee1d5bbb9a91d9 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" + +#: ../../src/faq.md:229 +#: 37c0474e48164160b23c4094d583d2d3 +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 +#: 3b2be0a4a87041b7a5bda20c6df2ffc8 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" + +#: ../../src/faq.md:247 +#: 886300d2dcff4861aae503d34b0bee44 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: fe393ecdff25428da6cbcd30171c7811 +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: ebfd4991d917413b858da8b437a55805 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: 2919ff4f51254e69aea40146e2d911f1 +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 61ed4e87457c41eea31f51740557597e +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 +#: 1e6624104b024eb092682cd0dd0f6a3c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: b741b8333e104feaa6d1f41fd4476304 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 +#: 334673ae870a4dada817857f3a49326e +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: 362f85270df04712b2e2f21c7019e3cb +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: ad6997f24c7c42fe965b5d7bfd1e633e +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99dce9d60b6a4f99bc39899b7c8c10ef +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 6b68fe24cbf64624b49ea56fce2eecad +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: d23326837eb74e7faf1f54e25f8309c4 +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 2e2eabe92670412e95474b25ad9cda4c +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: 81f9308adbee4a3c9e585b8e0f0c4844 +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 +#: a5d3ed6cac28415288e7fc7fbfc6e8a6 +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: 72f9692803304daf9f846e2b90139660 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: a7eb20c817704811b3bcf2f94ec2e51d +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 20fa869849ef4b358a11db46111017de +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: 35032fcd9f23403ca006d62a7d6e7be7 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: f6d6a4e3691446378c8fb01a2d19f8ad +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: 44608fed1048458e999e13b014327e7e +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 96ede8a8f1f34786aabd4004bf2e7acc +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 84634a368e704e8d828678785c784595 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 545c4db9c24f42ee946081254d9ca7a8 +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 1c1e6d583d5646a8a5c9316dcd743d9f +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: cf7d336d444e4f59aa83585b7abb1fe5 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" diff --git a/locales/pt/LC_MESSAGES/index.po b/locales/pt/LC_MESSAGES/index.po new file mode 100644 index 00000000..0a5d7d38 --- /dev/null +++ b/locales/pt/LC_MESSAGES/index.po @@ -0,0 +1,57 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/index.md:1 +#: a58ca61ccefc401588f91699bc98bd32 +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: 6dcf12053f104cb3a8d23ce8d4f90363 +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 1cc90206170d46119c5756f31a9e8799 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: b54801d84a944dadb4e4637551e3f7b9 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 860afd2eda4847e0a0d8834de3af4aa8 +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: d6046316c84b40ffb5478c90b2604911 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: c3c89ac756a74d9688e179b8718c9bf0 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: 0eb795062b484537b090c4d5c361f7f4 +msgid "Table of Contents" +msgstr "" diff --git a/locales/pt/LC_MESSAGES/setup.po b/locales/pt/LC_MESSAGES/setup.po new file mode 100644 index 00000000..06186f03 --- /dev/null +++ b/locales/pt/LC_MESSAGES/setup.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/setup.md:5 +#: 29bb5c68be6042e5aa4a370e9c4024b3 +msgid "This page has moved" +msgstr "" + +#: ../../src/setup.md:9 +#: 8bcf31398c34491da1a1590422a72cbe +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" diff --git a/locales/pt/LC_MESSAGES/sphinx.po b/locales/pt/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..68ce7729 --- /dev/null +++ b/locales/pt/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:27+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: b896fd5e11fe4674a7f46ad489476692 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: acede4e78f7e4aefa0ad9425928cbb42 +msgid "Section Navigation" +msgstr "" diff --git a/locales/pt/LC_MESSAGES/tutorials.po b/locales/pt/LC_MESSAGES/tutorials.po new file mode 100644 index 00000000..f893e551 --- /dev/null +++ b/locales/pt/LC_MESSAGES/tutorials.po @@ -0,0 +1,57 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/tutorials.md:1 +#: d32522e2993f4b48a789f46537fa5ebf +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 63a51dccb29045fd8f78d5e396c6e050 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: cb5f8748a5544be2835467ab07eb7a1c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 685d0cb2faa04703bcef408ecc2b92f4 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 20f45705145d45fc8420c4119b06a49f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 2bccd19d542d4458a1ba8616236f1840 +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: c491c73e4c00476980438ffc79c6e4d3 +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: b8485449206542e097584eca7363c8ce +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" From f067761345c6dc0ef62645648feb424f5c93ac22 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Wed, 25 Jan 2023 09:03:16 +0100 Subject: [PATCH 035/179] Translations update from Hosted Weblate (#363) * Added translation using Weblate (Portuguese) * Added translation using Weblate (Portuguese) * Added translation using Weblate (Portuguese) --- locales/pt/LC_MESSAGES/_includes.po | 22 + locales/pt/LC_MESSAGES/introduction.po | 607 +++++++ locales/pt/LC_MESSAGES/topics.po | 2083 ++++++++++++++++++++++++ 3 files changed, 2712 insertions(+) create mode 100644 locales/pt/LC_MESSAGES/_includes.po create mode 100644 locales/pt/LC_MESSAGES/introduction.po create mode 100644 locales/pt/LC_MESSAGES/topics.po diff --git a/locales/pt/LC_MESSAGES/_includes.po b/locales/pt/LC_MESSAGES/_includes.po new file mode 100644 index 00000000..6d6635cc --- /dev/null +++ b/locales/pt/LC_MESSAGES/_includes.po @@ -0,0 +1,22 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_includes/what-is-cwl.md:1 +#: 46f474e1b364495181698bd13ce28a1e +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" diff --git a/locales/pt/LC_MESSAGES/introduction.po b/locales/pt/LC_MESSAGES/introduction.po new file mode 100644 index 00000000..fe9de9a5 --- /dev/null +++ b/locales/pt/LC_MESSAGES/introduction.po @@ -0,0 +1,607 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/introduction/basic-concepts.md:1 +#: 92c85569d9e746d8a5b7a5e8f9773545 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: 5e501be2f49044c9897f6e8d65186abb +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: a6f5f188f9af4b608b8401996a558e83 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:2 +#: 2ecb1a3a4c7546ba94e560924cfb09a8 +#: 3c0da8bd74824f8b88223c2a9dcc6ec2 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: 7fb9ad094d844047b0d35dc70c295400 +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 303d1a15612846c1b60a4d651f9d1d4a +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: c84c4bde07034846b043c4f281f8e00c +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: d774877d6e4447b7b83d56ebbaf09e96 +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: e8884f39f08c41bab29c4284077fd860 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: 984ac8cee64e4e41957d8c5a4aff0cfd +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 17381e8872414c49b178d91ace2e3e82 +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: c4cdbf2a42644e0eb4eb74512388e9f7 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 7d994284e320413bb8dbb2a42cd16a4e +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: ce92487ca4e3495ebd0693c502773626 +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 0ce512c3cd744652b5feb2d8dcfdb613 +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: dd7d6a1399b04923b25df70abb1becf5 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: ce4c76b46531416bb4006a9c01f45a23 +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 0256a343321447559471d731c86d3546 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: e1235589f24942babe54adaae4f169af +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 81baaa297562452f80afe68657c8099d +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: 0c8bbd88bd8c4c71b19011812e7487c3 +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 3b64da1f14964cea9e5cbf8376578789 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: bf33807babb64befab3385eca4c92131 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: afdb75d374624f4798f358a3dfe7752e +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: bc28744d5fa644218ef55672d726307f +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 24ffb5bfa767424585b6b6c93169de93 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: bd53afe50cc14f2ca428adddb0e60dc9 +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: 35c98c4b352c4f9bb9572c740894dc57 +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: f7fb57fdf9344a7eb0f334aca8d3e85f +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 0dc6a8f19fda4e9eaa80b8e1bd1fc5be +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: ff1224487c35402d8afee6da3803e19b +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 63c2dd9aaec54df088e82febfd7bc49c +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 18f310d11c9b48b4a447b6662446cd3e +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: a3922283fdce4f99832c816626d5f098 +#: 19245373c2e84793a72462b7d2fa1c34 +#: 7c3ea7150c7d41fead10ddf2a6205ec8 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: cf39d3563e344ad9b31d5268c4069972 +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 97b0113a847044b98f79b5e00941f4c3 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 8cf4edbb4b344ac7b3eae86ed52beff8 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: c1dfc170fdf54c9e846539a5170f204f +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: 778babbcfb2648a1ad7a7ad8f80653a8 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: 23abed59f5d44bfb96e8fa13aa213b83 +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: ee93304de4e447c1bd5626e72b99b6fe +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: a79f07e33fc5437c9fa204111d0290d8 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: 3cf08b553a814478b4b2c6c84ebe354e +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 98751950a97f44fdb16e826fece810fb +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: eac153b881fa47ab8bb08074dad8eed2 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: 806ff7b185d74538a9b0e20c6ad84ffe +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: 1f9573b6cd45479bae2481a251132d53 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: c3995fd5588741148e3b2c91ca011ca9 +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: 8a67b172ce524aa09858acd9d1a62762 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: a567e0f952bc46be8b82d0a357f2c209 +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: 21d3bb850bb14fdcb6d4c4a15c9966b6 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 62cbb29459b24e9fa83c7cd7994bdf12 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: aaa319d4446c41ba82bf925f29f7d9dd +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: c49938a0100a4850b67d067a61304d01 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 91e986d0c1f44d7f9c3b32366160da6a +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 301c5a3baaaf46bb81bdc25b53a31f23 +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: 1664589ced314daebfb163e6424f220f +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 1223fecd61f34ad98ebbb7e45eaf4ac7 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 242c496599d84a64959db275ee1e212e +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 9b749d47f48341cb9ac8cd14098e6c47 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: e8ec351d7b79447bb15f4d4518b8de87 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: 58d5613243914dc8bc4ce88676525783 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 731a6c30786f43d88160f9642cbb05d2 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: ca2088eb9565429dbc1ce0b28b2ef1fb +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 5ac9c6bfb50b48878aff52f1194e53c4 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: b8d0c12ff07f4269bba87cd653803345 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 83780c1b43f744b4ae87a917b26293f5 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 2919320c41e94930a0aa9bc6aacb5a87 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b8e799c075214d539aa0a7c04dbc33c0 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: ccbd51a29ca841efb74c5e0a25d1eb87 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 5f3330c1e15a402781c3325f9d3dc779 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: 314fbc9f866a405b86e7bd704781dea1 +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 9434e3680aa9487fab9ddb782c6ff3d0 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: 2ce0bda38d814b248a2c23ebc26bf462 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 105c3be6f5f34f4388b9999603275bb5 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: bd378c8483a14c93b5fe00d76e5b0a06 +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 5ace5416560247c7a3304c41caa000c6 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: 5d7a175b3c5a4f888daf037672211d61 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: 4e0c0c345527412eaf70e8efe67fab8f +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 6dd8379682824d1397c48ac10db4b894 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 57691f7bd87741d68f4e1a963da91654 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: 13a4d71f127b4bd09c12a37752d27c8b +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: a574ed30000541b2816fbfe66b32c314 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 9bb9c9052ad14c7c9fc0275c8f1b651b +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 5afcf2e79ceb424ea0a570797a712321 +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: cc5b91b8c5b14a40bdd09d3bd45fe9bb +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: d5e36c7827334fc69498459db5137d30 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 39d3eff64d004a0f8257d61f2a90b186 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 19946d0d9a6f42d487537273225b91cd +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: 66048204601a439d8245455c48b08826 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: dcc41d0ce48e42a0ba209ca1fa37220a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: e2ebe32f12b74608b35217cea30cd0e0 +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: 37a4f461b82f4e48948c5eab400b14a5 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 371c6801e92448f9875fff60a509f509 +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: e3fb51cd196542008cb16458fdef7c1f +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: d00cd96d47c6450a8c0955765eff9ac1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: e06fdf0744344d0193b99791b9b94c7d +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: 6e2191fbb8794f83a51897028a2e50f7 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 931b6b49a46d4d5581a05446ac2e9a7d +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: 5cb281f4d0ea4163af0f7203c150345e +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: 4e6c4c2b6bae49a2b2d93bc95538c7b9 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: b37ba76e0dd940559e13543ea241376e +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: 22d7ac26f2ca41b2aa141fd4774b6f5c +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 15033ad0574d46b2951bb2121c80c462 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 2b2fc79461674b9ebdef49750f7fb319 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 8b11c9920b97427aa2d29498664e24bb +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: d11de6ee015f46c991fbc8b48cd1fb60 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: 71adfebd042a4820ac533a2e6e07c0ca +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: 8f199e6778a84ba68d385b42169f6b26 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: 28ec66afdad24dfd871ef1a2686f9976 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: cccb84844ce0453cb77ce3db65ffbc1b +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 0c5a431846f241829975552ef8dd9c32 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 8e383a7ea5b54c56adb9cb0c6ed6c179 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 98473d00529345d4989f0f5d2101da1b +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: d105326cb76b455d907c283a509f038c +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d4d00a573e36474f9c915563d4ea8709 +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: aa8195d109974f9da3b9da97479525cb +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" diff --git a/locales/pt/LC_MESSAGES/topics.po b/locales/pt/LC_MESSAGES/topics.po new file mode 100644 index 00000000..7d6384c1 --- /dev/null +++ b/locales/pt/LC_MESSAGES/topics.po @@ -0,0 +1,2083 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 1a006f1604c0405aaa4b93e41edc5184 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: b61b4d7ed53a436486c1429987a2a21b +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: 1bf9e65f1cc249ee93656a53ddd354ca +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: 3329dc69c32f4b9092b196d79ae5d0c1 +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: a003a3d1de0e4dfe8c777905e55fb9fe +#: e2dc24c683054cd785326de2c3f3f136 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: aca6a0cd24a2411c8cfb1ad392f6d315 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: bcf37e403eb041269e351d7f98a19587 +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: c5f68f8a9f34445ebcbd5783f96cb046 +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: 4eca90c659ba43158db373d36ee681df +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 7474eeb128624dc4b1e980dbd0f04ca4 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 0c520e5add334609a1afddc559abe19a +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 125a69207077425fa54f346abc45342d +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 6ca38a04844c403b836942b2f2f1e1e2 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 1da05be0d97d429a84085459ebae54cf +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: fb1b2a8c54f34d78ac61dd4b5ffd9063 +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: a8b1b5caf9904fc5b9eef8c110474b84 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 42a5a8cb3b284549aabb817b73ce5810 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: eddd878eb0324851997de2a69bcbb43f +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: b05c8ff667174f6798feb811cdd3c41d +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: 9dc16d1a6b0546cead6967f5e9b1526a +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: b8bf85e8523a4553a58face698aa863b +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: 6fb9a1a2ffe14f39b01af8736a9698eb +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 0a935aa93e554c0987af7349f94ccd3a +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: cadb5982a13e4621807ad976cf9b1524 +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: bd7ab2cc6234458181e9b99938eba824 +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 7beb72d7dd5a405f9be8b6fb6a310f10 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: e5942c4d4b4d4e1a8c0e9ed3da80960e +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: 5a5dbc9b9d2242ba8d15ecf39123694b +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: dd3016d33b7d4340a09a7c8e5aec4f0b +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 45d110a660b348f58a1107476df18cee +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: 97a5b141592e4415aa4acef4f6228045 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: 85f624f8879348e8bb368ec2749925bf +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 20a851dae87941c7975173ed9cd1e360 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: bb19e1b689564a11bb9e72d5f82cf3d9 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: b14199173add4585be62c4e8278b49f4 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: 9e883f18843a41d7b10102bc11655839 +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: fe3a1468aa864742b92c6e8f4ff1a38f +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: e9dbf14538404cceb02507962a173ee8 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a650a7dacbb547db97158a8ac2c9d0dc +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 501217b98c424a319e70ef963de506f6 +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: 7143809471454e00880ad8faaf43f141 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: 7ad86e42708a465980a56f735644de9f +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a8f29712337b4d1daf3190cc8973b8f7 +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 534843389795437991fad0b5a702b483 +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2052170aa2624feeb2253477895aa838 +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d5ed098a33ae4c1ab2a30eba483ecc6f +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: 2b55c028602f41babb6e535b425ba5dc +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 47408669ae8b4432a43d763dba12a466 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: b2e5e925971849a09a8d54d9c649a32d +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 9a39f53bdcc94904a90effb507767645 +#: f296149bf19947528b134b01a4d7ce81 +#: 965fa9769dea4ac9b3dd252e0a3bc603 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 79d8ea95f0c34585a3dec4f83453de60 +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 4afab699247b4f619702c4086eb1b6f3 +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 693b91423f004118b806bb8ee7952eaf +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: e4a25f04a6fa4001bb1e58cb775cdd84 +#: c771cbc64607412a9164c28934e9e0f5 +#: bdd5a3eac1e3436496e05a13c4f06073 +#: 1e62b28ef0184081b4d6e53f34b753e1 +#: 33edd6deb38740ed98466b6e023b0393 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: a3a8bcdfadc4484ea5e4c13a25b2da85 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 7800570badf149b3bb1f81d470dbf4be +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 496313f8ec67403ca78ba66130df261e +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: f7cc0d1ac5dd47658093cd0360f90329 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 0d563f15c1cc4484b6b2955bdc70e1a9 +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: 06425b6cdaf244b198fdde312e864190 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: 26c3762a637a4492a6c12588544cb0a7 +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: 221433aa39104642af8afb70ebd08576 +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: 197bf36a5d7741b3a9ac56c19d4a7686 +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: d9249cf936d24ab3b3fc508d17d94745 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: 2ff7ce81cd3a492a8549484ba8d1f135 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 2bb45c56e2fc49e094be2cf742222e67 +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: e2a4a531c6164f15bc711618db058f52 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 90f7960bd24d4481bd05da1d61ef146b +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: a51814548e44467c841ca65b2ac63b2c +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: fa13573d9c174ca1accf20a449e5984f +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: f2912b17e3be47b0b7186efdb4c4010f +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 4d9c95d18c1a4880845e7194a99aed3c +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: c656a020978f465b85b8754346ea5b6d +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: ff4d0b6bc0264650a21adc811b8caf4c +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: 77e00be2c0984465af5bf501b4031f32 +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: 3d7b7238be974c0487f219cb5c030149 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 03a62f421c8241779c0e79f4dbad96cc +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 31a85893835748339b6c84fb98fde14b +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 08d9ecd7d3294c5b9dd4db228a1d8d5b +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: d94d6c69aaa64edd9c75624286713c2e +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: 020019b8aedb494fad022d19b7106f83 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: a6b66e0fc0de442e8f72f0d0c37c7e8c +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: 48b7d9ddac2940c0815e5c855bfca6d9 +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 894b843f9c064d56913e1a8c48093314 +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 2319e845caee41a3bc5888c3f1fc28d1 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 9ea661d749db428eacd2207dc7a01e36 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: 4ff76250f28144a4a9d8807a9d4ed3b4 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: 7f9f2df357a740feb89bfbcc44ff4d61 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: 12633ed841dd447a8753faeb4f9e5096 +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 4db64481d38c4896a85a8f6038a9931c +#: 1b4ff3eeddde4a9a8018235b9d706567 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: 50547062ee404e2ebeae7eeb54b9de4b +#: 88933bc02fa84412944673c3463af1ad +#: 4fde39d8a50e49f09bd28a8598760682 +#: b933cbf847d94c5fb8471918ce8cb4ad +#: 0145c520b85a4bc29302bb654f08f23b +#: a3e322ac8a0d4e2ba9bfbece6b5ae64b +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: d9b166225120432f9a2bf2cc7b6ffdfe +#: 28f8ec2fc5c0436aaba19e9d479aa466 +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: b866a0e5897e44329714f4c55eb20d2e +#: e64b5027878346d79f9ab52b3d3b916e +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: ed38ec582fbb48ff9f9cffa7962ef515 +#: 6cc0788250624fd69fa4e3881191ab7f +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 17eefb5f38534c1b87116c3a061ea1bb +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: ce0572fc81b343e6991c88ca0195149a +#: f8b77ad06ebe43d7b03b2135737902e2 +#: c7953486c99d4c7898c0155a6085dfd5 +#: 46d99b1f7f0747479bd58486cf7941d2 +#: cd0a797b3619404f964ba9efb33756bd +#: 528cd5e0d3994230b719fbfb39b1f13e +#: 324241aae8ff4505ab0467f2a7f27fe2 +#: f4086b1ad2e44c2b9de2636f8bc1eb90 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 764d7cf3fb5444d58dc9e0eb6b8fc649 +#: 0450a4b8de3046998d30ce1f09c10daf +#: fd6bf79cbb694dbb89e8731aed733e6c +#: e6048a64e09d46099132fee40a2e0644 +#: 9512391eb96440bd8e48c3754821e3d0 +#: 3e8669bf4a6741f9aba170864b251dac +#: a02ede726d3f4eec9602f72054c0d963 +#: 4ed593dfc39246789f1e4ecdc742323b +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 304de40206cb43d7b651245586cfa55b +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: 7855471c93bc44aabb1a2b9beb52b56a +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: f0452f324bfa451f9f3264f9a55e0e5d +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 6dc476cf8689465ea3993f49a9eead75 +#: 4dfc0be21065471d91def850bc2528fb +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: 09d69778a89044099b3e5d7cf02471bb +#: e3077bdff0dc4dfdae60eb60f3d66d8b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: b28843f7b57745db9cb3648ef23fda0f +#: 6a745fa266dd42849c95410775b690e0 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: be00ed49197f48ecb7cb244ecc214369 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: 90ad2b27f97b4ca089cf23a073cdf17b +#: 38d062892cb04bc7bbf0b56f263079e1 +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: c2d2756d617743b886c67160c2face21 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: 8681600183d1429cbd1b15639e1a222f +#: 1d49cd7337004fc38f4e8e9aa4270481 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: 24b7f85116cc4d2f904600555aa19b8b +#: c401a68b4f384d3eb13ab3e89a4a7195 +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: 0e1f9d22d0714bc5b80e420f63b34cff +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: 5fed95f16aaf42d4b41c569d9546b7f0 +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: b539a931f31d4cfe9d72aa5800115fb2 +#: 48e497c024bc4c38a86dd027aaa4fd2d +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: be638c80121948c99cc9fdb67a5d291e +#: 1fd8fe769ba8497eb8a9520af91ea33e +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: b5f3ad78a233411c97520c1fffdec18f +#: 7854e46c7fd24afd9c1942808521bee1 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 211bd57896494fca9ea8aa2fc142eea2 +#: 28ec0718d3114bfdaae4524c009da944 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: c6a421f7a0214d89958d4c258b58aac8 +#: 07bd0bc74ad74187bdc24c26041467ca +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 3afc146cde2e47d5b52e62fbd1f37426 +#: 2225f5acb44a4ce0ad16be5c4f6cba48 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 9acd61d4d67a4d2c82171a79462fb458 +#: cd7e7fea3b8346268618c31b70581326 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 140e449e46a84e3ca1a604176e583f44 +#: 3d8b717d4568458eb53b0b91695b3de8 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 76f35653e34b433d8e9fedc6d12ce856 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 1a2edf61fda8404689e3c0a7389d7d02 +#: 3bced6d84fa6453195be82dbc6d7ec83 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 0b5aceb6c9d24bd9bfe95cc04fdc61ad +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: 3523cc46c6324fca9053d6b1dd8c7495 +#: 21eee2c1cb6b430486446d223dcca0eb +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: b4f126415048402ca388c4c63f34ebe5 +#: fdf588cf8cd34d60bfb6cece3ef859e0 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 1b494245c14e4e22918c43ad9f26cc8d +#: df4d781178f2465b8a421651bdd2f66f +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: a88008a23ede4ea49ffcaccba7029d31 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: a256b51f1e944b7d9659b945d8ab05c9 +#: 23bbd631e73147e3af561eb4a14d2d6c +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: a446842e26e44781ad10cdaad73bc49d +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 3cc10263ab2f4dbfb6ccb12612b89cf1 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 995f6af5fc244293b34f5d840f01ce1c +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: b556a1d134764505aa25003d79a53e88 +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: ad23da5452bd46248606f6799ce93db0 +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: c63036ac68344465af6c7756be00b60b +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 2f7f270b0ac24f2f8df506f5dde72cf7 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: f49272e5e4c1491eb59c79d2dfb88a86 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 8b50c892d36d4d178ec4268c7c13887d +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: 9d22117a6f5a434593d5144bf824999f +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 4fbc454a144a466b9dd7ff74903fc5fb +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 281b129a76a24b0a818092acd1038757 +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 4dda6ca233d54c12b6ddceabae198495 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 59d87fecfd7f4438b68e0bcdecdcfb46 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: 0f7e33673ad349e5ad41a078032e5806 +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 77a7141f897048139ef3785b5f870b43 +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: 14ed183bc7e346598921445c0dea11e0 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 9406d05bf0ed4774af50fd66d24aa299 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: f5a9048ef9e047528c291505ef9a2c12 +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: 51e8c5a231eb45fb8c15be49b37a7bff +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 860a6f01ebac45938abd220758fd1109 +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 32155f96d47f4d76998a401aa9e9591f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: a62bbb9251794560ace0e52be3d9ebd3 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: e301af8f675444c69cfb6b578c02fdc7 +#: 3da1dec243994409bd764b133d4fc243 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 82c6efcfb5d5410eb316399b7c4f638e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: 29c3d25c657340a1bab7123a166b78c2 +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: ef8e7bd7e944429da78474d2fc5e0348 +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 08dd50bc6a5942ec8f3b6c201fc4497f +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 78c51215a68f40b280cc21d0e412eacf +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: bb8e2203374a4ae7b833c543ecc563b0 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: f34aa1e4d08944c497602b2a35f38a50 +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 2932972efc94447987b02a7707c62656 +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: 968f4e83c511425d8faf4c8d0f18097e +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 2eb89bdbaee04a899a961a7b87f0aef1 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: 3781fc7cd22d48bdb5aa4abc0c93b06f +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: f4af4a85efb243728d2ee783393dce14 +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: dbf8350f003a46b984b7432160e6def5 +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: db2993fe83814747a52f9db0b2fcc81e +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 39fe18bf5d4b4539b2f98e3bf0feea2a +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 58e7b0e7d0a149498e846dd2790c0eee +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: 4b78c5437904492ea3e692372d2fc163 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: f2626686125d4ec29fb2338373b54c93 +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 46327aca33cb49d1ba61149e94884991 +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 43f2e7020da94f77bce4e1f852ab11f1 +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 8342aa3f84624325aff8f7f4de788187 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: 2d54f11f99b245e5b2802b984bc024a5 +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: 83a357dc06b343549876035b03b8c5d1 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: 0461538fa12a44c5a9d230a928ae930d +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: 2b2552958f404447b711d09650d22395 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: 82c97e60f8634bd6b4d3e88524722412 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 0ae1393a80e94b899023c29f4af6084b +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 74339f624bba49d6b68e1dfc4724f673 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 3a4473864ec04d2e9a0d550b2051f717 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: 575661b36a2040699956f897bd6cc614 +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 3d18a704f5a94e2889e847c32a78aaab +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: fceca2b53d0646b2ae9f1cf9dbefe2fc +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: cba49054785b4ec2a7acd3aaa2e165d8 +#: 647c0e302af841d7b1789447281d7344 +#: d23de44d5d5b4bc7b32f3726afa97500 +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: dd867685663f4728b9fbe446a9b14a3d +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 67bf2c2cbbc44f6eb870af3a3a852676 +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 94d66455bfd04697814495e116176ffe +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: 39a9d3583f29451d8035158c54266ed6 +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: eba6af5cf8224d198fc04f090362307c +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: b48377cceff342e793e982c9fa2095d3 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: b64ef70d944c461b8ec7219e14e47795 +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 73cd08a2226f4cbe99fcde2d3636d640 +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 3c33bffa2c574ef888b041c1e6735b8e +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: 23bd067b32724dad9daba1e924757d86 +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 1be92fc3d0b44ea089273cfcd47318ef +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: 3d08125883b74f49bba042ed58d34648 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 7636c7e8b6e04d7089ba1cb10c4c475d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: e1c95ce96db043eb86ff9b3ae595017b +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: e6588c4b8fa64959b2dcac52403a6415 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: e7f85cb69a5342889525fbb81b44c86c +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: 71756719e0274300a839b38c8b4ea986 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: 88bf75fce3064eaf823b5d88be0ce053 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: 60374713dea84fff92b89b4ebaa8d7ac +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: 7616d5ea746f47ac972183150b97e8b0 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 0ca022c095334ec4a9fe41cb732e11a1 +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 1c807f8fd1c540ae8802092fbcec7159 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: c51956eb3ece432ea0ed5b676b2f037a +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: 45e6ab3a53b94f5b90136d68c1c0e479 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 7e05dc23d6be4428b4a414b3a65c4727 +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 96e7266ef25b429da42337c3582cc201 +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 9cb6959a877f4590bccb977416753410 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 7b54a3cd870d4b038dff685064bbca1a +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 0d661c96ac2d41ee94641a397aa3bdf7 +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: 94d39b79923a4a65b1a6ce5c464528c6 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 56801121f70b4cb2ab6207e254ec8bbf +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 42418ff882d44c1b9584fb9f7887f744 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 1118de96d202444d9bb4db74ebe4792d +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: aca51d371db84aa79418c79a18310055 +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: 3473e6d2942e4546a2c1590edeb502f8 +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: c210ad12f61047b68302e67da9b5dae0 +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: 1c15cff5a4614d88a62c8d2df97029fc +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: 4beae917368545688c01a4a929685cae +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 4f4f63b7107e4dc194760802c4581c2a +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: d942035c4c914ccb9de75836af9761c7 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 0e9064cf55fe43588053d37100634538 +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: aa1dcfc618e74a53b3c579380e5e1558 +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: 3ec3f4a2d1c547b18780db17fbff060c +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: 21e598983ce94d22b9d40a77577a6608 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 62f79a2c055b455d9626ca5a18d1bd72 +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 19c2b9b13bcc480aa7474301422faab3 +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 17bb520489a74f64b76ddbe2ffedcb5e +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 9e2b97aa3bfe4eae8524b325bf2ea3f1 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: 028c844ef208450f994b3949210ca996 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 2b758e44e4be4fdf89a5897385db6c59 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 16395173b7ee468f85ee8450493504de +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 51e2e929dadc41a78cea98f779e2e2a3 +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b757d4b151ef46fa96897bf00a0d9ab4 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: 2f2f46a81e8946bf8a9b48a5956c82f8 +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: 75177c797c704385bfa5ce86e03266c9 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: 4d05d16c3cb74eb291da7586fa859b90 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: c115b7ed044346d6a9c4c06306ee82d8 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 8f83261e3e91424b9a3c38280c643f02 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 269af269348e4da5b93cb25dcd10374a +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: c376ab464fec4ee78a33d42dfed5dc1c +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 53d468d14703494699478e6847d82e34 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: 32bd7abe387e4999a0864f6e6a48e435 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 0712e952fe2442daa9ceb0cee79a3ebf +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: ef2b8db0c8d64e41b839b47aae34d0ec +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: f9f45dcc2bcb4fd1a1021d2843137fa3 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 4ffbc016a5344e6e9272793d921e4900 +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7118718b98c5488c9d9a54e5ec84c055 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 20fe8fa105a84171972722158bafbc0d +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 836fa2a818854cf9af13d674f5bb859c +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: 5d56e1ac063d48c2b140a72db9f78540 +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: 0166655553ac4d8fb868138936176986 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: e43fe4a9340b458786c51499c75b5556 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: 0ba13966a1364d4e9992b5cfeb6871d1 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: feb8bce610be4a3a92053f2e2e5aab76 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: 0f5fd76c57e7412097b4ebdeb074f2fd +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: b645dd17256543b0a42d231171140c95 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: c8d5743769bd4fee93f77a52ba318883 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: af6cbb89b7a84bf78b7443b6746484fe +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: ad9394b163a94340975a66ea2bba7094 +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: 677bce1f24f449beb2bac5ed8469f624 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 4c0d14a24b354feabf4b6ad4852f9543 +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: d407e5c9aa9043b0b6ab234348467db0 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: f06b60c926204ca88b4355803f1b7b11 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 0a7c19b054d2400abd327736b6829670 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: cd1773f336544b3688bc76c28e9d1f79 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 6b7bbca601f04f7183bc75988bd6db13 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: 069d1dd1f03f4cd79e44f2dcd890b531 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 4924b1a69a5f48b0aa6af943b40ffc68 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: e100d8d8f23c4d6996ac59c5ad68acf0 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: a87dfd0dc0274ff4b34354678f2d49d2 +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 772078ff701a477cae9acb8dda16ef1f +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: d2d67048e93e40c4820b805f1ba28cc9 +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 580477152be041a8ae5c5f546ecbf21d +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: 05f8faea082b4fb9b9c22b8eff7eb356 +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 4c107fb18fb34c2dba7743118c51e8c8 +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: 729ea19aa03b49bdadccc6e6f0d2e7d9 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: e849cda9fb1d4a48b5b1f9a4e44213a1 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: bfc20f529d2d4797b87c63c7b2c05e91 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: 761a900275a044f28ddcebe509a4637a +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 59af21cf1ee848e993563ad47f7bb248 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: d711ce1ccdcf427aba25a2ab3d11165d +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: eaaaa01fe0894f479a42a9c3ce199819 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: 92489f186e3f449295b0dc864ebf17f7 +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 1360c3a2d43b48f3b3e1153bb26b3f30 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 2e993e21a3624910b4282bd088694fec +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: df5b4b041dc944be8580e43012339168 +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: 92ac2766d118428ea148094c022a8b0d +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: e4ddaca03eb449eabbf2d2fce752c367 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 0bc50411a4b748d8864305070d11a304 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 74453227279a46cea3644f3ca7df61b9 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 75ce3269886645eda46a6575fca186eb +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 1e7e5b46017a476a80d57ab7eb614758 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: 1ee41e983ca14a959caa199b1ce12700 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: 070e6a00d09e4675b89afec5d066aec1 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: fd37ebe3aad9473891cc764a47363f8e +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: 85176099018c4ae19bed1261e92e6e92 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 952e9a347f444ef496fa0cdf00160ffd +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 2b5ad46ca3024ce1b37e1c92a820aabf +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: ea17d17cd08b4c40a842598c8521af56 +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 6e5f1266974d4a32995aaa69fbbfd648 +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 20be823f70c348bbaad6bfc8b88201a9 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 02311e5310cb49d19bf2998513f73124 +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: ca6e4a3fe04145a9a21cc43cc53a07bc +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 75452467551a46a2b2b3685f1a4aae0d +#: 93efa8e941a7427f949afc794ed16e75 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: 39beed65cb114bd78c79aa4a5d6f4398 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: dd880d0589fe45dbaf9b7d799402f158 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 671d0bd54bb147518c35f0844a76c61d +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 66de58a51b034f6a8d5dbe742046f817 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 564e68d58e364715aa72183cb16b3d72 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: 558739ceb3fe40de8ea87ff1e7d3fe9d +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: fdc601ee1aa54e1f84cd00eed2e44e52 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: e4f4a76cee96473d9da3bc1c9e35324a +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: d524ed5f1e964688af9d74eef8e46e04 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: c646e4714d78437fb450127b119fbd70 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 8351ddfd726c40159d81c017ef221606 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: 456794c7274f4654b54aae8d4073a2df +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: 6485e8d6814144d1bcbe66bfe4fcbdb9 +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: a2b9e47cc923466f8bd2fbc4b33fc4fa +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 698cc640807247fd8d512c59ce32ee48 +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: dd658e10da624918b7dec1ea18bbf432 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: f6bd95a4fbc44ffdbfec7fcac90f6bb6 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: ac7b02a71d3544848d4fb539b2a4f115 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: 4380dbd066a44102a71c7e42ca7de8d8 +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: da946c9d59f44fb995daa6aadc44031d +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: 7c73bc555f604afd8491c1619d6905eb +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: e79ce424410e4682881fe14326955a14 +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: be8d2b89052e4f9d96ff2bf15526e229 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 967b064ec4284d0aaf374509915497e1 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 02d667b922264f8e8021844df0085578 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: db8734e07541495188d9ee97eaaaeff3 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: 22542da60ac24403827e2e2a14595770 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: d10f35716f9c4b878da0f2b4ff3d44aa +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 1fd555d1f8ca499ead8d5601eb62266a +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: f5fc85accf8c4bb9bc701ba0b4ee2e21 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: e69cb5e87f4b4670abbc1606197d804c +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: 15d763c45a2749a8926b1f965db9d97f +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: c2aac63fc0c347d9833d253039000fa3 +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: 06a23beb753c4a97b302943f59128d78 +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 45985434cfe9438cb558075e1fd73809 +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: e92da36d865142289b11d245221ff8d4 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 3ed7a2b9f77b4eadae3bf6e4a98d14b9 +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: fd66c4fb9c2a4beea0ed5ed8874fcd61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 65944dc8b32a46a4beb73dbdebb7b01a +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 6250fe161ab0421b8799040b79ce695a +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: cc40c0f1ade34ab3b400a02b59b7ba01 +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 29f53a5d64fa498bad0dbe94b238fd97 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: 037fccb419bc4e9f839c665ae31e28ee +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: fdd4bec90c484a618ed8e4d1199deff8 +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 11afb584f37947358963f6510935c5d5 +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: a77e0bfb589c40b6a61a9ca559961a7c +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: 3f4aa12588204fe5b33db590a9446283 +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 640c67f3bcd740c59f90c361024acbcc +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: 8c4d30cbbea146a584731d164d4ad9ef +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: 5d0fd4f8b58e4a8e8f46902e64e6556b +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: e98ab273645340f9a1446183a642e79e +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 37a83ed92d9e44689cfd3a31c2785418 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 7cebef0a9e1444149b1dc58d30f6c10e +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 0cd2bd98918b4622bc586d50f1ce1fa4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: 92458de979564d19a634bb8d3bf6f586 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: d4ee6cc8903f4e6992439ca2586246ed +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 62b438c4ed8a409f96974f3d59cc5854 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: f0f288aeae4f4649ba3615437b531e97 +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: f35023cb05504d1db0cbee41c4e5f371 +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: 01564f1d2038489685160f03db92085f +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: ad662dce1e4149728b8e17f74d8f975f +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 4f6a57f34f094418b7c13aa07eef95c7 +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: 373a6c24de9144e69f37418d6ce8857d +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: f804a8493c8e40178772d94bdc45b43e +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: b3c504b8ab1a42788ef4e3339d27b0dc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 2c2681fe72e24a5d8d98f0aa8e8c56a2 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 571e5c13552c4381bb6de53c02fe5f43 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: fd789f444d9a4061b4fc61bac70353bb +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 2cef838551994b078e460c63214517f9 +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: 2a3a8a553d3c455e9288f63b9a02898d +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: b0b8def4623a4018b1ac913a9256c0a2 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 3f0d4346f0104cc08c059eed9ab4b3a9 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 22e0ac963278414d8141ce5ce4031029 +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: 49cad54646d04adc8e5ac9f0f3c8f895 +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: c8776a4511b24f46bbe0a34d52cf3c8b +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 401b053bd08a4286b9059cb6ebf8d679 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: 8d48a277f37f458f88c54f362534d7b5 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: de90253a11f24f29a4a57348b4f60941 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: 1e20968f957441c58cabfbc46c21e8ca +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 4cf2e158afb348d7b3fd6274fe888129 +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 44c5c010c97a40068a6b930949dcd8cf +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: c6277b2a7a934f81a91e406ef317a1fb +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: 8b3ece04170c447e9b5a8f76374c4c23 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: 6b952b7369b447bdb0bf1e9ff8540194 +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: a6024fb7ce664896a6858d5ea3562fb7 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" From eb2c36b7c02b92feedf6f78e762a205461ef5b6e Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Wed, 25 Jan 2023 10:14:57 +0100 Subject: [PATCH 036/179] remove unused trademarks sections --- LICENSE.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/LICENSE.md b/LICENSE.md index 4345a729..75596a51 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -16,9 +16,9 @@ You are free: for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the -license terms. +license terms: + -Under the following terms: * **Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow @@ -53,7 +53,7 @@ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. -## Trademark + [cc-by-human]: https://creativecommons.org/licenses/by/4.0/ From ba5c9e53875937cc243c5ae9ea2c0d75eefba57c Mon Sep 17 00:00:00 2001 From: "Bruno P. Kinoshita" Date: Wed, 25 Jan 2023 12:54:27 +0100 Subject: [PATCH 037/179] Add troubleshooting docs (#364) --- CONTRIBUTING.md | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 7b954969..559a0293 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -125,6 +125,10 @@ source venv/bin/activate # Open in your browser ``` +You can use `udocker` or any other Docker compatible engine to build the +user guide, by setting the following environment variable: +`CWLTOOL_OPTIONS=--udocker`, or `CWLTOOL_OPTIONS=--podman` for Podman, or `CWLTOOL_OPTIONS=--singularity` for Singularity/Apptainer. + > NOTE: When you modify the packages installed with apt or pip, please verify > if the change needs to be applied to either or to both of CI and readthedocs. > ReadTheDocs builds and deploys previews. CI builds and deploys production @@ -185,6 +189,34 @@ If you are having trouble with links to sections or code blocks, it might be due to duplicated sections, or to spaces or other characters. To preview the generated links, use the `myst-anchors` tool. +### Troubleshooting + +General advice for troubleshooting is to increase the verbosity of Sphinx +logs. When using `make`, change your command to the following pattern: +`make SPHINXOPTS="-vvv" html`. Or if you are using `sphinx-build`, then +use the following: `sphinx-build -vvv -b html src build/`. + +It is also worth removing build directories and files such as `_build`, `build`, +and [`~/.cache/salad`](https://github.com/common-workflow-language/user_guide/issues/268#issuecomment-1276068865). +You may want to start afresh with a new Python virtual environment, +installing the dependencies from scratch. + +If running `make html` or `make watch` appears to run fine but [gets stuck +](https://github.com/common-workflow-language/user_guide/issues/268) at some +part of the process (`10%`, `33%`, `57%`, etc.) for longer than 2-5 minutes +you may have to try the following: + +1. Check if the Python dependencies installed in your Python virtual environment + have updates available (you can re-create the virtual environment, use `--upgrade` + for `pip`, or manually verify in PyPI and `pip`). +2. Use `top` or `htop` to find out if there is any `cwltool` command running. Then + try running that command individually to see what is the error message. +3. Upgrade your version of `docker` if you have [an error message]( + https://github.com/docker/compose/issues/8121#issuecomment-806055733) similar to + `docker: Failed to create the container ID file: open /tmp/....cid: no such file or directory.`. +4. Try using `udocker` instead of `docker`, by using `pip` to install it, and setting + `CWLTOOL_OPTIONS` to `--udocker`. + ## Other Resources General discussion of [Common Workflow Language][cwl-site] project From 2d7f5595882ed3d92143241536dbcdcb3947aa2c Mon Sep 17 00:00:00 2001 From: Michael Crusoe Date: Wed, 25 Jan 2023 14:37:58 +0100 Subject: [PATCH 038/179] Translated using Weblate (Spanish) Currently translated at 64.7% (11 of 17 strings) Translated using Weblate (Portuguese) Currently translated at 88.2% (15 of 17 strings) Co-authored-by: Michael Crusoe Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-license/es/ Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-license/pt/ Translation: Common Workflow Language/CWL User Guide: License --- locales/es/LC_MESSAGES/LICENSE.po | 67 +++++++++++++++++++++++++------ locales/pt/LC_MESSAGES/LICENSE.po | 61 +++++++++++++++++++++++----- 2 files changed, 105 insertions(+), 23 deletions(-) diff --git a/locales/es/LC_MESSAGES/LICENSE.po b/locales/es/LC_MESSAGES/LICENSE.po index 87af7480..719078bf 100644 --- a/locales/es/LC_MESSAGES/LICENSE.po +++ b/locales/es/LC_MESSAGES/LICENSE.po @@ -4,32 +4,38 @@ # Language User Guide package. # FIRST AUTHOR , 2023. # -#, fuzzy msgid "" msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" +"Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" +"PO-Revision-Date: 2023-01-25 13:37+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Spanish \n" +"Language: es\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" #: ../../LICENSE.md:2 385524707375429989b7b4fc7e4c7aa5 #: 3d749a78eb3e47c991d603c2cabd1b91 +#, fuzzy msgid "Licenses" -msgstr "" +msgstr "Licencias" #: ../../LICENSE.md:4 7682a147e3f74921948bde67ac684338 #: 4689ade8475a4c8a9d5e325f072c1392 +#, fuzzy msgid "Instructional Material" -msgstr "" +msgstr "Material didáctico" #: ../../LICENSE.md:6 7273f384601c4f18a4cc33c833f05e56 #: ef8ec0f072d947fbba997c4b2191abc2 +#, fuzzy msgid "" "All Common Workflow Language project instructional material and changes to " "the structure are also made available under the [Creative Commons " @@ -37,27 +43,34 @@ msgid "" "of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" "[cc-by-legal]." msgstr "" +"Todo el material instructivo del proyecto Common Workflow Language y los " +"cambios en la estructura también están disponibles bajo la [licencia " +"Creative Commons Attribution][cc-by-human]. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del [texto legal completo de la " +"licencia CC BY 4.0][cc-by-legal]." #: ../../LICENSE.md:12 2cd9327d0e2e43aaa963633db1320b96 #: 696f3824ca814c9eb314abae51be8202 msgid "You are free:" -msgstr "" +msgstr "Usted es libre de:" #: ../../LICENSE.md:14 793123b1e0ba4603a0c54c952ea4a590 #: 72ebe92edf58434e9d7a4fc6bddf8880 msgid "" "to **Share**---copy and redistribute the material in any medium or format" msgstr "" +"**Compartir**---copiar y redistribuir el material en cualquier medio o " +"formato" #: ../../LICENSE.md:15 151178e4c9a9444fb65dbf926edad28d #: 9b403f96d4194ffaab3f309d7d12f360 msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" +msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" #: ../../LICENSE.md:17 e44aed84ff0d48b3aea3946b3a7c85fc #: 10b1befd0f834d79880c8aeb70b595d4 msgid "for any purpose, even commercially." -msgstr "" +msgstr "para cualquier propósito, incluso comercialmente." #: ../../LICENSE.md:19 d8bb44ca55b642d6bb4a88eaa8292204 #: 9017d0b760bb4370926d511b97a604c6 @@ -65,11 +78,13 @@ msgid "" "The licensor cannot revoke these freedoms as long as you follow the license " "terms." msgstr "" +"La licenciante no puede revocar estas libertades en tanto usted siga los " +"términos de la licencia." #: ../../LICENSE.md:22 6859f286e52c417096b072c923b9f235 #: 1faadcaead6748dfb34886e5819af9b9 msgid "Under the following terms:" -msgstr "" +msgstr "Bajo los siguientes términos:" #: ../../LICENSE.md:24 ee4ea8e1fd044924b34b2d96ca158257 #: 7a49ed3a728349c9b486f3d0b1dbf577 @@ -81,6 +96,13 @@ msgid "" "made. You may do so in any reasonable manner, but not in any way that " "suggests the licensor endorses you or your use." msgstr "" +"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su " +"trabajo se deriva de un trabajo que tiene «Copyright © The Common Workflow " +"Language Project» y, cuando sea práctico, con un enlace a https://www." +"commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e indicar " +"si se han realizado cambios. Puede hacerlo en cualquier forma razonable, " +"pero no de forma tal que sugiera que usted o su uso tienen el apoyo de la " +"licenciante." #: ../../LICENSE.md:32 7598558aee3244b6b7892b06df94a393 #: 57da6294edce46eab00e7d15e6f6d4fa @@ -89,6 +111,9 @@ msgid "" "technological measures that legally restrict others from doing anything the " "license permits. With the understanding that:" msgstr "" +"**No hay restricciones adicionales**---No puede aplicar términos legales ni " +"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " +"permitido por la licencia. Con el entendimiento de que:" #: ../../LICENSE.md:36 a83123e7ae79486c80107d176ea951c7 #: 8fc8a30cd63c4a0a9d8ba1b913687029 @@ -97,6 +122,9 @@ msgid "" "the public domain or where your use is permitted by an applicable exception " "or limitation." msgstr "" +"No tiene que cumplir con la licencia para elementos del materiale en el " +"dominio público o cuando su uso esté permitido por una excepción o " +"limitación aplicable." #: ../../LICENSE.md:39 0cc05e8ed5274019998b1dfd6ab76824 #: fe59e74a4d024831a6d5cbcfd3e4ee38 @@ -105,22 +133,32 @@ msgid "" "necessary for your intended use. For example, other rights such as " "publicity, privacy, or moral rights may limit how you use the material." msgstr "" +"No se dan garantías. La licencia podría no darle todos los permisos que " +"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como " +"publicidad, privacidad, o derechos morales pueden limitar la forma en que " +"utilice el material." #: ../../LICENSE.md:44 d70e680300524c8583f1e7fd361ad2ba #: 3ea41d5a14ad46729cabb387a33814b0 msgid "Software" -msgstr "" +msgstr "Software" #: ../../LICENSE.md:46 d17e76d478354904b679b4f5ebde418d #: 23751e2552ff450c83e3dd255da56dac +#, fuzzy msgid "" "Except where otherwise noted, the example programs and other software " "provided by Common Workflow Language project are made available under the " "[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" +"Excepto cuando se indique lo contrario, los programas de ejemplo y otro " +"software proporcionado por el proyecto Common Workflow Language están " +"disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " +"la [OSI][Osi]." #: ../../LICENSE.md:51 015fba86005946eebc5959cc3b0493d0 #: 13fb5eb48a8a434e95dbbb717ccaef8a +#, fuzzy msgid "" "Unless required by applicable law or agreed to in writing, software " "distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " @@ -128,6 +166,11 @@ msgid "" "License for the specific language governing permissions and limitations " "under the License." msgstr "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." #: ../../LICENSE.md:57 524088befae04f5485dc731d505c769b #: e262fbd0e7de4f148f31afe39d1cb9e9 diff --git a/locales/pt/LC_MESSAGES/LICENSE.po b/locales/pt/LC_MESSAGES/LICENSE.po index c3591ece..885e610a 100644 --- a/locales/pt/LC_MESSAGES/LICENSE.po +++ b/locales/pt/LC_MESSAGES/LICENSE.po @@ -8,95 +8,134 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" +"PO-Revision-Date: 2023-01-25 13:37+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Portuguese \n" "Language: pt\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.16-dev\n" #: ../../LICENSE.md:2 #: 3d749a78eb3e47c991d603c2cabd1b91 msgid "Licenses" -msgstr "" +msgstr "Licenças" #: ../../LICENSE.md:4 #: 4689ade8475a4c8a9d5e325f072c1392 msgid "Instructional Material" -msgstr "" +msgstr "Material instrucional" #: ../../LICENSE.md:6 #: ef8ec0f072d947fbba997c4b2191abc2 +#, fuzzy msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." msgstr "" +"Todo o material instrucional do projeto Common Workflow Language e " +"alterações na estrutura também são disponibilizados sob a [licença Creative " +"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " +"humanos de (e não um substituto para) o [texto legal completo da licença CC " +"BY 4.0][cc-by-legal]." #: ../../LICENSE.md:12 #: 696f3824ca814c9eb314abae51be8202 msgid "You are free:" -msgstr "" +msgstr "Você tem o direito de:" #: ../../LICENSE.md:14 #: 72ebe92edf58434e9d7a4fc6bddf8880 msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" +"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " +"formato" #: ../../LICENSE.md:15 #: 9b403f96d4194ffaab3f309d7d12f360 msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" +msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" #: ../../LICENSE.md:17 #: 10b1befd0f834d79880c8aeb70b595d4 msgid "for any purpose, even commercially." -msgstr "" +msgstr "para qualquer fim, mesmo que comercial." #: ../../LICENSE.md:19 #: 9017d0b760bb4370926d511b97a604c6 msgid "The licensor cannot revoke these freedoms as long as you follow the license terms." msgstr "" +"O licenciante não pode revogar estes direitos desde que você respeite os " +"termos da licença." #: ../../LICENSE.md:22 #: 1faadcaead6748dfb34886e5819af9b9 msgid "Under the following terms:" -msgstr "" +msgstr "De acordo com os termos seguintes:" #: ../../LICENSE.md:24 #: 7a49ed3a728349c9b486f3d0b1dbf577 msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" +"Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " +"trabalho deriva de um trabalho que é «Copyright © The Common Workflow " +"Language project», e, quando prático, criar uma ligação para https://www." +"commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " +"se foram feitas alterações. Você pode fazê-lo de qualquer forma razoável, " +"mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " +"uso." #: ../../LICENSE.md:32 #: 57da6294edce46eab00e7d15e6f6d4fa msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" +"**Sem restrições adicionais**---Você não pode aplicar termos jurídicos ou " +"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " +"algo que a licença permita. Com o entendimento de que:" #: ../../LICENSE.md:36 #: 8fc8a30cd63c4a0a9d8ba1b913687029 msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." msgstr "" +"Não tem de cumprir com os termos da licença relativamente a elementos do " +"material que estejam no domínio público ou cuja utilização seja permitida " +"por uma exceção ou limitação que seja aplicável." #: ../../LICENSE.md:39 #: fe59e74a4d024831a6d5cbcfd3e4ee38 msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" +"Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " +"autorizações necessárias para o uso pretendido. Por exemplo, outros " +"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " +"podem limitar o uso do material." #: ../../LICENSE.md:44 #: 3ea41d5a14ad46729cabb387a33814b0 msgid "Software" -msgstr "" +msgstr "Software" #: ../../LICENSE.md:46 #: 23751e2552ff450c83e3dd255da56dac msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" +"Salvo indicação em contrário, os programas de exemplo e outro software " +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a [" +"licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." #: ../../LICENSE.md:51 #: 13fb5eb48a8a434e95dbbb717ccaef8a msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." #: ../../LICENSE.md:57 #: e262fbd0e7de4f148f31afe39d1cb9e9 +#, fuzzy msgid "Trademark" -msgstr "" +msgstr "Marca registrada" From 055f34d9884ace18a47fb6a2d4be60bc000a62df Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 25 Jan 2023 12:54:27 +0100 Subject: [PATCH 039/179] Switch to a single gettext --- locales/LICENSE.pot | 102 - locales/_includes.pot | 22 - locales/episodes.pot | 27 - locales/es/LC_MESSAGES/LICENSE.po | 135 - locales/es/LC_MESSAGES/_includes.po | 28 - locales/es/LC_MESSAGES/episodes.po | 32 - locales/es/LC_MESSAGES/faq.po | 358 --- locales/es/LC_MESSAGES/index.po | 57 - locales/es/LC_MESSAGES/introduction.po | 746 ----- locales/es/LC_MESSAGES/setup.po | 32 - locales/es/LC_MESSAGES/sphinx.po | 9 +- locales/es/LC_MESSAGES/topics.po | 2577 ---------------- locales/es/LC_MESSAGES/tutorials.po | 64 - locales/es/LC_MESSAGES/user_guide.po | 3827 ++++++++++++++++++++++++ locales/faq.pot | 292 -- locales/index.pot | 57 - locales/introduction.pot | 607 ---- locales/pt/LC_MESSAGES/LICENSE.po | 102 - locales/pt/LC_MESSAGES/_includes.po | 22 - locales/pt/LC_MESSAGES/episodes.po | 27 - locales/pt/LC_MESSAGES/faq.po | 292 -- locales/pt/LC_MESSAGES/index.po | 57 - locales/pt/LC_MESSAGES/introduction.po | 607 ---- locales/pt/LC_MESSAGES/setup.po | 27 - locales/pt/LC_MESSAGES/sphinx.po | 25 +- locales/pt/LC_MESSAGES/topics.po | 2083 ------------- locales/pt/LC_MESSAGES/tutorials.po | 57 - locales/pt/LC_MESSAGES/user_guide.po | 3820 +++++++++++++++++++++++ locales/setup.pot | 27 - locales/sphinx.pot | 6 +- locales/tutorials.pot | 57 - locales/{topics.pot => user_guide.pot} | 1931 +++++++++--- src/conf.py | 2 +- 33 files changed, 9153 insertions(+), 8961 deletions(-) delete mode 100644 locales/LICENSE.pot delete mode 100644 locales/_includes.pot delete mode 100644 locales/episodes.pot delete mode 100644 locales/es/LC_MESSAGES/LICENSE.po delete mode 100644 locales/es/LC_MESSAGES/_includes.po delete mode 100644 locales/es/LC_MESSAGES/episodes.po delete mode 100644 locales/es/LC_MESSAGES/faq.po delete mode 100644 locales/es/LC_MESSAGES/index.po delete mode 100644 locales/es/LC_MESSAGES/introduction.po delete mode 100644 locales/es/LC_MESSAGES/setup.po delete mode 100644 locales/es/LC_MESSAGES/topics.po delete mode 100644 locales/es/LC_MESSAGES/tutorials.po create mode 100644 locales/es/LC_MESSAGES/user_guide.po delete mode 100644 locales/faq.pot delete mode 100644 locales/index.pot delete mode 100644 locales/introduction.pot delete mode 100644 locales/pt/LC_MESSAGES/LICENSE.po delete mode 100644 locales/pt/LC_MESSAGES/_includes.po delete mode 100644 locales/pt/LC_MESSAGES/episodes.po delete mode 100644 locales/pt/LC_MESSAGES/faq.po delete mode 100644 locales/pt/LC_MESSAGES/index.po delete mode 100644 locales/pt/LC_MESSAGES/introduction.po delete mode 100644 locales/pt/LC_MESSAGES/setup.po delete mode 100644 locales/pt/LC_MESSAGES/topics.po delete mode 100644 locales/pt/LC_MESSAGES/tutorials.po create mode 100644 locales/pt/LC_MESSAGES/user_guide.po delete mode 100644 locales/setup.pot delete mode 100644 locales/tutorials.pot rename locales/{topics.pot => user_guide.pot} (57%) diff --git a/locales/LICENSE.pot b/locales/LICENSE.pot deleted file mode 100644 index 67ae058a..00000000 --- a/locales/LICENSE.pot +++ /dev/null @@ -1,102 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../LICENSE.md:2 -#: 087fa59ef53947e683e1b0d1097cfa14 -msgid "Licenses" -msgstr "" - -#: ../../LICENSE.md:4 -#: e134424e12c14d46a8cfa417dbb39dbf -msgid "Instructional Material" -msgstr "" - -#: ../../LICENSE.md:6 -#: 44fc3047733e40408793ef3438e4a21c -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." -msgstr "" - -#: ../../LICENSE.md:12 -#: b2a65a97826d48aa859843a1dbe646a0 -msgid "You are free:" -msgstr "" - -#: ../../LICENSE.md:14 -#: 922b2a5bc70b49e299d0662622aca1b2 -msgid "to **Share**---copy and redistribute the material in any medium or format" -msgstr "" - -#: ../../LICENSE.md:15 -#: 51700e62261a4a20a887c6c5ef4d3f46 -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" - -#: ../../LICENSE.md:17 -#: f84b26c1e38e46d79fa6b5cdcc7c6434 -msgid "for any purpose, even commercially." -msgstr "" - -#: ../../LICENSE.md:19 -#: 435cf52ad40643139c4eaec84b263132 -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms." -msgstr "" - -#: ../../LICENSE.md:22 -#: 4eeaef6ed7304ea8ad815fb8b35f374c -msgid "Under the following terms:" -msgstr "" - -#: ../../LICENSE.md:24 -#: 9295c98517134bc0b8b08e088ad630fb -msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." -msgstr "" - -#: ../../LICENSE.md:32 -#: c07512980b6a4433944edf2e80a88c6c -msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" -msgstr "" - -#: ../../LICENSE.md:36 -#: 6a4d80c1331c470facd6ccc060a0cd94 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." -msgstr "" - -#: ../../LICENSE.md:39 -#: d00d862c37ef4371bc40ad101c433199 -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." -msgstr "" - -#: ../../LICENSE.md:44 -#: 93ba22a55b954a86af163557e05c52a4 -msgid "Software" -msgstr "" - -#: ../../LICENSE.md:46 -#: 367e01c9a6ad426a83bf5f5374e6a8ab -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." -msgstr "" - -#: ../../LICENSE.md:51 -#: 565193677802418693fdbc123b34dd2b -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." -msgstr "" - -#: ../../LICENSE.md:57 -#: a4a99fc7709a49c29482f6e992d9e2bc -msgid "Trademark" -msgstr "" diff --git a/locales/_includes.pot b/locales/_includes.pot deleted file mode 100644 index 41cc9fb0..00000000 --- a/locales/_includes.pot +++ /dev/null @@ -1,22 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/_includes/what-is-cwl.md:1 -#: 46f474e1b364495181698bd13ce28a1e -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" diff --git a/locales/episodes.pot b/locales/episodes.pot deleted file mode 100644 index ecff4e32..00000000 --- a/locales/episodes.pot +++ /dev/null @@ -1,27 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/episodes.md:5 -#: 5b500989fc13480681ecb39954c13fd7 -msgid "This page has moved" -msgstr "" - -#: ../../src/episodes.md:9 -#: ff7a3cc03e2048278bcb9af2429b8dee -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." -msgstr "" diff --git a/locales/es/LC_MESSAGES/LICENSE.po b/locales/es/LC_MESSAGES/LICENSE.po deleted file mode 100644 index 87af7480..00000000 --- a/locales/es/LC_MESSAGES/LICENSE.po +++ /dev/null @@ -1,135 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../LICENSE.md:2 385524707375429989b7b4fc7e4c7aa5 -#: 3d749a78eb3e47c991d603c2cabd1b91 -msgid "Licenses" -msgstr "" - -#: ../../LICENSE.md:4 7682a147e3f74921948bde67ac684338 -#: 4689ade8475a4c8a9d5e325f072c1392 -msgid "Instructional Material" -msgstr "" - -#: ../../LICENSE.md:6 7273f384601c4f18a4cc33c833f05e56 -#: ef8ec0f072d947fbba997c4b2191abc2 -msgid "" -"All Common Workflow Language project instructional material and changes to " -"the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable summary " -"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" -"[cc-by-legal]." -msgstr "" - -#: ../../LICENSE.md:12 2cd9327d0e2e43aaa963633db1320b96 -#: 696f3824ca814c9eb314abae51be8202 -msgid "You are free:" -msgstr "" - -#: ../../LICENSE.md:14 793123b1e0ba4603a0c54c952ea4a590 -#: 72ebe92edf58434e9d7a4fc6bddf8880 -msgid "" -"to **Share**---copy and redistribute the material in any medium or format" -msgstr "" - -#: ../../LICENSE.md:15 151178e4c9a9444fb65dbf926edad28d -#: 9b403f96d4194ffaab3f309d7d12f360 -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" - -#: ../../LICENSE.md:17 e44aed84ff0d48b3aea3946b3a7c85fc -#: 10b1befd0f834d79880c8aeb70b595d4 -msgid "for any purpose, even commercially." -msgstr "" - -#: ../../LICENSE.md:19 d8bb44ca55b642d6bb4a88eaa8292204 -#: 9017d0b760bb4370926d511b97a604c6 -msgid "" -"The licensor cannot revoke these freedoms as long as you follow the license " -"terms." -msgstr "" - -#: ../../LICENSE.md:22 6859f286e52c417096b072c923b9f235 -#: 1faadcaead6748dfb34886e5819af9b9 -msgid "Under the following terms:" -msgstr "" - -#: ../../LICENSE.md:24 ee4ea8e1fd044924b34b2d96ca158257 -#: 7a49ed3a728349c9b486f3d0b1dbf577 -msgid "" -"**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow Language " -"project, and, where practical, linking to https://www.commonwl.org/ ), " -"provide a [link to the license][cc-by-human], and indicate if changes were " -"made. You may do so in any reasonable manner, but not in any way that " -"suggests the licensor endorses you or your use." -msgstr "" - -#: ../../LICENSE.md:32 7598558aee3244b6b7892b06df94a393 -#: 57da6294edce46eab00e7d15e6f6d4fa -msgid "" -"**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything the " -"license permits. With the understanding that:" -msgstr "" - -#: ../../LICENSE.md:36 a83123e7ae79486c80107d176ea951c7 -#: 8fc8a30cd63c4a0a9d8ba1b913687029 -msgid "" -"You do not have to comply with the license for elements of the material in " -"the public domain or where your use is permitted by an applicable exception " -"or limitation." -msgstr "" - -#: ../../LICENSE.md:39 0cc05e8ed5274019998b1dfd6ab76824 -#: fe59e74a4d024831a6d5cbcfd3e4ee38 -msgid "" -"No warranties are given. The license may not give you all of the permissions " -"necessary for your intended use. For example, other rights such as " -"publicity, privacy, or moral rights may limit how you use the material." -msgstr "" - -#: ../../LICENSE.md:44 d70e680300524c8583f1e7fd361ad2ba -#: 3ea41d5a14ad46729cabb387a33814b0 -msgid "Software" -msgstr "" - -#: ../../LICENSE.md:46 d17e76d478354904b679b4f5ebde418d -#: 23751e2552ff450c83e3dd255da56dac -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the " -"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." -msgstr "" - -#: ../../LICENSE.md:51 015fba86005946eebc5959cc3b0493d0 -#: 13fb5eb48a8a434e95dbbb717ccaef8a -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." -msgstr "" - -#: ../../LICENSE.md:57 524088befae04f5485dc731d505c769b -#: e262fbd0e7de4f148f31afe39d1cb9e9 -msgid "Trademark" -msgstr "" diff --git a/locales/es/LC_MESSAGES/_includes.po b/locales/es/LC_MESSAGES/_includes.po deleted file mode 100644 index ed23c04f..00000000 --- a/locales/es/LC_MESSAGES/_includes.po +++ /dev/null @@ -1,28 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/_includes/what-is-cwl.md:1 66189f9a18df470791d7e6ab690b3475 -msgid "" -"CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." -msgstr "" - diff --git a/locales/es/LC_MESSAGES/episodes.po b/locales/es/LC_MESSAGES/episodes.po deleted file mode 100644 index 897540f7..00000000 --- a/locales/es/LC_MESSAGES/episodes.po +++ /dev/null @@ -1,32 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/episodes.md:5 49382fe02e4f4aae96ce4d1b666d649a -#: 0cbb5e7334a647c3bcae7333ec3ced90 -msgid "This page has moved" -msgstr "" - -#: ../../src/episodes.md:9 ebd3b75bc9a347029e9e164e94b43374 -#: fabb221482cb4ac0a98bbe10943ed025 -msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. Please use the new [Table of Contents](index.md#table-of-" -"contents) to browse the User Guide." -msgstr "" diff --git a/locales/es/LC_MESSAGES/faq.po b/locales/es/LC_MESSAGES/faq.po deleted file mode 100644 index 4b38c453..00000000 --- a/locales/es/LC_MESSAGES/faq.po +++ /dev/null @@ -1,358 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/faq.md:1 e53c79b325b749a691434bf2f7825a5a -#: 5daa5afac36f46dd8329e5629056384c -msgid "FAQ" -msgstr "" - -#: ../../src/faq.md:11 d95bfefa6344474d9820a266922831f8 -#: 40c8efda3caf4c6089bda3027c522f37 -msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "" - -#: ../../src/faq.md:41 991a77ca372d4324843ed340ffbfbae7 -#: ee854bcb685941cab45ae7f33b0efe48 -msgid "Rename an Input File" -msgstr "" - -#: ../../src/faq.md:43 4654eac499464be4845a59bc281ec242 -#: a4cdd5ab6fe341a3ad3e3055556d96c3 -msgid "" -"This example demonstrates how to change the name of an input file as part of " -"a tool description. This could be useful when you are taking files produced " -"from another step in a workflow, and don't want to work with the default " -"names that these files were given when they were created." -msgstr "" - -#: ../../src/faq.md:59 4fcb9907771940d8857fab5b8211d337 -#: d1f359d47f124dfab23a75b196cd5884 -msgid "Rename an Output File" -msgstr "" - -#: ../../src/faq.md:61 9f3ed67bcb13459d9e7196e9d82cb58f -#: d83ced40605e411c92c4ae38761d7ffa -msgid "" -"This example demonstrates how to change the name of an output file from the " -"default name given to it by a tool:" -msgstr "" - -#: ../../src/faq.md:82 af6d80606de6412a8fe63ee379702eac -#: bc8997df2e6746cebc2068534f30ee82 -msgid "Referencing a Local Script" -msgstr "" - -#: ../../src/faq.md:84 fc7c21e08e8e45adb8f1265af494160e -#: 20b6ae57e1cf4410877a60fb3ef87264 -msgid "There are two ways to reference a local script:" -msgstr "" - -#: ../../src/faq.md:86 e37343ad3edd412f981397b995e6c841 -#: 73c66b809e9a4218b624338ccb88a05e -msgid "" -"The first method involves adding the folder containing your scripts to the " -"`PATH` environment variable. This allows you to run the shell script " -"directly without using `sh` or `bash` commands." -msgstr "" - -#: ../../src/faq.md:89 2b7e94e816fa46f4a221b5ce6b2214b2 -#: 9be72b7d5d604526b125b63148e99320 -msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" - -#: ../../src/faq.md:95 0fd0fd13672d48cda0f3ef7f2b0701da -#: fd96d178901545008a43fa99e3aa6cf3 -msgid "" -"After that, make the script executable with the command `chmod +x scriptname." -"sh`" -msgstr "" - -#: ../../src/faq.md:97 a21be18c313d430a8986760ee3725198 -#: db58a582e66244468f4d31e9213933d1 -msgid "" -"Finally, modify your `PATH` to add the directory where your script is " -"located. (It is good practice to use `$HOME/bin` for storing your own " -"scripts)." -msgstr "" - -#: ../../src/faq.md:104 404295b5792747c8a87306181d078cbc -#: 3e70f0da5cd7460b90c1690366f40820 -msgid "" -"Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "" - -#: ../../src/faq.md:113 92582f3845b446d08ca9cbc4ad76a0a7 -#: db28dc27c82b4b29a7a9a768550bba9b -msgid "" -"When you wish to share your work later, you can place your script in a " -"software container in the Docker format." -msgstr "" - -#: ../../src/faq.md:115 2d62b6e5d7944818acd0f43b7d37ce67 -#: 4474b16fb3fd4cdc85da931159804967 -msgid "" -"The second method involves including an input of `type: File` in the script " -"itself:" -msgstr "" - -#: ../../src/faq.md:135 c72fa80f79594d479cb99dc6bfcb207d -#: 23c9b2e21cec4ee8ade087e6630f62c2 -msgid "In CWL, everything must be directly stated." -msgstr "" - -#: ../../src/faq.md:138 5f2b7881a7c64cf29b05b4d78158e176 -#: c01309dcd65c4f1080c396e6a9efb75d -msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "" - -#: ../../src/faq.md:140 eb11641ac17e496384a60e4aacc5209b -#: 0a36801172fd4e24a04b3ba85cf74e29 -msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their input " -"binding makes use of `self`. Below is an example workaround for this, " -"pending a more sophisticated fix." -msgstr "" - -#: ../../src/faq.md:165 c0aee2cf9ee046128002b09a8aa397d8 -#: 433e788ba01141e98ea5a9e73ef71e6f -msgid "Model a \"one-or-the-other\" Parameter" -msgstr "" - -#: ../../src/faq.md:167 34a04d6d09e94fd796a5ee13c6b9856a -#: b6de2761ce454992904775a06b7ba326 -msgid "" -"Below is an example showing how to specify different strings to be added to " -"a command line, based on the value given to a Boolean parameter." -msgstr "" - -#: ../../src/faq.md:188 b1ee951a6e6e4f4c8e88de4dc93bd616 -#: e36c2d53e8ba40f4a602b489a6688e24 -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "" - -#: ../../src/faq.md:190 1664807c6b264fc3b58e9f2c40a9543c -#: a9310166cb514e4e8824bba7fcfcb277 -msgid "" -"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" -"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/faq.md:194 a7ab83c7f31e4e8d83fbfba1abadef2b -#: f6144f77152e4284963951abaa30adb2 -msgid "merge_nested" -msgstr "" - -#: ../../src/faq.md:196 908451dc6990489e88edc1012899c440 -#: 790709dfc2854e4a89fcc4769f84b0f4 -msgid "" -"The input must be an array consisting of exactly one entry for each input " -"link. If \"merge_nested\" is specified with a single link, the value from " -"the link must be wrapped in a single-item list." -msgstr "" - -#: ../../src/faq.md:199 30947198b46d4151a5d92076c30659c0 -#: 438789c8def549d1b4b8a187d5acc48e -msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "" - -#: ../../src/faq.md:201 0b320fb2e40442608137ed9d6f2a74cd -#: 23ede7dfd5c84492baee1d5bbb9a91d9 -msgid "" -"Or in other words: if the destination is of type `File[]` (an array of " -"`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " -"add `linkMerge: merge_nested` under the appropriate `in` entry of the " -"destination step." -msgstr "" - -#: ../../src/faq.md:229 a143590b23384ed79fc37b17a0abd46e -#: 37c0474e48164160b23c4094d583d2d3 -msgid "Optional Inputs 💯" -msgstr "" - -#: ../../src/faq.md:231 6b36effcb80040c79396a1df241f635e -#: 3b2be0a4a87041b7a5bda20c6df2ffc8 -msgid "" -"To make an input parameter optional, add a question mark to the type " -"declaration." -msgstr "" - -#: ../../src/faq.md:247 2873af63ee324fab948d16a9e14db5a7 -#: 886300d2dcff4861aae503d34b0bee44 -msgid "" -msgstr "" - -#: ../../src/faq.md:248 a11f170a082a4df2b4a0c068dd0573ed -#: fe393ecdff25428da6cbcd30171c7811 -msgid "Enum Inputs ⚜️" -msgstr "" - -#: ../../src/faq.md:250 bd2ccba5ac7e486c9af1d906ad96b07a -#: ebfd4991d917413b858da8b437a55805 -msgid "" -"For command line flags that require a specific input as the argument an enum " -"type can be declared in CWL. **Specifying null here is known as long form " -"style. It does the same thing as the question mark on the other inputs.**" -msgstr "" - -#: ../../src/faq.md:267 3f1d8cf3390c43f8b78ce33fc020f1a0 -#: 2919ff4f51254e69aea40146e2d911f1 -msgid "" -msgstr "" - -#: ../../src/faq.md:268 89626d59c2164bb99d0b123def33f701 -#: 61ed4e87457c41eea31f51740557597e -msgid "Record Inputs 📀" -msgstr "" - -#: ../../src/faq.md:270 028c6179803b4dc8a718669312804101 -#: 1e6624104b024eb092682cd0dd0f6a3c -msgid "" -"For commandline flags that are either **mutually exclusive** or " -"**dependent** a special record type can be defined. You can also specify " -"null here to create optional inputs." -msgstr "" - -#: ../../src/faq.md:322 23d9d603d4d44880aea5ebfd86e02d8d -#: b741b8333e104feaa6d1f41fd4476304 -msgid "Setting Mutually Exclusive Parameters" -msgstr "" - -#: ../../src/faq.md:324 06ae9317c6af481bbf4fd70236ca10a9 -#: 334673ae870a4dada817857f3a49326e -msgid "" -"To properly set fields in a record input type, you need to pass a dictionary " -"to the input to properly set the parameters. This is done by using inline " -"JavaScript and returning the dictionary with the key of the field you want " -"to set. The source field is set to indicate the input from the workflow to " -"be used as the value." -msgstr "" - -#: ../../src/faq.md:342 0c6c0af33a274a8cb64ae3111c014338 -#: 362f85270df04712b2e2f21c7019e3cb -msgid "Setting Booleans" -msgstr "" - -#: ../../src/faq.md:344 1139a2f4e58046f9aac4c64b7d5a2e4d -#: ad6997f24c7c42fe965b5d7bfd1e633e -msgid "These can be set by using the default field" -msgstr "" - -#: ../../src/faq.md:349 ca97418a37bb4ae99bce1b44eebefbad -#: 99dce9d60b6a4f99bc39899b7c8c10ef -msgid "Concatenating Strings in Inputs" -msgstr "" - -#: ../../src/faq.md:351 7a5d2d6c6474492fa65ffd8a5048c733 -#: 6b68fe24cbf64624b49ea56fce2eecad -msgid "The valueFrom field must be used instead of default." -msgstr "" - -#: ../../src/faq.md:359 2549c8887b204ddabe4221978dce7e57 -#: d23326837eb74e7faf1f54e25f8309c4 -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "" - -#: ../../src/faq.md:361 d15ae28e932446b48bfc1dbdc34d8eab -#: 2e2eabe92670412e95474b25ad9cda4c -msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "" - -#: ../../src/faq.md:363 925a0bb31c5f428b93232e42d96bddeb -#: 81f9308adbee4a3c9e585b8e0f0c4844 -msgid "" -"For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "" - -#: ../../src/faq.md:371 591dd97f12ca4b8ca263b17abe674fd6 -#: a5d3ed6cac28415288e7fc7fbfc6e8a6 -msgid "" -"If you can not avoid these dangerous characters, then pass `--relax-path-" -"checks` to `cwltool`." -msgstr "" - -#: ../../src/faq.md:373 3ccdf1a970c14cbe8e1d269dc4ae77b3 -#: 72f9692803304daf9f846e2b90139660 -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -msgstr "" - -#: ../../src/faq.md:375 4cefff22947f4d9eb2f66d1b6bca2a8f -#: a7eb20c817704811b3bcf2f94ec2e51d -msgid "If `cwltool --validate` returns valid" -msgstr "" - -#: ../../src/faq.md:384 bfcbe4003ccb4e59baeed0b631871970 -#: 20fa869849ef4b358a11db46111017de -msgid "But executing it causes an error like:" -msgstr "" - -#: ../../src/faq.md:396 d729277d8bc0488eadddf507ba63202f -#: 35032fcd9f23403ca006d62a7d6e7be7 -msgid "The file is here" -msgstr "" - -#: ../../src/faq.md:410 ca99353cf8f94d11add95ba36408ee46 -#: f6d6a4e3691446378c8fb01a2d19f8ad -msgid "Problem caused by `-` (hyphen character)." -msgstr "" - -#: ../../src/faq.md:423 deb9ae92120d4e30aebd6e4d0374a0a2 -#: 44608fed1048458e999e13b014327e7e -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" - -#: ../../src/faq.md:436 7f4054de28a243c89bd3aca1e2764b93 -#: 96ede8a8f1f34786aabd4004bf2e7acc -msgid "" -"If it is not possible to change the input identifier, then you can use an " -"alternative CWL Parameter Reference syntax:" -msgstr "" - -#: ../../src/faq.md:442 29658fd7b5724addb5074891942f79fe -#: 84634a368e704e8d828678785c784595 -msgid "Use CWL and cwltool with Singularity" -msgstr "" - -#: ../../src/faq.md:445 2dd0d8092e5640e3a930478497b78efd -#: 545c4db9c24f42ee946081254d9ca7a8 -msgid "" -"The CWL standards are built around (optional) Docker format containers. The " -"reference runner and several other CWL implementations support running those " -"Docker format containers using the Singularity engine. Directly specifying a " -"Singularity format container is not part of the CWL standards." -msgstr "" - -#: ../../src/faq.md:450 0d385ebff8c14cbfa418fa45c9b42e51 -#: 1c1e6d583d5646a8a5c9316dcd743d9f -msgid "Debug JavaScript Expressions" -msgstr "" - -#: ../../src/faq.md:452 67d82ee82a184ed3921da6fd1928e83e -#: cf7d336d444e4f59aa83585b7abb1fe5 -msgid "" -"You can use the --js-console option of cwltool, or " -"you can try creating a JavaScript or TypeScript project for your code, and " -"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" -"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" -msgstr "" diff --git a/locales/es/LC_MESSAGES/index.po b/locales/es/LC_MESSAGES/index.po deleted file mode 100644 index b87c1d09..00000000 --- a/locales/es/LC_MESSAGES/index.po +++ /dev/null @@ -1,57 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: es\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/index.md:1 -#: a58ca61ccefc401588f91699bc98bd32 -msgid "Common Workflow Language User Guide" -msgstr "" - -#: ../../src/index.md:3 -#: 6dcf12053f104cb3a8d23ce8d4f90363 -msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." -msgstr "" - -#: ../../src/index.md:7 -#: 1cc90206170d46119c5756f31a9e8799 -msgid "Contributions and Feedback are Welcome!" -msgstr "" - -#: ../../src/index.md:9 -#: b54801d84a944dadb4e4637551e3f7b9 -msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." -msgstr "" - -#: ../../src/index.md:16 -#: 860afd2eda4847e0a0d8834de3af4aa8 -msgid "Navigating the User Guide" -msgstr "" - -#: ../../src/index.md:18 -#: d6046316c84b40ffb5478c90b2604911 -msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." -msgstr "" - -#: ../../src/index.md:23 -#: c3c89ac756a74d9688e179b8718c9bf0 -msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." -msgstr "" - -#: ../../src/index.md:28 -#: 0eb795062b484537b090c4d5c361f7f4 -msgid "Table of Contents" -msgstr "" diff --git a/locales/es/LC_MESSAGES/introduction.po b/locales/es/LC_MESSAGES/introduction.po deleted file mode 100644 index 3452a5bc..00000000 --- a/locales/es/LC_MESSAGES/introduction.po +++ /dev/null @@ -1,746 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/introduction/basic-concepts.md:1 7d238c155d6a40df8c8471ebb448a41e -msgid "Basic Concepts" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:3 4af76ab7bd674e6ab73765ddcc81d5bf -msgid "" -"This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are " -"expected to be familiar with workflow managers, YAML, and comfortable " -"with following instructions for the command-line. The other sections of " -"the user guide cover the same concepts, but in more detail. If you are " -"already familiar with CWL or you are looking for more advanced content, " -"you may want to skip this section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:10 4fafbbbfec734215872f455f1c7e62e9 -msgid "The CWL Specification" -msgstr "" - -#: ../../src/_includes/what-is-cwl.md:2 7250962d9fcc4338a7c9e64e0c2b3868 -#: f8759274ac67447ab61551060918d9bc -msgid "" -"CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:21 106e3e4dd19b42beaa90908e17529869 -msgid "" -"The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered " -"in this user guide is the {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:25 eb85aefcc6824c028479e299f3477c5a -msgid "" -"The specification version can have up to three numbers separated by `.`s " -"(dots). The first number is the major release, used for backward-" -"incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes " -"that are backward-compatible. The last number is used for bug fixes, like" -" typos and other corrections to the specification." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:33 59a0083e4e594253b5eb0a6d2756f271 -msgid "" -"The model used for the specification version is called Semantic " -"Versioning. See the end of this section to [learn more](#learn-more) " -"about it." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:37 19dbee8336704859b5bd9f232879e81e -msgid "Implementations" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:39 947d98768fef4c3cb5b87208303b5712 -msgid "" -"An implementation of the CWL specification is any software written " -"following what is defined in a version of the specification document. " -"However, implementations may not implement every aspect of the " -"specification. CWL implementations are licensed under both Open Source " -"and commercial licenses." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:44 de6edc23dc9b4759b2aaa0954050b6be -msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud" -" and high performance computing environments where tasks are scheduled in" -" parallel across many nodes." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:51 ccee7288b79745d9a6a4bb32e9249594 -msgid "CWL specification, implementations, and other tools." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:105 -#: 10b787163c2e418291616a7bc1caf0bd -msgid "Processes and Requirements" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:107 -#: 0176badcaff14e79ba00f1f26c40f42d -msgid "" -"A process is a computing unit that takes inputs and produces outputs. The" -" behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification" -" {{ cwl_version }}:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:112 -#: 36e1e02745a44b4ab7f80f593eb3c408 -msgid "A command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:113 -#: c3e19102cf7d44c795dbd57897e4ad8a -msgid "An expression tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:114 -#: 288483391ca742e18ed19cd89666c4a1 -msgid "An operation." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:115 -#: 5f5df951ffd6414eb054ca3af83a1abe -msgid "A workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:118 -#: 430425889a4c4f0a9f774d1b2e67debb -msgid "The processing units available in the CWL objects model." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:119 -#: 9e42047299834ec6b41edf6c1b6d6513 -msgid "" -"A command-line tool is a wrapper for a command-line utility like `echo`, " -"`ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:122 -#: f6d4657261e042fd8bd9782047d19ea9 -msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be " -"used to simplify workflows and command-line tools, moving common parts of" -" a workflow execution into reusable JavaScript code that takes inputs and" -" produces outputs like a command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:127 -#: fb8fa26ade2e4555bc5904a680d4de23 -msgid "" -"Operation is an abstract process that also takes inputs, produces " -"outputs, and can be used in a workflow. But it is a special operation not" -" so commonly used. It is discussed in the [Operations " -"section](../topics/operations.md) of this user guide." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:131 -#: 1eb86d0cb6c74685829e7f978b177212 -msgid "" -"The workflow is a process that contains steps. Steps can be other " -"workflows (nested workflows), command-line tools, or expression tools. " -"The inputs of a workflow can be passed to any of its steps, while the " -"outputs produced by its steps can be used in the final output of the " -"workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:137 -#: dda24aff00964493ae997f36dff74c04 -msgid "" -"The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through " -"*requirements*. There are many requirements defined in the CWL " -"specification, for instance:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:141 -#: e696bf67d6d04416b3f9c43f12376a10 -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:142 -#: b9746c3e3e554c2684be3917a31c7d10 -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:143 -#: 8605fc09a1a04ab7ad271ac2bea9a17b -msgid "" -"`InitialWorkDirRequirement` - controls staging files in the input " -"directory." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:145 -#: a1fb5f8dd8964b6fb8990f7e877f8e3f -msgid "" -"Some CWL runners may provide requirements that are not in the " -"specification. For example, GPU requirements are supported in `cwltool` " -"through the `cwltool:CUDARequirement` requirement, but it is not part of " -"the {{ cwl_version }} specification and may not be supported by other CWL" -" runners." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:151 -#: 8fe3e01579524ef2badf284092ce00de -msgid "" -"Hints are similar to requirements, but while requirements list features " -"that are required, hints list optional features. Requirements are " -"explained in detail in the [Requirements](../topics/requirements-and-" -"hints.md) section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:155 -#: c0ca689a49334564baf49359b582c491 -msgid "FAIR Workflows" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:157 -#: fa9a58da83a04493bee1d1e6c1cba8e1 -msgid "" -"The FAIR principles have laid a foundation for sharing and publishing " -"digital assets, and in particular, data. The FAIR principles emphasize " -"machine accessibility and that all digital assets should be Findable, " -"Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created." -" It is thus important that workflows support the creation of FAIR data " -"and adhere to the FAIR principles. — [FAIR Computational " -"Workflows](https://workflows.community/groups/fair/), Workflows Community" -" Initiative." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:167 -#: 93e390de3c1445e5afa0a8bc8ee99480 -msgid "" -"CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\"," -" CWL tasks are isolated, and you must be explicit about your inputs and " -"outputs." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:171 -#: 4b5b1dfad3aa4fee9a41463d5feeb8ea -msgid "" -"The benefit of explicitness and isolation are flexibility, portability, " -"and scalability; tools and workflows described with CWL can transparently" -" leverage technologies such as Docker and be used with CWL " -"implementations from different vendors." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:176 -#: 6c0621375a704ed0a79d4ae65538bb31 -msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 357ae9a25a644caab49ddb3c9ead1028 -#: 646006005df94092ac1134bc194d5fe7 e495fae55ee1480c88438ec4dcc1fc5c -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:180 -#: ab4a78d72dfa43b180615e565080d07a -msgid "Semantic Versioning - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:181 -#: ba8d7155363b4ed59912fc426b207ffc -msgid "" -"The CWL Specification page in the CWL website: " -"" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:182 -#: 37fc683fd3564bd698e3a8843ed7e401 -msgid "" -"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:183 -#: e6af1cb1c3484a1db8fa8577dd5684c6 -msgid "" -"The list of Implementations in the CWL website: " -"" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:184 -#: fe7682c04d344a71a2d1de3586f83f38 -msgid "PROV-O: The PROV Ontology - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:185 -#: caf02d5ff6c04255a2144ff453884b0b -msgid "" -"CWL Operations are covered in the [Operations](../topics/operations.md) " -"section of this user guide." -msgstr "" - -#: ../../src/introduction/index.md:1 a22112574264441eb4b775ce72f7ee62 -msgid "Introduction" -msgstr "" - -#: ../../src/introduction/index.md:3 fe9e792085024abb95180662bf0657a9 -msgid "" -"This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that" -" are useful to know before reading the rest of the user guide." -msgstr "" - -#: ../../src/introduction/prerequisites.md:1 23849325192045f5aa48c9f3d9a2080a -msgid "Prerequisites" -msgstr "" - -#: ../../src/introduction/prerequisites.md:6 c7c0e1cd18d54dcca7062d7d053dcc35 -msgid "" -"The software and configurations listed in this section are prerequisites " -"for following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements " -"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" -"compatible runner or workflow system, but the results and interface may " -"look different (though the exact workflow outputs should be identical)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:12 5d7a4a2cccbb47bbaa9ba2ca2de1eff2 -msgid "CWL Implementations" -msgstr "" - -#: ../../src/introduction/prerequisites.md:14 a0ebb398fd1944858fde855a37938446 -msgid "" -"There are many implementations of the CWL standards. Some are complete " -"CWL runners, while others could be plug-ins or extensions to workflow " -"engines. We have a better explanation in the [Implementations](basic-" -"concepts.md#implementations) section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:19 83d90d246db24c07a73bcd73a3c6bfb6 -msgid "Operating System" -msgstr "" - -#: ../../src/introduction/prerequisites.md:21 c2fd09dd72af46ca8e3284d0c1c7dffb -msgid "" -"We recommend using an up-to-date operating system. You can choose any of " -"the following options for your operating system:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:24 00694f21c8bd435f9de10785d2a829dc -msgid "Linux" -msgstr "" - -#: ../../src/introduction/prerequisites.md:25 3cd6a5a0a9754a678ec4eb5a9569a2ab -msgid "macOS" -msgstr "" - -#: ../../src/introduction/prerequisites.md:26 2b0d2a5dc85c4216840c2ce406e10413 -msgid "Windows" -msgstr "" - -#: ../../src/introduction/prerequisites.md:29 0f8ab0f07c9f4e92b6907685a21e0d09 -msgid "" -"If you are using Windows, you will have to install the [Windows Subsystem" -" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " -"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" -"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " -"details on installing WSL2. Your operating system also needs internet " -"access and a recent version of Python (3.6+)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:35 eb1b97c2f64c43c78cf620f0b3197707 -msgid "CWL Runner" -msgstr "" - -#: ../../src/introduction/prerequisites.md:41 b0fff1b3d67e4e01b7140def8004924a -msgid "" -"The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL " -"community. It is also the CWL reference runner, which means it must " -"support everything in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/prerequisites.md:46 dfad9ccfdc5949adb5785e57a3f0a345 -msgid "" -"`cwltool` can be installed with `pip`. We recommend using a virtual " -"environment like `venv` or `conda`. The following commands will create " -"and activate a Python virtual environment using the `venv` module, and " -"install `cwltool` in that environment:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:51 229d3b94015c46f89a7fcf3035a06e38 -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:62 bede33df513b4ff0bf31a1c4a1b76304 -msgid "" -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool#install) for other ways to install `cwltool` with `apt` " -"and `conda`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:65 f20e6ae025fc48cf82b490aa1e45d978 -msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:67 10c729f31bd94b2580a494a07e8c8c06 -msgid "`true.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:73 55571e0099af459bb38ef2cbb5ce3720 -msgid "" -"The `cwltool` command has an option to validate CWL tool and workflow " -"descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the " -"CWL standards. However, these actions will be performed without running " -"the document. To validate CWL workflows (or even a standalone command " -"line tool description like the above) pass the `--validate` option to the" -" `cwltool` command:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:79 436d10464d0540da9227bff0e7721928 -msgid "Validating `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:84 db76c196cff7476c9f0059410071109e -msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:86 5c34965d08704905af72df2d02f399ea -msgid "Running `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:91 c4b1c6f7a6214a2a8cda037dfd1ce5e7 -msgid "Cwl-runner Python Module" -msgstr "" - -#: ../../src/introduction/prerequisites.md:93 22b70a1995e24ae1a5e688b08d69be78 -msgid "" -"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be " -"invoked independently, and is not reliant on a particular CWL runner " -"program name. Users can invoke `cwl-runner` instead of invoking a CWL " -"runner like `cwltool` directly. The `cwl-runner` is installed by a system" -" administrator or user to point to the preferred CWL implementation. This" -" is convenient for environments with multiple CWL runners." -msgstr "" - -#: ../../src/introduction/prerequisites.md:101 2b078afe85c9496ebe7c4fd5fa849506 -msgid "" -"The CWL community publishes a Python package with the name `cwlref-" -"runner` that installs an alias for `cwltool` under the name `cwl-runner`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:104 edb107bbbef94363a531344862b0646b -msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:111 c92da002f02148e485fccabfb80f78c6 -msgid "" -"Now you can validate and run your workflow with the `cwl-runner` " -"executable, which will invoke `cwltool`. You should have the same results" -" and output as in the previous section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:115 5ff5383fffc646cf860b9e6adffe0d4a -msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:120 3fb6539b1da24c6d8cab103ebaa728e9 -msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:125 56f8f92a8e4e46de9def7d33926a9354 -msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For" -" that, the first thing you need to do is copy `true.cwl` workflow into a " -"new file: `true_shebang.cwl`, and include a special first line, a " -"*shebang*:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:129 f024c312097941cc838f6e4684709e2d -msgid "`true_shebang.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:135 27eb4624fa6a4fbca5c842bc69e277ff -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:137 a086a591e5034a768d6ed9f95ccffb41 -msgid "Making `true.cwl` executable." -msgstr "" - -#: ../../src/introduction/prerequisites.md:144 dacb4f334ee64afa9da1418b806fbb8a -msgid "" -"And finally, you can execute it directly in the command-line. On " -"execution, the program specified in the shebang (`cwl-runner`) will be " -"used to execute the rest of the file." -msgstr "" - -#: ../../src/introduction/prerequisites.md:148 64cb2e80ed554f75aa64bc856c011e74 -msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" - -#: ../../src/introduction/prerequisites.md:154 7c008d7286b242c4989809773075e369 -msgid "" -"The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute " -"the script using the executable specified after the shebang. It is " -"considered a good practice to use `/usr/bin/env ` rather than" -" using a hard-coded location, since `/usr/bin/env ` looks for" -" the `` program in the system `PATH`," -msgstr "" - -#: ../../src/introduction/prerequisites.md:161 3d0c3d9473b64745aaadd1c97f86e6bd -msgid "Text Editor" -msgstr "" - -#: ../../src/introduction/prerequisites.md:163 f87429becda74bdab6e9e8956da16786 -msgid "" -"You can use any text editor with CWL, but for syntax highlighting we " -"recommend an editor with YAML support. Popular editors are Visual Studio " -"Code, Sublime, WebStorm, vim/neovim, and Emacs." -msgstr "" - -#: ../../src/introduction/prerequisites.md:167 40faebbbe3974365adbf4190ac9571af -msgid "" -"There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting" -" and better auto-complete:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:171 24ce76cffa4c4dc3b1471c932ce34d28 -msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " -"" -msgstr "" - -#: ../../src/introduction/prerequisites.md:172 1a14a5c5c15941ff8f957be9b7e346fd -msgid "" -"cwl-plugin for IntelliJ - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:174 6fccaea992b74740b91aa4dea1e9b6f6 -msgid "" -"The CWL community also maintains a list of editors and viewers: " -"" -msgstr "" - -#: ../../src/introduction/prerequisites.md:177 ff2d02dada844e349ce39147eaec02a0 -msgid "Docker" -msgstr "" - -#: ../../src/introduction/prerequisites.md:181 756d50a22d9944989e83fd49691b7dc1 -msgid "" -"`cwltool` uses Docker to run tools, workflows, and workflow steps that " -"specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: " -"." -msgstr "" - -#: ../../src/introduction/prerequisites.md:185 208ae40269d64a95922c3b6b88fa7af0 -msgid "" -"You do not need to know how to write and build Docker containers. In the " -"rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models " -"with and without containers." -msgstr "" - -#: ../../src/introduction/prerequisites.md:191 676cbeed9ecf468587f88adf03f088f2 -msgid "" -"`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for " -"pulling images." -msgstr "" - -#: ../../src/introduction/prerequisites.md:198 97048cb2351f4408946828ff46cd513e -msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the " -"next section, Basic Concepts." -msgstr "" - -#: ../../src/introduction/prerequisites.md:199 28810c389a8f480d8af7af37580fba6e -msgid "The Python `venv` module: " -msgstr "" - -#: ../../src/introduction/quick-start.md:1 6eba770f0a494294ada23cdfe563ada6 -msgid "Quick Start" -msgstr "" - -#: ../../src/introduction/quick-start.md:3 bc84e8e2bd7b4e2eadf8e09b64f8b11e -msgid "" -"This section will show you a brief overview of what CWL is, and where you" -" can learn more about it. No previous knowledge of CWL is required, but " -"you must be comfortable following instructions for the command-line." -msgstr "" - -#: ../../src/introduction/quick-start.md:7 244007c12d0e4c11b5bc5a50fbb7b263 -msgid "“Hello World”" -msgstr "" - -#: ../../src/introduction/quick-start.md:12 1b7f68f5a3214f4da4f1887d14ced464 -msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " -"The example below shows a simple CWL “Hello World” workflow annotated " -"with comments. Note that comments start with `#`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:16 aab574ceba8348b7a62c1c645c7ae300 -msgid "`hello_world.cwl`" -msgstr "" - -#: ../../src/introduction/quick-start.md:22 e3e88da22e65425292b19d8159e6bcdc -msgid "" -"The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the" -" same result as the command-line `echo \"Hello World\"`." -msgstr "" - -#: ../../src/introduction/quick-start.md:27 fbdbaead418f4246b4216acce9c6a51f -msgid "" -"In CWL, there is a distinction between a command-line tool and a " -"workflow. But for the sake of simplicity, we are using the term " -"“workflow” here. You will learn more about this in the [basic concepts" -"](basic-concepts.md) section." -msgstr "" - -#: ../../src/introduction/quick-start.md:32 008fc4481f1c4c7bb215fa3b6096048f -msgid "Installing a CWL Runner" -msgstr "" - -#: ../../src/introduction/quick-start.md:34 31d3ab3f31c44729989ee72a756c7242 -msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the " -"CWL *Reference Runner* for the specification, and it is compliant with " -"the latest version of the specification: {{ cwl_version }}. You can " -"install `cwltool` using `pip`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:39 069fa8bae74d4c24b680c4199d714277 -msgid "Installing `cwltool` with `pip`." -msgstr "" - -#: ../../src/introduction/quick-start.md:47 62cacbc189d0440ebe4a8dde4878450c -msgid "" -"If installing the cwltool using the pip command doesn't work for you, the" -" [prerequisites](prerequisites.md) section contains other ways to install" -" `cwltool` and a more detailed list of software and libraries used for " -"following the rest of this user guide." -msgstr "" - -#: ../../src/introduction/quick-start.md:51 f208e50c0089409aa7463c915be80092 -msgid "Running \"Hello World\"" -msgstr "" - -#: ../../src/introduction/quick-start.md:53 6c551e9af341475496b7b6b104330183 -msgid "" -"The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [INPUTS_OBJECT]`. You can run the " -"`hello_world.cwl` workflow without specifying any option:" -msgstr "" - -#: ../../src/introduction/quick-start.md:57 da2c9a63648342aab3f3b8a34660a4bc -msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:62 1217d999216f47aa8f1903e2417fc57a -msgid "" -"Or you can override the default value of the input parameter `message`, " -"similar to how you would change the argument of the `echo` base command:" -msgstr "" - -#: ../../src/introduction/quick-start.md:65 3559a76a1fc64f3eb61a503bf7c77757 -msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" - -#: ../../src/introduction/quick-start.md:70 21386999503341408b798efa9fc4f262 -msgid "" -"Another way of passing values to your workflow input parameters is via an" -" *Inputs Object*. This is a file containing the input fields with their " -"corresponding values. The Inputs Objects file can be written in JSON or " -"YAML. For example:" -msgstr "" - -#: ../../src/introduction/quick-start.md:74 215e425a5ae64cd0ac5e8d34d7f47b58 -msgid "`hello_world-job.json`" -msgstr "" - -#: ../../src/introduction/quick-start.md:80 963c003c4a334dbe874edc0ab38ea92f -msgid "" -"You can use this Inputs Object file now to execute the “Hello World” " -"workflow:" -msgstr "" - -#: ../../src/introduction/quick-start.md:82 83921375eed44fc695cbc172d9317032 -msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:88 9795092d234e4fa5a2bdfc4c9c02460f -msgid "" -"We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but " -"it is not a requirement. You can choose any name for your workflows and " -"Inputs Object files." -msgstr "" - -#: ../../src/introduction/quick-start.md:96 8846a5ff35b64859b8ec7b16be9f8f6b -msgid "Continue reading the next sections of this User Guide!" -msgstr "" - -#: ../../src/introduction/quick-start.md:97 785c9e2330b045b39bf02f77ab6513f6 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" - -#: ../../src/introduction/quick-start.md:98 b6d05398bca648b8ac25755fbaab91c0 -msgid "" -"The [`common-workflow-language` organization](https://github.com/common-" -"workflow-language) at GitHub." -msgstr "" - -#: ../../src/introduction/quick-start.md:99 2ccf7e847e0b476493ae514381ca3612 -msgid "" -"[Common Workflow Language at " -"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -msgstr "" - -#: ../../src/introduction/quick-start.md:100 d7168eb1f7384733be6316fe72f486eb -msgid "" -"[YAML.org](http://yaml.org/) and [YAML at " -"Wikipedia](https://en.wikipedia.org/wiki/YAML)." -msgstr "" - -#: ../../src/introduction/quick-start.md:101 14bbd3ce1f2a488ca919d4f26c8f1e5a -msgid "" -"The {{'[CWL Specification " -"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " -"cwl_version_text) }}." -msgstr "" - -#: ../../src/introduction/quick-start.md:102 86f1fc65d2d14a41ac282eb63fd9de86 -msgid "" -"[Workflow management system at " -"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -msgstr "" - diff --git a/locales/es/LC_MESSAGES/setup.po b/locales/es/LC_MESSAGES/setup.po deleted file mode 100644 index 6b6fd9db..00000000 --- a/locales/es/LC_MESSAGES/setup.po +++ /dev/null @@ -1,32 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/setup.md:5 715f40c8e3f544e4805ae2b456b9d699 -#: 29bb5c68be6042e5aa4a370e9c4024b3 -msgid "This page has moved" -msgstr "" - -#: ../../src/setup.md:9 c9641546c55a44eab9ae40ec272d5df8 -#: 8bcf31398c34491da1a1590422a72cbe -msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. The information on this page has been migrated to the [FAQ](/faq." -"md) section of the new user guide." -msgstr "" diff --git a/locales/es/LC_MESSAGES/sphinx.po b/locales/es/LC_MESSAGES/sphinx.po index 27d21259..38526232 100644 --- a/locales/es/LC_MESSAGES/sphinx.po +++ b/locales/es/LC_MESSAGES/sphinx.po @@ -9,7 +9,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -18,12 +18,11 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" "Generated-By: Babel 2.10.3\n" -#: ../../src/_templates/sidebar-nav-bs.html:1 ada5c93414a84374b3eaea93dc11ae74 -#: b896fd5e11fe4674a7f46ad489476692 +#: ../../src/_templates/sidebar-nav-bs.html:1 d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" msgstr "" -#: ../../src/_templates/sidebar-nav-bs.html:3 a3cc1c498bad434ebadd4a2e92dbf5f0 -#: acede4e78f7e4aefa0ad9425928cbb42 +#: ../../src/_templates/sidebar-nav-bs.html:3 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" msgstr "" + diff --git a/locales/es/LC_MESSAGES/topics.po b/locales/es/LC_MESSAGES/topics.po deleted file mode 100644 index 80ee8dd9..00000000 --- a/locales/es/LC_MESSAGES/topics.po +++ /dev/null @@ -1,2577 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/topics/additional-arguments-and-parameters.md:1 -#: be1d17fdb27345ffb7fe0cbe92002434 -msgid "Additional Arguments and Parameters" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:3 -#: 82ff1f5ebb0647e886d131f7a8c4f5c3 -msgid "" -"Sometimes tools require additional command line options that don't " -"correspond exactly to input parameters." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 4dbbc91d876746b59f53d3ba49df43f8 -msgid "" -"In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files " -"in the same directory as the source file. However, CWL input files (and " -"the directories in which they appear) may be read-only, so we need to " -"instruct \"javac\" to write the class file to the designated output " -"directory instead." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 82f4844017ec4f609c8f0f5bf9812f75 -msgid "`arguments.cwl`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 afb24d50c0a94693ab9ef9271068e58d -#: ca7a2bce1de34dd2ad8f77095854037b -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 23f9dcf2c7344a40aa2d512f1349135a -msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 3d26cfb6a1204ba89ac812bc4fe3df4f -msgid "" -"And now invoke `cwltool` providing the tool description and the input " -"object on the command line:" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 317f82f2a0d54af29baaf5e3fca1558e -msgid "" -"Here we use the `arguments` field to add an additional argument to the " -"command line that isn't tied to a specific input parameter." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:43 -#: c5f85db684c842a5a2d55afb8ea44e94 -msgid "" -"This example references a runtime parameter. Runtime parameters provide " -"information about the hardware or software environment when the tool is " -"actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include " -"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " -"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " -"Environment][runtime] section of the CWL specification for details." -msgstr "" - -#: ../../src/topics/best-practices.md:1 92154668e72240e48268a3dc593f65c5 -msgid "Best Practices" -msgstr "" - -#: ../../src/topics/best-practices.md:3 df0c80b10cde412c901b9bfa235b4521 -msgid "" -"The following are a set of recommended good practices to keep in mind " -"when writing a Common Workflow Language description for a tool or " -"workflow. These guidelines are presented for consideration on a scale of " -"usefulness: although more is better, not all are required." -msgstr "" - -#: ../../src/topics/best-practices.md:8 93e66f6c1c9643a3944ad3c7651464a1 -msgid "" -"No `type: string` parameters for names of input or reference " -"files/directories; use `type: File` or `type: Directory` as appropriate." -msgstr "" - -#: ../../src/topics/best-practices.md:11 7b54e111b9a2485d912b9c1dde0e6816 -msgid "" -"A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that" -" the usual rules of software licensing apply to this document. For " -"example, if the workflow is shared publicly, licensing terms must be " -"clear so that a future user understands under what conditions they can " -"run the workflow, modify it and/or combine it with other workflows. For " -"this reason, please consider including a license field in the document. " -"The authors of this guide urge you to choose a pre-existing license " -"rather than trying to write your own (see the link below to learn more " -"about choosing a license), and our recommended practice is to choose a " -"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" -"license]." -msgstr "" - -#: ../../src/topics/best-practices.md:20 c58100a01b034441b247e761df1f6a12 -msgid "" -"If possible, the license should be specified with its corresponding [SPDX" -" identifier][spdx]. Construct the metadata field for the license by " -"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " -"`SPDX-ID` is taken from the list of identifiers linked above. See the " -"example snippet below for guidance. For non-standard licenses without an " -"SPDX identifier, provide a URL to the license." -msgstr "" - -#: ../../src/topics/best-practices.md:26 53c3357a75df4704a96848aebc093327 -msgid "" -"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" -"Programmer][sci-license]\"" -msgstr "" - -#: ../../src/topics/best-practices.md:28 a9ae73ef4d3447038d1180032b41255c -msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" - -#: ../../src/topics/best-practices.md:37 a2a654e113d64f37bb3bfcb8828301ce -msgid "" -"For more examples of providing metadata within CWL descriptions, see " -"[the Metadata and Authorship section of this User Guide](../topics" -"/metadata-and-authorship.md)." -msgstr "" - -#: ../../src/topics/best-practices.md:40 66ad30cdce23481d90042b63c3bf8d16 -msgid "" -"Include [attribution information][license-example] for the author(s) of " -"the CWL tool or workflow description. Use unambiguous identifiers like " -"[ORCID][orcid]." -msgstr "" - -#: ../../src/topics/best-practices.md:44 f3c0be3d1a3249288a8cd3053bc1cdcf -msgid "" -"In tool descriptions, list dependencies using short name(s) under " -"`SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:47 07ad1cf2508d4cb780a6e703c07d5a5b -msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in " -"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." -msgstr "" - -#: ../../src/topics/best-practices.md:50 f0931e33e50a495aabd1c58daca72c3e -msgid "" -"All `input` and `output` identifiers should reflect their conceptual " -"identity. Use informative names like `unaligned_sequences`, " -"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " -"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." -msgstr "" - -#: ../../src/topics/best-practices.md:55 3da4c1e61c53469e8e313553130a5b28 -msgid "" -"In tool descriptions, include a list of version(s) of the tool that are " -"known to work with this description under `SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:58 8d3930c2039347beb1383b0dab7ea1d5 -msgid "" -"`format` should be specified for all input and output `File`s. " -"Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " -"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" -"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " -"types). For non-bioinformatics tools, use or build an appropriate " -"ontology/controlled vocabulary in the same way. Please edit this page to " -"let us know about it." -msgstr "" - -#: ../../src/topics/best-practices.md:66 275a541a634345d2b88a7e982d3a84cb -msgid "" -"Mark all input and output `File`s that are read from or written to in a " -"streaming compatible way (only once, no random-access), as `streamable: " -"true`." -msgstr "" - -#: ../../src/topics/best-practices.md:69 23e3e58d1b5245919d1be053b0c53ddc -msgid "" -"Each `CommandLineTool` description should focus on a single operation " -"only, even if the (sub)command is capable of more. Don't overcomplicate " -"your tool descriptions with options that you don't need or use." -msgstr "" - -#: ../../src/topics/best-practices.md:73 0a7b19343ab34220a615f9d5735f62f3 -msgid "" -"Custom types should be defined with one external YAML per type definition" -" for re-use." -msgstr "" - -#: ../../src/topics/best-practices.md:76 fbb538cc258a445a938333315248a4f8 -msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "" - -#: ../../src/topics/best-practices.md:78 dee070dbc0c54210a3b276dcd1e3b151 -msgid "" -"If useful, include a top-level `doc` as well. This should provide a " -"longer, more detailed description than was provided in the top-level " -"`label` (see above)." -msgstr "" - -#: ../../src/topics/best-practices.md:82 0d5c1c5e50de42809afdf4bcddeb86e0 -msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list" -" of valid values." -msgstr "" - -#: ../../src/topics/best-practices.md:85 63a5664bb6f043529e753fa27faa9104 -msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. " -"One common example: manipulating `File` names and paths? Consider whether" -" one of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc., could be used instead." -msgstr "" - -#: ../../src/topics/best-practices.md:90 e3832fa90bc540dd9c92dc606c8a3d1f -msgid "" -"Give the tool description to a colleague (preferably at a different " -"institution) to test and provide feedback." -msgstr "" - -#: ../../src/topics/best-practices.md:93 8a2e36ed7ae0486b9a569b8a7c336fe9 -msgid "" -"Complex workflows with individual components which can be abstracted " -"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" -" their workflow modular and allow sections of them to be easily reused." -msgstr "" - -#: ../../src/topics/best-practices.md:97 00dd50adbb734f0ab7e08d005cf30487 -msgid "" -"Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics" -" software\"][containers] (also useful to other disciplines)." -msgstr "" - -#: ../../src/topics/command-line-tool.md:1 eb2ea54b83304757ba4b835d4ae45642 -msgid "Command Line Tool" -msgstr "" - -#: ../../src/topics/command-line-tool.md:3 ad6f136a690e4c4d9320cbff4b1a3469 -msgid "" -"A command-line tool is a type of Process object that can be run by itself" -" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " -"`tar`, etc. The command-line tool is defined in the `baseCommand` " -"attribute of the command-line tool CWL document." -msgstr "" - -#: ../../src/topics/command-line-tool.md:8 3018247f156c470ca7b9c7801a6f59bd -msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The " -"following example contains a minimal example of a CWL command-line tool " -"for the `echo` Linux command, using inputs and outputs." -msgstr "" - -#: ../../src/topics/command-line-tool.md:19 7c07c9401a3d424089828def1d272842 -msgid "CWL command-line tool." -msgstr "" - -#: ../../src/topics/command-line-tool.md:50 d5300fa60ee942cc961594a504b0d08d -msgid "`echo.cwl`" -msgstr "" - -#: ../../src/topics/command-line-tool.md:57 f56c8f69d71f4f4da40fbb007008500e -msgid "" -"The example above uses a simplified form to define inputs and outputs. " -"You will learn more about in the [Inputs](../topics/inputs.md) and in the" -" [Outputs](../topics/outputs.md) sections." -msgstr "" - -#: ../../src/topics/command-line-tool.md:68 4621ef6fe81a4048944814aff22f508f -msgid "Network Access" -msgstr "" - -#: ../../src/topics/command-line-tool.md:69 1d3f1abb81ff4186843df880dc732ee2 -msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network " -"access. If a command-line tool is written manually in CWL v1.1+, there is" -" a need to specify when network access is required." -msgstr "" - -#: ../../src/topics/command-line-tool.md:83 93f0719b3b2c4c5297bf925801c93b45 -msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " -"Network Access automatically." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:1 -#: 46b4df81014846aea9e0fe7c5caade0d -msgid "Creating Files at Runtime" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:3 -#: 722ed10f0fed4ff59852fa09c45a92f1 -msgid "" -"Sometimes you need to create a file on the fly from input parameters, " -"such as tools that expect to read their input configuration from a file " -"rather than the command line parameters, or need a small wrapper shell " -"script." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:7 -#: 20b151c8c270433ab74288011f2ad47d -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:9 -#: 0625cac27fdc4127b50bd7f195117189 -msgid "`createfile.cwl`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:15 -#: 2035501f61434c339a5abdf693696c84 -msgid "" -"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the " -"value at the input `message`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:20 -#: f6e00a5502ef4bb386ee5f88b0085527 -msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later" -" during command line tool invocation. That means that any genuine need " -"for the character `$` must be **escaped** with `\\`. For instance, " -"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " -"be evaluated by the shell script instead of the CWL engine." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:27 -#: 4fbbc941c4f7412b936446fbf9115363 -msgid "" -"To test the above CWL tool, use this job to provide the input value " -"`message`:" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 9f546d2c6a454542a860ead319642479 e6c179499aee4824a5c02babbf26a869 -#: eb2052144d844cdaa0e9e4b3bc487628 -msgid "`echo-job.yml`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:35 -#: d9ea213b07e64d04b53cdb32a3650322 -msgid "" -"Before we run this, let us look at each step in a little more detail. The" -" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " -"command `sh example.sh`. This will run the file we create in the shell." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:40 -#: fcc7a6d59f8a4e13bf821d488fa17db7 -msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " -"YAML array, we need a `-` on the first line of each element of the array," -" in this case we have just one element. `entryname:` can have any value, " -"but it must match what was specified in the `baseCommand`. The final part" -" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " -"means that you are using a multiline string (without it, we would need to" -" write the whole script on one line)." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:51 -#: f7c967a182734c8ca47f873a0cb28093 -msgid "" -"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " -"formatting." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:54 -#: ../../src/topics/environment-variables.md:18 -#: ../../src/topics/file-formats.md:52 -#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 20f1807303474b5c8c18cede5df322a3 2c41b94f3196446ea483c630af9eea67 -#: 5735865bd655415a9a136f441eebafaf 7364d5ebf81e4949b3212b06788e2381 -#: f1195863b1b345f9a718776763466533 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - -#: ../../src/topics/custom-types.md:1 d2e58b004bfb4c6cae7c69658de21321 -msgid "Custom Types" -msgstr "" - -#: ../../src/topics/custom-types.md:3 484ff45699964c2996a0cdfea0fdb329 -msgid "" -"Sometimes you may want to write your own custom types for use and reuse " -"in CWL descriptions. Use of such custom types can reduce redundancy " -"between multiple descriptions that all use the same type, and also allow " -"for additional customisation/configuration of a tool/analysis without the" -" need to fiddle with the CWL description directly." -msgstr "" - -#: ../../src/topics/custom-types.md:9 c30f12911bb649c6b71e7ad73edd0b4c -msgid "" -"The example below is a CWL description of the [biom convert format][biom]" -" tool for converting a standard biom table file to hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:12 c8ecf2ef21fa4b8ba562625355ba8a65 -msgid "`custom-types.cwl`" -msgstr "" - -#: ../../src/topics/custom-types.md:18 3f328356740644a582ca21d5fa60b2f6 -msgid "`custom-types.yml`" -msgstr "" - -#: ../../src/topics/custom-types.md:24 b9569867a46745268f37ff47c18079fb -msgid "" -"___Note:___ To follow the example below, you need to [download the " -"example input file](https://github.com/common-workflow-" -"language/user_guide/blob/main/src/_includes/cwl/custom-" -"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " -"`wget`:" -msgstr "" - -#: ../../src/topics/custom-types.md:30 636449effdeb481da9ada5d283db2ab9 -msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to " -"be used in the table conversion are imported as a custom object:" -msgstr "" - -#: ../../src/topics/custom-types.md:46 d6d41dc3bbd746bab0a5905a8611a356 -msgid "" -"The reference to a custom type is a combination of the name of the file " -"in which the object is defined (`biom-convert-table.yaml`) and the name " -"of the object within that file (`table_type`) that defines the custom " -"type. In this case the `symbols` array from the imported `biom-convert-" -"table.yaml` file define the allowable table options. For example, in " -"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" -" to create an OTU table in hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:53 e742d68f3a994b9595bae07ee2099831 -msgid "The contents of the YAML file describing the custom type are given below:" -msgstr "" - -#: ../../src/topics/custom-types.md:55 f338008e7fb646038a7dcec456d9dce6 -msgid "`biom-convert-table.yaml`" -msgstr "" - -#: ../../src/topics/custom-types.md:61 e69fcaf1f01049d6824058969e87e0f0 -msgid "" -"In order for the custom type to be used in the CWL description, it must " -"be imported. Imports are described in " -"`requirements:SchemaDefRequirement`, as below in the example `custom-" -"types.cwl` description:" -msgstr "" - -#: ../../src/topics/custom-types.md:76 31abe821b66643d098ecdb4e207ed064 -msgid "" -"Note also that the author of this CWL description has also included " -"`ResourceRequirement`s, specifying the minimum amount of RAM and number " -"of cores required for the tool to run successfully, as well as details of" -" the version of the software that the description was written for and " -"other useful metadata. These features are discussed further in other " -"chapters of this user guide." -msgstr "" - -#: ../../src/topics/environment-variables.md:1 b2a8bdbc4e4347389dc9e2c34e7c71ca -msgid "Environment Variables" -msgstr "" - -#: ../../src/topics/environment-variables.md:3 8de1ffb0a81547f7a616d5ea912998c3 -msgid "" -"Tools run in a restricted environment and do not inherit most environment" -" variables from the parent process. You can set environment variables " -"for the tool using `EnvVarRequirement`." -msgstr "" - -#: ../../src/topics/environment-variables.md:7 9596b81e881549fba7910947a202ba5e -msgid "`env.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:1 8473228fc0104b4c940a967294276542 -msgid "Expression Tool" -msgstr "" - -#: ../../src/topics/expression-tool.md:3 75f469063959433a8ed459c2b09cd61f -msgid "" -"An expression tool is a type of Process that can be run by itself or as a" -" Workflow step. It executes a pure JavaScript expression. It is meant to " -"be used as a way to isolate complex JavaScript expressions that need to " -"operate on input data and produce some result as output." -msgstr "" - -#: ../../src/topics/expression-tool.md:8 6676f841711d43f682e18d954438fc65 -msgid "" -"Similar to the command-line tool it requires `inputs` and `outputs`. But " -"instead of `baseCommand`, it requires an `expression` attribute." -msgstr "" - -#: ../../src/topics/expression-tool.md:17 d6d043d8ce9a41c59ad0d3239f8f306e -msgid "CWL expression tool." -msgstr "" - -#: ../../src/topics/expression-tool.md:48 f3378c740b854b9695ea6ccfb0ab434a -msgid "`uppercase.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:67 c9d5c0dd3eeb4617891f90d1a081a3e7 -msgid "" -"We had to use an `InlineJavascriptRequirement` as our expression contains" -" a JavaScript call in `.toUpperCase()`. This means to tools using the " -"expression tool that JavaScript is a requirement." -msgstr "" - -#: ../../src/topics/expressions.md:1 08240053421545288788e84dec6d6614 -msgid "Expressions" -msgstr "" - -#: ../../src/topics/expressions.md:3 cf3ebc8d28d2443ca0e67b5974a963ab -msgid "" -"If you need to manipulate input parameters, include the requirement " -"`InlineJavascriptRequirement` and then anywhere a parameter reference is " -"legal you can provide a fragment of Javascript that will be evaluated by " -"the CWL runner." -msgstr "" - -#: ../../src/topics/expressions.md:9 767a6dc8370b4f9aad42e07a657e3e1f -msgid "" -"JavaScript expressions should only be used when absolutely necessary. " -"When manipulating file names, extensions, paths etc, consider whether one" -" of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " -"practices](best-practices.md)." -msgstr "" - -#: ../../src/topics/expressions.md:16 f38d9e8192614ba689d17c1cc48ac848 -msgid "`expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:22 ce88970e57f2427a905e1bc66c20ffe8 -msgid "" -"As this tool does not require any `inputs` we can run it with an (almost)" -" empty job file:" -msgstr "" - -#: ../../src/topics/expressions.md:25 e7238751e3604a34a15fff753136eada -msgid "`empty.yml`" -msgstr "" - -#: ../../src/topics/expressions.md:31 ff81d45c3f124c738871b40e5b717d7b -msgid "" -"`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object" -" is represented simply by a set of empty brackets." -msgstr "" - -#: ../../src/topics/expressions.md:35 f92515a70adc4366bc46e2eacf49e47b -msgid "We can then run `expression.cwl`:" -msgstr "" - -#: ../../src/topics/expressions.md:37 dcefffb5ecdc4ec3bcc216c21df896ec -msgid "Running `expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:47 bdb0a61e53cf4521bc0f16593eaa5fdd -msgid "" -"Note that requirements can be provided with the map syntax, as in the " -"example above:" -msgstr "" - -#: ../../src/topics/expressions.md:54 80c3b1fb37aa40038f0bc98905604c47 -msgid "" -"Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" -" describe the additional command line arguments." -msgstr "" - -#: ../../src/topics/expressions.md:62 22a6a66f05c94b988789edfc7acb7951 -msgid "Where are JavaScript expressions allowed?" -msgstr "" - -#: ../../src/topics/expressions.md:64 f09db29f329141e6b3dc3bf348e62b92 -msgid "" -"Just like [parameter references](parameter-references.md), you can use " -"JavaScript Expressions only in certain fields. These are:" -msgstr "" - -#: ../../src/topics/expressions.md:66 ae0f7e0009944da58df73fbc70600fc4 -msgid "" -"From " -"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 3c17c559cfbb4fbcabd0dd57afd0f710 -#: b2c2a86928eb40a18e72586ca43ac3f3 -msgid "`arguments`" -msgstr "" - -#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 -#: ../../src/topics/expressions.md:89 -#: ../../src/topics/parameter-references.md:65 -#: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 0042cbd326484bc985f48f469bedff14 -#: 447dcc99dc59453ca560d6c54bf8d7bb 996a1497269345569208c861d8bcba6b -#: ab62eac4484146cb83f26c5bc74a92e7 ac9c83c8605d47818cd2eceaa107e44a -#: ee13a1bcafb0428abc6f97816476b8a5 -msgid "`valueFrom`" -msgstr "" - -#: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 2054a8bc6ed643129482f73bd0b53823 -#: 4bcda5432fe74135ae0d31b4eb0d5d7b -msgid "`stdin`" -msgstr "" - -#: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 4e5551d884b74e5caa0cad273883fa11 -#: c37ea64ad4f54949b17e442698e25a49 -msgid "`stdout`" -msgstr "" - -#: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 28453a745d8f468b94157409007415de -#: 7b476f5cb3f64cafadbd962d465eacee -msgid "`stderr`" -msgstr "" - -#: ../../src/topics/expressions.md:72 12c9aeec38514f7193d41be7d2b81976 -msgid "" -"From " -"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 -#: ../../src/topics/parameter-references.md:70 -#: ../../src/topics/parameter-references.md:75 -#: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 280eea3ba89e4d84a5a8bbb14c74e36c -#: 447f71c801564eefa5b04659c834ea23 69f163066cc04c30a34d7b97ac7a4bc2 -#: 6a5d8d98b190442f9aadc2c074227835 89fba2d03ddd4cdc943e9175bd0ece33 -#: 9a9fa9f67e434ddeb38b339d004aec53 c533a40746e44835a82b1cc6461576b4 -#: cca5748633ab4899beddd115e0178db6 -msgid "`format`" -msgstr "" - -#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 -#: ../../src/topics/parameter-references.md:71 -#: ../../src/topics/parameter-references.md:76 -#: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 05182018082a474384e29c2ff90cb060 -#: 30217d1193e142729205e28e4cde49d7 308e0245ba0b48fc8f665d12ce5fa0c0 -#: 64bef9a598ed4adab4b517bb8f23fb25 7f7bbf1a07684e54b97ca1950c34930b -#: c3ae98ea21e244e3a76d06b87aa8bfae d4f067c6c06c4059b133c18affdac280 -#: dae8990502254aa99cc1ba44bd42bc89 -msgid "`secondaryFiles`" -msgstr "" - -#: ../../src/topics/expressions.md:75 88c61f4dc48f457b828143b1f0e86168 -msgid "" -"From " -"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:77 2473f34317664da3888f6696f1bce0e7 -msgid "" -"From " -"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:80 ced207b70446434bbe64d228a34c825d -msgid "" -"From " -"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 9b6ddcbbd00c4f5fa4088674586b8b60 -#: d02b26eba3b44df5bcc65436f66248f9 -msgid "`glob`" -msgstr "" - -#: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 38ebe3bb55484f61be01dbd31274b05c -#: c6018e429f30454cb30a33a92c39bda6 -msgid "`outputEval`" -msgstr "" - -#: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 a13cf40c0af743dea7589c4186465d1f -#: f51dc811ec154fd6a0b60d637ae42f06 -msgid "From `Workflow`" -msgstr "" - -#: ../../src/topics/expressions.md:84 a115dab301e34a958a9acea03c2b76a8 -msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 1540eea771934469b6b092c7eba2c223 -#: 6876d25a0d324dcabc7ae2e6202378a1 -msgid "From `steps`" -msgstr "" - -#: ../../src/topics/expressions.md:88 927df10417db4669916e08b9e4e37641 -msgid "" -"From " -"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 75ec03ffd3e64fabab680a2fcc66e0a4 -#: fa2635bff88c49b38401e2c87035d023 -msgid "" -"From " -"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 cbe310d7612e4f68b4832692cc0d145e -#: fa897f1a899141fc9e6be1b6af9c01ce -msgid "`expression`" -msgstr "" - -#: ../../src/topics/expressions.md:92 ba5b5e8410df4acab9ad6459df2ff061 -msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:95 935d707d1e31415e806b2bbcb851e322 -msgid "" -"From " -"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 89f051a47b99491b9ce17ded769ad1a3 -#: 9d59f22a9e734f8982b89830b4e7e6fc -msgid "`coresMin`" -msgstr "" - -#: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 182e1b73426e4367bf8fe430a415a9c6 -#: 5b5d3f05e6c647a38af612c10b2b8b71 -msgid "`coresMax`" -msgstr "" - -#: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 3fa480e44ffe473abb3af953f2d000f9 -#: 6375ee37a7fd4fa19be33c6f0ae75196 -msgid "`ramMin`" -msgstr "" - -#: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 b6d5c6ff972a4607873daa53817a6860 -#: d0a0be70585842d8b17a8ddc7fabfc3e -msgid "`ramMax`" -msgstr "" - -#: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 0d558c8e126f427ca9862d7dae8a2cb7 -#: 293d592f29e34a5aa4f7420368d2f24b -msgid "`tmpdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 43f37d9ec9b5429ab811039d1e8211d0 -#: b3a9149a14d346fbbc844d4de2cb3acb -msgid "`tmpdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 5dbe9152fa2b4554a4ceae0b5163a7f8 -#: e137a1254667427f816aa6b5219e7f26 -msgid "`outdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:103 -#: ../../src/topics/parameter-references.md:100 -#: 7af83d9455a944c180349d9f3123901c e8219f72a0854febb800511e2897cea1 -msgid "`outdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:104 f3f205c655eb4a2fb8c34407ee02fe76 -msgid "" -"From " -"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:105 -#: ../../src/topics/parameter-references.md:102 -#: 0f3325af2b674d07aba8d1b254b7bb67 92c818fc42b64e94b8a3bae737df6ac6 -msgid "`listing`" -msgstr "" - -#: ../../src/topics/expressions.md:106 a8bc743f7dc648889ce51d8a787597dd -msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/expressions.md:107 -#: ../../src/topics/parameter-references.md:104 -#: 04b9cd485e1342d0870c341321089d15 a07dc02fe7bd416994f9755934e6a524 -msgid "`entry`" -msgstr "" - -#: ../../src/topics/expressions.md:108 -#: ../../src/topics/parameter-references.md:105 -#: 69d9c547532644408b14655f50175684 df87b2c504dc4ae8865a0f4c94a84dff -msgid "`entryname`" -msgstr "" - -#: ../../src/topics/expressions.md:109 -#: ../../src/topics/parameter-references.md:106 -#: d248acde95024c94b3921e290276a2d1 f77892ff017d48fa833343150cdad6ca -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../src/topics/expressions.md:110 c0909df1820f40d599151a7b45db2f04 -msgid "" -"From " -"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/expressions.md:111 -#: ../../src/topics/parameter-references.md:108 -#: 2d62117b8b824035916716cc818348d4 9f0237a087b5445eb0a8fe474d3e3869 -msgid "`envValue`" -msgstr "" - -#: ../../src/topics/expressions.md:116 bdbae4965a344e778ed0e80a8e23845d -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" - -#: ../../src/topics/expressions.md:118 1af8bb96001e43d9b649044d9631f360 -msgid "" -"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" -" attribute that allows users to load external JavaScript files, or to " -"provide inline JavaScript code." -msgstr "" - -#: ../../src/topics/expressions.md:122 303ce6bcd17d4a219d2c3f4079e9b332 -msgid "" -"Entries added to the `expressionLib` attribute are parsed with the " -"JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts" -" of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:128 d4e0acefb25d458982b37167431c8364 -msgid "" -"The CWL standards (versions 1.0 through 1.2) " -"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" -" that the only version of JavaScript valid in CWL expressions is " -"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " -"that any code that you include or write in your CWL Document must be " -"compliant with ECMAScript 5.1." -msgstr "" - -#: ../../src/topics/expressions.md:135 b43add5b2d72451db8eee00a03b347a2 -msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a " -"JavaScript function inline in `expressionLib`. That function can then be " -"used in other parts of the CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:139 0908315609f1413392b2ed9b5769a62b -msgid "`hello-world-expressionlib-inline.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:146 d8aac17a8a9c4c209695ce760fc4cffb -msgid "" -"Running this CWL workflow will invoke the JavaScript function and result " -"in the `echo` command printing the input message with capital initial " -"letters:" -msgstr "" - -#: ../../src/topics/expressions.md:149 2deae9db0d394245bf21ba3e469fb64f -msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:155 6849411091ab422f8ebffc27e68c3286 -msgid "" -"Let's move the `capitalizeWords` function to an external file, `custom-" -"functions.js`, and import it in our CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:158 a74d3576acbc4694bbf75d371c57c4b0 -msgid "`custom-functions.js`" -msgstr "" - -#: ../../src/topics/expressions.md:164 330e32b4188141c083465fd77ac0d962 -msgid "`hello-world-expressionlib-external.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:171 61fae30939644f2e830107bb6815659a -msgid "" -"The `custom-functions.js` file is included in the CWL document with the " -"`$include: custom-functions.js` statement. That makes the functions and " -"variables available to be used in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:175 8e057a368eae43f892cdfcf1492fefae -msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:181 108a176667a74331a9c634537c6073be -msgid "" -"Finally, note that you can have both inline and external JavaScript code " -"in your CWL document. In this final example we have added another entry " -"to the `expressionLib` attribute with the new function " -"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" -" the external file `custom-functions.js`." -msgstr "" - -#: ../../src/topics/expressions.md:186 dc1a23ba61fe417aab857a2cf3b87d09 -msgid "`hello-world-expressionlib.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:193 683b69656c23424d9a171f72cc1ee355 -msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:200 a2d926603ed24b13a77a64606b72f7db -msgid "" -"The `$include` statement can be used to include a file from the local " -"disk or from a remote location. It works with both relative and absolute " -"paths. Read the [text about " -"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " -"the CWL specification to learn more about it." -msgstr "" - -#: ../../src/topics/file-formats.md:1 f00b6549fb2b40c7a0930fa2d70f78e9 -msgid "File Formats" -msgstr "" - -#: ../../src/topics/file-formats.md:3 02364803949047ddbad575b3f7ed27a3 -msgid "" -"Tools and workflows can take `File` types as input and produce them as " -"output. We also recommend indicating the format for `File` types. This " -"helps document for others how to use your tool while allowing you to do " -"some simple type-checking when creating parameter files." -msgstr "" - -#: ../../src/topics/file-formats.md:8 8f25e0b9d6564f089bc07050eecd2cbe -msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM" -" in our example), reference a local ontology for your institution, or do " -"not add a file format initially for quick development before sharing your" -" tool with others. You can browse existing [IANA file format " -"listings][IANA] and [EDAM file format listings][EDAM] on their websites." -msgstr "" - -#: ../../src/topics/file-formats.md:14 051d96f1784a44478c888a692a43020e -msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` " -"section of the document in greater detail, so don't worry about these for" -" now." -msgstr "" - -#: ../../src/topics/file-formats.md:17 c0b16138c24243f7882de4ea02ef14e4 -msgid "" -"Note that for added value `cwltool` can do some basic reasoning based on " -"file formats and warn you if there seem to be some obvious mismatches." -msgstr "" - -#: ../../src/topics/file-formats.md:20 05c4a830b7084575bfd35263d9226104 -msgid "`metadata_example.cwl`" -msgstr "" - -#: ../../src/topics/file-formats.md:26 -#: ../../src/topics/metadata-and-authorship.md:22 -#: 1af1e2ed821a435088471aa1d28c039c 441a574563f246118f24fc1ab8324b2e -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../src/topics/file-formats.md:32 241dfed53c39469d9e340a2494f97572 -msgid "Sample Parameter Files" -msgstr "" - -#: ../../src/topics/file-formats.md:34 c377cf86598d4ca4bf5311a47978e302 -msgid "" -"Below is an example of a parameter file for the example above. We " -"encourage checking in working examples of parameter files for your tool. " -"This allows others to quickly work with your tool, starting from a " -"\"known good\" parameterization." -msgstr "" - -#: ../../src/topics/file-formats.md:39 53ff3c58049a4096ae894c4b0214d5cb -msgid "`sample.yml`" -msgstr "" - -#: ../../src/topics/file-formats.md:45 6c6c380437634412900e3f8dff4558f6 -msgid "" -"___Note:___ To follow the example below, you need to download the example" -" input file, *file-formats.bam*. The file is available from " -" and can be downloaded e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/index.md:1 4ca0f8c05d9e451387a1eda0e6a04dad -msgid "Topics" -msgstr "" - -#: ../../src/topics/inputs.md:1 339cc31ba40c4d2cba0ff21d668701b6 -msgid "Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:3 802f62184fd545eabc2afb78d90930c1 -msgid "Essential Input Parameters" -msgstr "" - -#: ../../src/topics/inputs.md:5 9b641ae58d834dcc8a79fc547ead64a0 -msgid "" -"The `inputs` of a tool is a list of input parameters that control how to " -"run the tool. Each parameter has an `id` for the name of parameter, and " -"`type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/inputs.md:9 8886c014968d4e32b0ce1cc44a9068a0 -msgid "" -"Available primitive types are *string*, *int*, *long*, *float*, *double*," -" and *null*; complex types are *array* and *record*; in addition there " -"are special types *File*, *Directory* and *Any*." -msgstr "" - -#: ../../src/topics/inputs.md:13 f40f938f5ac140cea72a4146a3329579 -msgid "" -"The following example demonstrates some input parameters with different " -"types and appearing on the command line in different ways." -msgstr "" - -#: ../../src/topics/inputs.md:16 415298524e35434ea19a25c31e9ae649 -msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "" - -#: ../../src/topics/inputs.md:18 e8b631d0d4e64779aa7333b8e756fcbe -msgid "`inp.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:24 c5f3fddee0734d2da9207d64e268463f -msgid "Create a file called `inp-job.yml`:" -msgstr "" - -#: ../../src/topics/inputs.md:26 fed45d1ab5574bd889af14787ac2cd20 -msgid "`inp-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:33 1654a2e9bca0443c8fb46f7191beb81a -msgid "" -"You can use `cwltool` to create a template input object. That saves you " -"from having to type all the input parameters in a input object file:" -msgstr "" - -#: ../../src/topics/inputs.md:40 b22b453eb5d0497e88243bcfc4d3cb1b -msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template " -"inp.cwl > inp-job.yml`, and then modify the default values with your " -"desired input values." -msgstr "" - -#: ../../src/topics/inputs.md:44 c136e4badbf3429b8c9c9efbc91d7f65 -msgid "" -"Notice that \"example_file\", as a `File` type, must be provided as an " -"object with the fields `class: File` and `path`." -msgstr "" - -#: ../../src/topics/inputs.md:47 31ddeb567d744c21bbfa76e8cdf95e6d -msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" -" command line." -msgstr "" - -#: ../../src/topics/inputs.md:53 b19099fa3f3a4b5491e094f1ababc4a2 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " -"following boxed text describes these two commands and the expected output" -" from the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:64 685e49311ba547f697fc90073168041b -msgid "" -"The CWL reference runner (cwltool) and other runners create temporary " -"directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not " -"explicitly specified" -msgstr "" - -#: ../../src/topics/inputs.md:70 d31fc4e804a34097ab506fa3aa469b1d -msgid "" -"The field `inputBinding` is optional and indicates whether and how the " -"input parameter should appear on the tool's command line. If " -"`inputBinding` is missing, the parameter does not appear on the command " -"line. Let's look at each example in detail." -msgstr "" - -#: ../../src/topics/inputs.md:83 26ca8366924a442d9a3fb26f7223b028 -msgid "" -"Boolean types are treated as a flag. If the input parameter " -"\"example_flag\" is \"true\", then `prefix` will be added to the command " -"line. If false, no flag is added." -msgstr "" - -#: ../../src/topics/inputs.md:95 e9ba36f7d5ff4776aad272c9a0a7a81b -msgid "" -"String types appear on the command line as literal values. The `prefix` " -"is optional, if provided, it appears as a separate argument on the " -"command line before the parameter . In the example above, this is " -"rendered as `--example-string hello`." -msgstr "" - -#: ../../src/topics/inputs.md:109 bde0dfcb13ea4ac8bab41a8c3fa024ec -msgid "" -"Integer (and floating point) types appear on the command line with " -"decimal text representation. When the option `separate` is false (the " -"default value is true), the prefix and value are combined into a single " -"argument. In the example above, this is rendered as `-i42`." -msgstr "" - -#: ../../src/topics/inputs.md:124 0a38fa331eaa41ad9d61c869e5b73574 -msgid "" -"File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the " -"parameter is optional. In the example above, this is rendered as " -"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " -"parameter were not provided in the input, nothing would appear on the " -"command line." -msgstr "" - -#: ../../src/topics/inputs.md:131 afe9f6fca7314610b25aa519d145f1c8 -msgid "" -"Input files are read-only. If you wish to update an input file, you must" -" [first copy it to the output directory](staging-input-files.md)." -msgstr "" - -#: ../../src/topics/inputs.md:134 e976913dca354fd1b027ceba53e279fd -msgid "" -"The value of `position` is used to determine where parameter should " -"appear on the command line. Positions are relative to one another, not " -"absolute. As a result, positions do not have to be sequential, three " -"parameters with positions 1, 3, 5 will result in the same command line as" -" 1, 2, 3. More than one parameter can have the same position (ties are " -"broken using the parameter name), and the position field itself is " -"optional. The default position is 0." -msgstr "" - -#: ../../src/topics/inputs.md:142 3f5437225c06473ca6d99f256b735771 -msgid "" -"The `baseCommand` field will always appear in the final command line " -"before the parameters." -msgstr "" - -#: ../../src/topics/inputs.md:146 e0a6c25648394dc4a06c1a1ab11656d1 -msgid "Array Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:148 895ca55530674398af4f3ab0a2ff8295 -msgid "" -"It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to " -"provide `type` field with `type: array` and `items` defining the valid " -"data types that may appear in the array. Alternatively, brackets `[]` may" -" be added after the type name to indicate that input parameter is array " -"of that type." -msgstr "" - -#: ../../src/topics/inputs.md:154 2c9f27b7c4534f5087194653288fc473 -msgid "`array-inputs.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:160 2f54898bb89b4f24abcbb9e032b14fac -msgid "`array-inputs-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 07e7e4b0f9d047aba2b860033e9c939c -#: 12a54ad82e994ce485e2996d4e804373 5fb5d18d006242c2ad4cd143c6e6b5c4 -msgid "" -"Now invoke `cwltool` providing the tool description and the input object " -"on the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:178 36d386d92a7a47099dff930b89063d26 -msgid "" -"The `inputBinding` can appear either on the outer array parameter " -"definition or the inner array element definition, and these produce " -"different behavior when constructing the command line, as shown above. In" -" addition, the `itemSeparator` field, if provided, specifies that array " -"values should be concatenated into a single argument separated by the " -"item separator string." -msgstr "" - -#: ../../src/topics/inputs.md:185 eb22abf9766e441f835aaad0d12fe198 -msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` " -"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " -"lines, where array values that are not defined with an associated key are" -" marked by a leading `-`. This will be demonstrated in the next lesson " -"and is discussed in more detail in the [YAML Guide](yaml-" -"guide.md#arrays). You can specify arrays of arrays, arrays of records, " -"and other complex types." -msgstr "" - -#: ../../src/topics/inputs.md:191 dad1426793764a71ab0a71c8f6872da4 -msgid "Inclusive and Exclusive Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:193 22c9fdaebc8c4e0f9e1e8b72ef87003a -msgid "" -"Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be " -"provided together (they are exclusive). You can use records and type " -"unions to group parameters together to describe these two conditions." -msgstr "" - -#: ../../src/topics/inputs.md:198 c1e21b305da34c6b8960ebe5ca0d60bc -msgid "`record.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:204 5f3e64b47249408c9a1e006d27826a48 -msgid "`record-job1.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:215 76984af8223c45688a49ca7082b24cc3 -msgid "" -"In the first example, you can't provide `itemA` without also providing " -"`itemB`." -msgstr "" - -#: ../../src/topics/inputs.md:217 ff1dff0c91ac4324acc01188f2ef2bab -msgid "`record-job2.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:233 951aff2f38bc43c8bd1086a9e62243fe -msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the " -"first matching item (`itemC`) is added to the command line and remaining " -"item (`itemD`) is ignored." -msgstr "" - -#: ../../src/topics/inputs.md:236 ac93b8f5dd1646b8bbb7f5edc86ad2c7 -msgid "`record-job3.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:252 baa943e150554186ace37f310442a8a0 -msgid "" -"In the third example, only `itemD` is provided, so it appears on the " -"command line." -msgstr "" - -#: ../../src/topics/inputs.md:255 53f7e15ad5dc472faf409f30d902d4ce -msgid "Exclusive Input Parameters with Expressions" -msgstr "" - -#: ../../src/topics/inputs.md:257 1c455770202547a0bc3c62c063a0b3ed -msgid "" -"If you use exclusive input parameters combined with expressions, you need" -" to be aware that the `inputs` JavaScript object will contain one of the " -"exclusive input values. This means that you might need to use an **or** " -"boolean operator to check which values are present." -msgstr "" - -#: ../../src/topics/inputs.md:262 918873fedf60421f9e3713f82ac0c207 -msgid "" -"Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from" -" an enum." -msgstr "" - -#: ../../src/topics/inputs.md:265 4999688d5c954eb48fc42524e7a33176 -msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:271 294545640c6148dc8043027d4e4ea7d4 -msgid "" -"Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you " -"provide a valid value, such as “fasta” (one of the values of the enum), " -"your command should execute successfully:" -msgstr "" - -#: ../../src/topics/inputs.md:280 258d3d9ec6bb410eb012f89b44bf4072 -msgid "" -"However, if you do not provide any input value, then `file_format` will " -"be evaluated to a `null` value, which does not match the expected type " -"for the output field (a `string`), resulting in failure when running your" -" workflow." -msgstr "" - -#: ../../src/topics/inputs.md:289 6470c55fcf5e45b09534705df1fb4e7b -msgid "" -"To correct it, you must remember to use an or operator in your JavaScript" -" expression when using exclusive parameters, or any parameter that allows" -" `null`. For example, the expression could be changed to " -"`$(inputs.file_format || 'auto')`, to have a default value if none was " -"provided in the command line or job input file." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:1 -#: 0bf3128f26ef41f7b31418f506dc83d4 -msgid "Metadata and Authorship" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:3 -#: ef7ddf8716214cfbb8a411a13967198a -msgid "" -"Implementation extensions not required for correct execution (for " -"example, fields related to GUI presentation) and metadata about the tool " -"or workflow itself (for example, authorship for use in citations) may be " -"provided as additional fields on any object. Such extensions fields (e.g." -" `format: edam:format_2572`) can use a namespace prefix listed in the " -"`$namespaces` section of the document (e.g. edam: " -"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" -"][schema-salad]. Once you add the namespace prefix, you can access it " -"anywhere in the document as shown below. Otherwise, one must use full " -"URLs: `format: http://edamontology.org/format_2572`." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:13 -#: 913df947afb7420097be3f15caede947 -msgid "" -"For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to " -"cite your tool." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:16 -#: 4c773c6b1db9460ba58d5d276781d6e7 -msgid "`metadata_example2.cwl`" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:28 -#: c593b5d1f7e1469da7e97ca737632bc2 -msgid "Extended Example" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:30 -#: 28f6bc9a1465450ead788703b8329902 -msgid "" -"For those that are highly motivated, it is also possible to annotate your" -" tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints" -" at hardware requirements in order to use the tool, and a few more " -"metadata fields." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:35 -#: 84b37f20f8cb4136b274ecef284039fa -msgid "`metadata_example3.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:1 391ca127d3594bf0bd12a3ed29a85fc7 -msgid "Operations" -msgstr "" - -#: ../../src/topics/operations.md:3 e58e02c974ca451ca7e52d4a7e14ad99 -msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-" -"line tool, or an expression tool. It is a step of a workflow that " -"specifies inputs and outputs, but it does not provide enough information " -"to be executed." -msgstr "" - -#: ../../src/topics/operations.md:7 b725956dd0ff4906b54a002afacafd09 -msgid "" -"You can create operations to visualize a workflow during development, " -"before you are ready to submit the workflow to a CWL runner:" -msgstr "" - -#: ../../src/topics/operations.md:10 42e684d404aa4715a538bc209e84b469 -msgid "`operations.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:16 3bc2f8d60cce460788cff24274fee913 -msgid "" -"The `uppercase` step of the workflow is an operation. It can be used like" -" a command line tool or an expression. You can also plot it with the CWL " -"Viewer or `cwltool`:" -msgstr "" - -#: ../../src/topics/operations.md:24 910029acb5864b919b452e62a365c789 -msgid "" -"The output of the command above can be rendered with a Graphviz renderer." -" The following image is rendered with the Sphinx Graphviz directive (this" -" user guide is built with Sphinx):" -msgstr "" - -#: ../../src/topics/operations.md:55 edcbb0fc660840f29309e24a1f934d25 -msgid "" -"If you try running it with `cwltool`, the command will fail since " -"`cwltool` does not have enough information to know how to execute it:" -msgstr "" - -#: ../../src/topics/operations.md:58 14bf9940996647ac91ea2de9e95dbe13 -msgid "`cwltool` does not know how to run operations" -msgstr "" - -#: ../../src/topics/operations.md:66 71459c6b3efa47a1856c8f22f1b529da -msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A" -" CWL runner could, for instance, use abstract operations with ID's that " -"correspond to steps executed by a different workflow engine." -msgstr "" - -#: ../../src/topics/outputs.md:1 77937377da354c46afb8c7d4988cf964 -msgid "Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:3 7dbd814741e4452e95af2bddbbd41c73 -msgid "Returning Output Files" -msgstr "" - -#: ../../src/topics/outputs.md:5 10965b18de5841eda0658840d0e726c4 -msgid "" -"The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name" -" of parameter, and `type` describing what types of values are valid for " -"that parameter." -msgstr "" - -#: ../../src/topics/outputs.md:10 d1ebab8483744101b29a095067495897 -msgid "" -"When a tool runs under CWL, the starting working directory is the " -"designated output directory. The underlying tool or script must record " -"its results in the form of files created in the output directory. The " -"output parameters returned by the CWL tool are either the output files " -"themselves, or come from examining the content of those files." -msgstr "" - -#: ../../src/topics/outputs.md:16 030b920fe9ee445f9f996aef68087129 -msgid "" -"The following example demonstrates how to return a file that has been " -"extracted from a tar file." -msgstr "" - -#: ../../src/topics/outputs.md:19 81f1b2d425f244728504cab01a06dfeb -msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "" - -#: ../../src/topics/outputs.md:21 d23514327fbd476d87e9a3308cac38e4 -msgid "" -"In previous examples, the `baseCommand` was just a string, with any " -"arguments passed as CWL inputs. Instead of a single string we can use an " -"_array of strings_. The first element is the command to run, and any " -"subsequent elements are mandatory command line arguments" -msgstr "" - -#: ../../src/topics/outputs.md:26 ebae564b85824cd1818837689b134af5 -msgid "`tar.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:32 94a88afd7acc4576b8cc22780991d629 -msgid "`tar-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:38 a4dc894fe82e4b779771b512424ce70c -msgid "Next, create a tar file for the example." -msgstr "" - -#: ../../src/topics/outputs.md:45 dfd9feebfc7049498f807dfeb91e70e3 -msgid "" -"And now invoke `cwltool` with the tool description and the input object " -"on the command line:" -msgstr "" - -#: ../../src/topics/outputs.md:51 343cba8708a14ff9bd281fdff790bf39 -msgid "" -"The field `outputBinding` describes how to set the value of each output " -"parameter." -msgstr "" - -#: ../../src/topics/outputs.md:62 485a5a4cba354640a53832e4c7460fcb -msgid "" -"The `glob` field consists of the name of a file in the output directory. " -"If you don't know name of the file in advance, you can use a wildcard " -"pattern like `glob: '*.txt'`." -msgstr "" - -#: ../../src/topics/outputs.md:65 bafc8ef1a46b4f97af05a146a8903e2f -msgid "Capturing Standard Output" -msgstr "" - -#: ../../src/topics/outputs.md:67 3fafdc8d21344bceb8262e8534e34afe -msgid "" -"To capture a tool's standard output stream, add the `stdout` field with " -"the name of the file where the output stream should go. Then add `type: " -"stdout` on the corresponding output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:71 14fff0b709774a4cbb9213dc97ae9d42 -msgid "`stdout.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:89 ae07eb32467f40189765939c2fb4f6ae -msgid "Array Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:91 98aa9d49f5b14429b5fb9e38ab9c594d -msgid "" -"You can also capture multiple output files into an array of files using " -"`glob`." -msgstr "" - -#: ../../src/topics/outputs.md:93 ddb1cc7a7f6f44cd96748c88753b5bdf -msgid "`array-outputs.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:99 af69c5bbfac241809fd6e882dc1cafdd -msgid "`array-outputs-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:112 7910b5ce6997467096db8d432cfb2088 -msgid "" -"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " -"expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions" -" to mark entries in arrays, as demonstrated in several of the upcoming " -"sections." -msgstr "" - -#: ../../src/topics/parameter-references.md:1 11452076e78d4ccd9773b301d831d350 -msgid "Parameter References" -msgstr "" - -#: ../../src/topics/parameter-references.md:3 f8227a94ae9544a189886f90e9a3433c -msgid "" -"In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file " -"we were interested in was called \"hello.txt\", and this was written into" -" the `.cwl` file. This is not the best way to do this, as the " -"\"hello.txt\" filename may vary or be dependent on the input file(s) " -"used. To avoid this we can specify the name of the file we want in the " -"job parameters file (`.yml`). In this example, you will see how to " -"reference the value of input parameters dynamically from other fields, " -"which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../src/topics/parameter-references.md:13 38a045a2b8614cbba3a02d4f27b50127 -msgid "`tar-param.cwl`" -msgstr "" - -#: ../../src/topics/parameter-references.md:19 13529a4cc80a4070b85bf29829c762b1 -msgid "`tar-param-job.yml`" -msgstr "" - -#: ../../src/topics/parameter-references.md:25 da5a588a3155445098b7ad81b78f1fa4 -msgid "" -"Create your input files and invoke `cwltool` with the tool description " -"and the input object on the command line:" -msgstr "" - -#: ../../src/topics/parameter-references.md:36 9e91e38ca0e4473384498c6e28b1f116 -msgid "" -"Certain fields permit parameter references which are enclosed in " -"`$(...)`. These are evaluated and replaced with value being referenced." -msgstr "" - -#: ../../src/topics/parameter-references.md:47 a0e0270144df4b6aa3bf0ad261938b17 -msgid "" -"References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " -"`$(inputs['extractfile'])` are equivalent." -msgstr "" - -#: ../../src/topics/parameter-references.md:51 a4a0147041724445b7ab3459cbc786b0 -msgid "" -"The value of the \"inputs\" variable is the input object provided when " -"the CWL tool was invoked." -msgstr "" - -#: ../../src/topics/parameter-references.md:54 ea5153744a3d41dc883c4bb7df4e16de -msgid "" -"Note that because `File` parameters are objects, to get the path to an " -"input file you must reference the path field on a file object; to " -"reference the path to the tar file in the above example you would write " -"`$(inputs.tarfile.path)`." -msgstr "" - -#: ../../src/topics/parameter-references.md:59 84270504a1c445d2917825b8e854a80d -msgid "Where are parameter references allowed?" -msgstr "" - -#: ../../src/topics/parameter-references.md:61 9616d24145e74d17ac76cbe80ee4972a -msgid "You can only use parameter references in certain fields. These are:" -msgstr "" - -#: ../../src/topics/parameter-references.md:63 fe869638aa4a4cd3a43bc071ed66cb37 -msgid "" -"From " -"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/parameter-references.md:69 1e3f77c12d1c48a7b2df7cdccfe92d41 -msgid "" -"From " -"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:72 2b86b2eb9a2e4310923aa3e3c16fac1a -msgid "" -"From " -"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:74 6ad56ee119684a83b42821f3b366cc73 -msgid "" -"From " -"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:77 11b45dd3f4a644b2b6175fb9bf4219ad -msgid "" -"From " -"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:81 c5446e59a6bd4a3cbfc0ed2cd21783f4 -msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:85 3fefaf0fbde94a85be6db02643d0a5ec -msgid "" -"From " -"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/parameter-references.md:89 3911b95f4a72415f968ed640f445bd00 -msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:92 841837a2edca4aff8231a0b955def3a4 -msgid "" -"From " -"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:101 -#: 665c8d7b622441cda2c1f6b20da5d664 -msgid "" -"From " -"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:103 -#: cb71700c69694a53a62a43ef11a62595 -msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/parameter-references.md:107 -#: 6be0e1471d164c5099c0ccc2824cf038 -msgid "" -"From " -"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/requirements-and-hints.md:5 -#: 5984d3f30ab14197bcc03ce556bad3ab -msgid "Requirements and Hints" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:1 -#: 5357d8f77e504324a2904e7dc327e46a -msgid "Specifying Software Requirements" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:3 -#: 1bbff970e33144148c394d7f18ebfd96 -msgid "" -"Often, tool descriptions will be written for a specific version of a " -"software. To make it easier for others to use your descriptions, you can " -"include a `SoftwareRequirement` field in the `hints` section. This may " -"also help to avoid confusion about which version of a tool the " -"description was written for." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:13 -#: 0774b6bc9c8f4ab0acf943ed07f4b0d4 -msgid "" -"In this example, the software requirement being described is InterProScan" -" version 5.21-60." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:25 -#: 5cadc31694ee45d99ffa369983971756 -msgid "" -"Depending on your CWL runner, these hints may be used to check that the " -"required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the " -"[dependency resolvers configuration][dependencies]." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:29 -#: a8a0b7191ce9404292df0699b96c51d6 -msgid "" -"As well as a version number, a unique resource identifier (URI) for the " -"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" -" looked up in the [SciCrunch][scicrunch] registry, which provides a " -"portal for finding, tracking, and referring to scientific resources " -"consistently. If you want to specify a tool as a `SoftwareRequirement`, " -"search for the tool on SciCrunch and use the RRID that it has been " -"assigned in the registry. (Follow this [Adding a Resource Tutorial" -"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " -"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " -"field of your requirement description. Other good choices, in order of " -"preference, are to include the DOI for the main tool citation and the URL" -" to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 86c81fb6d34b4b36ac8778c79cbc0306 -msgid "Staging Input Files" -msgstr "" - -#: ../../src/topics/staging-input-files.md:3 4bd8293be25d401a868df24fabfc6538 -msgid "" -"Normally, input files are located in a read-only directory separate from " -"the output directory. This causes problems if the underlying tool " -"expects to write its output files alongside the input file in the same " -"directory. You use `InitialWorkDirRequirement` to stage input files into" -" the output directory. In this example, we use a JavaScript expression to" -" extract the base name of the input file from its leading directory path." -msgstr "" - -#: ../../src/topics/staging-input-files.md:9 05c39f514e234bd88895716c99eabcda -msgid "`linkfile.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:1 83fa50745b7e486db93f4d7883a778cc -msgid "Troubleshooting" -msgstr "" - -#: ../../src/topics/troubleshooting.md:3 d8d67e5238d049479e9c1a1c4b9b62c3 -msgid "" -"In this section you will find ways to troubleshoot when you have problems" -" executing CWL. We focus on `cwltool` here but some of these techniques " -"may apply to other CWL Runners." -msgstr "" - -#: ../../src/topics/troubleshooting.md:6 60e89aea0d634296a9753910a55a4493 -msgid "Run `cwltool` with `cachedir`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:8 7ff74ba8fd9443cc9e1cdda32e38ca7c -msgid "" -"You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor " -"output files, but created while your workflow is running). By default, " -"these files are created in a temporary directory but writing them to a " -"separate directory makes accessing them easier." -msgstr "" - -#: ../../src/topics/troubleshooting.md:14 1c8afaa3ef0c41b2a1ebc57d329d6ed4 -msgid "" -"In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " -"World\" | rev`, which would print the message \"Hello World\" reversed, " -"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," -" where instead of executing the `rev` command it tries to execute `revv`," -" which fails." -msgstr "" - -#: ../../src/topics/troubleshooting.md:20 b540a4f7a25148098a369350e22c247a -msgid "`troubleshooting-wf1.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:27 1cda8c6f9ed6421bafb39554bdc9b5f7 -msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " -"value (`cwltool` will create the directory for you if it does not exist " -"already):" -msgstr "" - -#: ../../src/topics/troubleshooting.md:35 93b8b99518474d709a90f5442c0d2b65 -msgid "" -"The workflow is in the `permanentFail` status due to `step_b` failing to " -"execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. " -"You can inspect the intermediate files created:" -msgstr "" - -#: ../../src/topics/troubleshooting.md:44 059deec3f12448b8a673e1d957595d7d -msgid "" -"Each workflow step has received a unique ID (the long value that looks " -"like a hash). The `${HASH}.status` files display the status of each step " -"executed by the workflow. And the `step_a` output file `stdout.txt` is " -"visible in the output of the command above." -msgstr "" - -#: ../../src/topics/troubleshooting.md:48 9c40b03256274b43a484b2a1108186c5 -msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" -" in the `step_b`). After fixing the typo, when you execute `cwltool` with" -" the same arguments as the previous time, note that now `cwltool` output " -"contains information about pre-cached outputs for `step_a`, and about a " -"new cache entry for the output of `step_b`. Also note that the status of " -"`step_b` is now of success." -msgstr "" - -#: ../../src/topics/troubleshooting.md:59 45314aa766a5479f9855cbc054ad17b9 -msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had" -" been cached, and there was no change in its execution or output. " -"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for" -" troubleshooting your CWL documents and also as a way to prevent " -"`cwltool` to re-evaluate steps unnecessarily." -msgstr "" - -#: ../../src/topics/using-containers.md:1 8289b75b054040e5bfa71f482554eb4e -msgid "Using Containers" -msgstr "" - -#: ../../src/topics/using-containers.md:3 333b0ee71bde4ce8aacf4ff8946dfbfe -msgid "Running Tools Inside Docker" -msgstr "" - -#: ../../src/topics/using-containers.md:5 54ef32fbf91a4edfa0006f62b51bcbb9 -msgid "" -"[Docker][docker] containers simplify software installation by providing a" -" complete known-good runtime for software and its dependencies. However," -" containers are also purposefully isolated from the host system, so in " -"order to run a tool inside a Docker container there is additional work to" -" ensure that input files are available inside the container and output " -"files can be recovered from the container. A CWL runner can perform this" -" work automatically, allowing you to use Docker to simplify your software" -" management while avoiding the complexity of invoking and managing Docker" -" containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 de34c8de4fda441d80abb9990e75b494 -msgid "" -"One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the " -"container." -msgstr "" - -#: ../../src/topics/using-containers.md:18 fbd75c368e6444d89978f010a235709c -msgid "" -"This example runs a simple Node.js script inside a Docker container which" -" will then print \"Hello World\" to the standard output." -msgstr "" - -#: ../../src/topics/using-containers.md:21 88ba9fb9da1d493ca8a4e37982ff27dd -msgid "`docker.cwl`" -msgstr "" - -#: ../../src/topics/using-containers.md:27 76dc921551ac44de9f07583d304bde3a -msgid "`docker-job.yml`" -msgstr "" - -#: ../../src/topics/using-containers.md:33 20b169511e734f0fb8b047b06e442146 -msgid "" -"Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that " -"is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 bb3199ee47b746529f088a323a72a434 -msgid "" -"`baseCommand: node` tells CWL that we will be running this command using " -"the Node Js runtime that is meant for Javascript files. We then need to " -"specify some `hints` for how to find the container we want. In this case" -" we list just our requirements for the docker container in " -"`DockerRequirements`. The `dockerPull:` parameter takes the same value " -"that you would pass to a `docker pull` command. That is, the name of the " -"container image (you can even specify the tag, which is good idea for " -"best practices when using containers for reproducible research). In this " -"case we have used a container called `node:slim`." -msgstr "" - -#: ../../src/topics/using-containers.md:52 562109bed3cc4da896d8307f74244552 -msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` " -"providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/using-containers.md:55 417e5bfea2ac485b880ee544984996ea -msgid "`hello.js`" -msgstr "" - -#: ../../src/topics/using-containers.md:69 ecd67cff285a43b5b66777032c7f690c -msgid "" -"Notice the CWL runner has constructed a Docker command line to run the " -"script." -msgstr "" - -#: ../../src/topics/using-containers.md:72 e5b8c1e93fda4043839ef0dc204f2ec1 -msgid "" -"In this example, the path to the script `hello.js` is " -"`/home/me/cwl/user_guide/hello.js` outside the container but " -"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " -"reflected in the invocation of the `node` command." -msgstr "" - -#: ../../src/topics/workflows.md:1 d09c4c6d692548d4b317e5c74445795f -msgid "Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:3 9e3bc00a91f948eeb26624078dce6823 -msgid "" -"A workflow is a CWL processing unit that executes command-line tools, " -"expression tools, or workflows (sub-workflows) as steps. It must have " -"`inputs`, `outputs`, and `steps` defined in the CWL document." -msgstr "" - -#: ../../src/topics/workflows.md:13 177aaf8abaf940d1ac006423998974fa -msgid "CWL workflow." -msgstr "" - -#: ../../src/topics/workflows.md:41 28308117076d4adcaf0f923c3f52d666 -msgid "" -"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier " -"examples." -msgstr "" - -#: ../../src/topics/workflows.md:51 c851029a3fa542b6ac21e00675661ca1 -msgid "`echo-uppercase.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:81 30cb988a8f814823a5dfb2f6ca3928fc -msgid "" -"A command-line tool or expression tool can also be written directly in " -"the same CWL document as the workflow. For example, we can rewrite the " -"`echo-uppercase.cwl` workflow as a single file:" -msgstr "" - -#: ../../src/topics/workflows.md:91 a7c8734f60664e619c63b98e5d3399b9 -msgid "`echo-uppercase-single-file.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:150 f4bb9b7b6ada46a4a1701daaac993798 -msgid "" -"Having separate files helps with modularity and code organization. But it" -" can be helpful writing everything in a single file for development. " -"There are other ways to combine multiple files into a single file (e.g. " -"`cwltool --pack`) discussed further in other sections of this user guide." -msgstr "" - -#: ../../src/topics/workflows.md:160 f4da934d636f4455a63f5ecbda2cfdea -msgid "" -"For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this" -" user guide in more detail." -msgstr "" - -#: ../../src/topics/workflows.md:165 529d327e58f64544aa02b075976aee32 -msgid "Writing Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:167 a4207261aa314fd98cbfdc368d96c1b6 -msgid "" -"This workflow extracts a java source file from a tar file and then " -"compiles it." -msgstr "" - -#: ../../src/topics/workflows.md:170 7571eba01bc44d0a97d8f283f19a8b49 -msgid "`1st-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 8e58b0c4e12e4a1183fe7b33e8ee39e6 c8833b0a5dc04e35a48575713bed3f24 -msgid "Visualization of 1st-workflow.cwl" -msgstr "" - -#: ../../src/topics/workflows.md:180 6a0e9118c6ee49fbb9111504dcebe190 -msgid "" -"[![Visualization of 1st-" -"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-" -"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-workflow.cwl)" -msgstr "" - -#: ../../src/topics/workflows.md:183 87e0059d86b64212a1cceee185fe264d -msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a" -" run:" -msgstr "" - -#: ../../src/topics/workflows.md:185 77943b217ba34d409ed4a18fd262388f -msgid "`1st-workflow-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:191 aceb3bee46034a94bdb6784a8c1a484c -msgid "" -"Next, create a sample Java file and add it to a tar file to use with the " -"command-line tool." -msgstr "" - -#: ../../src/topics/workflows.md:205 916621f2ca5d47c4935d68d20c5ea616 -msgid "What's going on here? Let's break it down:" -msgstr "" - -#: ../../src/topics/workflows.md:212 4a0ceee7f9ac4e80994ac8a750d77855 -msgid "" -"The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a " -"workflow." -msgstr "" - -#: ../../src/topics/workflows.md:221 3408935eb4f945349e00486a8df27c39 -msgid "" -"The `inputs` section describes the inputs of the workflow. This is a " -"list of input parameters where each parameter consists of an identifier " -"and a data type. These parameters can be used as sources for input to " -"specific workflows steps." -msgstr "" - -#: ../../src/topics/workflows.md:233 c0790bc2b8a34016b2eb3d64f0b8903e -msgid "" -"The `outputs` section describes the outputs of the workflow. This is a " -"list of output parameters where each parameter consists of an identifier " -"and a data type. The `outputSource` connects the output parameter " -"`classfile` of the `compile` step to the workflow output parameter " -"`compiled_class`." -msgstr "" - -#: ../../src/topics/workflows.md:248 5ad0adb359db4652a4b7ebd98369190e -msgid "" -"The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second " -"step compiles the file from the first step using the java compiler. " -"Workflow steps are not necessarily run in the order they are listed, " -"instead the order is determined by the dependencies between steps (using " -"`source`). In addition, workflow steps which do not depend on one " -"another may run in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:256 753f0dc2fa3a45358dfc66e7a86fb65a -msgid "" -"The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input" -" parameters, `tarfile` and `extractfile` and one output parameter " -"`extracted_file`." -msgstr "" - -#: ../../src/topics/workflows.md:261 7eb328b2d93d4ee3b47ec26340bd3e98 -msgid "" -"The ``in`` section of the workflow step connects these two input " -"parameters to the inputs of the workflow, `tarball` and " -"`name_of_file_to_extract` using `source`. This means that when the " -"workflow step is executed, the values assigned to `tarball` and " -"`name_of_file_to_extract` will be used for the parameters `tarfile` and " -"`extractfile` in order to run the tool." -msgstr "" - -#: ../../src/topics/workflows.md:267 9b2cdf146f3d4906931ec9be50a194e8 -msgid "" -"The `out` section of the workflow step lists the output parameters that " -"are expected from the tool." -msgstr "" - -#: ../../src/topics/workflows.md:278 b48d08c1caa241e68a758934f6d934f9 -msgid "" -"The second step `compile` depends on the results from the first step by " -"connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described " -"previously in [Additional Arguments and Parameters](additional-arguments-" -"and-parameters.md)). The output of this step `classfile` is connected to " -"the `outputs` section for the Workflow, described above." -msgstr "" - -#: ../../src/topics/workflows.md:285 cac7f881e9984afcae77afd99b049334 -msgid "Nested Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:287 2a60f236d6194b2daebed0fa094edc30 -msgid "" -"Workflows are ways to combine multiple tools to perform a larger " -"operations. We can also think of a workflow as being a tool itself; a CWL" -" workflow can be used as a step in another CWL workflow, if the workflow " -"engine supports the `SubworkflowFeatureRequirement`:" -msgstr "" - -#: ../../src/topics/workflows.md:297 6cc53ff3acef4bbc87a5124a4f473b52 -msgid "" -"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " -"workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:300 635696160b8d4b2b9607986a761a0fa0 -msgid "`nestedworkflows.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:309 4511d99ea12f4389a18f9fd061e207ce -msgid "" -"This two-step workflow starts with the `create-tar` step which is " -"connected to the `compile` step in orange; `compile` is another workflow," -" diagrammed on the right. In purple we see the fixed string " -"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 dbd710aa7bd049018af5a693a16f93c6 -msgid "" -" \"Visualization" -msgstr "" - -#: ../../src/topics/workflows.md:322 f9f192f956eb47d7a4fa47c80f1b56c0 -msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " -"its CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " -"mapped to become the step's input/outputs." -msgstr "" - -#: ../../src/topics/workflows.md:336 711bc01e2e5c47f293abe478f43c1b92 -msgid "" -"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and " -"`*.java` filename. This is generally best-practice, as it means it can be" -" reused in multiple parent workflows, or even in multiple steps within " -"the same workflow." -msgstr "" - -#: ../../src/topics/workflows.md:341 68509d8627a14073aabfe2071faf5214 -msgid "" -"Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar" -" file at `tarball`, which we will prepare in the `create-tar` step. At " -"this point it is probably a good idea to refactor `1st-workflow.cwl` to " -"have more specific input/output names, as those also appear in its usage " -"as a tool." -msgstr "" - -#: ../../src/topics/workflows.md:347 0744ac6efec34b61a4a7c3d1060bdb42 -msgid "" -"It is also possible to do a less generic approach and avoid external " -"dependencies in the job file. So in this workflow we can generate a hard-" -"coded `Hello.java` file using the previously mentioned " -"`InitialWorkDirRequirement` requirement, before adding it to a tar file." -msgstr "" - -#: ../../src/topics/workflows.md:366 2f6f5592fb5d44eb8c9998d8d9e9b9f1 -msgid "" -"In this case our step can assume `Hello.java` rather than be " -"parameterized, so we can use hardcoded values `hello.tar` and " -"`Hello.java` in a `baseCommand` and the resulting `outputs`:" -msgstr "" - -#: ../../src/topics/workflows.md:383 af8995565822455388c9e32b59f7319b -msgid "" -"Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This " -"is generally not best practice, as the tool then can't be reused. The " -"reason for doing it in this case is because the command line is hard-" -"coded with filenames that only make sense within this workflow." -msgstr "" - -#: ../../src/topics/workflows.md:389 a71808fbee3349079bb3a4fd4382662c -msgid "" -"In this example we had to prepare a tar file outside, but only because " -"our inner workflow was designed to take that as an input. A better " -"refactoring of the inner workflow would be to take a list of Java files " -"to compile, which would simplify its usage as a tool step in other " -"workflows." -msgstr "" - -#: ../../src/topics/workflows.md:394 3684b45ee2b146c2a1470712375b8fb0 -msgid "" -"Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL" -" Tool description, care must be taken to improve its usability in " -"multiple workflows." -msgstr "" - -#: ../../src/topics/workflows.md:398 882cda0615624d7e94c1a8708c35733b -msgid "Scattering Steps" -msgstr "" - -#: ../../src/topics/workflows.md:400 3f5af7cf008446f3ad18a7ea5e8aab5b -msgid "" -"Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish " -"to run a tool or workflow multiple times over a list of inputs. The " -"workflow then takes the input(s) as an array and will run the specified " -"step(s) on each element of the array as if it were a single input. This " -"allows you to run the same workflow on multiple inputs without having to " -"generate many different commands or input yaml files." -msgstr "" - -#: ../../src/topics/workflows.md:411 d927b215d2e3400c941e490f1a102c97 -msgid "" -"The most common reason a new user might want to use scatter is to perform" -" the same analysis on different samples. Let's start with a simple " -"workflow that calls our first example (`hello_world.cwl`) and takes an " -"array of strings as input to the workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:415 52466df4530640d8bf65fa8f8dac87b1 -msgid "`scatter-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:421 15488985c612469d80d9c20b00f1569b -msgid "" -"Aside from the `requirements` section including " -"`ScatterFeatureRequirement`, what is going on here?" -msgstr "" - -#: ../../src/topics/workflows.md:429 ccc00c4b29134214ac79fc6815ba15e0 -msgid "" -"First of all, notice that the main workflow level input here requires an " -"array of strings." -msgstr "" - -#: ../../src/topics/workflows.md:441 93cf2c2587394b00828a7f944d201c84 -msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This " -"field tells the runner that we'd like to scatter over this input for this" -" particular step. Note that the input name listed after scatter is the " -"one of the step's input, not a workflow level input." -msgstr "" - -#: ../../src/topics/workflows.md:445 5151bd4448314e7c9aac6d4841539613 -msgid "" -"For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if " -"you expect that the final output of your workflow will now have multiple " -"outputs to collect, be sure to update that to an array type as well!" -msgstr "" - -#: ../../src/topics/workflows.md:450 9154dd4987ad44e3bcb227324179a854 -msgid "Using the following input file:" -msgstr "" - -#: ../../src/topics/workflows.md:452 636ad7e5c8ec4b8b9f9ea1e70f166695 -msgid "`scatter-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:458 c3f371626c2f49da9092cd5aabc8e075 -msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" -" calls the command `echo` on a message. If we invoke `cwltool scatter-" -"workflow.cwl scatter-job.yml` on the command line:" -msgstr "" - -#: ../../src/topics/workflows.md:466 5b186b36c71d42d19b8ef294384a0365 -msgid "" -"You can see that the workflow calls echo multiple times on each element " -"of our `message_array`. Ok, so how about if we want to scatter over two " -"steps in a workflow?" -msgstr "" - -#: ../../src/topics/workflows.md:469 67f8b32d49284698ad5248f7960cb95b -msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding " -"the following lines instead of `outputs: []`" -msgstr "" - -#: ../../src/topics/workflows.md:472 e49cbede4a4942e99b6f90e878898362 -msgid "`hello_world_to_stdout.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:480 168b8b8983f84a49ab94c09be99753b4 -msgid "" -"And add a second step that uses `wc` to count the characters in each " -"file. See the tool below:" -msgstr "" - -#: ../../src/topics/workflows.md:483 9d2f8b5fc572494e8e1ff54be1ba146e -msgid "`wc-tool.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:489 0448518b8c514ec18fea6b32676528ce -msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under " -"each step:" -msgstr "" - -#: ../../src/topics/workflows.md:491 315b8d60537c4e1b98136ffed099df1e -msgid "`scatter-two-steps.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:497 fc4d347151574b95907c3db531b3467d -msgid "" -"Here we have placed the scatter field under each step. This is fine for " -"this example since it runs quickly, but if you're running many samples " -"for a more complex workflow, you may wish to consider an alternative. " -"Here we are running scatter on each step independently, but since the " -"second step is not dependent on the first step completing all languages, " -"we aren't using the scatter functionality efficiently. The second step " -"expects an array as input from the first step, so it will wait until " -"everything in step one is finished before doing anything. Pretend that " -"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " -"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " -"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " -"could finish in 4 minutes, it will actually finish in 8 minutes because " -"the first step must wait on `echo Hallo welt!`. You can see how this " -"might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 235259da671547188634a55a5616b32c -msgid "" -"Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can" -" make an entire workflow a single step in another workflow! Convert our " -"two-step workflow to a single step subworkflow:" -msgstr "" - -#: ../../src/topics/workflows.md:513 8621d777883f41dead6ec6de0bb01094 -msgid "`scatter-nested-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:519 87f8702d0b88446ca01018b08b42e5d7 -msgid "" -"Now the scatter acts on a single step, but that step consists of two " -"steps so each step is performed in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:522 c5dacc8526fa4341a13ce9872c1fcba1 -msgid "Conditional Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:524 9dfd2c7d475245d68052fc30d44b90d3 -msgid "" -"This workflow contains a conditional step and is executed based on the " -"input. This allows workflows to skip additional steps based on input " -"parameters given at the start of the program or by previous steps." -msgstr "" - -#: ../../src/topics/workflows.md:527 c48070836d1a4e53a9256f4e40716f3c -msgid "`conditional-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:566 88fc7b9654734d838aaf202083a6dcd1 -msgid "" -"The first thing you'll notice is that this workflow is only compatible " -"for version 1.2 or greater of the CWL standards." -msgstr "" - -#: ../../src/topics/workflows.md:573 2fc5956dbad1411f86aeefe5b8655b07 -msgid "" -"The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when`" -" is where the condition validation takes place. In this case only when " -"`in1` from the workflow contains a value `< 1` this step will be " -"executed." -msgstr "" - -#: ../../src/topics/workflows.md:587 e8a7a80a070148e4958af6b4d70250a1 -msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" -" will pass the first conditional step and will therefore be executed and " -"is shown in the log by `INFO [step step1] start` whereas the second step " -"is skipped as indicated by `INFO [step step2] will be skipped`." -msgstr "" - -#: ../../src/topics/workflows.md:607 6c2980f728e44c82bfad95316f405be8 -msgid "" -"When a value of 3 is given the first conditional step will not be " -"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." -msgstr "" - -#: ../../src/topics/workflows.md:627 8d0fbfb49a3a4aefa3ec7d71e782dbab -msgid "" -"If no conditions are met for example when using `--val 2` the workflow " -"will raise a permanentFail." -msgstr "" - -#: ../../src/topics/yaml-guide.md:1 b847adf4f9b343518c45eec4b5fb881b -msgid "YAML Guide" -msgstr "" - -#: ../../src/topics/yaml-guide.md:6 51d36eca415b4040ae7cd2dea438b829 -msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers " -"and humans. This guide introduces the features of YAML that are relevant " -"when writing CWL descriptions and input parameter files." -msgstr "" - -#: ../../src/topics/yaml-guide.md:13 12816605aedd40e5babe852973366a9d -msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" - -#: ../../src/topics/yaml-guide.md:16 9a5c688b2c584362b78fe3041832ee6d -msgid "Contents" -msgstr "" - -#: ../../src/topics/yaml-guide.md:18 b9c062f153ae40f8ae59164f6096a0fa -msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:19 2bd3b6f3998a461f9b4f5babe423242e -msgid "[Comments](#comments)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:20 6a7a52d67e954928b57731d64f9962d5 -msgid "[Maps](#maps)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:21 c0fe4464296e448d89fba9adae04ab71 -msgid "[Arrays](#arrays)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:22 c5f7a9a163884b18a7dfd3cccbf6bfae -msgid "[JSON Style](#json-style)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:24 5ebef4a028ef4f0dabd3caae4a0b0bfe -msgid "Key-Value Pairs" -msgstr "" - -#: ../../src/topics/yaml-guide.md:26 08f3b7b52d0d48499445fd30cd71640c -msgid "" -"Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the " -"`:` is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have " -"special meaning in the CWL specification and underscored key names " -"otherwise. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:42 888ae81b155f41a6860428e200948950 -msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, " -"`age_years`, and `home` - with their four respective values. Values can " -"be character strings, numeric (integer, floating point, or scientific " -"representation), Boolean (`true` or `false`), or more complex nested " -"types (see below)." -msgstr "" - -#: ../../src/topics/yaml-guide.md:51 4aa3831e2b9f4fb5b4161c198b9f6419 -msgid "" -"Values may be wrapped in quotation marks, but be aware that this may " -"change the way that they are interpreted i.e. `\"1234\"` will be treated " -"as a character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a" -" command: in CWL all parts of `baseCommand` must be strings so, if you " -"want to specify a fixed numeric value to a command, make sure that you " -"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." -msgstr "" - -#: ../../src/topics/yaml-guide.md:61 952c18ae0fb24c3ab42ae3f7b7db0844 -msgid "Comments" -msgstr "" - -#: ../../src/topics/yaml-guide.md:63 bd5835e2b35349679b1e69a50b958ee6 -msgid "" -"You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program " -"interpreting the YAML. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:76 2d36d90d86c3484c9f767e3fcdb29b25 -msgid "" -"If there is anything on the line before the comment, be sure to add at " -"least one space before the `#`!" -msgstr "" - -#: ../../src/topics/yaml-guide.md:79 48ca1f4243e343c2a3da3c9b5596097d -msgid "Maps" -msgstr "" - -#: ../../src/topics/yaml-guide.md:81 5d15caab19694c58a78d566b2897f6cc -msgid "" -"When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, " -"these hierarchical structures are described in YAML by providing " -"additional key-value pairs as the value of any key. These pairs " -"(sometimes referred to as \"children\") are written on new lines under " -"the key to which they belong (the \"parent\"), and should be indented " -"with two spaces (⇥tab characters are not allowed). For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:104 42cb06c103784fb087a44e55f570cc79 -msgid "" -"The YAML above illustrates how to build up complex nested object " -"descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and " -"`inputBinding`, while one of these children, `inputBinding`, contains a " -"further two key-value pairs (`position` and `prefix`). See the " -"[Arrays](#arrays) section below for more information about providing " -"multiple values/key-value pairs for a single key. For comparison with the" -" example YAML above, here is a graphical representation of the `inputs` " -"object it describes." -msgstr "" - -#: ../../src/topics/yaml-guide.md:127 90b1474dba5442a48f9fdd07b07ed9fd -msgid "Arrays" -msgstr "" - -#: ../../src/topics/yaml-guide.md:129 76a1a131ac7648f9aa14ce14b09d17fe -msgid "" -"In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) " -"section above, more than one key-value pair can be mapped to a single " -"key. However, it is also possible to define multiple values for a key " -"without having to provide a unique key for each value. We can achieve " -"this with an _array_, where each value is defined on its own line and " -"preceded by `-`. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:146 f04cae70233848f7bd051fd553a89b9b -msgid "and a more complex example combining maps and arrays:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:167 b6b1ad435b13428cb56c22fc135b303f -msgid "JSON Style" -msgstr "" - -#: ../../src/topics/yaml-guide.md:169 4a45ba50729c42ec949780bbcf495ef7 -msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " -"arrays can also be defined in YAML using the native JSON syntax. For " -"example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:177 57fa577b531645ae890c634c6549d680 -msgid "and:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:184 0cef0765d01e4525878389bb5ae8f6c5 -msgid "" -"Native JSON can be useful in indicating where a field is intentionally " -"left empty (such as `[]` for an empty array), as well as where it makes " -"more sense for the values to be located on the same line (For example, " -"when providing option flags and their values in a shell command). " -"However, as the second example above shows, it can severely affect the " -"readability of a YAML file, and should be used sparingly." -msgstr "" - -#: ../../src/topics/yaml-guide.md:194 1730e578bf2f4a7b8836d0a41e059de8 -msgid "Reference" -msgstr "" - -#: ../../src/topics/yaml-guide.md:196 f5e7fb0d74924c9e9b4ca1434f724ff0 -msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" -" us while we wrote this guide, though it also covers features that are " -"not valid in CWL." -msgstr "" - diff --git a/locales/es/LC_MESSAGES/tutorials.po b/locales/es/LC_MESSAGES/tutorials.po deleted file mode 100644 index 0c412e90..00000000 --- a/locales/es/LC_MESSAGES/tutorials.po +++ /dev/null @@ -1,64 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/tutorials.md:1 cba829ebca95427ca72b0c259e199cc1 -#: d32522e2993f4b48a789f46537fa5ebf -msgid "Tutorials" -msgstr "" - -#: ../../src/tutorials.md:5 413874a8cfb84860b7bce0ee5f4e6022 -#: 63a51dccb29045fd8f78d5e396c6e050 -msgid "" -"This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to the " -"list." -msgstr "" - -#: ../../src/tutorials.md:7 5242c591a9814c9793856f432d06adc1 -#: cb5f8748a5544be2835467ab07eb7a1c -msgid "Beginner Tutorials" -msgstr "" - -#: ../../src/tutorials.md:9 4a3e41ee134d491eafc9a7b07776b926 -#: 685d0cb2faa04703bcef408ecc2b92f4 -msgid "" -"[Introduction to Workflows with Common Workflow Language: For Contributors.]" -"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" -msgstr "" - -#: ../../src/tutorials.md:11 207a4a90ec2f406b8541f687540a71a5 -#: 20f45705145d45fc8420c4119b06a49f -msgid "Advanced Tutorials" -msgstr "" - -#: ../../src/tutorials.md:13 ead7b80dc37647289f83036eef8ca959 -#: 2bccd19d542d4458a1ba8616236f1840 -msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" - -#: ../../src/tutorials.md:15 95a0dd8e5c354219a3eb3140565aa853 -#: c491c73e4c00476980438ffc79c6e4d3 -msgid "Bioinformatics Tutorials" -msgstr "" - -#: ../../src/tutorials.md:17 82e0cb6989494cef91c464d45cc64728 -#: b8485449206542e097584eca7363c8ce -msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..ba080ed4 --- /dev/null +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -0,0 +1,3827 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"PO-Revision-Date: 2023-01-25 13:37+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Spanish \n" +"Language: es\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 4.16-dev\n" +"Generated-By: Babel 2.10.3\n" + +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "Licencias" + +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "Material didáctico" + +#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." +msgstr "" +"Todo el material instructivo del proyecto Common Workflow Language y los " +"cambios en la estructura también están disponibles bajo la [licencia " +"Creative Commons Attribution][cc-by-human]. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del [texto legal completo de la " +"licencia CC BY 4.0][cc-by-legal]." + +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "Usted es libre de:" + +#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" +"**Compartir**---copiar y redistribuir el material en cualquier medio o " +"formato" + +#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" + +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "para cualquier propósito, incluso comercialmente." + +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" +msgstr "" +"La licenciante no puede revocar estas libertades en tanto usted siga los " +"términos de la licencia." + +#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." +msgstr "" +"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su " +"trabajo se deriva de un trabajo que tiene «Copyright © The Common Workflow " +"Language Project» y, cuando sea práctico, con un enlace a https://www." +"commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e indicar " +"si se han realizado cambios. Puede hacerlo en cualquier forma razonable, " +"pero no de forma tal que sugiera que usted o su uso tienen el apoyo de la " +"licenciante." + +#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" +msgstr "" +"**No hay restricciones adicionales**---No puede aplicar términos legales ni " +"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " +"permitido por la licencia. Con el entendimiento de que:" + +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." +msgstr "" +"No tiene que cumplir con la licencia para elementos del materiale en el " +"dominio público o cuando su uso esté permitido por una excepción o " +"limitación aplicable." + +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." +msgstr "" +"No se dan garantías. La licencia podría no darle todos los permisos que " +"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como " +"publicidad, privacidad, o derechos morales pueden limitar la forma en que " +"utilice el material." + +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "Software" + +#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" +"Excepto cuando se indique lo contrario, los programas de ejemplo y otro " +"software proporcionado por el proyecto Common Workflow Language están " +"disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " +"la [OSI][Osi]." + +#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." +msgstr "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." + +#: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 +#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 +#: eab02dc13915490bb3c9ba744d78b6a7 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +msgid "" +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +msgid "" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +msgid "" +"The first method involves adding the folder containing your scripts to " +"the `PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +msgid "" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." +msgstr "" + +#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +msgid "" +"The second method involves including an input of `type: File` in the " +"script itself:" +msgstr "" + +#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +msgid "" +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +msgid "" +"Using " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +msgid "" +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." +msgstr "" + +#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." +msgstr "" + +#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +msgid "" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" +msgstr "" + +#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +msgid "" +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +msgid "" +"For example, the filename `a space is here.txt` includes 3 space " +"characters." +msgstr "" + +#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +msgid "" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +msgid "" +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." +msgstr "" + +#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +msgid "" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +msgid "" +"This guide will introduce you to writing workflows using the [Common " +"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " +"guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +msgid "" +"If you find that something is missing from this guide, or if you would " +"like to provide other feedback, file an Issue on the [project repository " +"for this guide][repo]. You can also suggest changes directly in a Pull " +"Request by clicking the \"Edit this page\" button at the right sidebar of" +" each page." +msgstr "" + +#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +msgid "" +"If you are a beginner user get started with the " +"[Introduction](/introduction/index.md) section. For advanced users the " +"subsections of the [Topics](/topics/index.md) have detailed information " +"about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +msgid "" +"The Table of Contents is displayed at the top menu and also on the left " +"sidebar. It also appears further down this page but with links to " +"subsections. The right sidebar contains links to the sections of each " +"page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +msgid "" +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "" +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "" +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "" +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "" +"`InitialWorkDirRequirement` - controls staging files in the input " +"directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "" +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "" +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows support the creation of FAIR data " +"and adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 +#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "" +"The CWL Specification page in the CWL website: " +"" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "" +"The list of Implementations in the CWL website: " +"" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +msgid "" +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +msgid "" +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +msgid "" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "" +"If you are using Windows, you will have to install the [Windows Subsystem" +" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " +"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" +"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " +"details on installing WSL2. Your operating system also needs internet " +"access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +msgid "" +"`cwltool` can be installed with `pip`. We recommend using a virtual " +"environment like `venv` or `conda`. The following commands will create " +"and activate a Python virtual environment using the `venv` module, and " +"install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +msgid "" +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool#install) for other ways to install `cwltool` with `apt` " +"and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +msgid "" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +msgid "" +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env ` rather than" +" using a hard-coded location, since `/usr/bin/env ` looks for" +" the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " +"" +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +msgid "" +"cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +msgid "" +"The CWL community also maintains a list of editors and viewers: " +"" +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: " +"." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models " +"with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for " +"pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +msgid "" +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "" +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +msgid "" +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +msgid "" +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +msgid "" +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "" +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "" +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "" +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +msgid "" +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "" +"For more examples of providing metadata within CWL descriptions, see " +"[the Metadata and Authorship section of this User Guide](../topics" +"/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +msgid "" +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"`SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "" +"Each `CommandLineTool` description should focus on a single operation " +"only, even if the (sub)command is capable of more. Don't overcomplicate " +"your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "" +"Custom types should be defined with one external YAML per type definition" +" for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +msgid "" +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +msgid "" +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +msgid "" +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +msgid "" +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. If a command-line tool is written manually in CWL v1.1+, there is" +" a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " +"Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "" +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 +#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "" +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 +#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f +#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 +#: f924d65fed0c4cb5b0a019b084a8b535 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +msgid "" +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +msgid "" +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +msgid "" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +msgid "" +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +msgid "" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +msgid "" +"Note also that the author of this CWL description has also included " +"`ResourceRequirement`s, specifying the minimum amount of RAM and number " +"of cores required for the tool to run successfully, as well as details of" +" the version of the software that the description was written for and " +"other useful metadata. These features are discussed further in other " +"chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "" +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +msgid "" +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +msgid "" +"We had to use an `InlineJavascriptRequirement` as our expression contains" +" a JavaScript call in `.toUpperCase()`. This means to tools using the " +"expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +msgid "" +"If you need to manipulate input parameters, include the requirement " +"`InlineJavascriptRequirement` and then anywhere a parameter reference is " +"legal you can provide a fragment of Javascript that will be evaluated by " +"the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "" +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +msgid "" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 +#: 1acb064f7a4a482aa0174bdc847c6382 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e +#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 +#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +msgid "" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc +#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd +#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 +#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 +#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d +#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f +#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c +#: f760465a49d64d4c8468ad9c4fea62b1 +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +msgid "" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +msgid "" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b +#: d555a3d991e344a5a8e1289168d7c6d1 +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c +#: e9fa9430535c424fa3e8be5d460d2ba4 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c +#: b0290d1a477b48119e17cf1fed9d6dff +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 +#: e1cde4aa32c041238ed2596173c6d824 +msgid "" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf +#: c2a92d3eca7f4ee39cec649170eeea53 +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +msgid "" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 +#: 718ceee9973240ec9c100977bbcc8921 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 +#: c07ab08eb75d4528949c56a3d7c12b28 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +msgid "" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +msgid "" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +msgid "" +"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" +" attribute that allows users to load external JavaScript files, or to " +"provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +msgid "" +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +msgid "" +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +msgid "" +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +msgid "" +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +msgid "" +"Tools and workflows can take `File` types as input and produce them as " +"output. We also recommend indicating the format for `File` types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +msgid "" +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +msgid "" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +msgid "" +"Available primitive types are *string*, *int*, *long*, *float*, *double*," +" and *null*; complex types are *array* and *record*; in addition there " +"are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "" +"The field `inputBinding` is optional and indicates whether and how the " +"input parameter should appear on the tool's command line. If " +"`inputBinding` is missing, the parameter does not appear on the command " +"line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +msgid "" +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +msgid "" +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +msgid "" +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +msgid "" +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "" +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +msgid "" +"The `baseCommand` field will always appear in the final command line " +"before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 +#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d +msgid "" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +msgid "" +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +msgid "" +"In the third example, only `itemD` is provided, so it appears on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +msgid "" +"If you use exclusive input parameters combined with expressions, you need" +" to be aware that the `inputs` JavaScript object will contain one of the " +"exclusive input values. This means that you might need to use an **or** " +"boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as “fasta” (one of the values of the enum), " +"your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +msgid "" +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to a `null` value, which does not match the expected type " +"for the output field (a `string`), resulting in failure when running your" +" workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +msgid "" +"To correct it, you must remember to use an or operator in your JavaScript" +" expression when using exclusive parameters, or any parameter that allows" +" `null`. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value if none was " +"provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "" +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "" +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +msgid "" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +msgid "" +"The `uppercase` step of the workflow is an operation. It can be used like" +" a command line tool or an expression. You can also plot it with the CWL " +"Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx Graphviz directive (this" +" user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +msgid "" +"If you try running it with `cwltool`, the command will fail since " +"`cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +msgid "" +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string we can use an " +"_array of strings_. The first element is the command to run, and any " +"subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +msgid "" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +msgid "" +"The field `outputBinding` describes how to set the value of each output " +"parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +msgid "" +"The `glob` field consists of the name of a file in the output directory. " +"If you don't know name of the file in advance, you can use a wildcard " +"pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "" +"To capture a tool's standard output stream, add the `stdout` field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +msgid "" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "" +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +msgid "" +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +msgid "" +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +msgid "" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +msgid "" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +msgid "" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +msgid "" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +msgid "" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +msgid "" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a `SoftwareRequirement` field in the `hints` section. This may " +"also help to avoid confusion about which version of a tool the " +"description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "" +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a `SoftwareRequirement`, " +"search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "" +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use `InitialWorkDirRequirement` to stage input files into" +" the output directory. In this example, we use a JavaScript expression to" +" extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +msgid "" +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +msgid "" +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +msgid "" +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the " +"container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +msgid "" +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that " +"is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +msgid "" +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier " +"examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +msgid "" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "" +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +msgid "" +"This workflow extracts a java source file from a tar file and then " +"compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +msgid "" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a " +"workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +msgid "" +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +msgid "" +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +msgid "" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +msgid "" +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +msgid "" +" \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +msgid "" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +msgid "" +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +msgid "" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +msgid "" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +msgid "" +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +msgid "" +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +msgid "" +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +msgid "" +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +msgid "" +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +msgid "" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +msgid "" +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to " +"the list." +msgstr "" + +#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +msgid "" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" + diff --git a/locales/faq.pot b/locales/faq.pot deleted file mode 100644 index f4ead324..00000000 --- a/locales/faq.pot +++ /dev/null @@ -1,292 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/faq.md:1 -#: 38d96ecb6f4f4835a94fce7389f64290 -msgid "FAQ" -msgstr "" - -#: ../../src/faq.md:11 -#: cf04e2bcede444ec84829b20873bb458 -msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "" - -#: ../../src/faq.md:41 -#: 7f5a8ebf64a6457290031a9878fcadb4 -msgid "Rename an Input File" -msgstr "" - -#: ../../src/faq.md:43 -#: d2da25aa3d4149c6a839e5a9d260d637 -msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." -msgstr "" - -#: ../../src/faq.md:59 -#: bb7a7c1994c44fd984a3d6daee56ca77 -msgid "Rename an Output File" -msgstr "" - -#: ../../src/faq.md:61 -#: ab649294dceb4701b50840614da498e9 -msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" -msgstr "" - -#: ../../src/faq.md:82 -#: 38a2bfda017f48af91062768c29228d6 -msgid "Referencing a Local Script" -msgstr "" - -#: ../../src/faq.md:84 -#: 73d6982c5a414307943c5100df766a29 -msgid "There are two ways to reference a local script:" -msgstr "" - -#: ../../src/faq.md:86 -#: 81acda6459354bf08b4f1454b3b2dcc4 -msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." -msgstr "" - -#: ../../src/faq.md:89 -#: c06ed26bc9d54aa2803014ba69e9ac78 -msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" - -#: ../../src/faq.md:95 -#: eb25e79af23e4104b38f6265e677c6a8 -msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" -msgstr "" - -#: ../../src/faq.md:97 -#: b618a3759865456f9ceb02a6a16ccba1 -msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." -msgstr "" - -#: ../../src/faq.md:104 -#: 455b1a1f10044b5c98b7fab451f48ed5 -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "" - -#: ../../src/faq.md:113 -#: 6b44a7665da14b6aa887224b2fe3c15f -msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." -msgstr "" - -#: ../../src/faq.md:115 -#: a05b7978ef76413588e211bd9bf9250c -msgid "The second method involves including an input of `type: File` in the script itself:" -msgstr "" - -#: ../../src/faq.md:135 -#: 6caf0ac2ccad4e449dfe5578ff75ec0e -msgid "In CWL, everything must be directly stated." -msgstr "" - -#: ../../src/faq.md:138 -#: ffe1586183ab4a3199639b1f9e8062c1 -msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "" - -#: ../../src/faq.md:140 -#: a8314e810d564e198e9fad0e32c23117 -msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." -msgstr "" - -#: ../../src/faq.md:165 -#: 77c15e3d59c74848b3b6ad85f213b30c -msgid "Model a \"one-or-the-other\" Parameter" -msgstr "" - -#: ../../src/faq.md:167 -#: f3d50a6a37494ce9883a4d9cd0ce7870 -msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." -msgstr "" - -#: ../../src/faq.md:188 -#: 9d7e8ab5d8864376814d12f10b52c6a4 -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "" - -#: ../../src/faq.md:190 -#: 93b78d5afe4541eaba53b6ea29150658 -msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/faq.md:194 -#: 8bfb650cce844e31a30a6e1773d92a48 -msgid "merge_nested" -msgstr "" - -#: ../../src/faq.md:196 -#: 0624c44a35e944c2b463146331c9ba4d -msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." -msgstr "" - -#: ../../src/faq.md:199 -#: 1f4df1cd685e4bd5a695e7ace5a9159d -msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "" - -#: ../../src/faq.md:201 -#: 1f057777e7a9430bbbc2036e53a6e4fb -msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." -msgstr "" - -#: ../../src/faq.md:229 -#: f64dbbcaac5642cebbd7cbd96d85c40d -msgid "Optional Inputs 💯" -msgstr "" - -#: ../../src/faq.md:231 -#: 71f80d93e08342ad8b6db87ec9c837cf -msgid "To make an input parameter optional, add a question mark to the type declaration." -msgstr "" - -#: ../../src/faq.md:247 -#: 7dec6a02cc364c8a9723043a3e8b7d79 -msgid "" -msgstr "" - -#: ../../src/faq.md:248 -#: 8a06fc5a9f80481888418234671702cd -msgid "Enum Inputs ⚜️" -msgstr "" - -#: ../../src/faq.md:250 -#: 2f3dc891f5b64378abc449947a5117cc -msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" -msgstr "" - -#: ../../src/faq.md:267 -#: b5324b01d6614202b0fac7026a450caa -msgid "" -msgstr "" - -#: ../../src/faq.md:268 -#: 1198ce319b4847f8b74a14d2ec5248d5 -msgid "Record Inputs 📀" -msgstr "" - -#: ../../src/faq.md:270 -#: d9e2a621f8ae455092120ebb711d1f99 -msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." -msgstr "" - -#: ../../src/faq.md:322 -#: 2c4153eb18d94ad7bbad6acab1b5b61a -msgid "Setting Mutually Exclusive Parameters" -msgstr "" - -#: ../../src/faq.md:324 -#: 77b90349be254ceb8de2cf58aa410e6d -msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." -msgstr "" - -#: ../../src/faq.md:342 -#: 31e2b62687b84efda4924d7108e23cb3 -msgid "Setting Booleans" -msgstr "" - -#: ../../src/faq.md:344 -#: 8c72738f5aaa4fcd8457a10e799d0e8d -msgid "These can be set by using the default field" -msgstr "" - -#: ../../src/faq.md:349 -#: 3a83df07178945d4822e3520674d6308 -msgid "Concatenating Strings in Inputs" -msgstr "" - -#: ../../src/faq.md:351 -#: 2aca2690fdac4922bfdc9e5a9f2741b8 -msgid "The valueFrom field must be used instead of default." -msgstr "" - -#: ../../src/faq.md:359 -#: 3d072aa6b914445ca8326ffe260b4e35 -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "" - -#: ../../src/faq.md:361 -#: fb653b6af6a74231904d2d0f850d1116 -msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "" - -#: ../../src/faq.md:363 -#: d3d261dd88a94fa8ae8bf65c39eef6a1 -msgid "For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "" - -#: ../../src/faq.md:371 -#: f7125b78a28c4924bdd3fcb37a184ff6 -msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." -msgstr "" - -#: ../../src/faq.md:373 -#: dc28c1a8e15b4499b4af492ac3cd2c1e -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -msgstr "" - -#: ../../src/faq.md:375 -#: db57566297534dea82c6f66dd9c14b51 -msgid "If `cwltool --validate` returns valid" -msgstr "" - -#: ../../src/faq.md:384 -#: 09a115ecb8d2487da88cd31e1bac337f -msgid "But executing it causes an error like:" -msgstr "" - -#: ../../src/faq.md:396 -#: 4537ae8ebd5c49f3857b2cbe81032d29 -msgid "The file is here" -msgstr "" - -#: ../../src/faq.md:410 -#: d31aa1c1adf343e8b2b71322511bf7f1 -msgid "Problem caused by `-` (hyphen character)." -msgstr "" - -#: ../../src/faq.md:423 -#: 096f725de9ee4c558d72695a84c40cbb -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" - -#: ../../src/faq.md:436 -#: 58316efc7814473383abb738c5c0b5ef -msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" -msgstr "" - -#: ../../src/faq.md:442 -#: 2ac3f24fd4074acb8e96542b350d5771 -msgid "Use CWL and cwltool with Singularity" -msgstr "" - -#: ../../src/faq.md:445 -#: ef3c267c3282458f891a76e5d467ec8e -msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." -msgstr "" - -#: ../../src/faq.md:450 -#: aa97ef90186747f7b9d0aaccf17535d1 -msgid "Debug JavaScript Expressions" -msgstr "" - -#: ../../src/faq.md:452 -#: bb5bc05d377d441abe02a09e3f1d1a03 -msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" -msgstr "" diff --git a/locales/index.pot b/locales/index.pot deleted file mode 100644 index 9000da74..00000000 --- a/locales/index.pot +++ /dev/null @@ -1,57 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/index.md:1 -#: 1e479cad716c478689be58d4b4aabd82 -msgid "Common Workflow Language User Guide" -msgstr "" - -#: ../../src/index.md:3 -#: 0afc69049ce0403695a03e30416fd9f9 -msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." -msgstr "" - -#: ../../src/index.md:7 -#: 852b4bfd1a374deb803accb90c7fea8c -msgid "Contributions and Feedback are Welcome!" -msgstr "" - -#: ../../src/index.md:9 -#: d702011b81064e65af1fcbd230d9977e -msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." -msgstr "" - -#: ../../src/index.md:16 -#: 884f157b64ce4787ab8da8f9e674c233 -msgid "Navigating the User Guide" -msgstr "" - -#: ../../src/index.md:18 -#: fd0133a1a0214ef49b763ba33e282a9e -msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." -msgstr "" - -#: ../../src/index.md:23 -#: e699c33ef40045528c31d74b2d797742 -msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." -msgstr "" - -#: ../../src/index.md:28 -#: 21aacf872e7a444c891c41ca3411ee06 -msgid "Table of Contents" -msgstr "" diff --git a/locales/introduction.pot b/locales/introduction.pot deleted file mode 100644 index 32cc94f9..00000000 --- a/locales/introduction.pot +++ /dev/null @@ -1,607 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/introduction/basic-concepts.md:1 -#: 92c85569d9e746d8a5b7a5e8f9773545 -msgid "Basic Concepts" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:3 -#: 5e501be2f49044c9897f6e8d65186abb -msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:10 -#: a6f5f188f9af4b608b8401996a558e83 -msgid "The CWL Specification" -msgstr "" - -#: ../../src/_includes/what-is-cwl.md:2 -#: 2ecb1a3a4c7546ba94e560924cfb09a8 -#: 3c0da8bd74824f8b88223c2a9dcc6ec2 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:21 -#: 7fb9ad094d844047b0d35dc70c295400 -msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:25 -#: 303d1a15612846c1b60a4d651f9d1d4a -msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:33 -#: c84c4bde07034846b043c4f281f8e00c -msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:37 -#: d774877d6e4447b7b83d56ebbaf09e96 -msgid "Implementations" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:39 -#: e8884f39f08c41bab29c4284077fd860 -msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:44 -#: 984ac8cee64e4e41957d8c5a4aff0cfd -msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:51 -#: 17381e8872414c49b178d91ace2e3e82 -msgid "CWL specification, implementations, and other tools." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:105 -#: c4cdbf2a42644e0eb4eb74512388e9f7 -msgid "Processes and Requirements" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:107 -#: 7d994284e320413bb8dbb2a42cd16a4e -msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:112 -#: ce92487ca4e3495ebd0693c502773626 -msgid "A command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:113 -#: 0ce512c3cd744652b5feb2d8dcfdb613 -msgid "An expression tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:114 -#: dd7d6a1399b04923b25df70abb1becf5 -msgid "An operation." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:115 -#: ce4c76b46531416bb4006a9c01f45a23 -msgid "A workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:118 -#: 0256a343321447559471d731c86d3546 -msgid "The processing units available in the CWL objects model." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:119 -#: e1235589f24942babe54adaae4f169af -msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:122 -#: 81baaa297562452f80afe68657c8099d -msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:127 -#: 0c8bbd88bd8c4c71b19011812e7487c3 -msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:131 -#: 3b64da1f14964cea9e5cbf8376578789 -msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:137 -#: bf33807babb64befab3385eca4c92131 -msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:141 -#: afdb75d374624f4798f358a3dfe7752e -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:142 -#: bc28744d5fa644218ef55672d726307f -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:143 -#: 24ffb5bfa767424585b6b6c93169de93 -msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:145 -#: bd53afe50cc14f2ca428adddb0e60dc9 -msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:151 -#: 35c98c4b352c4f9bb9572c740894dc57 -msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:155 -#: f7fb57fdf9344a7eb0f334aca8d3e85f -msgid "FAIR Workflows" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:157 -#: 0dc6a8f19fda4e9eaa80b8e1bd1fc5be -msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:167 -#: ff1224487c35402d8afee6da3803e19b -msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:171 -#: 63c2dd9aaec54df088e82febfd7bc49c -msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:176 -#: 18f310d11c9b48b4a447b6662446cd3e -msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 -#: a3922283fdce4f99832c816626d5f098 -#: 19245373c2e84793a72462b7d2fa1c34 -#: 7c3ea7150c7d41fead10ddf2a6205ec8 -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:180 -#: cf39d3563e344ad9b31d5268c4069972 -msgid "Semantic Versioning - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:181 -#: 97b0113a847044b98f79b5e00941f4c3 -msgid "The CWL Specification page in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:182 -#: 8cf4edbb4b344ac7b3eae86ed52beff8 -msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:183 -#: c1dfc170fdf54c9e846539a5170f204f -msgid "The list of Implementations in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:184 -#: 778babbcfb2648a1ad7a7ad8f80653a8 -msgid "PROV-O: The PROV Ontology - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:185 -#: 23abed59f5d44bfb96e8fa13aa213b83 -msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." -msgstr "" - -#: ../../src/introduction/index.md:1 -#: ee93304de4e447c1bd5626e72b99b6fe -msgid "Introduction" -msgstr "" - -#: ../../src/introduction/index.md:3 -#: a79f07e33fc5437c9fa204111d0290d8 -msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." -msgstr "" - -#: ../../src/introduction/prerequisites.md:1 -#: 3cf08b553a814478b4b2c6c84ebe354e -msgid "Prerequisites" -msgstr "" - -#: ../../src/introduction/prerequisites.md:6 -#: 98751950a97f44fdb16e826fece810fb -msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:12 -#: eac153b881fa47ab8bb08074dad8eed2 -msgid "CWL Implementations" -msgstr "" - -#: ../../src/introduction/prerequisites.md:14 -#: 806ff7b185d74538a9b0e20c6ad84ffe -msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:19 -#: 1f9573b6cd45479bae2481a251132d53 -msgid "Operating System" -msgstr "" - -#: ../../src/introduction/prerequisites.md:21 -#: c3995fd5588741148e3b2c91ca011ca9 -msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:24 -#: 8a67b172ce524aa09858acd9d1a62762 -msgid "Linux" -msgstr "" - -#: ../../src/introduction/prerequisites.md:25 -#: a567e0f952bc46be8b82d0a357f2c209 -msgid "macOS" -msgstr "" - -#: ../../src/introduction/prerequisites.md:26 -#: 21d3bb850bb14fdcb6d4c4a15c9966b6 -msgid "Windows" -msgstr "" - -#: ../../src/introduction/prerequisites.md:29 -#: 62cbb29459b24e9fa83c7cd7994bdf12 -msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:35 -#: aaa319d4446c41ba82bf925f29f7d9dd -msgid "CWL Runner" -msgstr "" - -#: ../../src/introduction/prerequisites.md:41 -#: c49938a0100a4850b67d067a61304d01 -msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/prerequisites.md:46 -#: 91e986d0c1f44d7f9c3b32366160da6a -msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:51 -#: 301c5a3baaaf46bb81bdc25b53a31f23 -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:62 -#: 1664589ced314daebfb163e6424f220f -msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:65 -#: 1223fecd61f34ad98ebbb7e45eaf4ac7 -msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:67 -#: 242c496599d84a64959db275ee1e212e -msgid "`true.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:73 -#: 9b749d47f48341cb9ac8cd14098e6c47 -msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:79 -#: e8ec351d7b79447bb15f4d4518b8de87 -msgid "Validating `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:84 -#: 58d5613243914dc8bc4ce88676525783 -msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:86 -#: 731a6c30786f43d88160f9642cbb05d2 -msgid "Running `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:91 -#: ca2088eb9565429dbc1ce0b28b2ef1fb -msgid "Cwl-runner Python Module" -msgstr "" - -#: ../../src/introduction/prerequisites.md:93 -#: 5ac9c6bfb50b48878aff52f1194e53c4 -msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." -msgstr "" - -#: ../../src/introduction/prerequisites.md:101 -#: b8d0c12ff07f4269bba87cd653803345 -msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:104 -#: 83780c1b43f744b4ae87a917b26293f5 -msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:111 -#: 2919320c41e94930a0aa9bc6aacb5a87 -msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:115 -#: b8e799c075214d539aa0a7c04dbc33c0 -msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:120 -#: ccbd51a29ca841efb74c5e0a25d1eb87 -msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:125 -#: 5f3330c1e15a402781c3325f9d3dc779 -msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:129 -#: 314fbc9f866a405b86e7bd704781dea1 -msgid "`true_shebang.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:135 -#: 9434e3680aa9487fab9ddb782c6ff3d0 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:137 -#: 2ce0bda38d814b248a2c23ebc26bf462 -msgid "Making `true.cwl` executable." -msgstr "" - -#: ../../src/introduction/prerequisites.md:144 -#: 105c3be6f5f34f4388b9999603275bb5 -msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." -msgstr "" - -#: ../../src/introduction/prerequisites.md:148 -#: bd378c8483a14c93b5fe00d76e5b0a06 -msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" - -#: ../../src/introduction/prerequisites.md:154 -#: 5ace5416560247c7a3304c41caa000c6 -msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," -msgstr "" - -#: ../../src/introduction/prerequisites.md:161 -#: 5d7a175b3c5a4f888daf037672211d61 -msgid "Text Editor" -msgstr "" - -#: ../../src/introduction/prerequisites.md:163 -#: 4e0c0c345527412eaf70e8efe67fab8f -msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." -msgstr "" - -#: ../../src/introduction/prerequisites.md:167 -#: 6dd8379682824d1397c48ac10db4b894 -msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:171 -#: 57691f7bd87741d68f4e1a963da91654 -msgid "Visual Studio Code with the Benten (CWL) plugin - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:172 -#: 13a4d71f127b4bd09c12a37752d27c8b -msgid "cwl-plugin for IntelliJ - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:174 -#: a574ed30000541b2816fbfe66b32c314 -msgid "The CWL community also maintains a list of editors and viewers: " -msgstr "" - -#: ../../src/introduction/prerequisites.md:177 -#: 9bb9c9052ad14c7c9fc0275c8f1b651b -msgid "Docker" -msgstr "" - -#: ../../src/introduction/prerequisites.md:181 -#: 5afcf2e79ceb424ea0a570797a712321 -msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." -msgstr "" - -#: ../../src/introduction/prerequisites.md:185 -#: cc5b91b8c5b14a40bdd09d3bd45fe9bb -msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." -msgstr "" - -#: ../../src/introduction/prerequisites.md:191 -#: d5e36c7827334fc69498459db5137d30 -msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." -msgstr "" - -#: ../../src/introduction/prerequisites.md:198 -#: 39d3eff64d004a0f8257d61f2a90b186 -msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." -msgstr "" - -#: ../../src/introduction/prerequisites.md:199 -#: 19946d0d9a6f42d487537273225b91cd -msgid "The Python `venv` module: " -msgstr "" - -#: ../../src/introduction/quick-start.md:1 -#: 66048204601a439d8245455c48b08826 -msgid "Quick Start" -msgstr "" - -#: ../../src/introduction/quick-start.md:3 -#: dcc41d0ce48e42a0ba209ca1fa37220a -msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." -msgstr "" - -#: ../../src/introduction/quick-start.md:7 -#: e2ebe32f12b74608b35217cea30cd0e0 -msgid "“Hello World”" -msgstr "" - -#: ../../src/introduction/quick-start.md:12 -#: 37a4f461b82f4e48948c5eab400b14a5 -msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:16 -#: 371c6801e92448f9875fff60a509f509 -msgid "`hello_world.cwl`" -msgstr "" - -#: ../../src/introduction/quick-start.md:22 -#: e3fb51cd196542008cb16458fdef7c1f -msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." -msgstr "" - -#: ../../src/introduction/quick-start.md:27 -#: d00cd96d47c6450a8c0955765eff9ac1 -msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." -msgstr "" - -#: ../../src/introduction/quick-start.md:32 -#: e06fdf0744344d0193b99791b9b94c7d -msgid "Installing a CWL Runner" -msgstr "" - -#: ../../src/introduction/quick-start.md:34 -#: 6e2191fbb8794f83a51897028a2e50f7 -msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:39 -#: 931b6b49a46d4d5581a05446ac2e9a7d -msgid "Installing `cwltool` with `pip`." -msgstr "" - -#: ../../src/introduction/quick-start.md:47 -#: 5cb281f4d0ea4163af0f7203c150345e -msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." -msgstr "" - -#: ../../src/introduction/quick-start.md:51 -#: 4e6c4c2b6bae49a2b2d93bc95538c7b9 -msgid "Running \"Hello World\"" -msgstr "" - -#: ../../src/introduction/quick-start.md:53 -#: b37ba76e0dd940559e13543ea241376e -msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" -msgstr "" - -#: ../../src/introduction/quick-start.md:57 -#: 22d7ac26f2ca41b2aa141fd4774b6f5c -msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:62 -#: 15033ad0574d46b2951bb2121c80c462 -msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" -msgstr "" - -#: ../../src/introduction/quick-start.md:65 -#: 2b2fc79461674b9ebdef49750f7fb319 -msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" - -#: ../../src/introduction/quick-start.md:70 -#: 8b11c9920b97427aa2d29498664e24bb -msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" -msgstr "" - -#: ../../src/introduction/quick-start.md:74 -#: d11de6ee015f46c991fbc8b48cd1fb60 -msgid "`hello_world-job.json`" -msgstr "" - -#: ../../src/introduction/quick-start.md:80 -#: 71adfebd042a4820ac533a2e6e07c0ca -msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" -msgstr "" - -#: ../../src/introduction/quick-start.md:82 -#: 8f199e6778a84ba68d385b42169f6b26 -msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:88 -#: 28ec66afdad24dfd871ef1a2686f9976 -msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." -msgstr "" - -#: ../../src/introduction/quick-start.md:96 -#: cccb84844ce0453cb77ce3db65ffbc1b -msgid "Continue reading the next sections of this User Guide!" -msgstr "" - -#: ../../src/introduction/quick-start.md:97 -#: 0c5a431846f241829975552ef8dd9c32 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" - -#: ../../src/introduction/quick-start.md:98 -#: 8e383a7ea5b54c56adb9cb0c6ed6c179 -msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." -msgstr "" - -#: ../../src/introduction/quick-start.md:99 -#: 98473d00529345d4989f0f5d2101da1b -msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -msgstr "" - -#: ../../src/introduction/quick-start.md:100 -#: d105326cb76b455d907c283a509f038c -msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." -msgstr "" - -#: ../../src/introduction/quick-start.md:101 -#: d4d00a573e36474f9c915563d4ea8709 -msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." -msgstr "" - -#: ../../src/introduction/quick-start.md:102 -#: aa8195d109974f9da3b9da97479525cb -msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/LICENSE.po b/locales/pt/LC_MESSAGES/LICENSE.po deleted file mode 100644 index c3591ece..00000000 --- a/locales/pt/LC_MESSAGES/LICENSE.po +++ /dev/null @@ -1,102 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../LICENSE.md:2 -#: 3d749a78eb3e47c991d603c2cabd1b91 -msgid "Licenses" -msgstr "" - -#: ../../LICENSE.md:4 -#: 4689ade8475a4c8a9d5e325f072c1392 -msgid "Instructional Material" -msgstr "" - -#: ../../LICENSE.md:6 -#: ef8ec0f072d947fbba997c4b2191abc2 -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." -msgstr "" - -#: ../../LICENSE.md:12 -#: 696f3824ca814c9eb314abae51be8202 -msgid "You are free:" -msgstr "" - -#: ../../LICENSE.md:14 -#: 72ebe92edf58434e9d7a4fc6bddf8880 -msgid "to **Share**---copy and redistribute the material in any medium or format" -msgstr "" - -#: ../../LICENSE.md:15 -#: 9b403f96d4194ffaab3f309d7d12f360 -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" - -#: ../../LICENSE.md:17 -#: 10b1befd0f834d79880c8aeb70b595d4 -msgid "for any purpose, even commercially." -msgstr "" - -#: ../../LICENSE.md:19 -#: 9017d0b760bb4370926d511b97a604c6 -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms." -msgstr "" - -#: ../../LICENSE.md:22 -#: 1faadcaead6748dfb34886e5819af9b9 -msgid "Under the following terms:" -msgstr "" - -#: ../../LICENSE.md:24 -#: 7a49ed3a728349c9b486f3d0b1dbf577 -msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." -msgstr "" - -#: ../../LICENSE.md:32 -#: 57da6294edce46eab00e7d15e6f6d4fa -msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" -msgstr "" - -#: ../../LICENSE.md:36 -#: 8fc8a30cd63c4a0a9d8ba1b913687029 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." -msgstr "" - -#: ../../LICENSE.md:39 -#: fe59e74a4d024831a6d5cbcfd3e4ee38 -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." -msgstr "" - -#: ../../LICENSE.md:44 -#: 3ea41d5a14ad46729cabb387a33814b0 -msgid "Software" -msgstr "" - -#: ../../LICENSE.md:46 -#: 23751e2552ff450c83e3dd255da56dac -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." -msgstr "" - -#: ../../LICENSE.md:51 -#: 13fb5eb48a8a434e95dbbb717ccaef8a -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." -msgstr "" - -#: ../../LICENSE.md:57 -#: e262fbd0e7de4f148f31afe39d1cb9e9 -msgid "Trademark" -msgstr "" diff --git a/locales/pt/LC_MESSAGES/_includes.po b/locales/pt/LC_MESSAGES/_includes.po deleted file mode 100644 index 6d6635cc..00000000 --- a/locales/pt/LC_MESSAGES/_includes.po +++ /dev/null @@ -1,22 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/_includes/what-is-cwl.md:1 -#: 46f474e1b364495181698bd13ce28a1e -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/episodes.po b/locales/pt/LC_MESSAGES/episodes.po deleted file mode 100644 index 94101eb0..00000000 --- a/locales/pt/LC_MESSAGES/episodes.po +++ /dev/null @@ -1,27 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/episodes.md:5 -#: 0cbb5e7334a647c3bcae7333ec3ced90 -msgid "This page has moved" -msgstr "" - -#: ../../src/episodes.md:9 -#: fabb221482cb4ac0a98bbe10943ed025 -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/faq.po b/locales/pt/LC_MESSAGES/faq.po deleted file mode 100644 index ce416d3d..00000000 --- a/locales/pt/LC_MESSAGES/faq.po +++ /dev/null @@ -1,292 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/faq.md:1 -#: 5daa5afac36f46dd8329e5629056384c -msgid "FAQ" -msgstr "" - -#: ../../src/faq.md:11 -#: 40c8efda3caf4c6089bda3027c522f37 -msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "" - -#: ../../src/faq.md:41 -#: ee854bcb685941cab45ae7f33b0efe48 -msgid "Rename an Input File" -msgstr "" - -#: ../../src/faq.md:43 -#: a4cdd5ab6fe341a3ad3e3055556d96c3 -msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." -msgstr "" - -#: ../../src/faq.md:59 -#: d1f359d47f124dfab23a75b196cd5884 -msgid "Rename an Output File" -msgstr "" - -#: ../../src/faq.md:61 -#: d83ced40605e411c92c4ae38761d7ffa -msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" -msgstr "" - -#: ../../src/faq.md:82 -#: bc8997df2e6746cebc2068534f30ee82 -msgid "Referencing a Local Script" -msgstr "" - -#: ../../src/faq.md:84 -#: 20b6ae57e1cf4410877a60fb3ef87264 -msgid "There are two ways to reference a local script:" -msgstr "" - -#: ../../src/faq.md:86 -#: 73c66b809e9a4218b624338ccb88a05e -msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." -msgstr "" - -#: ../../src/faq.md:89 -#: 9be72b7d5d604526b125b63148e99320 -msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" - -#: ../../src/faq.md:95 -#: fd96d178901545008a43fa99e3aa6cf3 -msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" -msgstr "" - -#: ../../src/faq.md:97 -#: db58a582e66244468f4d31e9213933d1 -msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." -msgstr "" - -#: ../../src/faq.md:104 -#: 3e70f0da5cd7460b90c1690366f40820 -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "" - -#: ../../src/faq.md:113 -#: db28dc27c82b4b29a7a9a768550bba9b -msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." -msgstr "" - -#: ../../src/faq.md:115 -#: 4474b16fb3fd4cdc85da931159804967 -msgid "The second method involves including an input of `type: File` in the script itself:" -msgstr "" - -#: ../../src/faq.md:135 -#: 23c9b2e21cec4ee8ade087e6630f62c2 -msgid "In CWL, everything must be directly stated." -msgstr "" - -#: ../../src/faq.md:138 -#: c01309dcd65c4f1080c396e6a9efb75d -msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "" - -#: ../../src/faq.md:140 -#: 0a36801172fd4e24a04b3ba85cf74e29 -msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." -msgstr "" - -#: ../../src/faq.md:165 -#: 433e788ba01141e98ea5a9e73ef71e6f -msgid "Model a \"one-or-the-other\" Parameter" -msgstr "" - -#: ../../src/faq.md:167 -#: b6de2761ce454992904775a06b7ba326 -msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." -msgstr "" - -#: ../../src/faq.md:188 -#: e36c2d53e8ba40f4a602b489a6688e24 -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "" - -#: ../../src/faq.md:190 -#: a9310166cb514e4e8824bba7fcfcb277 -msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/faq.md:194 -#: f6144f77152e4284963951abaa30adb2 -msgid "merge_nested" -msgstr "" - -#: ../../src/faq.md:196 -#: 790709dfc2854e4a89fcc4769f84b0f4 -msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." -msgstr "" - -#: ../../src/faq.md:199 -#: 438789c8def549d1b4b8a187d5acc48e -msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "" - -#: ../../src/faq.md:201 -#: 23ede7dfd5c84492baee1d5bbb9a91d9 -msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." -msgstr "" - -#: ../../src/faq.md:229 -#: 37c0474e48164160b23c4094d583d2d3 -msgid "Optional Inputs 💯" -msgstr "" - -#: ../../src/faq.md:231 -#: 3b2be0a4a87041b7a5bda20c6df2ffc8 -msgid "To make an input parameter optional, add a question mark to the type declaration." -msgstr "" - -#: ../../src/faq.md:247 -#: 886300d2dcff4861aae503d34b0bee44 -msgid "" -msgstr "" - -#: ../../src/faq.md:248 -#: fe393ecdff25428da6cbcd30171c7811 -msgid "Enum Inputs ⚜️" -msgstr "" - -#: ../../src/faq.md:250 -#: ebfd4991d917413b858da8b437a55805 -msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" -msgstr "" - -#: ../../src/faq.md:267 -#: 2919ff4f51254e69aea40146e2d911f1 -msgid "" -msgstr "" - -#: ../../src/faq.md:268 -#: 61ed4e87457c41eea31f51740557597e -msgid "Record Inputs 📀" -msgstr "" - -#: ../../src/faq.md:270 -#: 1e6624104b024eb092682cd0dd0f6a3c -msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." -msgstr "" - -#: ../../src/faq.md:322 -#: b741b8333e104feaa6d1f41fd4476304 -msgid "Setting Mutually Exclusive Parameters" -msgstr "" - -#: ../../src/faq.md:324 -#: 334673ae870a4dada817857f3a49326e -msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." -msgstr "" - -#: ../../src/faq.md:342 -#: 362f85270df04712b2e2f21c7019e3cb -msgid "Setting Booleans" -msgstr "" - -#: ../../src/faq.md:344 -#: ad6997f24c7c42fe965b5d7bfd1e633e -msgid "These can be set by using the default field" -msgstr "" - -#: ../../src/faq.md:349 -#: 99dce9d60b6a4f99bc39899b7c8c10ef -msgid "Concatenating Strings in Inputs" -msgstr "" - -#: ../../src/faq.md:351 -#: 6b68fe24cbf64624b49ea56fce2eecad -msgid "The valueFrom field must be used instead of default." -msgstr "" - -#: ../../src/faq.md:359 -#: d23326837eb74e7faf1f54e25f8309c4 -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "" - -#: ../../src/faq.md:361 -#: 2e2eabe92670412e95474b25ad9cda4c -msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "" - -#: ../../src/faq.md:363 -#: 81f9308adbee4a3c9e585b8e0f0c4844 -msgid "For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "" - -#: ../../src/faq.md:371 -#: a5d3ed6cac28415288e7fc7fbfc6e8a6 -msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." -msgstr "" - -#: ../../src/faq.md:373 -#: 72f9692803304daf9f846e2b90139660 -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -msgstr "" - -#: ../../src/faq.md:375 -#: a7eb20c817704811b3bcf2f94ec2e51d -msgid "If `cwltool --validate` returns valid" -msgstr "" - -#: ../../src/faq.md:384 -#: 20fa869849ef4b358a11db46111017de -msgid "But executing it causes an error like:" -msgstr "" - -#: ../../src/faq.md:396 -#: 35032fcd9f23403ca006d62a7d6e7be7 -msgid "The file is here" -msgstr "" - -#: ../../src/faq.md:410 -#: f6d6a4e3691446378c8fb01a2d19f8ad -msgid "Problem caused by `-` (hyphen character)." -msgstr "" - -#: ../../src/faq.md:423 -#: 44608fed1048458e999e13b014327e7e -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" - -#: ../../src/faq.md:436 -#: 96ede8a8f1f34786aabd4004bf2e7acc -msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" -msgstr "" - -#: ../../src/faq.md:442 -#: 84634a368e704e8d828678785c784595 -msgid "Use CWL and cwltool with Singularity" -msgstr "" - -#: ../../src/faq.md:445 -#: 545c4db9c24f42ee946081254d9ca7a8 -msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." -msgstr "" - -#: ../../src/faq.md:450 -#: 1c1e6d583d5646a8a5c9316dcd743d9f -msgid "Debug JavaScript Expressions" -msgstr "" - -#: ../../src/faq.md:452 -#: cf7d336d444e4f59aa83585b7abb1fe5 -msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" -msgstr "" diff --git a/locales/pt/LC_MESSAGES/index.po b/locales/pt/LC_MESSAGES/index.po deleted file mode 100644 index 0a5d7d38..00000000 --- a/locales/pt/LC_MESSAGES/index.po +++ /dev/null @@ -1,57 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/index.md:1 -#: a58ca61ccefc401588f91699bc98bd32 -msgid "Common Workflow Language User Guide" -msgstr "" - -#: ../../src/index.md:3 -#: 6dcf12053f104cb3a8d23ce8d4f90363 -msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." -msgstr "" - -#: ../../src/index.md:7 -#: 1cc90206170d46119c5756f31a9e8799 -msgid "Contributions and Feedback are Welcome!" -msgstr "" - -#: ../../src/index.md:9 -#: b54801d84a944dadb4e4637551e3f7b9 -msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." -msgstr "" - -#: ../../src/index.md:16 -#: 860afd2eda4847e0a0d8834de3af4aa8 -msgid "Navigating the User Guide" -msgstr "" - -#: ../../src/index.md:18 -#: d6046316c84b40ffb5478c90b2604911 -msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." -msgstr "" - -#: ../../src/index.md:23 -#: c3c89ac756a74d9688e179b8718c9bf0 -msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." -msgstr "" - -#: ../../src/index.md:28 -#: 0eb795062b484537b090c4d5c361f7f4 -msgid "Table of Contents" -msgstr "" diff --git a/locales/pt/LC_MESSAGES/introduction.po b/locales/pt/LC_MESSAGES/introduction.po deleted file mode 100644 index fe9de9a5..00000000 --- a/locales/pt/LC_MESSAGES/introduction.po +++ /dev/null @@ -1,607 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/introduction/basic-concepts.md:1 -#: 92c85569d9e746d8a5b7a5e8f9773545 -msgid "Basic Concepts" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:3 -#: 5e501be2f49044c9897f6e8d65186abb -msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:10 -#: a6f5f188f9af4b608b8401996a558e83 -msgid "The CWL Specification" -msgstr "" - -#: ../../src/_includes/what-is-cwl.md:2 -#: 2ecb1a3a4c7546ba94e560924cfb09a8 -#: 3c0da8bd74824f8b88223c2a9dcc6ec2 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:21 -#: 7fb9ad094d844047b0d35dc70c295400 -msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:25 -#: 303d1a15612846c1b60a4d651f9d1d4a -msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:33 -#: c84c4bde07034846b043c4f281f8e00c -msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:37 -#: d774877d6e4447b7b83d56ebbaf09e96 -msgid "Implementations" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:39 -#: e8884f39f08c41bab29c4284077fd860 -msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:44 -#: 984ac8cee64e4e41957d8c5a4aff0cfd -msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:51 -#: 17381e8872414c49b178d91ace2e3e82 -msgid "CWL specification, implementations, and other tools." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:105 -#: c4cdbf2a42644e0eb4eb74512388e9f7 -msgid "Processes and Requirements" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:107 -#: 7d994284e320413bb8dbb2a42cd16a4e -msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:112 -#: ce92487ca4e3495ebd0693c502773626 -msgid "A command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:113 -#: 0ce512c3cd744652b5feb2d8dcfdb613 -msgid "An expression tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:114 -#: dd7d6a1399b04923b25df70abb1becf5 -msgid "An operation." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:115 -#: ce4c76b46531416bb4006a9c01f45a23 -msgid "A workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:118 -#: 0256a343321447559471d731c86d3546 -msgid "The processing units available in the CWL objects model." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:119 -#: e1235589f24942babe54adaae4f169af -msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:122 -#: 81baaa297562452f80afe68657c8099d -msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:127 -#: 0c8bbd88bd8c4c71b19011812e7487c3 -msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:131 -#: 3b64da1f14964cea9e5cbf8376578789 -msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:137 -#: bf33807babb64befab3385eca4c92131 -msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:141 -#: afdb75d374624f4798f358a3dfe7752e -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:142 -#: bc28744d5fa644218ef55672d726307f -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:143 -#: 24ffb5bfa767424585b6b6c93169de93 -msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:145 -#: bd53afe50cc14f2ca428adddb0e60dc9 -msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:151 -#: 35c98c4b352c4f9bb9572c740894dc57 -msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:155 -#: f7fb57fdf9344a7eb0f334aca8d3e85f -msgid "FAIR Workflows" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:157 -#: 0dc6a8f19fda4e9eaa80b8e1bd1fc5be -msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:167 -#: ff1224487c35402d8afee6da3803e19b -msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:171 -#: 63c2dd9aaec54df088e82febfd7bc49c -msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:176 -#: 18f310d11c9b48b4a447b6662446cd3e -msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 -#: a3922283fdce4f99832c816626d5f098 -#: 19245373c2e84793a72462b7d2fa1c34 -#: 7c3ea7150c7d41fead10ddf2a6205ec8 -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:180 -#: cf39d3563e344ad9b31d5268c4069972 -msgid "Semantic Versioning - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:181 -#: 97b0113a847044b98f79b5e00941f4c3 -msgid "The CWL Specification page in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:182 -#: 8cf4edbb4b344ac7b3eae86ed52beff8 -msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:183 -#: c1dfc170fdf54c9e846539a5170f204f -msgid "The list of Implementations in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:184 -#: 778babbcfb2648a1ad7a7ad8f80653a8 -msgid "PROV-O: The PROV Ontology - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:185 -#: 23abed59f5d44bfb96e8fa13aa213b83 -msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." -msgstr "" - -#: ../../src/introduction/index.md:1 -#: ee93304de4e447c1bd5626e72b99b6fe -msgid "Introduction" -msgstr "" - -#: ../../src/introduction/index.md:3 -#: a79f07e33fc5437c9fa204111d0290d8 -msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." -msgstr "" - -#: ../../src/introduction/prerequisites.md:1 -#: 3cf08b553a814478b4b2c6c84ebe354e -msgid "Prerequisites" -msgstr "" - -#: ../../src/introduction/prerequisites.md:6 -#: 98751950a97f44fdb16e826fece810fb -msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:12 -#: eac153b881fa47ab8bb08074dad8eed2 -msgid "CWL Implementations" -msgstr "" - -#: ../../src/introduction/prerequisites.md:14 -#: 806ff7b185d74538a9b0e20c6ad84ffe -msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:19 -#: 1f9573b6cd45479bae2481a251132d53 -msgid "Operating System" -msgstr "" - -#: ../../src/introduction/prerequisites.md:21 -#: c3995fd5588741148e3b2c91ca011ca9 -msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:24 -#: 8a67b172ce524aa09858acd9d1a62762 -msgid "Linux" -msgstr "" - -#: ../../src/introduction/prerequisites.md:25 -#: a567e0f952bc46be8b82d0a357f2c209 -msgid "macOS" -msgstr "" - -#: ../../src/introduction/prerequisites.md:26 -#: 21d3bb850bb14fdcb6d4c4a15c9966b6 -msgid "Windows" -msgstr "" - -#: ../../src/introduction/prerequisites.md:29 -#: 62cbb29459b24e9fa83c7cd7994bdf12 -msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:35 -#: aaa319d4446c41ba82bf925f29f7d9dd -msgid "CWL Runner" -msgstr "" - -#: ../../src/introduction/prerequisites.md:41 -#: c49938a0100a4850b67d067a61304d01 -msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/prerequisites.md:46 -#: 91e986d0c1f44d7f9c3b32366160da6a -msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:51 -#: 301c5a3baaaf46bb81bdc25b53a31f23 -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:62 -#: 1664589ced314daebfb163e6424f220f -msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:65 -#: 1223fecd61f34ad98ebbb7e45eaf4ac7 -msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:67 -#: 242c496599d84a64959db275ee1e212e -msgid "`true.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:73 -#: 9b749d47f48341cb9ac8cd14098e6c47 -msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:79 -#: e8ec351d7b79447bb15f4d4518b8de87 -msgid "Validating `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:84 -#: 58d5613243914dc8bc4ce88676525783 -msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:86 -#: 731a6c30786f43d88160f9642cbb05d2 -msgid "Running `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:91 -#: ca2088eb9565429dbc1ce0b28b2ef1fb -msgid "Cwl-runner Python Module" -msgstr "" - -#: ../../src/introduction/prerequisites.md:93 -#: 5ac9c6bfb50b48878aff52f1194e53c4 -msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." -msgstr "" - -#: ../../src/introduction/prerequisites.md:101 -#: b8d0c12ff07f4269bba87cd653803345 -msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:104 -#: 83780c1b43f744b4ae87a917b26293f5 -msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:111 -#: 2919320c41e94930a0aa9bc6aacb5a87 -msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:115 -#: b8e799c075214d539aa0a7c04dbc33c0 -msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:120 -#: ccbd51a29ca841efb74c5e0a25d1eb87 -msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:125 -#: 5f3330c1e15a402781c3325f9d3dc779 -msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:129 -#: 314fbc9f866a405b86e7bd704781dea1 -msgid "`true_shebang.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:135 -#: 9434e3680aa9487fab9ddb782c6ff3d0 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:137 -#: 2ce0bda38d814b248a2c23ebc26bf462 -msgid "Making `true.cwl` executable." -msgstr "" - -#: ../../src/introduction/prerequisites.md:144 -#: 105c3be6f5f34f4388b9999603275bb5 -msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." -msgstr "" - -#: ../../src/introduction/prerequisites.md:148 -#: bd378c8483a14c93b5fe00d76e5b0a06 -msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" - -#: ../../src/introduction/prerequisites.md:154 -#: 5ace5416560247c7a3304c41caa000c6 -msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," -msgstr "" - -#: ../../src/introduction/prerequisites.md:161 -#: 5d7a175b3c5a4f888daf037672211d61 -msgid "Text Editor" -msgstr "" - -#: ../../src/introduction/prerequisites.md:163 -#: 4e0c0c345527412eaf70e8efe67fab8f -msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." -msgstr "" - -#: ../../src/introduction/prerequisites.md:167 -#: 6dd8379682824d1397c48ac10db4b894 -msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:171 -#: 57691f7bd87741d68f4e1a963da91654 -msgid "Visual Studio Code with the Benten (CWL) plugin - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:172 -#: 13a4d71f127b4bd09c12a37752d27c8b -msgid "cwl-plugin for IntelliJ - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:174 -#: a574ed30000541b2816fbfe66b32c314 -msgid "The CWL community also maintains a list of editors and viewers: " -msgstr "" - -#: ../../src/introduction/prerequisites.md:177 -#: 9bb9c9052ad14c7c9fc0275c8f1b651b -msgid "Docker" -msgstr "" - -#: ../../src/introduction/prerequisites.md:181 -#: 5afcf2e79ceb424ea0a570797a712321 -msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." -msgstr "" - -#: ../../src/introduction/prerequisites.md:185 -#: cc5b91b8c5b14a40bdd09d3bd45fe9bb -msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." -msgstr "" - -#: ../../src/introduction/prerequisites.md:191 -#: d5e36c7827334fc69498459db5137d30 -msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." -msgstr "" - -#: ../../src/introduction/prerequisites.md:198 -#: 39d3eff64d004a0f8257d61f2a90b186 -msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." -msgstr "" - -#: ../../src/introduction/prerequisites.md:199 -#: 19946d0d9a6f42d487537273225b91cd -msgid "The Python `venv` module: " -msgstr "" - -#: ../../src/introduction/quick-start.md:1 -#: 66048204601a439d8245455c48b08826 -msgid "Quick Start" -msgstr "" - -#: ../../src/introduction/quick-start.md:3 -#: dcc41d0ce48e42a0ba209ca1fa37220a -msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." -msgstr "" - -#: ../../src/introduction/quick-start.md:7 -#: e2ebe32f12b74608b35217cea30cd0e0 -msgid "“Hello World”" -msgstr "" - -#: ../../src/introduction/quick-start.md:12 -#: 37a4f461b82f4e48948c5eab400b14a5 -msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:16 -#: 371c6801e92448f9875fff60a509f509 -msgid "`hello_world.cwl`" -msgstr "" - -#: ../../src/introduction/quick-start.md:22 -#: e3fb51cd196542008cb16458fdef7c1f -msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." -msgstr "" - -#: ../../src/introduction/quick-start.md:27 -#: d00cd96d47c6450a8c0955765eff9ac1 -msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." -msgstr "" - -#: ../../src/introduction/quick-start.md:32 -#: e06fdf0744344d0193b99791b9b94c7d -msgid "Installing a CWL Runner" -msgstr "" - -#: ../../src/introduction/quick-start.md:34 -#: 6e2191fbb8794f83a51897028a2e50f7 -msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:39 -#: 931b6b49a46d4d5581a05446ac2e9a7d -msgid "Installing `cwltool` with `pip`." -msgstr "" - -#: ../../src/introduction/quick-start.md:47 -#: 5cb281f4d0ea4163af0f7203c150345e -msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." -msgstr "" - -#: ../../src/introduction/quick-start.md:51 -#: 4e6c4c2b6bae49a2b2d93bc95538c7b9 -msgid "Running \"Hello World\"" -msgstr "" - -#: ../../src/introduction/quick-start.md:53 -#: b37ba76e0dd940559e13543ea241376e -msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" -msgstr "" - -#: ../../src/introduction/quick-start.md:57 -#: 22d7ac26f2ca41b2aa141fd4774b6f5c -msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:62 -#: 15033ad0574d46b2951bb2121c80c462 -msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" -msgstr "" - -#: ../../src/introduction/quick-start.md:65 -#: 2b2fc79461674b9ebdef49750f7fb319 -msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" - -#: ../../src/introduction/quick-start.md:70 -#: 8b11c9920b97427aa2d29498664e24bb -msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" -msgstr "" - -#: ../../src/introduction/quick-start.md:74 -#: d11de6ee015f46c991fbc8b48cd1fb60 -msgid "`hello_world-job.json`" -msgstr "" - -#: ../../src/introduction/quick-start.md:80 -#: 71adfebd042a4820ac533a2e6e07c0ca -msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" -msgstr "" - -#: ../../src/introduction/quick-start.md:82 -#: 8f199e6778a84ba68d385b42169f6b26 -msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:88 -#: 28ec66afdad24dfd871ef1a2686f9976 -msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." -msgstr "" - -#: ../../src/introduction/quick-start.md:96 -#: cccb84844ce0453cb77ce3db65ffbc1b -msgid "Continue reading the next sections of this User Guide!" -msgstr "" - -#: ../../src/introduction/quick-start.md:97 -#: 0c5a431846f241829975552ef8dd9c32 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" - -#: ../../src/introduction/quick-start.md:98 -#: 8e383a7ea5b54c56adb9cb0c6ed6c179 -msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." -msgstr "" - -#: ../../src/introduction/quick-start.md:99 -#: 98473d00529345d4989f0f5d2101da1b -msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -msgstr "" - -#: ../../src/introduction/quick-start.md:100 -#: d105326cb76b455d907c283a509f038c -msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." -msgstr "" - -#: ../../src/introduction/quick-start.md:101 -#: d4d00a573e36474f9c915563d4ea8709 -msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." -msgstr "" - -#: ../../src/introduction/quick-start.md:102 -#: aa8195d109974f9da3b9da97479525cb -msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/setup.po b/locales/pt/LC_MESSAGES/setup.po deleted file mode 100644 index 06186f03..00000000 --- a/locales/pt/LC_MESSAGES/setup.po +++ /dev/null @@ -1,27 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/setup.md:5 -#: 29bb5c68be6042e5aa4a370e9c4024b3 -msgid "This page has moved" -msgstr "" - -#: ../../src/setup.md:9 -#: 8bcf31398c34491da1a1590422a72cbe -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/sphinx.po b/locales/pt/LC_MESSAGES/sphinx.po index 68ce7729..38526232 100644 --- a/locales/pt/LC_MESSAGES/sphinx.po +++ b/locales/pt/LC_MESSAGES/sphinx.po @@ -1,27 +1,28 @@ # SOME DESCRIPTIVE TITLE. # Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. # +#, fuzzy msgid "" msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" +"Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:27+0100\n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" +"Last-Translator: FULL NAME \n" +"Language-Team: LANGUAGE \n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" +"Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.10.3\n" -#: ../../src/_templates/sidebar-nav-bs.html:1 -#: b896fd5e11fe4674a7f46ad489476692 +#: ../../src/_templates/sidebar-nav-bs.html:1 d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" msgstr "" -#: ../../src/_templates/sidebar-nav-bs.html:3 -#: acede4e78f7e4aefa0ad9425928cbb42 +#: ../../src/_templates/sidebar-nav-bs.html:3 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" msgstr "" + diff --git a/locales/pt/LC_MESSAGES/topics.po b/locales/pt/LC_MESSAGES/topics.po deleted file mode 100644 index 7d6384c1..00000000 --- a/locales/pt/LC_MESSAGES/topics.po +++ /dev/null @@ -1,2083 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 1a006f1604c0405aaa4b93e41edc5184 -msgid "Additional Arguments and Parameters" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:3 -#: b61b4d7ed53a436486c1429987a2a21b -msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 1bf9e65f1cc249ee93656a53ddd354ca -msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 3329dc69c32f4b9092b196d79ae5d0c1 -msgid "`arguments.cwl`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 -#: a003a3d1de0e4dfe8c777905e55fb9fe -#: e2dc24c683054cd785326de2c3f3f136 -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:24 -#: aca6a0cd24a2411c8cfb1ad392f6d315 -msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:30 -#: bcf37e403eb041269e351d7f98a19587 -msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:36 -#: c5f68f8a9f34445ebcbd5783f96cb046 -msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:43 -#: 4eca90c659ba43158db373d36ee681df -msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." -msgstr "" - -#: ../../src/topics/best-practices.md:1 -#: 7474eeb128624dc4b1e980dbd0f04ca4 -msgid "Best Practices" -msgstr "" - -#: ../../src/topics/best-practices.md:3 -#: 0c520e5add334609a1afddc559abe19a -msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." -msgstr "" - -#: ../../src/topics/best-practices.md:8 -#: 125a69207077425fa54f346abc45342d -msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." -msgstr "" - -#: ../../src/topics/best-practices.md:11 -#: 6ca38a04844c403b836942b2f2f1e1e2 -msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." -msgstr "" - -#: ../../src/topics/best-practices.md:20 -#: 1da05be0d97d429a84085459ebae54cf -msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." -msgstr "" - -#: ../../src/topics/best-practices.md:26 -#: fb1b2a8c54f34d78ac61dd4b5ffd9063 -msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" -msgstr "" - -#: ../../src/topics/best-practices.md:28 -#: a8b1b5caf9904fc5b9eef8c110474b84 -msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" - -#: ../../src/topics/best-practices.md:37 -#: 42a5a8cb3b284549aabb817b73ce5810 -msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." -msgstr "" - -#: ../../src/topics/best-practices.md:40 -#: eddd878eb0324851997de2a69bcbb43f -msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." -msgstr "" - -#: ../../src/topics/best-practices.md:44 -#: b05c8ff667174f6798feb811cdd3c41d -msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:47 -#: 9dc16d1a6b0546cead6967f5e9b1526a -msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." -msgstr "" - -#: ../../src/topics/best-practices.md:50 -#: b8bf85e8523a4553a58face698aa863b -msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." -msgstr "" - -#: ../../src/topics/best-practices.md:55 -#: 6fb9a1a2ffe14f39b01af8736a9698eb -msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:58 -#: 0a935aa93e554c0987af7349f94ccd3a -msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." -msgstr "" - -#: ../../src/topics/best-practices.md:66 -#: cadb5982a13e4621807ad976cf9b1524 -msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." -msgstr "" - -#: ../../src/topics/best-practices.md:69 -#: bd7ab2cc6234458181e9b99938eba824 -msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." -msgstr "" - -#: ../../src/topics/best-practices.md:73 -#: 7beb72d7dd5a405f9be8b6fb6a310f10 -msgid "Custom types should be defined with one external YAML per type definition for re-use." -msgstr "" - -#: ../../src/topics/best-practices.md:76 -#: e5942c4d4b4d4e1a8c0e9ed3da80960e -msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "" - -#: ../../src/topics/best-practices.md:78 -#: 5a5dbc9b9d2242ba8d15ecf39123694b -msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." -msgstr "" - -#: ../../src/topics/best-practices.md:82 -#: dd3016d33b7d4340a09a7c8e5aec4f0b -msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." -msgstr "" - -#: ../../src/topics/best-practices.md:85 -#: 45d110a660b348f58a1107476df18cee -msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." -msgstr "" - -#: ../../src/topics/best-practices.md:90 -#: 97a5b141592e4415aa4acef4f6228045 -msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." -msgstr "" - -#: ../../src/topics/best-practices.md:93 -#: 85f624f8879348e8bb368ec2749925bf -msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." -msgstr "" - -#: ../../src/topics/best-practices.md:97 -#: 20a851dae87941c7975173ed9cd1e360 -msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." -msgstr "" - -#: ../../src/topics/command-line-tool.md:1 -#: bb19e1b689564a11bb9e72d5f82cf3d9 -msgid "Command Line Tool" -msgstr "" - -#: ../../src/topics/command-line-tool.md:3 -#: b14199173add4585be62c4e8278b49f4 -msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." -msgstr "" - -#: ../../src/topics/command-line-tool.md:8 -#: 9e883f18843a41d7b10102bc11655839 -msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." -msgstr "" - -#: ../../src/topics/command-line-tool.md:19 -#: fe3a1468aa864742b92c6e8f4ff1a38f -msgid "CWL command-line tool." -msgstr "" - -#: ../../src/topics/command-line-tool.md:50 -#: e9dbf14538404cceb02507962a173ee8 -msgid "`echo.cwl`" -msgstr "" - -#: ../../src/topics/command-line-tool.md:57 -#: a650a7dacbb547db97158a8ac2c9d0dc -msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." -msgstr "" - -#: ../../src/topics/command-line-tool.md:68 -#: 501217b98c424a319e70ef963de506f6 -msgid "Network Access" -msgstr "" - -#: ../../src/topics/command-line-tool.md:69 -#: 7143809471454e00880ad8faaf43f141 -msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." -msgstr "" - -#: ../../src/topics/command-line-tool.md:83 -#: 7ad86e42708a465980a56f735644de9f -msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:1 -#: a8f29712337b4d1daf3190cc8973b8f7 -msgid "Creating Files at Runtime" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:3 -#: 534843389795437991fad0b5a702b483 -msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:7 -#: 2052170aa2624feeb2253477895aa838 -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:9 -#: d5ed098a33ae4c1ab2a30eba483ecc6f -msgid "`createfile.cwl`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:15 -#: 2b55c028602f41babb6e535b425ba5dc -msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:20 -#: 47408669ae8b4432a43d763dba12a466 -msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:27 -#: b2e5e925971849a09a8d54d9c649a32d -msgid "To test the above CWL tool, use this job to provide the input value `message`:" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 -#: ../../src/topics/outputs.md:77 -#: 9a39f53bdcc94904a90effb507767645 -#: f296149bf19947528b134b01a4d7ce81 -#: 965fa9769dea4ac9b3dd252e0a3bc603 -msgid "`echo-job.yml`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:35 -#: 79d8ea95f0c34585a3dec4f83453de60 -msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:40 -#: 4afab699247b4f619702c4086eb1b6f3 -msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:51 -#: 693b91423f004118b806bb8ee7952eaf -msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:54 -#: ../../src/topics/environment-variables.md:18 -#: ../../src/topics/file-formats.md:52 -#: ../../src/topics/staging-input-files.md:20 -#: ../../src/topics/workflows.md:198 -#: e4a25f04a6fa4001bb1e58cb775cdd84 -#: c771cbc64607412a9164c28934e9e0f5 -#: bdd5a3eac1e3436496e05a13c4f06073 -#: 1e62b28ef0184081b4d6e53f34b753e1 -#: 33edd6deb38740ed98466b6e023b0393 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/custom-types.md:1 -#: a3a8bcdfadc4484ea5e4c13a25b2da85 -msgid "Custom Types" -msgstr "" - -#: ../../src/topics/custom-types.md:3 -#: 7800570badf149b3bb1f81d470dbf4be -msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." -msgstr "" - -#: ../../src/topics/custom-types.md:9 -#: 496313f8ec67403ca78ba66130df261e -msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:12 -#: f7cc0d1ac5dd47658093cd0360f90329 -msgid "`custom-types.cwl`" -msgstr "" - -#: ../../src/topics/custom-types.md:18 -#: 0d563f15c1cc4484b6b2955bdc70e1a9 -msgid "`custom-types.yml`" -msgstr "" - -#: ../../src/topics/custom-types.md:24 -#: 06425b6cdaf244b198fdde312e864190 -msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/custom-types.md:30 -#: 26c3762a637a4492a6c12588544cb0a7 -msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" -msgstr "" - -#: ../../src/topics/custom-types.md:46 -#: 221433aa39104642af8afb70ebd08576 -msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:53 -#: 197bf36a5d7741b3a9ac56c19d4a7686 -msgid "The contents of the YAML file describing the custom type are given below:" -msgstr "" - -#: ../../src/topics/custom-types.md:55 -#: d9249cf936d24ab3b3fc508d17d94745 -msgid "`biom-convert-table.yaml`" -msgstr "" - -#: ../../src/topics/custom-types.md:61 -#: 2ff7ce81cd3a492a8549484ba8d1f135 -msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" -msgstr "" - -#: ../../src/topics/custom-types.md:76 -#: 2bb45c56e2fc49e094be2cf742222e67 -msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." -msgstr "" - -#: ../../src/topics/environment-variables.md:1 -#: e2a4a531c6164f15bc711618db058f52 -msgid "Environment Variables" -msgstr "" - -#: ../../src/topics/environment-variables.md:3 -#: 90f7960bd24d4481bd05da1d61ef146b -msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." -msgstr "" - -#: ../../src/topics/environment-variables.md:7 -#: a51814548e44467c841ca65b2ac63b2c -msgid "`env.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:1 -#: fa13573d9c174ca1accf20a449e5984f -msgid "Expression Tool" -msgstr "" - -#: ../../src/topics/expression-tool.md:3 -#: f2912b17e3be47b0b7186efdb4c4010f -msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." -msgstr "" - -#: ../../src/topics/expression-tool.md:8 -#: 4d9c95d18c1a4880845e7194a99aed3c -msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." -msgstr "" - -#: ../../src/topics/expression-tool.md:17 -#: c656a020978f465b85b8754346ea5b6d -msgid "CWL expression tool." -msgstr "" - -#: ../../src/topics/expression-tool.md:48 -#: ff4d0b6bc0264650a21adc811b8caf4c -msgid "`uppercase.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:67 -#: 77e00be2c0984465af5bf501b4031f32 -msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." -msgstr "" - -#: ../../src/topics/expressions.md:1 -#: 3d7b7238be974c0487f219cb5c030149 -msgid "Expressions" -msgstr "" - -#: ../../src/topics/expressions.md:3 -#: 03a62f421c8241779c0e79f4dbad96cc -msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." -msgstr "" - -#: ../../src/topics/expressions.md:9 -#: 31a85893835748339b6c84fb98fde14b -msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." -msgstr "" - -#: ../../src/topics/expressions.md:16 -#: 08d9ecd7d3294c5b9dd4db228a1d8d5b -msgid "`expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:22 -#: d94d6c69aaa64edd9c75624286713c2e -msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" -msgstr "" - -#: ../../src/topics/expressions.md:25 -#: 020019b8aedb494fad022d19b7106f83 -msgid "`empty.yml`" -msgstr "" - -#: ../../src/topics/expressions.md:31 -#: a6b66e0fc0de442e8f72f0d0c37c7e8c -msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." -msgstr "" - -#: ../../src/topics/expressions.md:35 -#: 48b7d9ddac2940c0815e5c855bfca6d9 -msgid "We can then run `expression.cwl`:" -msgstr "" - -#: ../../src/topics/expressions.md:37 -#: 894b843f9c064d56913e1a8c48093314 -msgid "Running `expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:47 -#: 2319e845caee41a3bc5888c3f1fc28d1 -msgid "Note that requirements can be provided with the map syntax, as in the example above:" -msgstr "" - -#: ../../src/topics/expressions.md:54 -#: 9ea661d749db428eacd2207dc7a01e36 -msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." -msgstr "" - -#: ../../src/topics/expressions.md:62 -#: 4ff76250f28144a4a9d8807a9d4ed3b4 -msgid "Where are JavaScript expressions allowed?" -msgstr "" - -#: ../../src/topics/expressions.md:64 -#: 7f9f2df357a740feb89bfbcc44ff4d61 -msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" -msgstr "" - -#: ../../src/topics/expressions.md:66 -#: 12633ed841dd447a8753faeb4f9e5096 -msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 -#: 4db64481d38c4896a85a8f6038a9931c -#: 1b4ff3eeddde4a9a8018235b9d706567 -msgid "`arguments`" -msgstr "" - -#: ../../src/topics/expressions.md:68 -#: ../../src/topics/expressions.md:76 -#: ../../src/topics/expressions.md:89 -#: ../../src/topics/parameter-references.md:65 -#: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 -#: 50547062ee404e2ebeae7eeb54b9de4b -#: 88933bc02fa84412944673c3463af1ad -#: 4fde39d8a50e49f09bd28a8598760682 -#: b933cbf847d94c5fb8471918ce8cb4ad -#: 0145c520b85a4bc29302bb654f08f23b -#: a3e322ac8a0d4e2ba9bfbece6b5ae64b -msgid "`valueFrom`" -msgstr "" - -#: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 -#: d9b166225120432f9a2bf2cc7b6ffdfe -#: 28f8ec2fc5c0436aaba19e9d479aa466 -msgid "`stdin`" -msgstr "" - -#: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 -#: b866a0e5897e44329714f4c55eb20d2e -#: e64b5027878346d79f9ab52b3d3b916e -msgid "`stdout`" -msgstr "" - -#: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 -#: ed38ec582fbb48ff9f9cffa7962ef515 -#: 6cc0788250624fd69fa4e3881191ab7f -msgid "`stderr`" -msgstr "" - -#: ../../src/topics/expressions.md:72 -#: 17eefb5f38534c1b87116c3a061ea1bb -msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:73 -#: ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 -#: ../../src/topics/expressions.md:93 -#: ../../src/topics/parameter-references.md:70 -#: ../../src/topics/parameter-references.md:75 -#: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 -#: ce0572fc81b343e6991c88ca0195149a -#: f8b77ad06ebe43d7b03b2135737902e2 -#: c7953486c99d4c7898c0155a6085dfd5 -#: 46d99b1f7f0747479bd58486cf7941d2 -#: cd0a797b3619404f964ba9efb33756bd -#: 528cd5e0d3994230b719fbfb39b1f13e -#: 324241aae8ff4505ab0467f2a7f27fe2 -#: f4086b1ad2e44c2b9de2636f8bc1eb90 -msgid "`format`" -msgstr "" - -#: ../../src/topics/expressions.md:74 -#: ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 -#: ../../src/topics/expressions.md:94 -#: ../../src/topics/parameter-references.md:71 -#: ../../src/topics/parameter-references.md:76 -#: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 -#: 764d7cf3fb5444d58dc9e0eb6b8fc649 -#: 0450a4b8de3046998d30ce1f09c10daf -#: fd6bf79cbb694dbb89e8731aed733e6c -#: e6048a64e09d46099132fee40a2e0644 -#: 9512391eb96440bd8e48c3754821e3d0 -#: 3e8669bf4a6741f9aba170864b251dac -#: a02ede726d3f4eec9602f72054c0d963 -#: 4ed593dfc39246789f1e4ecdc742323b -msgid "`secondaryFiles`" -msgstr "" - -#: ../../src/topics/expressions.md:75 -#: 304de40206cb43d7b651245586cfa55b -msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:77 -#: 7855471c93bc44aabb1a2b9beb52b56a -msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:80 -#: f0452f324bfa451f9f3264f9a55e0e5d -msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 -#: 6dc476cf8689465ea3993f49a9eead75 -#: 4dfc0be21065471d91def850bc2528fb -msgid "`glob`" -msgstr "" - -#: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 -#: 09d69778a89044099b3e5d7cf02471bb -#: e3077bdff0dc4dfdae60eb60f3d66d8b -msgid "`outputEval`" -msgstr "" - -#: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 -#: b28843f7b57745db9cb3648ef23fda0f -#: 6a745fa266dd42849c95410775b690e0 -msgid "From `Workflow`" -msgstr "" - -#: ../../src/topics/expressions.md:84 -#: be00ed49197f48ecb7cb244ecc214369 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 -#: 90ad2b27f97b4ca089cf23a073cdf17b -#: 38d062892cb04bc7bbf0b56f263079e1 -msgid "From `steps`" -msgstr "" - -#: ../../src/topics/expressions.md:88 -#: c2d2756d617743b886c67160c2face21 -msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 -#: 8681600183d1429cbd1b15639e1a222f -#: 1d49cd7337004fc38f4e8e9aa4270481 -msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 -#: 24b7f85116cc4d2f904600555aa19b8b -#: c401a68b4f384d3eb13ab3e89a4a7195 -msgid "`expression`" -msgstr "" - -#: ../../src/topics/expressions.md:92 -#: 0e1f9d22d0714bc5b80e420f63b34cff -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:95 -#: 5fed95f16aaf42d4b41c569d9546b7f0 -msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 -#: b539a931f31d4cfe9d72aa5800115fb2 -#: 48e497c024bc4c38a86dd027aaa4fd2d -msgid "`coresMin`" -msgstr "" - -#: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 -#: be638c80121948c99cc9fdb67a5d291e -#: 1fd8fe769ba8497eb8a9520af91ea33e -msgid "`coresMax`" -msgstr "" - -#: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 -#: b5f3ad78a233411c97520c1fffdec18f -#: 7854e46c7fd24afd9c1942808521bee1 -msgid "`ramMin`" -msgstr "" - -#: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 -#: 211bd57896494fca9ea8aa2fc142eea2 -#: 28ec0718d3114bfdaae4524c009da944 -msgid "`ramMax`" -msgstr "" - -#: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 -#: c6a421f7a0214d89958d4c258b58aac8 -#: 07bd0bc74ad74187bdc24c26041467ca -msgid "`tmpdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 -#: 3afc146cde2e47d5b52e62fbd1f37426 -#: 2225f5acb44a4ce0ad16be5c4f6cba48 -msgid "`tmpdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 -#: 9acd61d4d67a4d2c82171a79462fb458 -#: cd7e7fea3b8346268618c31b70581326 -msgid "`outdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:103 -#: ../../src/topics/parameter-references.md:100 -#: 140e449e46a84e3ca1a604176e583f44 -#: 3d8b717d4568458eb53b0b91695b3de8 -msgid "`outdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:104 -#: 76f35653e34b433d8e9fedc6d12ce856 -msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:105 -#: ../../src/topics/parameter-references.md:102 -#: 1a2edf61fda8404689e3c0a7389d7d02 -#: 3bced6d84fa6453195be82dbc6d7ec83 -msgid "`listing`" -msgstr "" - -#: ../../src/topics/expressions.md:106 -#: 0b5aceb6c9d24bd9bfe95cc04fdc61ad -msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/expressions.md:107 -#: ../../src/topics/parameter-references.md:104 -#: 3523cc46c6324fca9053d6b1dd8c7495 -#: 21eee2c1cb6b430486446d223dcca0eb -msgid "`entry`" -msgstr "" - -#: ../../src/topics/expressions.md:108 -#: ../../src/topics/parameter-references.md:105 -#: b4f126415048402ca388c4c63f34ebe5 -#: fdf588cf8cd34d60bfb6cece3ef859e0 -msgid "`entryname`" -msgstr "" - -#: ../../src/topics/expressions.md:109 -#: ../../src/topics/parameter-references.md:106 -#: 1b494245c14e4e22918c43ad9f26cc8d -#: df4d781178f2465b8a421651bdd2f66f -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../src/topics/expressions.md:110 -#: a88008a23ede4ea49ffcaccba7029d31 -msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/expressions.md:111 -#: ../../src/topics/parameter-references.md:108 -#: a256b51f1e944b7d9659b945d8ab05c9 -#: 23bbd631e73147e3af561eb4a14d2d6c -msgid "`envValue`" -msgstr "" - -#: ../../src/topics/expressions.md:116 -#: a446842e26e44781ad10cdaad73bc49d -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" - -#: ../../src/topics/expressions.md:118 -#: 3cc10263ab2f4dbfb6ccb12612b89cf1 -msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." -msgstr "" - -#: ../../src/topics/expressions.md:122 -#: 995f6af5fc244293b34f5d840f01ce1c -msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:128 -#: b556a1d134764505aa25003d79a53e88 -msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." -msgstr "" - -#: ../../src/topics/expressions.md:135 -#: ad23da5452bd46248606f6799ce93db0 -msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:139 -#: c63036ac68344465af6c7756be00b60b -msgid "`hello-world-expressionlib-inline.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:146 -#: 2f7f270b0ac24f2f8df506f5dde72cf7 -msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" -msgstr "" - -#: ../../src/topics/expressions.md:149 -#: f49272e5e4c1491eb59c79d2dfb88a86 -msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:155 -#: 8b50c892d36d4d178ec4268c7c13887d -msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:158 -#: 9d22117a6f5a434593d5144bf824999f -msgid "`custom-functions.js`" -msgstr "" - -#: ../../src/topics/expressions.md:164 -#: 4fbc454a144a466b9dd7ff74903fc5fb -msgid "`hello-world-expressionlib-external.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:171 -#: 281b129a76a24b0a818092acd1038757 -msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:175 -#: 4dda6ca233d54c12b6ddceabae198495 -msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:181 -#: 59d87fecfd7f4438b68e0bcdecdcfb46 -msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." -msgstr "" - -#: ../../src/topics/expressions.md:186 -#: 0f7e33673ad349e5ad41a078032e5806 -msgid "`hello-world-expressionlib.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:193 -#: 77a7141f897048139ef3785b5f870b43 -msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:200 -#: 14ed183bc7e346598921445c0dea11e0 -msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." -msgstr "" - -#: ../../src/topics/file-formats.md:1 -#: 9406d05bf0ed4774af50fd66d24aa299 -msgid "File Formats" -msgstr "" - -#: ../../src/topics/file-formats.md:3 -#: f5a9048ef9e047528c291505ef9a2c12 -msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." -msgstr "" - -#: ../../src/topics/file-formats.md:8 -#: 51e8c5a231eb45fb8c15be49b37a7bff -msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." -msgstr "" - -#: ../../src/topics/file-formats.md:14 -#: 860a6f01ebac45938abd220758fd1109 -msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." -msgstr "" - -#: ../../src/topics/file-formats.md:17 -#: 32155f96d47f4d76998a401aa9e9591f -msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." -msgstr "" - -#: ../../src/topics/file-formats.md:20 -#: a62bbb9251794560ace0e52be3d9ebd3 -msgid "`metadata_example.cwl`" -msgstr "" - -#: ../../src/topics/file-formats.md:26 -#: ../../src/topics/metadata-and-authorship.md:22 -#: e301af8f675444c69cfb6b578c02fdc7 -#: 3da1dec243994409bd764b133d4fc243 -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../src/topics/file-formats.md:32 -#: 82c6efcfb5d5410eb316399b7c4f638e -msgid "Sample Parameter Files" -msgstr "" - -#: ../../src/topics/file-formats.md:34 -#: 29c3d25c657340a1bab7123a166b78c2 -msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." -msgstr "" - -#: ../../src/topics/file-formats.md:39 -#: ef8e7bd7e944429da78474d2fc5e0348 -msgid "`sample.yml`" -msgstr "" - -#: ../../src/topics/file-formats.md:45 -#: 08dd50bc6a5942ec8f3b6c201fc4497f -msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/index.md:1 -#: 78c51215a68f40b280cc21d0e412eacf -msgid "Topics" -msgstr "" - -#: ../../src/topics/inputs.md:1 -#: bb8e2203374a4ae7b833c543ecc563b0 -msgid "Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:3 -#: f34aa1e4d08944c497602b2a35f38a50 -msgid "Essential Input Parameters" -msgstr "" - -#: ../../src/topics/inputs.md:5 -#: 2932972efc94447987b02a7707c62656 -msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/inputs.md:9 -#: 968f4e83c511425d8faf4c8d0f18097e -msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." -msgstr "" - -#: ../../src/topics/inputs.md:13 -#: 2eb89bdbaee04a899a961a7b87f0aef1 -msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." -msgstr "" - -#: ../../src/topics/inputs.md:16 -#: 3781fc7cd22d48bdb5aa4abc0c93b06f -msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "" - -#: ../../src/topics/inputs.md:18 -#: f4af4a85efb243728d2ee783393dce14 -msgid "`inp.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:24 -#: dbf8350f003a46b984b7432160e6def5 -msgid "Create a file called `inp-job.yml`:" -msgstr "" - -#: ../../src/topics/inputs.md:26 -#: db2993fe83814747a52f9db0b2fcc81e -msgid "`inp-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:33 -#: 39fe18bf5d4b4539b2f98e3bf0feea2a -msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" -msgstr "" - -#: ../../src/topics/inputs.md:40 -#: 58e7b0e7d0a149498e846dd2790c0eee -msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." -msgstr "" - -#: ../../src/topics/inputs.md:44 -#: 4b78c5437904492ea3e692372d2fc163 -msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." -msgstr "" - -#: ../../src/topics/inputs.md:47 -#: f2626686125d4ec29fb2338373b54c93 -msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:53 -#: 46327aca33cb49d1ba61149e94884991 -msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:64 -#: 43f2e7020da94f77bce4e1f852ab11f1 -msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" -msgstr "" - -#: ../../src/topics/inputs.md:70 -#: 8342aa3f84624325aff8f7f4de788187 -msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." -msgstr "" - -#: ../../src/topics/inputs.md:83 -#: 2d54f11f99b245e5b2802b984bc024a5 -msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." -msgstr "" - -#: ../../src/topics/inputs.md:95 -#: 83a357dc06b343549876035b03b8c5d1 -msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." -msgstr "" - -#: ../../src/topics/inputs.md:109 -#: 0461538fa12a44c5a9d230a928ae930d -msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." -msgstr "" - -#: ../../src/topics/inputs.md:124 -#: 2b2552958f404447b711d09650d22395 -msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:131 -#: 82c97e60f8634bd6b4d3e88524722412 -msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." -msgstr "" - -#: ../../src/topics/inputs.md:134 -#: 0ae1393a80e94b899023c29f4af6084b -msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." -msgstr "" - -#: ../../src/topics/inputs.md:142 -#: 74339f624bba49d6b68e1dfc4724f673 -msgid "The `baseCommand` field will always appear in the final command line before the parameters." -msgstr "" - -#: ../../src/topics/inputs.md:146 -#: 3a4473864ec04d2e9a0d550b2051f717 -msgid "Array Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:148 -#: 575661b36a2040699956f897bd6cc614 -msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." -msgstr "" - -#: ../../src/topics/inputs.md:154 -#: 3d18a704f5a94e2889e847c32a78aaab -msgid "`array-inputs.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:160 -#: fceca2b53d0646b2ae9f1cf9dbefe2fc -msgid "`array-inputs-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:166 -#: ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 -#: cba49054785b4ec2a7acd3aaa2e165d8 -#: 647c0e302af841d7b1789447281d7344 -#: d23de44d5d5b4bc7b32f3726afa97500 -msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:178 -#: dd867685663f4728b9fbe446a9b14a3d -msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." -msgstr "" - -#: ../../src/topics/inputs.md:185 -#: 67bf2c2cbbc44f6eb870af3a3a852676 -msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." -msgstr "" - -#: ../../src/topics/inputs.md:191 -#: 94d66455bfd04697814495e116176ffe -msgid "Inclusive and Exclusive Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:193 -#: 39a9d3583f29451d8035158c54266ed6 -msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." -msgstr "" - -#: ../../src/topics/inputs.md:198 -#: eba6af5cf8224d198fc04f090362307c -msgid "`record.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:204 -#: b48377cceff342e793e982c9fa2095d3 -msgid "`record-job1.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:215 -#: b64ef70d944c461b8ec7219e14e47795 -msgid "In the first example, you can't provide `itemA` without also providing `itemB`." -msgstr "" - -#: ../../src/topics/inputs.md:217 -#: 73cd08a2226f4cbe99fcde2d3636d640 -msgid "`record-job2.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:233 -#: 3c33bffa2c574ef888b041c1e6735b8e -msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." -msgstr "" - -#: ../../src/topics/inputs.md:236 -#: 23bd067b32724dad9daba1e924757d86 -msgid "`record-job3.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:252 -#: 1be92fc3d0b44ea089273cfcd47318ef -msgid "In the third example, only `itemD` is provided, so it appears on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:255 -#: 3d08125883b74f49bba042ed58d34648 -msgid "Exclusive Input Parameters with Expressions" -msgstr "" - -#: ../../src/topics/inputs.md:257 -#: 7636c7e8b6e04d7089ba1cb10c4c475d -msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." -msgstr "" - -#: ../../src/topics/inputs.md:262 -#: e1c95ce96db043eb86ff9b3ae595017b -msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." -msgstr "" - -#: ../../src/topics/inputs.md:265 -#: e6588c4b8fa64959b2dcac52403a6415 -msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:271 -#: e7f85cb69a5342889525fbb81b44c86c -msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" -msgstr "" - -#: ../../src/topics/inputs.md:280 -#: 71756719e0274300a839b38c8b4ea986 -msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." -msgstr "" - -#: ../../src/topics/inputs.md:289 -#: 88bf75fce3064eaf823b5d88be0ce053 -msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:1 -#: 60374713dea84fff92b89b4ebaa8d7ac -msgid "Metadata and Authorship" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:3 -#: 7616d5ea746f47ac972183150b97e8b0 -msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:13 -#: 0ca022c095334ec4a9fe41cb732e11a1 -msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:16 -#: 1c807f8fd1c540ae8802092fbcec7159 -msgid "`metadata_example2.cwl`" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:28 -#: c51956eb3ece432ea0ed5b676b2f037a -msgid "Extended Example" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:30 -#: 45e6ab3a53b94f5b90136d68c1c0e479 -msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:35 -#: 7e05dc23d6be4428b4a414b3a65c4727 -msgid "`metadata_example3.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:1 -#: 96e7266ef25b429da42337c3582cc201 -msgid "Operations" -msgstr "" - -#: ../../src/topics/operations.md:3 -#: 9cb6959a877f4590bccb977416753410 -msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." -msgstr "" - -#: ../../src/topics/operations.md:7 -#: 7b54a3cd870d4b038dff685064bbca1a -msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" -msgstr "" - -#: ../../src/topics/operations.md:10 -#: 0d661c96ac2d41ee94641a397aa3bdf7 -msgid "`operations.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:16 -#: 94d39b79923a4a65b1a6ce5c464528c6 -msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" -msgstr "" - -#: ../../src/topics/operations.md:24 -#: 56801121f70b4cb2ab6207e254ec8bbf -msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" -msgstr "" - -#: ../../src/topics/operations.md:55 -#: 42418ff882d44c1b9584fb9f7887f744 -msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" -msgstr "" - -#: ../../src/topics/operations.md:58 -#: 1118de96d202444d9bb4db74ebe4792d -msgid "`cwltool` does not know how to run operations" -msgstr "" - -#: ../../src/topics/operations.md:66 -#: aca51d371db84aa79418c79a18310055 -msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." -msgstr "" - -#: ../../src/topics/outputs.md:1 -#: 3473e6d2942e4546a2c1590edeb502f8 -msgid "Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:3 -#: c210ad12f61047b68302e67da9b5dae0 -msgid "Returning Output Files" -msgstr "" - -#: ../../src/topics/outputs.md:5 -#: 1c15cff5a4614d88a62c8d2df97029fc -msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/outputs.md:10 -#: 4beae917368545688c01a4a929685cae -msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." -msgstr "" - -#: ../../src/topics/outputs.md:16 -#: 4f4f63b7107e4dc194760802c4581c2a -msgid "The following example demonstrates how to return a file that has been extracted from a tar file." -msgstr "" - -#: ../../src/topics/outputs.md:19 -#: d942035c4c914ccb9de75836af9761c7 -msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "" - -#: ../../src/topics/outputs.md:21 -#: 0e9064cf55fe43588053d37100634538 -msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" -msgstr "" - -#: ../../src/topics/outputs.md:26 -#: aa1dcfc618e74a53b3c579380e5e1558 -msgid "`tar.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:32 -#: 3ec3f4a2d1c547b18780db17fbff060c -msgid "`tar-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:38 -#: 21e598983ce94d22b9d40a77577a6608 -msgid "Next, create a tar file for the example." -msgstr "" - -#: ../../src/topics/outputs.md:45 -#: 62f79a2c055b455d9626ca5a18d1bd72 -msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/outputs.md:51 -#: 19c2b9b13bcc480aa7474301422faab3 -msgid "The field `outputBinding` describes how to set the value of each output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:62 -#: 17bb520489a74f64b76ddbe2ffedcb5e -msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." -msgstr "" - -#: ../../src/topics/outputs.md:65 -#: 9e2b97aa3bfe4eae8524b325bf2ea3f1 -msgid "Capturing Standard Output" -msgstr "" - -#: ../../src/topics/outputs.md:67 -#: 028c844ef208450f994b3949210ca996 -msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:71 -#: 2b758e44e4be4fdf89a5897385db6c59 -msgid "`stdout.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:89 -#: 16395173b7ee468f85ee8450493504de -msgid "Array Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:91 -#: 51e2e929dadc41a78cea98f779e2e2a3 -msgid "You can also capture multiple output files into an array of files using `glob`." -msgstr "" - -#: ../../src/topics/outputs.md:93 -#: b757d4b151ef46fa96897bf00a0d9ab4 -msgid "`array-outputs.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:99 -#: 2f2f46a81e8946bf8a9b48a5956c82f8 -msgid "`array-outputs-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:112 -#: 75177c797c704385bfa5ce86e03266c9 -msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." -msgstr "" - -#: ../../src/topics/parameter-references.md:1 -#: 4d05d16c3cb74eb291da7586fa859b90 -msgid "Parameter References" -msgstr "" - -#: ../../src/topics/parameter-references.md:3 -#: c115b7ed044346d6a9c4c06306ee82d8 -msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../src/topics/parameter-references.md:13 -#: 8f83261e3e91424b9a3c38280c643f02 -msgid "`tar-param.cwl`" -msgstr "" - -#: ../../src/topics/parameter-references.md:19 -#: 269af269348e4da5b93cb25dcd10374a -msgid "`tar-param-job.yml`" -msgstr "" - -#: ../../src/topics/parameter-references.md:25 -#: c376ab464fec4ee78a33d42dfed5dc1c -msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/parameter-references.md:36 -#: 53d468d14703494699478e6847d82e34 -msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." -msgstr "" - -#: ../../src/topics/parameter-references.md:47 -#: 32bd7abe387e4999a0864f6e6a48e435 -msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." -msgstr "" - -#: ../../src/topics/parameter-references.md:51 -#: 0712e952fe2442daa9ceb0cee79a3ebf -msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." -msgstr "" - -#: ../../src/topics/parameter-references.md:54 -#: ef2b8db0c8d64e41b839b47aae34d0ec -msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." -msgstr "" - -#: ../../src/topics/parameter-references.md:59 -#: f9f45dcc2bcb4fd1a1021d2843137fa3 -msgid "Where are parameter references allowed?" -msgstr "" - -#: ../../src/topics/parameter-references.md:61 -#: 4ffbc016a5344e6e9272793d921e4900 -msgid "You can only use parameter references in certain fields. These are:" -msgstr "" - -#: ../../src/topics/parameter-references.md:63 -#: 7118718b98c5488c9d9a54e5ec84c055 -msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/parameter-references.md:69 -#: 20fe8fa105a84171972722158bafbc0d -msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:72 -#: 836fa2a818854cf9af13d674f5bb859c -msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:74 -#: 5d56e1ac063d48c2b140a72db9f78540 -msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:77 -#: 0166655553ac4d8fb868138936176986 -msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:81 -#: e43fe4a9340b458786c51499c75b5556 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:85 -#: 0ba13966a1364d4e9992b5cfeb6871d1 -msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/parameter-references.md:89 -#: feb8bce610be4a3a92053f2e2e5aab76 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:92 -#: 0f5fd76c57e7412097b4ebdeb074f2fd -msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:101 -#: b645dd17256543b0a42d231171140c95 -msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:103 -#: c8d5743769bd4fee93f77a52ba318883 -msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/parameter-references.md:107 -#: af6cbb89b7a84bf78b7443b6746484fe -msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/requirements-and-hints.md:5 -#: ad9394b163a94340975a66ea2bba7094 -msgid "Requirements and Hints" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:1 -#: 677bce1f24f449beb2bac5ed8469f624 -msgid "Specifying Software Requirements" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:3 -#: 4c0d14a24b354feabf4b6ad4852f9543 -msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:13 -#: d407e5c9aa9043b0b6ab234348467db0 -msgid "In this example, the software requirement being described is InterProScan version 5.21-60." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:25 -#: f06b60c926204ca88b4355803f1b7b11 -msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:29 -#: 0a7c19b054d2400abd327736b6829670 -msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 -#: cd1773f336544b3688bc76c28e9d1f79 -msgid "Staging Input Files" -msgstr "" - -#: ../../src/topics/staging-input-files.md:3 -#: 6b7bbca601f04f7183bc75988bd6db13 -msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." -msgstr "" - -#: ../../src/topics/staging-input-files.md:9 -#: 069d1dd1f03f4cd79e44f2dcd890b531 -msgid "`linkfile.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:1 -#: 4924b1a69a5f48b0aa6af943b40ffc68 -msgid "Troubleshooting" -msgstr "" - -#: ../../src/topics/troubleshooting.md:3 -#: e100d8d8f23c4d6996ac59c5ad68acf0 -msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." -msgstr "" - -#: ../../src/topics/troubleshooting.md:6 -#: a87dfd0dc0274ff4b34354678f2d49d2 -msgid "Run `cwltool` with `cachedir`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:8 -#: 772078ff701a477cae9acb8dda16ef1f -msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." -msgstr "" - -#: ../../src/topics/troubleshooting.md:14 -#: d2d67048e93e40c4820b805f1ba28cc9 -msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." -msgstr "" - -#: ../../src/topics/troubleshooting.md:20 -#: 580477152be041a8ae5c5f546ecbf21d -msgid "`troubleshooting-wf1.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:27 -#: 05f8faea082b4fb9b9c22b8eff7eb356 -msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" -msgstr "" - -#: ../../src/topics/troubleshooting.md:35 -#: 4c107fb18fb34c2dba7743118c51e8c8 -msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" -msgstr "" - -#: ../../src/topics/troubleshooting.md:44 -#: 729ea19aa03b49bdadccc6e6f0d2e7d9 -msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." -msgstr "" - -#: ../../src/topics/troubleshooting.md:48 -#: e849cda9fb1d4a48b5b1f9a4e44213a1 -msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." -msgstr "" - -#: ../../src/topics/troubleshooting.md:59 -#: bfc20f529d2d4797b87c63c7b2c05e91 -msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." -msgstr "" - -#: ../../src/topics/using-containers.md:1 -#: 761a900275a044f28ddcebe509a4637a -msgid "Using Containers" -msgstr "" - -#: ../../src/topics/using-containers.md:3 -#: 59af21cf1ee848e993563ad47f7bb248 -msgid "Running Tools Inside Docker" -msgstr "" - -#: ../../src/topics/using-containers.md:5 -#: d711ce1ccdcf427aba25a2ab3d11165d -msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 -#: eaaaa01fe0894f479a42a9c3ce199819 -msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." -msgstr "" - -#: ../../src/topics/using-containers.md:18 -#: 92489f186e3f449295b0dc864ebf17f7 -msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." -msgstr "" - -#: ../../src/topics/using-containers.md:21 -#: 1360c3a2d43b48f3b3e1153bb26b3f30 -msgid "`docker.cwl`" -msgstr "" - -#: ../../src/topics/using-containers.md:27 -#: 2e993e21a3624910b4282bd088694fec -msgid "`docker-job.yml`" -msgstr "" - -#: ../../src/topics/using-containers.md:33 -#: df5b4b041dc944be8580e43012339168 -msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 -#: 92ac2766d118428ea148094c022a8b0d -msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." -msgstr "" - -#: ../../src/topics/using-containers.md:52 -#: e4ddaca03eb449eabbf2d2fce752c367 -msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/using-containers.md:55 -#: 0bc50411a4b748d8864305070d11a304 -msgid "`hello.js`" -msgstr "" - -#: ../../src/topics/using-containers.md:69 -#: 74453227279a46cea3644f3ca7df61b9 -msgid "Notice the CWL runner has constructed a Docker command line to run the script." -msgstr "" - -#: ../../src/topics/using-containers.md:72 -#: 75ce3269886645eda46a6575fca186eb -msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." -msgstr "" - -#: ../../src/topics/workflows.md:1 -#: 1e7e5b46017a476a80d57ab7eb614758 -msgid "Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:3 -#: 1ee41e983ca14a959caa199b1ce12700 -msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." -msgstr "" - -#: ../../src/topics/workflows.md:13 -#: 070e6a00d09e4675b89afec5d066aec1 -msgid "CWL workflow." -msgstr "" - -#: ../../src/topics/workflows.md:41 -#: fd37ebe3aad9473891cc764a47363f8e -msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." -msgstr "" - -#: ../../src/topics/workflows.md:51 -#: 85176099018c4ae19bed1261e92e6e92 -msgid "`echo-uppercase.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:81 -#: 952e9a347f444ef496fa0cdf00160ffd -msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" -msgstr "" - -#: ../../src/topics/workflows.md:91 -#: 2b5ad46ca3024ce1b37e1c92a820aabf -msgid "`echo-uppercase-single-file.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:150 -#: ea17d17cd08b4c40a842598c8521af56 -msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." -msgstr "" - -#: ../../src/topics/workflows.md:160 -#: 6e5f1266974d4a32995aaa69fbbfd648 -msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." -msgstr "" - -#: ../../src/topics/workflows.md:165 -#: 20be823f70c348bbaad6bfc8b88201a9 -msgid "Writing Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:167 -#: 02311e5310cb49d19bf2998513f73124 -msgid "This workflow extracts a java source file from a tar file and then compiles it." -msgstr "" - -#: ../../src/topics/workflows.md:170 -#: ca6e4a3fe04145a9a21cc43cc53a07bc -msgid "`1st-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:179 -#: ../../src/topics/workflows.md:180 -#: 75452467551a46a2b2b3685f1a4aae0d -#: 93efa8e941a7427f949afc794ed16e75 -msgid "Visualization of 1st-workflow.cwl" -msgstr "" - -#: ../../src/topics/workflows.md:180 -#: 39beed65cb114bd78c79aa4a5d6f4398 -msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" -msgstr "" - -#: ../../src/topics/workflows.md:183 -#: dd880d0589fe45dbaf9b7d799402f158 -msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" -msgstr "" - -#: ../../src/topics/workflows.md:185 -#: 671d0bd54bb147518c35f0844a76c61d -msgid "`1st-workflow-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:191 -#: 66de58a51b034f6a8d5dbe742046f817 -msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." -msgstr "" - -#: ../../src/topics/workflows.md:205 -#: 564e68d58e364715aa72183cb16b3d72 -msgid "What's going on here? Let's break it down:" -msgstr "" - -#: ../../src/topics/workflows.md:212 -#: 558739ceb3fe40de8ea87ff1e7d3fe9d -msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." -msgstr "" - -#: ../../src/topics/workflows.md:221 -#: fdc601ee1aa54e1f84cd00eed2e44e52 -msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." -msgstr "" - -#: ../../src/topics/workflows.md:233 -#: e4f4a76cee96473d9da3bc1c9e35324a -msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." -msgstr "" - -#: ../../src/topics/workflows.md:248 -#: d524ed5f1e964688af9d74eef8e46e04 -msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:256 -#: c646e4714d78437fb450127b119fbd70 -msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." -msgstr "" - -#: ../../src/topics/workflows.md:261 -#: 8351ddfd726c40159d81c017ef221606 -msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." -msgstr "" - -#: ../../src/topics/workflows.md:267 -#: 456794c7274f4654b54aae8d4073a2df -msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." -msgstr "" - -#: ../../src/topics/workflows.md:278 -#: 6485e8d6814144d1bcbe66bfe4fcbdb9 -msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." -msgstr "" - -#: ../../src/topics/workflows.md:285 -#: a2b9e47cc923466f8bd2fbc4b33fc4fa -msgid "Nested Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:287 -#: 698cc640807247fd8d512c59ce32ee48 -msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" -msgstr "" - -#: ../../src/topics/workflows.md:297 -#: dd658e10da624918b7dec1ea18bbf432 -msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:300 -#: f6bd95a4fbc44ffdbfec7fcac90f6bb6 -msgid "`nestedworkflows.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:309 -#: ac7b02a71d3544848d4fb539b2a4f115 -msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 -#: 4380dbd066a44102a71c7e42ca7de8d8 -msgid "\"Visualization \"Visualization" -msgstr "" - -#: ../../src/topics/workflows.md:322 -#: da946c9d59f44fb995daa6aadc44031d -msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." -msgstr "" - -#: ../../src/topics/workflows.md:336 -#: 7c73bc555f604afd8491c1619d6905eb -msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." -msgstr "" - -#: ../../src/topics/workflows.md:341 -#: e79ce424410e4682881fe14326955a14 -msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." -msgstr "" - -#: ../../src/topics/workflows.md:347 -#: be8d2b89052e4f9d96ff2bf15526e229 -msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." -msgstr "" - -#: ../../src/topics/workflows.md:366 -#: 967b064ec4284d0aaf374509915497e1 -msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" -msgstr "" - -#: ../../src/topics/workflows.md:383 -#: 02d667b922264f8e8021844df0085578 -msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." -msgstr "" - -#: ../../src/topics/workflows.md:389 -#: db8734e07541495188d9ee97eaaaeff3 -msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." -msgstr "" - -#: ../../src/topics/workflows.md:394 -#: 22542da60ac24403827e2e2a14595770 -msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." -msgstr "" - -#: ../../src/topics/workflows.md:398 -#: d10f35716f9c4b878da0f2b4ff3d44aa -msgid "Scattering Steps" -msgstr "" - -#: ../../src/topics/workflows.md:400 -#: 1fd555d1f8ca499ead8d5601eb62266a -msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." -msgstr "" - -#: ../../src/topics/workflows.md:411 -#: f5fc85accf8c4bb9bc701ba0b4ee2e21 -msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:415 -#: e69cb5e87f4b4670abbc1606197d804c -msgid "`scatter-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:421 -#: 15d763c45a2749a8926b1f965db9d97f -msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" -msgstr "" - -#: ../../src/topics/workflows.md:429 -#: c2aac63fc0c347d9833d253039000fa3 -msgid "First of all, notice that the main workflow level input here requires an array of strings." -msgstr "" - -#: ../../src/topics/workflows.md:441 -#: 06a23beb753c4a97b302943f59128d78 -msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." -msgstr "" - -#: ../../src/topics/workflows.md:445 -#: 45985434cfe9438cb558075e1fd73809 -msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" -msgstr "" - -#: ../../src/topics/workflows.md:450 -#: e92da36d865142289b11d245221ff8d4 -msgid "Using the following input file:" -msgstr "" - -#: ../../src/topics/workflows.md:452 -#: 3ed7a2b9f77b4eadae3bf6e4a98d14b9 -msgid "`scatter-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:458 -#: fd66c4fb9c2a4beea0ed5ed8874fcd61 -msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" -msgstr "" - -#: ../../src/topics/workflows.md:466 -#: 65944dc8b32a46a4beb73dbdebb7b01a -msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" -msgstr "" - -#: ../../src/topics/workflows.md:469 -#: 6250fe161ab0421b8799040b79ce695a -msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" -msgstr "" - -#: ../../src/topics/workflows.md:472 -#: cc40c0f1ade34ab3b400a02b59b7ba01 -msgid "`hello_world_to_stdout.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:480 -#: 29f53a5d64fa498bad0dbe94b238fd97 -msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" -msgstr "" - -#: ../../src/topics/workflows.md:483 -#: 037fccb419bc4e9f839c665ae31e28ee -msgid "`wc-tool.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:489 -#: fdd4bec90c484a618ed8e4d1199deff8 -msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" -msgstr "" - -#: ../../src/topics/workflows.md:491 -#: 11afb584f37947358963f6510935c5d5 -msgid "`scatter-two-steps.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:497 -#: a77e0bfb589c40b6a61a9ca559961a7c -msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 -#: 3f4aa12588204fe5b33db590a9446283 -msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" -msgstr "" - -#: ../../src/topics/workflows.md:513 -#: 640c67f3bcd740c59f90c361024acbcc -msgid "`scatter-nested-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:519 -#: 8c4d30cbbea146a584731d164d4ad9ef -msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:522 -#: 5d0fd4f8b58e4a8e8f46902e64e6556b -msgid "Conditional Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:524 -#: e98ab273645340f9a1446183a642e79e -msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." -msgstr "" - -#: ../../src/topics/workflows.md:527 -#: 37a83ed92d9e44689cfd3a31c2785418 -msgid "`conditional-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:566 -#: 7cebef0a9e1444149b1dc58d30f6c10e -msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." -msgstr "" - -#: ../../src/topics/workflows.md:573 -#: 0cd2bd98918b4622bc586d50f1ce1fa4 -msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." -msgstr "" - -#: ../../src/topics/workflows.md:587 -#: 92458de979564d19a634bb8d3bf6f586 -msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." -msgstr "" - -#: ../../src/topics/workflows.md:607 -#: d4ee6cc8903f4e6992439ca2586246ed -msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." -msgstr "" - -#: ../../src/topics/workflows.md:627 -#: 62b438c4ed8a409f96974f3d59cc5854 -msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." -msgstr "" - -#: ../../src/topics/yaml-guide.md:1 -#: f0f288aeae4f4649ba3615437b531e97 -msgid "YAML Guide" -msgstr "" - -#: ../../src/topics/yaml-guide.md:6 -#: f35023cb05504d1db0cbee41c4e5f371 -msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." -msgstr "" - -#: ../../src/topics/yaml-guide.md:13 -#: 01564f1d2038489685160f03db92085f -msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" - -#: ../../src/topics/yaml-guide.md:16 -#: ad662dce1e4149728b8e17f74d8f975f -msgid "Contents" -msgstr "" - -#: ../../src/topics/yaml-guide.md:18 -#: 4f6a57f34f094418b7c13aa07eef95c7 -msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:19 -#: 373a6c24de9144e69f37418d6ce8857d -msgid "[Comments](#comments)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:20 -#: f804a8493c8e40178772d94bdc45b43e -msgid "[Maps](#maps)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:21 -#: b3c504b8ab1a42788ef4e3339d27b0dc -msgid "[Arrays](#arrays)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:22 -#: 2c2681fe72e24a5d8d98f0aa8e8c56a2 -msgid "[JSON Style](#json-style)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:24 -#: 571e5c13552c4381bb6de53c02fe5f43 -msgid "Key-Value Pairs" -msgstr "" - -#: ../../src/topics/yaml-guide.md:26 -#: fd789f444d9a4061b4fc61bac70353bb -msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:42 -#: 2cef838551994b078e460c63214517f9 -msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." -msgstr "" - -#: ../../src/topics/yaml-guide.md:51 -#: 2a3a8a553d3c455e9288f63b9a02898d -msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." -msgstr "" - -#: ../../src/topics/yaml-guide.md:61 -#: b0b8def4623a4018b1ac913a9256c0a2 -msgid "Comments" -msgstr "" - -#: ../../src/topics/yaml-guide.md:63 -#: 3f0d4346f0104cc08c059eed9ab4b3a9 -msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:76 -#: 22e0ac963278414d8141ce5ce4031029 -msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" -msgstr "" - -#: ../../src/topics/yaml-guide.md:79 -#: 49cad54646d04adc8e5ac9f0f3c8f895 -msgid "Maps" -msgstr "" - -#: ../../src/topics/yaml-guide.md:81 -#: c8776a4511b24f46bbe0a34d52cf3c8b -msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:104 -#: 401b053bd08a4286b9059cb6ebf8d679 -msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." -msgstr "" - -#: ../../src/topics/yaml-guide.md:127 -#: 8d48a277f37f458f88c54f362534d7b5 -msgid "Arrays" -msgstr "" - -#: ../../src/topics/yaml-guide.md:129 -#: de90253a11f24f29a4a57348b4f60941 -msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:146 -#: 1e20968f957441c58cabfbc46c21e8ca -msgid "and a more complex example combining maps and arrays:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:167 -#: 4cf2e158afb348d7b3fd6274fe888129 -msgid "JSON Style" -msgstr "" - -#: ../../src/topics/yaml-guide.md:169 -#: 44c5c010c97a40068a6b930949dcd8cf -msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:177 -#: c6277b2a7a934f81a91e406ef317a1fb -msgid "and:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:184 -#: 8b3ece04170c447e9b5a8f76374c4c23 -msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." -msgstr "" - -#: ../../src/topics/yaml-guide.md:194 -#: 6b952b7369b447bdb0bf1e9ff8540194 -msgid "Reference" -msgstr "" - -#: ../../src/topics/yaml-guide.md:196 -#: a6024fb7ce664896a6858d5ea3562fb7 -msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/tutorials.po b/locales/pt/LC_MESSAGES/tutorials.po deleted file mode 100644 index f893e551..00000000 --- a/locales/pt/LC_MESSAGES/tutorials.po +++ /dev/null @@ -1,57 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/tutorials.md:1 -#: d32522e2993f4b48a789f46537fa5ebf -msgid "Tutorials" -msgstr "" - -#: ../../src/tutorials.md:5 -#: 63a51dccb29045fd8f78d5e396c6e050 -msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." -msgstr "" - -#: ../../src/tutorials.md:7 -#: cb5f8748a5544be2835467ab07eb7a1c -msgid "Beginner Tutorials" -msgstr "" - -#: ../../src/tutorials.md:9 -#: 685d0cb2faa04703bcef408ecc2b92f4 -msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" -msgstr "" - -#: ../../src/tutorials.md:11 -#: 20f45705145d45fc8420c4119b06a49f -msgid "Advanced Tutorials" -msgstr "" - -#: ../../src/tutorials.md:13 -#: 2bccd19d542d4458a1ba8616236f1840 -msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" - -#: ../../src/tutorials.md:15 -#: c491c73e4c00476980438ffc79c6e4d3 -msgid "Bioinformatics Tutorials" -msgstr "" - -#: ../../src/tutorials.md:17 -#: b8485449206542e097584eca7363c8ce -msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..3584ce39 --- /dev/null +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -0,0 +1,3820 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. +# +#, fuzzy +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"PO-Revision-Date: 2023-01-25 13:37+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Portuguese \n" +"Language: pt\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.16-dev\n" + +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "Licenças" + +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." +msgstr "" +"Todo o material instrucional do projeto Common Workflow Language e " +"alterações na estrutura também são disponibilizados sob a [licença Creative " +"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " +"humanos de (e não um substituto para) o [texto legal completo da licença CC " +"BY 4.0][cc-by-legal]." + +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "Você tem o direito de:" + +#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" +"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " +"formato" + +#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" + +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "para qualquer fim, mesmo que comercial." + +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" +msgstr "" +"O licenciante não pode revogar estes direitos desde que você respeite os " +"termos da licença." + +#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." +msgstr "" +"Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " +"trabalho deriva de um trabalho que é «Copyright © The Common Workflow " +"Language project», e, quando prático, criar uma ligação para https://www." +"commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " +"se foram feitas alterações. Você pode fazê-lo de qualquer forma razoável, " +"mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " +"uso." + +#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" +msgstr "" +"**Sem restrições adicionais**---Você não pode aplicar termos jurídicos ou " +"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " +"algo que a licença permita. Com o entendimento de que:" + +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." +msgstr "" +"Não tem de cumprir com os termos da licença relativamente a elementos do " +"material que estejam no domínio público ou cuja utilização seja permitida " +"por uma exceção ou limitação que seja aplicável." + +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." +msgstr "" +"Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " +"autorizações necessárias para o uso pretendido. Por exemplo, outros " +"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " +"podem limitar o uso do material." + +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "Software" + +#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" +"Salvo indicação em contrário, os programas de exemplo e outro software " +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a [" +"licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." + +#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 +#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 +#: eab02dc13915490bb3c9ba744d78b6a7 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +msgid "" +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +msgid "" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +msgid "" +"The first method involves adding the folder containing your scripts to " +"the `PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +msgid "" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." +msgstr "" + +#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +msgid "" +"The second method involves including an input of `type: File` in the " +"script itself:" +msgstr "" + +#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +msgid "" +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +msgid "" +"Using " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +msgid "" +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." +msgstr "" + +#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." +msgstr "" + +#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +msgid "" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" +msgstr "" + +#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +msgid "" +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +msgid "" +"For example, the filename `a space is here.txt` includes 3 space " +"characters." +msgstr "" + +#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +msgid "" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +msgid "" +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." +msgstr "" + +#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +msgid "" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +msgid "" +"This guide will introduce you to writing workflows using the [Common " +"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " +"guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +msgid "" +"If you find that something is missing from this guide, or if you would " +"like to provide other feedback, file an Issue on the [project repository " +"for this guide][repo]. You can also suggest changes directly in a Pull " +"Request by clicking the \"Edit this page\" button at the right sidebar of" +" each page." +msgstr "" + +#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +msgid "" +"If you are a beginner user get started with the " +"[Introduction](/introduction/index.md) section. For advanced users the " +"subsections of the [Topics](/topics/index.md) have detailed information " +"about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +msgid "" +"The Table of Contents is displayed at the top menu and also on the left " +"sidebar. It also appears further down this page but with links to " +"subsections. The right sidebar contains links to the sections of each " +"page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +msgid "" +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "" +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "" +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "" +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "" +"`InitialWorkDirRequirement` - controls staging files in the input " +"directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "" +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "" +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows support the creation of FAIR data " +"and adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 +#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "" +"The CWL Specification page in the CWL website: " +"" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "" +"The list of Implementations in the CWL website: " +"" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +msgid "" +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +msgid "" +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +msgid "" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "" +"If you are using Windows, you will have to install the [Windows Subsystem" +" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " +"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" +"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " +"details on installing WSL2. Your operating system also needs internet " +"access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +msgid "" +"`cwltool` can be installed with `pip`. We recommend using a virtual " +"environment like `venv` or `conda`. The following commands will create " +"and activate a Python virtual environment using the `venv` module, and " +"install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +msgid "" +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool#install) for other ways to install `cwltool` with `apt` " +"and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +msgid "" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +msgid "" +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env ` rather than" +" using a hard-coded location, since `/usr/bin/env ` looks for" +" the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " +"" +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +msgid "" +"cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +msgid "" +"The CWL community also maintains a list of editors and viewers: " +"" +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: " +"." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models " +"with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for " +"pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +msgid "" +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "" +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +msgid "" +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +msgid "" +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +msgid "" +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "" +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "" +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "" +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +msgid "" +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "" +"For more examples of providing metadata within CWL descriptions, see " +"[the Metadata and Authorship section of this User Guide](../topics" +"/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +msgid "" +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"`SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "" +"Each `CommandLineTool` description should focus on a single operation " +"only, even if the (sub)command is capable of more. Don't overcomplicate " +"your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "" +"Custom types should be defined with one external YAML per type definition" +" for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +msgid "" +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +msgid "" +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +msgid "" +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +msgid "" +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. If a command-line tool is written manually in CWL v1.1+, there is" +" a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " +"Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "" +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 +#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "" +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 +#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f +#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 +#: f924d65fed0c4cb5b0a019b084a8b535 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +msgid "" +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +msgid "" +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +msgid "" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +msgid "" +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +msgid "" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +msgid "" +"Note also that the author of this CWL description has also included " +"`ResourceRequirement`s, specifying the minimum amount of RAM and number " +"of cores required for the tool to run successfully, as well as details of" +" the version of the software that the description was written for and " +"other useful metadata. These features are discussed further in other " +"chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "" +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +msgid "" +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +msgid "" +"We had to use an `InlineJavascriptRequirement` as our expression contains" +" a JavaScript call in `.toUpperCase()`. This means to tools using the " +"expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +msgid "" +"If you need to manipulate input parameters, include the requirement " +"`InlineJavascriptRequirement` and then anywhere a parameter reference is " +"legal you can provide a fragment of Javascript that will be evaluated by " +"the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "" +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +msgid "" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 +#: 1acb064f7a4a482aa0174bdc847c6382 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e +#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 +#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +msgid "" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc +#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd +#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 +#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 +#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d +#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f +#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c +#: f760465a49d64d4c8468ad9c4fea62b1 +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +msgid "" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +msgid "" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b +#: d555a3d991e344a5a8e1289168d7c6d1 +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c +#: e9fa9430535c424fa3e8be5d460d2ba4 +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c +#: b0290d1a477b48119e17cf1fed9d6dff +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 +#: e1cde4aa32c041238ed2596173c6d824 +msgid "" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf +#: c2a92d3eca7f4ee39cec649170eeea53 +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +msgid "" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 +#: 718ceee9973240ec9c100977bbcc8921 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 +#: c07ab08eb75d4528949c56a3d7c12b28 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +msgid "" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +msgid "" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +msgid "" +"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" +" attribute that allows users to load external JavaScript files, or to " +"provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +msgid "" +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +msgid "" +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +msgid "" +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +msgid "" +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +msgid "" +"Tools and workflows can take `File` types as input and produce them as " +"output. We also recommend indicating the format for `File` types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +msgid "" +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +msgid "" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +msgid "" +"Available primitive types are *string*, *int*, *long*, *float*, *double*," +" and *null*; complex types are *array* and *record*; in addition there " +"are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "" +"The field `inputBinding` is optional and indicates whether and how the " +"input parameter should appear on the tool's command line. If " +"`inputBinding` is missing, the parameter does not appear on the command " +"line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +msgid "" +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +msgid "" +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +msgid "" +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +msgid "" +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "" +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +msgid "" +"The `baseCommand` field will always appear in the final command line " +"before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 +#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d +msgid "" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +msgid "" +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +msgid "" +"In the third example, only `itemD` is provided, so it appears on the " +"command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +msgid "" +"If you use exclusive input parameters combined with expressions, you need" +" to be aware that the `inputs` JavaScript object will contain one of the " +"exclusive input values. This means that you might need to use an **or** " +"boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as “fasta” (one of the values of the enum), " +"your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +msgid "" +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to a `null` value, which does not match the expected type " +"for the output field (a `string`), resulting in failure when running your" +" workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +msgid "" +"To correct it, you must remember to use an or operator in your JavaScript" +" expression when using exclusive parameters, or any parameter that allows" +" `null`. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value if none was " +"provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "" +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "" +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +msgid "" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +msgid "" +"The `uppercase` step of the workflow is an operation. It can be used like" +" a command line tool or an expression. You can also plot it with the CWL " +"Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx Graphviz directive (this" +" user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +msgid "" +"If you try running it with `cwltool`, the command will fail since " +"`cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +msgid "" +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string we can use an " +"_array of strings_. The first element is the command to run, and any " +"subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +msgid "" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +msgid "" +"The field `outputBinding` describes how to set the value of each output " +"parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +msgid "" +"The `glob` field consists of the name of a file in the output directory. " +"If you don't know name of the file in advance, you can use a wildcard " +"pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "" +"To capture a tool's standard output stream, add the `stdout` field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +msgid "" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "" +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +msgid "" +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +msgid "" +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +msgid "" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +msgid "" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +msgid "" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +msgid "" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +msgid "" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +msgid "" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a `SoftwareRequirement` field in the `hints` section. This may " +"also help to avoid confusion about which version of a tool the " +"description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "" +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a `SoftwareRequirement`, " +"search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "" +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use `InitialWorkDirRequirement` to stage input files into" +" the output directory. In this example, we use a JavaScript expression to" +" extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +msgid "" +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +msgid "" +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +msgid "" +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the " +"container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +msgid "" +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that " +"is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +msgid "" +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier " +"examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +msgid "" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "" +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +msgid "" +"This workflow extracts a java source file from a tar file and then " +"compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +msgid "" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a " +"workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +msgid "" +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +msgid "" +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +msgid "" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +msgid "" +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +msgid "" +" \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +msgid "" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +msgid "" +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +msgid "" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +msgid "" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +msgid "" +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +msgid "" +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +msgid "" +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +msgid "" +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +msgid "" +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +msgid "" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +msgid "" +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to " +"the list." +msgstr "" + +#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +msgid "" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" + diff --git a/locales/setup.pot b/locales/setup.pot deleted file mode 100644 index 961f7927..00000000 --- a/locales/setup.pot +++ /dev/null @@ -1,27 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/setup.md:5 -#: 8395100e210f4ac5a87cc2aeb3d7067c -msgid "This page has moved" -msgstr "" - -#: ../../src/setup.md:9 -#: 1e47ac8e393541d19b9499e307fe69e7 -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." -msgstr "" diff --git a/locales/sphinx.pot b/locales/sphinx.pot index f8448bb7..e7779e0d 100644 --- a/locales/sphinx.pot +++ b/locales/sphinx.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -17,11 +17,11 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" #: ../../src/_templates/sidebar-nav-bs.html:1 -#: 1c343f1abfaa4e14b7f1b645c77c595c +#: d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" msgstr "" #: ../../src/_templates/sidebar-nav-bs.html:3 -#: 3c55f014feb3477889c4df5a158a8804 +#: 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" msgstr "" diff --git a/locales/tutorials.pot b/locales/tutorials.pot deleted file mode 100644 index f989fb64..00000000 --- a/locales/tutorials.pot +++ /dev/null @@ -1,57 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -#, fuzzy -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/tutorials.md:1 -#: b963a4be60544dec9a0c34e04aa43371 -msgid "Tutorials" -msgstr "" - -#: ../../src/tutorials.md:5 -#: f9246ba9313948f7b8547822aae2305d -msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." -msgstr "" - -#: ../../src/tutorials.md:7 -#: 9a3d1f4c2d0b438188e84b692f831dc5 -msgid "Beginner Tutorials" -msgstr "" - -#: ../../src/tutorials.md:9 -#: 3c4d6087706b4c90ac69005cebed9adc -msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" -msgstr "" - -#: ../../src/tutorials.md:11 -#: 585908b83f854dd7a28715a4a0f6b1c4 -msgid "Advanced Tutorials" -msgstr "" - -#: ../../src/tutorials.md:13 -#: 8934504b3c924a7d812014c344d58dce -msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" - -#: ../../src/tutorials.md:15 -#: 0c6b1dbd9f464c698322783bd55d6d6c -msgid "Bioinformatics Tutorials" -msgstr "" - -#: ../../src/tutorials.md:17 -#: 9a767964b3cb4f619f0b7a7d5d08a97d -msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" diff --git a/locales/topics.pot b/locales/user_guide.pot similarity index 57% rename from locales/topics.pot rename to locales/user_guide.pot index 1f40bff2..0a669946 100644 --- a/locales/topics.pot +++ b/locales/user_guide.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:44+0100\n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -16,274 +16,1273 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" + #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 1a006f1604c0405aaa4b93e41edc5184 +#: 9c87c76c690948ac8e18088a0fffe679 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: b61b4d7ed53a436486c1429987a2a21b +#: ad00d94d4fb64bbdac356e64dd3803b9 msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 1bf9e65f1cc249ee93656a53ddd354ca +#: d8110ed19da94ad8a9f56e7006c4a2cf msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 3329dc69c32f4b9092b196d79ae5d0c1 +#: a74935dc31664e979ca8f90a6a4ba53c msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 -#: a003a3d1de0e4dfe8c777905e55fb9fe -#: e2dc24c683054cd785326de2c3f3f136 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: aca6a0cd24a2411c8cfb1ad392f6d315 +#: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: bcf37e403eb041269e351d7f98a19587 +#: 9643449da1da46d7861866dce490cbcb msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: c5f68f8a9f34445ebcbd5783f96cb046 +#: 713666580a0a4466b4ba6e3eb2b54f0a msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: 4eca90c659ba43158db373d36ee681df +#: d50574c8b9694f83aa376d39b9a6fcd6 msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." msgstr "" #: ../../src/topics/best-practices.md:1 -#: 7474eeb128624dc4b1e980dbd0f04ca4 +#: 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "" #: ../../src/topics/best-practices.md:3 -#: 0c520e5add334609a1afddc559abe19a +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." msgstr "" #: ../../src/topics/best-practices.md:8 -#: 125a69207077425fa54f346abc45342d +#: 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" #: ../../src/topics/best-practices.md:11 -#: 6ca38a04844c403b836942b2f2f1e1e2 +#: 4dee8504a8e5496081dadc386ab45540 msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." msgstr "" #: ../../src/topics/best-practices.md:20 -#: 1da05be0d97d429a84085459ebae54cf +#: 674c238b25e240eda05e22e399f2f78f msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." msgstr "" #: ../../src/topics/best-practices.md:26 -#: fb1b2a8c54f34d78ac61dd4b5ffd9063 +#: b651f80f47b4442fbf29454a233697fc msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" msgstr "" #: ../../src/topics/best-practices.md:28 -#: a8b1b5caf9904fc5b9eef8c110474b84 +#: 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" #: ../../src/topics/best-practices.md:37 -#: 42a5a8cb3b284549aabb817b73ce5810 +#: 3a87a0fb2a364e3da5aaa4017e430b19 msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." msgstr "" #: ../../src/topics/best-practices.md:40 -#: eddd878eb0324851997de2a69bcbb43f +#: ecf2b9c0b1664afe9c4e180610610021 msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." msgstr "" #: ../../src/topics/best-practices.md:44 -#: b05c8ff667174f6798feb811cdd3c41d +#: e24cb13d98014e558b6a6946758359e0 msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:47 -#: 9dc16d1a6b0546cead6967f5e9b1526a +#: f2b14a92374e449d9fb1e8c86ae0dd61 msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" #: ../../src/topics/best-practices.md:50 -#: b8bf85e8523a4553a58face698aa863b +#: 928e3df7ca3e479ca6474a8e72cf36eb msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" #: ../../src/topics/best-practices.md:55 -#: 6fb9a1a2ffe14f39b01af8736a9698eb +#: d355f035676446c88b028f327aeb4829 msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:58 -#: 0a935aa93e554c0987af7349f94ccd3a +#: 339b852df24242189d6efcd2898a3396 msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." msgstr "" #: ../../src/topics/best-practices.md:66 -#: cadb5982a13e4621807ad976cf9b1524 +#: 3ef57e6862f240bebcf193a52397af0a msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." msgstr "" #: ../../src/topics/best-practices.md:69 -#: bd7ab2cc6234458181e9b99938eba824 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." msgstr "" #: ../../src/topics/best-practices.md:73 -#: 7beb72d7dd5a405f9be8b6fb6a310f10 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 msgid "Custom types should be defined with one external YAML per type definition for re-use." msgstr "" #: ../../src/topics/best-practices.md:76 -#: e5942c4d4b4d4e1a8c0e9ed3da80960e +#: c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" #: ../../src/topics/best-practices.md:78 -#: 5a5dbc9b9d2242ba8d15ecf39123694b +#: fae385da16aa443da996fa23ac03d6ae msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." msgstr "" #: ../../src/topics/best-practices.md:82 -#: dd3016d33b7d4340a09a7c8e5aec4f0b +#: 92430be71ecc40e18bbbb80d5576c613 msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." msgstr "" #: ../../src/topics/best-practices.md:85 -#: 45d110a660b348f58a1107476df18cee +#: 387d83db81024f65aa9a890c2d07874a msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." msgstr "" #: ../../src/topics/best-practices.md:90 -#: 97a5b141592e4415aa4acef4f6228045 +#: d8e2280a75a74916a1630afaa2fe2ae3 msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." msgstr "" #: ../../src/topics/best-practices.md:93 -#: 85f624f8879348e8bb368ec2749925bf +#: f1c1340f9745458980e0fbd641738687 msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." msgstr "" #: ../../src/topics/best-practices.md:97 -#: 20a851dae87941c7975173ed9cd1e360 +#: 5424e5472c3d466fa2a3d2022c6cb475 msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." msgstr "" #: ../../src/topics/command-line-tool.md:1 -#: bb19e1b689564a11bb9e72d5f82cf3d9 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" #: ../../src/topics/command-line-tool.md:3 -#: b14199173add4585be62c4e8278b49f4 +#: 12f57b2ba76b492abe1816e06bfb1417 msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." msgstr "" #: ../../src/topics/command-line-tool.md:8 -#: 9e883f18843a41d7b10102bc11655839 +#: e1f657a46ce94a0d83671540e2cc2dab msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." msgstr "" #: ../../src/topics/command-line-tool.md:19 -#: fe3a1468aa864742b92c6e8f4ff1a38f +#: abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" #: ../../src/topics/command-line-tool.md:50 -#: e9dbf14538404cceb02507962a173ee8 +#: 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" #: ../../src/topics/command-line-tool.md:57 -#: a650a7dacbb547db97158a8ac2c9d0dc +#: a5eacdbc9aa142c890b177869da4143d msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." msgstr "" #: ../../src/topics/command-line-tool.md:68 -#: 501217b98c424a319e70ef963de506f6 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" #: ../../src/topics/command-line-tool.md:69 -#: 7143809471454e00880ad8faaf43f141 +#: e3bdaceae8784ab0807b2cf356a98580 msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." msgstr "" #: ../../src/topics/command-line-tool.md:83 -#: 7ad86e42708a465980a56f735644de9f +#: ed521ac365db4a6ba5a1051fbaa2932e msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a8f29712337b4d1daf3190cc8973b8f7 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 534843389795437991fad0b5a702b483 +#: 0cf51b6da6884065ae42032abc20eb0d msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2052170aa2624feeb2253477895aa838 +#: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d5ed098a33ae4c1ab2a30eba483ecc6f +#: d3f74c3b094a427fbec831afab657d50 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 2b55c028602f41babb6e535b425ba5dc +#: cfffc518ba6e4ed1a80762ed6f7d25df msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 47408669ae8b4432a43d763dba12a466 +#: 9454a330b9324744b89448f2694b1b03 msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: b2e5e925971849a09a8d54d9c649a32d +#: 7f8d99a30b644457a62ac1523d0c72aa msgid "To test the above CWL tool, use this job to provide the input value `message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 #: ../../src/topics/outputs.md:77 -#: 9a39f53bdcc94904a90effb507767645 -#: f296149bf19947528b134b01a4d7ce81 -#: 965fa9769dea4ac9b3dd252e0a3bc603 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 79d8ea95f0c34585a3dec4f83453de60 +#: 10d1373bb14a4a3cacd3b92a2f83382d msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 4afab699247b4f619702c4086eb1b6f3 +#: 70e257091bdb456e8957f90a8fa90e8c msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 693b91423f004118b806bb8ee7952eaf +#: 1741804e33aa43ce88b4320c11ae5973 msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." msgstr "" @@ -292,193 +1291,193 @@ msgstr "" #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 #: ../../src/topics/workflows.md:198 -#: e4a25f04a6fa4001bb1e58cb775cdd84 -#: c771cbc64607412a9164c28934e9e0f5 -#: bdd5a3eac1e3436496e05a13c4f06073 -#: 1e62b28ef0184081b4d6e53f34b753e1 -#: 33edd6deb38740ed98466b6e023b0393 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/custom-types.md:1 -#: a3a8bcdfadc4484ea5e4c13a25b2da85 +#: cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" #: ../../src/topics/custom-types.md:3 -#: 7800570badf149b3bb1f81d470dbf4be +#: 67573252cc064b27ab13eebc468ac58a msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." msgstr "" #: ../../src/topics/custom-types.md:9 -#: 496313f8ec67403ca78ba66130df261e +#: 73e68b3af9cf41338d843c0c40e50cdc msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:12 -#: f7cc0d1ac5dd47658093cd0360f90329 +#: ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" #: ../../src/topics/custom-types.md:18 -#: 0d563f15c1cc4484b6b2955bdc70e1a9 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" #: ../../src/topics/custom-types.md:24 -#: 06425b6cdaf244b198fdde312e864190 +#: a999b1acda2641598086648c64aa3831 msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" #: ../../src/topics/custom-types.md:30 -#: 26c3762a637a4492a6c12588544cb0a7 +#: f8c12a58cb0b46a488823c6ae95f25ea msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" msgstr "" #: ../../src/topics/custom-types.md:46 -#: 221433aa39104642af8afb70ebd08576 +#: f25a63e0926d4932bbe64b2e4bdabf9e msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:53 -#: 197bf36a5d7741b3a9ac56c19d4a7686 +#: b0a4df0fd3ca42338cff4689235dcf4e msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" #: ../../src/topics/custom-types.md:55 -#: d9249cf936d24ab3b3fc508d17d94745 +#: fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" #: ../../src/topics/custom-types.md:61 -#: 2ff7ce81cd3a492a8549484ba8d1f135 +#: d718630a296545f3a989c8c71e9ddc77 msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" msgstr "" #: ../../src/topics/custom-types.md:76 -#: 2bb45c56e2fc49e094be2cf742222e67 +#: 9a97acd430064710bcdf76edbd9f711c msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." msgstr "" #: ../../src/topics/environment-variables.md:1 -#: e2a4a531c6164f15bc711618db058f52 +#: 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" #: ../../src/topics/environment-variables.md:3 -#: 90f7960bd24d4481bd05da1d61ef146b +#: 3c821c9c46d841ec89b8a5b1018f3af8 msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." msgstr "" #: ../../src/topics/environment-variables.md:7 -#: a51814548e44467c841ca65b2ac63b2c +#: bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:1 -#: fa13573d9c174ca1accf20a449e5984f +#: 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" #: ../../src/topics/expression-tool.md:3 -#: f2912b17e3be47b0b7186efdb4c4010f +#: 48deb71f361a43e48a56ed483075bca8 msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." msgstr "" #: ../../src/topics/expression-tool.md:8 -#: 4d9c95d18c1a4880845e7194a99aed3c +#: 716b56506ca7470299899c5d820a9ea2 msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." msgstr "" #: ../../src/topics/expression-tool.md:17 -#: c656a020978f465b85b8754346ea5b6d +#: b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" #: ../../src/topics/expression-tool.md:48 -#: ff4d0b6bc0264650a21adc811b8caf4c +#: 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:67 -#: 77e00be2c0984465af5bf501b4031f32 +#: e3ecac0a8e604f2b98a2a12b0579990a msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." msgstr "" #: ../../src/topics/expressions.md:1 -#: 3d7b7238be974c0487f219cb5c030149 +#: c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" #: ../../src/topics/expressions.md:3 -#: 03a62f421c8241779c0e79f4dbad96cc +#: 007a345b4bad49cf996c4301b8386473 msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." msgstr "" #: ../../src/topics/expressions.md:9 -#: 31a85893835748339b6c84fb98fde14b +#: 2edbd398eadb458b8eacd5fa5496f0a2 msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." msgstr "" #: ../../src/topics/expressions.md:16 -#: 08d9ecd7d3294c5b9dd4db228a1d8d5b +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:22 -#: d94d6c69aaa64edd9c75624286713c2e +#: efb5fd14988c4e2a8f834ee5369d4102 msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" msgstr "" #: ../../src/topics/expressions.md:25 -#: 020019b8aedb494fad022d19b7106f83 +#: e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" #: ../../src/topics/expressions.md:31 -#: a6b66e0fc0de442e8f72f0d0c37c7e8c +#: 276f688ba7cc471a842f085ca852b1d9 msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." msgstr "" #: ../../src/topics/expressions.md:35 -#: 48b7d9ddac2940c0815e5c855bfca6d9 +#: ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" #: ../../src/topics/expressions.md:37 -#: 894b843f9c064d56913e1a8c48093314 +#: 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:47 -#: 2319e845caee41a3bc5888c3f1fc28d1 +#: 8b70a1ad70514039b97164fa630c12e4 msgid "Note that requirements can be provided with the map syntax, as in the example above:" msgstr "" #: ../../src/topics/expressions.md:54 -#: 9ea661d749db428eacd2207dc7a01e36 +#: 2f28ab412d2843ffa5f14acdc01fc732 msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." msgstr "" #: ../../src/topics/expressions.md:62 -#: 4ff76250f28144a4a9d8807a9d4ed3b4 +#: d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" #: ../../src/topics/expressions.md:64 -#: 7f9f2df357a740feb89bfbcc44ff4d61 +#: cbec9277b5004e50af2728cbda0df740 msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" msgstr "" #: ../../src/topics/expressions.md:66 -#: 12633ed841dd447a8753faeb4f9e5096 +#: e259f55f8000479bbd8009e25cf0ca6c msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 -#: 4db64481d38c4896a85a8f6038a9931c -#: 1b4ff3eeddde4a9a8018235b9d706567 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 msgid "`arguments`" msgstr "" @@ -488,38 +1487,38 @@ msgstr "" #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 #: ../../src/topics/parameter-references.md:86 -#: 50547062ee404e2ebeae7eeb54b9de4b -#: 88933bc02fa84412944673c3463af1ad -#: 4fde39d8a50e49f09bd28a8598760682 -#: b933cbf847d94c5fb8471918ce8cb4ad -#: 0145c520b85a4bc29302bb654f08f23b -#: a3e322ac8a0d4e2ba9bfbece6b5ae64b +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 #: ../../src/topics/parameter-references.md:66 -#: d9b166225120432f9a2bf2cc7b6ffdfe -#: 28f8ec2fc5c0436aaba19e9d479aa466 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 #: ../../src/topics/parameter-references.md:67 -#: b866a0e5897e44329714f4c55eb20d2e -#: e64b5027878346d79f9ab52b3d3b916e +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 #: ../../src/topics/parameter-references.md:68 -#: ed38ec582fbb48ff9f9cffa7962ef515 -#: 6cc0788250624fd69fa4e3881191ab7f +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" #: ../../src/topics/expressions.md:72 -#: 17eefb5f38534c1b87116c3a061ea1bb +#: 8210b36347a749889450529ecdf4ff0e msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" @@ -531,14 +1530,14 @@ msgstr "" #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 #: ../../src/topics/parameter-references.md:90 -#: ce0572fc81b343e6991c88ca0195149a -#: f8b77ad06ebe43d7b03b2135737902e2 -#: c7953486c99d4c7898c0155a6085dfd5 -#: 46d99b1f7f0747479bd58486cf7941d2 -#: cd0a797b3619404f964ba9efb33756bd -#: 528cd5e0d3994230b719fbfb39b1f13e -#: 324241aae8ff4505ab0467f2a7f27fe2 -#: f4086b1ad2e44c2b9de2636f8bc1eb90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" @@ -550,1534 +1549,1574 @@ msgstr "" #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 #: ../../src/topics/parameter-references.md:91 -#: 764d7cf3fb5444d58dc9e0eb6b8fc649 -#: 0450a4b8de3046998d30ce1f09c10daf -#: fd6bf79cbb694dbb89e8731aed733e6c -#: e6048a64e09d46099132fee40a2e0644 -#: 9512391eb96440bd8e48c3754821e3d0 -#: 3e8669bf4a6741f9aba170864b251dac -#: a02ede726d3f4eec9602f72054c0d963 -#: 4ed593dfc39246789f1e4ecdc742323b +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae msgid "`secondaryFiles`" msgstr "" #: ../../src/topics/expressions.md:75 -#: 304de40206cb43d7b651245586cfa55b +#: 23088850ad02459696f6bbd385109aac msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/expressions.md:77 -#: 7855471c93bc44aabb1a2b9beb52b56a +#: f02257a822ad46ac93c5981531cc85d5 msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:80 -#: f0452f324bfa451f9f3264f9a55e0e5d +#: 989a1c4aaa1143be9f53b90cd8b6d500 msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 -#: 6dc476cf8689465ea3993f49a9eead75 -#: 4dfc0be21065471d91def850bc2528fb +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 #: ../../src/topics/parameter-references.md:79 -#: 09d69778a89044099b3e5d7cf02471bb -#: e3077bdff0dc4dfdae60eb60f3d66d8b +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 -#: b28843f7b57745db9cb3648ef23fda0f -#: 6a745fa266dd42849c95410775b690e0 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c msgid "From `Workflow`" msgstr "" #: ../../src/topics/expressions.md:84 -#: be00ed49197f48ecb7cb244ecc214369 +#: d289541e460147aa933f7878996f8649 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 -#: 90ad2b27f97b4ca089cf23a073cdf17b -#: 38d062892cb04bc7bbf0b56f263079e1 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c msgid "From `steps`" msgstr "" #: ../../src/topics/expressions.md:88 -#: c2d2756d617743b886c67160c2face21 +#: 81b4d1f23a3642bfa9bb395b94260cd1 msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 -#: 8681600183d1429cbd1b15639e1a222f -#: 1d49cd7337004fc38f4e8e9aa4270481 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 -#: 24b7f85116cc4d2f904600555aa19b8b -#: c401a68b4f384d3eb13ab3e89a4a7195 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf msgid "`expression`" msgstr "" #: ../../src/topics/expressions.md:92 -#: 0e1f9d22d0714bc5b80e420f63b34cff +#: f495da32f05a4a5ba9539be0a54c1a59 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:95 -#: 5fed95f16aaf42d4b41c569d9546b7f0 +#: bdb4c68a175047ddbe141ca24960127f msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 -#: b539a931f31d4cfe9d72aa5800115fb2 -#: 48e497c024bc4c38a86dd027aaa4fd2d +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 #: ../../src/topics/parameter-references.md:94 -#: be638c80121948c99cc9fdb67a5d291e -#: 1fd8fe769ba8497eb8a9520af91ea33e +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 #: ../../src/topics/parameter-references.md:95 -#: b5f3ad78a233411c97520c1fffdec18f -#: 7854e46c7fd24afd9c1942808521bee1 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 -#: 211bd57896494fca9ea8aa2fc142eea2 -#: 28ec0718d3114bfdaae4524c009da944 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 #: ../../src/topics/parameter-references.md:97 -#: c6a421f7a0214d89958d4c258b58aac8 -#: 07bd0bc74ad74187bdc24c26041467ca +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 -#: 3afc146cde2e47d5b52e62fbd1f37426 -#: 2225f5acb44a4ce0ad16be5c4f6cba48 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 #: ../../src/topics/parameter-references.md:99 -#: 9acd61d4d67a4d2c82171a79462fb458 -#: cd7e7fea3b8346268618c31b70581326 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 140e449e46a84e3ca1a604176e583f44 -#: 3d8b717d4568458eb53b0b91695b3de8 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" #: ../../src/topics/expressions.md:104 -#: 76f35653e34b433d8e9fedc6d12ce856 +#: 97b61352363f47cb890e8937c5613fa3 msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 1a2edf61fda8404689e3c0a7389d7d02 -#: 3bced6d84fa6453195be82dbc6d7ec83 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" #: ../../src/topics/expressions.md:106 -#: 0b5aceb6c9d24bd9bfe95cc04fdc61ad +#: 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 3523cc46c6324fca9053d6b1dd8c7495 -#: 21eee2c1cb6b430486446d223dcca0eb +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: b4f126415048402ca388c4c63f34ebe5 -#: fdf588cf8cd34d60bfb6cece3ef859e0 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 1b494245c14e4e22918c43ad9f26cc8d -#: df4d781178f2465b8a421651bdd2f66f +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" #: ../../src/topics/expressions.md:110 -#: a88008a23ede4ea49ffcaccba7029d31 +#: 0bc424ef2ca346099f29b937379908a0 msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: a256b51f1e944b7d9659b945d8ab05c9 -#: 23bbd631e73147e3af561eb4a14d2d6c +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" #: ../../src/topics/expressions.md:116 -#: a446842e26e44781ad10cdaad73bc49d +#: 10d36a1adfd04144b401c993b12b4094 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" #: ../../src/topics/expressions.md:118 -#: 3cc10263ab2f4dbfb6ccb12612b89cf1 +#: 29b73e1dd72744f68377f0a38c10f062 msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." msgstr "" #: ../../src/topics/expressions.md:122 -#: 995f6af5fc244293b34f5d840f01ce1c +#: 38a2afaf4a6c4d04909af22c93f2808d msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:128 -#: b556a1d134764505aa25003d79a53e88 +#: cd74f34b21af4de9be96fd897efc469b msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" #: ../../src/topics/expressions.md:135 -#: ad23da5452bd46248606f6799ce93db0 +#: f12e371f3f1a4b0cb2cff9800352d48c msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" msgstr "" #: ../../src/topics/expressions.md:139 -#: c63036ac68344465af6c7756be00b60b +#: 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" #: ../../src/topics/expressions.md:146 -#: 2f7f270b0ac24f2f8df506f5dde72cf7 +#: 8f0e8f050e334ac08334e9215e1dcf61 msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" msgstr "" #: ../../src/topics/expressions.md:149 -#: f49272e5e4c1491eb59c79d2dfb88a86 +#: 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" #: ../../src/topics/expressions.md:155 -#: 8b50c892d36d4d178ec4268c7c13887d +#: 7a6be0005a6441feb67f036d005d7885 msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" msgstr "" #: ../../src/topics/expressions.md:158 -#: 9d22117a6f5a434593d5144bf824999f +#: ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" #: ../../src/topics/expressions.md:164 -#: 4fbc454a144a466b9dd7ff74903fc5fb +#: 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" #: ../../src/topics/expressions.md:171 -#: 281b129a76a24b0a818092acd1038757 +#: 06635145b441418aaae84dc804f3d6ac msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:175 -#: 4dda6ca233d54c12b6ddceabae198495 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" #: ../../src/topics/expressions.md:181 -#: 59d87fecfd7f4438b68e0bcdecdcfb46 +#: 04eaf1f7c630450db318dcd8b7626e15 msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." msgstr "" #: ../../src/topics/expressions.md:186 -#: 0f7e33673ad349e5ad41a078032e5806 +#: c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" #: ../../src/topics/expressions.md:193 -#: 77a7141f897048139ef3785b5f870b43 +#: 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" #: ../../src/topics/expressions.md:200 -#: 14ed183bc7e346598921445c0dea11e0 +#: fd4579a3c9844492b314b5c3c1775fc7 msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." msgstr "" #: ../../src/topics/file-formats.md:1 -#: 9406d05bf0ed4774af50fd66d24aa299 +#: 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" #: ../../src/topics/file-formats.md:3 -#: f5a9048ef9e047528c291505ef9a2c12 +#: e024bcb70e04412e90e1838426d1b69a msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." msgstr "" #: ../../src/topics/file-formats.md:8 -#: 51e8c5a231eb45fb8c15be49b37a7bff +#: a3db21c0b3114802a8a5b610e252ef13 msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" #: ../../src/topics/file-formats.md:14 -#: 860a6f01ebac45938abd220758fd1109 +#: 0f5bc8520d6a4dafa37c65343da9702a msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." msgstr "" #: ../../src/topics/file-formats.md:17 -#: 32155f96d47f4d76998a401aa9e9591f +#: 5cb830da47464a8b9c3950983fa4d56f msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." msgstr "" #: ../../src/topics/file-formats.md:20 -#: a62bbb9251794560ace0e52be3d9ebd3 +#: 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: e301af8f675444c69cfb6b578c02fdc7 -#: 3da1dec243994409bd764b133d4fc243 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" #: ../../src/topics/file-formats.md:32 -#: 82c6efcfb5d5410eb316399b7c4f638e +#: 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" #: ../../src/topics/file-formats.md:34 -#: 29c3d25c657340a1bab7123a166b78c2 +#: a2ce43b391864e8bbde16328cc19b32b msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." msgstr "" #: ../../src/topics/file-formats.md:39 -#: ef8e7bd7e944429da78474d2fc5e0348 +#: aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "" #: ../../src/topics/file-formats.md:45 -#: 08dd50bc6a5942ec8f3b6c201fc4497f +#: 56ee4dcfff6141d5bef80eb96559876d msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" #: ../../src/topics/index.md:1 -#: 78c51215a68f40b280cc21d0e412eacf +#: 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" #: ../../src/topics/inputs.md:1 -#: bb8e2203374a4ae7b833c543ecc563b0 +#: 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" #: ../../src/topics/inputs.md:3 -#: f34aa1e4d08944c497602b2a35f38a50 +#: d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" #: ../../src/topics/inputs.md:5 -#: 2932972efc94447987b02a7707c62656 +#: 96671c56523c4ea9992fb5dfcfa6490e msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/inputs.md:9 -#: 968f4e83c511425d8faf4c8d0f18097e +#: bcc6246742cb46bfb185e415c4a3431a msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." msgstr "" #: ../../src/topics/inputs.md:13 -#: 2eb89bdbaee04a899a961a7b87f0aef1 +#: 86dce36de687449c88fb5eb9d64eb045 msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." msgstr "" #: ../../src/topics/inputs.md:16 -#: 3781fc7cd22d48bdb5aa4abc0c93b06f +#: cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" #: ../../src/topics/inputs.md:18 -#: f4af4a85efb243728d2ee783393dce14 +#: 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" #: ../../src/topics/inputs.md:24 -#: dbf8350f003a46b984b7432160e6def5 +#: c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" #: ../../src/topics/inputs.md:26 -#: db2993fe83814747a52f9db0b2fcc81e +#: dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" #: ../../src/topics/inputs.md:33 -#: 39fe18bf5d4b4539b2f98e3bf0feea2a +#: 36ab1d9edafc4831bb1bca5f123b04b0 msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" msgstr "" #: ../../src/topics/inputs.md:40 -#: 58e7b0e7d0a149498e846dd2790c0eee +#: 7dc630ea86464b1dba3a4e5079260b3b msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." msgstr "" #: ../../src/topics/inputs.md:44 -#: 4b78c5437904492ea3e692372d2fc163 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." msgstr "" #: ../../src/topics/inputs.md:47 -#: f2626686125d4ec29fb2338373b54c93 +#: 651e032007ea4a119d20c820bb61f86b msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." msgstr "" #: ../../src/topics/inputs.md:53 -#: 46327aca33cb49d1ba61149e94884991 +#: 0b056dde9e87428996e47870b12119da msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" msgstr "" #: ../../src/topics/inputs.md:64 -#: 43f2e7020da94f77bce4e1f852ab11f1 +#: 628124a1670b4b058bb0fb6e495a099c msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" msgstr "" #: ../../src/topics/inputs.md:70 -#: 8342aa3f84624325aff8f7f4de788187 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." msgstr "" #: ../../src/topics/inputs.md:83 -#: 2d54f11f99b245e5b2802b984bc024a5 +#: ec2adb3912bc46e28891229e9e0d9a1c msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." msgstr "" #: ../../src/topics/inputs.md:95 -#: 83a357dc06b343549876035b03b8c5d1 +#: a519be60726a44af9941fdce04735353 msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." msgstr "" #: ../../src/topics/inputs.md:109 -#: 0461538fa12a44c5a9d230a928ae930d +#: cb8fc8c4c79e467eac5fab4ca685201e msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." msgstr "" #: ../../src/topics/inputs.md:124 -#: 2b2552958f404447b711d09650d22395 +#: a26cc105716f47cb807174c9003153b0 msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." msgstr "" #: ../../src/topics/inputs.md:131 -#: 82c97e60f8634bd6b4d3e88524722412 +#: cc159dd5fe5748caac838862f5b8c4d1 msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." msgstr "" #: ../../src/topics/inputs.md:134 -#: 0ae1393a80e94b899023c29f4af6084b +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." msgstr "" #: ../../src/topics/inputs.md:142 -#: 74339f624bba49d6b68e1dfc4724f673 +#: 6812698e9ad84d3385de5e88e9dde0b3 msgid "The `baseCommand` field will always appear in the final command line before the parameters." msgstr "" #: ../../src/topics/inputs.md:146 -#: 3a4473864ec04d2e9a0d550b2051f717 +#: 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" #: ../../src/topics/inputs.md:148 -#: 575661b36a2040699956f897bd6cc614 +#: d1f02be278754267893dfce5a940997d msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." msgstr "" #: ../../src/topics/inputs.md:154 -#: 3d18a704f5a94e2889e847c32a78aaab +#: 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" #: ../../src/topics/inputs.md:160 -#: fceca2b53d0646b2ae9f1cf9dbefe2fc +#: 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 #: ../../src/topics/outputs.md:82 #: ../../src/topics/outputs.md:105 -#: cba49054785b4ec2a7acd3aaa2e165d8 -#: 647c0e302af841d7b1789447281d7344 -#: d23de44d5d5b4bc7b32f3726afa97500 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/inputs.md:178 -#: dd867685663f4728b9fbe446a9b14a3d +#: 75d59e395c66416cae9b352db5081516 msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." msgstr "" #: ../../src/topics/inputs.md:185 -#: 67bf2c2cbbc44f6eb870af3a3a852676 +#: 874c6f19abbf45d7ab7d30a378c4048d msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." msgstr "" #: ../../src/topics/inputs.md:191 -#: 94d66455bfd04697814495e116176ffe +#: 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" #: ../../src/topics/inputs.md:193 -#: 39a9d3583f29451d8035158c54266ed6 +#: dea0d4b681f94e73b13965dcfe75cf7d msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." msgstr "" #: ../../src/topics/inputs.md:198 -#: eba6af5cf8224d198fc04f090362307c +#: ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" #: ../../src/topics/inputs.md:204 -#: b48377cceff342e793e982c9fa2095d3 +#: d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" #: ../../src/topics/inputs.md:215 -#: b64ef70d944c461b8ec7219e14e47795 +#: 750474486a84482292eeba45f118287f msgid "In the first example, you can't provide `itemA` without also providing `itemB`." msgstr "" #: ../../src/topics/inputs.md:217 -#: 73cd08a2226f4cbe99fcde2d3636d640 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" #: ../../src/topics/inputs.md:233 -#: 3c33bffa2c574ef888b041c1e6735b8e +#: 1eb0e39bb6d04b8cab300f44a79f3add msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." msgstr "" #: ../../src/topics/inputs.md:236 -#: 23bd067b32724dad9daba1e924757d86 +#: bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" #: ../../src/topics/inputs.md:252 -#: 1be92fc3d0b44ea089273cfcd47318ef +#: 4b2ab812f62c4f949dd25c8527f2411c msgid "In the third example, only `itemD` is provided, so it appears on the command line." msgstr "" #: ../../src/topics/inputs.md:255 -#: 3d08125883b74f49bba042ed58d34648 +#: b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" #: ../../src/topics/inputs.md:257 -#: 7636c7e8b6e04d7089ba1cb10c4c475d +#: 2c3b884cb1c54521900cc90782e8a58d msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." msgstr "" #: ../../src/topics/inputs.md:262 -#: e1c95ce96db043eb86ff9b3ae595017b +#: a1073b6306044dffb414319ae01f68bb msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." msgstr "" #: ../../src/topics/inputs.md:265 -#: e6588c4b8fa64959b2dcac52403a6415 +#: 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" #: ../../src/topics/inputs.md:271 -#: e7f85cb69a5342889525fbb81b44c86c +#: 9a1d92334685449386dfa3b3a899ed48 msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" msgstr "" #: ../../src/topics/inputs.md:280 -#: 71756719e0274300a839b38c8b4ea986 +#: fb623af4c480411b8fde28d01c981411 msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." msgstr "" #: ../../src/topics/inputs.md:289 -#: 88bf75fce3064eaf823b5d88be0ce053 +#: e98e165f6bba40809c90473d72f9d592 msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 60374713dea84fff92b89b4ebaa8d7ac +#: d33aa2353ad44fb885d3a1ee48263dc4 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: 7616d5ea746f47ac972183150b97e8b0 +#: cd64d2d828834cbbb24ea5358caf5405 msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 0ca022c095334ec4a9fe41cb732e11a1 +#: 80af387fe3ff4e2da999903385bd602b msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 1c807f8fd1c540ae8802092fbcec7159 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: c51956eb3ece432ea0ed5b676b2f037a +#: d402bf528c7f4eb69aaaa275be2bf1d4 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: 45e6ab3a53b94f5b90136d68c1c0e479 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 7e05dc23d6be4428b4a414b3a65c4727 +#: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" msgstr "" #: ../../src/topics/operations.md:1 -#: 96e7266ef25b429da42337c3582cc201 +#: 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" #: ../../src/topics/operations.md:3 -#: 9cb6959a877f4590bccb977416753410 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." msgstr "" #: ../../src/topics/operations.md:7 -#: 7b54a3cd870d4b038dff685064bbca1a +#: 5565c1b2d8a349169a305a9b26b4574d msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" msgstr "" #: ../../src/topics/operations.md:10 -#: 0d661c96ac2d41ee94641a397aa3bdf7 +#: 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "" #: ../../src/topics/operations.md:16 -#: 94d39b79923a4a65b1a6ce5c464528c6 +#: 88160cef4cfa4add9020aa89511a5749 msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" msgstr "" #: ../../src/topics/operations.md:24 -#: 56801121f70b4cb2ab6207e254ec8bbf +#: 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" msgstr "" #: ../../src/topics/operations.md:55 -#: 42418ff882d44c1b9584fb9f7887f744 +#: 730ba1434a1445ae847ec6153b6a3b72 msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" msgstr "" #: ../../src/topics/operations.md:58 -#: 1118de96d202444d9bb4db74ebe4792d +#: 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" #: ../../src/topics/operations.md:66 -#: aca51d371db84aa79418c79a18310055 +#: a25d0b1e13324b40a6b8fcd227948c4f msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." msgstr "" #: ../../src/topics/outputs.md:1 -#: 3473e6d2942e4546a2c1590edeb502f8 +#: da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" #: ../../src/topics/outputs.md:3 -#: c210ad12f61047b68302e67da9b5dae0 +#: 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" #: ../../src/topics/outputs.md:5 -#: 1c15cff5a4614d88a62c8d2df97029fc +#: d661df070e3040869da412d07a71f716 msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/outputs.md:10 -#: 4beae917368545688c01a4a929685cae +#: a11585474d3849cca5467512ed964743 msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." msgstr "" #: ../../src/topics/outputs.md:16 -#: 4f4f63b7107e4dc194760802c4581c2a +#: 2682f9ca8e604a0c9986f7746fdec960 msgid "The following example demonstrates how to return a file that has been extracted from a tar file." msgstr "" #: ../../src/topics/outputs.md:19 -#: d942035c4c914ccb9de75836af9761c7 +#: 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" #: ../../src/topics/outputs.md:21 -#: 0e9064cf55fe43588053d37100634538 +#: 22447a560f6f4317bf67bd7c4336126c msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" msgstr "" #: ../../src/topics/outputs.md:26 -#: aa1dcfc618e74a53b3c579380e5e1558 +#: f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" #: ../../src/topics/outputs.md:32 -#: 3ec3f4a2d1c547b18780db17fbff060c +#: ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" #: ../../src/topics/outputs.md:38 -#: 21e598983ce94d22b9d40a77577a6608 +#: dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "" #: ../../src/topics/outputs.md:45 -#: 62f79a2c055b455d9626ca5a18d1bd72 +#: 52703d6b7f914097934bfad13663abeb msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/outputs.md:51 -#: 19c2b9b13bcc480aa7474301422faab3 +#: 5e1c79df657d4a6e84e055dd6b300a5d msgid "The field `outputBinding` describes how to set the value of each output parameter." msgstr "" #: ../../src/topics/outputs.md:62 -#: 17bb520489a74f64b76ddbe2ffedcb5e +#: 329d2809dfae4f90bc638f5f03a47ee3 msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." msgstr "" #: ../../src/topics/outputs.md:65 -#: 9e2b97aa3bfe4eae8524b325bf2ea3f1 +#: 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" #: ../../src/topics/outputs.md:67 -#: 028c844ef208450f994b3949210ca996 +#: c6bcf7c6a8774dd6be41cc775848c3b8 msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." msgstr "" #: ../../src/topics/outputs.md:71 -#: 2b758e44e4be4fdf89a5897385db6c59 +#: 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" #: ../../src/topics/outputs.md:89 -#: 16395173b7ee468f85ee8450493504de +#: 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" #: ../../src/topics/outputs.md:91 -#: 51e2e929dadc41a78cea98f779e2e2a3 +#: 9647019d8c37466886e7aab6f176634d msgid "You can also capture multiple output files into an array of files using `glob`." msgstr "" #: ../../src/topics/outputs.md:93 -#: b757d4b151ef46fa96897bf00a0d9ab4 +#: b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" #: ../../src/topics/outputs.md:99 -#: 2f2f46a81e8946bf8a9b48a5956c82f8 +#: cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" #: ../../src/topics/outputs.md:112 -#: 75177c797c704385bfa5ce86e03266c9 +#: cc067051f22f433bbece08f60933e002 msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" #: ../../src/topics/parameter-references.md:1 -#: 4d05d16c3cb74eb291da7586fa859b90 +#: a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" #: ../../src/topics/parameter-references.md:3 -#: c115b7ed044346d6a9c4c06306ee82d8 +#: dbfe2c1123144316aa026374b0f353d3 msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." msgstr "" #: ../../src/topics/parameter-references.md:13 -#: 8f83261e3e91424b9a3c38280c643f02 +#: 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" #: ../../src/topics/parameter-references.md:19 -#: 269af269348e4da5b93cb25dcd10374a +#: 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "" #: ../../src/topics/parameter-references.md:25 -#: c376ab464fec4ee78a33d42dfed5dc1c +#: 074cf5d912854d8c864607cc24b15302 msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/parameter-references.md:36 -#: 53d468d14703494699478e6847d82e34 +#: 0290af3e3cbb4b32b0450c8771f3bf95 msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." msgstr "" #: ../../src/topics/parameter-references.md:47 -#: 32bd7abe387e4999a0864f6e6a48e435 +#: b54240bb94f746bba7511633aa969db0 msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." msgstr "" #: ../../src/topics/parameter-references.md:51 -#: 0712e952fe2442daa9ceb0cee79a3ebf +#: 8b70a072aa87414c88e89a3e19af0a51 msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." msgstr "" #: ../../src/topics/parameter-references.md:54 -#: ef2b8db0c8d64e41b839b47aae34d0ec +#: eea20f89c45f424a888178df53713b28 msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." msgstr "" #: ../../src/topics/parameter-references.md:59 -#: f9f45dcc2bcb4fd1a1021d2843137fa3 +#: cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" #: ../../src/topics/parameter-references.md:61 -#: 4ffbc016a5344e6e9272793d921e4900 +#: 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" #: ../../src/topics/parameter-references.md:63 -#: 7118718b98c5488c9d9a54e5ec84c055 +#: 7647e0229a924f988cf02b7812a55c06 msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/parameter-references.md:69 -#: 20fe8fa105a84171972722158bafbc0d +#: 9d663249666045618a0d3acddb85a9a9 msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:72 -#: 836fa2a818854cf9af13d674f5bb859c +#: 5fed4984f6784347b4cbe0630b1dd2c2 msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/parameter-references.md:74 -#: 5d56e1ac063d48c2b140a72db9f78540 +#: dbf6153cd02542a6a01c172803122b7f msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:77 -#: 0166655553ac4d8fb868138936176986 +#: b6250cf6fa8a4a0c94b33302e0decca5 msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/parameter-references.md:81 -#: e43fe4a9340b458786c51499c75b5556 +#: fa6ca3bbc6784380a03a950a6f49a180 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:85 -#: 0ba13966a1364d4e9992b5cfeb6871d1 +#: b92b516e537a4773ad67b4af586e7a25 msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/parameter-references.md:89 -#: feb8bce610be4a3a92053f2e2e5aab76 +#: 467a701228504d06b971b79a59c69064 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:92 -#: 0f5fd76c57e7412097b4ebdeb074f2fd +#: 2634f989eb304009a8568d70ed42786c msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: b645dd17256543b0a42d231171140c95 +#: 5d8bed66282c408695292ea92a03b2c4 msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: c8d5743769bd4fee93f77a52ba318883 +#: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: af6cbb89b7a84bf78b7443b6746484fe +#: 9a6b311ded8d4e43ae635b1b927dbdf2 msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: ad9394b163a94340975a66ea2bba7094 +#: aac74f957774479a83aab4c6ff1390ae msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: 677bce1f24f449beb2bac5ed8469f624 +#: b75d29d1d55d44488338f9689f156855 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 4c0d14a24b354feabf4b6ad4852f9543 +#: 574d93d1d592458a985f259519c036cb msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: d407e5c9aa9043b0b6ab234348467db0 +#: 82e48b3e3c3f451480cc0b6a529271f6 msgid "In this example, the software requirement being described is InterProScan version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: f06b60c926204ca88b4355803f1b7b11 +#: 02e40154eac74ecc98d0447d03475b44 msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 0a7c19b054d2400abd327736b6829670 +#: 8cb1c5d9b1a54c40924099494eb766c6 msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." msgstr "" #: ../../src/topics/staging-input-files.md:1 -#: cd1773f336544b3688bc76c28e9d1f79 +#: b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" #: ../../src/topics/staging-input-files.md:3 -#: 6b7bbca601f04f7183bc75988bd6db13 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." msgstr "" #: ../../src/topics/staging-input-files.md:9 -#: 069d1dd1f03f4cd79e44f2dcd890b531 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:1 -#: 4924b1a69a5f48b0aa6af943b40ffc68 +#: 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "" #: ../../src/topics/troubleshooting.md:3 -#: e100d8d8f23c4d6996ac59c5ad68acf0 +#: fbe0c65b444441f785d0054176d036a6 msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." msgstr "" #: ../../src/topics/troubleshooting.md:6 -#: a87dfd0dc0274ff4b34354678f2d49d2 +#: 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" #: ../../src/topics/troubleshooting.md:8 -#: 772078ff701a477cae9acb8dda16ef1f +#: 9a710602e00c4934ae3a3b471aa68458 msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." msgstr "" #: ../../src/topics/troubleshooting.md:14 -#: d2d67048e93e40c4820b805f1ba28cc9 +#: 21b5be7270a14f0987240c81d1ec879b msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" #: ../../src/topics/troubleshooting.md:20 -#: 580477152be041a8ae5c5f546ecbf21d +#: 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:27 -#: 05f8faea082b4fb9b9c22b8eff7eb356 +#: cfe9d8241fe84bd5b74042a5625d933f msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" msgstr "" #: ../../src/topics/troubleshooting.md:35 -#: 4c107fb18fb34c2dba7743118c51e8c8 +#: 764d933cc4da446abd8dd8f913f05dac msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" msgstr "" #: ../../src/topics/troubleshooting.md:44 -#: 729ea19aa03b49bdadccc6e6f0d2e7d9 +#: c93efc6d4e004859981ee7f5fa28ed03 msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." msgstr "" #: ../../src/topics/troubleshooting.md:48 -#: e849cda9fb1d4a48b5b1f9a4e44213a1 +#: 546601da44cb49bd9611b1c85807fd90 msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." msgstr "" #: ../../src/topics/troubleshooting.md:59 -#: bfc20f529d2d4797b87c63c7b2c05e91 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." msgstr "" #: ../../src/topics/using-containers.md:1 -#: 761a900275a044f28ddcebe509a4637a +#: eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "" #: ../../src/topics/using-containers.md:3 -#: 59af21cf1ee848e993563ad47f7bb248 +#: 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" #: ../../src/topics/using-containers.md:5 -#: d711ce1ccdcf427aba25a2ab3d11165d +#: e07f33d01b804663a25ffb08aad74821 msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." msgstr "" #: ../../src/topics/using-containers.md:15 -#: eaaaa01fe0894f479a42a9c3ce199819 +#: 7a644506619a4f08958ec7d4540cd557 msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." msgstr "" #: ../../src/topics/using-containers.md:18 -#: 92489f186e3f449295b0dc864ebf17f7 +#: b5195b7d8eaa419fb2b90cb33a57783a msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." msgstr "" #: ../../src/topics/using-containers.md:21 -#: 1360c3a2d43b48f3b3e1153bb26b3f30 +#: 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" #: ../../src/topics/using-containers.md:27 -#: 2e993e21a3624910b4282bd088694fec +#: 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" #: ../../src/topics/using-containers.md:33 -#: df5b4b041dc944be8580e43012339168 +#: 2713594c937d4c528fc8d04d9e9819ed msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." msgstr "" #: ../../src/topics/using-containers.md:44 -#: 92ac2766d118428ea148094c022a8b0d +#: cf94c1424fc2413c85647fd1ee73d951 msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." msgstr "" #: ../../src/topics/using-containers.md:52 -#: e4ddaca03eb449eabbf2d2fce752c367 +#: dc0452107c604e29bdf32bb289fe5db8 msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/using-containers.md:55 -#: 0bc50411a4b748d8864305070d11a304 +#: 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" #: ../../src/topics/using-containers.md:69 -#: 74453227279a46cea3644f3ca7df61b9 +#: 483181f498fc4d968b5fe6ef427709f7 msgid "Notice the CWL runner has constructed a Docker command line to run the script." msgstr "" #: ../../src/topics/using-containers.md:72 -#: 75ce3269886645eda46a6575fca186eb +#: 7487485d6aa4458089a4b4bdf107ea64 msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." msgstr "" #: ../../src/topics/workflows.md:1 -#: 1e7e5b46017a476a80d57ab7eb614758 +#: 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" #: ../../src/topics/workflows.md:3 -#: 1ee41e983ca14a959caa199b1ce12700 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" #: ../../src/topics/workflows.md:13 -#: 070e6a00d09e4675b89afec5d066aec1 +#: f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" #: ../../src/topics/workflows.md:41 -#: fd37ebe3aad9473891cc764a47363f8e +#: 5870ac44e4c24b8daf5f06c49f95ce04 msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." msgstr "" #: ../../src/topics/workflows.md:51 -#: 85176099018c4ae19bed1261e92e6e92 +#: a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" #: ../../src/topics/workflows.md:81 -#: 952e9a347f444ef496fa0cdf00160ffd +#: 93188ed43ee949cc98b3ea679ce14feb msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" msgstr "" #: ../../src/topics/workflows.md:91 -#: 2b5ad46ca3024ce1b37e1c92a820aabf +#: 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" #: ../../src/topics/workflows.md:150 -#: ea17d17cd08b4c40a842598c8521af56 +#: 1cc17ad26e9c474b895ba5cd20c8b66a msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." msgstr "" #: ../../src/topics/workflows.md:160 -#: 6e5f1266974d4a32995aaa69fbbfd648 +#: 24aca0bea4d94e3593b844cf0586cffe msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." msgstr "" #: ../../src/topics/workflows.md:165 -#: 20be823f70c348bbaad6bfc8b88201a9 +#: 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" #: ../../src/topics/workflows.md:167 -#: 02311e5310cb49d19bf2998513f73124 +#: 9c56528acd5f49deb139e034dfbfac7c msgid "This workflow extracts a java source file from a tar file and then compiles it." msgstr "" #: ../../src/topics/workflows.md:170 -#: ca6e4a3fe04145a9a21cc43cc53a07bc +#: 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 #: ../../src/topics/workflows.md:180 -#: 75452467551a46a2b2b3685f1a4aae0d -#: 93efa8e941a7427f949afc794ed16e75 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" #: ../../src/topics/workflows.md:180 -#: 39beed65cb114bd78c79aa4a5d6f4398 +#: a2dd833fdca4443181648e41051a5232 msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" #: ../../src/topics/workflows.md:183 -#: dd880d0589fe45dbaf9b7d799402f158 +#: 7e40cc9f9e1341c195e843c009575b94 msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" msgstr "" #: ../../src/topics/workflows.md:185 -#: 671d0bd54bb147518c35f0844a76c61d +#: 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "" #: ../../src/topics/workflows.md:191 -#: 66de58a51b034f6a8d5dbe742046f817 +#: 6fcf8ad3d1bd49afa4a105622437bd59 msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." msgstr "" #: ../../src/topics/workflows.md:205 -#: 564e68d58e364715aa72183cb16b3d72 +#: 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" #: ../../src/topics/workflows.md:212 -#: 558739ceb3fe40de8ea87ff1e7d3fe9d +#: def35d6021394def80a53ae49a2cdbde msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." msgstr "" #: ../../src/topics/workflows.md:221 -#: fdc601ee1aa54e1f84cd00eed2e44e52 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." msgstr "" #: ../../src/topics/workflows.md:233 -#: e4f4a76cee96473d9da3bc1c9e35324a +#: c84d4450bc6a475dbf34e0b22cea9130 msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." msgstr "" #: ../../src/topics/workflows.md:248 -#: d524ed5f1e964688af9d74eef8e46e04 +#: cca9665f6daa44b49233baf34ab9fcc7 msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." msgstr "" #: ../../src/topics/workflows.md:256 -#: c646e4714d78437fb450127b119fbd70 +#: 547edbf5fa424b8286cc21674ff159b0 msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." msgstr "" #: ../../src/topics/workflows.md:261 -#: 8351ddfd726c40159d81c017ef221606 +#: 7ca248888b9d484cb544cd76ba538662 msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" #: ../../src/topics/workflows.md:267 -#: 456794c7274f4654b54aae8d4073a2df +#: ae6b240718104380b08db5552d7355ea msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." msgstr "" #: ../../src/topics/workflows.md:278 -#: 6485e8d6814144d1bcbe66bfe4fcbdb9 +#: e5a8b7f84be64020b191099f3fad30ed msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." msgstr "" #: ../../src/topics/workflows.md:285 -#: a2b9e47cc923466f8bd2fbc4b33fc4fa +#: f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" #: ../../src/topics/workflows.md:287 -#: 698cc640807247fd8d512c59ce32ee48 +#: 12a06d8358534102b202965d4258c18e msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" msgstr "" #: ../../src/topics/workflows.md:297 -#: dd658e10da624918b7dec1ea18bbf432 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" msgstr "" #: ../../src/topics/workflows.md:300 -#: f6bd95a4fbc44ffdbfec7fcac90f6bb6 +#: 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "" #: ../../src/topics/workflows.md:309 -#: ac7b02a71d3544848d4fb539b2a4f115 +#: b7f93705e5b8416696be01850072e8c0 msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" #: ../../src/topics/workflows.md:314 -#: 4380dbd066a44102a71c7e42ca7de8d8 +#: e87045829b344089ab59dc27063ddd7a msgid "\"Visualization \"Visualization" msgstr "" #: ../../src/topics/workflows.md:322 -#: da946c9d59f44fb995daa6aadc44031d +#: 42ef2f145b824d69b63abc1da175c216 msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." msgstr "" #: ../../src/topics/workflows.md:336 -#: 7c73bc555f604afd8491c1619d6905eb +#: c61cedf543664d388183e04b3939cc39 msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." msgstr "" #: ../../src/topics/workflows.md:341 -#: e79ce424410e4682881fe14326955a14 +#: 9e39e3f1501c4fcaab3e8962e090f6be msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." msgstr "" #: ../../src/topics/workflows.md:347 -#: be8d2b89052e4f9d96ff2bf15526e229 +#: 03e2f767c4da461982fc3c0f3ba94762 msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" #: ../../src/topics/workflows.md:366 -#: 967b064ec4284d0aaf374509915497e1 +#: 3bea5822b8694e2aa32c446e1c54a045 msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" #: ../../src/topics/workflows.md:383 -#: 02d667b922264f8e8021844df0085578 +#: 426023bd6e3a471cbb30dbda3d6f9e57 msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." msgstr "" #: ../../src/topics/workflows.md:389 -#: db8734e07541495188d9ee97eaaaeff3 +#: 0d498cd4caf54c15891ca1afe58e2727 msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." msgstr "" #: ../../src/topics/workflows.md:394 -#: 22542da60ac24403827e2e2a14595770 +#: b2d75045e02741b4850f5ff1243f7858 msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." msgstr "" #: ../../src/topics/workflows.md:398 -#: d10f35716f9c4b878da0f2b4ff3d44aa +#: cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" #: ../../src/topics/workflows.md:400 -#: 1fd555d1f8ca499ead8d5601eb62266a +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." msgstr "" #: ../../src/topics/workflows.md:411 -#: f5fc85accf8c4bb9bc701ba0b4ee2e21 +#: 5fa79c62049a447c8328ebf9db54ebf4 msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" msgstr "" #: ../../src/topics/workflows.md:415 -#: e69cb5e87f4b4670abbc1606197d804c +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:421 -#: 15d763c45a2749a8926b1f965db9d97f +#: 3a67d77a2e7b4c0bb61cc3585ceae942 msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" msgstr "" #: ../../src/topics/workflows.md:429 -#: c2aac63fc0c347d9833d253039000fa3 +#: f1cb55fc59824cc18a95fd6dcb32cf4c msgid "First of all, notice that the main workflow level input here requires an array of strings." msgstr "" #: ../../src/topics/workflows.md:441 -#: 06a23beb753c4a97b302943f59128d78 +#: d947c54933d64aad90df392a1cedd63f msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." msgstr "" #: ../../src/topics/workflows.md:445 -#: 45985434cfe9438cb558075e1fd73809 +#: 651d35997332404186aa6d5711da4a3d msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" msgstr "" #: ../../src/topics/workflows.md:450 -#: e92da36d865142289b11d245221ff8d4 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "" #: ../../src/topics/workflows.md:452 -#: 3ed7a2b9f77b4eadae3bf6e4a98d14b9 +#: 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" #: ../../src/topics/workflows.md:458 -#: fd66c4fb9c2a4beea0ed5ed8874fcd61 +#: b662c1a5a4424c8d8350a806356acc61 msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" msgstr "" #: ../../src/topics/workflows.md:466 -#: 65944dc8b32a46a4beb73dbdebb7b01a +#: 04d6babfd87343d7a5f13867ea02b65f msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" msgstr "" #: ../../src/topics/workflows.md:469 -#: 6250fe161ab0421b8799040b79ce695a +#: 2eaacf1a90204a2b9bd621344560f2a1 msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" msgstr "" #: ../../src/topics/workflows.md:472 -#: cc40c0f1ade34ab3b400a02b59b7ba01 +#: 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" #: ../../src/topics/workflows.md:480 -#: 29f53a5d64fa498bad0dbe94b238fd97 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" msgstr "" #: ../../src/topics/workflows.md:483 -#: 037fccb419bc4e9f839c665ae31e28ee +#: e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "" #: ../../src/topics/workflows.md:489 -#: fdd4bec90c484a618ed8e4d1199deff8 +#: e3a7182f00f440b8b5461da91194a64b msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" msgstr "" #: ../../src/topics/workflows.md:491 -#: 11afb584f37947358963f6510935c5d5 +#: 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" #: ../../src/topics/workflows.md:497 -#: a77e0bfb589c40b6a61a9ca559961a7c +#: b5338f39e8c74ff28e139da68089a742 msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." msgstr "" #: ../../src/topics/workflows.md:509 -#: 3f4aa12588204fe5b33db590a9446283 +#: f6d92156d67c4a339bcfd194cff897df msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" msgstr "" #: ../../src/topics/workflows.md:513 -#: 640c67f3bcd740c59f90c361024acbcc +#: 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:519 -#: 8c4d30cbbea146a584731d164d4ad9ef +#: d80ab383eec9402faba997b548fe42eb msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." msgstr "" #: ../../src/topics/workflows.md:522 -#: 5d0fd4f8b58e4a8e8f46902e64e6556b +#: f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "" #: ../../src/topics/workflows.md:524 -#: e98ab273645340f9a1446183a642e79e +#: 49217c02f58c43ff9ec00f10da8d4e84 msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." msgstr "" #: ../../src/topics/workflows.md:527 -#: 37a83ed92d9e44689cfd3a31c2785418 +#: 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:566 -#: 7cebef0a9e1444149b1dc58d30f6c10e +#: 8dbd56473f8c40c0bb12a48be06117e3 msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." msgstr "" #: ../../src/topics/workflows.md:573 -#: 0cd2bd98918b4622bc586d50f1ce1fa4 +#: 78d7f3ede2c746d482042adef050b2c4 msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." msgstr "" #: ../../src/topics/workflows.md:587 -#: 92458de979564d19a634bb8d3bf6f586 +#: cbbf93c70fe04ba7932ba25758ddc611 msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" #: ../../src/topics/workflows.md:607 -#: d4ee6cc8903f4e6992439ca2586246ed +#: cfa1c1fde4454df283f87cc54a9c59ec msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" #: ../../src/topics/workflows.md:627 -#: 62b438c4ed8a409f96974f3d59cc5854 +#: 1a8be2950cbb475bbb2617e005f0fac9 msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." msgstr "" #: ../../src/topics/yaml-guide.md:1 -#: f0f288aeae4f4649ba3615437b531e97 +#: 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "" #: ../../src/topics/yaml-guide.md:6 -#: f35023cb05504d1db0cbee41c4e5f371 +#: 5d83c56102e141cc978500f678dd0c1c msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." msgstr "" #: ../../src/topics/yaml-guide.md:13 -#: 01564f1d2038489685160f03db92085f +#: c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" #: ../../src/topics/yaml-guide.md:16 -#: ad662dce1e4149728b8e17f74d8f975f +#: fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "" #: ../../src/topics/yaml-guide.md:18 -#: 4f6a57f34f094418b7c13aa07eef95c7 +#: 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" #: ../../src/topics/yaml-guide.md:19 -#: 373a6c24de9144e69f37418d6ce8857d +#: b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" #: ../../src/topics/yaml-guide.md:20 -#: f804a8493c8e40178772d94bdc45b43e +#: b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" #: ../../src/topics/yaml-guide.md:21 -#: b3c504b8ab1a42788ef4e3339d27b0dc +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" #: ../../src/topics/yaml-guide.md:22 -#: 2c2681fe72e24a5d8d98f0aa8e8c56a2 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "" #: ../../src/topics/yaml-guide.md:24 -#: 571e5c13552c4381bb6de53c02fe5f43 +#: 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "" #: ../../src/topics/yaml-guide.md:26 -#: fd789f444d9a4061b4fc61bac70353bb +#: cda73485875d4c8e9464679a20558616 msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:42 -#: 2cef838551994b078e460c63214517f9 +#: 98cae24919b74c088a5d89706aec581b msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" #: ../../src/topics/yaml-guide.md:51 -#: 2a3a8a553d3c455e9288f63b9a02898d +#: b4b0940b4b5743c09637b36b964202d0 msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" #: ../../src/topics/yaml-guide.md:61 -#: b0b8def4623a4018b1ac913a9256c0a2 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" #: ../../src/topics/yaml-guide.md:63 -#: 3f0d4346f0104cc08c059eed9ab4b3a9 +#: 9ca3554d771d45998e88aaede525b227 msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:76 -#: 22e0ac963278414d8141ce5ce4031029 +#: 3fca839cede94cfd8e4f605c73ba699d msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" msgstr "" #: ../../src/topics/yaml-guide.md:79 -#: 49cad54646d04adc8e5ac9f0f3c8f895 +#: da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "" #: ../../src/topics/yaml-guide.md:81 -#: c8776a4511b24f46bbe0a34d52cf3c8b +#: 3ded0f125249485c921994b6e6b93ac9 msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" msgstr "" #: ../../src/topics/yaml-guide.md:104 -#: 401b053bd08a4286b9059cb6ebf8d679 +#: 53ece35d309a4c8d99f1efb2122a7092 msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." msgstr "" #: ../../src/topics/yaml-guide.md:127 -#: 8d48a277f37f458f88c54f362534d7b5 +#: d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" #: ../../src/topics/yaml-guide.md:129 -#: de90253a11f24f29a4a57348b4f60941 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:146 -#: 1e20968f957441c58cabfbc46c21e8ca +#: fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" #: ../../src/topics/yaml-guide.md:167 -#: 4cf2e158afb348d7b3fd6274fe888129 +#: 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "" #: ../../src/topics/yaml-guide.md:169 -#: 44c5c010c97a40068a6b930949dcd8cf +#: 87bafb845c714b109874f6137b84462d msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:177 -#: c6277b2a7a934f81a91e406ef317a1fb +#: 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "" #: ../../src/topics/yaml-guide.md:184 -#: 8b3ece04170c447e9b5a8f76374c4c23 +#: fcd05b1ef31a4046946a2399c7fc5575 msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." msgstr "" #: ../../src/topics/yaml-guide.md:194 -#: 6b952b7369b447bdb0bf1e9ff8540194 +#: f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "" #: ../../src/topics/yaml-guide.md:196 -#: a6024fb7ce664896a6858d5ea3562fb7 +#: 859368c1f25c4a4aad57abfd046c63f5 msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." msgstr "" + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" diff --git a/src/conf.py b/src/conf.py index 60ece96c..990751ba 100644 --- a/src/conf.py +++ b/src/conf.py @@ -236,5 +236,5 @@ } gettext_uuid = True -gettext_compact = True +gettext_compact = "user_guide" locale_dirs = ['locales/'] From 3a715f91e821d471ddf4883a3c5543c29eaf12ac Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 25 Jan 2023 15:35:18 +0100 Subject: [PATCH 040/179] add Weblate to README --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index de079218..d6817cc9 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,8 @@ [![Syntax Check](https://app.travis-ci.com/common-workflow-language/user_guide.svg?branch=main)](https://app.travis-ci.com/common-workflow-language/user_guide) +[![Translation status](https://hosted.weblate.org/widgets/commonwl/-/user-guide/svg-badge.svg)](https://hosted.weblate.org/engage/commonwl/) + This is the source of the official user guide for the Common Workflow Language standards. Releases are published at from the `release` branch. From a8098340780f4db905c755358391ddc75417727a Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Thu, 26 Jan 2023 14:55:11 +0100 Subject: [PATCH 041/179] convert license to RST to restore indirect links (#366) --- LICENSE.md | 63 -- LICENSE.rst | 59 ++ locales/es/LC_MESSAGES/user_guide.po | 1380 +++++++++++++------------ locales/pt/LC_MESSAGES/user_guide.po | 1385 +++++++++++++------------- locales/user_guide.pot | 1358 ++++++++++++------------- src/LICENSE.md | 2 - src/LICENSE.rst | 1 + src/conf.py | 2 +- src/index.md | 2 +- 9 files changed, 2098 insertions(+), 2154 deletions(-) delete mode 100644 LICENSE.md create mode 100644 LICENSE.rst delete mode 100644 src/LICENSE.md create mode 100644 src/LICENSE.rst diff --git a/LICENSE.md b/LICENSE.md deleted file mode 100644 index 75596a51..00000000 --- a/LICENSE.md +++ /dev/null @@ -1,63 +0,0 @@ -# Licenses - -## Instructional Material - -All Common Workflow Language project instructional material and changes -to the structure are also made available under the [Creative Commons Attribution -license][cc-by-human]. The following is a human-readable summary of -(and not a substitute for) the [full legal text of the CC BY 4.0 -license][cc-by-legal]. - -You are free: - -* to **Share**---copy and redistribute the material in any medium or format -* to **Adapt**---remix, transform, and build upon the material - -for any purpose, even commercially. - -The licensor cannot revoke these freedoms as long as you follow the -license terms: - - - -* **Attribution**---You must give appropriate credit (mentioning that - your work is derived from work that is Copyright © the Common Workflow - Language project, and, where practical, linking to - https://www.commonwl.org/ ), provide a [link to the - license][cc-by-human], and indicate if changes were made. You may do - so in any reasonable manner, but not in any way that suggests the - licensor endorses you or your use. - -* **No additional restrictions**---You may not apply legal terms or -technological measures that legally restrict others from doing -anything the license permits. With the understanding that: - - * You do not have to comply with the license for elements of the - material in the public domain or where your use is permitted by an - applicable exception or limitation. - * No warranties are given. The license may not give you all of the - permissions necessary for your intended use. For example, other - rights such as publicity, privacy, or moral rights may limit how you - use the material. - -## Software - -Except where otherwise noted, the example programs and other software -provided by Common Workflow Language project are made available under the -[OSI][osi]-approved -[Apache 2.0 license][apache-2.0-license]. - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - - - - -[cc-by-human]: https://creativecommons.org/licenses/by/4.0/ -[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode -[apache-2.0-license]: https://opensource.org/licenses/Apache-2.0 -[mit-license]: https://opensource.org/licenses/mit-license.html -[osi]: https://opensource.org diff --git a/LICENSE.rst b/LICENSE.rst new file mode 100644 index 00000000..cc6a19b0 --- /dev/null +++ b/LICENSE.rst @@ -0,0 +1,59 @@ +Licenses +======== + +Instructional Material +---------------------- + +All Common Workflow Language project instructional material and changes +to the structure are also made available under the `Creative Commons +Attribution license `_. The following is a human-readable summary of (and +not a substitute for) the `full legal text of the CC BY 4.0 license `_. + +You are free: + +- to **Share**—copy and redistribute the material in any medium or + format +- to **Adapt**—remix, transform, and build upon the material + +for any purpose, even commercially. + +The licensor cannot revoke these freedoms as long as you follow the +license terms: + +- **Attribution**—You must give appropriate credit (mentioning that + your work is derived from work that is Copyright © the Common + Workflow Language project, and, where practical, linking to + https://www.commonwl.org/ ), provide a `link to the license `_, and + indicate if changes were made. You may do so in any reasonable + manner, but not in any way that suggests the licensor endorses you or + your use. + +- **No additional restrictions**—You may not apply legal terms or + technological measures that legally restrict others from doing + anything the license permits. With the understanding that: + + - You do not have to comply with the license for elements of the + material in the public domain or where your use is permitted by an + applicable exception or limitation. + - No warranties are given. The license may not give you all of the + permissions necessary for your intended use. For example, other + rights such as publicity, privacy, or moral rights may limit how + you use the material. + +Software +-------- + +Except where otherwise noted, the example programs and other software +provided by Common Workflow Language project are made available under +the `OSI`_-approved `Apache 2.0 license `_. + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an “AS IS” BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +.. _cc-by-human: https://creativecommons.org/licenses/by/4.0/ +.. _cc-by-legal: https://creativecommons.org/licenses/by/4.0/legalcode +.. _OSI: https://opensource.org +.. _Apache-2.0: https://opensource.org/licenses/Apache-2.0 diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index ba080ed4..3fa6daab 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,149 +9,113 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"POT-Creation-Date: 2023-01-25 16:53+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" -"Language-Team: Spanish \n" "Language: es\n" +"Language-Team: Spanish \n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=2; plural=n != 1;\n" -"X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.rst:2 dcdc2e8da0ec4d9e9453601fdd83bac5 msgid "Licenses" -msgstr "Licencias" +msgstr "" +"Licencias" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.rst:5 3e165520ca56481b8f8d494a8d471de3 msgid "Instructional Material" -msgstr "Material didáctico" +msgstr "" +"Material didáctico" -#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d -msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable " -"summary of (and not a substitute for) the [full legal text of the CC BY " -"4.0 license][cc-by-legal]." +#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." msgstr "" "Todo el material instructivo del proyecto Common Workflow Language y los " -"cambios en la estructura también están disponibles bajo la [licencia " -"Creative Commons Attribution][cc-by-human]. Lo que sigue es un resumen " -"legible por humanos (y no un sustituto) del [texto legal completo de la " -"licencia CC BY 4.0][cc-by-legal]." +"cambios en la estructura también están disponibles bajo la `licencia " +"Creative Commons Attribution `_. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del `texto legal completo de la " +"licencia CC BY 4.0 `_." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.rst:12 b7a7a0fb40344fe087c1cc3ec19308aa msgid "You are free:" msgstr "Usted es libre de:" -#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" +#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 +msgid "to **Share**—copy and redistribute the material in any medium or format" msgstr "" -"**Compartir**---copiar y redistribuir el material en cualquier medio o " +"**Compartir**—copiar y redistribuir el material en cualquier medio o " "formato" -#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" +#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 +msgid "to **Adapt**—remix, transform, and build upon the material" +msgstr "**Adaptar**—remezclar, transformar y construir a partir del material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.rst:18 430ff4de74924bc3a3b2c7e809ea4456 msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e -msgid "" -"The licensor cannot revoke these freedoms as long as you follow the " -"license terms:" +#: ../../LICENSE.rst:20 2173e2af49be41ee97a74c4e879faf25 +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " "términos de la licencia." -#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 -msgid "" -"**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow " -"Language project, and, where practical, linking to " -"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" -"human], and indicate if changes were made. You may do so in any " -"reasonable manner, but not in any way that suggests the licensor endorses" -" you or your use." +#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 +msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" -"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su " -"trabajo se deriva de un trabajo que tiene «Copyright © The Common Workflow " -"Language Project» y, cuando sea práctico, con un enlace a https://www." -"commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e indicar " -"si se han realizado cambios. Puede hacerlo en cualquier forma razonable, " -"pero no de forma tal que sugiera que usted o su uso tienen el apoyo de la " -"licenciante." +"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su" +" trabajo se deriva de un trabajo que tiene «Copyright © The Common " +"Workflow Language Project» y, cuando sea práctico, con un enlace a " +"https://www.commonwl.org/%20),%20brindar%20un%20%60enlace%20a%20la%20licencia%20%3Ccc-by-" +"human_>`_, e indicar si se han realizado cambios. Puede hacerlo en cualquier" +" forma razonable, pero no de forma tal que sugiera que usted o su uso " +"tienen el apoyo de la licenciante." -#: ../../LICENSE.md:32 8161753b7526445db319210044566200 -msgid "" -"**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything " -"the license permits. With the understanding that:" +#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 +msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" -"**No hay restricciones adicionales**---No puede aplicar términos legales ni " -"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " -"permitido por la licencia. Con el entendimiento de que:" +"**No hay restricciones adicionales**---No puede aplicar términos legales " +"ni medidas tecnológicas que restrinjan legalmente a otras a hacer " +"cualquier uso permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 -msgid "" -"You do not have to comply with the license for elements of the material " -"in the public domain or where your use is permitted by an applicable " -"exception or limitation." +#: ../../LICENSE.rst:35 f6aae4a5cd0547118c8a3240ca2b4be6 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limit msgstr "" "No tiene que cumplir con la licencia para elementos del materiale en el " "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 -msgid "" -"No warranties are given. The license may not give you all of the " -"permissions necessary for your intended use. For example, other rights " -"such as publicity, privacy, or moral rights may limit how you use the " -"material." +#: ../../LICENSE.rst:38 a40c173be35b4c1b92e83f42bfe2382c +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" "No se dan garantías. La licencia podría no darle todos los permisos que " -"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como " -"publicidad, privacidad, o derechos morales pueden limitar la forma en que " -"utilice el material." +"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como" +" publicidad, privacidad, o derechos morales pueden limitar la forma en " +"que utilice el material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.rst:44 3d7ca3f2cede4d5f998bf014bd970748 msgid "Software" msgstr "Software" -#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." msgstr "" "Excepto cuando se indique lo contrario, los programas de ejemplo y otro " "software proporcionado por el proyecto Common Workflow Language están " -"disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " -"la [OSI][Osi]." +"disponibles bajo la `licencia Apache 2.0 `_ aprobada " +"por la `OSI`_." -#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, " -"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " -"See the License for the specific language governing permissions and " -"limitations under the License." +#: ../../LICENSE.rst:50 4ee4d68b90fe422880da856cd539b982 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 -#: eab02dc13915490bb3c9ba744d78b6a7 +#: 5ad4be9b62d54c95a913795b514676fd bdd540403a5746ff99edf2dcad0e3122 +#: dfc7702e073140c985cf47272a20214d msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -160,30 +124,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +#: ../../src/episodes.md:9 3060770b3bef41d7bcfcdfb413d7689c msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +#: ../../src/faq.md:1 48bb9f628b344ba1a3b67ae1cb264e3c msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +#: ../../src/faq.md:11 7e3684e9672643738846756e1ebafd18 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 +#: ../../src/faq.md:41 187ceabb7fd9480bb8cf0f2da47f65ef msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +#: ../../src/faq.md:43 b548b76bcc85420a9b30792386105139 msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -191,94 +155,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f +#: ../../src/faq.md:59 9ce692b78ead47e4b0f8cdae8837d35b msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +#: ../../src/faq.md:61 6df1201c159343da9e7515379980d6a0 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 +#: ../../src/faq.md:82 f9ab1d0dc1c842b6abb5385268c1d3bd msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +#: ../../src/faq.md:84 9f6a84ab6a9343b6ad7db826f8964362 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +#: ../../src/faq.md:86 fa50e4fa990b42d1ba4c0f4ae1e5caa1 msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +#: ../../src/faq.md:89 3a871012fcfd4f3ebeca0cb86ec93435 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +#: ../../src/faq.md:95 d954edfff2584288ac8c600733070d2e msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +#: ../../src/faq.md:97 af6b1e37d6be4450a761854480ec9aab msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be +#: ../../src/faq.md:104 31f4a2d43062493ca64c648f80afc8e9 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +#: ../../src/faq.md:113 41c54e71b6cd4f63b2a619a515240d34 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +#: ../../src/faq.md:115 8edc3541ad134ab5a1d23c724f1f0a4e msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 +#: ../../src/faq.md:135 ac0ea81eba8842a18801ab03cbf80a57 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +#: ../../src/faq.md:138 52be1a5640234feabe958ff7ade33653 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +#: ../../src/faq.md:140 c6db734d5aef4f4f99676bdebf9c83c9 msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 +#: ../../src/faq.md:165 a9f7b47c0dd741739795da39bf114879 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +#: ../../src/faq.md:167 e3fdd9228b924905a4a1f4b2b7ad7159 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +#: ../../src/faq.md:188 3f7cda1437cc48f18745a827ebb74582 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +#: ../../src/faq.md:190 5aeaba2cae64442e816bbd458aee833a msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -286,22 +250,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +#: ../../src/faq.md:194 5af827a402834978addd82c70be6b5ab msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +#: ../../src/faq.md:196 6d69e42bd8e443c4b19d80807c7efd6b msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +#: ../../src/faq.md:199 404640397b6e40c2a2cd5cf85ab3b1c0 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +#: ../../src/faq.md:201 1682c2486e224770b62269709a8663cf msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -310,25 +274,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd +#: ../../src/faq.md:229 9078fc009bc145808813c9cc2b734b58 msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +#: ../../src/faq.md:231 d4b5a54a400c409cb7984428f6a03ec8 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +#: ../../src/faq.md:247 9e8dbee6e8f84d08b1a54fffa06394ef msgid "" msgstr "" -#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c +#: ../../src/faq.md:248 1d846bfb5f054d09a4afad1da8e4b642 msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +#: ../../src/faq.md:250 2d0e95fec8084787b734388d60188574 msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -336,26 +300,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +#: ../../src/faq.md:267 eccc4a364330470fa474dcaaa3433390 msgid "" msgstr "" -#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 +#: ../../src/faq.md:268 e945f6a337af4e4686bed482a4fe6c39 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +#: ../../src/faq.md:270 8a3efaa0ad1548428bcfd6e01d135cdc msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 +#: ../../src/faq.md:322 cdab644adc5643708870fb08c06cbfca msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +#: ../../src/faq.md:324 089a5a0b076b44aeaab4d69ee3c79f97 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -364,77 +328,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 +#: ../../src/faq.md:342 561172559c6f41a68819608fd9e58bb0 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +#: ../../src/faq.md:344 c5ee4946d2e840abaa3dc796a62652c7 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 +#: ../../src/faq.md:349 4f2069a2113c414db18eca95550e9e09 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +#: ../../src/faq.md:351 31f3390e6771414ba7bf57c044c4b0c4 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c +#: ../../src/faq.md:359 3b77ce4930ae46d5be9f6965e8c54727 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +#: ../../src/faq.md:361 06f36bbe4d3840229b7374f27b86ae80 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +#: ../../src/faq.md:363 3cb2f70d00274a4dafd972ccd8c519c2 msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +#: ../../src/faq.md:371 093a1529262043ef84a99675054938e0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +#: ../../src/faq.md:373 45b6d9acbfaa47e5984184f7da554d0a msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +#: ../../src/faq.md:375 5705c9bacca5405ca6f14315a5575db8 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +#: ../../src/faq.md:384 82bfc285b59a439ca97d3278997f0fce msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +#: ../../src/faq.md:396 181d5130101d45ccb22aebae3d154c2f msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +#: ../../src/faq.md:410 e864390b5ddb423aaa10e9d33d257dc1 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 +#: ../../src/faq.md:423 fe637c32fb15427a9045679b5da42ec5 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +#: ../../src/faq.md:436 1f8004b9df8547029d82e57f9abdc979 msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 +#: ../../src/faq.md:442 70990dc5a0034099921ceb89c89e2dcc msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +#: ../../src/faq.md:445 f679e26f18d9455f945fd13361a9c906 msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -443,11 +407,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 +#: ../../src/faq.md:450 fcd0273dbdd84e728cfd8fbe239f2a01 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +#: ../../src/faq.md:452 173ddbd1e7c64927a8dcb12a2a2140f8 msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -458,22 +422,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +#: ../../src/index.md:1 662fe273e2fb4042b688512955e450a1 msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +#: ../../src/index.md:3 a15b52205f0145feaac298510e4d678a msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +#: ../../src/index.md:7 512aa0c7166b429e8116f71eef007f79 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +#: ../../src/index.md:9 b1b19e17a18540939cb3bb7f8a700cab msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -482,11 +446,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +#: ../../src/index.md:16 d58b36ac43ac44139897be752fbb1f87 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +#: ../../src/index.md:18 6726cf3585a646a8b4cbeb543cf84a38 msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -494,7 +458,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +#: ../../src/index.md:23 2e504aa7c46a426fa959e7254e9a84a5 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -502,15 +466,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +#: ../../src/index.md:28 e7be0df0838b432d9c7f296d777f120b msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +#: ../../src/introduction/basic-concepts.md:1 173e0816db20432c8d9dba1de5393dee msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +#: ../../src/introduction/basic-concepts.md:3 30eacc583f6841719e2142d283811d97 msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -521,18 +485,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +#: ../../src/introduction/basic-concepts.md:10 791b8f38a14147bbaa174c7eb595f17e msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +#: ../../src/introduction/basic-concepts.md:21 1a3989dcbb9844b39d84bf6df6b352ed msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +#: ../../src/introduction/basic-concepts.md:25 db1bbc6e980f404f9f3fcd08e92ee9a3 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -542,18 +506,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +#: ../../src/introduction/basic-concepts.md:33 acc7887c65974114996f700a38a7eccc msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +#: ../../src/introduction/basic-concepts.md:37 d2476d9bcff44f21b8d84a3a0d87a246 msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +#: ../../src/introduction/basic-concepts.md:39 f86415e4d78e48c4a8a76ced81221b98 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -562,24 +526,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +#: ../../src/introduction/basic-concepts.md:44 c5524d73708c4c779980528864506fd4 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +#: ../../src/introduction/basic-concepts.md:51 ac46a9f8850a434bac5bc2b41ee6294e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: 9bba7c4f783942e4a299603430601363 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 +#: e2140e0f0e7747ef8383887c20a7945a msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -588,39 +552,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 15bf490724cd46dcbcfab44633c5a9a2 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 51d52d051e654a8395239f88df7c9d8c msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: eb496cc818524fa7bae5a22ddd00a19c msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: c4a22d12e7f149ff901d27de32b9361d msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 7618de899a7043989d77baacf62eb7b2 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a +#: 6f1544a220664b79b04bf008058b5a91 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 +#: fbd14ac9a2f541478a320ed4cbc69e13 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -629,7 +593,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef +#: da4dba50d25d4533b3dbb92f54d32a30 msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -638,7 +602,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#: ce11c9f8d65c4268984d0384d95144cc msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -648,7 +612,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 +#: 3a201aa497e84f70855bb2251e7e3281 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -657,24 +621,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 +#: b78f7fa2be1c4bb090f6da895457ad1e msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 +#: f7e95d264ffa4e2db0864faccd9e5a0e msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 +#: 3f1e5b01e49a4dc1b1c99936a4589afc msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee +#: 03c3048f38ae4938a484cf02001877b3 msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -684,7 +648,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e +#: f9715b5ec65c405c849bb030c1927060 msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -693,12 +657,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: 442662f50e9e4620970ce32b1b127969 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 +#: 2b34c786af3840e88f29d214e19dc837 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -712,7 +676,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a +#: dd6aadff8cf54ce78ea6b317afbaddb0 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -721,7 +685,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee +#: fe7f1f0b28434f8aaf0f6ac6589a83f0 msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -730,71 +694,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: d10cf45b3c7f49dc98bc0e5d1246f224 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 -#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf +#: ../../src/introduction/quick-start.md:94 332b6e8b831e4bc5aed3745938230a57 +#: ce7fc63b808d4499b9bf9828c2dafe35 ebf339ed376a4d3b89b15b4d5afe593b msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 8badec9987ba40609cf1f626172b2b2d msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 +#: c75a8b4bf0e24781bf6713cf6f013cd1 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 +#: 79b146ffe6d74e1b8f6019251dc4b7c2 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 +#: 07cca9a33d8f4b77ac6ad35ca8b95655 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: 31db11c8ddf2423192a8b2063b3e91c2 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b +#: d81dd96143ea444aa78ff45cfa0584b3 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +#: ../../src/introduction/index.md:1 c54984605872472190ae7771809a20db msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +#: ../../src/introduction/index.md:3 01a237b8ec2f46c9acd31d142591ce75 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +#: ../../src/introduction/prerequisites.md:1 3fb9888b666945eab1e3ff109646c574 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +#: ../../src/introduction/prerequisites.md:6 5fb0486762354f93853fff209f835c08 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -804,11 +768,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +#: ../../src/introduction/prerequisites.md:12 5f1e7a608e0b455196d191c845a5c98e msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +#: ../../src/introduction/prerequisites.md:14 7ba4b5c51be24f5392949d06ee42e018 msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -816,29 +780,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +#: ../../src/introduction/prerequisites.md:19 e2d3e6dd13b14d819a504c35da6fe8e7 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +#: ../../src/introduction/prerequisites.md:21 91251d1f0efb4d4cb083b4517ff3107a msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +#: ../../src/introduction/prerequisites.md:24 6ad263e267514c5fb05794d3d76d418d msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +#: ../../src/introduction/prerequisites.md:25 8a3bfd72dccf4a8c874a96aebcbe5cb7 msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +#: ../../src/introduction/prerequisites.md:26 5195706d9c6c4573aff135fd539759a2 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +#: ../../src/introduction/prerequisites.md:29 9c4506915e4c40599527bc1d2b18645b msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -848,11 +812,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +#: ../../src/introduction/prerequisites.md:35 37d9eb784ec1425786158f98e3f63890 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +#: ../../src/introduction/prerequisites.md:41 572f493a985141a1b92dafbdba92790d msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -860,7 +824,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +#: ../../src/introduction/prerequisites.md:46 9606d3c4849f4b17b2e55a298210f055 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -868,26 +832,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +#: ../../src/introduction/prerequisites.md:51 754fc59967d94ffa935284676d55ffed msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +#: ../../src/introduction/prerequisites.md:62 2905c6362d4146e8b35bc74744841972 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +#: ../../src/introduction/prerequisites.md:65 091278ece252483a9838fb771de3e04e msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +#: ../../src/introduction/prerequisites.md:67 0928a5c668c3414a945bc9eda147892c msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +#: ../../src/introduction/prerequisites.md:73 56f3c481762848298214a88e559fc0f9 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -898,23 +862,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +#: ../../src/introduction/prerequisites.md:79 710c266ab4a5477b84d6ea987420fa20 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 +#: ../../src/introduction/prerequisites.md:84 cc353db5da2546bb88a77ce1a202ff9d msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +#: ../../src/introduction/prerequisites.md:86 b62df08ec96f4cdb887600079856dd76 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: ../../src/introduction/prerequisites.md:91 97e02557293440d1a58ba659dad21113 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +#: ../../src/introduction/prerequisites.md:93 0935c3ff01634c75b5c91546dc36c7b9 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -925,32 +889,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +#: ../../src/introduction/prerequisites.md:101 cfb37fd605164a8d9cc75bf892ce97c0 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +#: ../../src/introduction/prerequisites.md:104 5f06a7a6aae343d989a5b30979c600f6 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +#: ../../src/introduction/prerequisites.md:111 5f956260f3874b6dbeaf3ad7ecc09c9a msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +#: ../../src/introduction/prerequisites.md:115 d35e4effec554a638d6c3047ef3fd05f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +#: ../../src/introduction/prerequisites.md:120 15a1f944a0d642729d3736ed1c907074 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +#: ../../src/introduction/prerequisites.md:125 fa34c808bb494ddfa3f3926bc42e650c msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -958,30 +922,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: ../../src/introduction/prerequisites.md:129 0c15f62eb7534e809f625f3fa213e92d msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 +#: ../../src/introduction/prerequisites.md:135 d67719a6f0ce4ba1bb6152a10507b729 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +#: ../../src/introduction/prerequisites.md:137 1c96e75281844bfab0578bab2e816854 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +#: ../../src/introduction/prerequisites.md:144 bece1fc3c3f842b0b30d8f1b7fbfc200 msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +#: ../../src/introduction/prerequisites.md:148 a7caa36b0f83448b91ef2e76e30abc51 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +#: ../../src/introduction/prerequisites.md:154 39321e93e9994fcca20b425aa45c2894 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -991,47 +955,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +#: ../../src/introduction/prerequisites.md:161 601cf500d76c4e0287af4429a46b36d2 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +#: ../../src/introduction/prerequisites.md:163 b286d5359e184ef58054c72df4014629 msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +#: ../../src/introduction/prerequisites.md:167 e14423edd829401faed0950772123240 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +#: ../../src/introduction/prerequisites.md:171 889c44360bd54a0e85e7f0e61aa6593c msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +#: ../../src/introduction/prerequisites.md:172 7b9bff73624947ac90a99c7880e2e911 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +#: ../../src/introduction/prerequisites.md:174 c5ff687c86ef4ccaae25d8bcfbd5f873 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +#: ../../src/introduction/prerequisites.md:177 0a610a9632064deb824afd0719429d3a msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +#: ../../src/introduction/prerequisites.md:181 ec0c47438a5242cb99dffa7a4997e95a msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1039,7 +1003,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +#: ../../src/introduction/prerequisites.md:185 aae94ac2114641f186eac0f4117223eb msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1047,57 +1011,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +#: ../../src/introduction/prerequisites.md:191 209e072724ed4d27b37e9bff6d55d811 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +#: ../../src/introduction/prerequisites.md:198 3bf47876e3694e6cadb05123326459cb msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +#: ../../src/introduction/prerequisites.md:199 459a65b8e67c4a9aaa03138c1abe94ad msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +#: ../../src/introduction/quick-start.md:1 898eb29ac7714c69840b795633953a05 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +#: ../../src/introduction/quick-start.md:3 2a658bd2d8ce4533ab7e056fc3a3ffcf msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +#: ../../src/introduction/quick-start.md:7 32dd2e28cf0f40b6930750f0162355eb msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +#: ../../src/introduction/quick-start.md:12 471c47d311074ecfac071b6d52d9cfb6 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +#: ../../src/introduction/quick-start.md:16 5078140028ea4d04973cb9cd20f0607e msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +#: ../../src/introduction/quick-start.md:22 ab127d4ba0a44526ab129587a8160923 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +#: ../../src/introduction/quick-start.md:27 d5cc6b4295a74f3586f022b0227759b3 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1105,11 +1069,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +#: ../../src/introduction/quick-start.md:32 585a4fe583ce44e180a062742b3b0849 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +#: ../../src/introduction/quick-start.md:34 0d81b0c9ea58420789d1d71cca32ce88 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1117,11 +1081,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +#: ../../src/introduction/quick-start.md:39 ea4ab0782d8049d8b1b89cea4ae60048 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +#: ../../src/introduction/quick-start.md:47 f6f3b7453a254f828bd4c9e9fef92bed msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1129,32 +1093,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +#: ../../src/introduction/quick-start.md:51 3bf9050175d4444ebbbabe219412574f msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +#: ../../src/introduction/quick-start.md:53 e03f72a14dcf4bf38ce8232598ca761d msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +#: ../../src/introduction/quick-start.md:57 3dcfb2facd324dccb3084c02487625dc msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +#: ../../src/introduction/quick-start.md:62 b8531da183964b02bca19f818ec076d4 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +#: ../../src/introduction/quick-start.md:65 7ba1ddebeb2843179fe99fc410b193c6 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +#: ../../src/introduction/quick-start.md:70 a6dc303e9d284b60bf1102212505ca27 msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1162,21 +1126,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +#: ../../src/introduction/quick-start.md:74 59ac7830ae3e4d7cb1bf503e8c90fe30 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +#: ../../src/introduction/quick-start.md:80 6d1d6f42ada2418ba0a1de1371825b9f msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +#: ../../src/introduction/quick-start.md:82 1cd924fe8ace4a82ad8701f37b5e7d84 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +#: ../../src/introduction/quick-start.md:88 aa297c52cd964291a47bb91c0135156b msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1184,46 +1148,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +#: ../../src/introduction/quick-start.md:96 28b02c90397745bfbacc03c3b1034939 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 +#: ../../src/introduction/quick-start.md:97 ef2a4f39f01049b891868b84d968c0dd msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +#: ../../src/introduction/quick-start.md:98 89e3fa8dceda4f0cb1cfdfd1f17fe4df msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +#: ../../src/introduction/quick-start.md:99 7cd178223ba94d1ab3ee8cc5f13a8dcf msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +#: ../../src/introduction/quick-start.md:100 46f6f8d050ce4f8c897056167d9707a7 msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +#: ../../src/introduction/quick-start.md:101 5ee00ee409b746dc951ca1d4c360e624 msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +#: ../../src/introduction/quick-start.md:102 d4af972281174b8999eab55ee0ab1a0e msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +#: ../../src/setup.md:9 80401cfffae042ab9ec4b3754af04b25 msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1231,19 +1195,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 32f86f911ebe4a4c94975f81742333f3 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 +#: d5f1ad2b95ad46d48f8f2ca5e357bb5d msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf +#: c53ceee943ad4acea779e072b9137889 msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1254,37 +1218,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: 7dfe9dffbf5744299bf232599644c7f6 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: ../../src/topics/staging-input-files.md:15 00709fa451134ee09a0d808e101f28ed +#: 991172e201ec4796992a349dee44f090 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: 1f3c23a4769043ca985b8ddfed19391d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb +#: f81b43c7cb194a1cad8672129223c833 msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a +#: a20073a8f5374eb1bc8531ff33e622b6 msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 +#: d08869beca3a4774baf1097b63e79474 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1295,11 +1259,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +#: ../../src/topics/best-practices.md:1 109b773789024b2b9c063a6169c6169f msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +#: ../../src/topics/best-practices.md:3 959fa04f88e54d42b9b774cc95d85ee0 msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1307,13 +1271,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +#: ../../src/topics/best-practices.md:8 64674980c3f24c45bbfbf3f957dda55e msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +#: ../../src/topics/best-practices.md:11 90f2e4265919446a902e17627f4420e2 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1329,7 +1293,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +#: ../../src/topics/best-practices.md:20 6b5f91a749fd44b5acfd6071c9913342 msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1339,43 +1303,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +#: ../../src/topics/best-practices.md:26 5fe2962837b14f0e9989063be4a506c3 msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +#: ../../src/topics/best-practices.md:28 4e1bdea962ed4618884cb9d1d59d7509 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +#: ../../src/topics/best-practices.md:37 37eff4ca02e843259f6ffa38e4a87a04 msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +#: ../../src/topics/best-practices.md:40 ae47231c203d40a98c10045038ea9b65 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +#: ../../src/topics/best-practices.md:44 018a6d5dbf1044559b365c7b9017eb3f msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +#: ../../src/topics/best-practices.md:47 e073d8f990c44b09a73d642cfe49bebd msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +#: ../../src/topics/best-practices.md:50 e04fae88d9b64493ac69eaee24585098 msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1383,13 +1347,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +#: ../../src/topics/best-practices.md:55 b26b9c9b1c4346a297a31c9721f0172a msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +#: ../../src/topics/best-practices.md:58 b50500c3c3f54b16a535a16175a44653 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1401,44 +1365,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +#: ../../src/topics/best-practices.md:66 623f3a804199449bb85e23e00c8bb507 msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +#: ../../src/topics/best-practices.md:69 effea0b1356447c0899ca0746667ea31 msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +#: ../../src/topics/best-practices.md:73 00e8ef87864c4ca2b2c1c0548b02b38d msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +#: ../../src/topics/best-practices.md:76 6e6f48d70b894a6c959ca30fe6bad772 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +#: ../../src/topics/best-practices.md:78 02fe08760a4a4ab49e96f4e51316a81d msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +#: ../../src/topics/best-practices.md:82 172ed7915a654964ba63f860b2d65330 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +#: ../../src/topics/best-practices.md:85 4d0a2871a7484e21b3c39c4dbaaa63fc msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1446,31 +1410,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +#: ../../src/topics/best-practices.md:90 1eea9f1e284447718141f5417b6bb433 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +#: ../../src/topics/best-practices.md:93 509411d353fe4314b087b81b09ea960b msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +#: ../../src/topics/best-practices.md:97 a54bc80bf08243bba67d98dd682ee134 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +#: ../../src/topics/command-line-tool.md:1 69ecdaea24ef42eebef9d86e5d716b11 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +#: ../../src/topics/command-line-tool.md:3 3cc5847468d1478bb5589dee68147189 msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1478,52 +1442,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +#: ../../src/topics/command-line-tool.md:8 98c6bc409420485095ae65d6b0b9a3a0 msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +#: ../../src/topics/command-line-tool.md:19 ebe23e5378514f888a9ec32a2adb1e98 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +#: ../../src/topics/command-line-tool.md:50 387cfe85604f424f8d31c4a4c9c15edb msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +#: ../../src/topics/command-line-tool.md:57 7b1d65754e854693bb60289c97d3fb5d msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +#: ../../src/topics/command-line-tool.md:68 f440cef729c8410281432307a4da8d55 msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +#: ../../src/topics/command-line-tool.md:69 4fbb8ceb1b59480583ac611142167049 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +#: ../../src/topics/command-line-tool.md:83 b87869204838415bbf694214e3680593 msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: 12cf5f2264504c44a2173e858bb2c283 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d +#: 7694f9cabfe04308bbddd2c88ae6d9b9 msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1532,17 +1496,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff +#: b557dc4f8ef549b98f59412a918643de msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: 3011eb003c084285b30cfa56a8da45b6 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df +#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1550,7 +1514,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 +#: ce78b2d147054da895beba66d0ecdab4 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1560,7 +1524,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa +#: a973846ec5a946eeaff02c5b00997da9 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1568,13 +1532,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb -#: ca03defa3ad14cf698171cb09e3055c1 +#: 294fd83a97a64249bac38f7482159372 9e8eb1542db640ff9e300649ce50dc9d +#: ccec7f73b9d948e79a6cdf32bc124092 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d +#: 22948f19cb78485f8f86244686a35c09 msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1582,7 +1546,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c +#: 001d9579bfce438e865377fb9c2df776 msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1594,7 +1558,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 +#: e62618db8995428bb3f260e03ac8f459 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1604,19 +1568,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f -#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 -#: f924d65fed0c4cb5b0a019b084a8b535 +#: 457756c4e9544f068af897113358cc89 6d5ae75431424ea788c3440606f22940 +#: 98e0548845fa447fb05a29c9fc2f17b5 de5e8aad4e3046bf9bfc2ad8ccba17d0 +#: e9801b2142cd45368a73ef9b121c1d08 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +#: ../../src/topics/custom-types.md:1 ee2bca9bdbb74b60a706c3118d6a17ba msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +#: ../../src/topics/custom-types.md:3 e63ae9694f40438d872d141ae824a42d msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1625,21 +1589,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +#: ../../src/topics/custom-types.md:9 750fdd4c270e46a09f79e867358f7414 msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +#: ../../src/topics/custom-types.md:12 b3f688cc82444ef7a7a0aa63dac39cac msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +#: ../../src/topics/custom-types.md:18 3638be18b4f64cf08053d512e590dda3 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +#: ../../src/topics/custom-types.md:24 7d5b9c21739c48f18c13614ca6967f6b msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1648,13 +1612,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +#: ../../src/topics/custom-types.md:30 8fea29993f944d8d8d3181afa29bd0a6 msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +#: ../../src/topics/custom-types.md:46 02d0b648d70f49d7892f690be06df585 msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1665,15 +1629,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e +#: ../../src/topics/custom-types.md:53 0743bef42b9a42328849c8c2f9da9eed msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +#: ../../src/topics/custom-types.md:55 85c5d0cbbc6243a6823f5eeac0f85dd9 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +#: ../../src/topics/custom-types.md:61 be848f30769543eb9c0be55263e3f758 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1681,7 +1645,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +#: ../../src/topics/custom-types.md:76 cbff44a64ba4432cb59a82f82c2f0103 msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1691,26 +1655,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +#: ../../src/topics/environment-variables.md:1 617f1c0084cf42d9be4c7a8fa5a48432 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +#: ../../src/topics/environment-variables.md:3 cee79afa3c6f43c29ef05e06b7843d35 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +#: ../../src/topics/environment-variables.md:7 225903b11efa417989df42de86ad2451 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +#: ../../src/topics/expression-tool.md:1 1a5f058290064c1cad05e63eb127fcbb msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +#: ../../src/topics/expression-tool.md:3 74ad8d69cf294ae880dbbe28e25b3545 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1718,32 +1682,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +#: ../../src/topics/expression-tool.md:8 5293e8ee9b3b4f59947cfc164ef111c4 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +#: ../../src/topics/expression-tool.md:17 ffa1955c759942c68e7589429e5ea86b msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +#: ../../src/topics/expression-tool.md:48 038bc0ba5f6a405a8255a7be76979baf msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +#: ../../src/topics/expression-tool.md:67 fae1c63de02e48c0969a98e4c49b2e06 msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +#: ../../src/topics/expressions.md:1 7093a94695524851a5463193f0701b78 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +#: ../../src/topics/expressions.md:3 dc8274ecb15948c29a31db89b12a58bd msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1751,7 +1715,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +#: ../../src/topics/expressions.md:9 cec8eef8a5aa49778ecedd4195ab9f2c msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1760,67 +1724,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: ../../src/topics/expressions.md:16 df100967597043c78112bf43b520cfab msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +#: ../../src/topics/expressions.md:22 59ccf4daba39406581a6bc2d9bb1b7d2 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +#: ../../src/topics/expressions.md:25 570cc75699dd4e0a987fc9aca9a01ee4 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +#: ../../src/topics/expressions.md:31 9e123723048546d495ed5110d7177708 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +#: ../../src/topics/expressions.md:35 26543894f6e04270b89ab702451bcc89 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +#: ../../src/topics/expressions.md:37 f403c1d4e43a4aa0aef8488d2b5a6262 msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +#: ../../src/topics/expressions.md:47 249dffb569a944c897ce5862e5f28fad msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +#: ../../src/topics/expressions.md:54 1641c96aca2f4923885fe8a509eb3a49 msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +#: ../../src/topics/expressions.md:62 bc63405a0d964df2bd9493996abc48fe msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +#: ../../src/topics/expressions.md:64 5c191d1420db4e26aca31c1b1e34cb75 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +#: ../../src/topics/expressions.md:66 d6a5c65e824a4bbc94578df9597d4716 msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 -#: 1acb064f7a4a482aa0174bdc847c6382 +#: ../../src/topics/parameter-references.md:64 a7ff51fe564748229a88a0d3044dbc17 +#: c12625211cc542b68cb51365a63eef00 msgid "`arguments`" msgstr "" @@ -1828,32 +1792,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e -#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 -#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: ../../src/topics/parameter-references.md:86 05c34a5a2e404a14b9d284a9d0c73bd3 +#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe +#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 +#: e7f1993580f0425098a719e83a64cc7f msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: ../../src/topics/parameter-references.md:66 2fd5b42cafe34d3185888de041818dff +#: c158e9ee5fbf4e868b152a0a5880092f msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: ../../src/topics/parameter-references.md:67 3f29e4a3087847e9af6f19166a8def9a +#: 92697d3179ec48898eaea9aba3c24dcd msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: ../../src/topics/parameter-references.md:68 c0eaef93bc3743279549bcfb8b014ca3 +#: d6722e3093884ad7b62696fbb2f48fdc msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +#: ../../src/topics/expressions.md:72 37c493fdc2f0410a9748f8faf09ce5b5 msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1864,11 +1828,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc -#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd -#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 -#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb -#: ed875a006df64f9e8a55fa5e9fa87404 +#: ../../src/topics/parameter-references.md:90 04e3eefe4ec445cb90c2fa42344aaed5 +#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 +#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef +#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 +#: c610220d06484d589313dc29faf8222c msgid "`format`" msgstr "" @@ -1877,51 +1841,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 -#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d -#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f -#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c -#: f760465a49d64d4c8468ad9c4fea62b1 +#: ../../src/topics/parameter-references.md:91 662b36e3505f4ac3bb5070bb6e055217 +#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da +#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c +#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b +#: f71216a4b35e4157aece5ffa2602d8bf msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +#: ../../src/topics/expressions.md:75 a3c775a0f04b4541a9b712bfe2e4e69a msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +#: ../../src/topics/expressions.md:77 ef16c4a9a7ea415fa399297b63b9710c msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +#: ../../src/topics/expressions.md:80 2592e429c74c4ff5b8ba68a36f060c1a msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: ../../src/topics/parameter-references.md:78 5cca4c2ad617400eb6efad4066b1839b +#: ba1fff3ebb274dfba845b3ee20ebd71f msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b -#: d555a3d991e344a5a8e1289168d7c6d1 +#: ../../src/topics/parameter-references.md:79 6914526c0a7c43a2a05438519508ee0f +#: 722d3bd7184841639b9f9a38914002da msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c -#: e9fa9430535c424fa3e8be5d460d2ba4 +#: ../../src/topics/parameter-references.md:80 737b0f9392154241ae5b56c6caa823f5 +#: 7b46d408e7e7481b91a950b2d4010c9a msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +#: ../../src/topics/expressions.md:84 f09e7371708b4c0685eef2a314791ccd msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1930,32 +1894,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c -#: b0290d1a477b48119e17cf1fed9d6dff +#: ../../src/topics/parameter-references.md:84 aa6ca1def2024c98b9d5542de1a81425 +#: e9fc5f7fa4474dfc95039b94167fe894 msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +#: ../../src/topics/expressions.md:88 6c37a1ff939748bf83a86c07c3d017fe msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 -#: e1cde4aa32c041238ed2596173c6d824 +#: ../../src/topics/parameter-references.md:87 3a8126b0a0334df890b2be2c693ea5d5 +#: 61744122b7d7494890cbe6b2fb72b9f7 msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf -#: c2a92d3eca7f4ee39cec649170eeea53 +#: ../../src/topics/parameter-references.md:88 93cb9015dacc4b50a4ef177ce4ece2e7 +#: e0c7ccc8f8664cf794cbb7330355f3fe msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +#: ../../src/topics/expressions.md:92 58a1773b1cf546d7890010fdebd47388 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1963,61 +1927,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +#: ../../src/topics/expressions.md:95 230f3227ed1144f7abe0f8c231bebbd5 msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: ../../src/topics/parameter-references.md:93 5c77dc9f8afe4dd88933943030e836f2 +#: c9534670f5f04769aa3749c3778eb705 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 -#: 718ceee9973240ec9c100977bbcc8921 +#: ../../src/topics/parameter-references.md:94 4ec8bbac5fb14371a6a4cd53d7cd6450 +#: 7b0887a8caed41b2acccf7021bb323d3 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 -#: c07ab08eb75d4528949c56a3d7c12b28 +#: ../../src/topics/parameter-references.md:95 aceedfb558b246bc87eb3eaedea187fd +#: e5e8b8c75f0f43cbb6e160e5bf810c6e msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: ../../src/topics/parameter-references.md:96 266dfb5fe6a842078baf66073cac9623 +#: fe3b9fb45e01490498c5a35c012b3de8 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: ../../src/topics/parameter-references.md:97 85f424cbfc85460f9da310aee1ff0b82 +#: ddf82b12b12d416fb65f3ce3f51bbdf0 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: ../../src/topics/parameter-references.md:98 966e88656ae5402a975022ee60646283 +#: af14fda3cca645fbb2f3c5825fe0788e msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: ../../src/topics/parameter-references.md:99 09120baec1464afb8aed4edd773bf509 +#: fec70bb106ad4d95a2d55ebdcf711afc msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +#: ../../src/topics/expressions.md:104 1dc4148caef748428a7d13caff37b1b1 msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -2025,33 +1989,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +#: ../../src/topics/expressions.md:106 947b1ca132a54ed39745cd12ebcd65e1 msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b +#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 +#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +#: ../../src/topics/expressions.md:110 5fa512d352d945e7a3e0d59b0987cd1b msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2059,22 +2023,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +#: ../../src/topics/expressions.md:116 81e91df082834d2cab7ef1f62d8ba57a msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +#: ../../src/topics/expressions.md:118 e6bfd1dc2e324992b6c3332c11ae3445 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +#: ../../src/topics/expressions.md:122 acf10261df2944ec890d754fd56c6b28 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2082,7 +2046,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +#: ../../src/topics/expressions.md:128 bda6b8f398554b0c946c2c7d96308a42 msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2092,54 +2056,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +#: ../../src/topics/expressions.md:135 454c02c3918647039c90ae387005dea6 msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +#: ../../src/topics/expressions.md:139 e1fad28bf9cb4c4c85eb74dd520ba107 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +#: ../../src/topics/expressions.md:146 9835d0b399b84a0084fe5a4d9e7e6405 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +#: ../../src/topics/expressions.md:149 410ba7a5ac6349a98460c6337ee5c4fb msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +#: ../../src/topics/expressions.md:155 d2daf50d7f3d4de18331c8fd2c8a5786 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +#: ../../src/topics/expressions.md:158 8f2015c12b2b4d5d9a800ddeaf428f25 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +#: ../../src/topics/expressions.md:164 f0ff919ffc12439d89d7b40f51ade84c msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +#: ../../src/topics/expressions.md:171 307a17a893fc4dafaec2a63a95704644 msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +#: ../../src/topics/expressions.md:175 7f393e86b114470f8dda47b2deec63aa msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +#: ../../src/topics/expressions.md:181 c3f459b87b96435583637b3f1573e658 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2148,15 +2112,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +#: ../../src/topics/expressions.md:186 9f676022eb2744839ca2109920250cb6 msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +#: ../../src/topics/expressions.md:193 ede7285f77864fb0aee6cfecc2c97fa0 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +#: ../../src/topics/expressions.md:200 c55fb184bc614ee2b6e5e64611e5df9b msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2165,11 +2129,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +#: ../../src/topics/file-formats.md:1 66b522f46ce242149386e79f63b32cf8 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +#: ../../src/topics/file-formats.md:3 64a20285785d48ca86227a0cf6353ad4 msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2177,7 +2141,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +#: ../../src/topics/file-formats.md:8 5f71bbe2c74e4260b79d4d9230d35397 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2186,34 +2150,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +#: ../../src/topics/file-formats.md:14 63bfff437e3348428f7e33ece7ec55e7 msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +#: ../../src/topics/file-formats.md:17 6ce83d9c06e4436881aa47d94ef41e0b msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +#: ../../src/topics/file-formats.md:20 55006c594abf4e70a38e979568fadcf4 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +#: ../../src/topics/file-formats.md:32 1a1905ff2d624eca952c8a53b3bee678 msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +#: ../../src/topics/file-formats.md:34 368ff92476b14f5c8331260eafc5acb5 msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2221,11 +2185,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +#: ../../src/topics/file-formats.md:39 5d530afa23f349a79f54d51d40724747 msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +#: ../../src/topics/file-formats.md:45 16f965f86712483aa7f95dfa3f944a17 msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2234,80 +2198,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +#: ../../src/topics/index.md:1 dc629e2c90ed458b96107a6994676434 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +#: ../../src/topics/inputs.md:1 cf2f077cf8044079a7005e6e508dcd8c msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +#: ../../src/topics/inputs.md:3 129e1d2a71894d28b009f4846754a75d msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +#: ../../src/topics/inputs.md:5 d6791bbe575042b9a7282c69407dd907 msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +#: ../../src/topics/inputs.md:9 e8da87f8bb664334adf831995601f462 msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +#: ../../src/topics/inputs.md:13 de6c322618304207b6d1364d1ec2dc13 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +#: ../../src/topics/inputs.md:16 43bdcf6dc1b14030bff27fa53289c02c msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +#: ../../src/topics/inputs.md:18 056510b42ea64717996ab49c307bda86 msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +#: ../../src/topics/inputs.md:24 6852f5dbd9094c99bb68f2a88f76c9bc msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +#: ../../src/topics/inputs.md:26 f33b6800367248b7927d97ad7b4be5b5 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +#: ../../src/topics/inputs.md:33 8ad812d7e88f4cbba83228ffb1711576 msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +#: ../../src/topics/inputs.md:40 cc680bbf091a46f8b4b3dbe6324c040a msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +#: ../../src/topics/inputs.md:44 446ac81f078d46289a18f494748f482c msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +#: ../../src/topics/inputs.md:47 3d6d958d111943f3a2139b4dbb7810db msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +#: ../../src/topics/inputs.md:53 ba0ec9157709430c822f4e91459288e2 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2315,7 +2279,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +#: ../../src/topics/inputs.md:64 2565f8fd4a15429e887aeb71eacdff1e msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2323,7 +2287,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +#: ../../src/topics/inputs.md:70 659ed5c64fb546399b741553a347b8e8 msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2331,14 +2295,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +#: ../../src/topics/inputs.md:83 3d87e69d41374fbab23b26d36c1aee03 msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +#: ../../src/topics/inputs.md:95 07bc81683e2c4ac68b379462bae95207 msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2346,7 +2310,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +#: ../../src/topics/inputs.md:109 3e304da2150f448d9e39715ac5f5deaa msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2354,7 +2318,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +#: ../../src/topics/inputs.md:124 fd8a98686e3c4c609f79ae427f1558d3 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2364,13 +2328,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +#: ../../src/topics/inputs.md:131 f1a2e1bbb1104a4fab5a7f04cac845c7 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +#: ../../src/topics/inputs.md:134 6a7f0ccd227e4f90a8c8ca96744bda68 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2381,17 +2345,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +#: ../../src/topics/inputs.md:142 1f79d115d8a145189638c68c3095396c msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +#: ../../src/topics/inputs.md:146 6e1b3e2d90184e34925891099d2b5cc1 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +#: ../../src/topics/inputs.md:148 4f6df7f13e42448eb4a53f03bc477b56 msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2401,23 +2365,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +#: ../../src/topics/inputs.md:154 dbc0b52627514ad0908969d0b4ddfdf4 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +#: ../../src/topics/inputs.md:160 f173dd96ad124470a53573c86a8df203 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 -#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d +#: ../../src/topics/outputs.md:105 af25945b530048b685891b1de4e35e72 +#: cb07caa4ff0149b3ae832be53f8d76f6 e0098a77080d4349b05ceb7735a5fdf5 msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +#: ../../src/topics/inputs.md:178 2445d2c7c2794fd3ad8b6ed8b4a9440b msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2427,7 +2391,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +#: ../../src/topics/inputs.md:185 4459819ba75647d185986a3386939494 msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2438,11 +2402,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +#: ../../src/topics/inputs.md:191 8f163bd34ded4785b6e28c8e2147e0dd msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +#: ../../src/topics/inputs.md:193 1799e11a7b9c4929a3d1379d7ea45d03 msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2450,46 +2414,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +#: ../../src/topics/inputs.md:198 9510c0b431a44b5e84e0b583de7c5446 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +#: ../../src/topics/inputs.md:204 efb4eb6f5e994b50a52fa2c707dad1ce msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +#: ../../src/topics/inputs.md:215 34599c6f10ce4104be2359a1b37f91cb msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: ../../src/topics/inputs.md:217 0663ea7918994d3f9c45c652a3ed12db msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +#: ../../src/topics/inputs.md:233 a98dda6ca4b14edba467de638bba28fc msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +#: ../../src/topics/inputs.md:236 10d0e9f8df8c47788703073b17529bc8 msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +#: ../../src/topics/inputs.md:252 9a0e1a130fba4d24a9168ca3e455cd23 msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +#: ../../src/topics/inputs.md:255 992a8c801ceb4233acf56b6bff315188 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +#: ../../src/topics/inputs.md:257 9027d23fa7074b789c3b86ca5ea17fa4 msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2497,18 +2461,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +#: ../../src/topics/inputs.md:262 68b47710a8ea4b978428b42c627944e9 msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +#: ../../src/topics/inputs.md:265 d33e4cac65d14111a89c838c4d1759b9 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +#: ../../src/topics/inputs.md:271 24cea1cf7d774b6ab56959f289cab39d msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2516,7 +2480,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +#: ../../src/topics/inputs.md:280 b866867d6f8e4d3999b62a85e6884ebc msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2524,7 +2488,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +#: ../../src/topics/inputs.md:289 80c49ed168b14d25b2f09b3b0186b44f msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2534,12 +2498,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: 71628ebe908b4cd28dd1fa17e3d2e2fb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 +#: f123ca244c23413c91405a4b84887525 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2554,7 +2518,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b +#: 23299ae1bec94b00a32a8af7eeac350f msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2562,17 +2526,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: 2495a9f2032a47c188338cb81ba429eb msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: 3fd2f3cf7bdf44089df2ce3122534801 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 +#: d5a5b8b490b640439db92da949266e4e msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2582,15 +2546,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: 5935ed94331d4b2f8ce597f31edea843 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +#: ../../src/topics/operations.md:1 5feb559552194ba58da7206c601292fe msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +#: ../../src/topics/operations.md:3 b7124ba4df9042baadc1641ee09545d6 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2598,56 +2562,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +#: ../../src/topics/operations.md:7 d34b698c62114041a64e0abce25ca935 msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +#: ../../src/topics/operations.md:10 cba2c31262bd450cbafc7ca77f4fb8fa msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +#: ../../src/topics/operations.md:16 b01be5f632104096b5af6193aab34d90 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +#: ../../src/topics/operations.md:24 60a6a02c1367403db6df3ec10f75eb69 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +#: ../../src/topics/operations.md:55 314ea7bc35154f41b2af5fa6683ca389 msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +#: ../../src/topics/operations.md:58 d81e679b13474f74bc5e1ce1e31c2bc6 msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +#: ../../src/topics/operations.md:66 d7fb27131ee44bfc82f698ee44b2bae0 msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +#: ../../src/topics/outputs.md:1 b8ef11eafd1d46e088f1277f4ac372bc msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +#: ../../src/topics/outputs.md:3 d2382ed1f644459594655d5b5b4d838a msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +#: ../../src/topics/outputs.md:5 6651632d977b44479b721174fffeda2d msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2655,7 +2619,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +#: ../../src/topics/outputs.md:10 bee5f532554241088764ac9e56abbe85 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2664,17 +2628,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +#: ../../src/topics/outputs.md:16 0c7c506f38be421399073871f64e99b0 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +#: ../../src/topics/outputs.md:19 8b60286e56cc42a8ab5f751a97adf771 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +#: ../../src/topics/outputs.md:21 fa0ad674f15348339a1eee771a6ba9e2 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2682,71 +2646,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +#: ../../src/topics/outputs.md:26 177b5f1b95a34fb9b2eb42f733d79ac8 msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +#: ../../src/topics/outputs.md:32 a08a6d8aca8e490482e127a8fd5e650e msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +#: ../../src/topics/outputs.md:38 c2c60f68b1e045f88844076e191fda9b msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +#: ../../src/topics/outputs.md:45 6d939f62526e4e6d95acb57d72f60a84 msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +#: ../../src/topics/outputs.md:51 c48edd9034364b81ad42540a98b51d91 msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +#: ../../src/topics/outputs.md:62 9ebe0186a7124dfaa30e558e8f59653a msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +#: ../../src/topics/outputs.md:65 9381b7d7c9904df0a5e16dac29c2e08f msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +#: ../../src/topics/outputs.md:67 2aa9c6916e3546b7b92fa64bb83275d1 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +#: ../../src/topics/outputs.md:71 63afb7a597fc4e459b6a7dbd40bbf6ff msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +#: ../../src/topics/outputs.md:89 7418915470f041c9af5bd39ea652de36 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +#: ../../src/topics/outputs.md:91 f82db001b58c4969b2d8bc1dcbd7cf8a msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +#: ../../src/topics/outputs.md:93 26d9f0b28d384617a8e490c1f8e26e52 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +#: ../../src/topics/outputs.md:99 cf46c971b31b4e10bf0fefb4cd028c2f msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +#: ../../src/topics/outputs.md:112 a4347983fb9945a4a2773af88e426dc9 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2755,11 +2719,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +#: ../../src/topics/parameter-references.md:1 c5489e0633114372b273098ee2c9ffd9 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +#: ../../src/topics/parameter-references.md:3 75de9fd63393429daf1ca10a85339aa7 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2772,40 +2736,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +#: ../../src/topics/parameter-references.md:13 8b5d0ada32d645be9359f43a431f5f91 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +#: ../../src/topics/parameter-references.md:19 2ed93dc8778e44209194f41b9ad193d5 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +#: ../../src/topics/parameter-references.md:25 a80dd6d9920540e9880514e04035af86 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +#: ../../src/topics/parameter-references.md:36 9de300f7b9da49f59d1c9fd96dec4a8b msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +#: ../../src/topics/parameter-references.md:47 a61f52d3c1024c3692899e05fcea4bee msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +#: ../../src/topics/parameter-references.md:51 dafc9ba578c14fd79d075160e6b7bd6b msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +#: ../../src/topics/parameter-references.md:54 28ca6cae42904559bcec98fb9d2b07cb msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2813,45 +2777,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +#: ../../src/topics/parameter-references.md:59 616c9ff9fcae489285f0bbbc67f07d29 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +#: ../../src/topics/parameter-references.md:61 ac17acd83ddb43dc9fb7a5e595ab1153 msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +#: ../../src/topics/parameter-references.md:63 156573324cde41ee8b3c47deabf43db8 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +#: ../../src/topics/parameter-references.md:69 c9725be01e8a401fb3ad9ff01339f81e msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +#: ../../src/topics/parameter-references.md:72 6797335256e2412cbbe7636507931455 msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +#: ../../src/topics/parameter-references.md:74 05a5f0fcb7454cb697e3d810d55fac26 msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +#: ../../src/topics/parameter-references.md:77 406e68280b5c4ee494632f94b635b7ad msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +#: ../../src/topics/parameter-references.md:81 2d6e2a4ff391494591bbdf8dbcc4a6ae msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2859,13 +2823,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +#: ../../src/topics/parameter-references.md:85 e71a974b29624210a107fc2d097d4196 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +#: ../../src/topics/parameter-references.md:89 b59df98754e24654bfef0b1fe1d91660 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2873,43 +2837,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +#: ../../src/topics/parameter-references.md:92 d2bccbff1ce646348fe38c776ad183e1 msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 +#: 943ba46512ce48fe8c5b62327734c503 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: bbcd43d5af7d44108aeb65075a6bd2be msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 +#: 834295755af841a78e466eea43864861 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: a6b626489bfa468e8f059ab3aa669201 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: e1dbea105aa845c38cb1f90b43847271 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb +#: e9640f47d40e45bca184eb30700df648 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2919,14 +2883,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 +#: 0456efb3718b4356ad2b277ee16de967 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 +#: f7e97f926505407f8f8e9a427e055e43 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2935,7 +2899,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 +#: ec597ff8f6ee47bc815b069335869f1f msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2951,11 +2915,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +#: ../../src/topics/staging-input-files.md:1 7467a7f6f26a459ba4ce83e4e6dfcc2b msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +#: ../../src/topics/staging-input-files.md:3 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2965,26 +2929,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: ../../src/topics/staging-input-files.md:9 a03372581fa44f9b8e3e088a4099cdd9 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +#: ../../src/topics/troubleshooting.md:1 36e082be73464be0ad5d0b681cc510da msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +#: ../../src/topics/troubleshooting.md:3 4464455b51ad4873ac13c4a63ee5fb54 msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +#: ../../src/topics/troubleshooting.md:6 ed7ff0753d1743a995f4cfedd6e5dcc2 msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +#: ../../src/topics/troubleshooting.md:8 4c2dd10dd66446058477a52fb8d2c602 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2993,7 +2957,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +#: ../../src/topics/troubleshooting.md:14 978b6a5fd5fa425fa9a18d9f0e8788da msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -3003,18 +2967,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +#: ../../src/topics/troubleshooting.md:20 000c0d6ae8bf414d9293b9f13fd2e448 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +#: ../../src/topics/troubleshooting.md:27 7e91b8811be14f8e80df39ac4c5bd316 msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +#: ../../src/topics/troubleshooting.md:35 d42799cc5bd4484bb6beb309a61e103e msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -3022,7 +2986,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +#: ../../src/topics/troubleshooting.md:44 48bb0f6666ac48648c7d969608b3bd48 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -3030,7 +2994,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +#: ../../src/topics/troubleshooting.md:48 f8876044db184cbaaca56579d0c773df msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3040,7 +3004,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +#: ../../src/topics/troubleshooting.md:59 a5a3d408dbe34cfda4dd0b2abe67e7d7 msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3050,15 +3014,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +#: ../../src/topics/using-containers.md:1 4c240a18c4e6441189489011242c1efd msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +#: ../../src/topics/using-containers.md:3 e37e76ef376a4ee695e600998906ec1c msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +#: ../../src/topics/using-containers.md:5 51a307b0ba7c4c1d89309ba8d2250471 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3071,35 +3035,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +#: ../../src/topics/using-containers.md:15 13cc38d72d34468fa4eb6d91f23ff105 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +#: ../../src/topics/using-containers.md:18 42a48398d3ef4b03bd7395120f2cfb42 msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +#: ../../src/topics/using-containers.md:21 d59387b433bc4ecfaf7e72026624db02 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +#: ../../src/topics/using-containers.md:27 d963418ccc0b4803bbc758d718ccb5aa msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +#: ../../src/topics/using-containers.md:33 a224d1510c9e46aab23d8bdc03c349dd msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +#: ../../src/topics/using-containers.md:44 0a82f8a45b0546aaac4c976dcc98014a msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3112,23 +3076,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +#: ../../src/topics/using-containers.md:52 bc418a2a535e49359c4cd44b373bbe02 msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +#: ../../src/topics/using-containers.md:55 a799fba2322944cea00e413c08066536 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +#: ../../src/topics/using-containers.md:69 35379c6b972940bd8451f10b74dd793e msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +#: ../../src/topics/using-containers.md:72 2d5265525ad544a0b64ad2cf07aacc26 msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3136,44 +3100,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +#: ../../src/topics/workflows.md:1 e2521b89596d42f8a87a3207fd6c32f2 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +#: ../../src/topics/workflows.md:3 3676f23b63e142cb8e5715ae07216a47 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +#: ../../src/topics/workflows.md:13 00725aed13a440ca8b3c4f9155fbee99 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +#: ../../src/topics/workflows.md:41 2e38a4f9072b4ad9bbb74f943d22084d msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +#: ../../src/topics/workflows.md:51 2b9f4035ea864b6db50c861a1819289d msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +#: ../../src/topics/workflows.md:81 28e9064780e7418a8e02a22f92e34404 msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +#: ../../src/topics/workflows.md:91 66ce14a10d2d4dc497d3ed71e11ed8b8 msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +#: ../../src/topics/workflows.md:150 8dc00528c3d2426c8a3492a8191f1d81 msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3181,33 +3145,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +#: ../../src/topics/workflows.md:160 f9ef5e258f7c4971a8543d1dfed711a8 msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +#: ../../src/topics/workflows.md:165 324bc51071d743ea80124c23880ddc0a msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +#: ../../src/topics/workflows.md:167 d8c13e01976b43a1af34c11a7bc36897 msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +#: ../../src/topics/workflows.md:170 43910a8ab4484e529a17df418b1aedbb msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +#: ../../src/topics/workflows.md:180 7ad12d67e815400c94080804b9285629 msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3220,34 +3184,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +#: ../../src/topics/workflows.md:183 457d5a31c79143acae2683d95d27f7a3 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +#: ../../src/topics/workflows.md:185 a2a73901bf634547900d08b9a1ac8889 msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +#: ../../src/topics/workflows.md:191 f347d80e62384b14acf6423675e5359a msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +#: ../../src/topics/workflows.md:205 2a845a4f3f98428fb82f3ca7ce038a6e msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +#: ../../src/topics/workflows.md:212 e2007c74d5f449a882809d6b91c010bf msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#: ../../src/topics/workflows.md:221 7f5e53ee7cf94be2bff45ef64db28a24 msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3255,7 +3219,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +#: ../../src/topics/workflows.md:233 a0d076b7b8b048478580c99ef0c8429f msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3264,7 +3228,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +#: ../../src/topics/workflows.md:248 7fd926c18ad548e98845e9b5134dd6f2 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3275,7 +3239,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +#: ../../src/topics/workflows.md:256 789fbd47f8564cceb430ef3c0bc90e9b msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3283,7 +3247,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +#: ../../src/topics/workflows.md:261 45c4d0492d6143ca9cebe81e9b2cf3ae msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3293,13 +3257,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +#: ../../src/topics/workflows.md:267 73bd3da2af8545928d5ea71d0f7454f6 msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +#: ../../src/topics/workflows.md:278 15ce3d2700424f0fbb280d602ccebcf6 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3309,11 +3273,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +#: ../../src/topics/workflows.md:285 af4268f19202436eb0a7e8c6bed5e386 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +#: ../../src/topics/workflows.md:287 94a4eadca6b949d79de2990a0150eee8 msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3321,17 +3285,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +#: ../../src/topics/workflows.md:297 09c1619e8cbd4febbb637f7e99ad5890 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +#: ../../src/topics/workflows.md:300 677ea7a27eb64568ab3689142d6efe70 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +#: ../../src/topics/workflows.md:309 097e6d47f9394e62b80110700492783a msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3339,7 +3303,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +#: ../../src/topics/workflows.md:314 e93affce8c104bf6977182047c1f1077 msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +#: ../../src/topics/workflows.md:322 06c9e04ba890473b851240a0fa9c3b12 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3361,7 +3325,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +#: ../../src/topics/workflows.md:336 0380dc1fe3aa48e4b62283b7b2a611d8 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3370,7 +3334,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +#: ../../src/topics/workflows.md:341 49b251f7a313492ea60504b00109e526 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3380,7 +3344,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +#: ../../src/topics/workflows.md:347 7ee55702d7dd4679a24ff052f6f0cbeb msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3388,14 +3352,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +#: ../../src/topics/workflows.md:366 85d7e2e270874aa6b9f477cec0f48154 msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +#: ../../src/topics/workflows.md:383 570e94513c984c09ad6aa255f534216d msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3404,7 +3368,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +#: ../../src/topics/workflows.md:389 a107258662fb4bd4a9a3d8754e34d1e9 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3413,7 +3377,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +#: ../../src/topics/workflows.md:394 fc1a6502d831458ab8371a575cea47e2 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3421,11 +3385,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +#: ../../src/topics/workflows.md:398 2d10806bf1ce4e26b92adda61efc0862 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +#: ../../src/topics/workflows.md:400 046c5e134de94b629cc22d416f3c9182 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3436,7 +3400,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +#: ../../src/topics/workflows.md:411 52fa22d3277940049fbb589a3ea73433 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3444,23 +3408,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: ../../src/topics/workflows.md:415 6043beb96c2c49648011ec556aa9e986 msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +#: ../../src/topics/workflows.md:421 5ac4310515124e2986724425bed5651f msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +#: ../../src/topics/workflows.md:429 7958e91d5c2f4046aa9d2070a900f9ae msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +#: ../../src/topics/workflows.md:441 2db234d776fe4fd38bab07245dcb783a msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3468,7 +3432,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +#: ../../src/topics/workflows.md:445 7cfb17230e284ee7b6e2a00efe8eeb74 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3476,59 +3440,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: ../../src/topics/workflows.md:450 4311ac98544e4fb0b2f4b24985710a01 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +#: ../../src/topics/workflows.md:452 780f9c72e6c34c39918642c7e2477355 msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +#: ../../src/topics/workflows.md:458 cc4a7316db644b438cbaa181ad9ef2d3 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +#: ../../src/topics/workflows.md:466 dfc461a03fe8487794837904febb8b63 msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +#: ../../src/topics/workflows.md:469 1e83485b00b64dfaba897bd8d772e0f0 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +#: ../../src/topics/workflows.md:472 d0321d6805ec4d3abf3877d02a0a417f msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +#: ../../src/topics/workflows.md:480 d7d77e807b3048c7bdf89558f76804cb msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +#: ../../src/topics/workflows.md:483 8d9b8be147fc4a71922dde858842e543 msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +#: ../../src/topics/workflows.md:489 34b7705416a745a6a42e6d402c0757ed msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +#: ../../src/topics/workflows.md:491 257adcee9da64d5c987f3b64efd20ab0 msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +#: ../../src/topics/workflows.md:497 fa6ed5d0c14f42f4aa3c5144648db22c msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3546,7 +3510,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +#: ../../src/topics/workflows.md:509 333e8ce458d54de394526769f96d12d2 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3554,38 +3518,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +#: ../../src/topics/workflows.md:513 b819e8a5df6e4fa495924095709669ef msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +#: ../../src/topics/workflows.md:519 f1955468a1364d44a930db77c9c4b495 msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +#: ../../src/topics/workflows.md:522 8c3b9b645a204d02b2c73a205e8ec296 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +#: ../../src/topics/workflows.md:524 4d88b9c186cd4502adbf752e8a70b6ce msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +#: ../../src/topics/workflows.md:527 9927673564024ba5833b5ac271737857 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +#: ../../src/topics/workflows.md:566 84f4ed7ce2004742b8db9087104a469a msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +#: ../../src/topics/workflows.md:573 2b5f9757adca4490a149c7f45e14fcb5 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3594,7 +3558,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +#: ../../src/topics/workflows.md:587 0418de720813442f81ecff293c9448b5 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3602,62 +3566,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +#: ../../src/topics/workflows.md:607 524eec63be8248ae982939c975ef50a2 msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +#: ../../src/topics/workflows.md:627 5e99f9912cc549a7890e2934425eb943 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +#: ../../src/topics/yaml-guide.md:1 b0121ee087d6424fbb0ea5957a7b0b8c msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +#: ../../src/topics/yaml-guide.md:6 49e9f6b3a06840289decf3f557860f87 msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +#: ../../src/topics/yaml-guide.md:13 ed9eebec0b3d4b72ba65507d37757a37 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +#: ../../src/topics/yaml-guide.md:16 bf9b255a24a84f3ba989a223492b8f41 msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +#: ../../src/topics/yaml-guide.md:18 e79fa0b7f8b14810a3a20908ef92bc55 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +#: ../../src/topics/yaml-guide.md:19 290e2035f903417cbecb5dc5f09d6ebe msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +#: ../../src/topics/yaml-guide.md:20 d420730151534f1a89076588a3358f09 msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: ../../src/topics/yaml-guide.md:21 a6b5378bbe1e4bee9e37a765bddf75f7 msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: ../../src/topics/yaml-guide.md:22 6e4d9465dc2b454d96b02d7ad1817795 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +#: ../../src/topics/yaml-guide.md:24 a649d4af5f434dac9395e013ec4836bb msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +#: ../../src/topics/yaml-guide.md:26 446190a298834b73bda068286e8490cf msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3667,7 +3631,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +#: ../../src/topics/yaml-guide.md:42 2f35c012ff174721bffe66a3f58a804f msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3676,7 +3640,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +#: ../../src/topics/yaml-guide.md:51 43127c98c9d94aedac61cee67929c1a6 msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3687,28 +3651,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: ../../src/topics/yaml-guide.md:61 dc4fe561203c4c38a9caea5bd6eff2cd msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +#: ../../src/topics/yaml-guide.md:63 f924e4896db2424d99ce8c9da14c599a msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +#: ../../src/topics/yaml-guide.md:76 bf7646f5f925485c842a6d34140e40b8 msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +#: ../../src/topics/yaml-guide.md:79 c483e61dec8949fa96bb893d422888a0 msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +#: ../../src/topics/yaml-guide.md:81 85fcb523d0e34a499eae04d304887f7b msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3719,7 +3683,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +#: ../../src/topics/yaml-guide.md:104 83d47c8736a34f3cbf09e3997845e4f4 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3732,11 +3696,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +#: ../../src/topics/yaml-guide.md:127 c698fb3d37bc403e9aeb679b8fc0e15e msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +#: ../../src/topics/yaml-guide.md:129 ae8af2f0eeda4aec97201211dfa965c7 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3747,26 +3711,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +#: ../../src/topics/yaml-guide.md:146 2ee87aa465cd41fda16a61e242f8c9d0 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +#: ../../src/topics/yaml-guide.md:167 0a6fd4469ff24b61b3ad001b09eead18 msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +#: ../../src/topics/yaml-guide.md:169 b96ba19bce9341d39c46054e1f10fe8f msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +#: ../../src/topics/yaml-guide.md:177 903f30af3d0c45cfb61063936a8097a7 msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +#: ../../src/topics/yaml-guide.md:184 ede8db7c0a58432e8a1c416e937a06d2 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3776,52 +3740,52 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +#: ../../src/topics/yaml-guide.md:194 c8b53615476a4a1fbef2420d93bac94e msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +#: ../../src/topics/yaml-guide.md:196 ea03cb5525cc491f9feb5c4780b38fee msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +#: ../../src/tutorials.md:1 92fd3a5e31714eab859dd630af2e78cf msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +#: ../../src/tutorials.md:5 de660ecdb5b44c97a0e519d00b232497 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +#: ../../src/tutorials.md:7 5afc1e1288e74ed0985e61e5164479c7 msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +#: ../../src/tutorials.md:9 862dc7ac81e54b1fb3d4c2f961b8810e msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +#: ../../src/tutorials.md:11 e2c94c0e1c7048d38cd7aa2c465a859d msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +#: ../../src/tutorials.md:13 b63253780f51467a95207d820d13ac39 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +#: ../../src/tutorials.md:15 6d06ca7ed5df4560aaed286f4fe33928 msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +#: ../../src/tutorials.md:17 5448df4a6a8f431d80e269bcd480e19e msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po index 3584ce39..3ed0733d 100644 --- a/locales/pt/LC_MESSAGES/user_guide.po +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -9,142 +9,115 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-25 16:53+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" -"Language-Team: Portuguese \n" "Language: pt\n" +"Language-Team: Portuguese \n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" +"Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=2; plural=n > 1;\n" -"X-Generator: Weblate 4.16-dev\n" +"Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.rst:2 75de2be8809847b8bf1ccd42aa694a24 msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.rst:5 2edd71801f6245ef821887a74f21b94c msgid "Instructional Material" msgstr "" -#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d -msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable " -"summary of (and not a substitute for) the [full legal text of the CC BY " -"4.0 license][cc-by-legal]." +#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." msgstr "" "Todo o material instrucional do projeto Common Workflow Language e " -"alterações na estrutura também são disponibilizados sob a [licença Creative " -"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " -"humanos de (e não um substituto para) o [texto legal completo da licença CC " -"BY 4.0][cc-by-legal]." +"alterações na estrutura também são disponibilizados sob a `licença " +"Creative Commons Attribution `_. O seguinte é um resumo " +"legível por humanos de (e não um substituto para) o `texto legal completo" +" da licença CC BY 4.0 `_." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.rst:12 90cc755d172e4c82b882b4ee620fe652 msgid "You are free:" msgstr "Você tem o direito de:" -#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" +#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 +msgid "to **Share**—copy and redistribute the material in any medium or format" msgstr "" -"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " -"formato" +"**Compartilhar**—copiar e redistribuir o material em qualquer suporte " +"ou formato" -#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" +#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 +msgid "to **Adapt**—remix, transform, and build upon the material" +msgstr "**Adaptar**—remixar, transformar, e criar a partir do material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.rst:18 430ff4de74924bc3a3b2c7e809ea4456 msgid "for any purpose, even commercially." msgstr "para qualquer fim, mesmo que comercial." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e -msgid "" -"The licensor cannot revoke these freedoms as long as you follow the " -"license terms:" +#: ../../LICENSE.rst:20 2173e2af49be41ee97a74c4e879faf25 +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" msgstr "" "O licenciante não pode revogar estes direitos desde que você respeite os " "termos da licença." -#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 -msgid "" -"**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow " -"Language project, and, where practical, linking to " -"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" -"human], and indicate if changes were made. You may do so in any " -"reasonable manner, but not in any way that suggests the licensor endorses" -" you or your use." +#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 +msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" "Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " "trabalho deriva de um trabalho que é «Copyright © The Common Workflow " -"Language project», e, quando prático, criar uma ligação para https://www." -"commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " -"se foram feitas alterações. Você pode fazê-lo de qualquer forma razoável, " -"mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " -"uso." +"Language project», e, quando prático, criar uma ligação para " +"https://www.commonwl.org/%20),%20fornecer%20um%20%60link%20para%20a%20licen%C3%A7a%20%3Ccc-by-" +"human_>`_, e indicar se foram feitas alterações. Você pode fazê-lo de " +"qualquer forma razoável, mas não de uma forma que sugira que o " +"licenciante o apoia ou aprova o seu uso." -#: ../../LICENSE.md:32 8161753b7526445db319210044566200 -msgid "" -"**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything " -"the license permits. With the understanding that:" +#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 +msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" -"**Sem restrições adicionais**---Você não pode aplicar termos jurídicos ou " -"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " -"algo que a licença permita. Com o entendimento de que:" +"**Sem restrições adicionais**—Você não pode aplicar termos jurídicos ou" +" medidas de caráter tecnológico que restrinjam legalmente outros de " +"fazerem algo que a licença permita. Com o entendimento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 -msgid "" -"You do not have to comply with the license for elements of the material " -"in the public domain or where your use is permitted by an applicable " -"exception or limitation." +#: ../../LICENSE.rst:35 f6aae4a5cd0547118c8a3240ca2b4be6 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." msgstr "" "Não tem de cumprir com os termos da licença relativamente a elementos do " -"material que estejam no domínio público ou cuja utilização seja permitida " -"por uma exceção ou limitação que seja aplicável." +"material que estejam no domínio público ou cuja utilização seja permitida" +" por uma exceção ou limitação que seja aplicável." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 -msgid "" -"No warranties are given. The license may not give you all of the " -"permissions necessary for your intended use. For example, other rights " -"such as publicity, privacy, or moral rights may limit how you use the " -"material." +#: ../../LICENSE.rst:38 a40c173be35b4c1b92e83f42bfe2382c +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" "Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " "autorizações necessárias para o uso pretendido. Por exemplo, outros " -"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " -"podem limitar o uso do material." +"direitos, tais como direitos de imagem, de privacidade ou direitos " +"morais, podem limitar o uso do material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.rst:44 3d7ca3f2cede4d5f998bf014bd970748 msgid "Software" msgstr "Software" -#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." msgstr "" "Salvo indicação em contrário, os programas de exemplo e outro software " -"fornecido pelo projecto Common Workflow Language são disponibilizados sob a [" -"licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." +"fornecido pelo projecto Common Workflow Language são disponibilizados sob" +" a `licença Apache 2.0 `_ aprovada pela `OSI`_." -#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +#: ../../LICENSE.rst:50 9c4d58a1129a4d4eb4db1bfabbeddb6e msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, " -"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " -"See the License for the specific language governing permissions and " -"limitations under the License." +"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT" +" WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the" +" License for the specific language governing permissions and limitations " +"under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 -#: eab02dc13915490bb3c9ba744d78b6a7 +#: 5ad4be9b62d54c95a913795b514676fd bdd540403a5746ff99edf2dcad0e3122 +#: dfc7702e073140c985cf47272a20214d msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -153,30 +126,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +#: ../../src/episodes.md:9 3060770b3bef41d7bcfcdfb413d7689c msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +#: ../../src/faq.md:1 48bb9f628b344ba1a3b67ae1cb264e3c msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +#: ../../src/faq.md:11 7e3684e9672643738846756e1ebafd18 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 +#: ../../src/faq.md:41 187ceabb7fd9480bb8cf0f2da47f65ef msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +#: ../../src/faq.md:43 b548b76bcc85420a9b30792386105139 msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -184,94 +157,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f +#: ../../src/faq.md:59 9ce692b78ead47e4b0f8cdae8837d35b msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +#: ../../src/faq.md:61 6df1201c159343da9e7515379980d6a0 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 +#: ../../src/faq.md:82 f9ab1d0dc1c842b6abb5385268c1d3bd msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +#: ../../src/faq.md:84 9f6a84ab6a9343b6ad7db826f8964362 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +#: ../../src/faq.md:86 fa50e4fa990b42d1ba4c0f4ae1e5caa1 msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +#: ../../src/faq.md:89 3a871012fcfd4f3ebeca0cb86ec93435 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +#: ../../src/faq.md:95 d954edfff2584288ac8c600733070d2e msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +#: ../../src/faq.md:97 af6b1e37d6be4450a761854480ec9aab msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be +#: ../../src/faq.md:104 31f4a2d43062493ca64c648f80afc8e9 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +#: ../../src/faq.md:113 41c54e71b6cd4f63b2a619a515240d34 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +#: ../../src/faq.md:115 8edc3541ad134ab5a1d23c724f1f0a4e msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 +#: ../../src/faq.md:135 ac0ea81eba8842a18801ab03cbf80a57 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +#: ../../src/faq.md:138 52be1a5640234feabe958ff7ade33653 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +#: ../../src/faq.md:140 c6db734d5aef4f4f99676bdebf9c83c9 msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 +#: ../../src/faq.md:165 a9f7b47c0dd741739795da39bf114879 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +#: ../../src/faq.md:167 e3fdd9228b924905a4a1f4b2b7ad7159 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +#: ../../src/faq.md:188 3f7cda1437cc48f18745a827ebb74582 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +#: ../../src/faq.md:190 5aeaba2cae64442e816bbd458aee833a msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -279,22 +252,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +#: ../../src/faq.md:194 5af827a402834978addd82c70be6b5ab msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +#: ../../src/faq.md:196 6d69e42bd8e443c4b19d80807c7efd6b msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +#: ../../src/faq.md:199 404640397b6e40c2a2cd5cf85ab3b1c0 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +#: ../../src/faq.md:201 1682c2486e224770b62269709a8663cf msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -303,25 +276,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd +#: ../../src/faq.md:229 9078fc009bc145808813c9cc2b734b58 msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +#: ../../src/faq.md:231 d4b5a54a400c409cb7984428f6a03ec8 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +#: ../../src/faq.md:247 9e8dbee6e8f84d08b1a54fffa06394ef msgid "" msgstr "" -#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c +#: ../../src/faq.md:248 1d846bfb5f054d09a4afad1da8e4b642 msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +#: ../../src/faq.md:250 2d0e95fec8084787b734388d60188574 msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -329,26 +302,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +#: ../../src/faq.md:267 eccc4a364330470fa474dcaaa3433390 msgid "" msgstr "" -#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 +#: ../../src/faq.md:268 e945f6a337af4e4686bed482a4fe6c39 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +#: ../../src/faq.md:270 8a3efaa0ad1548428bcfd6e01d135cdc msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 +#: ../../src/faq.md:322 cdab644adc5643708870fb08c06cbfca msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +#: ../../src/faq.md:324 089a5a0b076b44aeaab4d69ee3c79f97 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -357,77 +330,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 +#: ../../src/faq.md:342 561172559c6f41a68819608fd9e58bb0 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +#: ../../src/faq.md:344 c5ee4946d2e840abaa3dc796a62652c7 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 +#: ../../src/faq.md:349 4f2069a2113c414db18eca95550e9e09 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +#: ../../src/faq.md:351 31f3390e6771414ba7bf57c044c4b0c4 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c +#: ../../src/faq.md:359 3b77ce4930ae46d5be9f6965e8c54727 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +#: ../../src/faq.md:361 06f36bbe4d3840229b7374f27b86ae80 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +#: ../../src/faq.md:363 3cb2f70d00274a4dafd972ccd8c519c2 msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +#: ../../src/faq.md:371 093a1529262043ef84a99675054938e0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +#: ../../src/faq.md:373 45b6d9acbfaa47e5984184f7da554d0a msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +#: ../../src/faq.md:375 5705c9bacca5405ca6f14315a5575db8 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +#: ../../src/faq.md:384 82bfc285b59a439ca97d3278997f0fce msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +#: ../../src/faq.md:396 181d5130101d45ccb22aebae3d154c2f msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +#: ../../src/faq.md:410 e864390b5ddb423aaa10e9d33d257dc1 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 +#: ../../src/faq.md:423 fe637c32fb15427a9045679b5da42ec5 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +#: ../../src/faq.md:436 1f8004b9df8547029d82e57f9abdc979 msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 +#: ../../src/faq.md:442 70990dc5a0034099921ceb89c89e2dcc msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +#: ../../src/faq.md:445 f679e26f18d9455f945fd13361a9c906 msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -436,11 +409,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 +#: ../../src/faq.md:450 fcd0273dbdd84e728cfd8fbe239f2a01 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +#: ../../src/faq.md:452 173ddbd1e7c64927a8dcb12a2a2140f8 msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -451,22 +424,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +#: ../../src/index.md:1 662fe273e2fb4042b688512955e450a1 msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +#: ../../src/index.md:3 a15b52205f0145feaac298510e4d678a msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +#: ../../src/index.md:7 512aa0c7166b429e8116f71eef007f79 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +#: ../../src/index.md:9 b1b19e17a18540939cb3bb7f8a700cab msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -475,11 +448,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +#: ../../src/index.md:16 d58b36ac43ac44139897be752fbb1f87 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +#: ../../src/index.md:18 6726cf3585a646a8b4cbeb543cf84a38 msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -487,7 +460,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +#: ../../src/index.md:23 2e504aa7c46a426fa959e7254e9a84a5 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -495,15 +468,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +#: ../../src/index.md:28 e7be0df0838b432d9c7f296d777f120b msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +#: ../../src/introduction/basic-concepts.md:1 173e0816db20432c8d9dba1de5393dee msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +#: ../../src/introduction/basic-concepts.md:3 30eacc583f6841719e2142d283811d97 msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -514,18 +487,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +#: ../../src/introduction/basic-concepts.md:10 791b8f38a14147bbaa174c7eb595f17e msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +#: ../../src/introduction/basic-concepts.md:21 1a3989dcbb9844b39d84bf6df6b352ed msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +#: ../../src/introduction/basic-concepts.md:25 db1bbc6e980f404f9f3fcd08e92ee9a3 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -535,18 +508,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +#: ../../src/introduction/basic-concepts.md:33 acc7887c65974114996f700a38a7eccc msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +#: ../../src/introduction/basic-concepts.md:37 d2476d9bcff44f21b8d84a3a0d87a246 msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +#: ../../src/introduction/basic-concepts.md:39 f86415e4d78e48c4a8a76ced81221b98 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -555,24 +528,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +#: ../../src/introduction/basic-concepts.md:44 c5524d73708c4c779980528864506fd4 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +#: ../../src/introduction/basic-concepts.md:51 ac46a9f8850a434bac5bc2b41ee6294e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: 9bba7c4f783942e4a299603430601363 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 +#: e2140e0f0e7747ef8383887c20a7945a msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -581,39 +554,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 15bf490724cd46dcbcfab44633c5a9a2 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 51d52d051e654a8395239f88df7c9d8c msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: eb496cc818524fa7bae5a22ddd00a19c msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: c4a22d12e7f149ff901d27de32b9361d msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 7618de899a7043989d77baacf62eb7b2 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a +#: 6f1544a220664b79b04bf008058b5a91 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 +#: fbd14ac9a2f541478a320ed4cbc69e13 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -622,7 +595,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef +#: da4dba50d25d4533b3dbb92f54d32a30 msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -631,7 +604,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#: ce11c9f8d65c4268984d0384d95144cc msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -641,7 +614,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 +#: 3a201aa497e84f70855bb2251e7e3281 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -650,24 +623,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 +#: b78f7fa2be1c4bb090f6da895457ad1e msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 +#: f7e95d264ffa4e2db0864faccd9e5a0e msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 +#: 3f1e5b01e49a4dc1b1c99936a4589afc msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee +#: 03c3048f38ae4938a484cf02001877b3 msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -677,7 +650,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e +#: f9715b5ec65c405c849bb030c1927060 msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -686,12 +659,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: 442662f50e9e4620970ce32b1b127969 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 +#: 2b34c786af3840e88f29d214e19dc837 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -705,7 +678,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a +#: dd6aadff8cf54ce78ea6b317afbaddb0 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -714,7 +687,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee +#: fe7f1f0b28434f8aaf0f6ac6589a83f0 msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -723,71 +696,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: d10cf45b3c7f49dc98bc0e5d1246f224 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 -#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf +#: ../../src/introduction/quick-start.md:94 332b6e8b831e4bc5aed3745938230a57 +#: ce7fc63b808d4499b9bf9828c2dafe35 ebf339ed376a4d3b89b15b4d5afe593b msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 8badec9987ba40609cf1f626172b2b2d msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 +#: c75a8b4bf0e24781bf6713cf6f013cd1 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 +#: 79b146ffe6d74e1b8f6019251dc4b7c2 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 +#: 07cca9a33d8f4b77ac6ad35ca8b95655 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: 31db11c8ddf2423192a8b2063b3e91c2 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b +#: d81dd96143ea444aa78ff45cfa0584b3 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +#: ../../src/introduction/index.md:1 c54984605872472190ae7771809a20db msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +#: ../../src/introduction/index.md:3 01a237b8ec2f46c9acd31d142591ce75 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +#: ../../src/introduction/prerequisites.md:1 3fb9888b666945eab1e3ff109646c574 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +#: ../../src/introduction/prerequisites.md:6 5fb0486762354f93853fff209f835c08 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -797,11 +770,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +#: ../../src/introduction/prerequisites.md:12 5f1e7a608e0b455196d191c845a5c98e msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +#: ../../src/introduction/prerequisites.md:14 7ba4b5c51be24f5392949d06ee42e018 msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -809,29 +782,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +#: ../../src/introduction/prerequisites.md:19 e2d3e6dd13b14d819a504c35da6fe8e7 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +#: ../../src/introduction/prerequisites.md:21 91251d1f0efb4d4cb083b4517ff3107a msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +#: ../../src/introduction/prerequisites.md:24 6ad263e267514c5fb05794d3d76d418d msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +#: ../../src/introduction/prerequisites.md:25 8a3bfd72dccf4a8c874a96aebcbe5cb7 msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +#: ../../src/introduction/prerequisites.md:26 5195706d9c6c4573aff135fd539759a2 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +#: ../../src/introduction/prerequisites.md:29 9c4506915e4c40599527bc1d2b18645b msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -841,11 +814,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +#: ../../src/introduction/prerequisites.md:35 37d9eb784ec1425786158f98e3f63890 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +#: ../../src/introduction/prerequisites.md:41 572f493a985141a1b92dafbdba92790d msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -853,7 +826,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +#: ../../src/introduction/prerequisites.md:46 9606d3c4849f4b17b2e55a298210f055 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -861,26 +834,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +#: ../../src/introduction/prerequisites.md:51 754fc59967d94ffa935284676d55ffed msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +#: ../../src/introduction/prerequisites.md:62 2905c6362d4146e8b35bc74744841972 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +#: ../../src/introduction/prerequisites.md:65 091278ece252483a9838fb771de3e04e msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +#: ../../src/introduction/prerequisites.md:67 0928a5c668c3414a945bc9eda147892c msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +#: ../../src/introduction/prerequisites.md:73 56f3c481762848298214a88e559fc0f9 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -891,23 +864,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +#: ../../src/introduction/prerequisites.md:79 710c266ab4a5477b84d6ea987420fa20 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 +#: ../../src/introduction/prerequisites.md:84 cc353db5da2546bb88a77ce1a202ff9d msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +#: ../../src/introduction/prerequisites.md:86 b62df08ec96f4cdb887600079856dd76 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: ../../src/introduction/prerequisites.md:91 97e02557293440d1a58ba659dad21113 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +#: ../../src/introduction/prerequisites.md:93 0935c3ff01634c75b5c91546dc36c7b9 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -918,32 +891,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +#: ../../src/introduction/prerequisites.md:101 cfb37fd605164a8d9cc75bf892ce97c0 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +#: ../../src/introduction/prerequisites.md:104 5f06a7a6aae343d989a5b30979c600f6 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +#: ../../src/introduction/prerequisites.md:111 5f956260f3874b6dbeaf3ad7ecc09c9a msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +#: ../../src/introduction/prerequisites.md:115 d35e4effec554a638d6c3047ef3fd05f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +#: ../../src/introduction/prerequisites.md:120 15a1f944a0d642729d3736ed1c907074 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +#: ../../src/introduction/prerequisites.md:125 fa34c808bb494ddfa3f3926bc42e650c msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -951,30 +924,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: ../../src/introduction/prerequisites.md:129 0c15f62eb7534e809f625f3fa213e92d msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 +#: ../../src/introduction/prerequisites.md:135 d67719a6f0ce4ba1bb6152a10507b729 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +#: ../../src/introduction/prerequisites.md:137 1c96e75281844bfab0578bab2e816854 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +#: ../../src/introduction/prerequisites.md:144 bece1fc3c3f842b0b30d8f1b7fbfc200 msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +#: ../../src/introduction/prerequisites.md:148 a7caa36b0f83448b91ef2e76e30abc51 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +#: ../../src/introduction/prerequisites.md:154 39321e93e9994fcca20b425aa45c2894 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -984,47 +957,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +#: ../../src/introduction/prerequisites.md:161 601cf500d76c4e0287af4429a46b36d2 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +#: ../../src/introduction/prerequisites.md:163 b286d5359e184ef58054c72df4014629 msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +#: ../../src/introduction/prerequisites.md:167 e14423edd829401faed0950772123240 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +#: ../../src/introduction/prerequisites.md:171 889c44360bd54a0e85e7f0e61aa6593c msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +#: ../../src/introduction/prerequisites.md:172 7b9bff73624947ac90a99c7880e2e911 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +#: ../../src/introduction/prerequisites.md:174 c5ff687c86ef4ccaae25d8bcfbd5f873 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +#: ../../src/introduction/prerequisites.md:177 0a610a9632064deb824afd0719429d3a msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +#: ../../src/introduction/prerequisites.md:181 ec0c47438a5242cb99dffa7a4997e95a msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1032,7 +1005,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +#: ../../src/introduction/prerequisites.md:185 aae94ac2114641f186eac0f4117223eb msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1040,57 +1013,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +#: ../../src/introduction/prerequisites.md:191 209e072724ed4d27b37e9bff6d55d811 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +#: ../../src/introduction/prerequisites.md:198 3bf47876e3694e6cadb05123326459cb msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +#: ../../src/introduction/prerequisites.md:199 459a65b8e67c4a9aaa03138c1abe94ad msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +#: ../../src/introduction/quick-start.md:1 898eb29ac7714c69840b795633953a05 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +#: ../../src/introduction/quick-start.md:3 2a658bd2d8ce4533ab7e056fc3a3ffcf msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +#: ../../src/introduction/quick-start.md:7 32dd2e28cf0f40b6930750f0162355eb msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +#: ../../src/introduction/quick-start.md:12 471c47d311074ecfac071b6d52d9cfb6 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +#: ../../src/introduction/quick-start.md:16 5078140028ea4d04973cb9cd20f0607e msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +#: ../../src/introduction/quick-start.md:22 ab127d4ba0a44526ab129587a8160923 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +#: ../../src/introduction/quick-start.md:27 d5cc6b4295a74f3586f022b0227759b3 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1098,11 +1071,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +#: ../../src/introduction/quick-start.md:32 585a4fe583ce44e180a062742b3b0849 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +#: ../../src/introduction/quick-start.md:34 0d81b0c9ea58420789d1d71cca32ce88 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1110,11 +1083,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +#: ../../src/introduction/quick-start.md:39 ea4ab0782d8049d8b1b89cea4ae60048 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +#: ../../src/introduction/quick-start.md:47 f6f3b7453a254f828bd4c9e9fef92bed msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1122,32 +1095,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +#: ../../src/introduction/quick-start.md:51 3bf9050175d4444ebbbabe219412574f msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +#: ../../src/introduction/quick-start.md:53 e03f72a14dcf4bf38ce8232598ca761d msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +#: ../../src/introduction/quick-start.md:57 3dcfb2facd324dccb3084c02487625dc msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +#: ../../src/introduction/quick-start.md:62 b8531da183964b02bca19f818ec076d4 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +#: ../../src/introduction/quick-start.md:65 7ba1ddebeb2843179fe99fc410b193c6 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +#: ../../src/introduction/quick-start.md:70 a6dc303e9d284b60bf1102212505ca27 msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1155,21 +1128,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +#: ../../src/introduction/quick-start.md:74 59ac7830ae3e4d7cb1bf503e8c90fe30 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +#: ../../src/introduction/quick-start.md:80 6d1d6f42ada2418ba0a1de1371825b9f msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +#: ../../src/introduction/quick-start.md:82 1cd924fe8ace4a82ad8701f37b5e7d84 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +#: ../../src/introduction/quick-start.md:88 aa297c52cd964291a47bb91c0135156b msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1177,46 +1150,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +#: ../../src/introduction/quick-start.md:96 28b02c90397745bfbacc03c3b1034939 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 +#: ../../src/introduction/quick-start.md:97 ef2a4f39f01049b891868b84d968c0dd msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +#: ../../src/introduction/quick-start.md:98 89e3fa8dceda4f0cb1cfdfd1f17fe4df msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +#: ../../src/introduction/quick-start.md:99 7cd178223ba94d1ab3ee8cc5f13a8dcf msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +#: ../../src/introduction/quick-start.md:100 46f6f8d050ce4f8c897056167d9707a7 msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +#: ../../src/introduction/quick-start.md:101 5ee00ee409b746dc951ca1d4c360e624 msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +#: ../../src/introduction/quick-start.md:102 d4af972281174b8999eab55ee0ab1a0e msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +#: ../../src/setup.md:9 80401cfffae042ab9ec4b3754af04b25 msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1224,19 +1197,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 32f86f911ebe4a4c94975f81742333f3 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 +#: d5f1ad2b95ad46d48f8f2ca5e357bb5d msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf +#: c53ceee943ad4acea779e072b9137889 msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1247,37 +1220,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: 7dfe9dffbf5744299bf232599644c7f6 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: ../../src/topics/staging-input-files.md:15 00709fa451134ee09a0d808e101f28ed +#: 991172e201ec4796992a349dee44f090 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: 1f3c23a4769043ca985b8ddfed19391d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb +#: f81b43c7cb194a1cad8672129223c833 msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a +#: a20073a8f5374eb1bc8531ff33e622b6 msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 +#: d08869beca3a4774baf1097b63e79474 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1288,11 +1261,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +#: ../../src/topics/best-practices.md:1 109b773789024b2b9c063a6169c6169f msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +#: ../../src/topics/best-practices.md:3 959fa04f88e54d42b9b774cc95d85ee0 msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1300,13 +1273,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +#: ../../src/topics/best-practices.md:8 64674980c3f24c45bbfbf3f957dda55e msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +#: ../../src/topics/best-practices.md:11 90f2e4265919446a902e17627f4420e2 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1322,7 +1295,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +#: ../../src/topics/best-practices.md:20 6b5f91a749fd44b5acfd6071c9913342 msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1332,43 +1305,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +#: ../../src/topics/best-practices.md:26 5fe2962837b14f0e9989063be4a506c3 msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +#: ../../src/topics/best-practices.md:28 4e1bdea962ed4618884cb9d1d59d7509 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +#: ../../src/topics/best-practices.md:37 37eff4ca02e843259f6ffa38e4a87a04 msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +#: ../../src/topics/best-practices.md:40 ae47231c203d40a98c10045038ea9b65 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +#: ../../src/topics/best-practices.md:44 018a6d5dbf1044559b365c7b9017eb3f msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +#: ../../src/topics/best-practices.md:47 e073d8f990c44b09a73d642cfe49bebd msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +#: ../../src/topics/best-practices.md:50 e04fae88d9b64493ac69eaee24585098 msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1376,13 +1349,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +#: ../../src/topics/best-practices.md:55 b26b9c9b1c4346a297a31c9721f0172a msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +#: ../../src/topics/best-practices.md:58 b50500c3c3f54b16a535a16175a44653 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1394,44 +1367,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +#: ../../src/topics/best-practices.md:66 623f3a804199449bb85e23e00c8bb507 msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +#: ../../src/topics/best-practices.md:69 effea0b1356447c0899ca0746667ea31 msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +#: ../../src/topics/best-practices.md:73 00e8ef87864c4ca2b2c1c0548b02b38d msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +#: ../../src/topics/best-practices.md:76 6e6f48d70b894a6c959ca30fe6bad772 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +#: ../../src/topics/best-practices.md:78 02fe08760a4a4ab49e96f4e51316a81d msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +#: ../../src/topics/best-practices.md:82 172ed7915a654964ba63f860b2d65330 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +#: ../../src/topics/best-practices.md:85 4d0a2871a7484e21b3c39c4dbaaa63fc msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1439,31 +1412,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +#: ../../src/topics/best-practices.md:90 1eea9f1e284447718141f5417b6bb433 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +#: ../../src/topics/best-practices.md:93 509411d353fe4314b087b81b09ea960b msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +#: ../../src/topics/best-practices.md:97 a54bc80bf08243bba67d98dd682ee134 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +#: ../../src/topics/command-line-tool.md:1 69ecdaea24ef42eebef9d86e5d716b11 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +#: ../../src/topics/command-line-tool.md:3 3cc5847468d1478bb5589dee68147189 msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1471,52 +1444,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +#: ../../src/topics/command-line-tool.md:8 98c6bc409420485095ae65d6b0b9a3a0 msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +#: ../../src/topics/command-line-tool.md:19 ebe23e5378514f888a9ec32a2adb1e98 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +#: ../../src/topics/command-line-tool.md:50 387cfe85604f424f8d31c4a4c9c15edb msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +#: ../../src/topics/command-line-tool.md:57 7b1d65754e854693bb60289c97d3fb5d msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +#: ../../src/topics/command-line-tool.md:68 f440cef729c8410281432307a4da8d55 msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +#: ../../src/topics/command-line-tool.md:69 4fbb8ceb1b59480583ac611142167049 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +#: ../../src/topics/command-line-tool.md:83 b87869204838415bbf694214e3680593 msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: 12cf5f2264504c44a2173e858bb2c283 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d +#: 7694f9cabfe04308bbddd2c88ae6d9b9 msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1525,17 +1498,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff +#: b557dc4f8ef549b98f59412a918643de msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: 3011eb003c084285b30cfa56a8da45b6 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df +#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1543,7 +1516,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 +#: ce78b2d147054da895beba66d0ecdab4 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1553,7 +1526,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa +#: a973846ec5a946eeaff02c5b00997da9 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1561,13 +1534,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb -#: ca03defa3ad14cf698171cb09e3055c1 +#: 294fd83a97a64249bac38f7482159372 9e8eb1542db640ff9e300649ce50dc9d +#: ccec7f73b9d948e79a6cdf32bc124092 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d +#: 22948f19cb78485f8f86244686a35c09 msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1575,7 +1548,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c +#: 001d9579bfce438e865377fb9c2df776 msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1587,7 +1560,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 +#: e62618db8995428bb3f260e03ac8f459 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1597,19 +1570,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f -#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 -#: f924d65fed0c4cb5b0a019b084a8b535 +#: 457756c4e9544f068af897113358cc89 6d5ae75431424ea788c3440606f22940 +#: 98e0548845fa447fb05a29c9fc2f17b5 de5e8aad4e3046bf9bfc2ad8ccba17d0 +#: e9801b2142cd45368a73ef9b121c1d08 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +#: ../../src/topics/custom-types.md:1 ee2bca9bdbb74b60a706c3118d6a17ba msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +#: ../../src/topics/custom-types.md:3 e63ae9694f40438d872d141ae824a42d msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1618,21 +1591,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +#: ../../src/topics/custom-types.md:9 750fdd4c270e46a09f79e867358f7414 msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +#: ../../src/topics/custom-types.md:12 b3f688cc82444ef7a7a0aa63dac39cac msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +#: ../../src/topics/custom-types.md:18 3638be18b4f64cf08053d512e590dda3 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +#: ../../src/topics/custom-types.md:24 7d5b9c21739c48f18c13614ca6967f6b msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1641,13 +1614,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +#: ../../src/topics/custom-types.md:30 8fea29993f944d8d8d3181afa29bd0a6 msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +#: ../../src/topics/custom-types.md:46 02d0b648d70f49d7892f690be06df585 msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1658,15 +1631,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e +#: ../../src/topics/custom-types.md:53 0743bef42b9a42328849c8c2f9da9eed msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +#: ../../src/topics/custom-types.md:55 85c5d0cbbc6243a6823f5eeac0f85dd9 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +#: ../../src/topics/custom-types.md:61 be848f30769543eb9c0be55263e3f758 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1674,7 +1647,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +#: ../../src/topics/custom-types.md:76 cbff44a64ba4432cb59a82f82c2f0103 msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1684,26 +1657,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +#: ../../src/topics/environment-variables.md:1 617f1c0084cf42d9be4c7a8fa5a48432 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +#: ../../src/topics/environment-variables.md:3 cee79afa3c6f43c29ef05e06b7843d35 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +#: ../../src/topics/environment-variables.md:7 225903b11efa417989df42de86ad2451 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +#: ../../src/topics/expression-tool.md:1 1a5f058290064c1cad05e63eb127fcbb msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +#: ../../src/topics/expression-tool.md:3 74ad8d69cf294ae880dbbe28e25b3545 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1711,32 +1684,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +#: ../../src/topics/expression-tool.md:8 5293e8ee9b3b4f59947cfc164ef111c4 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +#: ../../src/topics/expression-tool.md:17 ffa1955c759942c68e7589429e5ea86b msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +#: ../../src/topics/expression-tool.md:48 038bc0ba5f6a405a8255a7be76979baf msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +#: ../../src/topics/expression-tool.md:67 fae1c63de02e48c0969a98e4c49b2e06 msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +#: ../../src/topics/expressions.md:1 7093a94695524851a5463193f0701b78 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +#: ../../src/topics/expressions.md:3 dc8274ecb15948c29a31db89b12a58bd msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1744,7 +1717,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +#: ../../src/topics/expressions.md:9 cec8eef8a5aa49778ecedd4195ab9f2c msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1753,67 +1726,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: ../../src/topics/expressions.md:16 df100967597043c78112bf43b520cfab msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +#: ../../src/topics/expressions.md:22 59ccf4daba39406581a6bc2d9bb1b7d2 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +#: ../../src/topics/expressions.md:25 570cc75699dd4e0a987fc9aca9a01ee4 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +#: ../../src/topics/expressions.md:31 9e123723048546d495ed5110d7177708 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +#: ../../src/topics/expressions.md:35 26543894f6e04270b89ab702451bcc89 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +#: ../../src/topics/expressions.md:37 f403c1d4e43a4aa0aef8488d2b5a6262 msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +#: ../../src/topics/expressions.md:47 249dffb569a944c897ce5862e5f28fad msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +#: ../../src/topics/expressions.md:54 1641c96aca2f4923885fe8a509eb3a49 msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +#: ../../src/topics/expressions.md:62 bc63405a0d964df2bd9493996abc48fe msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +#: ../../src/topics/expressions.md:64 5c191d1420db4e26aca31c1b1e34cb75 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +#: ../../src/topics/expressions.md:66 d6a5c65e824a4bbc94578df9597d4716 msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 -#: 1acb064f7a4a482aa0174bdc847c6382 +#: ../../src/topics/parameter-references.md:64 a7ff51fe564748229a88a0d3044dbc17 +#: c12625211cc542b68cb51365a63eef00 msgid "`arguments`" msgstr "" @@ -1821,32 +1794,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e -#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 -#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: ../../src/topics/parameter-references.md:86 05c34a5a2e404a14b9d284a9d0c73bd3 +#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe +#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 +#: e7f1993580f0425098a719e83a64cc7f msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: ../../src/topics/parameter-references.md:66 2fd5b42cafe34d3185888de041818dff +#: c158e9ee5fbf4e868b152a0a5880092f msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: ../../src/topics/parameter-references.md:67 3f29e4a3087847e9af6f19166a8def9a +#: 92697d3179ec48898eaea9aba3c24dcd msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: ../../src/topics/parameter-references.md:68 c0eaef93bc3743279549bcfb8b014ca3 +#: d6722e3093884ad7b62696fbb2f48fdc msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +#: ../../src/topics/expressions.md:72 37c493fdc2f0410a9748f8faf09ce5b5 msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1857,11 +1830,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc -#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd -#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 -#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb -#: ed875a006df64f9e8a55fa5e9fa87404 +#: ../../src/topics/parameter-references.md:90 04e3eefe4ec445cb90c2fa42344aaed5 +#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 +#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef +#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 +#: c610220d06484d589313dc29faf8222c msgid "`format`" msgstr "" @@ -1870,51 +1843,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 -#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d -#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f -#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c -#: f760465a49d64d4c8468ad9c4fea62b1 +#: ../../src/topics/parameter-references.md:91 662b36e3505f4ac3bb5070bb6e055217 +#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da +#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c +#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b +#: f71216a4b35e4157aece5ffa2602d8bf msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +#: ../../src/topics/expressions.md:75 a3c775a0f04b4541a9b712bfe2e4e69a msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +#: ../../src/topics/expressions.md:77 ef16c4a9a7ea415fa399297b63b9710c msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +#: ../../src/topics/expressions.md:80 2592e429c74c4ff5b8ba68a36f060c1a msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: ../../src/topics/parameter-references.md:78 5cca4c2ad617400eb6efad4066b1839b +#: ba1fff3ebb274dfba845b3ee20ebd71f msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b -#: d555a3d991e344a5a8e1289168d7c6d1 +#: ../../src/topics/parameter-references.md:79 6914526c0a7c43a2a05438519508ee0f +#: 722d3bd7184841639b9f9a38914002da msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c -#: e9fa9430535c424fa3e8be5d460d2ba4 +#: ../../src/topics/parameter-references.md:80 737b0f9392154241ae5b56c6caa823f5 +#: 7b46d408e7e7481b91a950b2d4010c9a msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +#: ../../src/topics/expressions.md:84 f09e7371708b4c0685eef2a314791ccd msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1923,32 +1896,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c -#: b0290d1a477b48119e17cf1fed9d6dff +#: ../../src/topics/parameter-references.md:84 aa6ca1def2024c98b9d5542de1a81425 +#: e9fc5f7fa4474dfc95039b94167fe894 msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +#: ../../src/topics/expressions.md:88 6c37a1ff939748bf83a86c07c3d017fe msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 -#: e1cde4aa32c041238ed2596173c6d824 +#: ../../src/topics/parameter-references.md:87 3a8126b0a0334df890b2be2c693ea5d5 +#: 61744122b7d7494890cbe6b2fb72b9f7 msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf -#: c2a92d3eca7f4ee39cec649170eeea53 +#: ../../src/topics/parameter-references.md:88 93cb9015dacc4b50a4ef177ce4ece2e7 +#: e0c7ccc8f8664cf794cbb7330355f3fe msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +#: ../../src/topics/expressions.md:92 58a1773b1cf546d7890010fdebd47388 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1956,61 +1929,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +#: ../../src/topics/expressions.md:95 230f3227ed1144f7abe0f8c231bebbd5 msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: ../../src/topics/parameter-references.md:93 5c77dc9f8afe4dd88933943030e836f2 +#: c9534670f5f04769aa3749c3778eb705 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 -#: 718ceee9973240ec9c100977bbcc8921 +#: ../../src/topics/parameter-references.md:94 4ec8bbac5fb14371a6a4cd53d7cd6450 +#: 7b0887a8caed41b2acccf7021bb323d3 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 -#: c07ab08eb75d4528949c56a3d7c12b28 +#: ../../src/topics/parameter-references.md:95 aceedfb558b246bc87eb3eaedea187fd +#: e5e8b8c75f0f43cbb6e160e5bf810c6e msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: ../../src/topics/parameter-references.md:96 266dfb5fe6a842078baf66073cac9623 +#: fe3b9fb45e01490498c5a35c012b3de8 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: ../../src/topics/parameter-references.md:97 85f424cbfc85460f9da310aee1ff0b82 +#: ddf82b12b12d416fb65f3ce3f51bbdf0 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: ../../src/topics/parameter-references.md:98 966e88656ae5402a975022ee60646283 +#: af14fda3cca645fbb2f3c5825fe0788e msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: ../../src/topics/parameter-references.md:99 09120baec1464afb8aed4edd773bf509 +#: fec70bb106ad4d95a2d55ebdcf711afc msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +#: ../../src/topics/expressions.md:104 1dc4148caef748428a7d13caff37b1b1 msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -2018,33 +1991,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +#: ../../src/topics/expressions.md:106 947b1ca132a54ed39745cd12ebcd65e1 msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b +#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 +#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +#: ../../src/topics/expressions.md:110 5fa512d352d945e7a3e0d59b0987cd1b msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2052,22 +2025,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +#: ../../src/topics/expressions.md:116 81e91df082834d2cab7ef1f62d8ba57a msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +#: ../../src/topics/expressions.md:118 e6bfd1dc2e324992b6c3332c11ae3445 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +#: ../../src/topics/expressions.md:122 acf10261df2944ec890d754fd56c6b28 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2075,7 +2048,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +#: ../../src/topics/expressions.md:128 bda6b8f398554b0c946c2c7d96308a42 msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2085,54 +2058,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +#: ../../src/topics/expressions.md:135 454c02c3918647039c90ae387005dea6 msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +#: ../../src/topics/expressions.md:139 e1fad28bf9cb4c4c85eb74dd520ba107 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +#: ../../src/topics/expressions.md:146 9835d0b399b84a0084fe5a4d9e7e6405 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +#: ../../src/topics/expressions.md:149 410ba7a5ac6349a98460c6337ee5c4fb msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +#: ../../src/topics/expressions.md:155 d2daf50d7f3d4de18331c8fd2c8a5786 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +#: ../../src/topics/expressions.md:158 8f2015c12b2b4d5d9a800ddeaf428f25 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +#: ../../src/topics/expressions.md:164 f0ff919ffc12439d89d7b40f51ade84c msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +#: ../../src/topics/expressions.md:171 307a17a893fc4dafaec2a63a95704644 msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +#: ../../src/topics/expressions.md:175 7f393e86b114470f8dda47b2deec63aa msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +#: ../../src/topics/expressions.md:181 c3f459b87b96435583637b3f1573e658 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2141,15 +2114,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +#: ../../src/topics/expressions.md:186 9f676022eb2744839ca2109920250cb6 msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +#: ../../src/topics/expressions.md:193 ede7285f77864fb0aee6cfecc2c97fa0 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +#: ../../src/topics/expressions.md:200 c55fb184bc614ee2b6e5e64611e5df9b msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2158,11 +2131,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +#: ../../src/topics/file-formats.md:1 66b522f46ce242149386e79f63b32cf8 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +#: ../../src/topics/file-formats.md:3 64a20285785d48ca86227a0cf6353ad4 msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2170,7 +2143,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +#: ../../src/topics/file-formats.md:8 5f71bbe2c74e4260b79d4d9230d35397 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2179,34 +2152,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +#: ../../src/topics/file-formats.md:14 63bfff437e3348428f7e33ece7ec55e7 msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +#: ../../src/topics/file-formats.md:17 6ce83d9c06e4436881aa47d94ef41e0b msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +#: ../../src/topics/file-formats.md:20 55006c594abf4e70a38e979568fadcf4 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +#: ../../src/topics/file-formats.md:32 1a1905ff2d624eca952c8a53b3bee678 msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +#: ../../src/topics/file-formats.md:34 368ff92476b14f5c8331260eafc5acb5 msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2214,11 +2187,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +#: ../../src/topics/file-formats.md:39 5d530afa23f349a79f54d51d40724747 msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +#: ../../src/topics/file-formats.md:45 16f965f86712483aa7f95dfa3f944a17 msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2227,80 +2200,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +#: ../../src/topics/index.md:1 dc629e2c90ed458b96107a6994676434 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +#: ../../src/topics/inputs.md:1 cf2f077cf8044079a7005e6e508dcd8c msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +#: ../../src/topics/inputs.md:3 129e1d2a71894d28b009f4846754a75d msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +#: ../../src/topics/inputs.md:5 d6791bbe575042b9a7282c69407dd907 msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +#: ../../src/topics/inputs.md:9 e8da87f8bb664334adf831995601f462 msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +#: ../../src/topics/inputs.md:13 de6c322618304207b6d1364d1ec2dc13 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +#: ../../src/topics/inputs.md:16 43bdcf6dc1b14030bff27fa53289c02c msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +#: ../../src/topics/inputs.md:18 056510b42ea64717996ab49c307bda86 msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +#: ../../src/topics/inputs.md:24 6852f5dbd9094c99bb68f2a88f76c9bc msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +#: ../../src/topics/inputs.md:26 f33b6800367248b7927d97ad7b4be5b5 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +#: ../../src/topics/inputs.md:33 8ad812d7e88f4cbba83228ffb1711576 msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +#: ../../src/topics/inputs.md:40 cc680bbf091a46f8b4b3dbe6324c040a msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +#: ../../src/topics/inputs.md:44 446ac81f078d46289a18f494748f482c msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +#: ../../src/topics/inputs.md:47 3d6d958d111943f3a2139b4dbb7810db msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +#: ../../src/topics/inputs.md:53 ba0ec9157709430c822f4e91459288e2 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2308,7 +2281,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +#: ../../src/topics/inputs.md:64 2565f8fd4a15429e887aeb71eacdff1e msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2316,7 +2289,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +#: ../../src/topics/inputs.md:70 659ed5c64fb546399b741553a347b8e8 msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2324,14 +2297,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +#: ../../src/topics/inputs.md:83 3d87e69d41374fbab23b26d36c1aee03 msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +#: ../../src/topics/inputs.md:95 07bc81683e2c4ac68b379462bae95207 msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2339,7 +2312,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +#: ../../src/topics/inputs.md:109 3e304da2150f448d9e39715ac5f5deaa msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2347,7 +2320,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +#: ../../src/topics/inputs.md:124 fd8a98686e3c4c609f79ae427f1558d3 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2357,13 +2330,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +#: ../../src/topics/inputs.md:131 f1a2e1bbb1104a4fab5a7f04cac845c7 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +#: ../../src/topics/inputs.md:134 6a7f0ccd227e4f90a8c8ca96744bda68 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2374,17 +2347,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +#: ../../src/topics/inputs.md:142 1f79d115d8a145189638c68c3095396c msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +#: ../../src/topics/inputs.md:146 6e1b3e2d90184e34925891099d2b5cc1 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +#: ../../src/topics/inputs.md:148 4f6df7f13e42448eb4a53f03bc477b56 msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2394,23 +2367,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +#: ../../src/topics/inputs.md:154 dbc0b52627514ad0908969d0b4ddfdf4 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +#: ../../src/topics/inputs.md:160 f173dd96ad124470a53573c86a8df203 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 -#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d +#: ../../src/topics/outputs.md:105 af25945b530048b685891b1de4e35e72 +#: cb07caa4ff0149b3ae832be53f8d76f6 e0098a77080d4349b05ceb7735a5fdf5 msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +#: ../../src/topics/inputs.md:178 2445d2c7c2794fd3ad8b6ed8b4a9440b msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2420,7 +2393,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +#: ../../src/topics/inputs.md:185 4459819ba75647d185986a3386939494 msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2431,11 +2404,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +#: ../../src/topics/inputs.md:191 8f163bd34ded4785b6e28c8e2147e0dd msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +#: ../../src/topics/inputs.md:193 1799e11a7b9c4929a3d1379d7ea45d03 msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2443,46 +2416,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +#: ../../src/topics/inputs.md:198 9510c0b431a44b5e84e0b583de7c5446 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +#: ../../src/topics/inputs.md:204 efb4eb6f5e994b50a52fa2c707dad1ce msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +#: ../../src/topics/inputs.md:215 34599c6f10ce4104be2359a1b37f91cb msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: ../../src/topics/inputs.md:217 0663ea7918994d3f9c45c652a3ed12db msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +#: ../../src/topics/inputs.md:233 a98dda6ca4b14edba467de638bba28fc msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +#: ../../src/topics/inputs.md:236 10d0e9f8df8c47788703073b17529bc8 msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +#: ../../src/topics/inputs.md:252 9a0e1a130fba4d24a9168ca3e455cd23 msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +#: ../../src/topics/inputs.md:255 992a8c801ceb4233acf56b6bff315188 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +#: ../../src/topics/inputs.md:257 9027d23fa7074b789c3b86ca5ea17fa4 msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2490,18 +2463,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +#: ../../src/topics/inputs.md:262 68b47710a8ea4b978428b42c627944e9 msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +#: ../../src/topics/inputs.md:265 d33e4cac65d14111a89c838c4d1759b9 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +#: ../../src/topics/inputs.md:271 24cea1cf7d774b6ab56959f289cab39d msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2509,7 +2482,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +#: ../../src/topics/inputs.md:280 b866867d6f8e4d3999b62a85e6884ebc msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2517,7 +2490,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +#: ../../src/topics/inputs.md:289 80c49ed168b14d25b2f09b3b0186b44f msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2527,12 +2500,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: 71628ebe908b4cd28dd1fa17e3d2e2fb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 +#: f123ca244c23413c91405a4b84887525 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2547,7 +2520,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b +#: 23299ae1bec94b00a32a8af7eeac350f msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2555,17 +2528,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: 2495a9f2032a47c188338cb81ba429eb msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: 3fd2f3cf7bdf44089df2ce3122534801 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 +#: d5a5b8b490b640439db92da949266e4e msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2575,15 +2548,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: 5935ed94331d4b2f8ce597f31edea843 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +#: ../../src/topics/operations.md:1 5feb559552194ba58da7206c601292fe msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +#: ../../src/topics/operations.md:3 b7124ba4df9042baadc1641ee09545d6 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2591,56 +2564,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +#: ../../src/topics/operations.md:7 d34b698c62114041a64e0abce25ca935 msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +#: ../../src/topics/operations.md:10 cba2c31262bd450cbafc7ca77f4fb8fa msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +#: ../../src/topics/operations.md:16 b01be5f632104096b5af6193aab34d90 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +#: ../../src/topics/operations.md:24 60a6a02c1367403db6df3ec10f75eb69 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +#: ../../src/topics/operations.md:55 314ea7bc35154f41b2af5fa6683ca389 msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +#: ../../src/topics/operations.md:58 d81e679b13474f74bc5e1ce1e31c2bc6 msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +#: ../../src/topics/operations.md:66 d7fb27131ee44bfc82f698ee44b2bae0 msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +#: ../../src/topics/outputs.md:1 b8ef11eafd1d46e088f1277f4ac372bc msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +#: ../../src/topics/outputs.md:3 d2382ed1f644459594655d5b5b4d838a msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +#: ../../src/topics/outputs.md:5 6651632d977b44479b721174fffeda2d msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2648,7 +2621,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +#: ../../src/topics/outputs.md:10 bee5f532554241088764ac9e56abbe85 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2657,17 +2630,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +#: ../../src/topics/outputs.md:16 0c7c506f38be421399073871f64e99b0 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +#: ../../src/topics/outputs.md:19 8b60286e56cc42a8ab5f751a97adf771 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +#: ../../src/topics/outputs.md:21 fa0ad674f15348339a1eee771a6ba9e2 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2675,71 +2648,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +#: ../../src/topics/outputs.md:26 177b5f1b95a34fb9b2eb42f733d79ac8 msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +#: ../../src/topics/outputs.md:32 a08a6d8aca8e490482e127a8fd5e650e msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +#: ../../src/topics/outputs.md:38 c2c60f68b1e045f88844076e191fda9b msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +#: ../../src/topics/outputs.md:45 6d939f62526e4e6d95acb57d72f60a84 msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +#: ../../src/topics/outputs.md:51 c48edd9034364b81ad42540a98b51d91 msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +#: ../../src/topics/outputs.md:62 9ebe0186a7124dfaa30e558e8f59653a msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +#: ../../src/topics/outputs.md:65 9381b7d7c9904df0a5e16dac29c2e08f msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +#: ../../src/topics/outputs.md:67 2aa9c6916e3546b7b92fa64bb83275d1 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +#: ../../src/topics/outputs.md:71 63afb7a597fc4e459b6a7dbd40bbf6ff msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +#: ../../src/topics/outputs.md:89 7418915470f041c9af5bd39ea652de36 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +#: ../../src/topics/outputs.md:91 f82db001b58c4969b2d8bc1dcbd7cf8a msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +#: ../../src/topics/outputs.md:93 26d9f0b28d384617a8e490c1f8e26e52 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +#: ../../src/topics/outputs.md:99 cf46c971b31b4e10bf0fefb4cd028c2f msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +#: ../../src/topics/outputs.md:112 a4347983fb9945a4a2773af88e426dc9 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2748,11 +2721,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +#: ../../src/topics/parameter-references.md:1 c5489e0633114372b273098ee2c9ffd9 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +#: ../../src/topics/parameter-references.md:3 75de9fd63393429daf1ca10a85339aa7 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2765,40 +2738,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +#: ../../src/topics/parameter-references.md:13 8b5d0ada32d645be9359f43a431f5f91 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +#: ../../src/topics/parameter-references.md:19 2ed93dc8778e44209194f41b9ad193d5 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +#: ../../src/topics/parameter-references.md:25 a80dd6d9920540e9880514e04035af86 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +#: ../../src/topics/parameter-references.md:36 9de300f7b9da49f59d1c9fd96dec4a8b msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +#: ../../src/topics/parameter-references.md:47 a61f52d3c1024c3692899e05fcea4bee msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +#: ../../src/topics/parameter-references.md:51 dafc9ba578c14fd79d075160e6b7bd6b msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +#: ../../src/topics/parameter-references.md:54 28ca6cae42904559bcec98fb9d2b07cb msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2806,45 +2779,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +#: ../../src/topics/parameter-references.md:59 616c9ff9fcae489285f0bbbc67f07d29 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +#: ../../src/topics/parameter-references.md:61 ac17acd83ddb43dc9fb7a5e595ab1153 msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +#: ../../src/topics/parameter-references.md:63 156573324cde41ee8b3c47deabf43db8 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +#: ../../src/topics/parameter-references.md:69 c9725be01e8a401fb3ad9ff01339f81e msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +#: ../../src/topics/parameter-references.md:72 6797335256e2412cbbe7636507931455 msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +#: ../../src/topics/parameter-references.md:74 05a5f0fcb7454cb697e3d810d55fac26 msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +#: ../../src/topics/parameter-references.md:77 406e68280b5c4ee494632f94b635b7ad msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +#: ../../src/topics/parameter-references.md:81 2d6e2a4ff391494591bbdf8dbcc4a6ae msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2852,13 +2825,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +#: ../../src/topics/parameter-references.md:85 e71a974b29624210a107fc2d097d4196 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +#: ../../src/topics/parameter-references.md:89 b59df98754e24654bfef0b1fe1d91660 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2866,43 +2839,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +#: ../../src/topics/parameter-references.md:92 d2bccbff1ce646348fe38c776ad183e1 msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 +#: 943ba46512ce48fe8c5b62327734c503 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: bbcd43d5af7d44108aeb65075a6bd2be msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 +#: 834295755af841a78e466eea43864861 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: a6b626489bfa468e8f059ab3aa669201 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: e1dbea105aa845c38cb1f90b43847271 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb +#: e9640f47d40e45bca184eb30700df648 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2912,14 +2885,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 +#: 0456efb3718b4356ad2b277ee16de967 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 +#: f7e97f926505407f8f8e9a427e055e43 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2928,7 +2901,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 +#: ec597ff8f6ee47bc815b069335869f1f msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2944,11 +2917,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +#: ../../src/topics/staging-input-files.md:1 7467a7f6f26a459ba4ce83e4e6dfcc2b msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +#: ../../src/topics/staging-input-files.md:3 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2958,26 +2931,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: ../../src/topics/staging-input-files.md:9 a03372581fa44f9b8e3e088a4099cdd9 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +#: ../../src/topics/troubleshooting.md:1 36e082be73464be0ad5d0b681cc510da msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +#: ../../src/topics/troubleshooting.md:3 4464455b51ad4873ac13c4a63ee5fb54 msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +#: ../../src/topics/troubleshooting.md:6 ed7ff0753d1743a995f4cfedd6e5dcc2 msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +#: ../../src/topics/troubleshooting.md:8 4c2dd10dd66446058477a52fb8d2c602 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2986,7 +2959,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +#: ../../src/topics/troubleshooting.md:14 978b6a5fd5fa425fa9a18d9f0e8788da msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -2996,18 +2969,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +#: ../../src/topics/troubleshooting.md:20 000c0d6ae8bf414d9293b9f13fd2e448 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +#: ../../src/topics/troubleshooting.md:27 7e91b8811be14f8e80df39ac4c5bd316 msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +#: ../../src/topics/troubleshooting.md:35 d42799cc5bd4484bb6beb309a61e103e msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -3015,7 +2988,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +#: ../../src/topics/troubleshooting.md:44 48bb0f6666ac48648c7d969608b3bd48 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -3023,7 +2996,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +#: ../../src/topics/troubleshooting.md:48 f8876044db184cbaaca56579d0c773df msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3033,7 +3006,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +#: ../../src/topics/troubleshooting.md:59 a5a3d408dbe34cfda4dd0b2abe67e7d7 msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3043,15 +3016,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +#: ../../src/topics/using-containers.md:1 4c240a18c4e6441189489011242c1efd msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +#: ../../src/topics/using-containers.md:3 e37e76ef376a4ee695e600998906ec1c msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +#: ../../src/topics/using-containers.md:5 51a307b0ba7c4c1d89309ba8d2250471 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3064,35 +3037,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +#: ../../src/topics/using-containers.md:15 13cc38d72d34468fa4eb6d91f23ff105 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +#: ../../src/topics/using-containers.md:18 42a48398d3ef4b03bd7395120f2cfb42 msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +#: ../../src/topics/using-containers.md:21 d59387b433bc4ecfaf7e72026624db02 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +#: ../../src/topics/using-containers.md:27 d963418ccc0b4803bbc758d718ccb5aa msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +#: ../../src/topics/using-containers.md:33 a224d1510c9e46aab23d8bdc03c349dd msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +#: ../../src/topics/using-containers.md:44 0a82f8a45b0546aaac4c976dcc98014a msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3105,23 +3078,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +#: ../../src/topics/using-containers.md:52 bc418a2a535e49359c4cd44b373bbe02 msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +#: ../../src/topics/using-containers.md:55 a799fba2322944cea00e413c08066536 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +#: ../../src/topics/using-containers.md:69 35379c6b972940bd8451f10b74dd793e msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +#: ../../src/topics/using-containers.md:72 2d5265525ad544a0b64ad2cf07aacc26 msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3129,44 +3102,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +#: ../../src/topics/workflows.md:1 e2521b89596d42f8a87a3207fd6c32f2 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +#: ../../src/topics/workflows.md:3 3676f23b63e142cb8e5715ae07216a47 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +#: ../../src/topics/workflows.md:13 00725aed13a440ca8b3c4f9155fbee99 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +#: ../../src/topics/workflows.md:41 2e38a4f9072b4ad9bbb74f943d22084d msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +#: ../../src/topics/workflows.md:51 2b9f4035ea864b6db50c861a1819289d msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +#: ../../src/topics/workflows.md:81 28e9064780e7418a8e02a22f92e34404 msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +#: ../../src/topics/workflows.md:91 66ce14a10d2d4dc497d3ed71e11ed8b8 msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +#: ../../src/topics/workflows.md:150 8dc00528c3d2426c8a3492a8191f1d81 msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3174,33 +3147,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +#: ../../src/topics/workflows.md:160 f9ef5e258f7c4971a8543d1dfed711a8 msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +#: ../../src/topics/workflows.md:165 324bc51071d743ea80124c23880ddc0a msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +#: ../../src/topics/workflows.md:167 d8c13e01976b43a1af34c11a7bc36897 msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +#: ../../src/topics/workflows.md:170 43910a8ab4484e529a17df418b1aedbb msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +#: ../../src/topics/workflows.md:180 7ad12d67e815400c94080804b9285629 msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3213,34 +3186,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +#: ../../src/topics/workflows.md:183 457d5a31c79143acae2683d95d27f7a3 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +#: ../../src/topics/workflows.md:185 a2a73901bf634547900d08b9a1ac8889 msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +#: ../../src/topics/workflows.md:191 f347d80e62384b14acf6423675e5359a msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +#: ../../src/topics/workflows.md:205 2a845a4f3f98428fb82f3ca7ce038a6e msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +#: ../../src/topics/workflows.md:212 e2007c74d5f449a882809d6b91c010bf msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#: ../../src/topics/workflows.md:221 7f5e53ee7cf94be2bff45ef64db28a24 msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3248,7 +3221,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +#: ../../src/topics/workflows.md:233 a0d076b7b8b048478580c99ef0c8429f msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3257,7 +3230,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +#: ../../src/topics/workflows.md:248 7fd926c18ad548e98845e9b5134dd6f2 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3268,7 +3241,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +#: ../../src/topics/workflows.md:256 789fbd47f8564cceb430ef3c0bc90e9b msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3276,7 +3249,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +#: ../../src/topics/workflows.md:261 45c4d0492d6143ca9cebe81e9b2cf3ae msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3286,13 +3259,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +#: ../../src/topics/workflows.md:267 73bd3da2af8545928d5ea71d0f7454f6 msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +#: ../../src/topics/workflows.md:278 15ce3d2700424f0fbb280d602ccebcf6 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3302,11 +3275,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +#: ../../src/topics/workflows.md:285 af4268f19202436eb0a7e8c6bed5e386 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +#: ../../src/topics/workflows.md:287 94a4eadca6b949d79de2990a0150eee8 msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3314,17 +3287,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +#: ../../src/topics/workflows.md:297 09c1619e8cbd4febbb637f7e99ad5890 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +#: ../../src/topics/workflows.md:300 677ea7a27eb64568ab3689142d6efe70 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +#: ../../src/topics/workflows.md:309 097e6d47f9394e62b80110700492783a msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3332,7 +3305,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +#: ../../src/topics/workflows.md:314 e93affce8c104bf6977182047c1f1077 msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +#: ../../src/topics/workflows.md:322 06c9e04ba890473b851240a0fa9c3b12 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3354,7 +3327,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +#: ../../src/topics/workflows.md:336 0380dc1fe3aa48e4b62283b7b2a611d8 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3363,7 +3336,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +#: ../../src/topics/workflows.md:341 49b251f7a313492ea60504b00109e526 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3373,7 +3346,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +#: ../../src/topics/workflows.md:347 7ee55702d7dd4679a24ff052f6f0cbeb msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3381,14 +3354,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +#: ../../src/topics/workflows.md:366 85d7e2e270874aa6b9f477cec0f48154 msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +#: ../../src/topics/workflows.md:383 570e94513c984c09ad6aa255f534216d msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3397,7 +3370,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +#: ../../src/topics/workflows.md:389 a107258662fb4bd4a9a3d8754e34d1e9 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3406,7 +3379,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +#: ../../src/topics/workflows.md:394 fc1a6502d831458ab8371a575cea47e2 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3414,11 +3387,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +#: ../../src/topics/workflows.md:398 2d10806bf1ce4e26b92adda61efc0862 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +#: ../../src/topics/workflows.md:400 046c5e134de94b629cc22d416f3c9182 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3429,7 +3402,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +#: ../../src/topics/workflows.md:411 52fa22d3277940049fbb589a3ea73433 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3437,23 +3410,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: ../../src/topics/workflows.md:415 6043beb96c2c49648011ec556aa9e986 msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +#: ../../src/topics/workflows.md:421 5ac4310515124e2986724425bed5651f msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +#: ../../src/topics/workflows.md:429 7958e91d5c2f4046aa9d2070a900f9ae msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +#: ../../src/topics/workflows.md:441 2db234d776fe4fd38bab07245dcb783a msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3461,7 +3434,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +#: ../../src/topics/workflows.md:445 7cfb17230e284ee7b6e2a00efe8eeb74 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3469,59 +3442,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: ../../src/topics/workflows.md:450 4311ac98544e4fb0b2f4b24985710a01 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +#: ../../src/topics/workflows.md:452 780f9c72e6c34c39918642c7e2477355 msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +#: ../../src/topics/workflows.md:458 cc4a7316db644b438cbaa181ad9ef2d3 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +#: ../../src/topics/workflows.md:466 dfc461a03fe8487794837904febb8b63 msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +#: ../../src/topics/workflows.md:469 1e83485b00b64dfaba897bd8d772e0f0 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +#: ../../src/topics/workflows.md:472 d0321d6805ec4d3abf3877d02a0a417f msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +#: ../../src/topics/workflows.md:480 d7d77e807b3048c7bdf89558f76804cb msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +#: ../../src/topics/workflows.md:483 8d9b8be147fc4a71922dde858842e543 msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +#: ../../src/topics/workflows.md:489 34b7705416a745a6a42e6d402c0757ed msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +#: ../../src/topics/workflows.md:491 257adcee9da64d5c987f3b64efd20ab0 msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +#: ../../src/topics/workflows.md:497 fa6ed5d0c14f42f4aa3c5144648db22c msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3539,7 +3512,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +#: ../../src/topics/workflows.md:509 333e8ce458d54de394526769f96d12d2 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3547,38 +3520,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +#: ../../src/topics/workflows.md:513 b819e8a5df6e4fa495924095709669ef msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +#: ../../src/topics/workflows.md:519 f1955468a1364d44a930db77c9c4b495 msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +#: ../../src/topics/workflows.md:522 8c3b9b645a204d02b2c73a205e8ec296 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +#: ../../src/topics/workflows.md:524 4d88b9c186cd4502adbf752e8a70b6ce msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +#: ../../src/topics/workflows.md:527 9927673564024ba5833b5ac271737857 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +#: ../../src/topics/workflows.md:566 84f4ed7ce2004742b8db9087104a469a msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +#: ../../src/topics/workflows.md:573 2b5f9757adca4490a149c7f45e14fcb5 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3587,7 +3560,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +#: ../../src/topics/workflows.md:587 0418de720813442f81ecff293c9448b5 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3595,62 +3568,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +#: ../../src/topics/workflows.md:607 524eec63be8248ae982939c975ef50a2 msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +#: ../../src/topics/workflows.md:627 5e99f9912cc549a7890e2934425eb943 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +#: ../../src/topics/yaml-guide.md:1 b0121ee087d6424fbb0ea5957a7b0b8c msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +#: ../../src/topics/yaml-guide.md:6 49e9f6b3a06840289decf3f557860f87 msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +#: ../../src/topics/yaml-guide.md:13 ed9eebec0b3d4b72ba65507d37757a37 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +#: ../../src/topics/yaml-guide.md:16 bf9b255a24a84f3ba989a223492b8f41 msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +#: ../../src/topics/yaml-guide.md:18 e79fa0b7f8b14810a3a20908ef92bc55 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +#: ../../src/topics/yaml-guide.md:19 290e2035f903417cbecb5dc5f09d6ebe msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +#: ../../src/topics/yaml-guide.md:20 d420730151534f1a89076588a3358f09 msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: ../../src/topics/yaml-guide.md:21 a6b5378bbe1e4bee9e37a765bddf75f7 msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: ../../src/topics/yaml-guide.md:22 6e4d9465dc2b454d96b02d7ad1817795 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +#: ../../src/topics/yaml-guide.md:24 a649d4af5f434dac9395e013ec4836bb msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +#: ../../src/topics/yaml-guide.md:26 446190a298834b73bda068286e8490cf msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3660,7 +3633,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +#: ../../src/topics/yaml-guide.md:42 2f35c012ff174721bffe66a3f58a804f msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3669,7 +3642,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +#: ../../src/topics/yaml-guide.md:51 43127c98c9d94aedac61cee67929c1a6 msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3680,28 +3653,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: ../../src/topics/yaml-guide.md:61 dc4fe561203c4c38a9caea5bd6eff2cd msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +#: ../../src/topics/yaml-guide.md:63 f924e4896db2424d99ce8c9da14c599a msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +#: ../../src/topics/yaml-guide.md:76 bf7646f5f925485c842a6d34140e40b8 msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +#: ../../src/topics/yaml-guide.md:79 c483e61dec8949fa96bb893d422888a0 msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +#: ../../src/topics/yaml-guide.md:81 85fcb523d0e34a499eae04d304887f7b msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3712,7 +3685,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +#: ../../src/topics/yaml-guide.md:104 83d47c8736a34f3cbf09e3997845e4f4 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3725,11 +3698,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +#: ../../src/topics/yaml-guide.md:127 c698fb3d37bc403e9aeb679b8fc0e15e msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +#: ../../src/topics/yaml-guide.md:129 ae8af2f0eeda4aec97201211dfa965c7 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3740,26 +3713,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +#: ../../src/topics/yaml-guide.md:146 2ee87aa465cd41fda16a61e242f8c9d0 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +#: ../../src/topics/yaml-guide.md:167 0a6fd4469ff24b61b3ad001b09eead18 msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +#: ../../src/topics/yaml-guide.md:169 b96ba19bce9341d39c46054e1f10fe8f msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +#: ../../src/topics/yaml-guide.md:177 903f30af3d0c45cfb61063936a8097a7 msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +#: ../../src/topics/yaml-guide.md:184 ede8db7c0a58432e8a1c416e937a06d2 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3769,52 +3742,64 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +#: ../../src/topics/yaml-guide.md:194 c8b53615476a4a1fbef2420d93bac94e msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +#: ../../src/topics/yaml-guide.md:196 ea03cb5525cc491f9feb5c4780b38fee msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +#: ../../src/tutorials.md:1 92fd3a5e31714eab859dd630af2e78cf msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +#: ../../src/tutorials.md:5 de660ecdb5b44c97a0e519d00b232497 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +#: ../../src/tutorials.md:7 5afc1e1288e74ed0985e61e5164479c7 msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +#: ../../src/tutorials.md:9 862dc7ac81e54b1fb3d4c2f961b8810e msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +#: ../../src/tutorials.md:11 e2c94c0e1c7048d38cd7aa2c465a859d msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +#: ../../src/tutorials.md:13 b63253780f51467a95207d820d13ac39 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +#: ../../src/tutorials.md:15 6d06ca7ed5df4560aaed286f4fe33928 msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +#: ../../src/tutorials.md:17 5448df4a6a8f431d80e269bcd480e19e msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" +#~ msgid "" +#~ "Unless required by applicable law or " +#~ "agreed to in writing, software " +#~ "distributed under the License is " +#~ "distributed on an \"AS IS\" BASIS, " +#~ "WITHOUT WARRANTIES OR CONDITIONS OF ANY" +#~ " KIND, either express or implied. See" +#~ " the License for the specific " +#~ "language governing permissions and limitations" +#~ " under the License." +#~ msgstr "" + diff --git a/locales/user_guide.pot b/locales/user_guide.pot index 0a669946..a806cea1 100644 --- a/locales/user_guide.pot +++ b/locales/user_guide.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"POT-Creation-Date: 2023-01-25 16:53+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -16,1273 +16,1273 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" -#: ../../LICENSE.md:2 -#: 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.rst:2 +#: 75de2be8809847b8bf1ccd42aa694a24 msgid "Licenses" msgstr "" -#: ../../LICENSE.md:4 -#: 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.rst:5 +#: 2edd71801f6245ef821887a74f21b94c msgid "Instructional Material" msgstr "" -#: ../../LICENSE.md:6 -#: 747f9dd48bc54f44adcd8b18c57f4d9d -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +#: ../../LICENSE.rst:7 +#: 3c0a9704ed8f4367893242a4f75d703f +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." msgstr "" -#: ../../LICENSE.md:12 -#: 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.rst:12 +#: 90cc755d172e4c82b882b4ee620fe652 msgid "You are free:" msgstr "" -#: ../../LICENSE.md:14 -#: 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" +#: ../../LICENSE.rst:14 +#: e5246890525144bda8547106b6643382 +msgid "to **Share**—copy and redistribute the material in any medium or format" msgstr "" -#: ../../LICENSE.md:15 -#: 18a3a0aec35743848c97bc178f9c94ff -msgid "to **Adapt**---remix, transform, and build upon the material" +#: ../../LICENSE.rst:16 +#: 4d96baa7ca7a4240b75be213696558ba +msgid "to **Adapt**—remix, transform, and build upon the material" msgstr "" -#: ../../LICENSE.md:17 -#: b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.rst:18 +#: e19adbba09d14d069534251a7ef70993 msgid "for any purpose, even commercially." msgstr "" -#: ../../LICENSE.md:19 -#: 6021e65292a149d5b15e14491f3eb05e +#: ../../LICENSE.rst:20 +#: 8bc6672f4a33428296226112a1be6fbe msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" msgstr "" -#: ../../LICENSE.md:24 -#: 8fb7a2946c384364814c6ec3910997d3 -msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.rst:23 +#: be38276e7b374f57b9997391bf898a62 +msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" -#: ../../LICENSE.md:32 -#: 8161753b7526445db319210044566200 -msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.rst:31 +#: f00d5c3846034c2ea116c2f74786d9fc +msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" -#: ../../LICENSE.md:36 -#: 15314ba527864eaa834cf1185cfcc4e3 +#: ../../LICENSE.rst:35 +#: 1798d65c10104040923c2fea2199bab2 msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." msgstr "" -#: ../../LICENSE.md:39 -#: b351ddf9847d48b1a2a87fc78eaba4d2 +#: ../../LICENSE.rst:38 +#: c65198b804f8436ba783643d51bc72d9 msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" -#: ../../LICENSE.md:44 -#: a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.rst:44 +#: 4777f6a958394b138c5b68eee0367734 msgid "Software" msgstr "" -#: ../../LICENSE.md:46 -#: 84b2c685bbab48449fdc72d2a1e42bf4 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +#: ../../LICENSE.rst:46 +#: 7dec2236137f4de5ac7df7a8c8eaf98b +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." msgstr "" -#: ../../LICENSE.md:51 -#: 0f68eafafaef4b54accba7e13bfaa702 -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +#: ../../LICENSE.rst:50 +#: 9c4d58a1129a4d4eb4db1bfabbeddb6e +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 #: ../../src/_includes/what-is-cwl.md:2 -#: eab02dc13915490bb3c9ba744d78b6a7 -#: d4f35995b0f6494d9771a4be0a82538f -#: d6ccd4b546254f56a597d67dd4fdc5d6 +#: bdd540403a5746ff99edf2dcad0e3122 +#: 5ad4be9b62d54c95a913795b514676fd +#: dfc7702e073140c985cf47272a20214d msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." msgstr "" #: ../../src/episodes.md:5 #: ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc -#: 436cfca6f857469bbff7c652df32160f +#: f1b89ae4325343f783bce8b7c9971047 +#: 810c4e8dd79247d6a6fd51a8f65d3975 msgid "This page has moved" msgstr "" #: ../../src/episodes.md:9 -#: cc11f5d29206492d9f2f0922882b6159 +#: 3060770b3bef41d7bcfcdfb413d7689c msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." msgstr "" #: ../../src/faq.md:1 -#: e2ed894d325a4f50a5e2dc69da5531a1 +#: 48bb9f628b344ba1a3b67ae1cb264e3c msgid "FAQ" msgstr "" #: ../../src/faq.md:11 -#: 61edb787dab04ca2ad3ed07616d878a0 +#: 7e3684e9672643738846756e1ebafd18 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" #: ../../src/faq.md:41 -#: d5321589e7ed4f0db3c630cc39800791 +#: 187ceabb7fd9480bb8cf0f2da47f65ef msgid "Rename an Input File" msgstr "" #: ../../src/faq.md:43 -#: fc62427c0a004810b055dee90ec5e2d9 +#: b548b76bcc85420a9b30792386105139 msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." msgstr "" #: ../../src/faq.md:59 -#: 1c6b8a4194a14611b4061b1540c3807f +#: 9ce692b78ead47e4b0f8cdae8837d35b msgid "Rename an Output File" msgstr "" #: ../../src/faq.md:61 -#: bc7ad10c929848a3a9a240a3c501d299 +#: 6df1201c159343da9e7515379980d6a0 msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" msgstr "" #: ../../src/faq.md:82 -#: 7225a993d281421b95c8e3df2846a0e3 +#: f9ab1d0dc1c842b6abb5385268c1d3bd msgid "Referencing a Local Script" msgstr "" #: ../../src/faq.md:84 -#: 7ef1dbb81993473f948d9c6f3c64b381 +#: 9f6a84ab6a9343b6ad7db826f8964362 msgid "There are two ways to reference a local script:" msgstr "" #: ../../src/faq.md:86 -#: 450edf800a18423195bea4fe8793a2cb +#: fa50e4fa990b42d1ba4c0f4ae1e5caa1 msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." msgstr "" #: ../../src/faq.md:89 -#: 1a8cc75ea6174b9297871b2e58971077 +#: 3a871012fcfd4f3ebeca0cb86ec93435 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" #: ../../src/faq.md:95 -#: a7d84f740a714ec588503ee084fbbc34 +#: d954edfff2584288ac8c600733070d2e msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" msgstr "" #: ../../src/faq.md:97 -#: 569d553abe85450c9d1c37456bf412f4 +#: af6b1e37d6be4450a761854480ec9aab msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." msgstr "" #: ../../src/faq.md:104 -#: 95f5dbbd21084a318413b9528fb867be +#: 31f4a2d43062493ca64c648f80afc8e9 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" #: ../../src/faq.md:113 -#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +#: 41c54e71b6cd4f63b2a619a515240d34 msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." msgstr "" #: ../../src/faq.md:115 -#: 8d86baa239364f799d4f9d5ea2b0e314 +#: 8edc3541ad134ab5a1d23c724f1f0a4e msgid "The second method involves including an input of `type: File` in the script itself:" msgstr "" #: ../../src/faq.md:135 -#: f2c109998c76434893ff16b17fdb2bd0 +#: ac0ea81eba8842a18801ab03cbf80a57 msgid "In CWL, everything must be directly stated." msgstr "" #: ../../src/faq.md:138 -#: c2c752b86bf94d6fb3751f4dd81bc7a7 +#: 52be1a5640234feabe958ff7ade33653 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" #: ../../src/faq.md:140 -#: 2c38cc58cbb340bc935a5f00e96ba95c +#: c6db734d5aef4f4f99676bdebf9c83c9 msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." msgstr "" #: ../../src/faq.md:165 -#: ce6db54bd0f54839a5beb948530a21f0 +#: a9f7b47c0dd741739795da39bf114879 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" #: ../../src/faq.md:167 -#: d06cbf89028b4638ad54c2529bcbfa25 +#: e3fdd9228b924905a4a1f4b2b7ad7159 msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." msgstr "" #: ../../src/faq.md:188 -#: d53fb28dcad04e7788cba9e280a2343c +#: 3f7cda1437cc48f18745a827ebb74582 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" #: ../../src/faq.md:190 -#: d9e30e11533b4d53a144f5df7041268d +#: 5aeaba2cae64442e816bbd458aee833a msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/faq.md:194 -#: 941077158ec54ae19bfa2e2ad6662da1 +#: 5af827a402834978addd82c70be6b5ab msgid "merge_nested" msgstr "" #: ../../src/faq.md:196 -#: 937cb94a370640c788fbc3fe0b19f2e5 +#: 6d69e42bd8e443c4b19d80807c7efd6b msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." msgstr "" #: ../../src/faq.md:199 -#: a1d57e15656548128a76a8b975c564c9 +#: 404640397b6e40c2a2cd5cf85ab3b1c0 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" #: ../../src/faq.md:201 -#: c8c235a9bf6240628f0b5493ffebf7e0 +#: 1682c2486e224770b62269709a8663cf msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." msgstr "" #: ../../src/faq.md:229 -#: 3da4dcb043eb4423a53a14182949d9cd +#: 9078fc009bc145808813c9cc2b734b58 msgid "Optional Inputs 💯" msgstr "" #: ../../src/faq.md:231 -#: 89b90d3bf1ea4ebd88482d435241fac5 +#: d4b5a54a400c409cb7984428f6a03ec8 msgid "To make an input parameter optional, add a question mark to the type declaration." msgstr "" #: ../../src/faq.md:247 -#: a854006054ce4ffe94bbfa73bdbecbf2 +#: 9e8dbee6e8f84d08b1a54fffa06394ef msgid "" msgstr "" #: ../../src/faq.md:248 -#: f80eb714e9df417fbba555b5dd5f4d8c +#: 1d846bfb5f054d09a4afad1da8e4b642 msgid "Enum Inputs ⚜️" msgstr "" #: ../../src/faq.md:250 -#: 10af80fa13af4158aec7060550485350 +#: 2d0e95fec8084787b734388d60188574 msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" msgstr "" #: ../../src/faq.md:267 -#: ad1c26711ccd4efd8fdb25f9293d33fd +#: eccc4a364330470fa474dcaaa3433390 msgid "" msgstr "" #: ../../src/faq.md:268 -#: 49e2095b51f84f609f5d4bc088ad9745 +#: e945f6a337af4e4686bed482a4fe6c39 msgid "Record Inputs 📀" msgstr "" #: ../../src/faq.md:270 -#: 52b8538177c64090af51f5f6a696c28c +#: 8a3efaa0ad1548428bcfd6e01d135cdc msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." msgstr "" #: ../../src/faq.md:322 -#: f96c9257e3734b8aa0cc5e065f74f944 +#: cdab644adc5643708870fb08c06cbfca msgid "Setting Mutually Exclusive Parameters" msgstr "" #: ../../src/faq.md:324 -#: 7dc0540508084a3495ff3b2ac90fd323 +#: 089a5a0b076b44aeaab4d69ee3c79f97 msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." msgstr "" #: ../../src/faq.md:342 -#: b53dc77466b24a67b52b8aadf4fab724 +#: 561172559c6f41a68819608fd9e58bb0 msgid "Setting Booleans" msgstr "" #: ../../src/faq.md:344 -#: cf4e7f3977ae4f9b877072c2b1c4b533 +#: c5ee4946d2e840abaa3dc796a62652c7 msgid "These can be set by using the default field" msgstr "" #: ../../src/faq.md:349 -#: 99b37739ef18443ca7c0e715a131e0c7 +#: 4f2069a2113c414db18eca95550e9e09 msgid "Concatenating Strings in Inputs" msgstr "" #: ../../src/faq.md:351 -#: 9b00b5a55ee941e1adbfe89e133791e3 +#: 31f3390e6771414ba7bf57c044c4b0c4 msgid "The valueFrom field must be used instead of default." msgstr "" #: ../../src/faq.md:359 -#: 07922147f7ab487ba2a1e7c43c9f410c +#: 3b77ce4930ae46d5be9f6965e8c54727 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" #: ../../src/faq.md:361 -#: 7a11806f0c7045b48fe58a271f814797 +#: 06f36bbe4d3840229b7374f27b86ae80 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" #: ../../src/faq.md:363 -#: fdaec25650ab4b0fb1c527610e24ae5a +#: 3cb2f70d00274a4dafd972ccd8c519c2 msgid "For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" #: ../../src/faq.md:371 -#: 182959fc9f4746d082994e07d05c8cde +#: 093a1529262043ef84a99675054938e0 msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." msgstr "" #: ../../src/faq.md:373 -#: cc7752e9989e4a6d957682f479d6fc60 +#: 45b6d9acbfaa47e5984184f7da554d0a msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 -#: 6db1ebd2d6c74ceca889662cd7df5cd5 +#: 5705c9bacca5405ca6f14315a5575db8 msgid "If `cwltool --validate` returns valid" msgstr "" #: ../../src/faq.md:384 -#: 3de2513c7d7b4569ba63f7e6d29137b7 +#: 82bfc285b59a439ca97d3278997f0fce msgid "But executing it causes an error like:" msgstr "" #: ../../src/faq.md:396 -#: ae3a9188706649e28f97bc4ec34c0821 +#: 181d5130101d45ccb22aebae3d154c2f msgid "The file is here" msgstr "" #: ../../src/faq.md:410 -#: e1ac97ab6ad3449b8c54933d25257f73 +#: e864390b5ddb423aaa10e9d33d257dc1 msgid "Problem caused by `-` (hyphen character)." msgstr "" #: ../../src/faq.md:423 -#: f6c402f7f6974edbbb5582c8e22f3869 +#: fe637c32fb15427a9045679b5da42ec5 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" #: ../../src/faq.md:436 -#: 190099a242a645c9b9f8bc3ce89d920d +#: 1f8004b9df8547029d82e57f9abdc979 msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" msgstr "" #: ../../src/faq.md:442 -#: 06a4f6ffc2da4d43b453d4784b42efd3 +#: 70990dc5a0034099921ceb89c89e2dcc msgid "Use CWL and cwltool with Singularity" msgstr "" #: ../../src/faq.md:445 -#: 1901c34201054a9cae199b0dbb8b945e +#: f679e26f18d9455f945fd13361a9c906 msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." msgstr "" #: ../../src/faq.md:450 -#: 2d498470524d47f18f9936ace6acebb0 +#: fcd0273dbdd84e728cfd8fbe239f2a01 msgid "Debug JavaScript Expressions" msgstr "" #: ../../src/faq.md:452 -#: d7b044f5224a48eda09bc949cf645193 +#: 173ddbd1e7c64927a8dcb12a2a2140f8 msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" #: ../../src/index.md:1 -#: 2754519265eb426b940bbbd2b8d64e1e +#: 662fe273e2fb4042b688512955e450a1 msgid "Common Workflow Language User Guide" msgstr "" #: ../../src/index.md:3 -#: f8d6e4cd54cb42c88182a43171d97bab +#: a15b52205f0145feaac298510e4d678a msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." msgstr "" #: ../../src/index.md:7 -#: 132d40fee3b84469afa80d5ff613bf77 +#: 512aa0c7166b429e8116f71eef007f79 msgid "Contributions and Feedback are Welcome!" msgstr "" #: ../../src/index.md:9 -#: 0f47157605a34ea58770ea898deebae4 +#: b1b19e17a18540939cb3bb7f8a700cab msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" #: ../../src/index.md:16 -#: 6d269e8d70184034bcb56385a6ca198f +#: d58b36ac43ac44139897be752fbb1f87 msgid "Navigating the User Guide" msgstr "" #: ../../src/index.md:18 -#: ed74c9a4b623464480e2c184668fcec0 +#: 6726cf3585a646a8b4cbeb543cf84a38 msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." msgstr "" #: ../../src/index.md:23 -#: cfa67cf5521b414da6f7d34cbed283f7 +#: 2e504aa7c46a426fa959e7254e9a84a5 msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." msgstr "" #: ../../src/index.md:28 -#: ee6b82bd86264e4bb1e8e4065b1e6b9c +#: e7be0df0838b432d9c7f296d777f120b msgid "Table of Contents" msgstr "" #: ../../src/introduction/basic-concepts.md:1 -#: e208c8a7506e41dcac9a403c5d2850c1 +#: 173e0816db20432c8d9dba1de5393dee msgid "Basic Concepts" msgstr "" #: ../../src/introduction/basic-concepts.md:3 -#: ac62d326a68145b695e46b714d4e8156 +#: 30eacc583f6841719e2142d283811d97 msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." msgstr "" #: ../../src/introduction/basic-concepts.md:10 -#: 984e6676b9d04c7092bc492f195dfb91 +#: 791b8f38a14147bbaa174c7eb595f17e msgid "The CWL Specification" msgstr "" #: ../../src/introduction/basic-concepts.md:21 -#: cbe1d761da5b403d9605fa1fb8e62fdf +#: 1a3989dcbb9844b39d84bf6df6b352ed msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." msgstr "" #: ../../src/introduction/basic-concepts.md:25 -#: 3a71b269bd3c49eb913cf69b60373c24 +#: db1bbc6e980f404f9f3fcd08e92ee9a3 msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." msgstr "" #: ../../src/introduction/basic-concepts.md:33 -#: b171b72c48d44050a3416a7a42c4021d +#: acc7887c65974114996f700a38a7eccc msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." msgstr "" #: ../../src/introduction/basic-concepts.md:37 -#: b3df1607e9d242d78b22dc44335fbe2d +#: d2476d9bcff44f21b8d84a3a0d87a246 msgid "Implementations" msgstr "" #: ../../src/introduction/basic-concepts.md:39 -#: 078b58ffc1cc4d25a7c4eea3bb76e025 +#: f86415e4d78e48c4a8a76ced81221b98 msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." msgstr "" #: ../../src/introduction/basic-concepts.md:44 -#: c3869b4ec5ff47d99e8da79770722e04 +#: c5524d73708c4c779980528864506fd4 msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." msgstr "" #: ../../src/introduction/basic-concepts.md:51 -#: 2482c84831fc4dfab629e7bfcfb41cbf +#: ac46a9f8850a434bac5bc2b41ee6294e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: 9bba7c4f783942e4a299603430601363 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 +#: e2140e0f0e7747ef8383887c20a7945a msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 15bf490724cd46dcbcfab44633c5a9a2 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 51d52d051e654a8395239f88df7c9d8c msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: eb496cc818524fa7bae5a22ddd00a19c msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: c4a22d12e7f149ff901d27de32b9361d msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 7618de899a7043989d77baacf62eb7b2 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a +#: 6f1544a220664b79b04bf008058b5a91 msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 +#: fbd14ac9a2f541478a320ed4cbc69e13 msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef +#: da4dba50d25d4533b3dbb92f54d32a30 msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#: ce11c9f8d65c4268984d0384d95144cc msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 +#: 3a201aa497e84f70855bb2251e7e3281 msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 +#: b78f7fa2be1c4bb090f6da895457ad1e msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 +#: f7e95d264ffa4e2db0864faccd9e5a0e msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 +#: 3f1e5b01e49a4dc1b1c99936a4589afc msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee +#: 03c3048f38ae4938a484cf02001877b3 msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e +#: f9715b5ec65c405c849bb030c1927060 msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: 442662f50e9e4620970ce32b1b127969 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 +#: 2b34c786af3840e88f29d214e19dc837 msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a +#: dd6aadff8cf54ce78ea6b317afbaddb0 msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee +#: fe7f1f0b28434f8aaf0f6ac6589a83f0 msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: d10cf45b3c7f49dc98bc0e5d1246f224 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 #: ../../src/introduction/quick-start.md:94 -#: 65c24244713741e196da08cb9ba237b2 -#: f059896039524095b4deb65d693f8ddf -#: 3439764fab0e49d2bcb7c9fbae556e65 +#: ebf339ed376a4d3b89b15b4d5afe593b +#: 332b6e8b831e4bc5aed3745938230a57 +#: ce7fc63b808d4499b9bf9828c2dafe35 msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 8badec9987ba40609cf1f626172b2b2d msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 +#: c75a8b4bf0e24781bf6713cf6f013cd1 msgid "The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 +#: 79b146ffe6d74e1b8f6019251dc4b7c2 msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 +#: 07cca9a33d8f4b77ac6ad35ca8b95655 msgid "The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: 31db11c8ddf2423192a8b2063b3e91c2 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b +#: d81dd96143ea444aa78ff45cfa0584b3 msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." msgstr "" #: ../../src/introduction/index.md:1 -#: 1769a0cbf4de4d77879c1f202cd11af9 +#: c54984605872472190ae7771809a20db msgid "Introduction" msgstr "" #: ../../src/introduction/index.md:3 -#: 950370f0a36048b38e1bde9b78f80816 +#: 01a237b8ec2f46c9acd31d142591ce75 msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." msgstr "" #: ../../src/introduction/prerequisites.md:1 -#: f01faaf1b253407cbbc2f353c24774f3 +#: 3fb9888b666945eab1e3ff109646c574 msgid "Prerequisites" msgstr "" #: ../../src/introduction/prerequisites.md:6 -#: 353b14f06ee845d0a06a829643e31534 +#: 5fb0486762354f93853fff209f835c08 msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." msgstr "" #: ../../src/introduction/prerequisites.md:12 -#: b5a0607096814c0aa577f977c3b57c54 +#: 5f1e7a608e0b455196d191c845a5c98e msgid "CWL Implementations" msgstr "" #: ../../src/introduction/prerequisites.md:14 -#: ff2bb4c6504b456bac7ca9c514414dbf +#: 7ba4b5c51be24f5392949d06ee42e018 msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." msgstr "" #: ../../src/introduction/prerequisites.md:19 -#: cbbcce4c2a96471b8b0ae3593ad59de4 +#: e2d3e6dd13b14d819a504c35da6fe8e7 msgid "Operating System" msgstr "" #: ../../src/introduction/prerequisites.md:21 -#: 5089fdba8aed4113983fa86e698df98b +#: 91251d1f0efb4d4cb083b4517ff3107a msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" msgstr "" #: ../../src/introduction/prerequisites.md:24 -#: dbaa4bae22fe4d05b18d7351967ddbc3 +#: 6ad263e267514c5fb05794d3d76d418d msgid "Linux" msgstr "" #: ../../src/introduction/prerequisites.md:25 -#: c05187af85be41b782678b79627f8fbf +#: 8a3bfd72dccf4a8c874a96aebcbe5cb7 msgid "macOS" msgstr "" #: ../../src/introduction/prerequisites.md:26 -#: beb6cf4d7c154eb9b6d7fe024a318ed7 +#: 5195706d9c6c4573aff135fd539759a2 msgid "Windows" msgstr "" #: ../../src/introduction/prerequisites.md:29 -#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +#: 9c4506915e4c40599527bc1d2b18645b msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." msgstr "" #: ../../src/introduction/prerequisites.md:35 -#: 56d78c95daa54135b6aa9b2bfdc34d01 +#: 37d9eb784ec1425786158f98e3f63890 msgid "CWL Runner" msgstr "" #: ../../src/introduction/prerequisites.md:41 -#: 0f2704bf1f7148be95e999e312899f11 +#: 572f493a985141a1b92dafbdba92790d msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." msgstr "" #: ../../src/introduction/prerequisites.md:46 -#: 86264c9e56104ecea9146407c379aae2 +#: 9606d3c4849f4b17b2e55a298210f055 msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" msgstr "" #: ../../src/introduction/prerequisites.md:51 -#: 0a0f0e5151ab4c498b4f8a12c016f28d +#: 754fc59967d94ffa935284676d55ffed msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" #: ../../src/introduction/prerequisites.md:62 -#: f7aaafeee230400da056464c853582c2 +#: 2905c6362d4146e8b35bc74744841972 msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." msgstr "" #: ../../src/introduction/prerequisites.md:65 -#: 5eced7e4cd084e8a806b1d3b12d0c000 +#: 091278ece252483a9838fb771de3e04e msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:67 -#: 040c019b6e844eda8c8c2b210852516b +#: 0928a5c668c3414a945bc9eda147892c msgid "`true.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:73 -#: 6391e08e0bde49f4b21286d8fdb97433 +#: 56f3c481762848298214a88e559fc0f9 msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" msgstr "" #: ../../src/introduction/prerequisites.md:79 -#: cdef47fca304479c9a9df75afc0afb35 +#: 710c266ab4a5477b84d6ea987420fa20 msgid "Validating `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:84 -#: d41c4bc740aa474ea09a7cbd267c8840 +#: cc353db5da2546bb88a77ce1a202ff9d msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" #: ../../src/introduction/prerequisites.md:86 -#: 24d7be55d3994f0b82c38da47918e0c9 +#: b62df08ec96f4cdb887600079856dd76 msgid "Running `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:91 -#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: 97e02557293440d1a58ba659dad21113 msgid "Cwl-runner Python Module" msgstr "" #: ../../src/introduction/prerequisites.md:93 -#: 096d0a50f69e48bd9915238d1b4264c1 +#: 0935c3ff01634c75b5c91546dc36c7b9 msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." msgstr "" #: ../../src/introduction/prerequisites.md:101 -#: f9df974a8e2645a6918e67466bd1fdc2 +#: cfb37fd605164a8d9cc75bf892ce97c0 msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" #: ../../src/introduction/prerequisites.md:104 -#: 71ebe91d4bda473abe87578929433212 +#: 5f06a7a6aae343d989a5b30979c600f6 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" #: ../../src/introduction/prerequisites.md:111 -#: 746c6fc9c29d466494458a08d4c96672 +#: 5f956260f3874b6dbeaf3ad7ecc09c9a msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." msgstr "" #: ../../src/introduction/prerequisites.md:115 -#: b9cc5a843a0f49daad56e9303657bdd5 +#: d35e4effec554a638d6c3047ef3fd05f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:120 -#: 34ab40437ab646488ba3ee86cd7fe071 +#: 15a1f944a0d642729d3736ed1c907074 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:125 -#: 705807fae182425dbf4244dbf2be1226 +#: fa34c808bb494ddfa3f3926bc42e650c msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" #: ../../src/introduction/prerequisites.md:129 -#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: 0c15f62eb7534e809f625f3fa213e92d msgid "`true_shebang.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:135 -#: 164c438baab54ec19bbb4584a10dd411 +#: d67719a6f0ce4ba1bb6152a10507b729 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" #: ../../src/introduction/prerequisites.md:137 -#: bf8be77af6154326b28442c5d2e2b852 +#: 1c96e75281844bfab0578bab2e816854 msgid "Making `true.cwl` executable." msgstr "" #: ../../src/introduction/prerequisites.md:144 -#: 695184d1b45a42f393e2da99c3721773 +#: bece1fc3c3f842b0b30d8f1b7fbfc200 msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." msgstr "" #: ../../src/introduction/prerequisites.md:148 -#: 7c4f45b3e7b549e186126693aa4a3d4f +#: a7caa36b0f83448b91ef2e76e30abc51 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" #: ../../src/introduction/prerequisites.md:154 -#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +#: 39321e93e9994fcca20b425aa45c2894 msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," msgstr "" #: ../../src/introduction/prerequisites.md:161 -#: eec6c07455384630809ff1c532bfe7d4 +#: 601cf500d76c4e0287af4429a46b36d2 msgid "Text Editor" msgstr "" #: ../../src/introduction/prerequisites.md:163 -#: f6b39b12bd5c495cb53e2795bf9200ed +#: b286d5359e184ef58054c72df4014629 msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" #: ../../src/introduction/prerequisites.md:167 -#: 2fdb62a13f9447bc89183426260ce781 +#: e14423edd829401faed0950772123240 msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" msgstr "" #: ../../src/introduction/prerequisites.md:171 -#: 1f07135156254f74a6b043bf33d00cc3 +#: 889c44360bd54a0e85e7f0e61aa6593c msgid "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" #: ../../src/introduction/prerequisites.md:172 -#: de344f356b1c466d9131cdbd4d7353a3 +#: 7b9bff73624947ac90a99c7880e2e911 msgid "cwl-plugin for IntelliJ - " msgstr "" #: ../../src/introduction/prerequisites.md:174 -#: 3f9324ede11441f58d93875867034cf0 +#: c5ff687c86ef4ccaae25d8bcfbd5f873 msgid "The CWL community also maintains a list of editors and viewers: " msgstr "" #: ../../src/introduction/prerequisites.md:177 -#: 6ce8b81560e341c580d316d69202b268 +#: 0a610a9632064deb824afd0719429d3a msgid "Docker" msgstr "" #: ../../src/introduction/prerequisites.md:181 -#: 40cfd559d6a848d1aae354d3bdaa8e9c +#: ec0c47438a5242cb99dffa7a4997e95a msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." msgstr "" #: ../../src/introduction/prerequisites.md:185 -#: 8a9a50b0ebe847ce90593881ffe0d69c +#: aae94ac2114641f186eac0f4117223eb msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." msgstr "" #: ../../src/introduction/prerequisites.md:191 -#: 923cf9dd6d6c417aabe42f9fa62ffa35 +#: 209e072724ed4d27b37e9bff6d55d811 msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." msgstr "" #: ../../src/introduction/prerequisites.md:198 -#: 9390b03889de44638141d705e0ef8322 +#: 3bf47876e3694e6cadb05123326459cb msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." msgstr "" #: ../../src/introduction/prerequisites.md:199 -#: 12042e411482458f8c35a2491f9433e0 +#: 459a65b8e67c4a9aaa03138c1abe94ad msgid "The Python `venv` module: " msgstr "" #: ../../src/introduction/quick-start.md:1 -#: cdd4196f9aa34beba115901ec97913b6 +#: 898eb29ac7714c69840b795633953a05 msgid "Quick Start" msgstr "" #: ../../src/introduction/quick-start.md:3 -#: c43d9675ed134b78b02acb5a102a764a +#: 2a658bd2d8ce4533ab7e056fc3a3ffcf msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." msgstr "" #: ../../src/introduction/quick-start.md:7 -#: 280936bb2a22469799b2c9e9ba22adee +#: 32dd2e28cf0f40b6930750f0162355eb msgid "“Hello World”" msgstr "" #: ../../src/introduction/quick-start.md:12 -#: cb203354977d42a58112d09357f62565 +#: 471c47d311074ecfac071b6d52d9cfb6 msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" msgstr "" #: ../../src/introduction/quick-start.md:16 -#: 9e51962a7e5c47248f3e20703ae101eb +#: 5078140028ea4d04973cb9cd20f0607e msgid "`hello_world.cwl`" msgstr "" #: ../../src/introduction/quick-start.md:22 -#: 7e475e3f3c4a4404bb0236124c0f7ce7 +#: ab127d4ba0a44526ab129587a8160923 msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." msgstr "" #: ../../src/introduction/quick-start.md:27 -#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +#: d5cc6b4295a74f3586f022b0227759b3 msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." msgstr "" #: ../../src/introduction/quick-start.md:32 -#: 498a43362a4749f3b8b433709d34a1d5 +#: 585a4fe583ce44e180a062742b3b0849 msgid "Installing a CWL Runner" msgstr "" #: ../../src/introduction/quick-start.md:34 -#: f3e56aedd56b4b93bdc3894273e8c144 +#: 0d81b0c9ea58420789d1d71cca32ce88 msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" msgstr "" #: ../../src/introduction/quick-start.md:39 -#: 81481f5b82e4488398f87f0a169bd359 +#: ea4ab0782d8049d8b1b89cea4ae60048 msgid "Installing `cwltool` with `pip`." msgstr "" #: ../../src/introduction/quick-start.md:47 -#: a81342e756d24c40acc15835d0a768f2 +#: f6f3b7453a254f828bd4c9e9fef92bed msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." msgstr "" #: ../../src/introduction/quick-start.md:51 -#: c12cf89f8b9a421ebd05330326e219b3 +#: 3bf9050175d4444ebbbabe219412574f msgid "Running \"Hello World\"" msgstr "" #: ../../src/introduction/quick-start.md:53 -#: 9b68bcb1a41849dc9601ab47c5bbb0fe +#: e03f72a14dcf4bf38ce8232598ca761d msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" msgstr "" #: ../../src/introduction/quick-start.md:57 -#: ce04027dfcfe4b7b91ea3c2136b18b23 +#: 3dcfb2facd324dccb3084c02487625dc msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:62 -#: 0d8a788402914ebd8f09a5ca80650011 +#: b8531da183964b02bca19f818ec076d4 msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" msgstr "" #: ../../src/introduction/quick-start.md:65 -#: 6d0b679efab24813a7a3b709ade940d1 +#: 7ba1ddebeb2843179fe99fc410b193c6 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" #: ../../src/introduction/quick-start.md:70 -#: 2ea056ab04b6419a9faf350de22a17f2 +#: a6dc303e9d284b60bf1102212505ca27 msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" msgstr "" #: ../../src/introduction/quick-start.md:74 -#: 1a44a545434b448aa956005deeed90a8 +#: 59ac7830ae3e4d7cb1bf503e8c90fe30 msgid "`hello_world-job.json`" msgstr "" #: ../../src/introduction/quick-start.md:80 -#: e76bfcc0c9f84bcdb3f6d5277869a88c +#: 6d1d6f42ada2418ba0a1de1371825b9f msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" msgstr "" #: ../../src/introduction/quick-start.md:82 -#: d4cdbe870a6f4a68b542ca719d989062 +#: 1cd924fe8ace4a82ad8701f37b5e7d84 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:88 -#: b6d59e4b9c854abab1b3f7a0fa26f504 +#: aa297c52cd964291a47bb91c0135156b msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." msgstr "" #: ../../src/introduction/quick-start.md:96 -#: 5535b98e8b1342f09f003ec6db2b44b1 +#: 28b02c90397745bfbacc03c3b1034939 msgid "Continue reading the next sections of this User Guide!" msgstr "" #: ../../src/introduction/quick-start.md:97 -#: 77e43c7117fd4c52b140f0dd52cc3963 +#: ef2a4f39f01049b891868b84d968c0dd msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" #: ../../src/introduction/quick-start.md:98 -#: 7282abfa7155497ca47c30f9abfb6474 +#: 89e3fa8dceda4f0cb1cfdfd1f17fe4df msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." msgstr "" #: ../../src/introduction/quick-start.md:99 -#: 176d8d47830f4031bb95dc231ebf1303 +#: 7cd178223ba94d1ab3ee8cc5f13a8dcf msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" #: ../../src/introduction/quick-start.md:100 -#: 82a7ca3703bc4f0daa18942a1ac8943b +#: 46f6f8d050ce4f8c897056167d9707a7 msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" #: ../../src/introduction/quick-start.md:101 -#: d039a9d6461c44628d4660c00d9ce6ff +#: 5ee00ee409b746dc951ca1d4c360e624 msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." msgstr "" #: ../../src/introduction/quick-start.md:102 -#: fbc3383d9e1c4eaca7931c3cc4f1752b +#: d4af972281174b8999eab55ee0ab1a0e msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" #: ../../src/setup.md:9 -#: 1330bd38c4b5495f890b98c669f81a9d +#: 80401cfffae042ab9ec4b3754af04b25 msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 32f86f911ebe4a4c94975f81742333f3 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 +#: d5f1ad2b95ad46d48f8f2ca5e357bb5d msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf +#: c53ceee943ad4acea779e072b9137889 msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: 7dfe9dffbf5744299bf232599644c7f6 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 -#: 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: 00709fa451134ee09a0d808e101f28ed +#: 991172e201ec4796992a349dee44f090 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: 1f3c23a4769043ca985b8ddfed19391d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb +#: f81b43c7cb194a1cad8672129223c833 msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a +#: a20073a8f5374eb1bc8531ff33e622b6 msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 +#: d08869beca3a4774baf1097b63e79474 msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." msgstr "" #: ../../src/topics/best-practices.md:1 -#: 612c4a66c36a43d4ac5d74c1757d6845 +#: 109b773789024b2b9c063a6169c6169f msgid "Best Practices" msgstr "" #: ../../src/topics/best-practices.md:3 -#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +#: 959fa04f88e54d42b9b774cc95d85ee0 msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." msgstr "" #: ../../src/topics/best-practices.md:8 -#: 4bcb84707acb40a0bfe2ea0853cb10b7 +#: 64674980c3f24c45bbfbf3f957dda55e msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" #: ../../src/topics/best-practices.md:11 -#: 4dee8504a8e5496081dadc386ab45540 +#: 90f2e4265919446a902e17627f4420e2 msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." msgstr "" #: ../../src/topics/best-practices.md:20 -#: 674c238b25e240eda05e22e399f2f78f +#: 6b5f91a749fd44b5acfd6071c9913342 msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." msgstr "" #: ../../src/topics/best-practices.md:26 -#: b651f80f47b4442fbf29454a233697fc +#: 5fe2962837b14f0e9989063be4a506c3 msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" msgstr "" #: ../../src/topics/best-practices.md:28 -#: 263a127a77cf4c41af76854f22f1f260 +#: 4e1bdea962ed4618884cb9d1d59d7509 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" #: ../../src/topics/best-practices.md:37 -#: 3a87a0fb2a364e3da5aaa4017e430b19 +#: 37eff4ca02e843259f6ffa38e4a87a04 msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." msgstr "" #: ../../src/topics/best-practices.md:40 -#: ecf2b9c0b1664afe9c4e180610610021 +#: ae47231c203d40a98c10045038ea9b65 msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." msgstr "" #: ../../src/topics/best-practices.md:44 -#: e24cb13d98014e558b6a6946758359e0 +#: 018a6d5dbf1044559b365c7b9017eb3f msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:47 -#: f2b14a92374e449d9fb1e8c86ae0dd61 +#: e073d8f990c44b09a73d642cfe49bebd msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" #: ../../src/topics/best-practices.md:50 -#: 928e3df7ca3e479ca6474a8e72cf36eb +#: e04fae88d9b64493ac69eaee24585098 msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" #: ../../src/topics/best-practices.md:55 -#: d355f035676446c88b028f327aeb4829 +#: b26b9c9b1c4346a297a31c9721f0172a msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:58 -#: 339b852df24242189d6efcd2898a3396 +#: b50500c3c3f54b16a535a16175a44653 msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." msgstr "" #: ../../src/topics/best-practices.md:66 -#: 3ef57e6862f240bebcf193a52397af0a +#: 623f3a804199449bb85e23e00c8bb507 msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." msgstr "" #: ../../src/topics/best-practices.md:69 -#: f1a7c4f896a04a80b0c5f6a1db61ff8c +#: effea0b1356447c0899ca0746667ea31 msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." msgstr "" #: ../../src/topics/best-practices.md:73 -#: 1ac4c3d8c3e44bd1af3fc5df70051926 +#: 00e8ef87864c4ca2b2c1c0548b02b38d msgid "Custom types should be defined with one external YAML per type definition for re-use." msgstr "" #: ../../src/topics/best-practices.md:76 -#: c858f64e66f048a5b0032ef3e4d83694 +#: 6e6f48d70b894a6c959ca30fe6bad772 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" #: ../../src/topics/best-practices.md:78 -#: fae385da16aa443da996fa23ac03d6ae +#: 02fe08760a4a4ab49e96f4e51316a81d msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." msgstr "" #: ../../src/topics/best-practices.md:82 -#: 92430be71ecc40e18bbbb80d5576c613 +#: 172ed7915a654964ba63f860b2d65330 msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." msgstr "" #: ../../src/topics/best-practices.md:85 -#: 387d83db81024f65aa9a890c2d07874a +#: 4d0a2871a7484e21b3c39c4dbaaa63fc msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." msgstr "" #: ../../src/topics/best-practices.md:90 -#: d8e2280a75a74916a1630afaa2fe2ae3 +#: 1eea9f1e284447718141f5417b6bb433 msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." msgstr "" #: ../../src/topics/best-practices.md:93 -#: f1c1340f9745458980e0fbd641738687 +#: 509411d353fe4314b087b81b09ea960b msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." msgstr "" #: ../../src/topics/best-practices.md:97 -#: 5424e5472c3d466fa2a3d2022c6cb475 +#: a54bc80bf08243bba67d98dd682ee134 msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." msgstr "" #: ../../src/topics/command-line-tool.md:1 -#: 3f4e98f6bfa141feba8c4b120e3d03e8 +#: 69ecdaea24ef42eebef9d86e5d716b11 msgid "Command Line Tool" msgstr "" #: ../../src/topics/command-line-tool.md:3 -#: 12f57b2ba76b492abe1816e06bfb1417 +#: 3cc5847468d1478bb5589dee68147189 msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." msgstr "" #: ../../src/topics/command-line-tool.md:8 -#: e1f657a46ce94a0d83671540e2cc2dab +#: 98c6bc409420485095ae65d6b0b9a3a0 msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." msgstr "" #: ../../src/topics/command-line-tool.md:19 -#: abb83f0097654a43bd78639d3dbb2bc8 +#: ebe23e5378514f888a9ec32a2adb1e98 msgid "CWL command-line tool." msgstr "" #: ../../src/topics/command-line-tool.md:50 -#: 3b1a9ae3412f4d6e96a39b9a16934232 +#: 387cfe85604f424f8d31c4a4c9c15edb msgid "`echo.cwl`" msgstr "" #: ../../src/topics/command-line-tool.md:57 -#: a5eacdbc9aa142c890b177869da4143d +#: 7b1d65754e854693bb60289c97d3fb5d msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." msgstr "" #: ../../src/topics/command-line-tool.md:68 -#: 1849b8f3ae1c4a84ae59a78ffd6b371e +#: f440cef729c8410281432307a4da8d55 msgid "Network Access" msgstr "" #: ../../src/topics/command-line-tool.md:69 -#: e3bdaceae8784ab0807b2cf356a98580 +#: 4fbb8ceb1b59480583ac611142167049 msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." msgstr "" #: ../../src/topics/command-line-tool.md:83 -#: ed521ac365db4a6ba5a1051fbaa2932e +#: b87869204838415bbf694214e3680593 msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: 12cf5f2264504c44a2173e858bb2c283 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d +#: 7694f9cabfe04308bbddd2c88ae6d9b9 msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff +#: b557dc4f8ef549b98f59412a918643de msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: 3011eb003c084285b30cfa56a8da45b6 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df +#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 +#: ce78b2d147054da895beba66d0ecdab4 msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa +#: a973846ec5a946eeaff02c5b00997da9 msgid "To test the above CWL tool, use this job to provide the input value `message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 #: ../../src/topics/outputs.md:77 -#: 2d2ef4769b2347e79db827655f1bcdeb -#: 2699fbc4376148af91b7a5a6cdac467c -#: ca03defa3ad14cf698171cb09e3055c1 +#: ccec7f73b9d948e79a6cdf32bc124092 +#: 9e8eb1542db640ff9e300649ce50dc9d +#: 294fd83a97a64249bac38f7482159372 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d +#: 22948f19cb78485f8f86244686a35c09 msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c +#: 001d9579bfce438e865377fb9c2df776 msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 +#: e62618db8995428bb3f260e03ac8f459 msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." msgstr "" @@ -1291,193 +1291,193 @@ msgstr "" #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 #: ../../src/topics/workflows.md:198 -#: b372f33c65bb4707b2a462a960bb1373 -#: 293fb1d428b849aebccad598a932992d -#: f924d65fed0c4cb5b0a019b084a8b535 -#: d6255506eebe44be94c5ce703c44a513 -#: 7bbd2d738fc54649aeb10f8d2bc38b6f +#: 98e0548845fa447fb05a29c9fc2f17b5 +#: e9801b2142cd45368a73ef9b121c1d08 +#: 457756c4e9544f068af897113358cc89 +#: de5e8aad4e3046bf9bfc2ad8ccba17d0 +#: 6d5ae75431424ea788c3440606f22940 msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/custom-types.md:1 -#: cb34fd4c8cb04053ada491a227651048 +#: ee2bca9bdbb74b60a706c3118d6a17ba msgid "Custom Types" msgstr "" #: ../../src/topics/custom-types.md:3 -#: 67573252cc064b27ab13eebc468ac58a +#: e63ae9694f40438d872d141ae824a42d msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." msgstr "" #: ../../src/topics/custom-types.md:9 -#: 73e68b3af9cf41338d843c0c40e50cdc +#: 750fdd4c270e46a09f79e867358f7414 msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:12 -#: ef5f35acb97f4ddfad7b688712f53484 +#: b3f688cc82444ef7a7a0aa63dac39cac msgid "`custom-types.cwl`" msgstr "" #: ../../src/topics/custom-types.md:18 -#: 7015dfa99a6f4cfb87ebf0ed61e8043c +#: 3638be18b4f64cf08053d512e590dda3 msgid "`custom-types.yml`" msgstr "" #: ../../src/topics/custom-types.md:24 -#: a999b1acda2641598086648c64aa3831 +#: 7d5b9c21739c48f18c13614ca6967f6b msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" #: ../../src/topics/custom-types.md:30 -#: f8c12a58cb0b46a488823c6ae95f25ea +#: 8fea29993f944d8d8d3181afa29bd0a6 msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" msgstr "" #: ../../src/topics/custom-types.md:46 -#: f25a63e0926d4932bbe64b2e4bdabf9e +#: 02d0b648d70f49d7892f690be06df585 msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:53 -#: b0a4df0fd3ca42338cff4689235dcf4e +#: 0743bef42b9a42328849c8c2f9da9eed msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" #: ../../src/topics/custom-types.md:55 -#: fecfbb44456640d8ba05e519bf2ff564 +#: 85c5d0cbbc6243a6823f5eeac0f85dd9 msgid "`biom-convert-table.yaml`" msgstr "" #: ../../src/topics/custom-types.md:61 -#: d718630a296545f3a989c8c71e9ddc77 +#: be848f30769543eb9c0be55263e3f758 msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" msgstr "" #: ../../src/topics/custom-types.md:76 -#: 9a97acd430064710bcdf76edbd9f711c +#: cbff44a64ba4432cb59a82f82c2f0103 msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." msgstr "" #: ../../src/topics/environment-variables.md:1 -#: 59014808cbef4c02aaef03129d8a29b0 +#: 617f1c0084cf42d9be4c7a8fa5a48432 msgid "Environment Variables" msgstr "" #: ../../src/topics/environment-variables.md:3 -#: 3c821c9c46d841ec89b8a5b1018f3af8 +#: cee79afa3c6f43c29ef05e06b7843d35 msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." msgstr "" #: ../../src/topics/environment-variables.md:7 -#: bfdebb32440a4034beb42135e38884e8 +#: 225903b11efa417989df42de86ad2451 msgid "`env.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:1 -#: 777d4a52f7554eff84db2df6d4d0f729 +#: 1a5f058290064c1cad05e63eb127fcbb msgid "Expression Tool" msgstr "" #: ../../src/topics/expression-tool.md:3 -#: 48deb71f361a43e48a56ed483075bca8 +#: 74ad8d69cf294ae880dbbe28e25b3545 msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." msgstr "" #: ../../src/topics/expression-tool.md:8 -#: 716b56506ca7470299899c5d820a9ea2 +#: 5293e8ee9b3b4f59947cfc164ef111c4 msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." msgstr "" #: ../../src/topics/expression-tool.md:17 -#: b63e6f5a2e89431c8fc7d04f47fd69fe +#: ffa1955c759942c68e7589429e5ea86b msgid "CWL expression tool." msgstr "" #: ../../src/topics/expression-tool.md:48 -#: 39727e9058f24b62b8746a46d3f812c2 +#: 038bc0ba5f6a405a8255a7be76979baf msgid "`uppercase.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:67 -#: e3ecac0a8e604f2b98a2a12b0579990a +#: fae1c63de02e48c0969a98e4c49b2e06 msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." msgstr "" #: ../../src/topics/expressions.md:1 -#: c8d648b765ec499a8e9c464590838492 +#: 7093a94695524851a5463193f0701b78 msgid "Expressions" msgstr "" #: ../../src/topics/expressions.md:3 -#: 007a345b4bad49cf996c4301b8386473 +#: dc8274ecb15948c29a31db89b12a58bd msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." msgstr "" #: ../../src/topics/expressions.md:9 -#: 2edbd398eadb458b8eacd5fa5496f0a2 +#: cec8eef8a5aa49778ecedd4195ab9f2c msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." msgstr "" #: ../../src/topics/expressions.md:16 -#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: df100967597043c78112bf43b520cfab msgid "`expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:22 -#: efb5fd14988c4e2a8f834ee5369d4102 +#: 59ccf4daba39406581a6bc2d9bb1b7d2 msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" msgstr "" #: ../../src/topics/expressions.md:25 -#: e833649b951841c49397796f996d29f3 +#: 570cc75699dd4e0a987fc9aca9a01ee4 msgid "`empty.yml`" msgstr "" #: ../../src/topics/expressions.md:31 -#: 276f688ba7cc471a842f085ca852b1d9 +#: 9e123723048546d495ed5110d7177708 msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." msgstr "" #: ../../src/topics/expressions.md:35 -#: ebf399ea4d5f47b9be03e24f04c69f2d +#: 26543894f6e04270b89ab702451bcc89 msgid "We can then run `expression.cwl`:" msgstr "" #: ../../src/topics/expressions.md:37 -#: 65e0cdd505b944caa40f65e612cdddfc +#: f403c1d4e43a4aa0aef8488d2b5a6262 msgid "Running `expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:47 -#: 8b70a1ad70514039b97164fa630c12e4 +#: 249dffb569a944c897ce5862e5f28fad msgid "Note that requirements can be provided with the map syntax, as in the example above:" msgstr "" #: ../../src/topics/expressions.md:54 -#: 2f28ab412d2843ffa5f14acdc01fc732 +#: 1641c96aca2f4923885fe8a509eb3a49 msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." msgstr "" #: ../../src/topics/expressions.md:62 -#: d957f55a6377422c9834f85d45e35009 +#: bc63405a0d964df2bd9493996abc48fe msgid "Where are JavaScript expressions allowed?" msgstr "" #: ../../src/topics/expressions.md:64 -#: cbec9277b5004e50af2728cbda0df740 +#: 5c191d1420db4e26aca31c1b1e34cb75 msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" msgstr "" #: ../../src/topics/expressions.md:66 -#: e259f55f8000479bbd8009e25cf0ca6c +#: d6a5c65e824a4bbc94578df9597d4716 msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 -#: 1acb064f7a4a482aa0174bdc847c6382 -#: 0222780b98ac48e89b1b4f57c9df8590 +#: a7ff51fe564748229a88a0d3044dbc17 +#: c12625211cc542b68cb51365a63eef00 msgid "`arguments`" msgstr "" @@ -1487,38 +1487,38 @@ msgstr "" #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 #: ../../src/topics/parameter-references.md:86 -#: ef2b8433778a40408f179c3e6f0cf99e -#: 224732683a9c41f3ba1b778851e745a8 -#: 17b10d1e91b24dc582df98fcd2ac850e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 -#: e4e68011dc5f42e4918c747afa7d764b -#: d44e3cfa661840eb851782e24caf1b68 +#: 3a64ccbbf70447d1a813a725e528b6fe +#: 5fb932af34a54a0ea691260d43053eba +#: 2a2286a9c8494e3b88db35bf63230f33 +#: e7f1993580f0425098a719e83a64cc7f +#: 05c34a5a2e404a14b9d284a9d0c73bd3 +#: e5b0293e6fcd4e9b8d7be3fc9fc127d3 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 #: ../../src/topics/parameter-references.md:66 -#: 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: 2fd5b42cafe34d3185888de041818dff +#: c158e9ee5fbf4e868b152a0a5880092f msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 #: ../../src/topics/parameter-references.md:67 -#: 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: 92697d3179ec48898eaea9aba3c24dcd +#: 3f29e4a3087847e9af6f19166a8def9a msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 #: ../../src/topics/parameter-references.md:68 -#: 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: d6722e3093884ad7b62696fbb2f48fdc +#: c0eaef93bc3743279549bcfb8b014ca3 msgid "`stderr`" msgstr "" #: ../../src/topics/expressions.md:72 -#: 8210b36347a749889450529ecdf4ff0e +#: 37c493fdc2f0410a9748f8faf09ce5b5 msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" @@ -1530,14 +1530,14 @@ msgstr "" #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 #: ../../src/topics/parameter-references.md:90 -#: d0a92a3792b549e9b5ddce4667d168d2 -#: 801729c7c71b4109824b035437e69bf9 -#: 1bc510d525f0414e88692e356e67fbbc -#: d2e246ae56a24e4abdd6b7d9812a86e2 -#: b1446bab2732412e91f721a08067b0bd -#: e89dbeb22f41430ca39c923d9fdf68cb -#: bd61499b71e64164878dea08d6d7141e -#: ed875a006df64f9e8a55fa5e9fa87404 +#: 9cfb6ca1255241aa9e5928ea981286e9 +#: 4ff7326e660f42d8b45c3353005554f8 +#: 04e3eefe4ec445cb90c2fa42344aaed5 +#: 07611b01b06a4afb808322a0dccccf30 +#: 6020618711d449a48618c11215453487 +#: c358a25b1f9543598b90d3df7c012b85 +#: c610220d06484d589313dc29faf8222c +#: 7b132c6e720f4256859757778f5c4fef msgid "`format`" msgstr "" @@ -1549,1574 +1549,1574 @@ msgstr "" #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 #: ../../src/topics/parameter-references.md:91 -#: 8a1748579de14f0888d5ee9023e37c2d -#: f760465a49d64d4c8468ad9c4fea62b1 -#: 28b6b5ffa7524374aaa9525ebfafb762 -#: d11f6a19ddf34cf19ec856bacf998e29 -#: bcb7cd10cb5947bb9d85c040f57f954f -#: da5188d3bedc4997a35bdf417f2f643c -#: cd7a0190511d4613b09600a3b1e9d55f -#: 47def3b078e2402182039be0227090ae +#: e193aebe7124444c90be1f6cad81482a +#: 74652fdbeaf14d82b9c5053e322504da +#: 93d2b17bb236426286ffd51bbecda61d +#: a44c278bde5849aeac122c981294332c +#: 6dfc264200a9496f9d2458fc759993d8 +#: f71216a4b35e4157aece5ffa2602d8bf +#: 662b36e3505f4ac3bb5070bb6e055217 +#: ee3d416cc68c4f11a79849bb67395f1b msgid "`secondaryFiles`" msgstr "" #: ../../src/topics/expressions.md:75 -#: 23088850ad02459696f6bbd385109aac +#: a3c775a0f04b4541a9b712bfe2e4e69a msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/expressions.md:77 -#: f02257a822ad46ac93c5981531cc85d5 +#: ef16c4a9a7ea415fa399297b63b9710c msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:80 -#: 989a1c4aaa1143be9f53b90cd8b6d500 +#: 2592e429c74c4ff5b8ba68a36f060c1a msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 -#: 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: 5cca4c2ad617400eb6efad4066b1839b +#: ba1fff3ebb274dfba845b3ee20ebd71f msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 #: ../../src/topics/parameter-references.md:79 -#: d555a3d991e344a5a8e1289168d7c6d1 -#: 44b3f123c9b04a308c1161b742a7b34b +#: 6914526c0a7c43a2a05438519508ee0f +#: 722d3bd7184841639b9f9a38914002da msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 -#: e9fa9430535c424fa3e8be5d460d2ba4 -#: 0e306cc923974d1db83fdfb45105a11c +#: 737b0f9392154241ae5b56c6caa823f5 +#: 7b46d408e7e7481b91a950b2d4010c9a msgid "From `Workflow`" msgstr "" #: ../../src/topics/expressions.md:84 -#: d289541e460147aa933f7878996f8649 +#: f09e7371708b4c0685eef2a314791ccd msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 -#: b0290d1a477b48119e17cf1fed9d6dff -#: 446f1190af7a40a0913ff04ce7aa938c +#: aa6ca1def2024c98b9d5542de1a81425 +#: e9fc5f7fa4474dfc95039b94167fe894 msgid "From `steps`" msgstr "" #: ../../src/topics/expressions.md:88 -#: 81b4d1f23a3642bfa9bb395b94260cd1 +#: 6c37a1ff939748bf83a86c07c3d017fe msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 -#: e1cde4aa32c041238ed2596173c6d824 -#: 557694f82e314baa9ccafba14d6ff2c9 +#: 3a8126b0a0334df890b2be2c693ea5d5 +#: 61744122b7d7494890cbe6b2fb72b9f7 msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 -#: c2a92d3eca7f4ee39cec649170eeea53 -#: 3c939769ede94602a67fc50c435741cf +#: 93cb9015dacc4b50a4ef177ce4ece2e7 +#: e0c7ccc8f8664cf794cbb7330355f3fe msgid "`expression`" msgstr "" #: ../../src/topics/expressions.md:92 -#: f495da32f05a4a5ba9539be0a54c1a59 +#: 58a1773b1cf546d7890010fdebd47388 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:95 -#: bdb4c68a175047ddbe141ca24960127f +#: 230f3227ed1144f7abe0f8c231bebbd5 msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 -#: 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: c9534670f5f04769aa3749c3778eb705 +#: 5c77dc9f8afe4dd88933943030e836f2 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 #: ../../src/topics/parameter-references.md:94 -#: 718ceee9973240ec9c100977bbcc8921 -#: 2b25152f6df5494a8632f3ce631c20d8 +#: 4ec8bbac5fb14371a6a4cd53d7cd6450 +#: 7b0887a8caed41b2acccf7021bb323d3 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 #: ../../src/topics/parameter-references.md:95 -#: c07ab08eb75d4528949c56a3d7c12b28 -#: 846cd427ae25410eae7c920b237edcb0 +#: aceedfb558b246bc87eb3eaedea187fd +#: e5e8b8c75f0f43cbb6e160e5bf810c6e msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 -#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: fe3b9fb45e01490498c5a35c012b3de8 +#: 266dfb5fe6a842078baf66073cac9623 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 #: ../../src/topics/parameter-references.md:97 -#: 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: 85f424cbfc85460f9da310aee1ff0b82 +#: ddf82b12b12d416fb65f3ce3f51bbdf0 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 -#: 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: 966e88656ae5402a975022ee60646283 +#: af14fda3cca645fbb2f3c5825fe0788e msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 #: ../../src/topics/parameter-references.md:99 -#: 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: fec70bb106ad4d95a2d55ebdcf711afc +#: 09120baec1464afb8aed4edd773bf509 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b -#: e3b76f42c924489f9a0bcf5a7b636d23 +#: c98db5b115ee4c4abb211481fe7214b0 +#: 2e128858cd06466680fc6bbfb577b818 msgid "`outdirMax`" msgstr "" #: ../../src/topics/expressions.md:104 -#: 97b61352363f47cb890e8937c5613fa3 +#: 1dc4148caef748428a7d13caff37b1b1 msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e -#: a258554d462f4f5f83ece28d5b2fc584 +#: 8caf296626024598b4450311ade09e56 +#: 568406e34c8642578396177b40043014 msgid "`listing`" msgstr "" #: ../../src/topics/expressions.md:106 -#: 8d0b142bb7ed4e61b8fb03de197240ce +#: 947b1ca132a54ed39745cd12ebcd65e1 msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: effc0208cf4f4551958db6e526c0528b -#: 9d4889c8cec24351a7a9e3c547e331b6 +#: 3af8e4ce750048e6b9de12d26b9647a6 +#: f56fb5fa08994fe08cc8ae8c193828d9 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: be6c1e85c7b6495d8086c262daad20e7 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +#: c6dbe0a66b9f47e5b4b47c44d9f54519 +#: 063e2ae9a0eb404e8c277ef7090eb6bc msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 -#: 6abeba392b0444b19f92a19f178a4682 +#: 72acfeef964841e7b65937b62b5850f0 +#: 39c6edc2866542cfa7da9f842fd3edd0 msgid "From `EnvVarRequirement`" msgstr "" #: ../../src/topics/expressions.md:110 -#: 0bc424ef2ca346099f29b937379908a0 +#: 5fa512d352d945e7a3e0d59b0987cd1b msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd -#: 949c376120d8441796ec9c89364f8851 +#: 79755be159fb45b0ad06cecce623ce2c +#: 520bf799546b4700a4f38f950ffd913b msgid "`envValue`" msgstr "" #: ../../src/topics/expressions.md:116 -#: 10d36a1adfd04144b401c993b12b4094 +#: 81e91df082834d2cab7ef1f62d8ba57a msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" #: ../../src/topics/expressions.md:118 -#: 29b73e1dd72744f68377f0a38c10f062 +#: e6bfd1dc2e324992b6c3332c11ae3445 msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." msgstr "" #: ../../src/topics/expressions.md:122 -#: 38a2afaf4a6c4d04909af22c93f2808d +#: acf10261df2944ec890d754fd56c6b28 msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:128 -#: cd74f34b21af4de9be96fd897efc469b +#: bda6b8f398554b0c946c2c7d96308a42 msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" #: ../../src/topics/expressions.md:135 -#: f12e371f3f1a4b0cb2cff9800352d48c +#: 454c02c3918647039c90ae387005dea6 msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" msgstr "" #: ../../src/topics/expressions.md:139 -#: 49d0fda2fc144e0b8b7c92afc1d8945e +#: e1fad28bf9cb4c4c85eb74dd520ba107 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" #: ../../src/topics/expressions.md:146 -#: 8f0e8f050e334ac08334e9215e1dcf61 +#: 9835d0b399b84a0084fe5a4d9e7e6405 msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" msgstr "" #: ../../src/topics/expressions.md:149 -#: 26c74b11bb1849cea0763bb74ec43e42 +#: 410ba7a5ac6349a98460c6337ee5c4fb msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" #: ../../src/topics/expressions.md:155 -#: 7a6be0005a6441feb67f036d005d7885 +#: d2daf50d7f3d4de18331c8fd2c8a5786 msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" msgstr "" #: ../../src/topics/expressions.md:158 -#: ed590f9e6f4f425da886b110295c45db +#: 8f2015c12b2b4d5d9a800ddeaf428f25 msgid "`custom-functions.js`" msgstr "" #: ../../src/topics/expressions.md:164 -#: 093235307d6f47d4858e559b780ef5e5 +#: f0ff919ffc12439d89d7b40f51ade84c msgid "`hello-world-expressionlib-external.cwl`" msgstr "" #: ../../src/topics/expressions.md:171 -#: 06635145b441418aaae84dc804f3d6ac +#: 307a17a893fc4dafaec2a63a95704644 msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:175 -#: 973a9b257b1a4f0dbd4444d4f11dadd7 +#: 7f393e86b114470f8dda47b2deec63aa msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" #: ../../src/topics/expressions.md:181 -#: 04eaf1f7c630450db318dcd8b7626e15 +#: c3f459b87b96435583637b3f1573e658 msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." msgstr "" #: ../../src/topics/expressions.md:186 -#: c4098489fbb049789f022cd3e5c3d49b +#: 9f676022eb2744839ca2109920250cb6 msgid "`hello-world-expressionlib.cwl`" msgstr "" #: ../../src/topics/expressions.md:193 -#: 5979e4ae5c424276bdbc47f69b379d0f +#: ede7285f77864fb0aee6cfecc2c97fa0 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" #: ../../src/topics/expressions.md:200 -#: fd4579a3c9844492b314b5c3c1775fc7 +#: c55fb184bc614ee2b6e5e64611e5df9b msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." msgstr "" #: ../../src/topics/file-formats.md:1 -#: 3f038e7371f84ed9b4547358dfb55a11 +#: 66b522f46ce242149386e79f63b32cf8 msgid "File Formats" msgstr "" #: ../../src/topics/file-formats.md:3 -#: e024bcb70e04412e90e1838426d1b69a +#: 64a20285785d48ca86227a0cf6353ad4 msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." msgstr "" #: ../../src/topics/file-formats.md:8 -#: a3db21c0b3114802a8a5b610e252ef13 +#: 5f71bbe2c74e4260b79d4d9230d35397 msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" #: ../../src/topics/file-formats.md:14 -#: 0f5bc8520d6a4dafa37c65343da9702a +#: 63bfff437e3348428f7e33ece7ec55e7 msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." msgstr "" #: ../../src/topics/file-formats.md:17 -#: 5cb830da47464a8b9c3950983fa4d56f +#: 6ce83d9c06e4436881aa47d94ef41e0b msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." msgstr "" #: ../../src/topics/file-formats.md:20 -#: 0535d5de416b4ea3b2f5996583deecc1 +#: 55006c594abf4e70a38e979568fadcf4 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 -#: fb47f73c38cf4ec59bd3021866a631f8 +#: 12ba2083a9ae4c78bf502ab762a29c7d +#: 5c8f1709fe61423bba3ceaca2fc7cf09 msgid "The equivalent of this CWL description in command line format is:" msgstr "" #: ../../src/topics/file-formats.md:32 -#: 74b28c1b09c6429b82e462e4ec61808e +#: 1a1905ff2d624eca952c8a53b3bee678 msgid "Sample Parameter Files" msgstr "" #: ../../src/topics/file-formats.md:34 -#: a2ce43b391864e8bbde16328cc19b32b +#: 368ff92476b14f5c8331260eafc5acb5 msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." msgstr "" #: ../../src/topics/file-formats.md:39 -#: aebee48b742c4145a600fd2daf8c75dc +#: 5d530afa23f349a79f54d51d40724747 msgid "`sample.yml`" msgstr "" #: ../../src/topics/file-formats.md:45 -#: 56ee4dcfff6141d5bef80eb96559876d +#: 16f965f86712483aa7f95dfa3f944a17 msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" #: ../../src/topics/index.md:1 -#: 8d3a6d83e2e54c56995893c41590b7ff +#: dc629e2c90ed458b96107a6994676434 msgid "Topics" msgstr "" #: ../../src/topics/inputs.md:1 -#: 5abcdebfa1cb401bb8892553be285fd3 +#: cf2f077cf8044079a7005e6e508dcd8c msgid "Inputs" msgstr "" #: ../../src/topics/inputs.md:3 -#: d3a55f71dc244026a97902de9ed819ea +#: 129e1d2a71894d28b009f4846754a75d msgid "Essential Input Parameters" msgstr "" #: ../../src/topics/inputs.md:5 -#: 96671c56523c4ea9992fb5dfcfa6490e +#: d6791bbe575042b9a7282c69407dd907 msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/inputs.md:9 -#: bcc6246742cb46bfb185e415c4a3431a +#: e8da87f8bb664334adf831995601f462 msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." msgstr "" #: ../../src/topics/inputs.md:13 -#: 86dce36de687449c88fb5eb9d64eb045 +#: de6c322618304207b6d1364d1ec2dc13 msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." msgstr "" #: ../../src/topics/inputs.md:16 -#: cd9cea15f57b492ba4098237cd7c5bed +#: 43bdcf6dc1b14030bff27fa53289c02c msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" #: ../../src/topics/inputs.md:18 -#: 8bdb875b63104f699efe28ea0abb1e3d +#: 056510b42ea64717996ab49c307bda86 msgid "`inp.cwl`" msgstr "" #: ../../src/topics/inputs.md:24 -#: c6a0151a68494c0cb0176781e65e252e +#: 6852f5dbd9094c99bb68f2a88f76c9bc msgid "Create a file called `inp-job.yml`:" msgstr "" #: ../../src/topics/inputs.md:26 -#: dc5e6b5e01d64226bd5dbbf3175fe010 +#: f33b6800367248b7927d97ad7b4be5b5 msgid "`inp-job.yml`" msgstr "" #: ../../src/topics/inputs.md:33 -#: 36ab1d9edafc4831bb1bca5f123b04b0 +#: 8ad812d7e88f4cbba83228ffb1711576 msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" msgstr "" #: ../../src/topics/inputs.md:40 -#: 7dc630ea86464b1dba3a4e5079260b3b +#: cc680bbf091a46f8b4b3dbe6324c040a msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." msgstr "" #: ../../src/topics/inputs.md:44 -#: ae37901a8dbe48a59e27ab4e2e6e2d30 +#: 446ac81f078d46289a18f494748f482c msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." msgstr "" #: ../../src/topics/inputs.md:47 -#: 651e032007ea4a119d20c820bb61f86b +#: 3d6d958d111943f3a2139b4dbb7810db msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." msgstr "" #: ../../src/topics/inputs.md:53 -#: 0b056dde9e87428996e47870b12119da +#: ba0ec9157709430c822f4e91459288e2 msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" msgstr "" #: ../../src/topics/inputs.md:64 -#: 628124a1670b4b058bb0fb6e495a099c +#: 2565f8fd4a15429e887aeb71eacdff1e msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" msgstr "" #: ../../src/topics/inputs.md:70 -#: 10ca6321ce3e4b08ab6a5bb380b19c11 +#: 659ed5c64fb546399b741553a347b8e8 msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." msgstr "" #: ../../src/topics/inputs.md:83 -#: ec2adb3912bc46e28891229e9e0d9a1c +#: 3d87e69d41374fbab23b26d36c1aee03 msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." msgstr "" #: ../../src/topics/inputs.md:95 -#: a519be60726a44af9941fdce04735353 +#: 07bc81683e2c4ac68b379462bae95207 msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." msgstr "" #: ../../src/topics/inputs.md:109 -#: cb8fc8c4c79e467eac5fab4ca685201e +#: 3e304da2150f448d9e39715ac5f5deaa msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." msgstr "" #: ../../src/topics/inputs.md:124 -#: a26cc105716f47cb807174c9003153b0 +#: fd8a98686e3c4c609f79ae427f1558d3 msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." msgstr "" #: ../../src/topics/inputs.md:131 -#: cc159dd5fe5748caac838862f5b8c4d1 +#: f1a2e1bbb1104a4fab5a7f04cac845c7 msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." msgstr "" #: ../../src/topics/inputs.md:134 -#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +#: 6a7f0ccd227e4f90a8c8ca96744bda68 msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." msgstr "" #: ../../src/topics/inputs.md:142 -#: 6812698e9ad84d3385de5e88e9dde0b3 +#: 1f79d115d8a145189638c68c3095396c msgid "The `baseCommand` field will always appear in the final command line before the parameters." msgstr "" #: ../../src/topics/inputs.md:146 -#: 9654e65b1c0642dbb5d4f34edb211989 +#: 6e1b3e2d90184e34925891099d2b5cc1 msgid "Array Inputs" msgstr "" #: ../../src/topics/inputs.md:148 -#: d1f02be278754267893dfce5a940997d +#: 4f6df7f13e42448eb4a53f03bc477b56 msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." msgstr "" #: ../../src/topics/inputs.md:154 -#: 01f30e38dfdd452dba3a996073936e16 +#: dbc0b52627514ad0908969d0b4ddfdf4 msgid "`array-inputs.cwl`" msgstr "" #: ../../src/topics/inputs.md:160 -#: 787d4bfb093c4ad287b902084706b751 +#: f173dd96ad124470a53573c86a8df203 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 #: ../../src/topics/outputs.md:82 #: ../../src/topics/outputs.md:105 -#: 588f0f7f967f4d69af27c9729d6d3119 -#: 02adef8ee8204842b5b4a0408f3bac33 -#: 9db68837918a4a349f32f15f12697a1d +#: e0098a77080d4349b05ceb7735a5fdf5 +#: af25945b530048b685891b1de4e35e72 +#: cb07caa4ff0149b3ae832be53f8d76f6 msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/inputs.md:178 -#: 75d59e395c66416cae9b352db5081516 +#: 2445d2c7c2794fd3ad8b6ed8b4a9440b msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." msgstr "" #: ../../src/topics/inputs.md:185 -#: 874c6f19abbf45d7ab7d30a378c4048d +#: 4459819ba75647d185986a3386939494 msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." msgstr "" #: ../../src/topics/inputs.md:191 -#: 5d7d7a28cc5d4862803032aec78174d9 +#: 8f163bd34ded4785b6e28c8e2147e0dd msgid "Inclusive and Exclusive Inputs" msgstr "" #: ../../src/topics/inputs.md:193 -#: dea0d4b681f94e73b13965dcfe75cf7d +#: 1799e11a7b9c4929a3d1379d7ea45d03 msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." msgstr "" #: ../../src/topics/inputs.md:198 -#: ddf598abf4f34aca9fffa045860fbf96 +#: 9510c0b431a44b5e84e0b583de7c5446 msgid "`record.cwl`" msgstr "" #: ../../src/topics/inputs.md:204 -#: d52a8089920e45bd89d582533b50e3a1 +#: efb4eb6f5e994b50a52fa2c707dad1ce msgid "`record-job1.yml`" msgstr "" #: ../../src/topics/inputs.md:215 -#: 750474486a84482292eeba45f118287f +#: 34599c6f10ce4104be2359a1b37f91cb msgid "In the first example, you can't provide `itemA` without also providing `itemB`." msgstr "" #: ../../src/topics/inputs.md:217 -#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: 0663ea7918994d3f9c45c652a3ed12db msgid "`record-job2.yml`" msgstr "" #: ../../src/topics/inputs.md:233 -#: 1eb0e39bb6d04b8cab300f44a79f3add +#: a98dda6ca4b14edba467de638bba28fc msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." msgstr "" #: ../../src/topics/inputs.md:236 -#: bc21ee10bff843689cc98ac6630edcea +#: 10d0e9f8df8c47788703073b17529bc8 msgid "`record-job3.yml`" msgstr "" #: ../../src/topics/inputs.md:252 -#: 4b2ab812f62c4f949dd25c8527f2411c +#: 9a0e1a130fba4d24a9168ca3e455cd23 msgid "In the third example, only `itemD` is provided, so it appears on the command line." msgstr "" #: ../../src/topics/inputs.md:255 -#: b771302d1bec4050a9417b080eef76c9 +#: 992a8c801ceb4233acf56b6bff315188 msgid "Exclusive Input Parameters with Expressions" msgstr "" #: ../../src/topics/inputs.md:257 -#: 2c3b884cb1c54521900cc90782e8a58d +#: 9027d23fa7074b789c3b86ca5ea17fa4 msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." msgstr "" #: ../../src/topics/inputs.md:262 -#: a1073b6306044dffb414319ae01f68bb +#: 68b47710a8ea4b978428b42c627944e9 msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." msgstr "" #: ../../src/topics/inputs.md:265 -#: 4a31c733092142b1af834eab1747c224 +#: d33e4cac65d14111a89c838c4d1759b9 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" #: ../../src/topics/inputs.md:271 -#: 9a1d92334685449386dfa3b3a899ed48 +#: 24cea1cf7d774b6ab56959f289cab39d msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" msgstr "" #: ../../src/topics/inputs.md:280 -#: fb623af4c480411b8fde28d01c981411 +#: b866867d6f8e4d3999b62a85e6884ebc msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." msgstr "" #: ../../src/topics/inputs.md:289 -#: e98e165f6bba40809c90473d72f9d592 +#: 80c49ed168b14d25b2f09b3b0186b44f msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: 71628ebe908b4cd28dd1fa17e3d2e2fb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 +#: f123ca244c23413c91405a4b84887525 msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b +#: 23299ae1bec94b00a32a8af7eeac350f msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: 2495a9f2032a47c188338cb81ba429eb msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: 3fd2f3cf7bdf44089df2ce3122534801 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 +#: d5a5b8b490b640439db92da949266e4e msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: 5935ed94331d4b2f8ce597f31edea843 msgid "`metadata_example3.cwl`" msgstr "" #: ../../src/topics/operations.md:1 -#: 8acf361cf77c4d45ba3f2e344146259f +#: 5feb559552194ba58da7206c601292fe msgid "Operations" msgstr "" #: ../../src/topics/operations.md:3 -#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +#: b7124ba4df9042baadc1641ee09545d6 msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." msgstr "" #: ../../src/topics/operations.md:7 -#: 5565c1b2d8a349169a305a9b26b4574d +#: d34b698c62114041a64e0abce25ca935 msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" msgstr "" #: ../../src/topics/operations.md:10 -#: 49cf614893d8438299b3bca384eb40cf +#: cba2c31262bd450cbafc7ca77f4fb8fa msgid "`operations.cwl`" msgstr "" #: ../../src/topics/operations.md:16 -#: 88160cef4cfa4add9020aa89511a5749 +#: b01be5f632104096b5af6193aab34d90 msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" msgstr "" #: ../../src/topics/operations.md:24 -#: 2f73a786b5d94dc0b23ed0cdd185afc8 +#: 60a6a02c1367403db6df3ec10f75eb69 msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" msgstr "" #: ../../src/topics/operations.md:55 -#: 730ba1434a1445ae847ec6153b6a3b72 +#: 314ea7bc35154f41b2af5fa6683ca389 msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" msgstr "" #: ../../src/topics/operations.md:58 -#: 98d9b8d867594543890af99e77e24edb +#: d81e679b13474f74bc5e1ce1e31c2bc6 msgid "`cwltool` does not know how to run operations" msgstr "" #: ../../src/topics/operations.md:66 -#: a25d0b1e13324b40a6b8fcd227948c4f +#: d7fb27131ee44bfc82f698ee44b2bae0 msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." msgstr "" #: ../../src/topics/outputs.md:1 -#: da077da5eb8a4ffebfde041fc16300de +#: b8ef11eafd1d46e088f1277f4ac372bc msgid "Outputs" msgstr "" #: ../../src/topics/outputs.md:3 -#: 1b3016f0462f42deb42ddaa33f28bf3d +#: d2382ed1f644459594655d5b5b4d838a msgid "Returning Output Files" msgstr "" #: ../../src/topics/outputs.md:5 -#: d661df070e3040869da412d07a71f716 +#: 6651632d977b44479b721174fffeda2d msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/outputs.md:10 -#: a11585474d3849cca5467512ed964743 +#: bee5f532554241088764ac9e56abbe85 msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." msgstr "" #: ../../src/topics/outputs.md:16 -#: 2682f9ca8e604a0c9986f7746fdec960 +#: 0c7c506f38be421399073871f64e99b0 msgid "The following example demonstrates how to return a file that has been extracted from a tar file." msgstr "" #: ../../src/topics/outputs.md:19 -#: 7e3fa7baf0f549ec89457e7004ac9545 +#: 8b60286e56cc42a8ab5f751a97adf771 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" #: ../../src/topics/outputs.md:21 -#: 22447a560f6f4317bf67bd7c4336126c +#: fa0ad674f15348339a1eee771a6ba9e2 msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" msgstr "" #: ../../src/topics/outputs.md:26 -#: f1ee2e00b0cc4112b51c9df3a919b73f +#: 177b5f1b95a34fb9b2eb42f733d79ac8 msgid "`tar.cwl`" msgstr "" #: ../../src/topics/outputs.md:32 -#: ad8e1acb251246d2a47c39b20d4e483a +#: a08a6d8aca8e490482e127a8fd5e650e msgid "`tar-job.yml`" msgstr "" #: ../../src/topics/outputs.md:38 -#: dc200c6960ae4476a772645d021f14b8 +#: c2c60f68b1e045f88844076e191fda9b msgid "Next, create a tar file for the example." msgstr "" #: ../../src/topics/outputs.md:45 -#: 52703d6b7f914097934bfad13663abeb +#: 6d939f62526e4e6d95acb57d72f60a84 msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/outputs.md:51 -#: 5e1c79df657d4a6e84e055dd6b300a5d +#: c48edd9034364b81ad42540a98b51d91 msgid "The field `outputBinding` describes how to set the value of each output parameter." msgstr "" #: ../../src/topics/outputs.md:62 -#: 329d2809dfae4f90bc638f5f03a47ee3 +#: 9ebe0186a7124dfaa30e558e8f59653a msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." msgstr "" #: ../../src/topics/outputs.md:65 -#: 96df2d45e42441d49ce193ccbfab78a3 +#: 9381b7d7c9904df0a5e16dac29c2e08f msgid "Capturing Standard Output" msgstr "" #: ../../src/topics/outputs.md:67 -#: c6bcf7c6a8774dd6be41cc775848c3b8 +#: 2aa9c6916e3546b7b92fa64bb83275d1 msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." msgstr "" #: ../../src/topics/outputs.md:71 -#: 9d86c03ab44841c785b924cc44727e31 +#: 63afb7a597fc4e459b6a7dbd40bbf6ff msgid "`stdout.cwl`" msgstr "" #: ../../src/topics/outputs.md:89 -#: 2fb58c2feaa84970bb5274c49f4b5b64 +#: 7418915470f041c9af5bd39ea652de36 msgid "Array Outputs" msgstr "" #: ../../src/topics/outputs.md:91 -#: 9647019d8c37466886e7aab6f176634d +#: f82db001b58c4969b2d8bc1dcbd7cf8a msgid "You can also capture multiple output files into an array of files using `glob`." msgstr "" #: ../../src/topics/outputs.md:93 -#: b9eaf21f5e014eefaae301c47dafd144 +#: 26d9f0b28d384617a8e490c1f8e26e52 msgid "`array-outputs.cwl`" msgstr "" #: ../../src/topics/outputs.md:99 -#: cffff6c43b4945daa3b2a49763bc50ae +#: cf46c971b31b4e10bf0fefb4cd028c2f msgid "`array-outputs-job.yml`" msgstr "" #: ../../src/topics/outputs.md:112 -#: cc067051f22f433bbece08f60933e002 +#: a4347983fb9945a4a2773af88e426dc9 msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" #: ../../src/topics/parameter-references.md:1 -#: a190a6440ec34898990cdac05d809f22 +#: c5489e0633114372b273098ee2c9ffd9 msgid "Parameter References" msgstr "" #: ../../src/topics/parameter-references.md:3 -#: dbfe2c1123144316aa026374b0f353d3 +#: 75de9fd63393429daf1ca10a85339aa7 msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." msgstr "" #: ../../src/topics/parameter-references.md:13 -#: 280f1a07d0ae41d7a4674504f832fcf0 +#: 8b5d0ada32d645be9359f43a431f5f91 msgid "`tar-param.cwl`" msgstr "" #: ../../src/topics/parameter-references.md:19 -#: 5c64d938862747cb9fb52515a656ce27 +#: 2ed93dc8778e44209194f41b9ad193d5 msgid "`tar-param-job.yml`" msgstr "" #: ../../src/topics/parameter-references.md:25 -#: 074cf5d912854d8c864607cc24b15302 +#: a80dd6d9920540e9880514e04035af86 msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/parameter-references.md:36 -#: 0290af3e3cbb4b32b0450c8771f3bf95 +#: 9de300f7b9da49f59d1c9fd96dec4a8b msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." msgstr "" #: ../../src/topics/parameter-references.md:47 -#: b54240bb94f746bba7511633aa969db0 +#: a61f52d3c1024c3692899e05fcea4bee msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." msgstr "" #: ../../src/topics/parameter-references.md:51 -#: 8b70a072aa87414c88e89a3e19af0a51 +#: dafc9ba578c14fd79d075160e6b7bd6b msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." msgstr "" #: ../../src/topics/parameter-references.md:54 -#: eea20f89c45f424a888178df53713b28 +#: 28ca6cae42904559bcec98fb9d2b07cb msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." msgstr "" #: ../../src/topics/parameter-references.md:59 -#: cb4ea13f5db84c0da43df3f7f2478d78 +#: 616c9ff9fcae489285f0bbbc67f07d29 msgid "Where are parameter references allowed?" msgstr "" #: ../../src/topics/parameter-references.md:61 -#: 6d3fb423e6c4434697cd113fb27e28ad +#: ac17acd83ddb43dc9fb7a5e595ab1153 msgid "You can only use parameter references in certain fields. These are:" msgstr "" #: ../../src/topics/parameter-references.md:63 -#: 7647e0229a924f988cf02b7812a55c06 +#: 156573324cde41ee8b3c47deabf43db8 msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/parameter-references.md:69 -#: 9d663249666045618a0d3acddb85a9a9 +#: c9725be01e8a401fb3ad9ff01339f81e msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:72 -#: 5fed4984f6784347b4cbe0630b1dd2c2 +#: 6797335256e2412cbbe7636507931455 msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/parameter-references.md:74 -#: dbf6153cd02542a6a01c172803122b7f +#: 05a5f0fcb7454cb697e3d810d55fac26 msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:77 -#: b6250cf6fa8a4a0c94b33302e0decca5 +#: 406e68280b5c4ee494632f94b635b7ad msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/parameter-references.md:81 -#: fa6ca3bbc6784380a03a950a6f49a180 +#: 2d6e2a4ff391494591bbdf8dbcc4a6ae msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:85 -#: b92b516e537a4773ad67b4af586e7a25 +#: e71a974b29624210a107fc2d097d4196 msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/parameter-references.md:89 -#: 467a701228504d06b971b79a59c69064 +#: b59df98754e24654bfef0b1fe1d91660 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:92 -#: 2634f989eb304009a8568d70ed42786c +#: d2bccbff1ce646348fe38c776ad183e1 msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 +#: 943ba46512ce48fe8c5b62327734c503 msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: bbcd43d5af7d44108aeb65075a6bd2be msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 +#: 834295755af841a78e466eea43864861 msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: a6b626489bfa468e8f059ab3aa669201 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: e1dbea105aa845c38cb1f90b43847271 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb +#: e9640f47d40e45bca184eb30700df648 msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 +#: 0456efb3718b4356ad2b277ee16de967 msgid "In this example, the software requirement being described is InterProScan version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 +#: f7e97f926505407f8f8e9a427e055e43 msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 +#: ec597ff8f6ee47bc815b069335869f1f msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." msgstr "" #: ../../src/topics/staging-input-files.md:1 -#: b85eb83e05e845d7a179f1b1d74db444 +#: 7467a7f6f26a459ba4ce83e4e6dfcc2b msgid "Staging Input Files" msgstr "" #: ../../src/topics/staging-input-files.md:3 -#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +#: 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." msgstr "" #: ../../src/topics/staging-input-files.md:9 -#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: a03372581fa44f9b8e3e088a4099cdd9 msgid "`linkfile.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:1 -#: 0f7508ce59754a7eb230dea6042244c6 +#: 36e082be73464be0ad5d0b681cc510da msgid "Troubleshooting" msgstr "" #: ../../src/topics/troubleshooting.md:3 -#: fbe0c65b444441f785d0054176d036a6 +#: 4464455b51ad4873ac13c4a63ee5fb54 msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." msgstr "" #: ../../src/topics/troubleshooting.md:6 -#: 1b6b7a75cc754775bf9dd80c0941e8da +#: ed7ff0753d1743a995f4cfedd6e5dcc2 msgid "Run `cwltool` with `cachedir`" msgstr "" #: ../../src/topics/troubleshooting.md:8 -#: 9a710602e00c4934ae3a3b471aa68458 +#: 4c2dd10dd66446058477a52fb8d2c602 msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." msgstr "" #: ../../src/topics/troubleshooting.md:14 -#: 21b5be7270a14f0987240c81d1ec879b +#: 978b6a5fd5fa425fa9a18d9f0e8788da msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" #: ../../src/topics/troubleshooting.md:20 -#: 0490b1fab86749e49b473949c52bbe8b +#: 000c0d6ae8bf414d9293b9f13fd2e448 msgid "`troubleshooting-wf1.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:27 -#: cfe9d8241fe84bd5b74042a5625d933f +#: 7e91b8811be14f8e80df39ac4c5bd316 msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" msgstr "" #: ../../src/topics/troubleshooting.md:35 -#: 764d933cc4da446abd8dd8f913f05dac +#: d42799cc5bd4484bb6beb309a61e103e msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" msgstr "" #: ../../src/topics/troubleshooting.md:44 -#: c93efc6d4e004859981ee7f5fa28ed03 +#: 48bb0f6666ac48648c7d969608b3bd48 msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." msgstr "" #: ../../src/topics/troubleshooting.md:48 -#: 546601da44cb49bd9611b1c85807fd90 +#: f8876044db184cbaaca56579d0c773df msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." msgstr "" #: ../../src/topics/troubleshooting.md:59 -#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +#: a5a3d408dbe34cfda4dd0b2abe67e7d7 msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." msgstr "" #: ../../src/topics/using-containers.md:1 -#: eff5f28ca83c458a9b07faf7a81f7e91 +#: 4c240a18c4e6441189489011242c1efd msgid "Using Containers" msgstr "" #: ../../src/topics/using-containers.md:3 -#: 2e634f3737d04d279ae78ceee4b0a664 +#: e37e76ef376a4ee695e600998906ec1c msgid "Running Tools Inside Docker" msgstr "" #: ../../src/topics/using-containers.md:5 -#: e07f33d01b804663a25ffb08aad74821 +#: 51a307b0ba7c4c1d89309ba8d2250471 msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." msgstr "" #: ../../src/topics/using-containers.md:15 -#: 7a644506619a4f08958ec7d4540cd557 +#: 13cc38d72d34468fa4eb6d91f23ff105 msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." msgstr "" #: ../../src/topics/using-containers.md:18 -#: b5195b7d8eaa419fb2b90cb33a57783a +#: 42a48398d3ef4b03bd7395120f2cfb42 msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." msgstr "" #: ../../src/topics/using-containers.md:21 -#: 7921a837ee744c5aa9a5bda04b0c8db1 +#: d59387b433bc4ecfaf7e72026624db02 msgid "`docker.cwl`" msgstr "" #: ../../src/topics/using-containers.md:27 -#: 387e9bc9381a4450af54aff77e4df6a2 +#: d963418ccc0b4803bbc758d718ccb5aa msgid "`docker-job.yml`" msgstr "" #: ../../src/topics/using-containers.md:33 -#: 2713594c937d4c528fc8d04d9e9819ed +#: a224d1510c9e46aab23d8bdc03c349dd msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." msgstr "" #: ../../src/topics/using-containers.md:44 -#: cf94c1424fc2413c85647fd1ee73d951 +#: 0a82f8a45b0546aaac4c976dcc98014a msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." msgstr "" #: ../../src/topics/using-containers.md:52 -#: dc0452107c604e29bdf32bb289fe5db8 +#: bc418a2a535e49359c4cd44b373bbe02 msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/using-containers.md:55 -#: 1a5596243cec4c948d9b6bf0bb12fad0 +#: a799fba2322944cea00e413c08066536 msgid "`hello.js`" msgstr "" #: ../../src/topics/using-containers.md:69 -#: 483181f498fc4d968b5fe6ef427709f7 +#: 35379c6b972940bd8451f10b74dd793e msgid "Notice the CWL runner has constructed a Docker command line to run the script." msgstr "" #: ../../src/topics/using-containers.md:72 -#: 7487485d6aa4458089a4b4bdf107ea64 +#: 2d5265525ad544a0b64ad2cf07aacc26 msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." msgstr "" #: ../../src/topics/workflows.md:1 -#: 7394e7690f934043af617436b40845f0 +#: e2521b89596d42f8a87a3207fd6c32f2 msgid "Workflows" msgstr "" #: ../../src/topics/workflows.md:3 -#: b9ae9e9a896048caad7e6c38a5bc1bd1 +#: 3676f23b63e142cb8e5715ae07216a47 msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" #: ../../src/topics/workflows.md:13 -#: f228fb7953ea48ed99d89880205f4620 +#: 00725aed13a440ca8b3c4f9155fbee99 msgid "CWL workflow." msgstr "" #: ../../src/topics/workflows.md:41 -#: 5870ac44e4c24b8daf5f06c49f95ce04 +#: 2e38a4f9072b4ad9bbb74f943d22084d msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." msgstr "" #: ../../src/topics/workflows.md:51 -#: a913c76d06164fa18718a8a6a7dcf0d6 +#: 2b9f4035ea864b6db50c861a1819289d msgid "`echo-uppercase.cwl`" msgstr "" #: ../../src/topics/workflows.md:81 -#: 93188ed43ee949cc98b3ea679ce14feb +#: 28e9064780e7418a8e02a22f92e34404 msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" msgstr "" #: ../../src/topics/workflows.md:91 -#: 36618126a4df4326b236ebe2ea42cffa +#: 66ce14a10d2d4dc497d3ed71e11ed8b8 msgid "`echo-uppercase-single-file.cwl`" msgstr "" #: ../../src/topics/workflows.md:150 -#: 1cc17ad26e9c474b895ba5cd20c8b66a +#: 8dc00528c3d2426c8a3492a8191f1d81 msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." msgstr "" #: ../../src/topics/workflows.md:160 -#: 24aca0bea4d94e3593b844cf0586cffe +#: f9ef5e258f7c4971a8543d1dfed711a8 msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." msgstr "" #: ../../src/topics/workflows.md:165 -#: 46cc4859856e4367a9e5e68eecd48b73 +#: 324bc51071d743ea80124c23880ddc0a msgid "Writing Workflows" msgstr "" #: ../../src/topics/workflows.md:167 -#: 9c56528acd5f49deb139e034dfbfac7c +#: d8c13e01976b43a1af34c11a7bc36897 msgid "This workflow extracts a java source file from a tar file and then compiles it." msgstr "" #: ../../src/topics/workflows.md:170 -#: 55ab007d472f43388e4c77aae8f165e7 +#: 43910a8ab4484e529a17df418b1aedbb msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 #: ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa -#: 307b6618a92948fca4203ccb497c77e6 +#: eab3ac7490f24645bbf0babb20aa9df0 +#: 56917e39cfa34470a7a88b52b1f955d9 msgid "Visualization of 1st-workflow.cwl" msgstr "" #: ../../src/topics/workflows.md:180 -#: a2dd833fdca4443181648e41051a5232 +#: 7ad12d67e815400c94080804b9285629 msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" #: ../../src/topics/workflows.md:183 -#: 7e40cc9f9e1341c195e843c009575b94 +#: 457d5a31c79143acae2683d95d27f7a3 msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" msgstr "" #: ../../src/topics/workflows.md:185 -#: 26c51dcb76364ed780376aecb7cbacda +#: a2a73901bf634547900d08b9a1ac8889 msgid "`1st-workflow-job.yml`" msgstr "" #: ../../src/topics/workflows.md:191 -#: 6fcf8ad3d1bd49afa4a105622437bd59 +#: f347d80e62384b14acf6423675e5359a msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." msgstr "" #: ../../src/topics/workflows.md:205 -#: 71cb81fa4511495b80422244849979e4 +#: 2a845a4f3f98428fb82f3ca7ce038a6e msgid "What's going on here? Let's break it down:" msgstr "" #: ../../src/topics/workflows.md:212 -#: def35d6021394def80a53ae49a2cdbde +#: e2007c74d5f449a882809d6b91c010bf msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." msgstr "" #: ../../src/topics/workflows.md:221 -#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#: 7f5e53ee7cf94be2bff45ef64db28a24 msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." msgstr "" #: ../../src/topics/workflows.md:233 -#: c84d4450bc6a475dbf34e0b22cea9130 +#: a0d076b7b8b048478580c99ef0c8429f msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." msgstr "" #: ../../src/topics/workflows.md:248 -#: cca9665f6daa44b49233baf34ab9fcc7 +#: 7fd926c18ad548e98845e9b5134dd6f2 msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." msgstr "" #: ../../src/topics/workflows.md:256 -#: 547edbf5fa424b8286cc21674ff159b0 +#: 789fbd47f8564cceb430ef3c0bc90e9b msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." msgstr "" #: ../../src/topics/workflows.md:261 -#: 7ca248888b9d484cb544cd76ba538662 +#: 45c4d0492d6143ca9cebe81e9b2cf3ae msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" #: ../../src/topics/workflows.md:267 -#: ae6b240718104380b08db5552d7355ea +#: 73bd3da2af8545928d5ea71d0f7454f6 msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." msgstr "" #: ../../src/topics/workflows.md:278 -#: e5a8b7f84be64020b191099f3fad30ed +#: 15ce3d2700424f0fbb280d602ccebcf6 msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." msgstr "" #: ../../src/topics/workflows.md:285 -#: f0b04849253c4693904512ddd7f9ce84 +#: af4268f19202436eb0a7e8c6bed5e386 msgid "Nested Workflows" msgstr "" #: ../../src/topics/workflows.md:287 -#: 12a06d8358534102b202965d4258c18e +#: 94a4eadca6b949d79de2990a0150eee8 msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" msgstr "" #: ../../src/topics/workflows.md:297 -#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +#: 09c1619e8cbd4febbb637f7e99ad5890 msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" msgstr "" #: ../../src/topics/workflows.md:300 -#: 49ed137fe996452a8534c68d100db941 +#: 677ea7a27eb64568ab3689142d6efe70 msgid "`nestedworkflows.cwl`" msgstr "" #: ../../src/topics/workflows.md:309 -#: b7f93705e5b8416696be01850072e8c0 +#: 097e6d47f9394e62b80110700492783a msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" #: ../../src/topics/workflows.md:314 -#: e87045829b344089ab59dc27063ddd7a +#: e93affce8c104bf6977182047c1f1077 msgid "\"Visualization \"Visualization" msgstr "" #: ../../src/topics/workflows.md:322 -#: 42ef2f145b824d69b63abc1da175c216 +#: 06c9e04ba890473b851240a0fa9c3b12 msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." msgstr "" #: ../../src/topics/workflows.md:336 -#: c61cedf543664d388183e04b3939cc39 +#: 0380dc1fe3aa48e4b62283b7b2a611d8 msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." msgstr "" #: ../../src/topics/workflows.md:341 -#: 9e39e3f1501c4fcaab3e8962e090f6be +#: 49b251f7a313492ea60504b00109e526 msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." msgstr "" #: ../../src/topics/workflows.md:347 -#: 03e2f767c4da461982fc3c0f3ba94762 +#: 7ee55702d7dd4679a24ff052f6f0cbeb msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" #: ../../src/topics/workflows.md:366 -#: 3bea5822b8694e2aa32c446e1c54a045 +#: 85d7e2e270874aa6b9f477cec0f48154 msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" #: ../../src/topics/workflows.md:383 -#: 426023bd6e3a471cbb30dbda3d6f9e57 +#: 570e94513c984c09ad6aa255f534216d msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." msgstr "" #: ../../src/topics/workflows.md:389 -#: 0d498cd4caf54c15891ca1afe58e2727 +#: a107258662fb4bd4a9a3d8754e34d1e9 msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." msgstr "" #: ../../src/topics/workflows.md:394 -#: b2d75045e02741b4850f5ff1243f7858 +#: fc1a6502d831458ab8371a575cea47e2 msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." msgstr "" #: ../../src/topics/workflows.md:398 -#: cfa765264a27411ab914de569aa3dac4 +#: 2d10806bf1ce4e26b92adda61efc0862 msgid "Scattering Steps" msgstr "" #: ../../src/topics/workflows.md:400 -#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +#: 046c5e134de94b629cc22d416f3c9182 msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." msgstr "" #: ../../src/topics/workflows.md:411 -#: 5fa79c62049a447c8328ebf9db54ebf4 +#: 52fa22d3277940049fbb589a3ea73433 msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" msgstr "" #: ../../src/topics/workflows.md:415 -#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: 6043beb96c2c49648011ec556aa9e986 msgid "`scatter-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:421 -#: 3a67d77a2e7b4c0bb61cc3585ceae942 +#: 5ac4310515124e2986724425bed5651f msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" msgstr "" #: ../../src/topics/workflows.md:429 -#: f1cb55fc59824cc18a95fd6dcb32cf4c +#: 7958e91d5c2f4046aa9d2070a900f9ae msgid "First of all, notice that the main workflow level input here requires an array of strings." msgstr "" #: ../../src/topics/workflows.md:441 -#: d947c54933d64aad90df392a1cedd63f +#: 2db234d776fe4fd38bab07245dcb783a msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." msgstr "" #: ../../src/topics/workflows.md:445 -#: 651d35997332404186aa6d5711da4a3d +#: 7cfb17230e284ee7b6e2a00efe8eeb74 msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" msgstr "" #: ../../src/topics/workflows.md:450 -#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: 4311ac98544e4fb0b2f4b24985710a01 msgid "Using the following input file:" msgstr "" #: ../../src/topics/workflows.md:452 -#: 842b926ae34542cb9023021f137b08be +#: 780f9c72e6c34c39918642c7e2477355 msgid "`scatter-job.yml`" msgstr "" #: ../../src/topics/workflows.md:458 -#: b662c1a5a4424c8d8350a806356acc61 +#: cc4a7316db644b438cbaa181ad9ef2d3 msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" msgstr "" #: ../../src/topics/workflows.md:466 -#: 04d6babfd87343d7a5f13867ea02b65f +#: dfc461a03fe8487794837904febb8b63 msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" msgstr "" #: ../../src/topics/workflows.md:469 -#: 2eaacf1a90204a2b9bd621344560f2a1 +#: 1e83485b00b64dfaba897bd8d772e0f0 msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" msgstr "" #: ../../src/topics/workflows.md:472 -#: 242993d42b164ee5abe7ca10d45856de +#: d0321d6805ec4d3abf3877d02a0a417f msgid "`hello_world_to_stdout.cwl`" msgstr "" #: ../../src/topics/workflows.md:480 -#: 4a94e5f7e1bc4d628702140e4e51d6d3 +#: d7d77e807b3048c7bdf89558f76804cb msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" msgstr "" #: ../../src/topics/workflows.md:483 -#: e61d93b848184c8e8e573928427b4d0a +#: 8d9b8be147fc4a71922dde858842e543 msgid "`wc-tool.cwl`" msgstr "" #: ../../src/topics/workflows.md:489 -#: e3a7182f00f440b8b5461da91194a64b +#: 34b7705416a745a6a42e6d402c0757ed msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" msgstr "" #: ../../src/topics/workflows.md:491 -#: 99fa96caacaa45cb97aded9a24fcac6d +#: 257adcee9da64d5c987f3b64efd20ab0 msgid "`scatter-two-steps.cwl`" msgstr "" #: ../../src/topics/workflows.md:497 -#: b5338f39e8c74ff28e139da68089a742 +#: fa6ed5d0c14f42f4aa3c5144648db22c msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." msgstr "" #: ../../src/topics/workflows.md:509 -#: f6d92156d67c4a339bcfd194cff897df +#: 333e8ce458d54de394526769f96d12d2 msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" msgstr "" #: ../../src/topics/workflows.md:513 -#: 1c9e386922324ec8a59306572c19fb8b +#: b819e8a5df6e4fa495924095709669ef msgid "`scatter-nested-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:519 -#: d80ab383eec9402faba997b548fe42eb +#: f1955468a1364d44a930db77c9c4b495 msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." msgstr "" #: ../../src/topics/workflows.md:522 -#: f7d2827d97db4bf4ab84b5d6621c3b48 +#: 8c3b9b645a204d02b2c73a205e8ec296 msgid "Conditional Workflows" msgstr "" #: ../../src/topics/workflows.md:524 -#: 49217c02f58c43ff9ec00f10da8d4e84 +#: 4d88b9c186cd4502adbf752e8a70b6ce msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." msgstr "" #: ../../src/topics/workflows.md:527 -#: 20b9f181420c401d8615c17a10027517 +#: 9927673564024ba5833b5ac271737857 msgid "`conditional-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:566 -#: 8dbd56473f8c40c0bb12a48be06117e3 +#: 84f4ed7ce2004742b8db9087104a469a msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." msgstr "" #: ../../src/topics/workflows.md:573 -#: 78d7f3ede2c746d482042adef050b2c4 +#: 2b5f9757adca4490a149c7f45e14fcb5 msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." msgstr "" #: ../../src/topics/workflows.md:587 -#: cbbf93c70fe04ba7932ba25758ddc611 +#: 0418de720813442f81ecff293c9448b5 msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" #: ../../src/topics/workflows.md:607 -#: cfa1c1fde4454df283f87cc54a9c59ec +#: 524eec63be8248ae982939c975ef50a2 msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" #: ../../src/topics/workflows.md:627 -#: 1a8be2950cbb475bbb2617e005f0fac9 +#: 5e99f9912cc549a7890e2934425eb943 msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." msgstr "" #: ../../src/topics/yaml-guide.md:1 -#: 5f09d4d897cf457d80b9a11b8c01747e +#: b0121ee087d6424fbb0ea5957a7b0b8c msgid "YAML Guide" msgstr "" #: ../../src/topics/yaml-guide.md:6 -#: 5d83c56102e141cc978500f678dd0c1c +#: 49e9f6b3a06840289decf3f557860f87 msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." msgstr "" #: ../../src/topics/yaml-guide.md:13 -#: c38438fbf9a04e729ec2e3c962435289 +#: ed9eebec0b3d4b72ba65507d37757a37 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" #: ../../src/topics/yaml-guide.md:16 -#: fdb9cc750cec43ee962517e637dc5fea +#: bf9b255a24a84f3ba989a223492b8f41 msgid "Contents" msgstr "" #: ../../src/topics/yaml-guide.md:18 -#: 08da9cd8056b4ddd8f5150cc85ba72ee +#: e79fa0b7f8b14810a3a20908ef92bc55 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" #: ../../src/topics/yaml-guide.md:19 -#: b027fc234ed943bbb00d4c6bc03c040a +#: 290e2035f903417cbecb5dc5f09d6ebe msgid "[Comments](#comments)" msgstr "" #: ../../src/topics/yaml-guide.md:20 -#: b8befec0d8684638aaa616a659e0100c +#: d420730151534f1a89076588a3358f09 msgid "[Maps](#maps)" msgstr "" #: ../../src/topics/yaml-guide.md:21 -#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: a6b5378bbe1e4bee9e37a765bddf75f7 msgid "[Arrays](#arrays)" msgstr "" #: ../../src/topics/yaml-guide.md:22 -#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: 6e4d9465dc2b454d96b02d7ad1817795 msgid "[JSON Style](#json-style)" msgstr "" #: ../../src/topics/yaml-guide.md:24 -#: 98056c5cfd5640ad9de0679360797cc7 +#: a649d4af5f434dac9395e013ec4836bb msgid "Key-Value Pairs" msgstr "" #: ../../src/topics/yaml-guide.md:26 -#: cda73485875d4c8e9464679a20558616 +#: 446190a298834b73bda068286e8490cf msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:42 -#: 98cae24919b74c088a5d89706aec581b +#: 2f35c012ff174721bffe66a3f58a804f msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" #: ../../src/topics/yaml-guide.md:51 -#: b4b0940b4b5743c09637b36b964202d0 +#: 43127c98c9d94aedac61cee67929c1a6 msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" #: ../../src/topics/yaml-guide.md:61 -#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: dc4fe561203c4c38a9caea5bd6eff2cd msgid "Comments" msgstr "" #: ../../src/topics/yaml-guide.md:63 -#: 9ca3554d771d45998e88aaede525b227 +#: f924e4896db2424d99ce8c9da14c599a msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:76 -#: 3fca839cede94cfd8e4f605c73ba699d +#: bf7646f5f925485c842a6d34140e40b8 msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" msgstr "" #: ../../src/topics/yaml-guide.md:79 -#: da34c635707345b2a5e85a2fcd30bbaf +#: c483e61dec8949fa96bb893d422888a0 msgid "Maps" msgstr "" #: ../../src/topics/yaml-guide.md:81 -#: 3ded0f125249485c921994b6e6b93ac9 +#: 85fcb523d0e34a499eae04d304887f7b msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" msgstr "" #: ../../src/topics/yaml-guide.md:104 -#: 53ece35d309a4c8d99f1efb2122a7092 +#: 83d47c8736a34f3cbf09e3997845e4f4 msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." msgstr "" #: ../../src/topics/yaml-guide.md:127 -#: d74321b111d84ae7a515f2f17dd39e23 +#: c698fb3d37bc403e9aeb679b8fc0e15e msgid "Arrays" msgstr "" #: ../../src/topics/yaml-guide.md:129 -#: 7fc0bdf2489a44f2a29e71b86f7c0055 +#: ae8af2f0eeda4aec97201211dfa965c7 msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:146 -#: fd64dd818ec64bb6aa9a11586a5747f6 +#: 2ee87aa465cd41fda16a61e242f8c9d0 msgid "and a more complex example combining maps and arrays:" msgstr "" #: ../../src/topics/yaml-guide.md:167 -#: 8c06e542dd4144fa83388d8142552c8d +#: 0a6fd4469ff24b61b3ad001b09eead18 msgid "JSON Style" msgstr "" #: ../../src/topics/yaml-guide.md:169 -#: 87bafb845c714b109874f6137b84462d +#: b96ba19bce9341d39c46054e1f10fe8f msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:177 -#: 5ab9ddf613a540a2b8228e37600cc5dc +#: 903f30af3d0c45cfb61063936a8097a7 msgid "and:" msgstr "" #: ../../src/topics/yaml-guide.md:184 -#: fcd05b1ef31a4046946a2399c7fc5575 +#: ede8db7c0a58432e8a1c416e937a06d2 msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." msgstr "" #: ../../src/topics/yaml-guide.md:194 -#: f4b8fc8236044fada420def13a02813d +#: c8b53615476a4a1fbef2420d93bac94e msgid "Reference" msgstr "" #: ../../src/topics/yaml-guide.md:196 -#: 859368c1f25c4a4aad57abfd046c63f5 +#: ea03cb5525cc491f9feb5c4780b38fee msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." msgstr "" #: ../../src/tutorials.md:1 -#: 2203c93f02ac4514a43508ecb98dfcc5 +#: 92fd3a5e31714eab859dd630af2e78cf msgid "Tutorials" msgstr "" #: ../../src/tutorials.md:5 -#: 5d92464923c245818c070fbef102be89 +#: de660ecdb5b44c97a0e519d00b232497 msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." msgstr "" #: ../../src/tutorials.md:7 -#: 8a5cd557dab5456bb41cdc24af73b50c +#: 5afc1e1288e74ed0985e61e5164479c7 msgid "Beginner Tutorials" msgstr "" #: ../../src/tutorials.md:9 -#: 13d7e2e92e96432787c712cf6a595424 +#: 862dc7ac81e54b1fb3d4c2f961b8810e msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" #: ../../src/tutorials.md:11 -#: 0abdd85c9b964a4e89ba3d80a6c78d6f +#: e2c94c0e1c7048d38cd7aa2c465a859d msgid "Advanced Tutorials" msgstr "" #: ../../src/tutorials.md:13 -#: 3cbf1f69a5514fd3bee90e68b201190f +#: b63253780f51467a95207d820d13ac39 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" #: ../../src/tutorials.md:15 -#: 68c97a7065634d02956f3f5c1d4eeb9f +#: 6d06ca7ed5df4560aaed286f4fe33928 msgid "Bioinformatics Tutorials" msgstr "" #: ../../src/tutorials.md:17 -#: a67c7e0eaf4e4d27b3e5db303333a088 +#: 5448df4a6a8f431d80e269bcd480e19e msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" diff --git a/src/LICENSE.md b/src/LICENSE.md deleted file mode 100644 index 84798e58..00000000 --- a/src/LICENSE.md +++ /dev/null @@ -1,2 +0,0 @@ -```{include} ../LICENSE.md -``` diff --git a/src/LICENSE.rst b/src/LICENSE.rst new file mode 100644 index 00000000..68c5792f --- /dev/null +++ b/src/LICENSE.rst @@ -0,0 +1 @@ +.. include:: ../LICENSE.rst diff --git a/src/conf.py b/src/conf.py index 990751ba..921ced1e 100644 --- a/src/conf.py +++ b/src/conf.py @@ -237,4 +237,4 @@ gettext_uuid = True gettext_compact = "user_guide" -locale_dirs = ['locales/'] +locale_dirs = ['../locales/'] diff --git a/src/index.md b/src/index.md index 8e10fa54..e1a0c0cb 100644 --- a/src/index.md +++ b/src/index.md @@ -35,7 +35,7 @@ introduction/index.md topics/index.md tutorials.md faq.md -LICENSE.md +LICENSE.rst ``` [repo]: https://github.com/common-workflow-language/user_guide/issues From 8efb720d8ee310a313510607bbeb5bc35195f9d2 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 27 Jan 2023 11:12:07 +0100 Subject: [PATCH 042/179] also fix the Spanish translation --- locales/es/LC_MESSAGES/user_guide.po | 1289 +++++++++++++------------- 1 file changed, 650 insertions(+), 639 deletions(-) diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index 3fa6daab..523946d0 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 16:53+0100\n" +"POT-Creation-Date: 2023-01-25 17:03+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" "Language: es\n" @@ -23,21 +23,24 @@ msgstr "" #: ../../LICENSE.rst:2 dcdc2e8da0ec4d9e9453601fdd83bac5 msgid "Licenses" -msgstr "" -"Licencias" +msgstr "Licencias" #: ../../LICENSE.rst:5 3e165520ca56481b8f8d494a8d471de3 msgid "Instructional Material" -msgstr "" -"Material didáctico" +msgstr "Material didáctico" #: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the `Creative Commons " +"Attribution license `_. The following is a human-readable " +"summary of (and not a substitute for) the `full legal text of the CC BY " +"4.0 license `_." msgstr "" "Todo el material instructivo del proyecto Common Workflow Language y los " "cambios en la estructura también están disponibles bajo la `licencia " -"Creative Commons Attribution `_. Lo que sigue es un resumen " -"legible por humanos (y no un sustituto) del `texto legal completo de la " +"Creative Commons Attribution `_. Lo que sigue es un resumen" +" legible por humanos (y no un sustituto) del `texto legal completo de la " "licencia CC BY 4.0 `_." #: ../../LICENSE.rst:12 b7a7a0fb40344fe087c1cc3ec19308aa @@ -58,38 +61,38 @@ msgstr "**Adaptar**—remezclar, transformar y construir a partir del material" msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.rst:20 2173e2af49be41ee97a74c4e879faf25 +#: ../../LICENSE.rst:20 8bc6672f4a33428296226112a1be6fbe msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " "términos de la licencia." -#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 +#: ../../LICENSE.rst:23 be38276e7b374f57b9997391bf898a62 msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" "Atribución — Usted debe dar crédito de manera adecuada(mencionando que su" " trabajo se deriva de un trabajo que tiene «Copyright © The Common " "Workflow Language Project» y, cuando sea práctico, con un enlace a " "https://www.commonwl.org/%20),%20brindar%20un%20%60enlace%20a%20la%20licencia%20%3Ccc-by-" -"human_>`_, e indicar si se han realizado cambios. Puede hacerlo en cualquier" -" forma razonable, pero no de forma tal que sugiera que usted o su uso " -"tienen el apoyo de la licenciante." +"human_>`_, e indicar si se han realizado cambios. Puede hacerlo en " +"cualquier forma razonable, pero no de forma tal que sugiera que usted o " +"su uso tienen el apoyo de la licenciante." -#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 +#: ../../LICENSE.rst:31 f00d5c3846034c2ea116c2f74786d9fc msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" "**No hay restricciones adicionales**---No puede aplicar términos legales " "ni medidas tecnológicas que restrinjan legalmente a otras a hacer " "cualquier uso permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.rst:35 f6aae4a5cd0547118c8a3240ca2b4be6 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limit +#: ../../LICENSE.rst:35 1798d65c10104040923c2fea2199bab2 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." msgstr "" "No tiene que cumplir con la licencia para elementos del materiale en el " "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.rst:38 a40c173be35b4c1b92e83f42bfe2382c +#: ../../LICENSE.rst:38 c65198b804f8436ba783643d51bc72d9 msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" "No se dan garantías. La licencia podría no darle todos los permisos que " @@ -102,20 +105,28 @@ msgid "Software" msgstr "Software" #: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" `OSI`_-approved `Apache 2.0 license `_." msgstr "" "Excepto cuando se indique lo contrario, los programas de ejemplo y otro " "software proporcionado por el proyecto Common Workflow Language están " -"disponibles bajo la `licencia Apache 2.0 `_ aprobada " -"por la `OSI`_." +"disponibles bajo la `licencia Apache 2.0 `_ aprobada por la " +"`OSI`_." #: ../../LICENSE.rst:50 4ee4d68b90fe422880da856cd539b982 -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT" +" WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the" +" License for the specific language governing permissions and limitations " +"under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 5ad4be9b62d54c95a913795b514676fd bdd540403a5746ff99edf2dcad0e3122 -#: dfc7702e073140c985cf47272a20214d +#: 271049c39d294b11b9bd94cb6be2857f 61af90891e2d4542b5f45fb3ec6480af +#: bf309fa01bed4355bf052ae4afbf9a67 msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -124,30 +135,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 +#: 055f0e960450410585b59760ef3ad284 6294af2e32e04207a87399c7f0780011 msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 3060770b3bef41d7bcfcdfb413d7689c +#: ../../src/episodes.md:9 6428125fc43c43bba8518ece2f5d150f msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 48bb9f628b344ba1a3b67ae1cb264e3c +#: ../../src/faq.md:1 ce8fade1e88e4b03ac0d3fc71d16f844 msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 7e3684e9672643738846756e1ebafd18 +#: ../../src/faq.md:11 9e7483b53a984b689964c69afcaa7123 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 187ceabb7fd9480bb8cf0f2da47f65ef +#: ../../src/faq.md:41 8c5a89257ef248cd99cba303713e5082 msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 b548b76bcc85420a9b30792386105139 +#: ../../src/faq.md:43 9e80d8eeefcf4a9d95fd5fe9d9fa124a msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -155,94 +166,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 9ce692b78ead47e4b0f8cdae8837d35b +#: ../../src/faq.md:59 c2e5f62490f940aab19166403a840597 msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 6df1201c159343da9e7515379980d6a0 +#: ../../src/faq.md:61 ffcffabdf25a4c398e8e53bc817ea769 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 f9ab1d0dc1c842b6abb5385268c1d3bd +#: ../../src/faq.md:82 c8a6b85cfca542ccb042a0269294e5e3 msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 9f6a84ab6a9343b6ad7db826f8964362 +#: ../../src/faq.md:84 98f583e5e36941c1856d719a16e58e4a msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 fa50e4fa990b42d1ba4c0f4ae1e5caa1 +#: ../../src/faq.md:86 fb9cac0954474b5284793330b7424949 msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 3a871012fcfd4f3ebeca0cb86ec93435 +#: ../../src/faq.md:89 cc45d609de1f423db86d58eea933e132 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 d954edfff2584288ac8c600733070d2e +#: ../../src/faq.md:95 27ee63895cb14321a1814f4372d3180f msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 af6b1e37d6be4450a761854480ec9aab +#: ../../src/faq.md:97 f1c841980f3d4364a2158a4eb2f0d257 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 31f4a2d43062493ca64c648f80afc8e9 +#: ../../src/faq.md:104 6d53d38ddcf244fb997db37eae7fcf90 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 41c54e71b6cd4f63b2a619a515240d34 +#: ../../src/faq.md:113 b6d60d66f3744ab3aea1b175ecb23d4a msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8edc3541ad134ab5a1d23c724f1f0a4e +#: ../../src/faq.md:115 cf4fa3ae602841d393b4143e9f6f5e82 msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 ac0ea81eba8842a18801ab03cbf80a57 +#: ../../src/faq.md:135 41a3c9aa55c5406f9b52af2243c79ccc msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 52be1a5640234feabe958ff7ade33653 +#: ../../src/faq.md:138 3b8eb247425a4a708f51c08cf258e30a msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 c6db734d5aef4f4f99676bdebf9c83c9 +#: ../../src/faq.md:140 388a6e091a054dc48afc928f46dac7b7 msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 a9f7b47c0dd741739795da39bf114879 +#: ../../src/faq.md:165 28c59d12156e44ea833822fd3ecaf824 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 e3fdd9228b924905a4a1f4b2b7ad7159 +#: ../../src/faq.md:167 8267843ff5c940c590b10047455f2102 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 3f7cda1437cc48f18745a827ebb74582 +#: ../../src/faq.md:188 6e6f55bc915e4cceb8e360544d6b4ae5 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 5aeaba2cae64442e816bbd458aee833a +#: ../../src/faq.md:190 1bc80953bd60405082a10a7798c1413d msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -250,22 +261,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 5af827a402834978addd82c70be6b5ab +#: ../../src/faq.md:194 a6cd4bf4dc314e66a951f7f1227c7bb7 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 6d69e42bd8e443c4b19d80807c7efd6b +#: ../../src/faq.md:196 7ab2440a92aa44b09e8a324cd67ca728 msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 404640397b6e40c2a2cd5cf85ab3b1c0 +#: ../../src/faq.md:199 152a529dfa2c42c1b6f0083589fa5aeb msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 1682c2486e224770b62269709a8663cf +#: ../../src/faq.md:201 b278c137167d4b958c099c0509edb79c msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -274,25 +285,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 9078fc009bc145808813c9cc2b734b58 +#: ../../src/faq.md:229 f0b38723838f479d9db8eb5142d28a1e msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 d4b5a54a400c409cb7984428f6a03ec8 +#: ../../src/faq.md:231 fc1e4a808e85422cbb4d128c5a1f4d0c msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 9e8dbee6e8f84d08b1a54fffa06394ef +#: ../../src/faq.md:247 d74964c9d19241848f4dd92a201e201f msgid "" msgstr "" -#: ../../src/faq.md:248 1d846bfb5f054d09a4afad1da8e4b642 +#: ../../src/faq.md:248 859b8e18e05a4c3285fb20bbb44c1ed4 msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 2d0e95fec8084787b734388d60188574 +#: ../../src/faq.md:250 eb6e932924a54afd9114c629b2d0e93b msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -300,26 +311,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 eccc4a364330470fa474dcaaa3433390 +#: ../../src/faq.md:267 31d70b41ddf042f6aa530b7bd6daae73 msgid "" msgstr "" -#: ../../src/faq.md:268 e945f6a337af4e4686bed482a4fe6c39 +#: ../../src/faq.md:268 9aa3ff8c957b42c8a30f37167a8177fd msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 8a3efaa0ad1548428bcfd6e01d135cdc +#: ../../src/faq.md:270 777ac7f6bde2470b981efc91feb01c81 msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 cdab644adc5643708870fb08c06cbfca +#: ../../src/faq.md:322 8647071efc0548a1807c03fe8a4ee54c msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 089a5a0b076b44aeaab4d69ee3c79f97 +#: ../../src/faq.md:324 4404233183124085990c44793a6b25f6 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -328,77 +339,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 561172559c6f41a68819608fd9e58bb0 +#: ../../src/faq.md:342 c5eecacfa07f47649f07ef9d888f4c5e msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 c5ee4946d2e840abaa3dc796a62652c7 +#: ../../src/faq.md:344 1efef04061fd48f1ab39a99508b5bc0b msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 4f2069a2113c414db18eca95550e9e09 +#: ../../src/faq.md:349 57e8ace8e8d64e7a90510e1ccea69612 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 31f3390e6771414ba7bf57c044c4b0c4 +#: ../../src/faq.md:351 138606e8d7be40bb960f278977f9107f msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 3b77ce4930ae46d5be9f6965e8c54727 +#: ../../src/faq.md:359 d0f668dc78464469a9f2bfc61a90aa76 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 06f36bbe4d3840229b7374f27b86ae80 +#: ../../src/faq.md:361 f2a49a7663e1456cac6b2eac0c46c662 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 3cb2f70d00274a4dafd972ccd8c519c2 +#: ../../src/faq.md:363 eefe4adebdba4063af0cac3ab5d46442 msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 093a1529262043ef84a99675054938e0 +#: ../../src/faq.md:371 526f2816123a43ecbcf09c46904b4b5f msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 45b6d9acbfaa47e5984184f7da554d0a +#: ../../src/faq.md:373 0ecf267c5f4d4557ad0d7ddef2f4b5e6 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 5705c9bacca5405ca6f14315a5575db8 +#: ../../src/faq.md:375 935a253376854d12928f00c2870ed4c0 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 82bfc285b59a439ca97d3278997f0fce +#: ../../src/faq.md:384 bc6c0bf679ae48e7822add7ab2cda220 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 181d5130101d45ccb22aebae3d154c2f +#: ../../src/faq.md:396 a63643806a2a4eee8ebd3502fd6ce2b5 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e864390b5ddb423aaa10e9d33d257dc1 +#: ../../src/faq.md:410 fc54964adcd648948d7baff02f47598e msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 fe637c32fb15427a9045679b5da42ec5 +#: ../../src/faq.md:423 aabc495306a149fdb15835ae1df93c42 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 1f8004b9df8547029d82e57f9abdc979 +#: ../../src/faq.md:436 2930faead8be45a6b9adbf51dcdfef6e msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 70990dc5a0034099921ceb89c89e2dcc +#: ../../src/faq.md:442 f885e4716a8d4de0b25d2d3356789672 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 f679e26f18d9455f945fd13361a9c906 +#: ../../src/faq.md:445 6487ff3c19c944eb8257b2cf60d0aac7 msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -407,11 +418,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 fcd0273dbdd84e728cfd8fbe239f2a01 +#: ../../src/faq.md:450 4cbacce539ce4f6cb5bb8ccf1574640c msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 173ddbd1e7c64927a8dcb12a2a2140f8 +#: ../../src/faq.md:452 27321576de714cd5b82c67f59b2e3e6f msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -422,22 +433,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 662fe273e2fb4042b688512955e450a1 +#: ../../src/index.md:1 6afded7ba21247099c9bfcedf40c9171 msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 a15b52205f0145feaac298510e4d678a +#: ../../src/index.md:3 17c386e7cd25496784207140f9876b90 msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 512aa0c7166b429e8116f71eef007f79 +#: ../../src/index.md:7 3bfd9bcf826a4400935dfad338612b12 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 b1b19e17a18540939cb3bb7f8a700cab +#: ../../src/index.md:9 4b38f1439da44ebb967b5b1e3df8f78a msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -446,11 +457,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 d58b36ac43ac44139897be752fbb1f87 +#: ../../src/index.md:16 a4a60a8d010448b0b8ad1e05cbc78f2b msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 6726cf3585a646a8b4cbeb543cf84a38 +#: ../../src/index.md:18 e23e00e89c81410ba8381fd81bc73b3c msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -458,7 +469,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 2e504aa7c46a426fa959e7254e9a84a5 +#: ../../src/index.md:23 7274d92e678a440eb0d3ae3109f4157a msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -466,15 +477,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 e7be0df0838b432d9c7f296d777f120b +#: ../../src/index.md:28 6ad5f2d254a24ac1b3faf382d08b58aa msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 173e0816db20432c8d9dba1de5393dee +#: ../../src/introduction/basic-concepts.md:1 7208cbccb84d45d58c7d5becec74b7d3 msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 30eacc583f6841719e2142d283811d97 +#: ../../src/introduction/basic-concepts.md:3 8b9809abb49840b195a89943ba15f78a msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -485,18 +496,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 791b8f38a14147bbaa174c7eb595f17e +#: ../../src/introduction/basic-concepts.md:10 9a934bf0848b438aaef7c4f00e0f2901 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 1a3989dcbb9844b39d84bf6df6b352ed +#: ../../src/introduction/basic-concepts.md:21 5a299600dc304fd886b7153de1a706f7 msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 db1bbc6e980f404f9f3fcd08e92ee9a3 +#: ../../src/introduction/basic-concepts.md:25 55f7696f07d64277ad1b39d283175b37 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -506,18 +517,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 acc7887c65974114996f700a38a7eccc +#: ../../src/introduction/basic-concepts.md:33 b854ca0af98347d2b66e74754eb92a50 msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 d2476d9bcff44f21b8d84a3a0d87a246 +#: ../../src/introduction/basic-concepts.md:37 d9785269c51e4902bf3a70e917d33238 msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 f86415e4d78e48c4a8a76ced81221b98 +#: ../../src/introduction/basic-concepts.md:39 b57a31b8d26545d1823fcd1fa2c83316 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -526,24 +537,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c5524d73708c4c779980528864506fd4 +#: ../../src/introduction/basic-concepts.md:44 4e264b1a40bd4935abb5bdeb75fa5c64 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 ac46a9f8850a434bac5bc2b41ee6294e +#: ../../src/introduction/basic-concepts.md:51 791b02bb1ee6459d8d8332fc2dee353c msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: 9bba7c4f783942e4a299603430601363 +#: 17300bbe695044e7b8917d23bd0aa597 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: e2140e0f0e7747ef8383887c20a7945a +#: 526614f195614818a614fc9a576e7cb5 msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -552,39 +563,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 15bf490724cd46dcbcfab44633c5a9a2 +#: 7b47991653054f2d9f49a91720754abf msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 51d52d051e654a8395239f88df7c9d8c +#: aa8838c0ee0a4b4285cb1b5dc6eb5d31 msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: eb496cc818524fa7bae5a22ddd00a19c +#: 457c73a37cb143d98005ebf6e67f5bf1 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: c4a22d12e7f149ff901d27de32b9361d +#: c28057f3b7814f8395dbc3ad54d5f6f9 msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 7618de899a7043989d77baacf62eb7b2 +#: 83afed0785cd4b0bb86863c2841ce982 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: 6f1544a220664b79b04bf008058b5a91 +#: f332864bcc1e49d582a82f3d721ff3cf msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: fbd14ac9a2f541478a320ed4cbc69e13 +#: 3005c6d669de412ab7f8e30d00752a20 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -593,7 +604,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: da4dba50d25d4533b3dbb92f54d32a30 +#: 2e4041cb402e4054a53ea5890b938ac1 msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -602,7 +613,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: ce11c9f8d65c4268984d0384d95144cc +#: 972f9a1e64394a63be3258d3af0b1d79 msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -612,7 +623,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 3a201aa497e84f70855bb2251e7e3281 +#: a572f0789084402fb2d216ac845bbfdb msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -621,24 +632,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: b78f7fa2be1c4bb090f6da895457ad1e +#: c7c5c9a1e98e47c0a5a6dfa69e96f921 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: f7e95d264ffa4e2db0864faccd9e5a0e +#: 357d42768e794286bf5463ca5850a7ed msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 3f1e5b01e49a4dc1b1c99936a4589afc +#: 61966aab989744c1b9b93f7751f35ebc msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 03c3048f38ae4938a484cf02001877b3 +#: e14a2082d2c44f3690a07d3cee5b13d1 msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -648,7 +659,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: f9715b5ec65c405c849bb030c1927060 +#: c128a76992e04d20bcc3edae8b6c0bc0 msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -657,12 +668,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 442662f50e9e4620970ce32b1b127969 +#: 42953a3d591c48c6b4e80e9ea4b97bb3 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 2b34c786af3840e88f29d214e19dc837 +#: e3762a763ba24571a9627efafe172441 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -676,7 +687,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: dd6aadff8cf54ce78ea6b317afbaddb0 +#: be8e01a012ed45d6b7e4e6aab1afcc32 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -685,7 +696,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: fe7f1f0b28434f8aaf0f6ac6589a83f0 +#: cf31aca4294d486cb0e25c6436996d17 msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -694,71 +705,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: d10cf45b3c7f49dc98bc0e5d1246f224 +#: cc7adbdc66df4aeaad1429f7268c90c0 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 332b6e8b831e4bc5aed3745938230a57 -#: ce7fc63b808d4499b9bf9828c2dafe35 ebf339ed376a4d3b89b15b4d5afe593b +#: ../../src/introduction/quick-start.md:94 71beb059c9e54a9ab5430f0dc44e07ea +#: 84679c5b03a3469294de849d9abe0a82 fd690fdd46344e0e8d9fc546f6d4013b msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 8badec9987ba40609cf1f626172b2b2d +#: 89ddaddb64f64b0c86c7e89da0edfaae msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: c75a8b4bf0e24781bf6713cf6f013cd1 +#: e920a824207746ffae63242d33137ac7 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 79b146ffe6d74e1b8f6019251dc4b7c2 +#: 51d619152aa44651889ff2006c8f5800 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 07cca9a33d8f4b77ac6ad35ca8b95655 +#: 88f3f5dd8aa6401793b89e8de3b8c7a7 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: 31db11c8ddf2423192a8b2063b3e91c2 +#: f1f9ee90d07c4381a8bb0851bdac231e msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: d81dd96143ea444aa78ff45cfa0584b3 +#: e3b710dabec2482d8ec1072d64d4e1f8 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 c54984605872472190ae7771809a20db +#: ../../src/introduction/index.md:1 418699fcb6c241dcbeeed81d82e9f84f msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 01a237b8ec2f46c9acd31d142591ce75 +#: ../../src/introduction/index.md:3 28b6521a55aa4ab190ca998a59c52609 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 3fb9888b666945eab1e3ff109646c574 +#: ../../src/introduction/prerequisites.md:1 0e4969399eda48b98d883a3fc1540633 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 5fb0486762354f93853fff209f835c08 +#: ../../src/introduction/prerequisites.md:6 6d59f082157b494ebcfff2f649abc524 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -768,11 +779,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 5f1e7a608e0b455196d191c845a5c98e +#: ../../src/introduction/prerequisites.md:12 2b83beccbc1b43969b705156b9c29482 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 7ba4b5c51be24f5392949d06ee42e018 +#: ../../src/introduction/prerequisites.md:14 594fe5e0aaf0499ebfa9218aaad4d08d msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -780,29 +791,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 e2d3e6dd13b14d819a504c35da6fe8e7 +#: ../../src/introduction/prerequisites.md:19 f69c7c75a36048f5af0ed1b56df9320d msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 91251d1f0efb4d4cb083b4517ff3107a +#: ../../src/introduction/prerequisites.md:21 f28638ffb8394ccead4ac52f30adc627 msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 6ad263e267514c5fb05794d3d76d418d +#: ../../src/introduction/prerequisites.md:24 8993d7d5c8d24fc5a9c7005800c0a1f1 msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 8a3bfd72dccf4a8c874a96aebcbe5cb7 +#: ../../src/introduction/prerequisites.md:25 2073109799e748d68304f5558c82b105 msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 5195706d9c6c4573aff135fd539759a2 +#: ../../src/introduction/prerequisites.md:26 9fb2c31bd36d495786397c7a7d6b3417 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 9c4506915e4c40599527bc1d2b18645b +#: ../../src/introduction/prerequisites.md:29 43e1957537034c5886574118fc2533da msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -812,11 +823,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 37d9eb784ec1425786158f98e3f63890 +#: ../../src/introduction/prerequisites.md:35 e3a3d9b94b1e44c48f298dfcdcd27104 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 572f493a985141a1b92dafbdba92790d +#: ../../src/introduction/prerequisites.md:41 8a385803ed3945ff81d38a3543a69d94 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -824,7 +835,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 9606d3c4849f4b17b2e55a298210f055 +#: ../../src/introduction/prerequisites.md:46 bf56727d93994d3995b0af0c68c2c583 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -832,26 +843,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 754fc59967d94ffa935284676d55ffed +#: ../../src/introduction/prerequisites.md:51 9a959bd914d543b78f9625f03df95765 msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 2905c6362d4146e8b35bc74744841972 +#: ../../src/introduction/prerequisites.md:62 198ce7d893a04fcb806ec1671838d588 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 091278ece252483a9838fb771de3e04e +#: ../../src/introduction/prerequisites.md:65 cc2be8feeab54a22a0b64a2a72991003 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 0928a5c668c3414a945bc9eda147892c +#: ../../src/introduction/prerequisites.md:67 749c672e8c234c1c9a5eb2cc9b77c4e3 msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 56f3c481762848298214a88e559fc0f9 +#: ../../src/introduction/prerequisites.md:73 29c64936318a4a2ba882e1eae8f03f57 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -862,23 +873,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 710c266ab4a5477b84d6ea987420fa20 +#: ../../src/introduction/prerequisites.md:79 44106744147f45bab675eb66148531c7 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 cc353db5da2546bb88a77ce1a202ff9d +#: ../../src/introduction/prerequisites.md:84 6d84c6890f564b4baf7b34f6a52cbfc4 msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 b62df08ec96f4cdb887600079856dd76 +#: ../../src/introduction/prerequisites.md:86 7eb67993e8ca48dc929e1a992f78cb39 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 97e02557293440d1a58ba659dad21113 +#: ../../src/introduction/prerequisites.md:91 52886c54c3c54b83896c52ebd7d53fad msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 0935c3ff01634c75b5c91546dc36c7b9 +#: ../../src/introduction/prerequisites.md:93 097945c33f7542e2bae2e9f7ba1cf84d msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -889,32 +900,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 cfb37fd605164a8d9cc75bf892ce97c0 +#: ../../src/introduction/prerequisites.md:101 3853bfc6a85747019c615a50c7ca6b40 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 5f06a7a6aae343d989a5b30979c600f6 +#: ../../src/introduction/prerequisites.md:104 662230f538504f44941c6f4801f6251c msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 5f956260f3874b6dbeaf3ad7ecc09c9a +#: ../../src/introduction/prerequisites.md:111 1c9eb9e2bb9e40a9985ada16c34eea2d msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 d35e4effec554a638d6c3047ef3fd05f +#: ../../src/introduction/prerequisites.md:115 7f53ba159979461393c0f278fe97fb30 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 15a1f944a0d642729d3736ed1c907074 +#: ../../src/introduction/prerequisites.md:120 7e8077c2dd584eda89ead60ecc5eabf3 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 fa34c808bb494ddfa3f3926bc42e650c +#: ../../src/introduction/prerequisites.md:125 1787a3c749ee48218b87c8401f6255d7 msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -922,30 +933,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 0c15f62eb7534e809f625f3fa213e92d +#: ../../src/introduction/prerequisites.md:129 a52ca4ce9a184e938c3a5cac9cb882ca msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 d67719a6f0ce4ba1bb6152a10507b729 +#: ../../src/introduction/prerequisites.md:135 41d3287a9a774a73aefd49bd709764bf msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 1c96e75281844bfab0578bab2e816854 +#: ../../src/introduction/prerequisites.md:137 3b9d30094611400b85b55db163cb303e msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 bece1fc3c3f842b0b30d8f1b7fbfc200 +#: ../../src/introduction/prerequisites.md:144 b6ea77357b4f45528ed1379f8fe67cfd msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 a7caa36b0f83448b91ef2e76e30abc51 +#: ../../src/introduction/prerequisites.md:148 8797ce327d7443fdb3d4617d3fc2cf7f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 39321e93e9994fcca20b425aa45c2894 +#: ../../src/introduction/prerequisites.md:154 896b6896b1e44d0cab5f35e7d0dd88e3 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -955,47 +966,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 601cf500d76c4e0287af4429a46b36d2 +#: ../../src/introduction/prerequisites.md:161 4b839d23d72f4d3fbe4f1ce7e568b20b msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 b286d5359e184ef58054c72df4014629 +#: ../../src/introduction/prerequisites.md:163 a42b9ab315b5402493e4ce0067d0a18e msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 e14423edd829401faed0950772123240 +#: ../../src/introduction/prerequisites.md:167 2f63483960634a7782f95e9e2feaa5a6 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 889c44360bd54a0e85e7f0e61aa6593c +#: ../../src/introduction/prerequisites.md:171 3471105073204d7998aaf790b73f785d msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 7b9bff73624947ac90a99c7880e2e911 +#: ../../src/introduction/prerequisites.md:172 0b8b47511b5e4296b7438be0ad2604ed msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 c5ff687c86ef4ccaae25d8bcfbd5f873 +#: ../../src/introduction/prerequisites.md:174 3e3eec00f23f4f21873ddb005204a875 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 0a610a9632064deb824afd0719429d3a +#: ../../src/introduction/prerequisites.md:177 2ceb25f2668442839e3e9f4512772a03 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 ec0c47438a5242cb99dffa7a4997e95a +#: ../../src/introduction/prerequisites.md:181 20c753c5371b43ed834fa741b0ce7692 msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1003,7 +1014,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 aae94ac2114641f186eac0f4117223eb +#: ../../src/introduction/prerequisites.md:185 a19c4fc9fa404912a0389337536d9c25 msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1011,57 +1022,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 209e072724ed4d27b37e9bff6d55d811 +#: ../../src/introduction/prerequisites.md:191 a0f38c1e28ca4850b3986617625acbf2 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 3bf47876e3694e6cadb05123326459cb +#: ../../src/introduction/prerequisites.md:198 37e1162f30894a1ca7dada9870ffa3da msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 459a65b8e67c4a9aaa03138c1abe94ad +#: ../../src/introduction/prerequisites.md:199 1c25a51edf6f47c5979c721b19cf11b5 msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 898eb29ac7714c69840b795633953a05 +#: ../../src/introduction/quick-start.md:1 ace930cf878d45a99f12b71bf0987a87 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 2a658bd2d8ce4533ab7e056fc3a3ffcf +#: ../../src/introduction/quick-start.md:3 46587a5e0d534af5867ae4f70a116bee msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 32dd2e28cf0f40b6930750f0162355eb +#: ../../src/introduction/quick-start.md:7 a0774d4e779e46f7a983922425203066 msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 471c47d311074ecfac071b6d52d9cfb6 +#: ../../src/introduction/quick-start.md:12 1658ee6f3cac4d04afc732aa758b1f48 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 5078140028ea4d04973cb9cd20f0607e +#: ../../src/introduction/quick-start.md:16 d8e2bc671b894f3fa8a091261754c728 msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 ab127d4ba0a44526ab129587a8160923 +#: ../../src/introduction/quick-start.md:22 683a469bf4824c64a8ea32e048d5df73 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 d5cc6b4295a74f3586f022b0227759b3 +#: ../../src/introduction/quick-start.md:27 b7c50413f7864a86815f3b581561cdb5 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1069,11 +1080,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 585a4fe583ce44e180a062742b3b0849 +#: ../../src/introduction/quick-start.md:32 d2ed66bdfcab4f7dad95b00c95d4a3d6 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 0d81b0c9ea58420789d1d71cca32ce88 +#: ../../src/introduction/quick-start.md:34 4dcbe776a70645e5a6c7513348fa6bee msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1081,11 +1092,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 ea4ab0782d8049d8b1b89cea4ae60048 +#: ../../src/introduction/quick-start.md:39 bae5b03fb74541e6ad79277a576e0516 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 f6f3b7453a254f828bd4c9e9fef92bed +#: ../../src/introduction/quick-start.md:47 8ff0d7a8d37b48488e4504ff8e3adcc5 msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1093,32 +1104,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 3bf9050175d4444ebbbabe219412574f +#: ../../src/introduction/quick-start.md:51 6255b499b9b144128afaeed64fabe8e5 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 e03f72a14dcf4bf38ce8232598ca761d +#: ../../src/introduction/quick-start.md:53 e861db9c43ed4b8ba262af8e435a350a msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 3dcfb2facd324dccb3084c02487625dc +#: ../../src/introduction/quick-start.md:57 c6318f06bcd74cda8c1f0caef9452b51 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 b8531da183964b02bca19f818ec076d4 +#: ../../src/introduction/quick-start.md:62 c862e745217244d28cd4c2f0842e203f msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 7ba1ddebeb2843179fe99fc410b193c6 +#: ../../src/introduction/quick-start.md:65 eba007736b92434a9711f683e64bb153 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 a6dc303e9d284b60bf1102212505ca27 +#: ../../src/introduction/quick-start.md:70 aebc2caf5d1b47f1b7cc0aa53e5a684e msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1126,21 +1137,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 59ac7830ae3e4d7cb1bf503e8c90fe30 +#: ../../src/introduction/quick-start.md:74 1242171f8b854562bb7848b06d2d065d msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 6d1d6f42ada2418ba0a1de1371825b9f +#: ../../src/introduction/quick-start.md:80 24e82ecf7926428386a89f18a34eb00c msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 1cd924fe8ace4a82ad8701f37b5e7d84 +#: ../../src/introduction/quick-start.md:82 00e75efe03554835bc33ebaed0652626 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 aa297c52cd964291a47bb91c0135156b +#: ../../src/introduction/quick-start.md:88 4ba34ec455704844a9cfcbac3522ea0c msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1148,46 +1159,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 28b02c90397745bfbacc03c3b1034939 +#: ../../src/introduction/quick-start.md:96 c0e9673440db454bb51af04432aeddbb msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 ef2a4f39f01049b891868b84d968c0dd +#: ../../src/introduction/quick-start.md:97 39a23a9d02ab4bccb36d6a714639509b msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 89e3fa8dceda4f0cb1cfdfd1f17fe4df +#: ../../src/introduction/quick-start.md:98 23a878e0166b40d78984a2263f63b760 msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 7cd178223ba94d1ab3ee8cc5f13a8dcf +#: ../../src/introduction/quick-start.md:99 5d9c435820674bf4b1c5d3fef5df736d msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 46f6f8d050ce4f8c897056167d9707a7 +#: ../../src/introduction/quick-start.md:100 e724ee53db1940b9b09a909f4db531a4 msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 5ee00ee409b746dc951ca1d4c360e624 +#: ../../src/introduction/quick-start.md:101 7820eb801a8145feb603145f153263b9 msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 d4af972281174b8999eab55ee0ab1a0e +#: ../../src/introduction/quick-start.md:102 e8db3f10be294f13abe3a4418bbae4b6 msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 80401cfffae042ab9ec4b3754af04b25 +#: ../../src/setup.md:9 95211ea6924148a6a1fa5ae8facc2c7b msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1195,19 +1206,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 32f86f911ebe4a4c94975f81742333f3 +#: b742a74d586e42e6b0480b7af3e49c9e msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: d5f1ad2b95ad46d48f8f2ca5e357bb5d +#: cd3da03d43044ec9843e476a54e704be msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: c53ceee943ad4acea779e072b9137889 +#: 0d48e2f07d784504a17cad0ae20262c2 msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1218,37 +1229,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 7dfe9dffbf5744299bf232599644c7f6 +#: 4d372b89f0ce451db2a505b1754b8356 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 00709fa451134ee09a0d808e101f28ed -#: 991172e201ec4796992a349dee44f090 +#: ../../src/topics/staging-input-files.md:15 573e903ef3d34514ab7b20e79c446567 +#: cfb40fbe52174d3799a6bec175db60a5 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 1f3c23a4769043ca985b8ddfed19391d +#: 95841b1c75c84f01bd5fcb7cf3afe78d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: f81b43c7cb194a1cad8672129223c833 +#: c8bca3654ebb4b29bf3f028b4c65fa35 msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: a20073a8f5374eb1bc8531ff33e622b6 +#: 1432105e38014a6d9d0cf80007141007 msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d08869beca3a4774baf1097b63e79474 +#: bcad473b34ec43f7906253123a1661fa msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1259,11 +1270,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 109b773789024b2b9c063a6169c6169f +#: ../../src/topics/best-practices.md:1 e1c8949e663b4debaf87735f1d62a2fc msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 959fa04f88e54d42b9b774cc95d85ee0 +#: ../../src/topics/best-practices.md:3 dcc991b647d34ffc8ea3bf9c3a38258d msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1271,13 +1282,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 64674980c3f24c45bbfbf3f957dda55e +#: ../../src/topics/best-practices.md:8 f26c222638e54187b8bb62fe30b66bc3 msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 90f2e4265919446a902e17627f4420e2 +#: ../../src/topics/best-practices.md:11 23720e4ab3d1407597f1d1c2a4d4d90c msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1293,7 +1304,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 6b5f91a749fd44b5acfd6071c9913342 +#: ../../src/topics/best-practices.md:20 b3638183c59744c897246af7dab5d10e msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1303,43 +1314,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 5fe2962837b14f0e9989063be4a506c3 +#: ../../src/topics/best-practices.md:26 2c0291133b964ad8b751f8a8ed2338fc msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 4e1bdea962ed4618884cb9d1d59d7509 +#: ../../src/topics/best-practices.md:28 325c8c4058f045aa8fbd705238122798 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 37eff4ca02e843259f6ffa38e4a87a04 +#: ../../src/topics/best-practices.md:37 05333866485b43479352f7ee9326c7fd msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ae47231c203d40a98c10045038ea9b65 +#: ../../src/topics/best-practices.md:40 f8140ec6e9cc41ee88ec4bde61a44d47 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 018a6d5dbf1044559b365c7b9017eb3f +#: ../../src/topics/best-practices.md:44 1d68f50dafaf4cc1851e2d67b3e78603 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 e073d8f990c44b09a73d642cfe49bebd +#: ../../src/topics/best-practices.md:47 b283942434c54456a3f29fbb0960b6c4 msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 e04fae88d9b64493ac69eaee24585098 +#: ../../src/topics/best-practices.md:50 0b4477c5b0184e59aa0c07161008a7bf msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1347,13 +1358,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 b26b9c9b1c4346a297a31c9721f0172a +#: ../../src/topics/best-practices.md:55 9741651d51f249ffba1820694ab78e92 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 b50500c3c3f54b16a535a16175a44653 +#: ../../src/topics/best-practices.md:58 5e76d4a9708244ff91f2587350d684a4 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1365,44 +1376,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 623f3a804199449bb85e23e00c8bb507 +#: ../../src/topics/best-practices.md:66 89e7028e55b54f968e87b9c1c3caeecf msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 effea0b1356447c0899ca0746667ea31 +#: ../../src/topics/best-practices.md:69 88e2338fb2614ef29dc497d8c01a2f2f msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 00e8ef87864c4ca2b2c1c0548b02b38d +#: ../../src/topics/best-practices.md:73 0f3aad35924344659eb5a6719ab2b8f0 msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 6e6f48d70b894a6c959ca30fe6bad772 +#: ../../src/topics/best-practices.md:76 877cbb1d537b46d3b6d05b2d8c025e70 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 02fe08760a4a4ab49e96f4e51316a81d +#: ../../src/topics/best-practices.md:78 5c0debbc1c1b428ebb32b589b99fe17d msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 172ed7915a654964ba63f860b2d65330 +#: ../../src/topics/best-practices.md:82 1ff97183191240edb98f0cc365cc028b msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 4d0a2871a7484e21b3c39c4dbaaa63fc +#: ../../src/topics/best-practices.md:85 22f7725deb07422fa0a7bc2e6f01e4d0 msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1410,31 +1421,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 1eea9f1e284447718141f5417b6bb433 +#: ../../src/topics/best-practices.md:90 982313839ccc4f5a8527fe9a854c78eb msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 509411d353fe4314b087b81b09ea960b +#: ../../src/topics/best-practices.md:93 267c9d10ab5e4b6c8a6104952deb1690 msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 a54bc80bf08243bba67d98dd682ee134 +#: ../../src/topics/best-practices.md:97 2eff0eec58c94f4d8986a4cb91b14b8e msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 69ecdaea24ef42eebef9d86e5d716b11 +#: ../../src/topics/command-line-tool.md:1 f38db701740b442c89ce58e937bd35c5 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 3cc5847468d1478bb5589dee68147189 +#: ../../src/topics/command-line-tool.md:3 034aac9e186645e384c28bb2a739cfff msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1442,52 +1453,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 98c6bc409420485095ae65d6b0b9a3a0 +#: ../../src/topics/command-line-tool.md:8 5f835cdfc0ae4f378d8dad6ae7ab1855 msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 ebe23e5378514f888a9ec32a2adb1e98 +#: ../../src/topics/command-line-tool.md:19 02900cb8ae4c4da89d264b76a984d6cd msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 387cfe85604f424f8d31c4a4c9c15edb +#: ../../src/topics/command-line-tool.md:50 753e48d6dfd54a88a12773b996f182d7 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 7b1d65754e854693bb60289c97d3fb5d +#: ../../src/topics/command-line-tool.md:57 c7ed6d1654c54bf390e933ef0f847b99 msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 f440cef729c8410281432307a4da8d55 +#: ../../src/topics/command-line-tool.md:68 0a0f855ce34449a0a37c036105c65839 msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 4fbb8ceb1b59480583ac611142167049 +#: ../../src/topics/command-line-tool.md:69 c4300454f49548f49e4bd186192515a1 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 b87869204838415bbf694214e3680593 +#: ../../src/topics/command-line-tool.md:83 f985d58070de4c0fb5f5a491fd4dc31c msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: 12cf5f2264504c44a2173e858bb2c283 +#: 2f4e2c85677a4e56a35b6bef36d67334 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 7694f9cabfe04308bbddd2c88ae6d9b9 +#: 13c6d5600a30406c81ffa25ce42eb0c8 msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1496,17 +1507,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: b557dc4f8ef549b98f59412a918643de +#: 3bf773b8560e44a3a37c68b6fcdc6a23 msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 3011eb003c084285b30cfa56a8da45b6 +#: 68b8578d2f6442929941ed2522b218ad msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 +#: 755149ed46c348c2b723b49c3b3152a8 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1514,7 +1525,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: ce78b2d147054da895beba66d0ecdab4 +#: 54b7ff590d52454eb87d9f23fca44501 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1524,7 +1535,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: a973846ec5a946eeaff02c5b00997da9 +#: a7c74a4a74c9414e9f29fa20bab7e295 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1532,13 +1543,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 294fd83a97a64249bac38f7482159372 9e8eb1542db640ff9e300649ce50dc9d -#: ccec7f73b9d948e79a6cdf32bc124092 +#: 0cbf233379024800bcebb963e0a3eb6f ae3bc02e4f3b404c89f3c461a62c5bc4 +#: dc32a2bacf2d4c8cb841be6eb8b839ad msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 22948f19cb78485f8f86244686a35c09 +#: 34a56bc23af44353a003ee295fb2c609 msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1546,7 +1557,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 001d9579bfce438e865377fb9c2df776 +#: c7855ec1f09d4945afcb0aec22567b31 msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1558,7 +1569,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: e62618db8995428bb3f260e03ac8f459 +#: 5c60492e27014735bb9a86307ee654d6 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1568,19 +1579,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 457756c4e9544f068af897113358cc89 6d5ae75431424ea788c3440606f22940 -#: 98e0548845fa447fb05a29c9fc2f17b5 de5e8aad4e3046bf9bfc2ad8ccba17d0 -#: e9801b2142cd45368a73ef9b121c1d08 +#: 80a9c04358e64ca28ef4879ad74ef733 a2b470f06ad94871970b7d95339fd369 +#: dc65b4b5e48e48a6ada03da0fac18a51 ea2360c5286b43ccabac202dfa97fbe7 +#: ee4ca94dadf64ab69a70b6cd4eaf451a msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 ee2bca9bdbb74b60a706c3118d6a17ba +#: ../../src/topics/custom-types.md:1 285d23ef9bbc46c9890ae7957d487c12 msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 e63ae9694f40438d872d141ae824a42d +#: ../../src/topics/custom-types.md:3 3edd322daad940d8957f88a2637876b5 msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1589,21 +1600,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 750fdd4c270e46a09f79e867358f7414 +#: ../../src/topics/custom-types.md:9 a1bd9b0dfa234e6caa6a684e981d89b5 msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 b3f688cc82444ef7a7a0aa63dac39cac +#: ../../src/topics/custom-types.md:12 0aeacb6ac20f4ebca3600425ca32f5f4 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 3638be18b4f64cf08053d512e590dda3 +#: ../../src/topics/custom-types.md:18 1c813ebce2904f008b5b33656f673ebc msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 7d5b9c21739c48f18c13614ca6967f6b +#: ../../src/topics/custom-types.md:24 cc36359e94c841d3aa5cbb26a094e1d5 msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1612,13 +1623,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 8fea29993f944d8d8d3181afa29bd0a6 +#: ../../src/topics/custom-types.md:30 dc79668b05e8439591a0beb4b57acc66 msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 02d0b648d70f49d7892f690be06df585 +#: ../../src/topics/custom-types.md:46 08aba4f77aa442d4a34aa1535f78c49e msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1629,15 +1640,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 0743bef42b9a42328849c8c2f9da9eed +#: ../../src/topics/custom-types.md:53 63431a972f994bccacf55d5fac0d614e msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 85c5d0cbbc6243a6823f5eeac0f85dd9 +#: ../../src/topics/custom-types.md:55 55e7695aca4f4319b1cf7551105a8782 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 be848f30769543eb9c0be55263e3f758 +#: ../../src/topics/custom-types.md:61 0c5ab34ebbf54ff6940b8ce3f080d744 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1645,7 +1656,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 cbff44a64ba4432cb59a82f82c2f0103 +#: ../../src/topics/custom-types.md:76 f97e18d2d3b946468c4fac227920e011 msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1655,26 +1666,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 617f1c0084cf42d9be4c7a8fa5a48432 +#: ../../src/topics/environment-variables.md:1 62644031403548898ff36addbc0b1f6f msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 cee79afa3c6f43c29ef05e06b7843d35 +#: ../../src/topics/environment-variables.md:3 595630b0687c4467aa65bfed289281f4 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 225903b11efa417989df42de86ad2451 +#: ../../src/topics/environment-variables.md:7 34e005c135864a89a00e817d79118e2e msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 1a5f058290064c1cad05e63eb127fcbb +#: ../../src/topics/expression-tool.md:1 b624f9f99c294e6996f212c8b62f20b0 msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 74ad8d69cf294ae880dbbe28e25b3545 +#: ../../src/topics/expression-tool.md:3 14df63ab847e4efca820f712548cd076 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1682,32 +1693,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 5293e8ee9b3b4f59947cfc164ef111c4 +#: ../../src/topics/expression-tool.md:8 91d4224b41c6473f936c03bd0ab9d370 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 ffa1955c759942c68e7589429e5ea86b +#: ../../src/topics/expression-tool.md:17 519989399dab493ea41941ed85cb9670 msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 038bc0ba5f6a405a8255a7be76979baf +#: ../../src/topics/expression-tool.md:48 28dd1cf24309404eaf717d417272e094 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 fae1c63de02e48c0969a98e4c49b2e06 +#: ../../src/topics/expression-tool.md:67 3f536ad8c86d442c8bbe61777dbb1a54 msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 7093a94695524851a5463193f0701b78 +#: ../../src/topics/expressions.md:1 b9e9894c6d024e60929d020dbaa553f0 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 dc8274ecb15948c29a31db89b12a58bd +#: ../../src/topics/expressions.md:3 482debe1a40f490b90d4ece1b3f9d732 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1715,7 +1726,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 cec8eef8a5aa49778ecedd4195ab9f2c +#: ../../src/topics/expressions.md:9 708346038be745d097685970cc462f4a msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1724,67 +1735,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 df100967597043c78112bf43b520cfab +#: ../../src/topics/expressions.md:16 99347b6b2c404a4b9bbcc96e0b4bd925 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 59ccf4daba39406581a6bc2d9bb1b7d2 +#: ../../src/topics/expressions.md:22 e6629f0914324c76a08fe179575b73d5 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 570cc75699dd4e0a987fc9aca9a01ee4 +#: ../../src/topics/expressions.md:25 2287002a87184fb9b95d775a368f0e46 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 9e123723048546d495ed5110d7177708 +#: ../../src/topics/expressions.md:31 c23d4543d9f949a9a7015fdcbb40dcd0 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 26543894f6e04270b89ab702451bcc89 +#: ../../src/topics/expressions.md:35 c04a9dcc84b84f37bcf32c3790672038 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 f403c1d4e43a4aa0aef8488d2b5a6262 +#: ../../src/topics/expressions.md:37 9f27c79365db455d9d31053576ebe05e msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 249dffb569a944c897ce5862e5f28fad +#: ../../src/topics/expressions.md:47 a2b3ad1e2c884e24948a915c3305aee1 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 1641c96aca2f4923885fe8a509eb3a49 +#: ../../src/topics/expressions.md:54 dd7665bbc5e9449588c9539e3c1910de msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 bc63405a0d964df2bd9493996abc48fe +#: ../../src/topics/expressions.md:62 0972c757f7c74ea9beabf6b9ef9dbf4c msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 5c191d1420db4e26aca31c1b1e34cb75 +#: ../../src/topics/expressions.md:64 175de3b9854546568f60a20cc19887de msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 d6a5c65e824a4bbc94578df9597d4716 +#: ../../src/topics/expressions.md:66 0c286e5ba1714a059a95b566fe49be31 msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 a7ff51fe564748229a88a0d3044dbc17 -#: c12625211cc542b68cb51365a63eef00 +#: ../../src/topics/parameter-references.md:64 3029c1dfe5424c2b812597b03ea76178 +#: a5503b6c524e4848aa308b0f4c26d774 msgid "`arguments`" msgstr "" @@ -1792,32 +1803,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 05c34a5a2e404a14b9d284a9d0c73bd3 -#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe -#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 -#: e7f1993580f0425098a719e83a64cc7f +#: ../../src/topics/parameter-references.md:86 0e03befa46c74dc2b09420e1eb2a6fbd +#: 50f81e7ab73a4713bbc60f6f5609b906 718dc3def33c462786174fb42097981f +#: 9c2acd930553458eb105f96213b5d7b0 d4bf86a995d546c0a9159b3f29a84125 +#: e98424244f554c7399e9e7ad560849a6 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 2fd5b42cafe34d3185888de041818dff -#: c158e9ee5fbf4e868b152a0a5880092f +#: ../../src/topics/parameter-references.md:66 2be930b5da674874a0b634eca3ad9346 +#: ce445ad0f00f403985eed1328103a500 msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 3f29e4a3087847e9af6f19166a8def9a -#: 92697d3179ec48898eaea9aba3c24dcd +#: ../../src/topics/parameter-references.md:67 2fe48d6404864ea39ef0634169f67be1 +#: 43453d90db244c558a815ca872dc716c msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 c0eaef93bc3743279549bcfb8b014ca3 -#: d6722e3093884ad7b62696fbb2f48fdc +#: ../../src/topics/parameter-references.md:68 78eaa318ba81407e9ca9c2c1702ead11 +#: f5da7058f7f146d584314a5bf4de5498 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 37c493fdc2f0410a9748f8faf09ce5b5 +#: ../../src/topics/expressions.md:72 7189f4415d204fb388c4a7e927e15b71 msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1828,11 +1839,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 04e3eefe4ec445cb90c2fa42344aaed5 -#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 -#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef -#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 -#: c610220d06484d589313dc29faf8222c +#: ../../src/topics/parameter-references.md:90 17a83cc91963434e89822a3e46df8401 +#: 194d3e48d38c476fa8f731e3bc2d8c7f 3a3000a6446b4ef4ac66a28acb13b136 +#: 5cc35210e95e4f2ba6a1a6f118926fdd 68b3d1481a4e4375b1b0c4fca8285374 +#: 94f2bc195bc0487da014bc3f4d2dc8fa b92b4eff2429437d9da911ca68cef954 +#: fc0a1353e87e479d8c8b6c973d547465 msgid "`format`" msgstr "" @@ -1841,51 +1852,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 662b36e3505f4ac3bb5070bb6e055217 -#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da -#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c -#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b -#: f71216a4b35e4157aece5ffa2602d8bf +#: ../../src/topics/parameter-references.md:91 5478cbeadc64412bbb32619fae9b9958 +#: 6950cbe52d334fe58bf4fa20e5f1f8ca 6b5bda581d0047819c6d92edd8ac9045 +#: 8248329fbe504b3a96bcd890908b070f 978c0fea8ed1481a9f06b6abb31ebd21 +#: a24ba514d66d49cea281fd4c9c7a2b8d b6e2c8e7abf74d64b2915063dda8479b +#: bc184adfad0e4642bc864d367b8779b7 msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 a3c775a0f04b4541a9b712bfe2e4e69a +#: ../../src/topics/expressions.md:75 5bba2d465e0a4c5d9575406d1294a225 msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 ef16c4a9a7ea415fa399297b63b9710c +#: ../../src/topics/expressions.md:77 da385d3cde614749887e195ea6d95291 msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 2592e429c74c4ff5b8ba68a36f060c1a +#: ../../src/topics/expressions.md:80 487c95417f8e48be8391163578ca9519 msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 5cca4c2ad617400eb6efad4066b1839b -#: ba1fff3ebb274dfba845b3ee20ebd71f +#: ../../src/topics/parameter-references.md:78 48437402c00147d4b4ca8bd6b38a5823 +#: bdcb3920048f4e578a4005fc2e30233b msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 6914526c0a7c43a2a05438519508ee0f -#: 722d3bd7184841639b9f9a38914002da +#: ../../src/topics/parameter-references.md:79 121556d49d584cc491a15ef8404ce462 +#: 183ba52666744f7ca5772939db2efd6c msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 737b0f9392154241ae5b56c6caa823f5 -#: 7b46d408e7e7481b91a950b2d4010c9a +#: ../../src/topics/parameter-references.md:80 08ad064936d8406f8c3852526f4f863d +#: 30c927925c6b483b80b583ca7c735437 msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 f09e7371708b4c0685eef2a314791ccd +#: ../../src/topics/expressions.md:84 32a26dd9c5f84e88995f093cda953ac9 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1894,32 +1905,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 aa6ca1def2024c98b9d5542de1a81425 -#: e9fc5f7fa4474dfc95039b94167fe894 +#: ../../src/topics/parameter-references.md:84 05ee6df2f9b247629d148fd59c293660 +#: e7b7d782b6ac49b3aa0c8d8ce7ff04d1 msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 6c37a1ff939748bf83a86c07c3d017fe +#: ../../src/topics/expressions.md:88 b0cccc07e5bb4effb60424623351499e msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 3a8126b0a0334df890b2be2c693ea5d5 -#: 61744122b7d7494890cbe6b2fb72b9f7 +#: ../../src/topics/parameter-references.md:87 4e5281c8663c4b6e8851be10f50143f1 +#: b5c22c66397e4268b4b3d53b9a253a3a msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 93cb9015dacc4b50a4ef177ce4ece2e7 -#: e0c7ccc8f8664cf794cbb7330355f3fe +#: ../../src/topics/parameter-references.md:88 98a28fec818e42af9e177e17fa12aa7a +#: c37d0b1fd75e44a28b3b6409f912e865 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 58a1773b1cf546d7890010fdebd47388 +#: ../../src/topics/expressions.md:92 dcc42c6c49964a4ca7bcf2124e26ebfd msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1927,61 +1938,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 230f3227ed1144f7abe0f8c231bebbd5 +#: ../../src/topics/expressions.md:95 d2ba352ac5fe427ea7ceb0bde01458ba msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 5c77dc9f8afe4dd88933943030e836f2 -#: c9534670f5f04769aa3749c3778eb705 +#: ../../src/topics/parameter-references.md:93 235cfd6e9baf48698102447fcb83e0e1 +#: 8aad01df8d8d4ab7905a5da7ce7f6bbf msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 4ec8bbac5fb14371a6a4cd53d7cd6450 -#: 7b0887a8caed41b2acccf7021bb323d3 +#: ../../src/topics/parameter-references.md:94 058ba8c9c2da4ebf8b2291600dafd611 +#: cea47d3e10f641a2b64f08ee100ea6bf msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 aceedfb558b246bc87eb3eaedea187fd -#: e5e8b8c75f0f43cbb6e160e5bf810c6e +#: ../../src/topics/parameter-references.md:95 3b039de5ad144207ae337aa88b3b1a1f +#: e0ecfe44b34e45dea513459b6b3e44a6 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 266dfb5fe6a842078baf66073cac9623 -#: fe3b9fb45e01490498c5a35c012b3de8 +#: ../../src/topics/parameter-references.md:96 1cfc6cb0be4e4ddd90f546adb796b805 +#: b62f6eaa7c394792929dda83a187c632 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 85f424cbfc85460f9da310aee1ff0b82 -#: ddf82b12b12d416fb65f3ce3f51bbdf0 +#: ../../src/topics/parameter-references.md:97 8b13b0e4071444179b26401929de8a10 +#: 8ffb471129c04fc6bb52b782fbd09f9b msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 966e88656ae5402a975022ee60646283 -#: af14fda3cca645fbb2f3c5825fe0788e +#: ../../src/topics/parameter-references.md:98 331f58b998cd4d309940ebfcc60a44f8 +#: 5041700e6ccc48989e395a6dcb1be3c4 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 09120baec1464afb8aed4edd773bf509 -#: fec70bb106ad4d95a2d55ebdcf711afc +#: ../../src/topics/parameter-references.md:99 14402b41c64548f8a9691c3b7ccaf3ac +#: cb4837a2b25343d2880a07143f85f40e msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 +#: 1d1c2894600544b686a8ec3c36cdf767 eaa30e987ec543ef8d6f7171de5525f0 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 1dc4148caef748428a7d13caff37b1b1 +#: ../../src/topics/expressions.md:104 065c97a553904db6ba61c20cf9d9939c msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -1989,33 +2000,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 +#: 36be05289972455ea4a60aa1f0b9cbdf 49e1ab5bc5734debb83060759d5c3236 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 947b1ca132a54ed39745cd12ebcd65e1 +#: ../../src/topics/expressions.md:106 f8e37cd35aea4bbb92d28e8d7e803ebb msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 +#: de816d1dc9f24c0cbef86fd6a09eff6b e265df9d1cfe439bb798ab6cd32485af msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 +#: 0363e32e12604eb896f4bdf6bbefd550 8b5289393b7f477699d007ded45a4df1 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 +#: 2c704cae43d64ecbbed33d18eb3f66f3 89acc8f8387d4643a844ac3efb186000 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 5fa512d352d945e7a3e0d59b0987cd1b +#: ../../src/topics/expressions.md:110 0597c6c214924e75ba2f212cd6b0c9f2 msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2023,22 +2034,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c +#: 1eb1c2432dd943f6a27a1f8b92e3981b 5b9ba9380f10425b809c6157a1f0b052 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 81e91df082834d2cab7ef1f62d8ba57a +#: ../../src/topics/expressions.md:116 b4cc7cc55cf04449b291a27514fc99ae msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 e6bfd1dc2e324992b6c3332c11ae3445 +#: ../../src/topics/expressions.md:118 cdb48eff43e7459fbf3ed21eb7791d66 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 acf10261df2944ec890d754fd56c6b28 +#: ../../src/topics/expressions.md:122 67a4dc675c0e444585d579954b99614e msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2046,7 +2057,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 bda6b8f398554b0c946c2c7d96308a42 +#: ../../src/topics/expressions.md:128 ea3238db48494ab7b044bab9f96590af msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2056,54 +2067,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 454c02c3918647039c90ae387005dea6 +#: ../../src/topics/expressions.md:135 baf2f6ac8d514705a1f7bf7ea8c71d2e msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 e1fad28bf9cb4c4c85eb74dd520ba107 +#: ../../src/topics/expressions.md:139 ef45f4e14fb943cd9fbf179f5d3680e5 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 9835d0b399b84a0084fe5a4d9e7e6405 +#: ../../src/topics/expressions.md:146 030261615c38485d83ed986c9c98ce15 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 410ba7a5ac6349a98460c6337ee5c4fb +#: ../../src/topics/expressions.md:149 1728e2370cbb49ab97bee4c2f74fff2d msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 d2daf50d7f3d4de18331c8fd2c8a5786 +#: ../../src/topics/expressions.md:155 4514fc0c99ac4688a37bf30bffe139e8 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 8f2015c12b2b4d5d9a800ddeaf428f25 +#: ../../src/topics/expressions.md:158 33804649720143e5a70e890af9ad9119 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 f0ff919ffc12439d89d7b40f51ade84c +#: ../../src/topics/expressions.md:164 c114496be4c243d6834776e17bf15010 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 307a17a893fc4dafaec2a63a95704644 +#: ../../src/topics/expressions.md:171 c784e86f14f54e4982db206741fbd96e msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 7f393e86b114470f8dda47b2deec63aa +#: ../../src/topics/expressions.md:175 f9de69aad9b44afabded71221c84adc2 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 c3f459b87b96435583637b3f1573e658 +#: ../../src/topics/expressions.md:181 b853c964611e45c2b37a8ac3c34a4133 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2112,15 +2123,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 9f676022eb2744839ca2109920250cb6 +#: ../../src/topics/expressions.md:186 a10d143210b94f83857f62e972d69134 msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 ede7285f77864fb0aee6cfecc2c97fa0 +#: ../../src/topics/expressions.md:193 b07734b172664040aff04f83bd4395a5 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 c55fb184bc614ee2b6e5e64611e5df9b +#: ../../src/topics/expressions.md:200 1f9a5377a1f04ee3b8a9ae22390e0cae msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2129,11 +2140,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 66b522f46ce242149386e79f63b32cf8 +#: ../../src/topics/file-formats.md:1 359bb6448aa140f8b940baf769c13db6 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 64a20285785d48ca86227a0cf6353ad4 +#: ../../src/topics/file-formats.md:3 c4aba730bee14931b051d6aead7c2dae msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2141,7 +2152,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 5f71bbe2c74e4260b79d4d9230d35397 +#: ../../src/topics/file-formats.md:8 c4dfcff573424bccb97580fdd1ef27a1 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2150,34 +2161,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 63bfff437e3348428f7e33ece7ec55e7 +#: ../../src/topics/file-formats.md:14 1457fa489c894f1bae8a3949ef200527 msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 6ce83d9c06e4436881aa47d94ef41e0b +#: ../../src/topics/file-formats.md:17 cc4fa87d57b344ed8961c31bc4397e71 msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 55006c594abf4e70a38e979568fadcf4 +#: ../../src/topics/file-formats.md:20 091815ab1d824787a1460ce11ffb834d msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 +#: 414b68dac4654163b3dc13e140ffdbf8 96fad38b4aea461493bf0827476163bd msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 1a1905ff2d624eca952c8a53b3bee678 +#: ../../src/topics/file-formats.md:32 4f71de1140974e73ab033fe7dd9dc165 msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 368ff92476b14f5c8331260eafc5acb5 +#: ../../src/topics/file-formats.md:34 b84e3294c8f648aab634e59b6f58441e msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2185,11 +2196,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 5d530afa23f349a79f54d51d40724747 +#: ../../src/topics/file-formats.md:39 6d9ae44900d64532906532432881d29d msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 16f965f86712483aa7f95dfa3f944a17 +#: ../../src/topics/file-formats.md:45 5b99384b3a854832bcca2fb02bdfc1b6 msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2198,80 +2209,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 dc629e2c90ed458b96107a6994676434 +#: ../../src/topics/index.md:1 3141fc6828024c3e8201e88ca10e19ee msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 cf2f077cf8044079a7005e6e508dcd8c +#: ../../src/topics/inputs.md:1 5f8c8ea68d7f46fead000315226ec164 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 129e1d2a71894d28b009f4846754a75d +#: ../../src/topics/inputs.md:3 86c18e5105b1400d86d413e28ad72f48 msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 d6791bbe575042b9a7282c69407dd907 +#: ../../src/topics/inputs.md:5 fa15037f9b0b4a2c9a1f4cff9b8fde43 msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 e8da87f8bb664334adf831995601f462 +#: ../../src/topics/inputs.md:9 fba6d2b7843e466abee33183103cf47d msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 de6c322618304207b6d1364d1ec2dc13 +#: ../../src/topics/inputs.md:13 09f5a55611d14e39b2266245b79ed763 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 43bdcf6dc1b14030bff27fa53289c02c +#: ../../src/topics/inputs.md:16 bdfb39c2656040858616afe731111d1a msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 056510b42ea64717996ab49c307bda86 +#: ../../src/topics/inputs.md:18 c306335ff07e4c03955fe87cad16efd1 msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 6852f5dbd9094c99bb68f2a88f76c9bc +#: ../../src/topics/inputs.md:24 50bd3db6bfb348eea13ba4714ecb2a20 msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 f33b6800367248b7927d97ad7b4be5b5 +#: ../../src/topics/inputs.md:26 5d32cfb6f6ed4dd8b11ed316830edba8 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 8ad812d7e88f4cbba83228ffb1711576 +#: ../../src/topics/inputs.md:33 b90fb1b2d38b42c1bad2d9667aaa22fd msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 cc680bbf091a46f8b4b3dbe6324c040a +#: ../../src/topics/inputs.md:40 6029a96abf9c4d7295eb86d435a1f58d msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 446ac81f078d46289a18f494748f482c +#: ../../src/topics/inputs.md:44 902e9df74f78431ca9cf1421a26e097a msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 3d6d958d111943f3a2139b4dbb7810db +#: ../../src/topics/inputs.md:47 9760d15bad144e70a86dc0a8da72363a msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 ba0ec9157709430c822f4e91459288e2 +#: ../../src/topics/inputs.md:53 75bf3fae131049308441bc496f543f6e msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2279,7 +2290,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 2565f8fd4a15429e887aeb71eacdff1e +#: ../../src/topics/inputs.md:64 38d8a9c157404bb496bc49f1e427bf99 msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2287,7 +2298,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 659ed5c64fb546399b741553a347b8e8 +#: ../../src/topics/inputs.md:70 502994ee84234f048e545633bb04cd3c msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2295,14 +2306,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 3d87e69d41374fbab23b26d36c1aee03 +#: ../../src/topics/inputs.md:83 551b06b8a3064bcd8d0f1693a4c0ee94 msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 07bc81683e2c4ac68b379462bae95207 +#: ../../src/topics/inputs.md:95 1838e7438be5449c91c6406a7e40d8cb msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2310,7 +2321,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 3e304da2150f448d9e39715ac5f5deaa +#: ../../src/topics/inputs.md:109 098bb02c941a4bf2a8d4dd9ab3bf052e msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2318,7 +2329,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 fd8a98686e3c4c609f79ae427f1558d3 +#: ../../src/topics/inputs.md:124 b43194d2b3ef4fc6a8c4b58741317b29 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2328,13 +2339,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 f1a2e1bbb1104a4fab5a7f04cac845c7 +#: ../../src/topics/inputs.md:131 e17c55c9ed034dd68f4d24272a61d2f1 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 6a7f0ccd227e4f90a8c8ca96744bda68 +#: ../../src/topics/inputs.md:134 c97a6945e4bc49888d280bbc43c3c069 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2345,17 +2356,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 1f79d115d8a145189638c68c3095396c +#: ../../src/topics/inputs.md:142 503666cda07b4d7397c65561714d8034 msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 6e1b3e2d90184e34925891099d2b5cc1 +#: ../../src/topics/inputs.md:146 e5463be0a00d42e386aa6fd3dfacaeaf msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 4f6df7f13e42448eb4a53f03bc477b56 +#: ../../src/topics/inputs.md:148 14b98bd0ef4a4065a24e66443458d607 msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2365,23 +2376,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 dbc0b52627514ad0908969d0b4ddfdf4 +#: ../../src/topics/inputs.md:154 98fa5dab117e41d4a42da8d78c533c64 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 f173dd96ad124470a53573c86a8df203 +#: ../../src/topics/inputs.md:160 116c212444da4488b32abdbd725db98a msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 af25945b530048b685891b1de4e35e72 -#: cb07caa4ff0149b3ae832be53f8d76f6 e0098a77080d4349b05ceb7735a5fdf5 +#: ../../src/topics/outputs.md:105 065e556e01b34c35b6be4b54b7cc0203 +#: 4745f370dcbd4ee8bbf4b3a20ac5b9fe d11761f2d576464f8a2c63bdec02d410 msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 2445d2c7c2794fd3ad8b6ed8b4a9440b +#: ../../src/topics/inputs.md:178 b3bf1d7e95704682b1bae17472eaa4bc msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2391,7 +2402,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 4459819ba75647d185986a3386939494 +#: ../../src/topics/inputs.md:185 04bc655130234786b06b2d5b9e693635 msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2402,11 +2413,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 8f163bd34ded4785b6e28c8e2147e0dd +#: ../../src/topics/inputs.md:191 e2c18a43b2794448b45c489dd2fa951e msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 1799e11a7b9c4929a3d1379d7ea45d03 +#: ../../src/topics/inputs.md:193 38968ed627514ef38e43b3d1e4a5e25f msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2414,46 +2425,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 9510c0b431a44b5e84e0b583de7c5446 +#: ../../src/topics/inputs.md:198 06aab84eceeb41d087b7e295ffa21586 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 efb4eb6f5e994b50a52fa2c707dad1ce +#: ../../src/topics/inputs.md:204 a0317edb8b964cd2a36c59eaa6df302a msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 34599c6f10ce4104be2359a1b37f91cb +#: ../../src/topics/inputs.md:215 5a3d1b82c79c4ccdb7d06381f4d0acda msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 0663ea7918994d3f9c45c652a3ed12db +#: ../../src/topics/inputs.md:217 e1fc6c3a324a46ee84b0eb59f8396552 msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 a98dda6ca4b14edba467de638bba28fc +#: ../../src/topics/inputs.md:233 f22e7d9e23b541ef88f3254095147519 msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 10d0e9f8df8c47788703073b17529bc8 +#: ../../src/topics/inputs.md:236 d473d2fa11f64e8fa86554b5777c98e4 msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 9a0e1a130fba4d24a9168ca3e455cd23 +#: ../../src/topics/inputs.md:252 290461c321d14d23b39003b93008a7cb msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 992a8c801ceb4233acf56b6bff315188 +#: ../../src/topics/inputs.md:255 add43f7531bb4c6988053ae799c366f0 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 9027d23fa7074b789c3b86ca5ea17fa4 +#: ../../src/topics/inputs.md:257 b12b6f5e34c14dbc9b40458d92e6797f msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2461,18 +2472,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 68b47710a8ea4b978428b42c627944e9 +#: ../../src/topics/inputs.md:262 4d8f38679952486095a77692387db2d3 msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 d33e4cac65d14111a89c838c4d1759b9 +#: ../../src/topics/inputs.md:265 47ec49759e274e59834192b794ec2d9b msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 24cea1cf7d774b6ab56959f289cab39d +#: ../../src/topics/inputs.md:271 0657044c742348fe9e63f662692570a1 msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2480,7 +2491,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 b866867d6f8e4d3999b62a85e6884ebc +#: ../../src/topics/inputs.md:280 30c21cafda144f848bfe79d8e232296e msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2488,7 +2499,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 80c49ed168b14d25b2f09b3b0186b44f +#: ../../src/topics/inputs.md:289 1cc8ea6abb684470b7790808acea2be1 msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2498,12 +2509,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 71628ebe908b4cd28dd1fa17e3d2e2fb +#: c3b84742343449f9b3866285d98b53bb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: f123ca244c23413c91405a4b84887525 +#: 0a1b08fe707c41089ad3d4895960ba17 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2518,7 +2529,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 23299ae1bec94b00a32a8af7eeac350f +#: 5bc4ef6584c74b948ffd5c0bddf8e569 msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2526,17 +2537,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 2495a9f2032a47c188338cb81ba429eb +#: 47ee25d60a4a4faa80476797954ec7a9 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 3fd2f3cf7bdf44089df2ce3122534801 +#: 195d4a8d5aad41159beffafd198d4640 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: d5a5b8b490b640439db92da949266e4e +#: b0c5946fbf79415aa74c8e72fa88cf85 msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2546,15 +2557,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 5935ed94331d4b2f8ce597f31edea843 +#: a98236fc1be745a69271855e1b5eecdb msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 5feb559552194ba58da7206c601292fe +#: ../../src/topics/operations.md:1 5f0da8d7e06a47fda38053dbadcbec18 msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 b7124ba4df9042baadc1641ee09545d6 +#: ../../src/topics/operations.md:3 23d41792b0524742878a6ab8f3ff0fe1 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2562,56 +2573,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 d34b698c62114041a64e0abce25ca935 +#: ../../src/topics/operations.md:7 c0f723242f11464392dfc32f67a3b67b msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 cba2c31262bd450cbafc7ca77f4fb8fa +#: ../../src/topics/operations.md:10 c9f3a48a3a064cb3b1759effe724301d msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 b01be5f632104096b5af6193aab34d90 +#: ../../src/topics/operations.md:16 fbad0b0144984ae78b84307ea68d0a03 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 60a6a02c1367403db6df3ec10f75eb69 +#: ../../src/topics/operations.md:24 59e9ff3276454ff19eb351ff33737f12 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 314ea7bc35154f41b2af5fa6683ca389 +#: ../../src/topics/operations.md:55 ba74f2ab7f6d4c178f3c4c43c461afbd msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 d81e679b13474f74bc5e1ce1e31c2bc6 +#: ../../src/topics/operations.md:58 93c8b61a12134991ae9bb78223e2017e msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 d7fb27131ee44bfc82f698ee44b2bae0 +#: ../../src/topics/operations.md:66 cbbdba36dc3841f2b1d820f369a8c680 msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 b8ef11eafd1d46e088f1277f4ac372bc +#: ../../src/topics/outputs.md:1 4649c8d743f448ab94ee589a1b3a342a msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 d2382ed1f644459594655d5b5b4d838a +#: ../../src/topics/outputs.md:3 1a9d6e2e33244d01b820cf11fe2beaff msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 6651632d977b44479b721174fffeda2d +#: ../../src/topics/outputs.md:5 233c8865faac4d6c8ec7704e9a997719 msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2619,7 +2630,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 bee5f532554241088764ac9e56abbe85 +#: ../../src/topics/outputs.md:10 5aab1c0db3d5449cbb4a0f0dad615d87 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2628,17 +2639,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 0c7c506f38be421399073871f64e99b0 +#: ../../src/topics/outputs.md:16 46b4eeb3ce8946dca0f8a94c399b4c96 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 8b60286e56cc42a8ab5f751a97adf771 +#: ../../src/topics/outputs.md:19 8d322609948a4d6e87d7962b3d29df2f msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 fa0ad674f15348339a1eee771a6ba9e2 +#: ../../src/topics/outputs.md:21 9fdcb55e965444ee8b5d74a2a9870d27 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2646,71 +2657,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 177b5f1b95a34fb9b2eb42f733d79ac8 +#: ../../src/topics/outputs.md:26 e4c490f599a0469a821aa8e74f4ef0ef msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 a08a6d8aca8e490482e127a8fd5e650e +#: ../../src/topics/outputs.md:32 b8ed6ebe6928455cb094ea430e21e5d4 msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 c2c60f68b1e045f88844076e191fda9b +#: ../../src/topics/outputs.md:38 3e65c52d218946fc83b8c3e6adcb21fe msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 6d939f62526e4e6d95acb57d72f60a84 +#: ../../src/topics/outputs.md:45 03751b45cdf647b689a3a69156989db5 msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 c48edd9034364b81ad42540a98b51d91 +#: ../../src/topics/outputs.md:51 1b6f59623f5d4cd984426da21b8438bf msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 9ebe0186a7124dfaa30e558e8f59653a +#: ../../src/topics/outputs.md:62 095902cca30944d19a0d5f17f582e3b0 msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 9381b7d7c9904df0a5e16dac29c2e08f +#: ../../src/topics/outputs.md:65 6d95fbfa321144a9932f26ab5f9ddc74 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 2aa9c6916e3546b7b92fa64bb83275d1 +#: ../../src/topics/outputs.md:67 8be7ef160e8b421a89124a639dc7fd84 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 63afb7a597fc4e459b6a7dbd40bbf6ff +#: ../../src/topics/outputs.md:71 fcf4490c351d4cd6a208345308168ef7 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 7418915470f041c9af5bd39ea652de36 +#: ../../src/topics/outputs.md:89 00f1bb92a38b4f3a8c0065ac75530689 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 f82db001b58c4969b2d8bc1dcbd7cf8a +#: ../../src/topics/outputs.md:91 1477d0fc5c4c4f82bcc1c8e6ba8eed4d msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 26d9f0b28d384617a8e490c1f8e26e52 +#: ../../src/topics/outputs.md:93 dee904cb678d4eb49dc829d6590b267a msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cf46c971b31b4e10bf0fefb4cd028c2f +#: ../../src/topics/outputs.md:99 a21c1fd3194a49ae992a743023653dc5 msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 a4347983fb9945a4a2773af88e426dc9 +#: ../../src/topics/outputs.md:112 e72c526da47a455da4b10e33938d1600 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2719,11 +2730,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 c5489e0633114372b273098ee2c9ffd9 +#: ../../src/topics/parameter-references.md:1 6447f4b8bb5f4f93bd8ec2c7b1fb09cb msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 75de9fd63393429daf1ca10a85339aa7 +#: ../../src/topics/parameter-references.md:3 1faea30495a440a68dbd1647dacc404c msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2736,40 +2747,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 8b5d0ada32d645be9359f43a431f5f91 +#: ../../src/topics/parameter-references.md:13 0c0a3f58a93f492dbfca14523809aacc msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 2ed93dc8778e44209194f41b9ad193d5 +#: ../../src/topics/parameter-references.md:19 460842f202db493dbb901be73a02797f msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 a80dd6d9920540e9880514e04035af86 +#: ../../src/topics/parameter-references.md:25 2591c2cf9e5f402281031ea8dd41a251 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 9de300f7b9da49f59d1c9fd96dec4a8b +#: ../../src/topics/parameter-references.md:36 b093abbff3614b2ba0141f07376a5220 msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 a61f52d3c1024c3692899e05fcea4bee +#: ../../src/topics/parameter-references.md:47 fda3718113354215bd2ac212553fb2d4 msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 dafc9ba578c14fd79d075160e6b7bd6b +#: ../../src/topics/parameter-references.md:51 271e78089c274154a0233289d705e628 msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 28ca6cae42904559bcec98fb9d2b07cb +#: ../../src/topics/parameter-references.md:54 29ab4fa0876b4c11a0c7482cca56ed80 msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2777,45 +2788,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 616c9ff9fcae489285f0bbbc67f07d29 +#: ../../src/topics/parameter-references.md:59 78e1857c5bd54af1b7ca4728879e6219 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 ac17acd83ddb43dc9fb7a5e595ab1153 +#: ../../src/topics/parameter-references.md:61 dae7873015254aa7874379164c90a8d0 msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 156573324cde41ee8b3c47deabf43db8 +#: ../../src/topics/parameter-references.md:63 7a45deb4682b49fd86d62fae41831db8 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 c9725be01e8a401fb3ad9ff01339f81e +#: ../../src/topics/parameter-references.md:69 442f77a69b314cba8e8857470263c706 msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 6797335256e2412cbbe7636507931455 +#: ../../src/topics/parameter-references.md:72 d4455241f14549b791e59fc1f942c8cb msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 05a5f0fcb7454cb697e3d810d55fac26 +#: ../../src/topics/parameter-references.md:74 ff4b1c05c5804ec7846043ae8814ad21 msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 406e68280b5c4ee494632f94b635b7ad +#: ../../src/topics/parameter-references.md:77 119e026b595f49c090d62aa7b7c77de4 msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 2d6e2a4ff391494591bbdf8dbcc4a6ae +#: ../../src/topics/parameter-references.md:81 5449d9c5687544a3bfbf8b2b25640a83 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2823,13 +2834,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 e71a974b29624210a107fc2d097d4196 +#: ../../src/topics/parameter-references.md:85 b3191a7bd03d4ff18802ae0f5d419676 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 b59df98754e24654bfef0b1fe1d91660 +#: ../../src/topics/parameter-references.md:89 ea9cfbbd4cbd4f26ba4b0cb50d58635b msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2837,43 +2848,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 d2bccbff1ce646348fe38c776ad183e1 +#: ../../src/topics/parameter-references.md:92 7d39ed2a3a724dc1a75e6b2cdf87d91d msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 943ba46512ce48fe8c5b62327734c503 +#: a1306ee650344278ae39d6086b1ed7d9 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: bbcd43d5af7d44108aeb65075a6bd2be +#: 21d76d22f3044460b925fee68ac74454 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 834295755af841a78e466eea43864861 +#: 6b8a5c59217c4928874710ead1456622 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: a6b626489bfa468e8f059ab3aa669201 +#: a9f6d09055c24029a5f85c3a663c4202 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: e1dbea105aa845c38cb1f90b43847271 +#: d3948618f9274ad0a333722567efeea5 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: e9640f47d40e45bca184eb30700df648 +#: 44623c81141345a0b0080e719e1418ab msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2883,14 +2894,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 0456efb3718b4356ad2b277ee16de967 +#: 6e80d82ed57b441b8292961ec3163213 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: f7e97f926505407f8f8e9a427e055e43 +#: fc61f369e720463f8a5cd6c751d1d5e6 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2899,7 +2910,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: ec597ff8f6ee47bc815b069335869f1f +#: f20aadbfc13243498ad199376c314e72 msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2915,11 +2926,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 7467a7f6f26a459ba4ce83e4e6dfcc2b +#: ../../src/topics/staging-input-files.md:1 e66956313b8f4f02bb96cfb256e2a7d4 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 +#: ../../src/topics/staging-input-files.md:3 f18c5a8fcbe84135a6e06cbf8008cd63 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2929,26 +2940,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 a03372581fa44f9b8e3e088a4099cdd9 +#: ../../src/topics/staging-input-files.md:9 87fe14c9a0594602aa56a7706e089458 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 36e082be73464be0ad5d0b681cc510da +#: ../../src/topics/troubleshooting.md:1 6e10063f55b747e1b07d6109ab7b046b msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 4464455b51ad4873ac13c4a63ee5fb54 +#: ../../src/topics/troubleshooting.md:3 e8831832b32449f4a8a3dde3c1b479cd msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 ed7ff0753d1743a995f4cfedd6e5dcc2 +#: ../../src/topics/troubleshooting.md:6 9c86467137864626a2079cb6cecb71c0 msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 4c2dd10dd66446058477a52fb8d2c602 +#: ../../src/topics/troubleshooting.md:8 24b66a3e2e464ec6a85b5dfbaad1cbf4 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2957,7 +2968,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 978b6a5fd5fa425fa9a18d9f0e8788da +#: ../../src/topics/troubleshooting.md:14 6d28f1cd40c045f384313c4d74073ed2 msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -2967,18 +2978,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 000c0d6ae8bf414d9293b9f13fd2e448 +#: ../../src/topics/troubleshooting.md:20 5235ff0c35c54396aceb799a65f6158e msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 7e91b8811be14f8e80df39ac4c5bd316 +#: ../../src/topics/troubleshooting.md:27 fc49344510594559b4f888bc45093b51 msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 d42799cc5bd4484bb6beb309a61e103e +#: ../../src/topics/troubleshooting.md:35 6e62be8d7d1344e8917904278b508518 msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -2986,7 +2997,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 48bb0f6666ac48648c7d969608b3bd48 +#: ../../src/topics/troubleshooting.md:44 c91b3a2818b143f58bd37da63479c560 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -2994,7 +3005,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 f8876044db184cbaaca56579d0c773df +#: ../../src/topics/troubleshooting.md:48 86f283bc522c4be2adfac16256f01b0e msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3004,7 +3015,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 a5a3d408dbe34cfda4dd0b2abe67e7d7 +#: ../../src/topics/troubleshooting.md:59 5362aa1d28344968953ab9cb389ccd8e msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3014,15 +3025,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 4c240a18c4e6441189489011242c1efd +#: ../../src/topics/using-containers.md:1 4bb1aafde4f745a083d3a276497523dc msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 e37e76ef376a4ee695e600998906ec1c +#: ../../src/topics/using-containers.md:3 b00987baf6974ff9b7e3b8cdfd7abd9a msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 51a307b0ba7c4c1d89309ba8d2250471 +#: ../../src/topics/using-containers.md:5 9ac51c5a2a0a45859e14d9e388edd5f0 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3035,35 +3046,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 13cc38d72d34468fa4eb6d91f23ff105 +#: ../../src/topics/using-containers.md:15 5494ccdb1a354b2386c82bd9a6f0b6a9 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 42a48398d3ef4b03bd7395120f2cfb42 +#: ../../src/topics/using-containers.md:18 4cfa8fc2bb224883946d5f63b372de82 msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 d59387b433bc4ecfaf7e72026624db02 +#: ../../src/topics/using-containers.md:21 e16c1922527a46e28bb5d933614cdaf7 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 d963418ccc0b4803bbc758d718ccb5aa +#: ../../src/topics/using-containers.md:27 7498a71704be462abef71c42e6b83d1b msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 a224d1510c9e46aab23d8bdc03c349dd +#: ../../src/topics/using-containers.md:33 ac0689bff9db46ea8bff8cd35cde86f3 msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 0a82f8a45b0546aaac4c976dcc98014a +#: ../../src/topics/using-containers.md:44 c4b7da5575674ca3ae734424022ef090 msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3076,23 +3087,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 bc418a2a535e49359c4cd44b373bbe02 +#: ../../src/topics/using-containers.md:52 d24fcecc17d0461cbd8689067f770c0d msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 a799fba2322944cea00e413c08066536 +#: ../../src/topics/using-containers.md:55 833d4d3b3f0e4c7cb8b1d35cb9a78a7e msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 35379c6b972940bd8451f10b74dd793e +#: ../../src/topics/using-containers.md:69 50fc0573276e4dd4a47208ed81109991 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 2d5265525ad544a0b64ad2cf07aacc26 +#: ../../src/topics/using-containers.md:72 f72e10e746604421904057ddf7078d3e msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3100,44 +3111,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 e2521b89596d42f8a87a3207fd6c32f2 +#: ../../src/topics/workflows.md:1 ee126833f6014e378c7841c4048dae85 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 3676f23b63e142cb8e5715ae07216a47 +#: ../../src/topics/workflows.md:3 0325bd610aa747b0b657afa0c978a1eb msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 00725aed13a440ca8b3c4f9155fbee99 +#: ../../src/topics/workflows.md:13 7c901105cf6949909d87be5681331368 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 2e38a4f9072b4ad9bbb74f943d22084d +#: ../../src/topics/workflows.md:41 74138d0c2ded4311bf688df4a28387b5 msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 2b9f4035ea864b6db50c861a1819289d +#: ../../src/topics/workflows.md:51 1ec4773e7319414b997d746d1965ff56 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 28e9064780e7418a8e02a22f92e34404 +#: ../../src/topics/workflows.md:81 5f860dd70e3b435188c61a538e5de0ef msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 66ce14a10d2d4dc497d3ed71e11ed8b8 +#: ../../src/topics/workflows.md:91 a9c56df6dca441dfabda7fa54fbe56c6 msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 8dc00528c3d2426c8a3492a8191f1d81 +#: ../../src/topics/workflows.md:150 586d561ddf724319b3da9ae857828648 msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3145,33 +3156,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 f9ef5e258f7c4971a8543d1dfed711a8 +#: ../../src/topics/workflows.md:160 f3e80b1903534065a30323611c267e9b msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 324bc51071d743ea80124c23880ddc0a +#: ../../src/topics/workflows.md:165 6ed53c6f9fb94d4ab3d10532c605c46b msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 d8c13e01976b43a1af34c11a7bc36897 +#: ../../src/topics/workflows.md:167 3fcfdf43b0a049388634625c45e0b1bb msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 43910a8ab4484e529a17df418b1aedbb +#: ../../src/topics/workflows.md:170 49415efafae64f94b66cb46ca2bbd40a msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 +#: 4806a2ef982944e8b073fafd416d3d74 d45701eeaa6e42feb4ef79d2fc4af756 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 7ad12d67e815400c94080804b9285629 +#: ../../src/topics/workflows.md:180 155cd684ff304258ae374b2e13090e5f msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3184,34 +3195,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 457d5a31c79143acae2683d95d27f7a3 +#: ../../src/topics/workflows.md:183 d8bdb44011274f94b606277799a6fa6f msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 a2a73901bf634547900d08b9a1ac8889 +#: ../../src/topics/workflows.md:185 9e1d9bc2f83743ea9964ec418d225200 msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 f347d80e62384b14acf6423675e5359a +#: ../../src/topics/workflows.md:191 a1240eab3ef746cf82a2c5451042b888 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 2a845a4f3f98428fb82f3ca7ce038a6e +#: ../../src/topics/workflows.md:205 a73cdc43a8e44973808027c29903afa3 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 e2007c74d5f449a882809d6b91c010bf +#: ../../src/topics/workflows.md:212 4277837a9fd443378d5ca3d9252993c9 msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 7f5e53ee7cf94be2bff45ef64db28a24 +#: ../../src/topics/workflows.md:221 09b714af60ee4ecc8ab1b95eac8284dd msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3219,7 +3230,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 a0d076b7b8b048478580c99ef0c8429f +#: ../../src/topics/workflows.md:233 3e99a3be9265463daf74b00a21d89cff msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3228,7 +3239,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 7fd926c18ad548e98845e9b5134dd6f2 +#: ../../src/topics/workflows.md:248 1c4a959d43b74686ab801a26ef412b3d msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3239,7 +3250,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 789fbd47f8564cceb430ef3c0bc90e9b +#: ../../src/topics/workflows.md:256 55daf180336d4045ac0cc4c14af98cfc msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3247,7 +3258,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 45c4d0492d6143ca9cebe81e9b2cf3ae +#: ../../src/topics/workflows.md:261 5ae40eb04d5440d5ba882a74aa5b9708 msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3257,13 +3268,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 73bd3da2af8545928d5ea71d0f7454f6 +#: ../../src/topics/workflows.md:267 f93e9b776a4544018877b7a13399609b msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 15ce3d2700424f0fbb280d602ccebcf6 +#: ../../src/topics/workflows.md:278 0e587435e3884334bc51a4abf4b4d785 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3273,11 +3284,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 af4268f19202436eb0a7e8c6bed5e386 +#: ../../src/topics/workflows.md:285 81b98764289245c79f18fcff478f4a9b msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 94a4eadca6b949d79de2990a0150eee8 +#: ../../src/topics/workflows.md:287 9baddec4015f40ad82ea2dee30305654 msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3285,17 +3296,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 09c1619e8cbd4febbb637f7e99ad5890 +#: ../../src/topics/workflows.md:297 986c3dd9460b42b3b20e2d01ba1fbe51 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 677ea7a27eb64568ab3689142d6efe70 +#: ../../src/topics/workflows.md:300 4558f174fea445fd97b80d963fc74f43 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 097e6d47f9394e62b80110700492783a +#: ../../src/topics/workflows.md:309 532823a13154401090e9fee3e018fda9 msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3303,7 +3314,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e93affce8c104bf6977182047c1f1077 +#: ../../src/topics/workflows.md:314 7b6f46b70bac4f848a956ea160243621 msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 06c9e04ba890473b851240a0fa9c3b12 +#: ../../src/topics/workflows.md:322 3861b4a31f71471b97bf9dc18cc80594 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3325,7 +3336,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 0380dc1fe3aa48e4b62283b7b2a611d8 +#: ../../src/topics/workflows.md:336 a10c37f65ac14ef2a5971872bc9b8f9a msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3334,7 +3345,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 49b251f7a313492ea60504b00109e526 +#: ../../src/topics/workflows.md:341 34175f932716406f836840732618caee msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3344,7 +3355,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 7ee55702d7dd4679a24ff052f6f0cbeb +#: ../../src/topics/workflows.md:347 0d132dc39cdf4818bc8e20132073f669 msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3352,14 +3363,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 85d7e2e270874aa6b9f477cec0f48154 +#: ../../src/topics/workflows.md:366 9f8c45f077974cf79612ee83df3d152b msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 570e94513c984c09ad6aa255f534216d +#: ../../src/topics/workflows.md:383 435f80d0599b4d93ae1339e8c7bc020a msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3368,7 +3379,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 a107258662fb4bd4a9a3d8754e34d1e9 +#: ../../src/topics/workflows.md:389 d39b024a1a8d4eae8d7fd3c929a782e9 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3377,7 +3388,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 fc1a6502d831458ab8371a575cea47e2 +#: ../../src/topics/workflows.md:394 3cbbe074843d4306b762d2fbc6fe9850 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3385,11 +3396,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 2d10806bf1ce4e26b92adda61efc0862 +#: ../../src/topics/workflows.md:398 7118b6e09b9f44129c7d98d90570f2c2 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 046c5e134de94b629cc22d416f3c9182 +#: ../../src/topics/workflows.md:400 70f3e73ee3714f22ad6ee43dd5ece703 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3400,7 +3411,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 52fa22d3277940049fbb589a3ea73433 +#: ../../src/topics/workflows.md:411 279495257ead4a4fa725c7d68c504162 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3408,23 +3419,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 6043beb96c2c49648011ec556aa9e986 +#: ../../src/topics/workflows.md:415 86d1d742bb5c4a9898aa573ce648f0ec msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 5ac4310515124e2986724425bed5651f +#: ../../src/topics/workflows.md:421 f4987847f46e4a2db54127ec7ebcadf7 msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 7958e91d5c2f4046aa9d2070a900f9ae +#: ../../src/topics/workflows.md:429 80e7c22dfe4d40749f2e9c3bf02bf8bc msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 2db234d776fe4fd38bab07245dcb783a +#: ../../src/topics/workflows.md:441 e930bb5d430a41d9b5bf49e473dd2ed1 msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3432,7 +3443,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 7cfb17230e284ee7b6e2a00efe8eeb74 +#: ../../src/topics/workflows.md:445 4076e9eb67ed4bd5942f089e394bad26 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3440,59 +3451,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 4311ac98544e4fb0b2f4b24985710a01 +#: ../../src/topics/workflows.md:450 1b44092e87b840de8f1d022676d0990d msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 780f9c72e6c34c39918642c7e2477355 +#: ../../src/topics/workflows.md:452 a8afac626f5d4240a57267085b9bef26 msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 cc4a7316db644b438cbaa181ad9ef2d3 +#: ../../src/topics/workflows.md:458 0896efc674bc402495c6e73c6c352523 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 dfc461a03fe8487794837904febb8b63 +#: ../../src/topics/workflows.md:466 91a53d918d4b47bdbe0b0a6d4adfc0dc msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 1e83485b00b64dfaba897bd8d772e0f0 +#: ../../src/topics/workflows.md:469 8325682d51d8421b9ea507f424f71e73 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 d0321d6805ec4d3abf3877d02a0a417f +#: ../../src/topics/workflows.md:472 503d068602d8477a820b91d835fa3f28 msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 d7d77e807b3048c7bdf89558f76804cb +#: ../../src/topics/workflows.md:480 4e768b91eb274a5cb157f1e3fe2f85cd msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 8d9b8be147fc4a71922dde858842e543 +#: ../../src/topics/workflows.md:483 18ec5231b7bf4c9ea59361b325fcdd01 msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 34b7705416a745a6a42e6d402c0757ed +#: ../../src/topics/workflows.md:489 87fd118dc2774cf08db0a3ba56520da5 msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 257adcee9da64d5c987f3b64efd20ab0 +#: ../../src/topics/workflows.md:491 8168ffcb23124b3f839a9862a7ec0958 msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 fa6ed5d0c14f42f4aa3c5144648db22c +#: ../../src/topics/workflows.md:497 37c222ea14904fd4a8fa93a1e0103239 msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3510,7 +3521,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 333e8ce458d54de394526769f96d12d2 +#: ../../src/topics/workflows.md:509 d392813fc6d14851a294a391426d41f6 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3518,38 +3529,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 b819e8a5df6e4fa495924095709669ef +#: ../../src/topics/workflows.md:513 652155460eaa42b6856c16cffdb845c0 msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 f1955468a1364d44a930db77c9c4b495 +#: ../../src/topics/workflows.md:519 6313cb377dc249e0b2262a3fe732fe32 msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 8c3b9b645a204d02b2c73a205e8ec296 +#: ../../src/topics/workflows.md:522 11f73cf24fb044e3a3afb3adb6137708 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 4d88b9c186cd4502adbf752e8a70b6ce +#: ../../src/topics/workflows.md:524 def9e62bf73f49eebce09677954e2a92 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 9927673564024ba5833b5ac271737857 +#: ../../src/topics/workflows.md:527 200dfe47d09d4b0b9e4acf29b7e038da msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 84f4ed7ce2004742b8db9087104a469a +#: ../../src/topics/workflows.md:566 858bda7fb6524e9dbfb35596ce6a6d07 msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 2b5f9757adca4490a149c7f45e14fcb5 +#: ../../src/topics/workflows.md:573 28897819504247a3a6cf9a9d9476b63b msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3558,7 +3569,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 0418de720813442f81ecff293c9448b5 +#: ../../src/topics/workflows.md:587 4f8fd11e29b048e1851299002c3a48c4 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3566,62 +3577,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 524eec63be8248ae982939c975ef50a2 +#: ../../src/topics/workflows.md:607 ed33196347d949eda752a081c7af4657 msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 5e99f9912cc549a7890e2934425eb943 +#: ../../src/topics/workflows.md:627 738c67568dbb4f2bbb5756fc5e727c01 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 b0121ee087d6424fbb0ea5957a7b0b8c +#: ../../src/topics/yaml-guide.md:1 19b016a1fec14056a9812c1c195c7c90 msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 49e9f6b3a06840289decf3f557860f87 +#: ../../src/topics/yaml-guide.md:6 a513367d60a74f559339c05d8ef10eb7 msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 ed9eebec0b3d4b72ba65507d37757a37 +#: ../../src/topics/yaml-guide.md:13 5e30680941164047a47f98417e916188 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 bf9b255a24a84f3ba989a223492b8f41 +#: ../../src/topics/yaml-guide.md:16 ca02f2bf1d754d5190f296674245b936 msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 e79fa0b7f8b14810a3a20908ef92bc55 +#: ../../src/topics/yaml-guide.md:18 466615194bb541fdbe2e6515b50531b3 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 290e2035f903417cbecb5dc5f09d6ebe +#: ../../src/topics/yaml-guide.md:19 33e664d59a30407891336db290a8a5b2 msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 d420730151534f1a89076588a3358f09 +#: ../../src/topics/yaml-guide.md:20 3e52ab079dcf4fc6a3f052a517f4d31b msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 a6b5378bbe1e4bee9e37a765bddf75f7 +#: ../../src/topics/yaml-guide.md:21 abcad6b7d37a4342a90c2d5952ea1232 msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 6e4d9465dc2b454d96b02d7ad1817795 +#: ../../src/topics/yaml-guide.md:22 500a489e4fae4d1abaa8883f632d1a24 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 a649d4af5f434dac9395e013ec4836bb +#: ../../src/topics/yaml-guide.md:24 546c1ef51a63487c91c98059dd46b0cb msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 446190a298834b73bda068286e8490cf +#: ../../src/topics/yaml-guide.md:26 72b4262833054edd9efe6078381de654 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3631,7 +3642,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 2f35c012ff174721bffe66a3f58a804f +#: ../../src/topics/yaml-guide.md:42 7b7e8242660744b791ba3868e4ed7e37 msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3640,7 +3651,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 43127c98c9d94aedac61cee67929c1a6 +#: ../../src/topics/yaml-guide.md:51 492d994a541c4c948fb5da9041153bcf msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3651,28 +3662,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dc4fe561203c4c38a9caea5bd6eff2cd +#: ../../src/topics/yaml-guide.md:61 e2209269db394f3988f18b147a57677c msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 f924e4896db2424d99ce8c9da14c599a +#: ../../src/topics/yaml-guide.md:63 e15c39c65aca47f690264d8008463bec msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 bf7646f5f925485c842a6d34140e40b8 +#: ../../src/topics/yaml-guide.md:76 afa546fcb7fb447d939d4a167f206f79 msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 c483e61dec8949fa96bb893d422888a0 +#: ../../src/topics/yaml-guide.md:79 7dd375e0fd964413af4957396d2a0474 msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 85fcb523d0e34a499eae04d304887f7b +#: ../../src/topics/yaml-guide.md:81 af8ef039a64a4c0783d7229dbdac65ef msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3683,7 +3694,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 83d47c8736a34f3cbf09e3997845e4f4 +#: ../../src/topics/yaml-guide.md:104 3ce968cb39a443059f6a828b3c8c2f33 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3696,11 +3707,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 c698fb3d37bc403e9aeb679b8fc0e15e +#: ../../src/topics/yaml-guide.md:127 3c2f48a8e616400b9a8ffb4b6f7efc9b msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 ae8af2f0eeda4aec97201211dfa965c7 +#: ../../src/topics/yaml-guide.md:129 c432b1656e0e49ef87aa3d6e42acad84 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3711,26 +3722,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 2ee87aa465cd41fda16a61e242f8c9d0 +#: ../../src/topics/yaml-guide.md:146 cac5e52767f74ce98693e2a19ee1eb0d msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 0a6fd4469ff24b61b3ad001b09eead18 +#: ../../src/topics/yaml-guide.md:167 101666907f8b4fb994e25ceffcf04a13 msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 b96ba19bce9341d39c46054e1f10fe8f +#: ../../src/topics/yaml-guide.md:169 5461960a469042a487b89e440f856aea msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 903f30af3d0c45cfb61063936a8097a7 +#: ../../src/topics/yaml-guide.md:177 e31349c164c84a9da46e2fb1861793df msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 ede8db7c0a58432e8a1c416e937a06d2 +#: ../../src/topics/yaml-guide.md:184 49a0b3dfdc9e4d58b6bc966db979ace8 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3740,52 +3751,52 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 c8b53615476a4a1fbef2420d93bac94e +#: ../../src/topics/yaml-guide.md:194 e08ec8c473e847f98e8a18b9ca0f2670 msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 ea03cb5525cc491f9feb5c4780b38fee +#: ../../src/topics/yaml-guide.md:196 6ee7bfb4a9e04dd19b5180bca5b02705 msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 92fd3a5e31714eab859dd630af2e78cf +#: ../../src/tutorials.md:1 42614ab7ba1546f89abeb8f48991271c msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 de660ecdb5b44c97a0e519d00b232497 +#: ../../src/tutorials.md:5 b8df5b8393ed4d869c066640fe83ec7b msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 5afc1e1288e74ed0985e61e5164479c7 +#: ../../src/tutorials.md:7 5b9aee5af41f438b9f4208294bf97f4a msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 862dc7ac81e54b1fb3d4c2f961b8810e +#: ../../src/tutorials.md:9 a71d3022dcfc44979cca4655ea51ad42 msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 e2c94c0e1c7048d38cd7aa2c465a859d +#: ../../src/tutorials.md:11 42b5a982e86f46dfbfcd7bfcc99d72a5 msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 b63253780f51467a95207d820d13ac39 +#: ../../src/tutorials.md:13 12dc402d053044b78d69927dd391fe9d msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 6d06ca7ed5df4560aaed286f4fe33928 +#: ../../src/tutorials.md:15 687c20e2e4bc4f869c7ee9390e61476a msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 5448df4a6a8f431d80e269bcd480e19e +#: ../../src/tutorials.md:17 a975fbb3ea7d467881ce0245de538295 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" From 354dbb22e2481aa41a1c14c47fbeec7da3440722 Mon Sep 17 00:00:00 2001 From: "Bruno P. Kinoshita" Date: Thu, 26 Jan 2023 23:37:13 +0100 Subject: [PATCH 043/179] Patch MyST to keep the context needed to translate Markdown files --- src/conf.py | 82 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 82 insertions(+) diff --git a/src/conf.py b/src/conf.py index 921ced1e..bcfe20a8 100644 --- a/src/conf.py +++ b/src/conf.py @@ -238,3 +238,85 @@ gettext_uuid = True gettext_compact = "user_guide" locale_dirs = ['../locales/'] + + +# Patched MyST parser +# from __future__ import annotations + +from docutils import nodes +from docutils.parsers.rst import Parser as RstParser +from sphinx.parsers import Parser as SphinxParser +from sphinx.util import logging + +from myst_parser.config.main import ( + MdParserConfig, + TopmatterReadError, + merge_file_level, + read_topmatter, +) +from myst_parser.mdit_to_docutils.sphinx_ import SphinxRenderer, create_warning +from myst_parser.parsers.mdit import create_md_parser + +SPHINX_LOGGER = logging.getLogger(__name__) + +class MystParser(SphinxParser): + """Sphinx parser for Markedly Structured Text (MyST).""" + + supported: tuple[str, ...] = ("md", "markdown", "myst") + """Aliases this parser supports.""" + + settings_spec = RstParser.settings_spec + """Runtime settings specification. + Defines runtime settings and associated command-line options, as used by + `docutils.frontend.OptionParser`. This is a concatenation of tuples of: + - Option group title (string or `None` which implies no group, just a list + of single options). + - Description (string or `None`). + - A sequence of option tuples + """ + + config_section = "myst parser" + config_section_dependencies = ("parsers",) + translate_section_name = None + + def parse(self, inputstring: str, document: nodes.document) -> None: + """Parse source text. + :param inputstring: The source string to parse + :param document: The root docutils node to add AST elements to + """ + # get the global config + config: MdParserConfig = document.settings.env.myst_config + + # update the global config with the file-level config + try: + topmatter = read_topmatter(inputstring) + except TopmatterReadError: + pass # this will be reported during the render + else: + if topmatter: + warning = lambda wtype, msg: create_warning( # noqa: E731 + document, msg, line=1, append_to=document, subtype=wtype + ) + config = merge_file_level(config, topmatter, warning) + + parser = create_md_parser(config, SphinxRenderer) + # TODO: In the first pass, the call above will use MarkdownIt over the whole document, + # populating the ``.md_env`` correctly. Over the next passes, from transforms as + # ``sphinx.transforms.i18n.Locale`` it will create a blank new document, as well + # as a new MarkdownIT parser but using just the Docutils document that is being + # translated. As a result of this, the translation has no reference-links, and it + # gives you the translation without resolving the links. Here we just re-use the + # ``md_env`` dictionary that contains the ``.references`` populated in the first + # pass, fixing i18n with MyST Parser. + env = {} if not hasattr(document.settings, 'md_env') else document.settings.md_env + parser.options["document"] = document + parser.render(inputstring, env) + document.settings.md_env = parser.renderer.md_env + + +def setup(app): + """Sphinx setup callback.""" + + # TODO: Here we replace the MySTParser (that replaces the Sphinx default parser...), + # with our patched version above. + app.add_source_parser(MystParser, override=True) From 43a5611de823f4160cf8bad6d02d045d5ab9a4b9 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 27 Jan 2023 11:19:15 +0100 Subject: [PATCH 044/179] Revert "also fix the Spanish translation" This reverts commit 8efb720d8ee310a313510607bbeb5bc35195f9d2. --- locales/es/LC_MESSAGES/user_guide.po | 1289 +++++++++++++------------- 1 file changed, 639 insertions(+), 650 deletions(-) diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index 523946d0..3fa6daab 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 17:03+0100\n" +"POT-Creation-Date: 2023-01-25 16:53+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" "Language: es\n" @@ -23,24 +23,21 @@ msgstr "" #: ../../LICENSE.rst:2 dcdc2e8da0ec4d9e9453601fdd83bac5 msgid "Licenses" -msgstr "Licencias" +msgstr "" +"Licencias" #: ../../LICENSE.rst:5 3e165520ca56481b8f8d494a8d471de3 msgid "Instructional Material" -msgstr "Material didáctico" +msgstr "" +"Material didáctico" #: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee -msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the `Creative Commons " -"Attribution license `_. The following is a human-readable " -"summary of (and not a substitute for) the `full legal text of the CC BY " -"4.0 license `_." +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." msgstr "" "Todo el material instructivo del proyecto Common Workflow Language y los " "cambios en la estructura también están disponibles bajo la `licencia " -"Creative Commons Attribution `_. Lo que sigue es un resumen" -" legible por humanos (y no un sustituto) del `texto legal completo de la " +"Creative Commons Attribution `_. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del `texto legal completo de la " "licencia CC BY 4.0 `_." #: ../../LICENSE.rst:12 b7a7a0fb40344fe087c1cc3ec19308aa @@ -61,38 +58,38 @@ msgstr "**Adaptar**—remezclar, transformar y construir a partir del material" msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.rst:20 8bc6672f4a33428296226112a1be6fbe +#: ../../LICENSE.rst:20 2173e2af49be41ee97a74c4e879faf25 msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " "términos de la licencia." -#: ../../LICENSE.rst:23 be38276e7b374f57b9997391bf898a62 +#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" "Atribución — Usted debe dar crédito de manera adecuada(mencionando que su" " trabajo se deriva de un trabajo que tiene «Copyright © The Common " "Workflow Language Project» y, cuando sea práctico, con un enlace a " "https://www.commonwl.org/%20),%20brindar%20un%20%60enlace%20a%20la%20licencia%20%3Ccc-by-" -"human_>`_, e indicar si se han realizado cambios. Puede hacerlo en " -"cualquier forma razonable, pero no de forma tal que sugiera que usted o " -"su uso tienen el apoyo de la licenciante." +"human_>`_, e indicar si se han realizado cambios. Puede hacerlo en cualquier" +" forma razonable, pero no de forma tal que sugiera que usted o su uso " +"tienen el apoyo de la licenciante." -#: ../../LICENSE.rst:31 f00d5c3846034c2ea116c2f74786d9fc +#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" "**No hay restricciones adicionales**---No puede aplicar términos legales " "ni medidas tecnológicas que restrinjan legalmente a otras a hacer " "cualquier uso permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.rst:35 1798d65c10104040923c2fea2199bab2 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +#: ../../LICENSE.rst:35 f6aae4a5cd0547118c8a3240ca2b4be6 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limit msgstr "" "No tiene que cumplir con la licencia para elementos del materiale en el " "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.rst:38 c65198b804f8436ba783643d51bc72d9 +#: ../../LICENSE.rst:38 a40c173be35b4c1b92e83f42bfe2382c msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" "No se dan garantías. La licencia podría no darle todos los permisos que " @@ -105,28 +102,20 @@ msgid "Software" msgstr "Software" #: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" `OSI`_-approved `Apache 2.0 license `_." +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." msgstr "" "Excepto cuando se indique lo contrario, los programas de ejemplo y otro " "software proporcionado por el proyecto Common Workflow Language están " -"disponibles bajo la `licencia Apache 2.0 `_ aprobada por la " -"`OSI`_." +"disponibles bajo la `licencia Apache 2.0 `_ aprobada " +"por la `OSI`_." #: ../../LICENSE.rst:50 4ee4d68b90fe422880da856cd539b982 -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT" -" WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the" -" License for the specific language governing permissions and limitations " -"under the License." +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 271049c39d294b11b9bd94cb6be2857f 61af90891e2d4542b5f45fb3ec6480af -#: bf309fa01bed4355bf052ae4afbf9a67 +#: 5ad4be9b62d54c95a913795b514676fd bdd540403a5746ff99edf2dcad0e3122 +#: dfc7702e073140c985cf47272a20214d msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -135,30 +124,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 055f0e960450410585b59760ef3ad284 6294af2e32e04207a87399c7f0780011 +#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 6428125fc43c43bba8518ece2f5d150f +#: ../../src/episodes.md:9 3060770b3bef41d7bcfcdfb413d7689c msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 ce8fade1e88e4b03ac0d3fc71d16f844 +#: ../../src/faq.md:1 48bb9f628b344ba1a3b67ae1cb264e3c msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 9e7483b53a984b689964c69afcaa7123 +#: ../../src/faq.md:11 7e3684e9672643738846756e1ebafd18 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 8c5a89257ef248cd99cba303713e5082 +#: ../../src/faq.md:41 187ceabb7fd9480bb8cf0f2da47f65ef msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 9e80d8eeefcf4a9d95fd5fe9d9fa124a +#: ../../src/faq.md:43 b548b76bcc85420a9b30792386105139 msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -166,94 +155,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 c2e5f62490f940aab19166403a840597 +#: ../../src/faq.md:59 9ce692b78ead47e4b0f8cdae8837d35b msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 ffcffabdf25a4c398e8e53bc817ea769 +#: ../../src/faq.md:61 6df1201c159343da9e7515379980d6a0 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 c8a6b85cfca542ccb042a0269294e5e3 +#: ../../src/faq.md:82 f9ab1d0dc1c842b6abb5385268c1d3bd msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 98f583e5e36941c1856d719a16e58e4a +#: ../../src/faq.md:84 9f6a84ab6a9343b6ad7db826f8964362 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 fb9cac0954474b5284793330b7424949 +#: ../../src/faq.md:86 fa50e4fa990b42d1ba4c0f4ae1e5caa1 msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 cc45d609de1f423db86d58eea933e132 +#: ../../src/faq.md:89 3a871012fcfd4f3ebeca0cb86ec93435 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 27ee63895cb14321a1814f4372d3180f +#: ../../src/faq.md:95 d954edfff2584288ac8c600733070d2e msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 f1c841980f3d4364a2158a4eb2f0d257 +#: ../../src/faq.md:97 af6b1e37d6be4450a761854480ec9aab msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 6d53d38ddcf244fb997db37eae7fcf90 +#: ../../src/faq.md:104 31f4a2d43062493ca64c648f80afc8e9 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 b6d60d66f3744ab3aea1b175ecb23d4a +#: ../../src/faq.md:113 41c54e71b6cd4f63b2a619a515240d34 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 cf4fa3ae602841d393b4143e9f6f5e82 +#: ../../src/faq.md:115 8edc3541ad134ab5a1d23c724f1f0a4e msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 41a3c9aa55c5406f9b52af2243c79ccc +#: ../../src/faq.md:135 ac0ea81eba8842a18801ab03cbf80a57 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 3b8eb247425a4a708f51c08cf258e30a +#: ../../src/faq.md:138 52be1a5640234feabe958ff7ade33653 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 388a6e091a054dc48afc928f46dac7b7 +#: ../../src/faq.md:140 c6db734d5aef4f4f99676bdebf9c83c9 msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 28c59d12156e44ea833822fd3ecaf824 +#: ../../src/faq.md:165 a9f7b47c0dd741739795da39bf114879 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 8267843ff5c940c590b10047455f2102 +#: ../../src/faq.md:167 e3fdd9228b924905a4a1f4b2b7ad7159 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 6e6f55bc915e4cceb8e360544d6b4ae5 +#: ../../src/faq.md:188 3f7cda1437cc48f18745a827ebb74582 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 1bc80953bd60405082a10a7798c1413d +#: ../../src/faq.md:190 5aeaba2cae64442e816bbd458aee833a msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -261,22 +250,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 a6cd4bf4dc314e66a951f7f1227c7bb7 +#: ../../src/faq.md:194 5af827a402834978addd82c70be6b5ab msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 7ab2440a92aa44b09e8a324cd67ca728 +#: ../../src/faq.md:196 6d69e42bd8e443c4b19d80807c7efd6b msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 152a529dfa2c42c1b6f0083589fa5aeb +#: ../../src/faq.md:199 404640397b6e40c2a2cd5cf85ab3b1c0 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 b278c137167d4b958c099c0509edb79c +#: ../../src/faq.md:201 1682c2486e224770b62269709a8663cf msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -285,25 +274,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 f0b38723838f479d9db8eb5142d28a1e +#: ../../src/faq.md:229 9078fc009bc145808813c9cc2b734b58 msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 fc1e4a808e85422cbb4d128c5a1f4d0c +#: ../../src/faq.md:231 d4b5a54a400c409cb7984428f6a03ec8 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 d74964c9d19241848f4dd92a201e201f +#: ../../src/faq.md:247 9e8dbee6e8f84d08b1a54fffa06394ef msgid "" msgstr "" -#: ../../src/faq.md:248 859b8e18e05a4c3285fb20bbb44c1ed4 +#: ../../src/faq.md:248 1d846bfb5f054d09a4afad1da8e4b642 msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 eb6e932924a54afd9114c629b2d0e93b +#: ../../src/faq.md:250 2d0e95fec8084787b734388d60188574 msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -311,26 +300,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 31d70b41ddf042f6aa530b7bd6daae73 +#: ../../src/faq.md:267 eccc4a364330470fa474dcaaa3433390 msgid "" msgstr "" -#: ../../src/faq.md:268 9aa3ff8c957b42c8a30f37167a8177fd +#: ../../src/faq.md:268 e945f6a337af4e4686bed482a4fe6c39 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 777ac7f6bde2470b981efc91feb01c81 +#: ../../src/faq.md:270 8a3efaa0ad1548428bcfd6e01d135cdc msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 8647071efc0548a1807c03fe8a4ee54c +#: ../../src/faq.md:322 cdab644adc5643708870fb08c06cbfca msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 4404233183124085990c44793a6b25f6 +#: ../../src/faq.md:324 089a5a0b076b44aeaab4d69ee3c79f97 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -339,77 +328,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 c5eecacfa07f47649f07ef9d888f4c5e +#: ../../src/faq.md:342 561172559c6f41a68819608fd9e58bb0 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 1efef04061fd48f1ab39a99508b5bc0b +#: ../../src/faq.md:344 c5ee4946d2e840abaa3dc796a62652c7 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 57e8ace8e8d64e7a90510e1ccea69612 +#: ../../src/faq.md:349 4f2069a2113c414db18eca95550e9e09 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 138606e8d7be40bb960f278977f9107f +#: ../../src/faq.md:351 31f3390e6771414ba7bf57c044c4b0c4 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 d0f668dc78464469a9f2bfc61a90aa76 +#: ../../src/faq.md:359 3b77ce4930ae46d5be9f6965e8c54727 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 f2a49a7663e1456cac6b2eac0c46c662 +#: ../../src/faq.md:361 06f36bbe4d3840229b7374f27b86ae80 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 eefe4adebdba4063af0cac3ab5d46442 +#: ../../src/faq.md:363 3cb2f70d00274a4dafd972ccd8c519c2 msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 526f2816123a43ecbcf09c46904b4b5f +#: ../../src/faq.md:371 093a1529262043ef84a99675054938e0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 0ecf267c5f4d4557ad0d7ddef2f4b5e6 +#: ../../src/faq.md:373 45b6d9acbfaa47e5984184f7da554d0a msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 935a253376854d12928f00c2870ed4c0 +#: ../../src/faq.md:375 5705c9bacca5405ca6f14315a5575db8 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 bc6c0bf679ae48e7822add7ab2cda220 +#: ../../src/faq.md:384 82bfc285b59a439ca97d3278997f0fce msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 a63643806a2a4eee8ebd3502fd6ce2b5 +#: ../../src/faq.md:396 181d5130101d45ccb22aebae3d154c2f msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 fc54964adcd648948d7baff02f47598e +#: ../../src/faq.md:410 e864390b5ddb423aaa10e9d33d257dc1 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 aabc495306a149fdb15835ae1df93c42 +#: ../../src/faq.md:423 fe637c32fb15427a9045679b5da42ec5 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 2930faead8be45a6b9adbf51dcdfef6e +#: ../../src/faq.md:436 1f8004b9df8547029d82e57f9abdc979 msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 f885e4716a8d4de0b25d2d3356789672 +#: ../../src/faq.md:442 70990dc5a0034099921ceb89c89e2dcc msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 6487ff3c19c944eb8257b2cf60d0aac7 +#: ../../src/faq.md:445 f679e26f18d9455f945fd13361a9c906 msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -418,11 +407,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 4cbacce539ce4f6cb5bb8ccf1574640c +#: ../../src/faq.md:450 fcd0273dbdd84e728cfd8fbe239f2a01 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 27321576de714cd5b82c67f59b2e3e6f +#: ../../src/faq.md:452 173ddbd1e7c64927a8dcb12a2a2140f8 msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -433,22 +422,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 6afded7ba21247099c9bfcedf40c9171 +#: ../../src/index.md:1 662fe273e2fb4042b688512955e450a1 msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 17c386e7cd25496784207140f9876b90 +#: ../../src/index.md:3 a15b52205f0145feaac298510e4d678a msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 3bfd9bcf826a4400935dfad338612b12 +#: ../../src/index.md:7 512aa0c7166b429e8116f71eef007f79 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 4b38f1439da44ebb967b5b1e3df8f78a +#: ../../src/index.md:9 b1b19e17a18540939cb3bb7f8a700cab msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -457,11 +446,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 a4a60a8d010448b0b8ad1e05cbc78f2b +#: ../../src/index.md:16 d58b36ac43ac44139897be752fbb1f87 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 e23e00e89c81410ba8381fd81bc73b3c +#: ../../src/index.md:18 6726cf3585a646a8b4cbeb543cf84a38 msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -469,7 +458,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 7274d92e678a440eb0d3ae3109f4157a +#: ../../src/index.md:23 2e504aa7c46a426fa959e7254e9a84a5 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -477,15 +466,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 6ad5f2d254a24ac1b3faf382d08b58aa +#: ../../src/index.md:28 e7be0df0838b432d9c7f296d777f120b msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 7208cbccb84d45d58c7d5becec74b7d3 +#: ../../src/introduction/basic-concepts.md:1 173e0816db20432c8d9dba1de5393dee msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 8b9809abb49840b195a89943ba15f78a +#: ../../src/introduction/basic-concepts.md:3 30eacc583f6841719e2142d283811d97 msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -496,18 +485,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 9a934bf0848b438aaef7c4f00e0f2901 +#: ../../src/introduction/basic-concepts.md:10 791b8f38a14147bbaa174c7eb595f17e msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 5a299600dc304fd886b7153de1a706f7 +#: ../../src/introduction/basic-concepts.md:21 1a3989dcbb9844b39d84bf6df6b352ed msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 55f7696f07d64277ad1b39d283175b37 +#: ../../src/introduction/basic-concepts.md:25 db1bbc6e980f404f9f3fcd08e92ee9a3 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -517,18 +506,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b854ca0af98347d2b66e74754eb92a50 +#: ../../src/introduction/basic-concepts.md:33 acc7887c65974114996f700a38a7eccc msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 d9785269c51e4902bf3a70e917d33238 +#: ../../src/introduction/basic-concepts.md:37 d2476d9bcff44f21b8d84a3a0d87a246 msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 b57a31b8d26545d1823fcd1fa2c83316 +#: ../../src/introduction/basic-concepts.md:39 f86415e4d78e48c4a8a76ced81221b98 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -537,24 +526,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 4e264b1a40bd4935abb5bdeb75fa5c64 +#: ../../src/introduction/basic-concepts.md:44 c5524d73708c4c779980528864506fd4 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 791b02bb1ee6459d8d8332fc2dee353c +#: ../../src/introduction/basic-concepts.md:51 ac46a9f8850a434bac5bc2b41ee6294e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: 17300bbe695044e7b8917d23bd0aa597 +#: 9bba7c4f783942e4a299603430601363 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 526614f195614818a614fc9a576e7cb5 +#: e2140e0f0e7747ef8383887c20a7945a msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -563,39 +552,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 7b47991653054f2d9f49a91720754abf +#: 15bf490724cd46dcbcfab44633c5a9a2 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: aa8838c0ee0a4b4285cb1b5dc6eb5d31 +#: 51d52d051e654a8395239f88df7c9d8c msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: 457c73a37cb143d98005ebf6e67f5bf1 +#: eb496cc818524fa7bae5a22ddd00a19c msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: c28057f3b7814f8395dbc3ad54d5f6f9 +#: c4a22d12e7f149ff901d27de32b9361d msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 83afed0785cd4b0bb86863c2841ce982 +#: 7618de899a7043989d77baacf62eb7b2 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: f332864bcc1e49d582a82f3d721ff3cf +#: 6f1544a220664b79b04bf008058b5a91 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 3005c6d669de412ab7f8e30d00752a20 +#: fbd14ac9a2f541478a320ed4cbc69e13 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -604,7 +593,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: 2e4041cb402e4054a53ea5890b938ac1 +#: da4dba50d25d4533b3dbb92f54d32a30 msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -613,7 +602,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 972f9a1e64394a63be3258d3af0b1d79 +#: ce11c9f8d65c4268984d0384d95144cc msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -623,7 +612,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: a572f0789084402fb2d216ac845bbfdb +#: 3a201aa497e84f70855bb2251e7e3281 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -632,24 +621,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: c7c5c9a1e98e47c0a5a6dfa69e96f921 +#: b78f7fa2be1c4bb090f6da895457ad1e msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 357d42768e794286bf5463ca5850a7ed +#: f7e95d264ffa4e2db0864faccd9e5a0e msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 61966aab989744c1b9b93f7751f35ebc +#: 3f1e5b01e49a4dc1b1c99936a4589afc msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: e14a2082d2c44f3690a07d3cee5b13d1 +#: 03c3048f38ae4938a484cf02001877b3 msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -659,7 +648,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: c128a76992e04d20bcc3edae8b6c0bc0 +#: f9715b5ec65c405c849bb030c1927060 msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -668,12 +657,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 42953a3d591c48c6b4e80e9ea4b97bb3 +#: 442662f50e9e4620970ce32b1b127969 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: e3762a763ba24571a9627efafe172441 +#: 2b34c786af3840e88f29d214e19dc837 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -687,7 +676,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: be8e01a012ed45d6b7e4e6aab1afcc32 +#: dd6aadff8cf54ce78ea6b317afbaddb0 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -696,7 +685,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: cf31aca4294d486cb0e25c6436996d17 +#: fe7f1f0b28434f8aaf0f6ac6589a83f0 msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -705,71 +694,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: cc7adbdc66df4aeaad1429f7268c90c0 +#: d10cf45b3c7f49dc98bc0e5d1246f224 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 71beb059c9e54a9ab5430f0dc44e07ea -#: 84679c5b03a3469294de849d9abe0a82 fd690fdd46344e0e8d9fc546f6d4013b +#: ../../src/introduction/quick-start.md:94 332b6e8b831e4bc5aed3745938230a57 +#: ce7fc63b808d4499b9bf9828c2dafe35 ebf339ed376a4d3b89b15b4d5afe593b msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 89ddaddb64f64b0c86c7e89da0edfaae +#: 8badec9987ba40609cf1f626172b2b2d msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: e920a824207746ffae63242d33137ac7 +#: c75a8b4bf0e24781bf6713cf6f013cd1 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 51d619152aa44651889ff2006c8f5800 +#: 79b146ffe6d74e1b8f6019251dc4b7c2 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 88f3f5dd8aa6401793b89e8de3b8c7a7 +#: 07cca9a33d8f4b77ac6ad35ca8b95655 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: f1f9ee90d07c4381a8bb0851bdac231e +#: 31db11c8ddf2423192a8b2063b3e91c2 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: e3b710dabec2482d8ec1072d64d4e1f8 +#: d81dd96143ea444aa78ff45cfa0584b3 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 418699fcb6c241dcbeeed81d82e9f84f +#: ../../src/introduction/index.md:1 c54984605872472190ae7771809a20db msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 28b6521a55aa4ab190ca998a59c52609 +#: ../../src/introduction/index.md:3 01a237b8ec2f46c9acd31d142591ce75 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 0e4969399eda48b98d883a3fc1540633 +#: ../../src/introduction/prerequisites.md:1 3fb9888b666945eab1e3ff109646c574 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 6d59f082157b494ebcfff2f649abc524 +#: ../../src/introduction/prerequisites.md:6 5fb0486762354f93853fff209f835c08 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -779,11 +768,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 2b83beccbc1b43969b705156b9c29482 +#: ../../src/introduction/prerequisites.md:12 5f1e7a608e0b455196d191c845a5c98e msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 594fe5e0aaf0499ebfa9218aaad4d08d +#: ../../src/introduction/prerequisites.md:14 7ba4b5c51be24f5392949d06ee42e018 msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -791,29 +780,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 f69c7c75a36048f5af0ed1b56df9320d +#: ../../src/introduction/prerequisites.md:19 e2d3e6dd13b14d819a504c35da6fe8e7 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 f28638ffb8394ccead4ac52f30adc627 +#: ../../src/introduction/prerequisites.md:21 91251d1f0efb4d4cb083b4517ff3107a msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 8993d7d5c8d24fc5a9c7005800c0a1f1 +#: ../../src/introduction/prerequisites.md:24 6ad263e267514c5fb05794d3d76d418d msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 2073109799e748d68304f5558c82b105 +#: ../../src/introduction/prerequisites.md:25 8a3bfd72dccf4a8c874a96aebcbe5cb7 msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 9fb2c31bd36d495786397c7a7d6b3417 +#: ../../src/introduction/prerequisites.md:26 5195706d9c6c4573aff135fd539759a2 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 43e1957537034c5886574118fc2533da +#: ../../src/introduction/prerequisites.md:29 9c4506915e4c40599527bc1d2b18645b msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -823,11 +812,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 e3a3d9b94b1e44c48f298dfcdcd27104 +#: ../../src/introduction/prerequisites.md:35 37d9eb784ec1425786158f98e3f63890 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 8a385803ed3945ff81d38a3543a69d94 +#: ../../src/introduction/prerequisites.md:41 572f493a985141a1b92dafbdba92790d msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -835,7 +824,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 bf56727d93994d3995b0af0c68c2c583 +#: ../../src/introduction/prerequisites.md:46 9606d3c4849f4b17b2e55a298210f055 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -843,26 +832,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 9a959bd914d543b78f9625f03df95765 +#: ../../src/introduction/prerequisites.md:51 754fc59967d94ffa935284676d55ffed msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 198ce7d893a04fcb806ec1671838d588 +#: ../../src/introduction/prerequisites.md:62 2905c6362d4146e8b35bc74744841972 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 cc2be8feeab54a22a0b64a2a72991003 +#: ../../src/introduction/prerequisites.md:65 091278ece252483a9838fb771de3e04e msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 749c672e8c234c1c9a5eb2cc9b77c4e3 +#: ../../src/introduction/prerequisites.md:67 0928a5c668c3414a945bc9eda147892c msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 29c64936318a4a2ba882e1eae8f03f57 +#: ../../src/introduction/prerequisites.md:73 56f3c481762848298214a88e559fc0f9 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -873,23 +862,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 44106744147f45bab675eb66148531c7 +#: ../../src/introduction/prerequisites.md:79 710c266ab4a5477b84d6ea987420fa20 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 6d84c6890f564b4baf7b34f6a52cbfc4 +#: ../../src/introduction/prerequisites.md:84 cc353db5da2546bb88a77ce1a202ff9d msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 7eb67993e8ca48dc929e1a992f78cb39 +#: ../../src/introduction/prerequisites.md:86 b62df08ec96f4cdb887600079856dd76 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 52886c54c3c54b83896c52ebd7d53fad +#: ../../src/introduction/prerequisites.md:91 97e02557293440d1a58ba659dad21113 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 097945c33f7542e2bae2e9f7ba1cf84d +#: ../../src/introduction/prerequisites.md:93 0935c3ff01634c75b5c91546dc36c7b9 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -900,32 +889,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 3853bfc6a85747019c615a50c7ca6b40 +#: ../../src/introduction/prerequisites.md:101 cfb37fd605164a8d9cc75bf892ce97c0 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 662230f538504f44941c6f4801f6251c +#: ../../src/introduction/prerequisites.md:104 5f06a7a6aae343d989a5b30979c600f6 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 1c9eb9e2bb9e40a9985ada16c34eea2d +#: ../../src/introduction/prerequisites.md:111 5f956260f3874b6dbeaf3ad7ecc09c9a msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 7f53ba159979461393c0f278fe97fb30 +#: ../../src/introduction/prerequisites.md:115 d35e4effec554a638d6c3047ef3fd05f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 7e8077c2dd584eda89ead60ecc5eabf3 +#: ../../src/introduction/prerequisites.md:120 15a1f944a0d642729d3736ed1c907074 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 1787a3c749ee48218b87c8401f6255d7 +#: ../../src/introduction/prerequisites.md:125 fa34c808bb494ddfa3f3926bc42e650c msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -933,30 +922,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 a52ca4ce9a184e938c3a5cac9cb882ca +#: ../../src/introduction/prerequisites.md:129 0c15f62eb7534e809f625f3fa213e92d msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 41d3287a9a774a73aefd49bd709764bf +#: ../../src/introduction/prerequisites.md:135 d67719a6f0ce4ba1bb6152a10507b729 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 3b9d30094611400b85b55db163cb303e +#: ../../src/introduction/prerequisites.md:137 1c96e75281844bfab0578bab2e816854 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 b6ea77357b4f45528ed1379f8fe67cfd +#: ../../src/introduction/prerequisites.md:144 bece1fc3c3f842b0b30d8f1b7fbfc200 msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 8797ce327d7443fdb3d4617d3fc2cf7f +#: ../../src/introduction/prerequisites.md:148 a7caa36b0f83448b91ef2e76e30abc51 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 896b6896b1e44d0cab5f35e7d0dd88e3 +#: ../../src/introduction/prerequisites.md:154 39321e93e9994fcca20b425aa45c2894 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -966,47 +955,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 4b839d23d72f4d3fbe4f1ce7e568b20b +#: ../../src/introduction/prerequisites.md:161 601cf500d76c4e0287af4429a46b36d2 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 a42b9ab315b5402493e4ce0067d0a18e +#: ../../src/introduction/prerequisites.md:163 b286d5359e184ef58054c72df4014629 msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 2f63483960634a7782f95e9e2feaa5a6 +#: ../../src/introduction/prerequisites.md:167 e14423edd829401faed0950772123240 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 3471105073204d7998aaf790b73f785d +#: ../../src/introduction/prerequisites.md:171 889c44360bd54a0e85e7f0e61aa6593c msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 0b8b47511b5e4296b7438be0ad2604ed +#: ../../src/introduction/prerequisites.md:172 7b9bff73624947ac90a99c7880e2e911 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 3e3eec00f23f4f21873ddb005204a875 +#: ../../src/introduction/prerequisites.md:174 c5ff687c86ef4ccaae25d8bcfbd5f873 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 2ceb25f2668442839e3e9f4512772a03 +#: ../../src/introduction/prerequisites.md:177 0a610a9632064deb824afd0719429d3a msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 20c753c5371b43ed834fa741b0ce7692 +#: ../../src/introduction/prerequisites.md:181 ec0c47438a5242cb99dffa7a4997e95a msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1014,7 +1003,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 a19c4fc9fa404912a0389337536d9c25 +#: ../../src/introduction/prerequisites.md:185 aae94ac2114641f186eac0f4117223eb msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1022,57 +1011,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 a0f38c1e28ca4850b3986617625acbf2 +#: ../../src/introduction/prerequisites.md:191 209e072724ed4d27b37e9bff6d55d811 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 37e1162f30894a1ca7dada9870ffa3da +#: ../../src/introduction/prerequisites.md:198 3bf47876e3694e6cadb05123326459cb msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 1c25a51edf6f47c5979c721b19cf11b5 +#: ../../src/introduction/prerequisites.md:199 459a65b8e67c4a9aaa03138c1abe94ad msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 ace930cf878d45a99f12b71bf0987a87 +#: ../../src/introduction/quick-start.md:1 898eb29ac7714c69840b795633953a05 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 46587a5e0d534af5867ae4f70a116bee +#: ../../src/introduction/quick-start.md:3 2a658bd2d8ce4533ab7e056fc3a3ffcf msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 a0774d4e779e46f7a983922425203066 +#: ../../src/introduction/quick-start.md:7 32dd2e28cf0f40b6930750f0162355eb msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 1658ee6f3cac4d04afc732aa758b1f48 +#: ../../src/introduction/quick-start.md:12 471c47d311074ecfac071b6d52d9cfb6 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 d8e2bc671b894f3fa8a091261754c728 +#: ../../src/introduction/quick-start.md:16 5078140028ea4d04973cb9cd20f0607e msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 683a469bf4824c64a8ea32e048d5df73 +#: ../../src/introduction/quick-start.md:22 ab127d4ba0a44526ab129587a8160923 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 b7c50413f7864a86815f3b581561cdb5 +#: ../../src/introduction/quick-start.md:27 d5cc6b4295a74f3586f022b0227759b3 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1080,11 +1069,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 d2ed66bdfcab4f7dad95b00c95d4a3d6 +#: ../../src/introduction/quick-start.md:32 585a4fe583ce44e180a062742b3b0849 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 4dcbe776a70645e5a6c7513348fa6bee +#: ../../src/introduction/quick-start.md:34 0d81b0c9ea58420789d1d71cca32ce88 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1092,11 +1081,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 bae5b03fb74541e6ad79277a576e0516 +#: ../../src/introduction/quick-start.md:39 ea4ab0782d8049d8b1b89cea4ae60048 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 8ff0d7a8d37b48488e4504ff8e3adcc5 +#: ../../src/introduction/quick-start.md:47 f6f3b7453a254f828bd4c9e9fef92bed msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1104,32 +1093,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 6255b499b9b144128afaeed64fabe8e5 +#: ../../src/introduction/quick-start.md:51 3bf9050175d4444ebbbabe219412574f msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 e861db9c43ed4b8ba262af8e435a350a +#: ../../src/introduction/quick-start.md:53 e03f72a14dcf4bf38ce8232598ca761d msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 c6318f06bcd74cda8c1f0caef9452b51 +#: ../../src/introduction/quick-start.md:57 3dcfb2facd324dccb3084c02487625dc msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 c862e745217244d28cd4c2f0842e203f +#: ../../src/introduction/quick-start.md:62 b8531da183964b02bca19f818ec076d4 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 eba007736b92434a9711f683e64bb153 +#: ../../src/introduction/quick-start.md:65 7ba1ddebeb2843179fe99fc410b193c6 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 aebc2caf5d1b47f1b7cc0aa53e5a684e +#: ../../src/introduction/quick-start.md:70 a6dc303e9d284b60bf1102212505ca27 msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1137,21 +1126,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 1242171f8b854562bb7848b06d2d065d +#: ../../src/introduction/quick-start.md:74 59ac7830ae3e4d7cb1bf503e8c90fe30 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 24e82ecf7926428386a89f18a34eb00c +#: ../../src/introduction/quick-start.md:80 6d1d6f42ada2418ba0a1de1371825b9f msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 00e75efe03554835bc33ebaed0652626 +#: ../../src/introduction/quick-start.md:82 1cd924fe8ace4a82ad8701f37b5e7d84 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 4ba34ec455704844a9cfcbac3522ea0c +#: ../../src/introduction/quick-start.md:88 aa297c52cd964291a47bb91c0135156b msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1159,46 +1148,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 c0e9673440db454bb51af04432aeddbb +#: ../../src/introduction/quick-start.md:96 28b02c90397745bfbacc03c3b1034939 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 39a23a9d02ab4bccb36d6a714639509b +#: ../../src/introduction/quick-start.md:97 ef2a4f39f01049b891868b84d968c0dd msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 23a878e0166b40d78984a2263f63b760 +#: ../../src/introduction/quick-start.md:98 89e3fa8dceda4f0cb1cfdfd1f17fe4df msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 5d9c435820674bf4b1c5d3fef5df736d +#: ../../src/introduction/quick-start.md:99 7cd178223ba94d1ab3ee8cc5f13a8dcf msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 e724ee53db1940b9b09a909f4db531a4 +#: ../../src/introduction/quick-start.md:100 46f6f8d050ce4f8c897056167d9707a7 msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 7820eb801a8145feb603145f153263b9 +#: ../../src/introduction/quick-start.md:101 5ee00ee409b746dc951ca1d4c360e624 msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 e8db3f10be294f13abe3a4418bbae4b6 +#: ../../src/introduction/quick-start.md:102 d4af972281174b8999eab55ee0ab1a0e msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 95211ea6924148a6a1fa5ae8facc2c7b +#: ../../src/setup.md:9 80401cfffae042ab9ec4b3754af04b25 msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1206,19 +1195,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: b742a74d586e42e6b0480b7af3e49c9e +#: 32f86f911ebe4a4c94975f81742333f3 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: cd3da03d43044ec9843e476a54e704be +#: d5f1ad2b95ad46d48f8f2ca5e357bb5d msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 0d48e2f07d784504a17cad0ae20262c2 +#: c53ceee943ad4acea779e072b9137889 msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1229,37 +1218,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 4d372b89f0ce451db2a505b1754b8356 +#: 7dfe9dffbf5744299bf232599644c7f6 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 573e903ef3d34514ab7b20e79c446567 -#: cfb40fbe52174d3799a6bec175db60a5 +#: ../../src/topics/staging-input-files.md:15 00709fa451134ee09a0d808e101f28ed +#: 991172e201ec4796992a349dee44f090 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 95841b1c75c84f01bd5fcb7cf3afe78d +#: 1f3c23a4769043ca985b8ddfed19391d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: c8bca3654ebb4b29bf3f028b4c65fa35 +#: f81b43c7cb194a1cad8672129223c833 msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 1432105e38014a6d9d0cf80007141007 +#: a20073a8f5374eb1bc8531ff33e622b6 msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: bcad473b34ec43f7906253123a1661fa +#: d08869beca3a4774baf1097b63e79474 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1270,11 +1259,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 e1c8949e663b4debaf87735f1d62a2fc +#: ../../src/topics/best-practices.md:1 109b773789024b2b9c063a6169c6169f msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 dcc991b647d34ffc8ea3bf9c3a38258d +#: ../../src/topics/best-practices.md:3 959fa04f88e54d42b9b774cc95d85ee0 msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1282,13 +1271,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 f26c222638e54187b8bb62fe30b66bc3 +#: ../../src/topics/best-practices.md:8 64674980c3f24c45bbfbf3f957dda55e msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 23720e4ab3d1407597f1d1c2a4d4d90c +#: ../../src/topics/best-practices.md:11 90f2e4265919446a902e17627f4420e2 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1304,7 +1293,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 b3638183c59744c897246af7dab5d10e +#: ../../src/topics/best-practices.md:20 6b5f91a749fd44b5acfd6071c9913342 msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1314,43 +1303,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 2c0291133b964ad8b751f8a8ed2338fc +#: ../../src/topics/best-practices.md:26 5fe2962837b14f0e9989063be4a506c3 msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 325c8c4058f045aa8fbd705238122798 +#: ../../src/topics/best-practices.md:28 4e1bdea962ed4618884cb9d1d59d7509 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 05333866485b43479352f7ee9326c7fd +#: ../../src/topics/best-practices.md:37 37eff4ca02e843259f6ffa38e4a87a04 msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 f8140ec6e9cc41ee88ec4bde61a44d47 +#: ../../src/topics/best-practices.md:40 ae47231c203d40a98c10045038ea9b65 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 1d68f50dafaf4cc1851e2d67b3e78603 +#: ../../src/topics/best-practices.md:44 018a6d5dbf1044559b365c7b9017eb3f msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 b283942434c54456a3f29fbb0960b6c4 +#: ../../src/topics/best-practices.md:47 e073d8f990c44b09a73d642cfe49bebd msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 0b4477c5b0184e59aa0c07161008a7bf +#: ../../src/topics/best-practices.md:50 e04fae88d9b64493ac69eaee24585098 msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1358,13 +1347,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 9741651d51f249ffba1820694ab78e92 +#: ../../src/topics/best-practices.md:55 b26b9c9b1c4346a297a31c9721f0172a msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 5e76d4a9708244ff91f2587350d684a4 +#: ../../src/topics/best-practices.md:58 b50500c3c3f54b16a535a16175a44653 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1376,44 +1365,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 89e7028e55b54f968e87b9c1c3caeecf +#: ../../src/topics/best-practices.md:66 623f3a804199449bb85e23e00c8bb507 msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 88e2338fb2614ef29dc497d8c01a2f2f +#: ../../src/topics/best-practices.md:69 effea0b1356447c0899ca0746667ea31 msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 0f3aad35924344659eb5a6719ab2b8f0 +#: ../../src/topics/best-practices.md:73 00e8ef87864c4ca2b2c1c0548b02b38d msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 877cbb1d537b46d3b6d05b2d8c025e70 +#: ../../src/topics/best-practices.md:76 6e6f48d70b894a6c959ca30fe6bad772 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 5c0debbc1c1b428ebb32b589b99fe17d +#: ../../src/topics/best-practices.md:78 02fe08760a4a4ab49e96f4e51316a81d msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 1ff97183191240edb98f0cc365cc028b +#: ../../src/topics/best-practices.md:82 172ed7915a654964ba63f860b2d65330 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 22f7725deb07422fa0a7bc2e6f01e4d0 +#: ../../src/topics/best-practices.md:85 4d0a2871a7484e21b3c39c4dbaaa63fc msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1421,31 +1410,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 982313839ccc4f5a8527fe9a854c78eb +#: ../../src/topics/best-practices.md:90 1eea9f1e284447718141f5417b6bb433 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 267c9d10ab5e4b6c8a6104952deb1690 +#: ../../src/topics/best-practices.md:93 509411d353fe4314b087b81b09ea960b msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 2eff0eec58c94f4d8986a4cb91b14b8e +#: ../../src/topics/best-practices.md:97 a54bc80bf08243bba67d98dd682ee134 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 f38db701740b442c89ce58e937bd35c5 +#: ../../src/topics/command-line-tool.md:1 69ecdaea24ef42eebef9d86e5d716b11 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 034aac9e186645e384c28bb2a739cfff +#: ../../src/topics/command-line-tool.md:3 3cc5847468d1478bb5589dee68147189 msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1453,52 +1442,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 5f835cdfc0ae4f378d8dad6ae7ab1855 +#: ../../src/topics/command-line-tool.md:8 98c6bc409420485095ae65d6b0b9a3a0 msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 02900cb8ae4c4da89d264b76a984d6cd +#: ../../src/topics/command-line-tool.md:19 ebe23e5378514f888a9ec32a2adb1e98 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 753e48d6dfd54a88a12773b996f182d7 +#: ../../src/topics/command-line-tool.md:50 387cfe85604f424f8d31c4a4c9c15edb msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 c7ed6d1654c54bf390e933ef0f847b99 +#: ../../src/topics/command-line-tool.md:57 7b1d65754e854693bb60289c97d3fb5d msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 0a0f855ce34449a0a37c036105c65839 +#: ../../src/topics/command-line-tool.md:68 f440cef729c8410281432307a4da8d55 msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 c4300454f49548f49e4bd186192515a1 +#: ../../src/topics/command-line-tool.md:69 4fbb8ceb1b59480583ac611142167049 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 f985d58070de4c0fb5f5a491fd4dc31c +#: ../../src/topics/command-line-tool.md:83 b87869204838415bbf694214e3680593 msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: 2f4e2c85677a4e56a35b6bef36d67334 +#: 12cf5f2264504c44a2173e858bb2c283 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 13c6d5600a30406c81ffa25ce42eb0c8 +#: 7694f9cabfe04308bbddd2c88ae6d9b9 msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1507,17 +1496,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 3bf773b8560e44a3a37c68b6fcdc6a23 +#: b557dc4f8ef549b98f59412a918643de msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 68b8578d2f6442929941ed2522b218ad +#: 3011eb003c084285b30cfa56a8da45b6 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 755149ed46c348c2b723b49c3b3152a8 +#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1525,7 +1514,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 54b7ff590d52454eb87d9f23fca44501 +#: ce78b2d147054da895beba66d0ecdab4 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1535,7 +1524,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: a7c74a4a74c9414e9f29fa20bab7e295 +#: a973846ec5a946eeaff02c5b00997da9 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1543,13 +1532,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 0cbf233379024800bcebb963e0a3eb6f ae3bc02e4f3b404c89f3c461a62c5bc4 -#: dc32a2bacf2d4c8cb841be6eb8b839ad +#: 294fd83a97a64249bac38f7482159372 9e8eb1542db640ff9e300649ce50dc9d +#: ccec7f73b9d948e79a6cdf32bc124092 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 34a56bc23af44353a003ee295fb2c609 +#: 22948f19cb78485f8f86244686a35c09 msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1557,7 +1546,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: c7855ec1f09d4945afcb0aec22567b31 +#: 001d9579bfce438e865377fb9c2df776 msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1569,7 +1558,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 5c60492e27014735bb9a86307ee654d6 +#: e62618db8995428bb3f260e03ac8f459 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1579,19 +1568,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 80a9c04358e64ca28ef4879ad74ef733 a2b470f06ad94871970b7d95339fd369 -#: dc65b4b5e48e48a6ada03da0fac18a51 ea2360c5286b43ccabac202dfa97fbe7 -#: ee4ca94dadf64ab69a70b6cd4eaf451a +#: 457756c4e9544f068af897113358cc89 6d5ae75431424ea788c3440606f22940 +#: 98e0548845fa447fb05a29c9fc2f17b5 de5e8aad4e3046bf9bfc2ad8ccba17d0 +#: e9801b2142cd45368a73ef9b121c1d08 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 285d23ef9bbc46c9890ae7957d487c12 +#: ../../src/topics/custom-types.md:1 ee2bca9bdbb74b60a706c3118d6a17ba msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 3edd322daad940d8957f88a2637876b5 +#: ../../src/topics/custom-types.md:3 e63ae9694f40438d872d141ae824a42d msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1600,21 +1589,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 a1bd9b0dfa234e6caa6a684e981d89b5 +#: ../../src/topics/custom-types.md:9 750fdd4c270e46a09f79e867358f7414 msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 0aeacb6ac20f4ebca3600425ca32f5f4 +#: ../../src/topics/custom-types.md:12 b3f688cc82444ef7a7a0aa63dac39cac msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 1c813ebce2904f008b5b33656f673ebc +#: ../../src/topics/custom-types.md:18 3638be18b4f64cf08053d512e590dda3 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 cc36359e94c841d3aa5cbb26a094e1d5 +#: ../../src/topics/custom-types.md:24 7d5b9c21739c48f18c13614ca6967f6b msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1623,13 +1612,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 dc79668b05e8439591a0beb4b57acc66 +#: ../../src/topics/custom-types.md:30 8fea29993f944d8d8d3181afa29bd0a6 msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 08aba4f77aa442d4a34aa1535f78c49e +#: ../../src/topics/custom-types.md:46 02d0b648d70f49d7892f690be06df585 msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1640,15 +1629,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 63431a972f994bccacf55d5fac0d614e +#: ../../src/topics/custom-types.md:53 0743bef42b9a42328849c8c2f9da9eed msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 55e7695aca4f4319b1cf7551105a8782 +#: ../../src/topics/custom-types.md:55 85c5d0cbbc6243a6823f5eeac0f85dd9 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 0c5ab34ebbf54ff6940b8ce3f080d744 +#: ../../src/topics/custom-types.md:61 be848f30769543eb9c0be55263e3f758 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1656,7 +1645,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 f97e18d2d3b946468c4fac227920e011 +#: ../../src/topics/custom-types.md:76 cbff44a64ba4432cb59a82f82c2f0103 msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1666,26 +1655,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 62644031403548898ff36addbc0b1f6f +#: ../../src/topics/environment-variables.md:1 617f1c0084cf42d9be4c7a8fa5a48432 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 595630b0687c4467aa65bfed289281f4 +#: ../../src/topics/environment-variables.md:3 cee79afa3c6f43c29ef05e06b7843d35 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 34e005c135864a89a00e817d79118e2e +#: ../../src/topics/environment-variables.md:7 225903b11efa417989df42de86ad2451 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 b624f9f99c294e6996f212c8b62f20b0 +#: ../../src/topics/expression-tool.md:1 1a5f058290064c1cad05e63eb127fcbb msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 14df63ab847e4efca820f712548cd076 +#: ../../src/topics/expression-tool.md:3 74ad8d69cf294ae880dbbe28e25b3545 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1693,32 +1682,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 91d4224b41c6473f936c03bd0ab9d370 +#: ../../src/topics/expression-tool.md:8 5293e8ee9b3b4f59947cfc164ef111c4 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 519989399dab493ea41941ed85cb9670 +#: ../../src/topics/expression-tool.md:17 ffa1955c759942c68e7589429e5ea86b msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 28dd1cf24309404eaf717d417272e094 +#: ../../src/topics/expression-tool.md:48 038bc0ba5f6a405a8255a7be76979baf msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 3f536ad8c86d442c8bbe61777dbb1a54 +#: ../../src/topics/expression-tool.md:67 fae1c63de02e48c0969a98e4c49b2e06 msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 b9e9894c6d024e60929d020dbaa553f0 +#: ../../src/topics/expressions.md:1 7093a94695524851a5463193f0701b78 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 482debe1a40f490b90d4ece1b3f9d732 +#: ../../src/topics/expressions.md:3 dc8274ecb15948c29a31db89b12a58bd msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1726,7 +1715,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 708346038be745d097685970cc462f4a +#: ../../src/topics/expressions.md:9 cec8eef8a5aa49778ecedd4195ab9f2c msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1735,67 +1724,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 99347b6b2c404a4b9bbcc96e0b4bd925 +#: ../../src/topics/expressions.md:16 df100967597043c78112bf43b520cfab msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 e6629f0914324c76a08fe179575b73d5 +#: ../../src/topics/expressions.md:22 59ccf4daba39406581a6bc2d9bb1b7d2 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 2287002a87184fb9b95d775a368f0e46 +#: ../../src/topics/expressions.md:25 570cc75699dd4e0a987fc9aca9a01ee4 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 c23d4543d9f949a9a7015fdcbb40dcd0 +#: ../../src/topics/expressions.md:31 9e123723048546d495ed5110d7177708 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 c04a9dcc84b84f37bcf32c3790672038 +#: ../../src/topics/expressions.md:35 26543894f6e04270b89ab702451bcc89 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 9f27c79365db455d9d31053576ebe05e +#: ../../src/topics/expressions.md:37 f403c1d4e43a4aa0aef8488d2b5a6262 msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 a2b3ad1e2c884e24948a915c3305aee1 +#: ../../src/topics/expressions.md:47 249dffb569a944c897ce5862e5f28fad msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 dd7665bbc5e9449588c9539e3c1910de +#: ../../src/topics/expressions.md:54 1641c96aca2f4923885fe8a509eb3a49 msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 0972c757f7c74ea9beabf6b9ef9dbf4c +#: ../../src/topics/expressions.md:62 bc63405a0d964df2bd9493996abc48fe msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 175de3b9854546568f60a20cc19887de +#: ../../src/topics/expressions.md:64 5c191d1420db4e26aca31c1b1e34cb75 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 0c286e5ba1714a059a95b566fe49be31 +#: ../../src/topics/expressions.md:66 d6a5c65e824a4bbc94578df9597d4716 msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 3029c1dfe5424c2b812597b03ea76178 -#: a5503b6c524e4848aa308b0f4c26d774 +#: ../../src/topics/parameter-references.md:64 a7ff51fe564748229a88a0d3044dbc17 +#: c12625211cc542b68cb51365a63eef00 msgid "`arguments`" msgstr "" @@ -1803,32 +1792,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 0e03befa46c74dc2b09420e1eb2a6fbd -#: 50f81e7ab73a4713bbc60f6f5609b906 718dc3def33c462786174fb42097981f -#: 9c2acd930553458eb105f96213b5d7b0 d4bf86a995d546c0a9159b3f29a84125 -#: e98424244f554c7399e9e7ad560849a6 +#: ../../src/topics/parameter-references.md:86 05c34a5a2e404a14b9d284a9d0c73bd3 +#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe +#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 +#: e7f1993580f0425098a719e83a64cc7f msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 2be930b5da674874a0b634eca3ad9346 -#: ce445ad0f00f403985eed1328103a500 +#: ../../src/topics/parameter-references.md:66 2fd5b42cafe34d3185888de041818dff +#: c158e9ee5fbf4e868b152a0a5880092f msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 2fe48d6404864ea39ef0634169f67be1 -#: 43453d90db244c558a815ca872dc716c +#: ../../src/topics/parameter-references.md:67 3f29e4a3087847e9af6f19166a8def9a +#: 92697d3179ec48898eaea9aba3c24dcd msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 78eaa318ba81407e9ca9c2c1702ead11 -#: f5da7058f7f146d584314a5bf4de5498 +#: ../../src/topics/parameter-references.md:68 c0eaef93bc3743279549bcfb8b014ca3 +#: d6722e3093884ad7b62696fbb2f48fdc msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 7189f4415d204fb388c4a7e927e15b71 +#: ../../src/topics/expressions.md:72 37c493fdc2f0410a9748f8faf09ce5b5 msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1839,11 +1828,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 17a83cc91963434e89822a3e46df8401 -#: 194d3e48d38c476fa8f731e3bc2d8c7f 3a3000a6446b4ef4ac66a28acb13b136 -#: 5cc35210e95e4f2ba6a1a6f118926fdd 68b3d1481a4e4375b1b0c4fca8285374 -#: 94f2bc195bc0487da014bc3f4d2dc8fa b92b4eff2429437d9da911ca68cef954 -#: fc0a1353e87e479d8c8b6c973d547465 +#: ../../src/topics/parameter-references.md:90 04e3eefe4ec445cb90c2fa42344aaed5 +#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 +#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef +#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 +#: c610220d06484d589313dc29faf8222c msgid "`format`" msgstr "" @@ -1852,51 +1841,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 5478cbeadc64412bbb32619fae9b9958 -#: 6950cbe52d334fe58bf4fa20e5f1f8ca 6b5bda581d0047819c6d92edd8ac9045 -#: 8248329fbe504b3a96bcd890908b070f 978c0fea8ed1481a9f06b6abb31ebd21 -#: a24ba514d66d49cea281fd4c9c7a2b8d b6e2c8e7abf74d64b2915063dda8479b -#: bc184adfad0e4642bc864d367b8779b7 +#: ../../src/topics/parameter-references.md:91 662b36e3505f4ac3bb5070bb6e055217 +#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da +#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c +#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b +#: f71216a4b35e4157aece5ffa2602d8bf msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 5bba2d465e0a4c5d9575406d1294a225 +#: ../../src/topics/expressions.md:75 a3c775a0f04b4541a9b712bfe2e4e69a msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 da385d3cde614749887e195ea6d95291 +#: ../../src/topics/expressions.md:77 ef16c4a9a7ea415fa399297b63b9710c msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 487c95417f8e48be8391163578ca9519 +#: ../../src/topics/expressions.md:80 2592e429c74c4ff5b8ba68a36f060c1a msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 48437402c00147d4b4ca8bd6b38a5823 -#: bdcb3920048f4e578a4005fc2e30233b +#: ../../src/topics/parameter-references.md:78 5cca4c2ad617400eb6efad4066b1839b +#: ba1fff3ebb274dfba845b3ee20ebd71f msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 121556d49d584cc491a15ef8404ce462 -#: 183ba52666744f7ca5772939db2efd6c +#: ../../src/topics/parameter-references.md:79 6914526c0a7c43a2a05438519508ee0f +#: 722d3bd7184841639b9f9a38914002da msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 08ad064936d8406f8c3852526f4f863d -#: 30c927925c6b483b80b583ca7c735437 +#: ../../src/topics/parameter-references.md:80 737b0f9392154241ae5b56c6caa823f5 +#: 7b46d408e7e7481b91a950b2d4010c9a msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 32a26dd9c5f84e88995f093cda953ac9 +#: ../../src/topics/expressions.md:84 f09e7371708b4c0685eef2a314791ccd msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1905,32 +1894,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 05ee6df2f9b247629d148fd59c293660 -#: e7b7d782b6ac49b3aa0c8d8ce7ff04d1 +#: ../../src/topics/parameter-references.md:84 aa6ca1def2024c98b9d5542de1a81425 +#: e9fc5f7fa4474dfc95039b94167fe894 msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 b0cccc07e5bb4effb60424623351499e +#: ../../src/topics/expressions.md:88 6c37a1ff939748bf83a86c07c3d017fe msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 4e5281c8663c4b6e8851be10f50143f1 -#: b5c22c66397e4268b4b3d53b9a253a3a +#: ../../src/topics/parameter-references.md:87 3a8126b0a0334df890b2be2c693ea5d5 +#: 61744122b7d7494890cbe6b2fb72b9f7 msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 98a28fec818e42af9e177e17fa12aa7a -#: c37d0b1fd75e44a28b3b6409f912e865 +#: ../../src/topics/parameter-references.md:88 93cb9015dacc4b50a4ef177ce4ece2e7 +#: e0c7ccc8f8664cf794cbb7330355f3fe msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 dcc42c6c49964a4ca7bcf2124e26ebfd +#: ../../src/topics/expressions.md:92 58a1773b1cf546d7890010fdebd47388 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1938,61 +1927,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 d2ba352ac5fe427ea7ceb0bde01458ba +#: ../../src/topics/expressions.md:95 230f3227ed1144f7abe0f8c231bebbd5 msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 235cfd6e9baf48698102447fcb83e0e1 -#: 8aad01df8d8d4ab7905a5da7ce7f6bbf +#: ../../src/topics/parameter-references.md:93 5c77dc9f8afe4dd88933943030e836f2 +#: c9534670f5f04769aa3749c3778eb705 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 058ba8c9c2da4ebf8b2291600dafd611 -#: cea47d3e10f641a2b64f08ee100ea6bf +#: ../../src/topics/parameter-references.md:94 4ec8bbac5fb14371a6a4cd53d7cd6450 +#: 7b0887a8caed41b2acccf7021bb323d3 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 3b039de5ad144207ae337aa88b3b1a1f -#: e0ecfe44b34e45dea513459b6b3e44a6 +#: ../../src/topics/parameter-references.md:95 aceedfb558b246bc87eb3eaedea187fd +#: e5e8b8c75f0f43cbb6e160e5bf810c6e msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 1cfc6cb0be4e4ddd90f546adb796b805 -#: b62f6eaa7c394792929dda83a187c632 +#: ../../src/topics/parameter-references.md:96 266dfb5fe6a842078baf66073cac9623 +#: fe3b9fb45e01490498c5a35c012b3de8 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 8b13b0e4071444179b26401929de8a10 -#: 8ffb471129c04fc6bb52b782fbd09f9b +#: ../../src/topics/parameter-references.md:97 85f424cbfc85460f9da310aee1ff0b82 +#: ddf82b12b12d416fb65f3ce3f51bbdf0 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 331f58b998cd4d309940ebfcc60a44f8 -#: 5041700e6ccc48989e395a6dcb1be3c4 +#: ../../src/topics/parameter-references.md:98 966e88656ae5402a975022ee60646283 +#: af14fda3cca645fbb2f3c5825fe0788e msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 14402b41c64548f8a9691c3b7ccaf3ac -#: cb4837a2b25343d2880a07143f85f40e +#: ../../src/topics/parameter-references.md:99 09120baec1464afb8aed4edd773bf509 +#: fec70bb106ad4d95a2d55ebdcf711afc msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1d1c2894600544b686a8ec3c36cdf767 eaa30e987ec543ef8d6f7171de5525f0 +#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 065c97a553904db6ba61c20cf9d9939c +#: ../../src/topics/expressions.md:104 1dc4148caef748428a7d13caff37b1b1 msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -2000,33 +1989,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 36be05289972455ea4a60aa1f0b9cbdf 49e1ab5bc5734debb83060759d5c3236 +#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 f8e37cd35aea4bbb92d28e8d7e803ebb +#: ../../src/topics/expressions.md:106 947b1ca132a54ed39745cd12ebcd65e1 msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: de816d1dc9f24c0cbef86fd6a09eff6b e265df9d1cfe439bb798ab6cd32485af +#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: 0363e32e12604eb896f4bdf6bbefd550 8b5289393b7f477699d007ded45a4df1 +#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2c704cae43d64ecbbed33d18eb3f66f3 89acc8f8387d4643a844ac3efb186000 +#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 0597c6c214924e75ba2f212cd6b0c9f2 +#: ../../src/topics/expressions.md:110 5fa512d352d945e7a3e0d59b0987cd1b msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2034,22 +2023,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 1eb1c2432dd943f6a27a1f8b92e3981b 5b9ba9380f10425b809c6157a1f0b052 +#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 b4cc7cc55cf04449b291a27514fc99ae +#: ../../src/topics/expressions.md:116 81e91df082834d2cab7ef1f62d8ba57a msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 cdb48eff43e7459fbf3ed21eb7791d66 +#: ../../src/topics/expressions.md:118 e6bfd1dc2e324992b6c3332c11ae3445 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 67a4dc675c0e444585d579954b99614e +#: ../../src/topics/expressions.md:122 acf10261df2944ec890d754fd56c6b28 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2057,7 +2046,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 ea3238db48494ab7b044bab9f96590af +#: ../../src/topics/expressions.md:128 bda6b8f398554b0c946c2c7d96308a42 msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2067,54 +2056,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 baf2f6ac8d514705a1f7bf7ea8c71d2e +#: ../../src/topics/expressions.md:135 454c02c3918647039c90ae387005dea6 msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 ef45f4e14fb943cd9fbf179f5d3680e5 +#: ../../src/topics/expressions.md:139 e1fad28bf9cb4c4c85eb74dd520ba107 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 030261615c38485d83ed986c9c98ce15 +#: ../../src/topics/expressions.md:146 9835d0b399b84a0084fe5a4d9e7e6405 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 1728e2370cbb49ab97bee4c2f74fff2d +#: ../../src/topics/expressions.md:149 410ba7a5ac6349a98460c6337ee5c4fb msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 4514fc0c99ac4688a37bf30bffe139e8 +#: ../../src/topics/expressions.md:155 d2daf50d7f3d4de18331c8fd2c8a5786 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 33804649720143e5a70e890af9ad9119 +#: ../../src/topics/expressions.md:158 8f2015c12b2b4d5d9a800ddeaf428f25 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 c114496be4c243d6834776e17bf15010 +#: ../../src/topics/expressions.md:164 f0ff919ffc12439d89d7b40f51ade84c msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 c784e86f14f54e4982db206741fbd96e +#: ../../src/topics/expressions.md:171 307a17a893fc4dafaec2a63a95704644 msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 f9de69aad9b44afabded71221c84adc2 +#: ../../src/topics/expressions.md:175 7f393e86b114470f8dda47b2deec63aa msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 b853c964611e45c2b37a8ac3c34a4133 +#: ../../src/topics/expressions.md:181 c3f459b87b96435583637b3f1573e658 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2123,15 +2112,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 a10d143210b94f83857f62e972d69134 +#: ../../src/topics/expressions.md:186 9f676022eb2744839ca2109920250cb6 msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 b07734b172664040aff04f83bd4395a5 +#: ../../src/topics/expressions.md:193 ede7285f77864fb0aee6cfecc2c97fa0 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 1f9a5377a1f04ee3b8a9ae22390e0cae +#: ../../src/topics/expressions.md:200 c55fb184bc614ee2b6e5e64611e5df9b msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2140,11 +2129,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 359bb6448aa140f8b940baf769c13db6 +#: ../../src/topics/file-formats.md:1 66b522f46ce242149386e79f63b32cf8 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 c4aba730bee14931b051d6aead7c2dae +#: ../../src/topics/file-formats.md:3 64a20285785d48ca86227a0cf6353ad4 msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2152,7 +2141,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 c4dfcff573424bccb97580fdd1ef27a1 +#: ../../src/topics/file-formats.md:8 5f71bbe2c74e4260b79d4d9230d35397 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2161,34 +2150,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 1457fa489c894f1bae8a3949ef200527 +#: ../../src/topics/file-formats.md:14 63bfff437e3348428f7e33ece7ec55e7 msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 cc4fa87d57b344ed8961c31bc4397e71 +#: ../../src/topics/file-formats.md:17 6ce83d9c06e4436881aa47d94ef41e0b msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 091815ab1d824787a1460ce11ffb834d +#: ../../src/topics/file-formats.md:20 55006c594abf4e70a38e979568fadcf4 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 414b68dac4654163b3dc13e140ffdbf8 96fad38b4aea461493bf0827476163bd +#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 4f71de1140974e73ab033fe7dd9dc165 +#: ../../src/topics/file-formats.md:32 1a1905ff2d624eca952c8a53b3bee678 msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 b84e3294c8f648aab634e59b6f58441e +#: ../../src/topics/file-formats.md:34 368ff92476b14f5c8331260eafc5acb5 msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2196,11 +2185,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 6d9ae44900d64532906532432881d29d +#: ../../src/topics/file-formats.md:39 5d530afa23f349a79f54d51d40724747 msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 5b99384b3a854832bcca2fb02bdfc1b6 +#: ../../src/topics/file-formats.md:45 16f965f86712483aa7f95dfa3f944a17 msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2209,80 +2198,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 3141fc6828024c3e8201e88ca10e19ee +#: ../../src/topics/index.md:1 dc629e2c90ed458b96107a6994676434 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 5f8c8ea68d7f46fead000315226ec164 +#: ../../src/topics/inputs.md:1 cf2f077cf8044079a7005e6e508dcd8c msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 86c18e5105b1400d86d413e28ad72f48 +#: ../../src/topics/inputs.md:3 129e1d2a71894d28b009f4846754a75d msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 fa15037f9b0b4a2c9a1f4cff9b8fde43 +#: ../../src/topics/inputs.md:5 d6791bbe575042b9a7282c69407dd907 msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 fba6d2b7843e466abee33183103cf47d +#: ../../src/topics/inputs.md:9 e8da87f8bb664334adf831995601f462 msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 09f5a55611d14e39b2266245b79ed763 +#: ../../src/topics/inputs.md:13 de6c322618304207b6d1364d1ec2dc13 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 bdfb39c2656040858616afe731111d1a +#: ../../src/topics/inputs.md:16 43bdcf6dc1b14030bff27fa53289c02c msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 c306335ff07e4c03955fe87cad16efd1 +#: ../../src/topics/inputs.md:18 056510b42ea64717996ab49c307bda86 msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 50bd3db6bfb348eea13ba4714ecb2a20 +#: ../../src/topics/inputs.md:24 6852f5dbd9094c99bb68f2a88f76c9bc msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 5d32cfb6f6ed4dd8b11ed316830edba8 +#: ../../src/topics/inputs.md:26 f33b6800367248b7927d97ad7b4be5b5 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 b90fb1b2d38b42c1bad2d9667aaa22fd +#: ../../src/topics/inputs.md:33 8ad812d7e88f4cbba83228ffb1711576 msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 6029a96abf9c4d7295eb86d435a1f58d +#: ../../src/topics/inputs.md:40 cc680bbf091a46f8b4b3dbe6324c040a msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 902e9df74f78431ca9cf1421a26e097a +#: ../../src/topics/inputs.md:44 446ac81f078d46289a18f494748f482c msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 9760d15bad144e70a86dc0a8da72363a +#: ../../src/topics/inputs.md:47 3d6d958d111943f3a2139b4dbb7810db msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 75bf3fae131049308441bc496f543f6e +#: ../../src/topics/inputs.md:53 ba0ec9157709430c822f4e91459288e2 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2290,7 +2279,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 38d8a9c157404bb496bc49f1e427bf99 +#: ../../src/topics/inputs.md:64 2565f8fd4a15429e887aeb71eacdff1e msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2298,7 +2287,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 502994ee84234f048e545633bb04cd3c +#: ../../src/topics/inputs.md:70 659ed5c64fb546399b741553a347b8e8 msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2306,14 +2295,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 551b06b8a3064bcd8d0f1693a4c0ee94 +#: ../../src/topics/inputs.md:83 3d87e69d41374fbab23b26d36c1aee03 msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 1838e7438be5449c91c6406a7e40d8cb +#: ../../src/topics/inputs.md:95 07bc81683e2c4ac68b379462bae95207 msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2321,7 +2310,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 098bb02c941a4bf2a8d4dd9ab3bf052e +#: ../../src/topics/inputs.md:109 3e304da2150f448d9e39715ac5f5deaa msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2329,7 +2318,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 b43194d2b3ef4fc6a8c4b58741317b29 +#: ../../src/topics/inputs.md:124 fd8a98686e3c4c609f79ae427f1558d3 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2339,13 +2328,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 e17c55c9ed034dd68f4d24272a61d2f1 +#: ../../src/topics/inputs.md:131 f1a2e1bbb1104a4fab5a7f04cac845c7 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 c97a6945e4bc49888d280bbc43c3c069 +#: ../../src/topics/inputs.md:134 6a7f0ccd227e4f90a8c8ca96744bda68 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2356,17 +2345,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 503666cda07b4d7397c65561714d8034 +#: ../../src/topics/inputs.md:142 1f79d115d8a145189638c68c3095396c msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 e5463be0a00d42e386aa6fd3dfacaeaf +#: ../../src/topics/inputs.md:146 6e1b3e2d90184e34925891099d2b5cc1 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 14b98bd0ef4a4065a24e66443458d607 +#: ../../src/topics/inputs.md:148 4f6df7f13e42448eb4a53f03bc477b56 msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2376,23 +2365,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 98fa5dab117e41d4a42da8d78c533c64 +#: ../../src/topics/inputs.md:154 dbc0b52627514ad0908969d0b4ddfdf4 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 116c212444da4488b32abdbd725db98a +#: ../../src/topics/inputs.md:160 f173dd96ad124470a53573c86a8df203 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 065e556e01b34c35b6be4b54b7cc0203 -#: 4745f370dcbd4ee8bbf4b3a20ac5b9fe d11761f2d576464f8a2c63bdec02d410 +#: ../../src/topics/outputs.md:105 af25945b530048b685891b1de4e35e72 +#: cb07caa4ff0149b3ae832be53f8d76f6 e0098a77080d4349b05ceb7735a5fdf5 msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 b3bf1d7e95704682b1bae17472eaa4bc +#: ../../src/topics/inputs.md:178 2445d2c7c2794fd3ad8b6ed8b4a9440b msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2402,7 +2391,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 04bc655130234786b06b2d5b9e693635 +#: ../../src/topics/inputs.md:185 4459819ba75647d185986a3386939494 msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2413,11 +2402,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 e2c18a43b2794448b45c489dd2fa951e +#: ../../src/topics/inputs.md:191 8f163bd34ded4785b6e28c8e2147e0dd msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 38968ed627514ef38e43b3d1e4a5e25f +#: ../../src/topics/inputs.md:193 1799e11a7b9c4929a3d1379d7ea45d03 msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2425,46 +2414,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 06aab84eceeb41d087b7e295ffa21586 +#: ../../src/topics/inputs.md:198 9510c0b431a44b5e84e0b583de7c5446 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 a0317edb8b964cd2a36c59eaa6df302a +#: ../../src/topics/inputs.md:204 efb4eb6f5e994b50a52fa2c707dad1ce msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 5a3d1b82c79c4ccdb7d06381f4d0acda +#: ../../src/topics/inputs.md:215 34599c6f10ce4104be2359a1b37f91cb msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 e1fc6c3a324a46ee84b0eb59f8396552 +#: ../../src/topics/inputs.md:217 0663ea7918994d3f9c45c652a3ed12db msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 f22e7d9e23b541ef88f3254095147519 +#: ../../src/topics/inputs.md:233 a98dda6ca4b14edba467de638bba28fc msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 d473d2fa11f64e8fa86554b5777c98e4 +#: ../../src/topics/inputs.md:236 10d0e9f8df8c47788703073b17529bc8 msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 290461c321d14d23b39003b93008a7cb +#: ../../src/topics/inputs.md:252 9a0e1a130fba4d24a9168ca3e455cd23 msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 add43f7531bb4c6988053ae799c366f0 +#: ../../src/topics/inputs.md:255 992a8c801ceb4233acf56b6bff315188 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 b12b6f5e34c14dbc9b40458d92e6797f +#: ../../src/topics/inputs.md:257 9027d23fa7074b789c3b86ca5ea17fa4 msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2472,18 +2461,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 4d8f38679952486095a77692387db2d3 +#: ../../src/topics/inputs.md:262 68b47710a8ea4b978428b42c627944e9 msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 47ec49759e274e59834192b794ec2d9b +#: ../../src/topics/inputs.md:265 d33e4cac65d14111a89c838c4d1759b9 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 0657044c742348fe9e63f662692570a1 +#: ../../src/topics/inputs.md:271 24cea1cf7d774b6ab56959f289cab39d msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2491,7 +2480,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 30c21cafda144f848bfe79d8e232296e +#: ../../src/topics/inputs.md:280 b866867d6f8e4d3999b62a85e6884ebc msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2499,7 +2488,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 1cc8ea6abb684470b7790808acea2be1 +#: ../../src/topics/inputs.md:289 80c49ed168b14d25b2f09b3b0186b44f msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2509,12 +2498,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: c3b84742343449f9b3866285d98b53bb +#: 71628ebe908b4cd28dd1fa17e3d2e2fb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: 0a1b08fe707c41089ad3d4895960ba17 +#: f123ca244c23413c91405a4b84887525 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2529,7 +2518,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 5bc4ef6584c74b948ffd5c0bddf8e569 +#: 23299ae1bec94b00a32a8af7eeac350f msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2537,17 +2526,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 47ee25d60a4a4faa80476797954ec7a9 +#: 2495a9f2032a47c188338cb81ba429eb msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 195d4a8d5aad41159beffafd198d4640 +#: 3fd2f3cf7bdf44089df2ce3122534801 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: b0c5946fbf79415aa74c8e72fa88cf85 +#: d5a5b8b490b640439db92da949266e4e msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2557,15 +2546,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: a98236fc1be745a69271855e1b5eecdb +#: 5935ed94331d4b2f8ce597f31edea843 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 5f0da8d7e06a47fda38053dbadcbec18 +#: ../../src/topics/operations.md:1 5feb559552194ba58da7206c601292fe msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 23d41792b0524742878a6ab8f3ff0fe1 +#: ../../src/topics/operations.md:3 b7124ba4df9042baadc1641ee09545d6 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2573,56 +2562,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 c0f723242f11464392dfc32f67a3b67b +#: ../../src/topics/operations.md:7 d34b698c62114041a64e0abce25ca935 msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 c9f3a48a3a064cb3b1759effe724301d +#: ../../src/topics/operations.md:10 cba2c31262bd450cbafc7ca77f4fb8fa msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 fbad0b0144984ae78b84307ea68d0a03 +#: ../../src/topics/operations.md:16 b01be5f632104096b5af6193aab34d90 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 59e9ff3276454ff19eb351ff33737f12 +#: ../../src/topics/operations.md:24 60a6a02c1367403db6df3ec10f75eb69 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 ba74f2ab7f6d4c178f3c4c43c461afbd +#: ../../src/topics/operations.md:55 314ea7bc35154f41b2af5fa6683ca389 msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 93c8b61a12134991ae9bb78223e2017e +#: ../../src/topics/operations.md:58 d81e679b13474f74bc5e1ce1e31c2bc6 msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 cbbdba36dc3841f2b1d820f369a8c680 +#: ../../src/topics/operations.md:66 d7fb27131ee44bfc82f698ee44b2bae0 msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 4649c8d743f448ab94ee589a1b3a342a +#: ../../src/topics/outputs.md:1 b8ef11eafd1d46e088f1277f4ac372bc msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 1a9d6e2e33244d01b820cf11fe2beaff +#: ../../src/topics/outputs.md:3 d2382ed1f644459594655d5b5b4d838a msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 233c8865faac4d6c8ec7704e9a997719 +#: ../../src/topics/outputs.md:5 6651632d977b44479b721174fffeda2d msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2630,7 +2619,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 5aab1c0db3d5449cbb4a0f0dad615d87 +#: ../../src/topics/outputs.md:10 bee5f532554241088764ac9e56abbe85 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2639,17 +2628,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 46b4eeb3ce8946dca0f8a94c399b4c96 +#: ../../src/topics/outputs.md:16 0c7c506f38be421399073871f64e99b0 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 8d322609948a4d6e87d7962b3d29df2f +#: ../../src/topics/outputs.md:19 8b60286e56cc42a8ab5f751a97adf771 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 9fdcb55e965444ee8b5d74a2a9870d27 +#: ../../src/topics/outputs.md:21 fa0ad674f15348339a1eee771a6ba9e2 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2657,71 +2646,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 e4c490f599a0469a821aa8e74f4ef0ef +#: ../../src/topics/outputs.md:26 177b5f1b95a34fb9b2eb42f733d79ac8 msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 b8ed6ebe6928455cb094ea430e21e5d4 +#: ../../src/topics/outputs.md:32 a08a6d8aca8e490482e127a8fd5e650e msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 3e65c52d218946fc83b8c3e6adcb21fe +#: ../../src/topics/outputs.md:38 c2c60f68b1e045f88844076e191fda9b msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 03751b45cdf647b689a3a69156989db5 +#: ../../src/topics/outputs.md:45 6d939f62526e4e6d95acb57d72f60a84 msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 1b6f59623f5d4cd984426da21b8438bf +#: ../../src/topics/outputs.md:51 c48edd9034364b81ad42540a98b51d91 msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 095902cca30944d19a0d5f17f582e3b0 +#: ../../src/topics/outputs.md:62 9ebe0186a7124dfaa30e558e8f59653a msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 6d95fbfa321144a9932f26ab5f9ddc74 +#: ../../src/topics/outputs.md:65 9381b7d7c9904df0a5e16dac29c2e08f msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 8be7ef160e8b421a89124a639dc7fd84 +#: ../../src/topics/outputs.md:67 2aa9c6916e3546b7b92fa64bb83275d1 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 fcf4490c351d4cd6a208345308168ef7 +#: ../../src/topics/outputs.md:71 63afb7a597fc4e459b6a7dbd40bbf6ff msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 00f1bb92a38b4f3a8c0065ac75530689 +#: ../../src/topics/outputs.md:89 7418915470f041c9af5bd39ea652de36 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 1477d0fc5c4c4f82bcc1c8e6ba8eed4d +#: ../../src/topics/outputs.md:91 f82db001b58c4969b2d8bc1dcbd7cf8a msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 dee904cb678d4eb49dc829d6590b267a +#: ../../src/topics/outputs.md:93 26d9f0b28d384617a8e490c1f8e26e52 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 a21c1fd3194a49ae992a743023653dc5 +#: ../../src/topics/outputs.md:99 cf46c971b31b4e10bf0fefb4cd028c2f msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 e72c526da47a455da4b10e33938d1600 +#: ../../src/topics/outputs.md:112 a4347983fb9945a4a2773af88e426dc9 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2730,11 +2719,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 6447f4b8bb5f4f93bd8ec2c7b1fb09cb +#: ../../src/topics/parameter-references.md:1 c5489e0633114372b273098ee2c9ffd9 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 1faea30495a440a68dbd1647dacc404c +#: ../../src/topics/parameter-references.md:3 75de9fd63393429daf1ca10a85339aa7 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2747,40 +2736,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 0c0a3f58a93f492dbfca14523809aacc +#: ../../src/topics/parameter-references.md:13 8b5d0ada32d645be9359f43a431f5f91 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 460842f202db493dbb901be73a02797f +#: ../../src/topics/parameter-references.md:19 2ed93dc8778e44209194f41b9ad193d5 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 2591c2cf9e5f402281031ea8dd41a251 +#: ../../src/topics/parameter-references.md:25 a80dd6d9920540e9880514e04035af86 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 b093abbff3614b2ba0141f07376a5220 +#: ../../src/topics/parameter-references.md:36 9de300f7b9da49f59d1c9fd96dec4a8b msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 fda3718113354215bd2ac212553fb2d4 +#: ../../src/topics/parameter-references.md:47 a61f52d3c1024c3692899e05fcea4bee msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 271e78089c274154a0233289d705e628 +#: ../../src/topics/parameter-references.md:51 dafc9ba578c14fd79d075160e6b7bd6b msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 29ab4fa0876b4c11a0c7482cca56ed80 +#: ../../src/topics/parameter-references.md:54 28ca6cae42904559bcec98fb9d2b07cb msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2788,45 +2777,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 78e1857c5bd54af1b7ca4728879e6219 +#: ../../src/topics/parameter-references.md:59 616c9ff9fcae489285f0bbbc67f07d29 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 dae7873015254aa7874379164c90a8d0 +#: ../../src/topics/parameter-references.md:61 ac17acd83ddb43dc9fb7a5e595ab1153 msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 7a45deb4682b49fd86d62fae41831db8 +#: ../../src/topics/parameter-references.md:63 156573324cde41ee8b3c47deabf43db8 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 442f77a69b314cba8e8857470263c706 +#: ../../src/topics/parameter-references.md:69 c9725be01e8a401fb3ad9ff01339f81e msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 d4455241f14549b791e59fc1f942c8cb +#: ../../src/topics/parameter-references.md:72 6797335256e2412cbbe7636507931455 msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 ff4b1c05c5804ec7846043ae8814ad21 +#: ../../src/topics/parameter-references.md:74 05a5f0fcb7454cb697e3d810d55fac26 msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 119e026b595f49c090d62aa7b7c77de4 +#: ../../src/topics/parameter-references.md:77 406e68280b5c4ee494632f94b635b7ad msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 5449d9c5687544a3bfbf8b2b25640a83 +#: ../../src/topics/parameter-references.md:81 2d6e2a4ff391494591bbdf8dbcc4a6ae msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2834,13 +2823,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 b3191a7bd03d4ff18802ae0f5d419676 +#: ../../src/topics/parameter-references.md:85 e71a974b29624210a107fc2d097d4196 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 ea9cfbbd4cbd4f26ba4b0cb50d58635b +#: ../../src/topics/parameter-references.md:89 b59df98754e24654bfef0b1fe1d91660 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2848,43 +2837,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 7d39ed2a3a724dc1a75e6b2cdf87d91d +#: ../../src/topics/parameter-references.md:92 d2bccbff1ce646348fe38c776ad183e1 msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: a1306ee650344278ae39d6086b1ed7d9 +#: 943ba46512ce48fe8c5b62327734c503 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 21d76d22f3044460b925fee68ac74454 +#: bbcd43d5af7d44108aeb65075a6bd2be msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 6b8a5c59217c4928874710ead1456622 +#: 834295755af841a78e466eea43864861 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: a9f6d09055c24029a5f85c3a663c4202 +#: a6b626489bfa468e8f059ab3aa669201 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: d3948618f9274ad0a333722567efeea5 +#: e1dbea105aa845c38cb1f90b43847271 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 44623c81141345a0b0080e719e1418ab +#: e9640f47d40e45bca184eb30700df648 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2894,14 +2883,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 6e80d82ed57b441b8292961ec3163213 +#: 0456efb3718b4356ad2b277ee16de967 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: fc61f369e720463f8a5cd6c751d1d5e6 +#: f7e97f926505407f8f8e9a427e055e43 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2910,7 +2899,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: f20aadbfc13243498ad199376c314e72 +#: ec597ff8f6ee47bc815b069335869f1f msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2926,11 +2915,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 e66956313b8f4f02bb96cfb256e2a7d4 +#: ../../src/topics/staging-input-files.md:1 7467a7f6f26a459ba4ce83e4e6dfcc2b msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 f18c5a8fcbe84135a6e06cbf8008cd63 +#: ../../src/topics/staging-input-files.md:3 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2940,26 +2929,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 87fe14c9a0594602aa56a7706e089458 +#: ../../src/topics/staging-input-files.md:9 a03372581fa44f9b8e3e088a4099cdd9 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 6e10063f55b747e1b07d6109ab7b046b +#: ../../src/topics/troubleshooting.md:1 36e082be73464be0ad5d0b681cc510da msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 e8831832b32449f4a8a3dde3c1b479cd +#: ../../src/topics/troubleshooting.md:3 4464455b51ad4873ac13c4a63ee5fb54 msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 9c86467137864626a2079cb6cecb71c0 +#: ../../src/topics/troubleshooting.md:6 ed7ff0753d1743a995f4cfedd6e5dcc2 msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 24b66a3e2e464ec6a85b5dfbaad1cbf4 +#: ../../src/topics/troubleshooting.md:8 4c2dd10dd66446058477a52fb8d2c602 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2968,7 +2957,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 6d28f1cd40c045f384313c4d74073ed2 +#: ../../src/topics/troubleshooting.md:14 978b6a5fd5fa425fa9a18d9f0e8788da msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -2978,18 +2967,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 5235ff0c35c54396aceb799a65f6158e +#: ../../src/topics/troubleshooting.md:20 000c0d6ae8bf414d9293b9f13fd2e448 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 fc49344510594559b4f888bc45093b51 +#: ../../src/topics/troubleshooting.md:27 7e91b8811be14f8e80df39ac4c5bd316 msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 6e62be8d7d1344e8917904278b508518 +#: ../../src/topics/troubleshooting.md:35 d42799cc5bd4484bb6beb309a61e103e msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -2997,7 +2986,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c91b3a2818b143f58bd37da63479c560 +#: ../../src/topics/troubleshooting.md:44 48bb0f6666ac48648c7d969608b3bd48 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -3005,7 +2994,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 86f283bc522c4be2adfac16256f01b0e +#: ../../src/topics/troubleshooting.md:48 f8876044db184cbaaca56579d0c773df msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3015,7 +3004,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 5362aa1d28344968953ab9cb389ccd8e +#: ../../src/topics/troubleshooting.md:59 a5a3d408dbe34cfda4dd0b2abe67e7d7 msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3025,15 +3014,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 4bb1aafde4f745a083d3a276497523dc +#: ../../src/topics/using-containers.md:1 4c240a18c4e6441189489011242c1efd msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 b00987baf6974ff9b7e3b8cdfd7abd9a +#: ../../src/topics/using-containers.md:3 e37e76ef376a4ee695e600998906ec1c msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 9ac51c5a2a0a45859e14d9e388edd5f0 +#: ../../src/topics/using-containers.md:5 51a307b0ba7c4c1d89309ba8d2250471 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3046,35 +3035,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 5494ccdb1a354b2386c82bd9a6f0b6a9 +#: ../../src/topics/using-containers.md:15 13cc38d72d34468fa4eb6d91f23ff105 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 4cfa8fc2bb224883946d5f63b372de82 +#: ../../src/topics/using-containers.md:18 42a48398d3ef4b03bd7395120f2cfb42 msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 e16c1922527a46e28bb5d933614cdaf7 +#: ../../src/topics/using-containers.md:21 d59387b433bc4ecfaf7e72026624db02 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 7498a71704be462abef71c42e6b83d1b +#: ../../src/topics/using-containers.md:27 d963418ccc0b4803bbc758d718ccb5aa msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 ac0689bff9db46ea8bff8cd35cde86f3 +#: ../../src/topics/using-containers.md:33 a224d1510c9e46aab23d8bdc03c349dd msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 c4b7da5575674ca3ae734424022ef090 +#: ../../src/topics/using-containers.md:44 0a82f8a45b0546aaac4c976dcc98014a msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3087,23 +3076,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 d24fcecc17d0461cbd8689067f770c0d +#: ../../src/topics/using-containers.md:52 bc418a2a535e49359c4cd44b373bbe02 msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 833d4d3b3f0e4c7cb8b1d35cb9a78a7e +#: ../../src/topics/using-containers.md:55 a799fba2322944cea00e413c08066536 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 50fc0573276e4dd4a47208ed81109991 +#: ../../src/topics/using-containers.md:69 35379c6b972940bd8451f10b74dd793e msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 f72e10e746604421904057ddf7078d3e +#: ../../src/topics/using-containers.md:72 2d5265525ad544a0b64ad2cf07aacc26 msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3111,44 +3100,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 ee126833f6014e378c7841c4048dae85 +#: ../../src/topics/workflows.md:1 e2521b89596d42f8a87a3207fd6c32f2 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 0325bd610aa747b0b657afa0c978a1eb +#: ../../src/topics/workflows.md:3 3676f23b63e142cb8e5715ae07216a47 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 7c901105cf6949909d87be5681331368 +#: ../../src/topics/workflows.md:13 00725aed13a440ca8b3c4f9155fbee99 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 74138d0c2ded4311bf688df4a28387b5 +#: ../../src/topics/workflows.md:41 2e38a4f9072b4ad9bbb74f943d22084d msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 1ec4773e7319414b997d746d1965ff56 +#: ../../src/topics/workflows.md:51 2b9f4035ea864b6db50c861a1819289d msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 5f860dd70e3b435188c61a538e5de0ef +#: ../../src/topics/workflows.md:81 28e9064780e7418a8e02a22f92e34404 msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 a9c56df6dca441dfabda7fa54fbe56c6 +#: ../../src/topics/workflows.md:91 66ce14a10d2d4dc497d3ed71e11ed8b8 msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 586d561ddf724319b3da9ae857828648 +#: ../../src/topics/workflows.md:150 8dc00528c3d2426c8a3492a8191f1d81 msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3156,33 +3145,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 f3e80b1903534065a30323611c267e9b +#: ../../src/topics/workflows.md:160 f9ef5e258f7c4971a8543d1dfed711a8 msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 6ed53c6f9fb94d4ab3d10532c605c46b +#: ../../src/topics/workflows.md:165 324bc51071d743ea80124c23880ddc0a msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 3fcfdf43b0a049388634625c45e0b1bb +#: ../../src/topics/workflows.md:167 d8c13e01976b43a1af34c11a7bc36897 msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 49415efafae64f94b66cb46ca2bbd40a +#: ../../src/topics/workflows.md:170 43910a8ab4484e529a17df418b1aedbb msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 4806a2ef982944e8b073fafd416d3d74 d45701eeaa6e42feb4ef79d2fc4af756 +#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 155cd684ff304258ae374b2e13090e5f +#: ../../src/topics/workflows.md:180 7ad12d67e815400c94080804b9285629 msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3195,34 +3184,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 d8bdb44011274f94b606277799a6fa6f +#: ../../src/topics/workflows.md:183 457d5a31c79143acae2683d95d27f7a3 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 9e1d9bc2f83743ea9964ec418d225200 +#: ../../src/topics/workflows.md:185 a2a73901bf634547900d08b9a1ac8889 msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 a1240eab3ef746cf82a2c5451042b888 +#: ../../src/topics/workflows.md:191 f347d80e62384b14acf6423675e5359a msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 a73cdc43a8e44973808027c29903afa3 +#: ../../src/topics/workflows.md:205 2a845a4f3f98428fb82f3ca7ce038a6e msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 4277837a9fd443378d5ca3d9252993c9 +#: ../../src/topics/workflows.md:212 e2007c74d5f449a882809d6b91c010bf msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 09b714af60ee4ecc8ab1b95eac8284dd +#: ../../src/topics/workflows.md:221 7f5e53ee7cf94be2bff45ef64db28a24 msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3230,7 +3219,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 3e99a3be9265463daf74b00a21d89cff +#: ../../src/topics/workflows.md:233 a0d076b7b8b048478580c99ef0c8429f msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3239,7 +3228,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 1c4a959d43b74686ab801a26ef412b3d +#: ../../src/topics/workflows.md:248 7fd926c18ad548e98845e9b5134dd6f2 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3250,7 +3239,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 55daf180336d4045ac0cc4c14af98cfc +#: ../../src/topics/workflows.md:256 789fbd47f8564cceb430ef3c0bc90e9b msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3258,7 +3247,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 5ae40eb04d5440d5ba882a74aa5b9708 +#: ../../src/topics/workflows.md:261 45c4d0492d6143ca9cebe81e9b2cf3ae msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3268,13 +3257,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 f93e9b776a4544018877b7a13399609b +#: ../../src/topics/workflows.md:267 73bd3da2af8545928d5ea71d0f7454f6 msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 0e587435e3884334bc51a4abf4b4d785 +#: ../../src/topics/workflows.md:278 15ce3d2700424f0fbb280d602ccebcf6 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3284,11 +3273,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 81b98764289245c79f18fcff478f4a9b +#: ../../src/topics/workflows.md:285 af4268f19202436eb0a7e8c6bed5e386 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 9baddec4015f40ad82ea2dee30305654 +#: ../../src/topics/workflows.md:287 94a4eadca6b949d79de2990a0150eee8 msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3296,17 +3285,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 986c3dd9460b42b3b20e2d01ba1fbe51 +#: ../../src/topics/workflows.md:297 09c1619e8cbd4febbb637f7e99ad5890 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 4558f174fea445fd97b80d963fc74f43 +#: ../../src/topics/workflows.md:300 677ea7a27eb64568ab3689142d6efe70 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 532823a13154401090e9fee3e018fda9 +#: ../../src/topics/workflows.md:309 097e6d47f9394e62b80110700492783a msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3314,7 +3303,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 7b6f46b70bac4f848a956ea160243621 +#: ../../src/topics/workflows.md:314 e93affce8c104bf6977182047c1f1077 msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 3861b4a31f71471b97bf9dc18cc80594 +#: ../../src/topics/workflows.md:322 06c9e04ba890473b851240a0fa9c3b12 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3336,7 +3325,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 a10c37f65ac14ef2a5971872bc9b8f9a +#: ../../src/topics/workflows.md:336 0380dc1fe3aa48e4b62283b7b2a611d8 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3345,7 +3334,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 34175f932716406f836840732618caee +#: ../../src/topics/workflows.md:341 49b251f7a313492ea60504b00109e526 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3355,7 +3344,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 0d132dc39cdf4818bc8e20132073f669 +#: ../../src/topics/workflows.md:347 7ee55702d7dd4679a24ff052f6f0cbeb msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3363,14 +3352,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 9f8c45f077974cf79612ee83df3d152b +#: ../../src/topics/workflows.md:366 85d7e2e270874aa6b9f477cec0f48154 msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 435f80d0599b4d93ae1339e8c7bc020a +#: ../../src/topics/workflows.md:383 570e94513c984c09ad6aa255f534216d msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3379,7 +3368,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 d39b024a1a8d4eae8d7fd3c929a782e9 +#: ../../src/topics/workflows.md:389 a107258662fb4bd4a9a3d8754e34d1e9 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3388,7 +3377,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 3cbbe074843d4306b762d2fbc6fe9850 +#: ../../src/topics/workflows.md:394 fc1a6502d831458ab8371a575cea47e2 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3396,11 +3385,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 7118b6e09b9f44129c7d98d90570f2c2 +#: ../../src/topics/workflows.md:398 2d10806bf1ce4e26b92adda61efc0862 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 70f3e73ee3714f22ad6ee43dd5ece703 +#: ../../src/topics/workflows.md:400 046c5e134de94b629cc22d416f3c9182 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3411,7 +3400,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 279495257ead4a4fa725c7d68c504162 +#: ../../src/topics/workflows.md:411 52fa22d3277940049fbb589a3ea73433 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3419,23 +3408,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 86d1d742bb5c4a9898aa573ce648f0ec +#: ../../src/topics/workflows.md:415 6043beb96c2c49648011ec556aa9e986 msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 f4987847f46e4a2db54127ec7ebcadf7 +#: ../../src/topics/workflows.md:421 5ac4310515124e2986724425bed5651f msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 80e7c22dfe4d40749f2e9c3bf02bf8bc +#: ../../src/topics/workflows.md:429 7958e91d5c2f4046aa9d2070a900f9ae msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 e930bb5d430a41d9b5bf49e473dd2ed1 +#: ../../src/topics/workflows.md:441 2db234d776fe4fd38bab07245dcb783a msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3443,7 +3432,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 4076e9eb67ed4bd5942f089e394bad26 +#: ../../src/topics/workflows.md:445 7cfb17230e284ee7b6e2a00efe8eeb74 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3451,59 +3440,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 1b44092e87b840de8f1d022676d0990d +#: ../../src/topics/workflows.md:450 4311ac98544e4fb0b2f4b24985710a01 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 a8afac626f5d4240a57267085b9bef26 +#: ../../src/topics/workflows.md:452 780f9c72e6c34c39918642c7e2477355 msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 0896efc674bc402495c6e73c6c352523 +#: ../../src/topics/workflows.md:458 cc4a7316db644b438cbaa181ad9ef2d3 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 91a53d918d4b47bdbe0b0a6d4adfc0dc +#: ../../src/topics/workflows.md:466 dfc461a03fe8487794837904febb8b63 msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 8325682d51d8421b9ea507f424f71e73 +#: ../../src/topics/workflows.md:469 1e83485b00b64dfaba897bd8d772e0f0 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 503d068602d8477a820b91d835fa3f28 +#: ../../src/topics/workflows.md:472 d0321d6805ec4d3abf3877d02a0a417f msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 4e768b91eb274a5cb157f1e3fe2f85cd +#: ../../src/topics/workflows.md:480 d7d77e807b3048c7bdf89558f76804cb msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 18ec5231b7bf4c9ea59361b325fcdd01 +#: ../../src/topics/workflows.md:483 8d9b8be147fc4a71922dde858842e543 msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 87fd118dc2774cf08db0a3ba56520da5 +#: ../../src/topics/workflows.md:489 34b7705416a745a6a42e6d402c0757ed msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 8168ffcb23124b3f839a9862a7ec0958 +#: ../../src/topics/workflows.md:491 257adcee9da64d5c987f3b64efd20ab0 msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 37c222ea14904fd4a8fa93a1e0103239 +#: ../../src/topics/workflows.md:497 fa6ed5d0c14f42f4aa3c5144648db22c msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3521,7 +3510,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 d392813fc6d14851a294a391426d41f6 +#: ../../src/topics/workflows.md:509 333e8ce458d54de394526769f96d12d2 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3529,38 +3518,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 652155460eaa42b6856c16cffdb845c0 +#: ../../src/topics/workflows.md:513 b819e8a5df6e4fa495924095709669ef msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 6313cb377dc249e0b2262a3fe732fe32 +#: ../../src/topics/workflows.md:519 f1955468a1364d44a930db77c9c4b495 msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 11f73cf24fb044e3a3afb3adb6137708 +#: ../../src/topics/workflows.md:522 8c3b9b645a204d02b2c73a205e8ec296 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 def9e62bf73f49eebce09677954e2a92 +#: ../../src/topics/workflows.md:524 4d88b9c186cd4502adbf752e8a70b6ce msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 200dfe47d09d4b0b9e4acf29b7e038da +#: ../../src/topics/workflows.md:527 9927673564024ba5833b5ac271737857 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 858bda7fb6524e9dbfb35596ce6a6d07 +#: ../../src/topics/workflows.md:566 84f4ed7ce2004742b8db9087104a469a msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 28897819504247a3a6cf9a9d9476b63b +#: ../../src/topics/workflows.md:573 2b5f9757adca4490a149c7f45e14fcb5 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3569,7 +3558,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 4f8fd11e29b048e1851299002c3a48c4 +#: ../../src/topics/workflows.md:587 0418de720813442f81ecff293c9448b5 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3577,62 +3566,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 ed33196347d949eda752a081c7af4657 +#: ../../src/topics/workflows.md:607 524eec63be8248ae982939c975ef50a2 msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 738c67568dbb4f2bbb5756fc5e727c01 +#: ../../src/topics/workflows.md:627 5e99f9912cc549a7890e2934425eb943 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 19b016a1fec14056a9812c1c195c7c90 +#: ../../src/topics/yaml-guide.md:1 b0121ee087d6424fbb0ea5957a7b0b8c msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 a513367d60a74f559339c05d8ef10eb7 +#: ../../src/topics/yaml-guide.md:6 49e9f6b3a06840289decf3f557860f87 msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 5e30680941164047a47f98417e916188 +#: ../../src/topics/yaml-guide.md:13 ed9eebec0b3d4b72ba65507d37757a37 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 ca02f2bf1d754d5190f296674245b936 +#: ../../src/topics/yaml-guide.md:16 bf9b255a24a84f3ba989a223492b8f41 msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 466615194bb541fdbe2e6515b50531b3 +#: ../../src/topics/yaml-guide.md:18 e79fa0b7f8b14810a3a20908ef92bc55 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 33e664d59a30407891336db290a8a5b2 +#: ../../src/topics/yaml-guide.md:19 290e2035f903417cbecb5dc5f09d6ebe msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 3e52ab079dcf4fc6a3f052a517f4d31b +#: ../../src/topics/yaml-guide.md:20 d420730151534f1a89076588a3358f09 msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 abcad6b7d37a4342a90c2d5952ea1232 +#: ../../src/topics/yaml-guide.md:21 a6b5378bbe1e4bee9e37a765bddf75f7 msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 500a489e4fae4d1abaa8883f632d1a24 +#: ../../src/topics/yaml-guide.md:22 6e4d9465dc2b454d96b02d7ad1817795 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 546c1ef51a63487c91c98059dd46b0cb +#: ../../src/topics/yaml-guide.md:24 a649d4af5f434dac9395e013ec4836bb msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 72b4262833054edd9efe6078381de654 +#: ../../src/topics/yaml-guide.md:26 446190a298834b73bda068286e8490cf msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3642,7 +3631,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 7b7e8242660744b791ba3868e4ed7e37 +#: ../../src/topics/yaml-guide.md:42 2f35c012ff174721bffe66a3f58a804f msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3651,7 +3640,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 492d994a541c4c948fb5da9041153bcf +#: ../../src/topics/yaml-guide.md:51 43127c98c9d94aedac61cee67929c1a6 msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3662,28 +3651,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 e2209269db394f3988f18b147a57677c +#: ../../src/topics/yaml-guide.md:61 dc4fe561203c4c38a9caea5bd6eff2cd msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 e15c39c65aca47f690264d8008463bec +#: ../../src/topics/yaml-guide.md:63 f924e4896db2424d99ce8c9da14c599a msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 afa546fcb7fb447d939d4a167f206f79 +#: ../../src/topics/yaml-guide.md:76 bf7646f5f925485c842a6d34140e40b8 msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 7dd375e0fd964413af4957396d2a0474 +#: ../../src/topics/yaml-guide.md:79 c483e61dec8949fa96bb893d422888a0 msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 af8ef039a64a4c0783d7229dbdac65ef +#: ../../src/topics/yaml-guide.md:81 85fcb523d0e34a499eae04d304887f7b msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3694,7 +3683,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 3ce968cb39a443059f6a828b3c8c2f33 +#: ../../src/topics/yaml-guide.md:104 83d47c8736a34f3cbf09e3997845e4f4 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3707,11 +3696,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 3c2f48a8e616400b9a8ffb4b6f7efc9b +#: ../../src/topics/yaml-guide.md:127 c698fb3d37bc403e9aeb679b8fc0e15e msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 c432b1656e0e49ef87aa3d6e42acad84 +#: ../../src/topics/yaml-guide.md:129 ae8af2f0eeda4aec97201211dfa965c7 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3722,26 +3711,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 cac5e52767f74ce98693e2a19ee1eb0d +#: ../../src/topics/yaml-guide.md:146 2ee87aa465cd41fda16a61e242f8c9d0 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 101666907f8b4fb994e25ceffcf04a13 +#: ../../src/topics/yaml-guide.md:167 0a6fd4469ff24b61b3ad001b09eead18 msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 5461960a469042a487b89e440f856aea +#: ../../src/topics/yaml-guide.md:169 b96ba19bce9341d39c46054e1f10fe8f msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 e31349c164c84a9da46e2fb1861793df +#: ../../src/topics/yaml-guide.md:177 903f30af3d0c45cfb61063936a8097a7 msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 49a0b3dfdc9e4d58b6bc966db979ace8 +#: ../../src/topics/yaml-guide.md:184 ede8db7c0a58432e8a1c416e937a06d2 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3751,52 +3740,52 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 e08ec8c473e847f98e8a18b9ca0f2670 +#: ../../src/topics/yaml-guide.md:194 c8b53615476a4a1fbef2420d93bac94e msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 6ee7bfb4a9e04dd19b5180bca5b02705 +#: ../../src/topics/yaml-guide.md:196 ea03cb5525cc491f9feb5c4780b38fee msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 42614ab7ba1546f89abeb8f48991271c +#: ../../src/tutorials.md:1 92fd3a5e31714eab859dd630af2e78cf msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 b8df5b8393ed4d869c066640fe83ec7b +#: ../../src/tutorials.md:5 de660ecdb5b44c97a0e519d00b232497 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 5b9aee5af41f438b9f4208294bf97f4a +#: ../../src/tutorials.md:7 5afc1e1288e74ed0985e61e5164479c7 msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 a71d3022dcfc44979cca4655ea51ad42 +#: ../../src/tutorials.md:9 862dc7ac81e54b1fb3d4c2f961b8810e msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 42b5a982e86f46dfbfcd7bfcc99d72a5 +#: ../../src/tutorials.md:11 e2c94c0e1c7048d38cd7aa2c465a859d msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 12dc402d053044b78d69927dd391fe9d +#: ../../src/tutorials.md:13 b63253780f51467a95207d820d13ac39 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 687c20e2e4bc4f869c7ee9390e61476a +#: ../../src/tutorials.md:15 6d06ca7ed5df4560aaed286f4fe33928 msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 a975fbb3ea7d467881ce0245de538295 +#: ../../src/tutorials.md:17 5448df4a6a8f431d80e269bcd480e19e msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" From eab42db5f89e05fd13496aa0600c3ff13008703c Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 27 Jan 2023 11:19:56 +0100 Subject: [PATCH 045/179] Revert "convert license to RST to restore indirect links (#366)" This reverts commit a8098340780f4db905c755358391ddc75417727a. --- LICENSE.md | 63 ++ LICENSE.rst | 59 -- locales/es/LC_MESSAGES/user_guide.po | 1380 ++++++++++++------------- locales/pt/LC_MESSAGES/user_guide.po | 1385 +++++++++++++------------- locales/user_guide.pot | 1358 ++++++++++++------------- src/LICENSE.md | 2 + src/LICENSE.rst | 1 - src/index.md | 2 +- 8 files changed, 2153 insertions(+), 2097 deletions(-) create mode 100644 LICENSE.md delete mode 100644 LICENSE.rst create mode 100644 src/LICENSE.md delete mode 100644 src/LICENSE.rst diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 00000000..75596a51 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,63 @@ +# Licenses + +## Instructional Material + +All Common Workflow Language project instructional material and changes +to the structure are also made available under the [Creative Commons Attribution +license][cc-by-human]. The following is a human-readable summary of +(and not a substitute for) the [full legal text of the CC BY 4.0 +license][cc-by-legal]. + +You are free: + +* to **Share**---copy and redistribute the material in any medium or format +* to **Adapt**---remix, transform, and build upon the material + +for any purpose, even commercially. + +The licensor cannot revoke these freedoms as long as you follow the +license terms: + + + +* **Attribution**---You must give appropriate credit (mentioning that + your work is derived from work that is Copyright © the Common Workflow + Language project, and, where practical, linking to + https://www.commonwl.org/ ), provide a [link to the + license][cc-by-human], and indicate if changes were made. You may do + so in any reasonable manner, but not in any way that suggests the + licensor endorses you or your use. + +* **No additional restrictions**---You may not apply legal terms or +technological measures that legally restrict others from doing +anything the license permits. With the understanding that: + + * You do not have to comply with the license for elements of the + material in the public domain or where your use is permitted by an + applicable exception or limitation. + * No warranties are given. The license may not give you all of the + permissions necessary for your intended use. For example, other + rights such as publicity, privacy, or moral rights may limit how you + use the material. + +## Software + +Except where otherwise noted, the example programs and other software +provided by Common Workflow Language project are made available under the +[OSI][osi]-approved +[Apache 2.0 license][apache-2.0-license]. + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + + + + +[cc-by-human]: https://creativecommons.org/licenses/by/4.0/ +[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode +[apache-2.0-license]: https://opensource.org/licenses/Apache-2.0 +[mit-license]: https://opensource.org/licenses/mit-license.html +[osi]: https://opensource.org diff --git a/LICENSE.rst b/LICENSE.rst deleted file mode 100644 index cc6a19b0..00000000 --- a/LICENSE.rst +++ /dev/null @@ -1,59 +0,0 @@ -Licenses -======== - -Instructional Material ----------------------- - -All Common Workflow Language project instructional material and changes -to the structure are also made available under the `Creative Commons -Attribution license `_. The following is a human-readable summary of (and -not a substitute for) the `full legal text of the CC BY 4.0 license `_. - -You are free: - -- to **Share**—copy and redistribute the material in any medium or - format -- to **Adapt**—remix, transform, and build upon the material - -for any purpose, even commercially. - -The licensor cannot revoke these freedoms as long as you follow the -license terms: - -- **Attribution**—You must give appropriate credit (mentioning that - your work is derived from work that is Copyright © the Common - Workflow Language project, and, where practical, linking to - https://www.commonwl.org/ ), provide a `link to the license `_, and - indicate if changes were made. You may do so in any reasonable - manner, but not in any way that suggests the licensor endorses you or - your use. - -- **No additional restrictions**—You may not apply legal terms or - technological measures that legally restrict others from doing - anything the license permits. With the understanding that: - - - You do not have to comply with the license for elements of the - material in the public domain or where your use is permitted by an - applicable exception or limitation. - - No warranties are given. The license may not give you all of the - permissions necessary for your intended use. For example, other - rights such as publicity, privacy, or moral rights may limit how - you use the material. - -Software --------- - -Except where otherwise noted, the example programs and other software -provided by Common Workflow Language project are made available under -the `OSI`_-approved `Apache 2.0 license `_. - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an “AS IS” BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - -.. _cc-by-human: https://creativecommons.org/licenses/by/4.0/ -.. _cc-by-legal: https://creativecommons.org/licenses/by/4.0/legalcode -.. _OSI: https://opensource.org -.. _Apache-2.0: https://opensource.org/licenses/Apache-2.0 diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index 3fa6daab..ba080ed4 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,113 +9,149 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 16:53+0100\n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" +"Language-Team: Spanish \n" "Language: es\n" -"Language-Team: Spanish \n" -"Plural-Forms: nplurals=2; plural=n != 1;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.rst:2 dcdc2e8da0ec4d9e9453601fdd83bac5 +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" -msgstr "" -"Licencias" +msgstr "Licencias" -#: ../../LICENSE.rst:5 3e165520ca56481b8f8d494a8d471de3 +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" -msgstr "" -"Material didáctico" +msgstr "Material didáctico" -#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." +#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." msgstr "" "Todo el material instructivo del proyecto Common Workflow Language y los " -"cambios en la estructura también están disponibles bajo la `licencia " -"Creative Commons Attribution `_. Lo que sigue es un resumen " -"legible por humanos (y no un sustituto) del `texto legal completo de la " -"licencia CC BY 4.0 `_." +"cambios en la estructura también están disponibles bajo la [licencia " +"Creative Commons Attribution][cc-by-human]. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del [texto legal completo de la " +"licencia CC BY 4.0][cc-by-legal]." -#: ../../LICENSE.rst:12 b7a7a0fb40344fe087c1cc3ec19308aa +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" msgstr "Usted es libre de:" -#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 -msgid "to **Share**—copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" -"**Compartir**—copiar y redistribuir el material en cualquier medio o " +"**Compartir**---copiar y redistribuir el material en cualquier medio o " "formato" -#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 -msgid "to **Adapt**—remix, transform, and build upon the material" -msgstr "**Adaptar**—remezclar, transformar y construir a partir del material" +#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" -#: ../../LICENSE.rst:18 430ff4de74924bc3a3b2c7e809ea4456 +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.rst:20 2173e2af49be41ee97a74c4e879faf25 -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " "términos de la licencia." -#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 -msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." msgstr "" -"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su" -" trabajo se deriva de un trabajo que tiene «Copyright © The Common " -"Workflow Language Project» y, cuando sea práctico, con un enlace a " -"https://www.commonwl.org/%20),%20brindar%20un%20%60enlace%20a%20la%20licencia%20%3Ccc-by-" -"human_>`_, e indicar si se han realizado cambios. Puede hacerlo en cualquier" -" forma razonable, pero no de forma tal que sugiera que usted o su uso " -"tienen el apoyo de la licenciante." +"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su " +"trabajo se deriva de un trabajo que tiene «Copyright © The Common Workflow " +"Language Project» y, cuando sea práctico, con un enlace a https://www." +"commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e indicar " +"si se han realizado cambios. Puede hacerlo en cualquier forma razonable, " +"pero no de forma tal que sugiera que usted o su uso tienen el apoyo de la " +"licenciante." -#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 -msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" msgstr "" -"**No hay restricciones adicionales**---No puede aplicar términos legales " -"ni medidas tecnológicas que restrinjan legalmente a otras a hacer " -"cualquier uso permitido por la licencia. Con el entendimiento de que:" +"**No hay restricciones adicionales**---No puede aplicar términos legales ni " +"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " +"permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.rst:35 f6aae4a5cd0547118c8a3240ca2b4be6 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limit +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." msgstr "" "No tiene que cumplir con la licencia para elementos del materiale en el " "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.rst:38 a40c173be35b4c1b92e83f42bfe2382c -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." msgstr "" "No se dan garantías. La licencia podría no darle todos los permisos que " -"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como" -" publicidad, privacidad, o derechos morales pueden limitar la forma en " -"que utilice el material." +"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como " +"publicidad, privacidad, o derechos morales pueden limitar la forma en que " +"utilice el material." -#: ../../LICENSE.rst:44 3d7ca3f2cede4d5f998bf014bd970748 +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea msgid "Software" msgstr "Software" -#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." +#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Excepto cuando se indique lo contrario, los programas de ejemplo y otro " "software proporcionado por el proyecto Common Workflow Language están " -"disponibles bajo la `licencia Apache 2.0 `_ aprobada " -"por la `OSI`_." +"disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " +"la [OSI][Osi]." -#: ../../LICENSE.rst:50 4ee4d68b90fe422880da856cd539b982 -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." msgstr "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 5ad4be9b62d54c95a913795b514676fd bdd540403a5746ff99edf2dcad0e3122 -#: dfc7702e073140c985cf47272a20214d +#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 +#: eab02dc13915490bb3c9ba744d78b6a7 msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -124,30 +160,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 3060770b3bef41d7bcfcdfb413d7689c +#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 48bb9f628b344ba1a3b67ae1cb264e3c +#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 7e3684e9672643738846756e1ebafd18 +#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 187ceabb7fd9480bb8cf0f2da47f65ef +#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 b548b76bcc85420a9b30792386105139 +#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -155,94 +191,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 9ce692b78ead47e4b0f8cdae8837d35b +#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 6df1201c159343da9e7515379980d6a0 +#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 f9ab1d0dc1c842b6abb5385268c1d3bd +#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 9f6a84ab6a9343b6ad7db826f8964362 +#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 fa50e4fa990b42d1ba4c0f4ae1e5caa1 +#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 3a871012fcfd4f3ebeca0cb86ec93435 +#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 d954edfff2584288ac8c600733070d2e +#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 af6b1e37d6be4450a761854480ec9aab +#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 31f4a2d43062493ca64c648f80afc8e9 +#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 41c54e71b6cd4f63b2a619a515240d34 +#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8edc3541ad134ab5a1d23c724f1f0a4e +#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 ac0ea81eba8842a18801ab03cbf80a57 +#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 52be1a5640234feabe958ff7ade33653 +#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 c6db734d5aef4f4f99676bdebf9c83c9 +#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 a9f7b47c0dd741739795da39bf114879 +#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 e3fdd9228b924905a4a1f4b2b7ad7159 +#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 3f7cda1437cc48f18745a827ebb74582 +#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 5aeaba2cae64442e816bbd458aee833a +#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -250,22 +286,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 5af827a402834978addd82c70be6b5ab +#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 6d69e42bd8e443c4b19d80807c7efd6b +#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 404640397b6e40c2a2cd5cf85ab3b1c0 +#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 1682c2486e224770b62269709a8663cf +#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -274,25 +310,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 9078fc009bc145808813c9cc2b734b58 +#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 d4b5a54a400c409cb7984428f6a03ec8 +#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 9e8dbee6e8f84d08b1a54fffa06394ef +#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 msgid "" msgstr "" -#: ../../src/faq.md:248 1d846bfb5f054d09a4afad1da8e4b642 +#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 2d0e95fec8084787b734388d60188574 +#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -300,26 +336,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 eccc4a364330470fa474dcaaa3433390 +#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd msgid "" msgstr "" -#: ../../src/faq.md:268 e945f6a337af4e4686bed482a4fe6c39 +#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 8a3efaa0ad1548428bcfd6e01d135cdc +#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 cdab644adc5643708870fb08c06cbfca +#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 089a5a0b076b44aeaab4d69ee3c79f97 +#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -328,77 +364,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 561172559c6f41a68819608fd9e58bb0 +#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 c5ee4946d2e840abaa3dc796a62652c7 +#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 4f2069a2113c414db18eca95550e9e09 +#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 31f3390e6771414ba7bf57c044c4b0c4 +#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 3b77ce4930ae46d5be9f6965e8c54727 +#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 06f36bbe4d3840229b7374f27b86ae80 +#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 3cb2f70d00274a4dafd972ccd8c519c2 +#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 093a1529262043ef84a99675054938e0 +#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 45b6d9acbfaa47e5984184f7da554d0a +#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 5705c9bacca5405ca6f14315a5575db8 +#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 82bfc285b59a439ca97d3278997f0fce +#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 181d5130101d45ccb22aebae3d154c2f +#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e864390b5ddb423aaa10e9d33d257dc1 +#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 fe637c32fb15427a9045679b5da42ec5 +#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 1f8004b9df8547029d82e57f9abdc979 +#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 70990dc5a0034099921ceb89c89e2dcc +#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 f679e26f18d9455f945fd13361a9c906 +#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -407,11 +443,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 fcd0273dbdd84e728cfd8fbe239f2a01 +#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 173ddbd1e7c64927a8dcb12a2a2140f8 +#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -422,22 +458,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 662fe273e2fb4042b688512955e450a1 +#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 a15b52205f0145feaac298510e4d678a +#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 512aa0c7166b429e8116f71eef007f79 +#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 b1b19e17a18540939cb3bb7f8a700cab +#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -446,11 +482,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 d58b36ac43ac44139897be752fbb1f87 +#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 6726cf3585a646a8b4cbeb543cf84a38 +#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -458,7 +494,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 2e504aa7c46a426fa959e7254e9a84a5 +#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -466,15 +502,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 e7be0df0838b432d9c7f296d777f120b +#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 173e0816db20432c8d9dba1de5393dee +#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 30eacc583f6841719e2142d283811d97 +#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -485,18 +521,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 791b8f38a14147bbaa174c7eb595f17e +#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 1a3989dcbb9844b39d84bf6df6b352ed +#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 db1bbc6e980f404f9f3fcd08e92ee9a3 +#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -506,18 +542,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 acc7887c65974114996f700a38a7eccc +#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 d2476d9bcff44f21b8d84a3a0d87a246 +#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 f86415e4d78e48c4a8a76ced81221b98 +#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -526,24 +562,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c5524d73708c4c779980528864506fd4 +#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 ac46a9f8850a434bac5bc2b41ee6294e +#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: 9bba7c4f783942e4a299603430601363 +#: a5ebc727fb3443f78e81d6b7ed5ac750 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: e2140e0f0e7747ef8383887c20a7945a +#: 86e6a06992dc4228bfda7add48e28ca3 msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -552,39 +588,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 15bf490724cd46dcbcfab44633c5a9a2 +#: 8c9772f96caf4169924d22eb929a4f0f msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 51d52d051e654a8395239f88df7c9d8c +#: 4fac209a62114798b79e4810f7a0148b msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: eb496cc818524fa7bae5a22ddd00a19c +#: b97ba368fd664caab0494e2392795697 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: c4a22d12e7f149ff901d27de32b9361d +#: 903a6796e3304a19ad885b2428b0e80f msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 7618de899a7043989d77baacf62eb7b2 +#: 6e352ac1f8e144c392ac5adf18c28298 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: 6f1544a220664b79b04bf008058b5a91 +#: cf2922f645904ac7955428ecddc37b8a msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: fbd14ac9a2f541478a320ed4cbc69e13 +#: 5f47aae608c041aeb4134d59dad314d2 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -593,7 +629,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: da4dba50d25d4533b3dbb92f54d32a30 +#: f6f589481d0c4891beaccb63160619ef msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -602,7 +638,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: ce11c9f8d65c4268984d0384d95144cc +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -612,7 +648,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 3a201aa497e84f70855bb2251e7e3281 +#: 4ace6b92f4e04a07aa202840ebe36417 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -621,24 +657,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: b78f7fa2be1c4bb090f6da895457ad1e +#: cc6cd8cb81564cadb8e6a4c49423b7f7 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: f7e95d264ffa4e2db0864faccd9e5a0e +#: 2d9f53b6ed5041dbb6c0b54835897856 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 3f1e5b01e49a4dc1b1c99936a4589afc +#: 907674a4ecff4826a2b880e28fc38f33 msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 03c3048f38ae4938a484cf02001877b3 +#: 037cd0e5ceda482eaeaca03d51745aee msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -648,7 +684,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: f9715b5ec65c405c849bb030c1927060 +#: e4643938445b48cc80eb8973ceeb126e msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -657,12 +693,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 442662f50e9e4620970ce32b1b127969 +#: c4c3315c96714e81b364f8cc003b87e6 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 2b34c786af3840e88f29d214e19dc837 +#: 3eb6a013a2a4478ca2ad134661f65c58 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -676,7 +712,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: dd6aadff8cf54ce78ea6b317afbaddb0 +#: 074af9633627470485e5225326d5f20a msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -685,7 +721,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: fe7f1f0b28434f8aaf0f6ac6589a83f0 +#: 847951c055b94a83b1e081594cef22ee msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -694,71 +730,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: d10cf45b3c7f49dc98bc0e5d1246f224 +#: 44bde1fae06b4678bcac4f3224601296 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 332b6e8b831e4bc5aed3745938230a57 -#: ce7fc63b808d4499b9bf9828c2dafe35 ebf339ed376a4d3b89b15b4d5afe593b +#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 +#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 8badec9987ba40609cf1f626172b2b2d +#: 9d5100c7d0a040aea1020bf633ad17de msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: c75a8b4bf0e24781bf6713cf6f013cd1 +#: 36eb4b3b966640af90faa55db3789cb6 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 79b146ffe6d74e1b8f6019251dc4b7c2 +#: 2ccb956baa6b4376a04ad9fcc4654631 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 07cca9a33d8f4b77ac6ad35ca8b95655 +#: 72889b830c514afe9a7cb1e64b5666a0 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: 31db11c8ddf2423192a8b2063b3e91c2 +#: e29bd7f973544600be589c3b3f84cf63 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: d81dd96143ea444aa78ff45cfa0584b3 +#: c377a7f5dbe645cebbb6c7eccf831a0b msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 c54984605872472190ae7771809a20db +#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 01a237b8ec2f46c9acd31d142591ce75 +#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 3fb9888b666945eab1e3ff109646c574 +#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 5fb0486762354f93853fff209f835c08 +#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -768,11 +804,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 5f1e7a608e0b455196d191c845a5c98e +#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 7ba4b5c51be24f5392949d06ee42e018 +#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -780,29 +816,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 e2d3e6dd13b14d819a504c35da6fe8e7 +#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 91251d1f0efb4d4cb083b4517ff3107a +#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 6ad263e267514c5fb05794d3d76d418d +#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 8a3bfd72dccf4a8c874a96aebcbe5cb7 +#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 5195706d9c6c4573aff135fd539759a2 +#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 9c4506915e4c40599527bc1d2b18645b +#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -812,11 +848,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 37d9eb784ec1425786158f98e3f63890 +#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 572f493a985141a1b92dafbdba92790d +#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -824,7 +860,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 9606d3c4849f4b17b2e55a298210f055 +#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -832,26 +868,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 754fc59967d94ffa935284676d55ffed +#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 2905c6362d4146e8b35bc74744841972 +#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 091278ece252483a9838fb771de3e04e +#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 0928a5c668c3414a945bc9eda147892c +#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 56f3c481762848298214a88e559fc0f9 +#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -862,23 +898,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 710c266ab4a5477b84d6ea987420fa20 +#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 cc353db5da2546bb88a77ce1a202ff9d +#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 b62df08ec96f4cdb887600079856dd76 +#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 97e02557293440d1a58ba659dad21113 +#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 0935c3ff01634c75b5c91546dc36c7b9 +#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -889,32 +925,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 cfb37fd605164a8d9cc75bf892ce97c0 +#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 5f06a7a6aae343d989a5b30979c600f6 +#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 5f956260f3874b6dbeaf3ad7ecc09c9a +#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 d35e4effec554a638d6c3047ef3fd05f +#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 15a1f944a0d642729d3736ed1c907074 +#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 fa34c808bb494ddfa3f3926bc42e650c +#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -922,30 +958,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 0c15f62eb7534e809f625f3fa213e92d +#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 d67719a6f0ce4ba1bb6152a10507b729 +#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 1c96e75281844bfab0578bab2e816854 +#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 bece1fc3c3f842b0b30d8f1b7fbfc200 +#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 a7caa36b0f83448b91ef2e76e30abc51 +#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 39321e93e9994fcca20b425aa45c2894 +#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -955,47 +991,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 601cf500d76c4e0287af4429a46b36d2 +#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 b286d5359e184ef58054c72df4014629 +#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 e14423edd829401faed0950772123240 +#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 889c44360bd54a0e85e7f0e61aa6593c +#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 7b9bff73624947ac90a99c7880e2e911 +#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 c5ff687c86ef4ccaae25d8bcfbd5f873 +#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 0a610a9632064deb824afd0719429d3a +#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 ec0c47438a5242cb99dffa7a4997e95a +#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1003,7 +1039,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 aae94ac2114641f186eac0f4117223eb +#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1011,57 +1047,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 209e072724ed4d27b37e9bff6d55d811 +#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 3bf47876e3694e6cadb05123326459cb +#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 459a65b8e67c4a9aaa03138c1abe94ad +#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 898eb29ac7714c69840b795633953a05 +#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 2a658bd2d8ce4533ab7e056fc3a3ffcf +#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 32dd2e28cf0f40b6930750f0162355eb +#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 471c47d311074ecfac071b6d52d9cfb6 +#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 5078140028ea4d04973cb9cd20f0607e +#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 ab127d4ba0a44526ab129587a8160923 +#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 d5cc6b4295a74f3586f022b0227759b3 +#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1069,11 +1105,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 585a4fe583ce44e180a062742b3b0849 +#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 0d81b0c9ea58420789d1d71cca32ce88 +#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1081,11 +1117,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 ea4ab0782d8049d8b1b89cea4ae60048 +#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 f6f3b7453a254f828bd4c9e9fef92bed +#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1093,32 +1129,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 3bf9050175d4444ebbbabe219412574f +#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 e03f72a14dcf4bf38ce8232598ca761d +#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 3dcfb2facd324dccb3084c02487625dc +#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 b8531da183964b02bca19f818ec076d4 +#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 7ba1ddebeb2843179fe99fc410b193c6 +#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 a6dc303e9d284b60bf1102212505ca27 +#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1126,21 +1162,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 59ac7830ae3e4d7cb1bf503e8c90fe30 +#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 6d1d6f42ada2418ba0a1de1371825b9f +#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 1cd924fe8ace4a82ad8701f37b5e7d84 +#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 aa297c52cd964291a47bb91c0135156b +#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1148,46 +1184,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 28b02c90397745bfbacc03c3b1034939 +#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 ef2a4f39f01049b891868b84d968c0dd +#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 89e3fa8dceda4f0cb1cfdfd1f17fe4df +#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 7cd178223ba94d1ab3ee8cc5f13a8dcf +#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 46f6f8d050ce4f8c897056167d9707a7 +#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 5ee00ee409b746dc951ca1d4c360e624 +#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 d4af972281174b8999eab55ee0ab1a0e +#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 80401cfffae042ab9ec4b3754af04b25 +#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1195,19 +1231,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 32f86f911ebe4a4c94975f81742333f3 +#: 9c87c76c690948ac8e18088a0fffe679 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: d5f1ad2b95ad46d48f8f2ca5e357bb5d +#: ad00d94d4fb64bbdac356e64dd3803b9 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: c53ceee943ad4acea779e072b9137889 +#: d8110ed19da94ad8a9f56e7006c4a2cf msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1218,37 +1254,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 7dfe9dffbf5744299bf232599644c7f6 +#: a74935dc31664e979ca8f90a6a4ba53c msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 00709fa451134ee09a0d808e101f28ed -#: 991172e201ec4796992a349dee44f090 +#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 1f3c23a4769043ca985b8ddfed19391d +#: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: f81b43c7cb194a1cad8672129223c833 +#: 9643449da1da46d7861866dce490cbcb msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: a20073a8f5374eb1bc8531ff33e622b6 +#: 713666580a0a4466b4ba6e3eb2b54f0a msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d08869beca3a4774baf1097b63e79474 +#: d50574c8b9694f83aa376d39b9a6fcd6 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1259,11 +1295,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 109b773789024b2b9c063a6169c6169f +#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 959fa04f88e54d42b9b774cc95d85ee0 +#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1271,13 +1307,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 64674980c3f24c45bbfbf3f957dda55e +#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 90f2e4265919446a902e17627f4420e2 +#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1293,7 +1329,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 6b5f91a749fd44b5acfd6071c9913342 +#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1303,43 +1339,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 5fe2962837b14f0e9989063be4a506c3 +#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 4e1bdea962ed4618884cb9d1d59d7509 +#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 37eff4ca02e843259f6ffa38e4a87a04 +#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ae47231c203d40a98c10045038ea9b65 +#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 018a6d5dbf1044559b365c7b9017eb3f +#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 e073d8f990c44b09a73d642cfe49bebd +#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 e04fae88d9b64493ac69eaee24585098 +#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1347,13 +1383,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 b26b9c9b1c4346a297a31c9721f0172a +#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 b50500c3c3f54b16a535a16175a44653 +#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1365,44 +1401,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 623f3a804199449bb85e23e00c8bb507 +#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 effea0b1356447c0899ca0746667ea31 +#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 00e8ef87864c4ca2b2c1c0548b02b38d +#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 6e6f48d70b894a6c959ca30fe6bad772 +#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 02fe08760a4a4ab49e96f4e51316a81d +#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 172ed7915a654964ba63f860b2d65330 +#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 4d0a2871a7484e21b3c39c4dbaaa63fc +#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1410,31 +1446,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 1eea9f1e284447718141f5417b6bb433 +#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 509411d353fe4314b087b81b09ea960b +#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 a54bc80bf08243bba67d98dd682ee134 +#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 69ecdaea24ef42eebef9d86e5d716b11 +#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 3cc5847468d1478bb5589dee68147189 +#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1442,52 +1478,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 98c6bc409420485095ae65d6b0b9a3a0 +#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 ebe23e5378514f888a9ec32a2adb1e98 +#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 387cfe85604f424f8d31c4a4c9c15edb +#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 7b1d65754e854693bb60289c97d3fb5d +#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 f440cef729c8410281432307a4da8d55 +#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 4fbb8ceb1b59480583ac611142167049 +#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 b87869204838415bbf694214e3680593 +#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: 12cf5f2264504c44a2173e858bb2c283 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 7694f9cabfe04308bbddd2c88ae6d9b9 +#: 0cf51b6da6884065ae42032abc20eb0d msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1496,17 +1532,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: b557dc4f8ef549b98f59412a918643de +#: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 3011eb003c084285b30cfa56a8da45b6 +#: d3f74c3b094a427fbec831afab657d50 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 +#: cfffc518ba6e4ed1a80762ed6f7d25df msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1514,7 +1550,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: ce78b2d147054da895beba66d0ecdab4 +#: 9454a330b9324744b89448f2694b1b03 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1524,7 +1560,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: a973846ec5a946eeaff02c5b00997da9 +#: 7f8d99a30b644457a62ac1523d0c72aa msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1532,13 +1568,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 294fd83a97a64249bac38f7482159372 9e8eb1542db640ff9e300649ce50dc9d -#: ccec7f73b9d948e79a6cdf32bc124092 +#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb +#: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 22948f19cb78485f8f86244686a35c09 +#: 10d1373bb14a4a3cacd3b92a2f83382d msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1546,7 +1582,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 001d9579bfce438e865377fb9c2df776 +#: 70e257091bdb456e8957f90a8fa90e8c msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1558,7 +1594,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: e62618db8995428bb3f260e03ac8f459 +#: 1741804e33aa43ce88b4320c11ae5973 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1568,19 +1604,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 457756c4e9544f068af897113358cc89 6d5ae75431424ea788c3440606f22940 -#: 98e0548845fa447fb05a29c9fc2f17b5 de5e8aad4e3046bf9bfc2ad8ccba17d0 -#: e9801b2142cd45368a73ef9b121c1d08 +#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f +#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 +#: f924d65fed0c4cb5b0a019b084a8b535 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 ee2bca9bdbb74b60a706c3118d6a17ba +#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 e63ae9694f40438d872d141ae824a42d +#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1589,21 +1625,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 750fdd4c270e46a09f79e867358f7414 +#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 b3f688cc82444ef7a7a0aa63dac39cac +#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 3638be18b4f64cf08053d512e590dda3 +#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 7d5b9c21739c48f18c13614ca6967f6b +#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1612,13 +1648,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 8fea29993f944d8d8d3181afa29bd0a6 +#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 02d0b648d70f49d7892f690be06df585 +#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1629,15 +1665,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 0743bef42b9a42328849c8c2f9da9eed +#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 85c5d0cbbc6243a6823f5eeac0f85dd9 +#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 be848f30769543eb9c0be55263e3f758 +#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1645,7 +1681,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 cbff44a64ba4432cb59a82f82c2f0103 +#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1655,26 +1691,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 617f1c0084cf42d9be4c7a8fa5a48432 +#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 cee79afa3c6f43c29ef05e06b7843d35 +#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 225903b11efa417989df42de86ad2451 +#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 1a5f058290064c1cad05e63eb127fcbb +#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 74ad8d69cf294ae880dbbe28e25b3545 +#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1682,32 +1718,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 5293e8ee9b3b4f59947cfc164ef111c4 +#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 ffa1955c759942c68e7589429e5ea86b +#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 038bc0ba5f6a405a8255a7be76979baf +#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 fae1c63de02e48c0969a98e4c49b2e06 +#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 7093a94695524851a5463193f0701b78 +#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 dc8274ecb15948c29a31db89b12a58bd +#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1715,7 +1751,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 cec8eef8a5aa49778ecedd4195ab9f2c +#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1724,67 +1760,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 df100967597043c78112bf43b520cfab +#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 59ccf4daba39406581a6bc2d9bb1b7d2 +#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 570cc75699dd4e0a987fc9aca9a01ee4 +#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 9e123723048546d495ed5110d7177708 +#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 26543894f6e04270b89ab702451bcc89 +#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 f403c1d4e43a4aa0aef8488d2b5a6262 +#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 249dffb569a944c897ce5862e5f28fad +#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 1641c96aca2f4923885fe8a509eb3a49 +#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 bc63405a0d964df2bd9493996abc48fe +#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 5c191d1420db4e26aca31c1b1e34cb75 +#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 d6a5c65e824a4bbc94578df9597d4716 +#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 a7ff51fe564748229a88a0d3044dbc17 -#: c12625211cc542b68cb51365a63eef00 +#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 +#: 1acb064f7a4a482aa0174bdc847c6382 msgid "`arguments`" msgstr "" @@ -1792,32 +1828,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 05c34a5a2e404a14b9d284a9d0c73bd3 -#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe -#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 -#: e7f1993580f0425098a719e83a64cc7f +#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e +#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 +#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 2fd5b42cafe34d3185888de041818dff -#: c158e9ee5fbf4e868b152a0a5880092f +#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 3f29e4a3087847e9af6f19166a8def9a -#: 92697d3179ec48898eaea9aba3c24dcd +#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 c0eaef93bc3743279549bcfb8b014ca3 -#: d6722e3093884ad7b62696fbb2f48fdc +#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 37c493fdc2f0410a9748f8faf09ce5b5 +#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1828,11 +1864,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 04e3eefe4ec445cb90c2fa42344aaed5 -#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 -#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef -#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 -#: c610220d06484d589313dc29faf8222c +#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc +#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd +#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 +#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb +#: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" @@ -1841,51 +1877,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 662b36e3505f4ac3bb5070bb6e055217 -#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da -#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c -#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b -#: f71216a4b35e4157aece5ffa2602d8bf +#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 +#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d +#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f +#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c +#: f760465a49d64d4c8468ad9c4fea62b1 msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 a3c775a0f04b4541a9b712bfe2e4e69a +#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 ef16c4a9a7ea415fa399297b63b9710c +#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 2592e429c74c4ff5b8ba68a36f060c1a +#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 5cca4c2ad617400eb6efad4066b1839b -#: ba1fff3ebb274dfba845b3ee20ebd71f +#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 6914526c0a7c43a2a05438519508ee0f -#: 722d3bd7184841639b9f9a38914002da +#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b +#: d555a3d991e344a5a8e1289168d7c6d1 msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 737b0f9392154241ae5b56c6caa823f5 -#: 7b46d408e7e7481b91a950b2d4010c9a +#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c +#: e9fa9430535c424fa3e8be5d460d2ba4 msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 f09e7371708b4c0685eef2a314791ccd +#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1894,32 +1930,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 aa6ca1def2024c98b9d5542de1a81425 -#: e9fc5f7fa4474dfc95039b94167fe894 +#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c +#: b0290d1a477b48119e17cf1fed9d6dff msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 6c37a1ff939748bf83a86c07c3d017fe +#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 3a8126b0a0334df890b2be2c693ea5d5 -#: 61744122b7d7494890cbe6b2fb72b9f7 +#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 +#: e1cde4aa32c041238ed2596173c6d824 msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 93cb9015dacc4b50a4ef177ce4ece2e7 -#: e0c7ccc8f8664cf794cbb7330355f3fe +#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf +#: c2a92d3eca7f4ee39cec649170eeea53 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 58a1773b1cf546d7890010fdebd47388 +#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1927,61 +1963,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 230f3227ed1144f7abe0f8c231bebbd5 +#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 5c77dc9f8afe4dd88933943030e836f2 -#: c9534670f5f04769aa3749c3778eb705 +#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 4ec8bbac5fb14371a6a4cd53d7cd6450 -#: 7b0887a8caed41b2acccf7021bb323d3 +#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 +#: 718ceee9973240ec9c100977bbcc8921 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 aceedfb558b246bc87eb3eaedea187fd -#: e5e8b8c75f0f43cbb6e160e5bf810c6e +#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 +#: c07ab08eb75d4528949c56a3d7c12b28 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 266dfb5fe6a842078baf66073cac9623 -#: fe3b9fb45e01490498c5a35c012b3de8 +#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 85f424cbfc85460f9da310aee1ff0b82 -#: ddf82b12b12d416fb65f3ce3f51bbdf0 +#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 966e88656ae5402a975022ee60646283 -#: af14fda3cca645fbb2f3c5825fe0788e +#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 09120baec1464afb8aed4edd773bf509 -#: fec70bb106ad4d95a2d55ebdcf711afc +#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 +#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 1dc4148caef748428a7d13caff37b1b1 +#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -1989,33 +2025,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 +#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 947b1ca132a54ed39745cd12ebcd65e1 +#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 +#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 +#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 5fa512d352d945e7a3e0d59b0987cd1b +#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2023,22 +2059,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c +#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 81e91df082834d2cab7ef1f62d8ba57a +#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 e6bfd1dc2e324992b6c3332c11ae3445 +#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 acf10261df2944ec890d754fd56c6b28 +#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2046,7 +2082,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 bda6b8f398554b0c946c2c7d96308a42 +#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2056,54 +2092,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 454c02c3918647039c90ae387005dea6 +#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 e1fad28bf9cb4c4c85eb74dd520ba107 +#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 9835d0b399b84a0084fe5a4d9e7e6405 +#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 410ba7a5ac6349a98460c6337ee5c4fb +#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 d2daf50d7f3d4de18331c8fd2c8a5786 +#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 8f2015c12b2b4d5d9a800ddeaf428f25 +#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 f0ff919ffc12439d89d7b40f51ade84c +#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 307a17a893fc4dafaec2a63a95704644 +#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 7f393e86b114470f8dda47b2deec63aa +#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 c3f459b87b96435583637b3f1573e658 +#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2112,15 +2148,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 9f676022eb2744839ca2109920250cb6 +#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 ede7285f77864fb0aee6cfecc2c97fa0 +#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 c55fb184bc614ee2b6e5e64611e5df9b +#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2129,11 +2165,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 66b522f46ce242149386e79f63b32cf8 +#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 64a20285785d48ca86227a0cf6353ad4 +#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2141,7 +2177,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 5f71bbe2c74e4260b79d4d9230d35397 +#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2150,34 +2186,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 63bfff437e3348428f7e33ece7ec55e7 +#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 6ce83d9c06e4436881aa47d94ef41e0b +#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 55006c594abf4e70a38e979568fadcf4 +#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 +#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 1a1905ff2d624eca952c8a53b3bee678 +#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 368ff92476b14f5c8331260eafc5acb5 +#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2185,11 +2221,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 5d530afa23f349a79f54d51d40724747 +#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 16f965f86712483aa7f95dfa3f944a17 +#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2198,80 +2234,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 dc629e2c90ed458b96107a6994676434 +#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 cf2f077cf8044079a7005e6e508dcd8c +#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 129e1d2a71894d28b009f4846754a75d +#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 d6791bbe575042b9a7282c69407dd907 +#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 e8da87f8bb664334adf831995601f462 +#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 de6c322618304207b6d1364d1ec2dc13 +#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 43bdcf6dc1b14030bff27fa53289c02c +#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 056510b42ea64717996ab49c307bda86 +#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 6852f5dbd9094c99bb68f2a88f76c9bc +#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 f33b6800367248b7927d97ad7b4be5b5 +#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 8ad812d7e88f4cbba83228ffb1711576 +#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 cc680bbf091a46f8b4b3dbe6324c040a +#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 446ac81f078d46289a18f494748f482c +#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 3d6d958d111943f3a2139b4dbb7810db +#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 ba0ec9157709430c822f4e91459288e2 +#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2279,7 +2315,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 2565f8fd4a15429e887aeb71eacdff1e +#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2287,7 +2323,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 659ed5c64fb546399b741553a347b8e8 +#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2295,14 +2331,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 3d87e69d41374fbab23b26d36c1aee03 +#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 07bc81683e2c4ac68b379462bae95207 +#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2310,7 +2346,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 3e304da2150f448d9e39715ac5f5deaa +#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2318,7 +2354,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 fd8a98686e3c4c609f79ae427f1558d3 +#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2328,13 +2364,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 f1a2e1bbb1104a4fab5a7f04cac845c7 +#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 6a7f0ccd227e4f90a8c8ca96744bda68 +#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2345,17 +2381,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 1f79d115d8a145189638c68c3095396c +#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 6e1b3e2d90184e34925891099d2b5cc1 +#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 4f6df7f13e42448eb4a53f03bc477b56 +#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2365,23 +2401,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 dbc0b52627514ad0908969d0b4ddfdf4 +#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 f173dd96ad124470a53573c86a8df203 +#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 af25945b530048b685891b1de4e35e72 -#: cb07caa4ff0149b3ae832be53f8d76f6 e0098a77080d4349b05ceb7735a5fdf5 +#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 +#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 2445d2c7c2794fd3ad8b6ed8b4a9440b +#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2391,7 +2427,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 4459819ba75647d185986a3386939494 +#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2402,11 +2438,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 8f163bd34ded4785b6e28c8e2147e0dd +#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 1799e11a7b9c4929a3d1379d7ea45d03 +#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2414,46 +2450,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 9510c0b431a44b5e84e0b583de7c5446 +#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 efb4eb6f5e994b50a52fa2c707dad1ce +#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 34599c6f10ce4104be2359a1b37f91cb +#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 0663ea7918994d3f9c45c652a3ed12db +#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 a98dda6ca4b14edba467de638bba28fc +#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 10d0e9f8df8c47788703073b17529bc8 +#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 9a0e1a130fba4d24a9168ca3e455cd23 +#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 992a8c801ceb4233acf56b6bff315188 +#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 9027d23fa7074b789c3b86ca5ea17fa4 +#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2461,18 +2497,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 68b47710a8ea4b978428b42c627944e9 +#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 d33e4cac65d14111a89c838c4d1759b9 +#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 24cea1cf7d774b6ab56959f289cab39d +#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2480,7 +2516,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 b866867d6f8e4d3999b62a85e6884ebc +#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2488,7 +2524,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 80c49ed168b14d25b2f09b3b0186b44f +#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2498,12 +2534,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 71628ebe908b4cd28dd1fa17e3d2e2fb +#: d33aa2353ad44fb885d3a1ee48263dc4 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: f123ca244c23413c91405a4b84887525 +#: cd64d2d828834cbbb24ea5358caf5405 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2518,7 +2554,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 23299ae1bec94b00a32a8af7eeac350f +#: 80af387fe3ff4e2da999903385bd602b msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2526,17 +2562,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 2495a9f2032a47c188338cb81ba429eb +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 3fd2f3cf7bdf44089df2ce3122534801 +#: d402bf528c7f4eb69aaaa275be2bf1d4 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: d5a5b8b490b640439db92da949266e4e +#: cb9980db4e5f4c74b01c2dec6d5e92d0 msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2546,15 +2582,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 5935ed94331d4b2f8ce597f31edea843 +#: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 5feb559552194ba58da7206c601292fe +#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 b7124ba4df9042baadc1641ee09545d6 +#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2562,56 +2598,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 d34b698c62114041a64e0abce25ca935 +#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 cba2c31262bd450cbafc7ca77f4fb8fa +#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 b01be5f632104096b5af6193aab34d90 +#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 60a6a02c1367403db6df3ec10f75eb69 +#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 314ea7bc35154f41b2af5fa6683ca389 +#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 d81e679b13474f74bc5e1ce1e31c2bc6 +#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 d7fb27131ee44bfc82f698ee44b2bae0 +#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 b8ef11eafd1d46e088f1277f4ac372bc +#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 d2382ed1f644459594655d5b5b4d838a +#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 6651632d977b44479b721174fffeda2d +#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2619,7 +2655,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 bee5f532554241088764ac9e56abbe85 +#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2628,17 +2664,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 0c7c506f38be421399073871f64e99b0 +#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 8b60286e56cc42a8ab5f751a97adf771 +#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 fa0ad674f15348339a1eee771a6ba9e2 +#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2646,71 +2682,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 177b5f1b95a34fb9b2eb42f733d79ac8 +#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 a08a6d8aca8e490482e127a8fd5e650e +#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 c2c60f68b1e045f88844076e191fda9b +#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 6d939f62526e4e6d95acb57d72f60a84 +#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 c48edd9034364b81ad42540a98b51d91 +#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 9ebe0186a7124dfaa30e558e8f59653a +#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 9381b7d7c9904df0a5e16dac29c2e08f +#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 2aa9c6916e3546b7b92fa64bb83275d1 +#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 63afb7a597fc4e459b6a7dbd40bbf6ff +#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 7418915470f041c9af5bd39ea652de36 +#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 f82db001b58c4969b2d8bc1dcbd7cf8a +#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 26d9f0b28d384617a8e490c1f8e26e52 +#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cf46c971b31b4e10bf0fefb4cd028c2f +#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 a4347983fb9945a4a2773af88e426dc9 +#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2719,11 +2755,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 c5489e0633114372b273098ee2c9ffd9 +#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 75de9fd63393429daf1ca10a85339aa7 +#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2736,40 +2772,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 8b5d0ada32d645be9359f43a431f5f91 +#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 2ed93dc8778e44209194f41b9ad193d5 +#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 a80dd6d9920540e9880514e04035af86 +#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 9de300f7b9da49f59d1c9fd96dec4a8b +#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 a61f52d3c1024c3692899e05fcea4bee +#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 dafc9ba578c14fd79d075160e6b7bd6b +#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 28ca6cae42904559bcec98fb9d2b07cb +#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2777,45 +2813,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 616c9ff9fcae489285f0bbbc67f07d29 +#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 ac17acd83ddb43dc9fb7a5e595ab1153 +#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 156573324cde41ee8b3c47deabf43db8 +#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 c9725be01e8a401fb3ad9ff01339f81e +#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 6797335256e2412cbbe7636507931455 +#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 05a5f0fcb7454cb697e3d810d55fac26 +#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 406e68280b5c4ee494632f94b635b7ad +#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 2d6e2a4ff391494591bbdf8dbcc4a6ae +#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2823,13 +2859,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 e71a974b29624210a107fc2d097d4196 +#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 b59df98754e24654bfef0b1fe1d91660 +#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2837,43 +2873,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 d2bccbff1ce646348fe38c776ad183e1 +#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 943ba46512ce48fe8c5b62327734c503 +#: 5d8bed66282c408695292ea92a03b2c4 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: bbcd43d5af7d44108aeb65075a6bd2be +#: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 834295755af841a78e466eea43864861 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: a6b626489bfa468e8f059ab3aa669201 +#: aac74f957774479a83aab4c6ff1390ae msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: e1dbea105aa845c38cb1f90b43847271 +#: b75d29d1d55d44488338f9689f156855 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: e9640f47d40e45bca184eb30700df648 +#: 574d93d1d592458a985f259519c036cb msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2883,14 +2919,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 0456efb3718b4356ad2b277ee16de967 +#: 82e48b3e3c3f451480cc0b6a529271f6 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: f7e97f926505407f8f8e9a427e055e43 +#: 02e40154eac74ecc98d0447d03475b44 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2899,7 +2935,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: ec597ff8f6ee47bc815b069335869f1f +#: 8cb1c5d9b1a54c40924099494eb766c6 msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2915,11 +2951,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 7467a7f6f26a459ba4ce83e4e6dfcc2b +#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 +#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2929,26 +2965,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 a03372581fa44f9b8e3e088a4099cdd9 +#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 36e082be73464be0ad5d0b681cc510da +#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 4464455b51ad4873ac13c4a63ee5fb54 +#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 ed7ff0753d1743a995f4cfedd6e5dcc2 +#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 4c2dd10dd66446058477a52fb8d2c602 +#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2957,7 +2993,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 978b6a5fd5fa425fa9a18d9f0e8788da +#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -2967,18 +3003,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 000c0d6ae8bf414d9293b9f13fd2e448 +#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 7e91b8811be14f8e80df39ac4c5bd316 +#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 d42799cc5bd4484bb6beb309a61e103e +#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -2986,7 +3022,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 48bb0f6666ac48648c7d969608b3bd48 +#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -2994,7 +3030,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 f8876044db184cbaaca56579d0c773df +#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3004,7 +3040,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 a5a3d408dbe34cfda4dd0b2abe67e7d7 +#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3014,15 +3050,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 4c240a18c4e6441189489011242c1efd +#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 e37e76ef376a4ee695e600998906ec1c +#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 51a307b0ba7c4c1d89309ba8d2250471 +#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3035,35 +3071,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 13cc38d72d34468fa4eb6d91f23ff105 +#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 42a48398d3ef4b03bd7395120f2cfb42 +#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 d59387b433bc4ecfaf7e72026624db02 +#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 d963418ccc0b4803bbc758d718ccb5aa +#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 a224d1510c9e46aab23d8bdc03c349dd +#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 0a82f8a45b0546aaac4c976dcc98014a +#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3076,23 +3112,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 bc418a2a535e49359c4cd44b373bbe02 +#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 a799fba2322944cea00e413c08066536 +#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 35379c6b972940bd8451f10b74dd793e +#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 2d5265525ad544a0b64ad2cf07aacc26 +#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3100,44 +3136,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 e2521b89596d42f8a87a3207fd6c32f2 +#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 3676f23b63e142cb8e5715ae07216a47 +#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 00725aed13a440ca8b3c4f9155fbee99 +#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 2e38a4f9072b4ad9bbb74f943d22084d +#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 2b9f4035ea864b6db50c861a1819289d +#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 28e9064780e7418a8e02a22f92e34404 +#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 66ce14a10d2d4dc497d3ed71e11ed8b8 +#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 8dc00528c3d2426c8a3492a8191f1d81 +#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3145,33 +3181,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 f9ef5e258f7c4971a8543d1dfed711a8 +#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 324bc51071d743ea80124c23880ddc0a +#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 d8c13e01976b43a1af34c11a7bc36897 +#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 43910a8ab4484e529a17df418b1aedbb +#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 +#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 7ad12d67e815400c94080804b9285629 +#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3184,34 +3220,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 457d5a31c79143acae2683d95d27f7a3 +#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 a2a73901bf634547900d08b9a1ac8889 +#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 f347d80e62384b14acf6423675e5359a +#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 2a845a4f3f98428fb82f3ca7ce038a6e +#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 e2007c74d5f449a882809d6b91c010bf +#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 7f5e53ee7cf94be2bff45ef64db28a24 +#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3219,7 +3255,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 a0d076b7b8b048478580c99ef0c8429f +#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3228,7 +3264,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 7fd926c18ad548e98845e9b5134dd6f2 +#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3239,7 +3275,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 789fbd47f8564cceb430ef3c0bc90e9b +#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3247,7 +3283,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 45c4d0492d6143ca9cebe81e9b2cf3ae +#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3257,13 +3293,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 73bd3da2af8545928d5ea71d0f7454f6 +#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 15ce3d2700424f0fbb280d602ccebcf6 +#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3273,11 +3309,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 af4268f19202436eb0a7e8c6bed5e386 +#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 94a4eadca6b949d79de2990a0150eee8 +#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3285,17 +3321,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 09c1619e8cbd4febbb637f7e99ad5890 +#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 677ea7a27eb64568ab3689142d6efe70 +#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 097e6d47f9394e62b80110700492783a +#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3303,7 +3339,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e93affce8c104bf6977182047c1f1077 +#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 06c9e04ba890473b851240a0fa9c3b12 +#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3325,7 +3361,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 0380dc1fe3aa48e4b62283b7b2a611d8 +#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3334,7 +3370,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 49b251f7a313492ea60504b00109e526 +#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3344,7 +3380,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 7ee55702d7dd4679a24ff052f6f0cbeb +#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3352,14 +3388,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 85d7e2e270874aa6b9f477cec0f48154 +#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 570e94513c984c09ad6aa255f534216d +#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3368,7 +3404,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 a107258662fb4bd4a9a3d8754e34d1e9 +#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3377,7 +3413,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 fc1a6502d831458ab8371a575cea47e2 +#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3385,11 +3421,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 2d10806bf1ce4e26b92adda61efc0862 +#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 046c5e134de94b629cc22d416f3c9182 +#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3400,7 +3436,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 52fa22d3277940049fbb589a3ea73433 +#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3408,23 +3444,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 6043beb96c2c49648011ec556aa9e986 +#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 5ac4310515124e2986724425bed5651f +#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 7958e91d5c2f4046aa9d2070a900f9ae +#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 2db234d776fe4fd38bab07245dcb783a +#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3432,7 +3468,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 7cfb17230e284ee7b6e2a00efe8eeb74 +#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3440,59 +3476,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 4311ac98544e4fb0b2f4b24985710a01 +#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 780f9c72e6c34c39918642c7e2477355 +#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 cc4a7316db644b438cbaa181ad9ef2d3 +#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 dfc461a03fe8487794837904febb8b63 +#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 1e83485b00b64dfaba897bd8d772e0f0 +#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 d0321d6805ec4d3abf3877d02a0a417f +#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 d7d77e807b3048c7bdf89558f76804cb +#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 8d9b8be147fc4a71922dde858842e543 +#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 34b7705416a745a6a42e6d402c0757ed +#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 257adcee9da64d5c987f3b64efd20ab0 +#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 fa6ed5d0c14f42f4aa3c5144648db22c +#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3510,7 +3546,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 333e8ce458d54de394526769f96d12d2 +#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3518,38 +3554,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 b819e8a5df6e4fa495924095709669ef +#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 f1955468a1364d44a930db77c9c4b495 +#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 8c3b9b645a204d02b2c73a205e8ec296 +#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 4d88b9c186cd4502adbf752e8a70b6ce +#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 9927673564024ba5833b5ac271737857 +#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 84f4ed7ce2004742b8db9087104a469a +#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 2b5f9757adca4490a149c7f45e14fcb5 +#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3558,7 +3594,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 0418de720813442f81ecff293c9448b5 +#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3566,62 +3602,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 524eec63be8248ae982939c975ef50a2 +#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 5e99f9912cc549a7890e2934425eb943 +#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 b0121ee087d6424fbb0ea5957a7b0b8c +#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 49e9f6b3a06840289decf3f557860f87 +#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 ed9eebec0b3d4b72ba65507d37757a37 +#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 bf9b255a24a84f3ba989a223492b8f41 +#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 e79fa0b7f8b14810a3a20908ef92bc55 +#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 290e2035f903417cbecb5dc5f09d6ebe +#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 d420730151534f1a89076588a3358f09 +#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 a6b5378bbe1e4bee9e37a765bddf75f7 +#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 6e4d9465dc2b454d96b02d7ad1817795 +#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 a649d4af5f434dac9395e013ec4836bb +#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 446190a298834b73bda068286e8490cf +#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3631,7 +3667,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 2f35c012ff174721bffe66a3f58a804f +#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3640,7 +3676,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 43127c98c9d94aedac61cee67929c1a6 +#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3651,28 +3687,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dc4fe561203c4c38a9caea5bd6eff2cd +#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 f924e4896db2424d99ce8c9da14c599a +#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 bf7646f5f925485c842a6d34140e40b8 +#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 c483e61dec8949fa96bb893d422888a0 +#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 85fcb523d0e34a499eae04d304887f7b +#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3683,7 +3719,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 83d47c8736a34f3cbf09e3997845e4f4 +#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3696,11 +3732,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 c698fb3d37bc403e9aeb679b8fc0e15e +#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 ae8af2f0eeda4aec97201211dfa965c7 +#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3711,26 +3747,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 2ee87aa465cd41fda16a61e242f8c9d0 +#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 0a6fd4469ff24b61b3ad001b09eead18 +#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 b96ba19bce9341d39c46054e1f10fe8f +#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 903f30af3d0c45cfb61063936a8097a7 +#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 ede8db7c0a58432e8a1c416e937a06d2 +#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3740,52 +3776,52 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 c8b53615476a4a1fbef2420d93bac94e +#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 ea03cb5525cc491f9feb5c4780b38fee +#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 92fd3a5e31714eab859dd630af2e78cf +#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 de660ecdb5b44c97a0e519d00b232497 +#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 5afc1e1288e74ed0985e61e5164479c7 +#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 862dc7ac81e54b1fb3d4c2f961b8810e +#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 e2c94c0e1c7048d38cd7aa2c465a859d +#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 b63253780f51467a95207d820d13ac39 +#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 6d06ca7ed5df4560aaed286f4fe33928 +#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 5448df4a6a8f431d80e269bcd480e19e +#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po index 3ed0733d..3584ce39 100644 --- a/locales/pt/LC_MESSAGES/user_guide.po +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -9,115 +9,142 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 16:53+0100\n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" +"Language-Team: Portuguese \n" "Language: pt\n" -"Language-Team: Portuguese \n" -"Plural-Forms: nplurals=2; plural=n > 1;\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" +"Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.16-dev\n" -#: ../../LICENSE.rst:2 75de2be8809847b8bf1ccd42aa694a24 +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.rst:5 2edd71801f6245ef821887a74f21b94c +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" msgstr "" -#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." +#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." msgstr "" "Todo o material instrucional do projeto Common Workflow Language e " -"alterações na estrutura também são disponibilizados sob a `licença " -"Creative Commons Attribution `_. O seguinte é um resumo " -"legível por humanos de (e não um substituto para) o `texto legal completo" -" da licença CC BY 4.0 `_." +"alterações na estrutura também são disponibilizados sob a [licença Creative " +"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " +"humanos de (e não um substituto para) o [texto legal completo da licença CC " +"BY 4.0][cc-by-legal]." -#: ../../LICENSE.rst:12 90cc755d172e4c82b882b4ee620fe652 +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" msgstr "Você tem o direito de:" -#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 -msgid "to **Share**—copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" -"**Compartilhar**—copiar e redistribuir o material em qualquer suporte " -"ou formato" +"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " +"formato" -#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 -msgid "to **Adapt**—remix, transform, and build upon the material" -msgstr "**Adaptar**—remixar, transformar, e criar a partir do material" +#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" -#: ../../LICENSE.rst:18 430ff4de74924bc3a3b2c7e809ea4456 +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." msgstr "para qualquer fim, mesmo que comercial." -#: ../../LICENSE.rst:20 2173e2af49be41ee97a74c4e879faf25 -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" msgstr "" "O licenciante não pode revogar estes direitos desde que você respeite os " "termos da licença." -#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 -msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." msgstr "" "Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " "trabalho deriva de um trabalho que é «Copyright © The Common Workflow " -"Language project», e, quando prático, criar uma ligação para " -"https://www.commonwl.org/%20),%20fornecer%20um%20%60link%20para%20a%20licen%C3%A7a%20%3Ccc-by-" -"human_>`_, e indicar se foram feitas alterações. Você pode fazê-lo de " -"qualquer forma razoável, mas não de uma forma que sugira que o " -"licenciante o apoia ou aprova o seu uso." +"Language project», e, quando prático, criar uma ligação para https://www." +"commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " +"se foram feitas alterações. Você pode fazê-lo de qualquer forma razoável, " +"mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " +"uso." -#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 -msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" msgstr "" -"**Sem restrições adicionais**—Você não pode aplicar termos jurídicos ou" -" medidas de caráter tecnológico que restrinjam legalmente outros de " -"fazerem algo que a licença permita. Com o entendimento de que:" +"**Sem restrições adicionais**---Você não pode aplicar termos jurídicos ou " +"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " +"algo que a licença permita. Com o entendimento de que:" -#: ../../LICENSE.rst:35 f6aae4a5cd0547118c8a3240ca2b4be6 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." msgstr "" "Não tem de cumprir com os termos da licença relativamente a elementos do " -"material que estejam no domínio público ou cuja utilização seja permitida" -" por uma exceção ou limitação que seja aplicável." +"material que estejam no domínio público ou cuja utilização seja permitida " +"por uma exceção ou limitação que seja aplicável." -#: ../../LICENSE.rst:38 a40c173be35b4c1b92e83f42bfe2382c -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." msgstr "" "Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " "autorizações necessárias para o uso pretendido. Por exemplo, outros " -"direitos, tais como direitos de imagem, de privacidade ou direitos " -"morais, podem limitar o uso do material." +"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " +"podem limitar o uso do material." -#: ../../LICENSE.rst:44 3d7ca3f2cede4d5f998bf014bd970748 +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea msgid "Software" msgstr "Software" -#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." +#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Salvo indicação em contrário, os programas de exemplo e outro software " -"fornecido pelo projecto Common Workflow Language são disponibilizados sob" -" a `licença Apache 2.0 `_ aprovada pela `OSI`_." +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a [" +"licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." -#: ../../LICENSE.rst:50 9c4d58a1129a4d4eb4db1bfabbeddb6e +#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT" -" WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the" -" License for the specific language governing permissions and limitations " -"under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 5ad4be9b62d54c95a913795b514676fd bdd540403a5746ff99edf2dcad0e3122 -#: dfc7702e073140c985cf47272a20214d +#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 +#: eab02dc13915490bb3c9ba744d78b6a7 msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -126,30 +153,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 3060770b3bef41d7bcfcdfb413d7689c +#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 48bb9f628b344ba1a3b67ae1cb264e3c +#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 7e3684e9672643738846756e1ebafd18 +#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 187ceabb7fd9480bb8cf0f2da47f65ef +#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 b548b76bcc85420a9b30792386105139 +#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -157,94 +184,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 9ce692b78ead47e4b0f8cdae8837d35b +#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 6df1201c159343da9e7515379980d6a0 +#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 f9ab1d0dc1c842b6abb5385268c1d3bd +#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 9f6a84ab6a9343b6ad7db826f8964362 +#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 fa50e4fa990b42d1ba4c0f4ae1e5caa1 +#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 3a871012fcfd4f3ebeca0cb86ec93435 +#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 d954edfff2584288ac8c600733070d2e +#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 af6b1e37d6be4450a761854480ec9aab +#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 31f4a2d43062493ca64c648f80afc8e9 +#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 41c54e71b6cd4f63b2a619a515240d34 +#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8edc3541ad134ab5a1d23c724f1f0a4e +#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 ac0ea81eba8842a18801ab03cbf80a57 +#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 52be1a5640234feabe958ff7ade33653 +#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 c6db734d5aef4f4f99676bdebf9c83c9 +#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 a9f7b47c0dd741739795da39bf114879 +#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 e3fdd9228b924905a4a1f4b2b7ad7159 +#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 3f7cda1437cc48f18745a827ebb74582 +#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 5aeaba2cae64442e816bbd458aee833a +#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -252,22 +279,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 5af827a402834978addd82c70be6b5ab +#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 6d69e42bd8e443c4b19d80807c7efd6b +#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 404640397b6e40c2a2cd5cf85ab3b1c0 +#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 1682c2486e224770b62269709a8663cf +#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -276,25 +303,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 9078fc009bc145808813c9cc2b734b58 +#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 d4b5a54a400c409cb7984428f6a03ec8 +#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 9e8dbee6e8f84d08b1a54fffa06394ef +#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 msgid "" msgstr "" -#: ../../src/faq.md:248 1d846bfb5f054d09a4afad1da8e4b642 +#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 2d0e95fec8084787b734388d60188574 +#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -302,26 +329,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 eccc4a364330470fa474dcaaa3433390 +#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd msgid "" msgstr "" -#: ../../src/faq.md:268 e945f6a337af4e4686bed482a4fe6c39 +#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 8a3efaa0ad1548428bcfd6e01d135cdc +#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 cdab644adc5643708870fb08c06cbfca +#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 089a5a0b076b44aeaab4d69ee3c79f97 +#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -330,77 +357,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 561172559c6f41a68819608fd9e58bb0 +#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 c5ee4946d2e840abaa3dc796a62652c7 +#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 4f2069a2113c414db18eca95550e9e09 +#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 31f3390e6771414ba7bf57c044c4b0c4 +#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 3b77ce4930ae46d5be9f6965e8c54727 +#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 06f36bbe4d3840229b7374f27b86ae80 +#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 3cb2f70d00274a4dafd972ccd8c519c2 +#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 093a1529262043ef84a99675054938e0 +#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 45b6d9acbfaa47e5984184f7da554d0a +#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 5705c9bacca5405ca6f14315a5575db8 +#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 82bfc285b59a439ca97d3278997f0fce +#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 181d5130101d45ccb22aebae3d154c2f +#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e864390b5ddb423aaa10e9d33d257dc1 +#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 fe637c32fb15427a9045679b5da42ec5 +#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 1f8004b9df8547029d82e57f9abdc979 +#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 70990dc5a0034099921ceb89c89e2dcc +#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 f679e26f18d9455f945fd13361a9c906 +#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -409,11 +436,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 fcd0273dbdd84e728cfd8fbe239f2a01 +#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 173ddbd1e7c64927a8dcb12a2a2140f8 +#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -424,22 +451,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 662fe273e2fb4042b688512955e450a1 +#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 a15b52205f0145feaac298510e4d678a +#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 512aa0c7166b429e8116f71eef007f79 +#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 b1b19e17a18540939cb3bb7f8a700cab +#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -448,11 +475,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 d58b36ac43ac44139897be752fbb1f87 +#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 6726cf3585a646a8b4cbeb543cf84a38 +#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -460,7 +487,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 2e504aa7c46a426fa959e7254e9a84a5 +#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -468,15 +495,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 e7be0df0838b432d9c7f296d777f120b +#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 173e0816db20432c8d9dba1de5393dee +#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 30eacc583f6841719e2142d283811d97 +#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -487,18 +514,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 791b8f38a14147bbaa174c7eb595f17e +#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 1a3989dcbb9844b39d84bf6df6b352ed +#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 db1bbc6e980f404f9f3fcd08e92ee9a3 +#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -508,18 +535,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 acc7887c65974114996f700a38a7eccc +#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 d2476d9bcff44f21b8d84a3a0d87a246 +#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 f86415e4d78e48c4a8a76ced81221b98 +#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -528,24 +555,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c5524d73708c4c779980528864506fd4 +#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 ac46a9f8850a434bac5bc2b41ee6294e +#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: 9bba7c4f783942e4a299603430601363 +#: a5ebc727fb3443f78e81d6b7ed5ac750 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: e2140e0f0e7747ef8383887c20a7945a +#: 86e6a06992dc4228bfda7add48e28ca3 msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -554,39 +581,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 15bf490724cd46dcbcfab44633c5a9a2 +#: 8c9772f96caf4169924d22eb929a4f0f msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 51d52d051e654a8395239f88df7c9d8c +#: 4fac209a62114798b79e4810f7a0148b msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: eb496cc818524fa7bae5a22ddd00a19c +#: b97ba368fd664caab0494e2392795697 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: c4a22d12e7f149ff901d27de32b9361d +#: 903a6796e3304a19ad885b2428b0e80f msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 7618de899a7043989d77baacf62eb7b2 +#: 6e352ac1f8e144c392ac5adf18c28298 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: 6f1544a220664b79b04bf008058b5a91 +#: cf2922f645904ac7955428ecddc37b8a msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: fbd14ac9a2f541478a320ed4cbc69e13 +#: 5f47aae608c041aeb4134d59dad314d2 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -595,7 +622,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: da4dba50d25d4533b3dbb92f54d32a30 +#: f6f589481d0c4891beaccb63160619ef msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -604,7 +631,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: ce11c9f8d65c4268984d0384d95144cc +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -614,7 +641,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 3a201aa497e84f70855bb2251e7e3281 +#: 4ace6b92f4e04a07aa202840ebe36417 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -623,24 +650,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: b78f7fa2be1c4bb090f6da895457ad1e +#: cc6cd8cb81564cadb8e6a4c49423b7f7 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: f7e95d264ffa4e2db0864faccd9e5a0e +#: 2d9f53b6ed5041dbb6c0b54835897856 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 3f1e5b01e49a4dc1b1c99936a4589afc +#: 907674a4ecff4826a2b880e28fc38f33 msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 03c3048f38ae4938a484cf02001877b3 +#: 037cd0e5ceda482eaeaca03d51745aee msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -650,7 +677,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: f9715b5ec65c405c849bb030c1927060 +#: e4643938445b48cc80eb8973ceeb126e msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -659,12 +686,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 442662f50e9e4620970ce32b1b127969 +#: c4c3315c96714e81b364f8cc003b87e6 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 2b34c786af3840e88f29d214e19dc837 +#: 3eb6a013a2a4478ca2ad134661f65c58 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -678,7 +705,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: dd6aadff8cf54ce78ea6b317afbaddb0 +#: 074af9633627470485e5225326d5f20a msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -687,7 +714,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: fe7f1f0b28434f8aaf0f6ac6589a83f0 +#: 847951c055b94a83b1e081594cef22ee msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -696,71 +723,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: d10cf45b3c7f49dc98bc0e5d1246f224 +#: 44bde1fae06b4678bcac4f3224601296 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 332b6e8b831e4bc5aed3745938230a57 -#: ce7fc63b808d4499b9bf9828c2dafe35 ebf339ed376a4d3b89b15b4d5afe593b +#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 +#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 8badec9987ba40609cf1f626172b2b2d +#: 9d5100c7d0a040aea1020bf633ad17de msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: c75a8b4bf0e24781bf6713cf6f013cd1 +#: 36eb4b3b966640af90faa55db3789cb6 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 79b146ffe6d74e1b8f6019251dc4b7c2 +#: 2ccb956baa6b4376a04ad9fcc4654631 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 07cca9a33d8f4b77ac6ad35ca8b95655 +#: 72889b830c514afe9a7cb1e64b5666a0 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: 31db11c8ddf2423192a8b2063b3e91c2 +#: e29bd7f973544600be589c3b3f84cf63 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: d81dd96143ea444aa78ff45cfa0584b3 +#: c377a7f5dbe645cebbb6c7eccf831a0b msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 c54984605872472190ae7771809a20db +#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 01a237b8ec2f46c9acd31d142591ce75 +#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 3fb9888b666945eab1e3ff109646c574 +#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 5fb0486762354f93853fff209f835c08 +#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -770,11 +797,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 5f1e7a608e0b455196d191c845a5c98e +#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 7ba4b5c51be24f5392949d06ee42e018 +#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -782,29 +809,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 e2d3e6dd13b14d819a504c35da6fe8e7 +#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 91251d1f0efb4d4cb083b4517ff3107a +#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 6ad263e267514c5fb05794d3d76d418d +#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 8a3bfd72dccf4a8c874a96aebcbe5cb7 +#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 5195706d9c6c4573aff135fd539759a2 +#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 9c4506915e4c40599527bc1d2b18645b +#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -814,11 +841,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 37d9eb784ec1425786158f98e3f63890 +#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 572f493a985141a1b92dafbdba92790d +#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -826,7 +853,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 9606d3c4849f4b17b2e55a298210f055 +#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -834,26 +861,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 754fc59967d94ffa935284676d55ffed +#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 2905c6362d4146e8b35bc74744841972 +#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 091278ece252483a9838fb771de3e04e +#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 0928a5c668c3414a945bc9eda147892c +#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 56f3c481762848298214a88e559fc0f9 +#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -864,23 +891,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 710c266ab4a5477b84d6ea987420fa20 +#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 cc353db5da2546bb88a77ce1a202ff9d +#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 b62df08ec96f4cdb887600079856dd76 +#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 97e02557293440d1a58ba659dad21113 +#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 0935c3ff01634c75b5c91546dc36c7b9 +#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -891,32 +918,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 cfb37fd605164a8d9cc75bf892ce97c0 +#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 5f06a7a6aae343d989a5b30979c600f6 +#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 5f956260f3874b6dbeaf3ad7ecc09c9a +#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 d35e4effec554a638d6c3047ef3fd05f +#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 15a1f944a0d642729d3736ed1c907074 +#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 fa34c808bb494ddfa3f3926bc42e650c +#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -924,30 +951,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 0c15f62eb7534e809f625f3fa213e92d +#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 d67719a6f0ce4ba1bb6152a10507b729 +#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 1c96e75281844bfab0578bab2e816854 +#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 bece1fc3c3f842b0b30d8f1b7fbfc200 +#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 a7caa36b0f83448b91ef2e76e30abc51 +#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 39321e93e9994fcca20b425aa45c2894 +#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -957,47 +984,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 601cf500d76c4e0287af4429a46b36d2 +#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 b286d5359e184ef58054c72df4014629 +#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 e14423edd829401faed0950772123240 +#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 889c44360bd54a0e85e7f0e61aa6593c +#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 7b9bff73624947ac90a99c7880e2e911 +#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 c5ff687c86ef4ccaae25d8bcfbd5f873 +#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 0a610a9632064deb824afd0719429d3a +#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 ec0c47438a5242cb99dffa7a4997e95a +#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1005,7 +1032,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 aae94ac2114641f186eac0f4117223eb +#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1013,57 +1040,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 209e072724ed4d27b37e9bff6d55d811 +#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 3bf47876e3694e6cadb05123326459cb +#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 459a65b8e67c4a9aaa03138c1abe94ad +#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 898eb29ac7714c69840b795633953a05 +#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 2a658bd2d8ce4533ab7e056fc3a3ffcf +#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 32dd2e28cf0f40b6930750f0162355eb +#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 471c47d311074ecfac071b6d52d9cfb6 +#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 5078140028ea4d04973cb9cd20f0607e +#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 ab127d4ba0a44526ab129587a8160923 +#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 d5cc6b4295a74f3586f022b0227759b3 +#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1071,11 +1098,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 585a4fe583ce44e180a062742b3b0849 +#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 0d81b0c9ea58420789d1d71cca32ce88 +#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1083,11 +1110,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 ea4ab0782d8049d8b1b89cea4ae60048 +#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 f6f3b7453a254f828bd4c9e9fef92bed +#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1095,32 +1122,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 3bf9050175d4444ebbbabe219412574f +#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 e03f72a14dcf4bf38ce8232598ca761d +#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 3dcfb2facd324dccb3084c02487625dc +#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 b8531da183964b02bca19f818ec076d4 +#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 7ba1ddebeb2843179fe99fc410b193c6 +#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 a6dc303e9d284b60bf1102212505ca27 +#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1128,21 +1155,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 59ac7830ae3e4d7cb1bf503e8c90fe30 +#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 6d1d6f42ada2418ba0a1de1371825b9f +#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 1cd924fe8ace4a82ad8701f37b5e7d84 +#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 aa297c52cd964291a47bb91c0135156b +#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1150,46 +1177,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 28b02c90397745bfbacc03c3b1034939 +#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 ef2a4f39f01049b891868b84d968c0dd +#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 89e3fa8dceda4f0cb1cfdfd1f17fe4df +#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 7cd178223ba94d1ab3ee8cc5f13a8dcf +#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 46f6f8d050ce4f8c897056167d9707a7 +#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 5ee00ee409b746dc951ca1d4c360e624 +#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 d4af972281174b8999eab55ee0ab1a0e +#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 80401cfffae042ab9ec4b3754af04b25 +#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1197,19 +1224,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 32f86f911ebe4a4c94975f81742333f3 +#: 9c87c76c690948ac8e18088a0fffe679 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: d5f1ad2b95ad46d48f8f2ca5e357bb5d +#: ad00d94d4fb64bbdac356e64dd3803b9 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: c53ceee943ad4acea779e072b9137889 +#: d8110ed19da94ad8a9f56e7006c4a2cf msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1220,37 +1247,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 7dfe9dffbf5744299bf232599644c7f6 +#: a74935dc31664e979ca8f90a6a4ba53c msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 00709fa451134ee09a0d808e101f28ed -#: 991172e201ec4796992a349dee44f090 +#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 1f3c23a4769043ca985b8ddfed19391d +#: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: f81b43c7cb194a1cad8672129223c833 +#: 9643449da1da46d7861866dce490cbcb msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: a20073a8f5374eb1bc8531ff33e622b6 +#: 713666580a0a4466b4ba6e3eb2b54f0a msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d08869beca3a4774baf1097b63e79474 +#: d50574c8b9694f83aa376d39b9a6fcd6 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1261,11 +1288,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 109b773789024b2b9c063a6169c6169f +#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 959fa04f88e54d42b9b774cc95d85ee0 +#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1273,13 +1300,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 64674980c3f24c45bbfbf3f957dda55e +#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 90f2e4265919446a902e17627f4420e2 +#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1295,7 +1322,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 6b5f91a749fd44b5acfd6071c9913342 +#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1305,43 +1332,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 5fe2962837b14f0e9989063be4a506c3 +#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 4e1bdea962ed4618884cb9d1d59d7509 +#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 37eff4ca02e843259f6ffa38e4a87a04 +#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ae47231c203d40a98c10045038ea9b65 +#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 018a6d5dbf1044559b365c7b9017eb3f +#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 e073d8f990c44b09a73d642cfe49bebd +#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 e04fae88d9b64493ac69eaee24585098 +#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1349,13 +1376,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 b26b9c9b1c4346a297a31c9721f0172a +#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 b50500c3c3f54b16a535a16175a44653 +#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1367,44 +1394,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 623f3a804199449bb85e23e00c8bb507 +#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 effea0b1356447c0899ca0746667ea31 +#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 00e8ef87864c4ca2b2c1c0548b02b38d +#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 6e6f48d70b894a6c959ca30fe6bad772 +#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 02fe08760a4a4ab49e96f4e51316a81d +#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 172ed7915a654964ba63f860b2d65330 +#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 4d0a2871a7484e21b3c39c4dbaaa63fc +#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1412,31 +1439,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 1eea9f1e284447718141f5417b6bb433 +#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 509411d353fe4314b087b81b09ea960b +#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 a54bc80bf08243bba67d98dd682ee134 +#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 69ecdaea24ef42eebef9d86e5d716b11 +#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 3cc5847468d1478bb5589dee68147189 +#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1444,52 +1471,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 98c6bc409420485095ae65d6b0b9a3a0 +#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 ebe23e5378514f888a9ec32a2adb1e98 +#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 387cfe85604f424f8d31c4a4c9c15edb +#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 7b1d65754e854693bb60289c97d3fb5d +#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 f440cef729c8410281432307a4da8d55 +#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 4fbb8ceb1b59480583ac611142167049 +#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 b87869204838415bbf694214e3680593 +#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: 12cf5f2264504c44a2173e858bb2c283 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 7694f9cabfe04308bbddd2c88ae6d9b9 +#: 0cf51b6da6884065ae42032abc20eb0d msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1498,17 +1525,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: b557dc4f8ef549b98f59412a918643de +#: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 3011eb003c084285b30cfa56a8da45b6 +#: d3f74c3b094a427fbec831afab657d50 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 +#: cfffc518ba6e4ed1a80762ed6f7d25df msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1516,7 +1543,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: ce78b2d147054da895beba66d0ecdab4 +#: 9454a330b9324744b89448f2694b1b03 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1526,7 +1553,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: a973846ec5a946eeaff02c5b00997da9 +#: 7f8d99a30b644457a62ac1523d0c72aa msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1534,13 +1561,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 294fd83a97a64249bac38f7482159372 9e8eb1542db640ff9e300649ce50dc9d -#: ccec7f73b9d948e79a6cdf32bc124092 +#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb +#: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 22948f19cb78485f8f86244686a35c09 +#: 10d1373bb14a4a3cacd3b92a2f83382d msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1548,7 +1575,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 001d9579bfce438e865377fb9c2df776 +#: 70e257091bdb456e8957f90a8fa90e8c msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1560,7 +1587,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: e62618db8995428bb3f260e03ac8f459 +#: 1741804e33aa43ce88b4320c11ae5973 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1570,19 +1597,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 457756c4e9544f068af897113358cc89 6d5ae75431424ea788c3440606f22940 -#: 98e0548845fa447fb05a29c9fc2f17b5 de5e8aad4e3046bf9bfc2ad8ccba17d0 -#: e9801b2142cd45368a73ef9b121c1d08 +#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f +#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 +#: f924d65fed0c4cb5b0a019b084a8b535 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 ee2bca9bdbb74b60a706c3118d6a17ba +#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 e63ae9694f40438d872d141ae824a42d +#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1591,21 +1618,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 750fdd4c270e46a09f79e867358f7414 +#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 b3f688cc82444ef7a7a0aa63dac39cac +#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 3638be18b4f64cf08053d512e590dda3 +#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 7d5b9c21739c48f18c13614ca6967f6b +#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1614,13 +1641,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 8fea29993f944d8d8d3181afa29bd0a6 +#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 02d0b648d70f49d7892f690be06df585 +#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1631,15 +1658,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 0743bef42b9a42328849c8c2f9da9eed +#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 85c5d0cbbc6243a6823f5eeac0f85dd9 +#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 be848f30769543eb9c0be55263e3f758 +#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1647,7 +1674,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 cbff44a64ba4432cb59a82f82c2f0103 +#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1657,26 +1684,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 617f1c0084cf42d9be4c7a8fa5a48432 +#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 cee79afa3c6f43c29ef05e06b7843d35 +#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 225903b11efa417989df42de86ad2451 +#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 1a5f058290064c1cad05e63eb127fcbb +#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 74ad8d69cf294ae880dbbe28e25b3545 +#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1684,32 +1711,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 5293e8ee9b3b4f59947cfc164ef111c4 +#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 ffa1955c759942c68e7589429e5ea86b +#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 038bc0ba5f6a405a8255a7be76979baf +#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 fae1c63de02e48c0969a98e4c49b2e06 +#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 7093a94695524851a5463193f0701b78 +#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 dc8274ecb15948c29a31db89b12a58bd +#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1717,7 +1744,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 cec8eef8a5aa49778ecedd4195ab9f2c +#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1726,67 +1753,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 df100967597043c78112bf43b520cfab +#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 59ccf4daba39406581a6bc2d9bb1b7d2 +#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 570cc75699dd4e0a987fc9aca9a01ee4 +#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 9e123723048546d495ed5110d7177708 +#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 26543894f6e04270b89ab702451bcc89 +#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 f403c1d4e43a4aa0aef8488d2b5a6262 +#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 249dffb569a944c897ce5862e5f28fad +#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 1641c96aca2f4923885fe8a509eb3a49 +#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 bc63405a0d964df2bd9493996abc48fe +#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 5c191d1420db4e26aca31c1b1e34cb75 +#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 d6a5c65e824a4bbc94578df9597d4716 +#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 a7ff51fe564748229a88a0d3044dbc17 -#: c12625211cc542b68cb51365a63eef00 +#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 +#: 1acb064f7a4a482aa0174bdc847c6382 msgid "`arguments`" msgstr "" @@ -1794,32 +1821,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 05c34a5a2e404a14b9d284a9d0c73bd3 -#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe -#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 -#: e7f1993580f0425098a719e83a64cc7f +#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e +#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 +#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 2fd5b42cafe34d3185888de041818dff -#: c158e9ee5fbf4e868b152a0a5880092f +#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 3f29e4a3087847e9af6f19166a8def9a -#: 92697d3179ec48898eaea9aba3c24dcd +#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 c0eaef93bc3743279549bcfb8b014ca3 -#: d6722e3093884ad7b62696fbb2f48fdc +#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 37c493fdc2f0410a9748f8faf09ce5b5 +#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1830,11 +1857,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 04e3eefe4ec445cb90c2fa42344aaed5 -#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 -#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef -#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 -#: c610220d06484d589313dc29faf8222c +#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc +#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd +#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 +#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb +#: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" @@ -1843,51 +1870,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 662b36e3505f4ac3bb5070bb6e055217 -#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da -#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c -#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b -#: f71216a4b35e4157aece5ffa2602d8bf +#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 +#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d +#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f +#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c +#: f760465a49d64d4c8468ad9c4fea62b1 msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 a3c775a0f04b4541a9b712bfe2e4e69a +#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 ef16c4a9a7ea415fa399297b63b9710c +#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 2592e429c74c4ff5b8ba68a36f060c1a +#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 5cca4c2ad617400eb6efad4066b1839b -#: ba1fff3ebb274dfba845b3ee20ebd71f +#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 6914526c0a7c43a2a05438519508ee0f -#: 722d3bd7184841639b9f9a38914002da +#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b +#: d555a3d991e344a5a8e1289168d7c6d1 msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 737b0f9392154241ae5b56c6caa823f5 -#: 7b46d408e7e7481b91a950b2d4010c9a +#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c +#: e9fa9430535c424fa3e8be5d460d2ba4 msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 f09e7371708b4c0685eef2a314791ccd +#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1896,32 +1923,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 aa6ca1def2024c98b9d5542de1a81425 -#: e9fc5f7fa4474dfc95039b94167fe894 +#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c +#: b0290d1a477b48119e17cf1fed9d6dff msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 6c37a1ff939748bf83a86c07c3d017fe +#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 3a8126b0a0334df890b2be2c693ea5d5 -#: 61744122b7d7494890cbe6b2fb72b9f7 +#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 +#: e1cde4aa32c041238ed2596173c6d824 msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 93cb9015dacc4b50a4ef177ce4ece2e7 -#: e0c7ccc8f8664cf794cbb7330355f3fe +#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf +#: c2a92d3eca7f4ee39cec649170eeea53 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 58a1773b1cf546d7890010fdebd47388 +#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1929,61 +1956,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 230f3227ed1144f7abe0f8c231bebbd5 +#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 5c77dc9f8afe4dd88933943030e836f2 -#: c9534670f5f04769aa3749c3778eb705 +#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 4ec8bbac5fb14371a6a4cd53d7cd6450 -#: 7b0887a8caed41b2acccf7021bb323d3 +#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 +#: 718ceee9973240ec9c100977bbcc8921 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 aceedfb558b246bc87eb3eaedea187fd -#: e5e8b8c75f0f43cbb6e160e5bf810c6e +#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 +#: c07ab08eb75d4528949c56a3d7c12b28 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 266dfb5fe6a842078baf66073cac9623 -#: fe3b9fb45e01490498c5a35c012b3de8 +#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 85f424cbfc85460f9da310aee1ff0b82 -#: ddf82b12b12d416fb65f3ce3f51bbdf0 +#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 966e88656ae5402a975022ee60646283 -#: af14fda3cca645fbb2f3c5825fe0788e +#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 09120baec1464afb8aed4edd773bf509 -#: fec70bb106ad4d95a2d55ebdcf711afc +#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 +#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 1dc4148caef748428a7d13caff37b1b1 +#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -1991,33 +2018,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 +#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 947b1ca132a54ed39745cd12ebcd65e1 +#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 +#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 +#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 5fa512d352d945e7a3e0d59b0987cd1b +#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2025,22 +2052,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c +#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 81e91df082834d2cab7ef1f62d8ba57a +#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 e6bfd1dc2e324992b6c3332c11ae3445 +#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 acf10261df2944ec890d754fd56c6b28 +#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2048,7 +2075,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 bda6b8f398554b0c946c2c7d96308a42 +#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2058,54 +2085,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 454c02c3918647039c90ae387005dea6 +#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 e1fad28bf9cb4c4c85eb74dd520ba107 +#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 9835d0b399b84a0084fe5a4d9e7e6405 +#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 410ba7a5ac6349a98460c6337ee5c4fb +#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 d2daf50d7f3d4de18331c8fd2c8a5786 +#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 8f2015c12b2b4d5d9a800ddeaf428f25 +#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 f0ff919ffc12439d89d7b40f51ade84c +#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 307a17a893fc4dafaec2a63a95704644 +#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 7f393e86b114470f8dda47b2deec63aa +#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 c3f459b87b96435583637b3f1573e658 +#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2114,15 +2141,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 9f676022eb2744839ca2109920250cb6 +#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 ede7285f77864fb0aee6cfecc2c97fa0 +#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 c55fb184bc614ee2b6e5e64611e5df9b +#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2131,11 +2158,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 66b522f46ce242149386e79f63b32cf8 +#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 64a20285785d48ca86227a0cf6353ad4 +#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2143,7 +2170,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 5f71bbe2c74e4260b79d4d9230d35397 +#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2152,34 +2179,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 63bfff437e3348428f7e33ece7ec55e7 +#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 6ce83d9c06e4436881aa47d94ef41e0b +#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 55006c594abf4e70a38e979568fadcf4 +#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 +#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 1a1905ff2d624eca952c8a53b3bee678 +#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 368ff92476b14f5c8331260eafc5acb5 +#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2187,11 +2214,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 5d530afa23f349a79f54d51d40724747 +#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 16f965f86712483aa7f95dfa3f944a17 +#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2200,80 +2227,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 dc629e2c90ed458b96107a6994676434 +#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 cf2f077cf8044079a7005e6e508dcd8c +#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 129e1d2a71894d28b009f4846754a75d +#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 d6791bbe575042b9a7282c69407dd907 +#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 e8da87f8bb664334adf831995601f462 +#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 de6c322618304207b6d1364d1ec2dc13 +#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 43bdcf6dc1b14030bff27fa53289c02c +#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 056510b42ea64717996ab49c307bda86 +#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 6852f5dbd9094c99bb68f2a88f76c9bc +#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 f33b6800367248b7927d97ad7b4be5b5 +#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 8ad812d7e88f4cbba83228ffb1711576 +#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 cc680bbf091a46f8b4b3dbe6324c040a +#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 446ac81f078d46289a18f494748f482c +#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 3d6d958d111943f3a2139b4dbb7810db +#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 ba0ec9157709430c822f4e91459288e2 +#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2281,7 +2308,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 2565f8fd4a15429e887aeb71eacdff1e +#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2289,7 +2316,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 659ed5c64fb546399b741553a347b8e8 +#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2297,14 +2324,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 3d87e69d41374fbab23b26d36c1aee03 +#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 07bc81683e2c4ac68b379462bae95207 +#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2312,7 +2339,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 3e304da2150f448d9e39715ac5f5deaa +#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2320,7 +2347,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 fd8a98686e3c4c609f79ae427f1558d3 +#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2330,13 +2357,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 f1a2e1bbb1104a4fab5a7f04cac845c7 +#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 6a7f0ccd227e4f90a8c8ca96744bda68 +#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2347,17 +2374,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 1f79d115d8a145189638c68c3095396c +#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 6e1b3e2d90184e34925891099d2b5cc1 +#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 4f6df7f13e42448eb4a53f03bc477b56 +#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2367,23 +2394,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 dbc0b52627514ad0908969d0b4ddfdf4 +#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 f173dd96ad124470a53573c86a8df203 +#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 af25945b530048b685891b1de4e35e72 -#: cb07caa4ff0149b3ae832be53f8d76f6 e0098a77080d4349b05ceb7735a5fdf5 +#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 +#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 2445d2c7c2794fd3ad8b6ed8b4a9440b +#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2393,7 +2420,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 4459819ba75647d185986a3386939494 +#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2404,11 +2431,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 8f163bd34ded4785b6e28c8e2147e0dd +#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 1799e11a7b9c4929a3d1379d7ea45d03 +#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2416,46 +2443,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 9510c0b431a44b5e84e0b583de7c5446 +#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 efb4eb6f5e994b50a52fa2c707dad1ce +#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 34599c6f10ce4104be2359a1b37f91cb +#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 0663ea7918994d3f9c45c652a3ed12db +#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 a98dda6ca4b14edba467de638bba28fc +#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 10d0e9f8df8c47788703073b17529bc8 +#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 9a0e1a130fba4d24a9168ca3e455cd23 +#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 992a8c801ceb4233acf56b6bff315188 +#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 9027d23fa7074b789c3b86ca5ea17fa4 +#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2463,18 +2490,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 68b47710a8ea4b978428b42c627944e9 +#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 d33e4cac65d14111a89c838c4d1759b9 +#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 24cea1cf7d774b6ab56959f289cab39d +#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2482,7 +2509,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 b866867d6f8e4d3999b62a85e6884ebc +#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2490,7 +2517,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 80c49ed168b14d25b2f09b3b0186b44f +#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2500,12 +2527,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 71628ebe908b4cd28dd1fa17e3d2e2fb +#: d33aa2353ad44fb885d3a1ee48263dc4 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: f123ca244c23413c91405a4b84887525 +#: cd64d2d828834cbbb24ea5358caf5405 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2520,7 +2547,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 23299ae1bec94b00a32a8af7eeac350f +#: 80af387fe3ff4e2da999903385bd602b msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2528,17 +2555,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 2495a9f2032a47c188338cb81ba429eb +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 3fd2f3cf7bdf44089df2ce3122534801 +#: d402bf528c7f4eb69aaaa275be2bf1d4 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: d5a5b8b490b640439db92da949266e4e +#: cb9980db4e5f4c74b01c2dec6d5e92d0 msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2548,15 +2575,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 5935ed94331d4b2f8ce597f31edea843 +#: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 5feb559552194ba58da7206c601292fe +#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 b7124ba4df9042baadc1641ee09545d6 +#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2564,56 +2591,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 d34b698c62114041a64e0abce25ca935 +#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 cba2c31262bd450cbafc7ca77f4fb8fa +#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 b01be5f632104096b5af6193aab34d90 +#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 60a6a02c1367403db6df3ec10f75eb69 +#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 314ea7bc35154f41b2af5fa6683ca389 +#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 d81e679b13474f74bc5e1ce1e31c2bc6 +#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 d7fb27131ee44bfc82f698ee44b2bae0 +#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 b8ef11eafd1d46e088f1277f4ac372bc +#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 d2382ed1f644459594655d5b5b4d838a +#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 6651632d977b44479b721174fffeda2d +#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2621,7 +2648,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 bee5f532554241088764ac9e56abbe85 +#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2630,17 +2657,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 0c7c506f38be421399073871f64e99b0 +#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 8b60286e56cc42a8ab5f751a97adf771 +#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 fa0ad674f15348339a1eee771a6ba9e2 +#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2648,71 +2675,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 177b5f1b95a34fb9b2eb42f733d79ac8 +#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 a08a6d8aca8e490482e127a8fd5e650e +#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 c2c60f68b1e045f88844076e191fda9b +#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 6d939f62526e4e6d95acb57d72f60a84 +#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 c48edd9034364b81ad42540a98b51d91 +#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 9ebe0186a7124dfaa30e558e8f59653a +#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 9381b7d7c9904df0a5e16dac29c2e08f +#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 2aa9c6916e3546b7b92fa64bb83275d1 +#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 63afb7a597fc4e459b6a7dbd40bbf6ff +#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 7418915470f041c9af5bd39ea652de36 +#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 f82db001b58c4969b2d8bc1dcbd7cf8a +#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 26d9f0b28d384617a8e490c1f8e26e52 +#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cf46c971b31b4e10bf0fefb4cd028c2f +#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 a4347983fb9945a4a2773af88e426dc9 +#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2721,11 +2748,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 c5489e0633114372b273098ee2c9ffd9 +#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 75de9fd63393429daf1ca10a85339aa7 +#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2738,40 +2765,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 8b5d0ada32d645be9359f43a431f5f91 +#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 2ed93dc8778e44209194f41b9ad193d5 +#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 a80dd6d9920540e9880514e04035af86 +#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 9de300f7b9da49f59d1c9fd96dec4a8b +#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 a61f52d3c1024c3692899e05fcea4bee +#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 dafc9ba578c14fd79d075160e6b7bd6b +#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 28ca6cae42904559bcec98fb9d2b07cb +#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2779,45 +2806,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 616c9ff9fcae489285f0bbbc67f07d29 +#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 ac17acd83ddb43dc9fb7a5e595ab1153 +#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 156573324cde41ee8b3c47deabf43db8 +#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 c9725be01e8a401fb3ad9ff01339f81e +#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 6797335256e2412cbbe7636507931455 +#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 05a5f0fcb7454cb697e3d810d55fac26 +#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 406e68280b5c4ee494632f94b635b7ad +#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 2d6e2a4ff391494591bbdf8dbcc4a6ae +#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2825,13 +2852,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 e71a974b29624210a107fc2d097d4196 +#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 b59df98754e24654bfef0b1fe1d91660 +#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2839,43 +2866,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 d2bccbff1ce646348fe38c776ad183e1 +#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 943ba46512ce48fe8c5b62327734c503 +#: 5d8bed66282c408695292ea92a03b2c4 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: bbcd43d5af7d44108aeb65075a6bd2be +#: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 834295755af841a78e466eea43864861 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: a6b626489bfa468e8f059ab3aa669201 +#: aac74f957774479a83aab4c6ff1390ae msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: e1dbea105aa845c38cb1f90b43847271 +#: b75d29d1d55d44488338f9689f156855 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: e9640f47d40e45bca184eb30700df648 +#: 574d93d1d592458a985f259519c036cb msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2885,14 +2912,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 0456efb3718b4356ad2b277ee16de967 +#: 82e48b3e3c3f451480cc0b6a529271f6 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: f7e97f926505407f8f8e9a427e055e43 +#: 02e40154eac74ecc98d0447d03475b44 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2901,7 +2928,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: ec597ff8f6ee47bc815b069335869f1f +#: 8cb1c5d9b1a54c40924099494eb766c6 msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2917,11 +2944,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 7467a7f6f26a459ba4ce83e4e6dfcc2b +#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 +#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2931,26 +2958,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 a03372581fa44f9b8e3e088a4099cdd9 +#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 36e082be73464be0ad5d0b681cc510da +#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 4464455b51ad4873ac13c4a63ee5fb54 +#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 ed7ff0753d1743a995f4cfedd6e5dcc2 +#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 4c2dd10dd66446058477a52fb8d2c602 +#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2959,7 +2986,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 978b6a5fd5fa425fa9a18d9f0e8788da +#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -2969,18 +2996,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 000c0d6ae8bf414d9293b9f13fd2e448 +#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 7e91b8811be14f8e80df39ac4c5bd316 +#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 d42799cc5bd4484bb6beb309a61e103e +#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -2988,7 +3015,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 48bb0f6666ac48648c7d969608b3bd48 +#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -2996,7 +3023,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 f8876044db184cbaaca56579d0c773df +#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3006,7 +3033,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 a5a3d408dbe34cfda4dd0b2abe67e7d7 +#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3016,15 +3043,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 4c240a18c4e6441189489011242c1efd +#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 e37e76ef376a4ee695e600998906ec1c +#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 51a307b0ba7c4c1d89309ba8d2250471 +#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3037,35 +3064,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 13cc38d72d34468fa4eb6d91f23ff105 +#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 42a48398d3ef4b03bd7395120f2cfb42 +#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 d59387b433bc4ecfaf7e72026624db02 +#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 d963418ccc0b4803bbc758d718ccb5aa +#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 a224d1510c9e46aab23d8bdc03c349dd +#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 0a82f8a45b0546aaac4c976dcc98014a +#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3078,23 +3105,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 bc418a2a535e49359c4cd44b373bbe02 +#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 a799fba2322944cea00e413c08066536 +#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 35379c6b972940bd8451f10b74dd793e +#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 2d5265525ad544a0b64ad2cf07aacc26 +#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3102,44 +3129,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 e2521b89596d42f8a87a3207fd6c32f2 +#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 3676f23b63e142cb8e5715ae07216a47 +#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 00725aed13a440ca8b3c4f9155fbee99 +#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 2e38a4f9072b4ad9bbb74f943d22084d +#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 2b9f4035ea864b6db50c861a1819289d +#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 28e9064780e7418a8e02a22f92e34404 +#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 66ce14a10d2d4dc497d3ed71e11ed8b8 +#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 8dc00528c3d2426c8a3492a8191f1d81 +#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3147,33 +3174,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 f9ef5e258f7c4971a8543d1dfed711a8 +#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 324bc51071d743ea80124c23880ddc0a +#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 d8c13e01976b43a1af34c11a7bc36897 +#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 43910a8ab4484e529a17df418b1aedbb +#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 +#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 7ad12d67e815400c94080804b9285629 +#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3186,34 +3213,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 457d5a31c79143acae2683d95d27f7a3 +#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 a2a73901bf634547900d08b9a1ac8889 +#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 f347d80e62384b14acf6423675e5359a +#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 2a845a4f3f98428fb82f3ca7ce038a6e +#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 e2007c74d5f449a882809d6b91c010bf +#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 7f5e53ee7cf94be2bff45ef64db28a24 +#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3221,7 +3248,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 a0d076b7b8b048478580c99ef0c8429f +#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3230,7 +3257,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 7fd926c18ad548e98845e9b5134dd6f2 +#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3241,7 +3268,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 789fbd47f8564cceb430ef3c0bc90e9b +#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3249,7 +3276,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 45c4d0492d6143ca9cebe81e9b2cf3ae +#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3259,13 +3286,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 73bd3da2af8545928d5ea71d0f7454f6 +#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 15ce3d2700424f0fbb280d602ccebcf6 +#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3275,11 +3302,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 af4268f19202436eb0a7e8c6bed5e386 +#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 94a4eadca6b949d79de2990a0150eee8 +#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3287,17 +3314,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 09c1619e8cbd4febbb637f7e99ad5890 +#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 677ea7a27eb64568ab3689142d6efe70 +#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 097e6d47f9394e62b80110700492783a +#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3305,7 +3332,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e93affce8c104bf6977182047c1f1077 +#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 06c9e04ba890473b851240a0fa9c3b12 +#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3327,7 +3354,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 0380dc1fe3aa48e4b62283b7b2a611d8 +#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3336,7 +3363,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 49b251f7a313492ea60504b00109e526 +#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3346,7 +3373,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 7ee55702d7dd4679a24ff052f6f0cbeb +#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3354,14 +3381,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 85d7e2e270874aa6b9f477cec0f48154 +#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 570e94513c984c09ad6aa255f534216d +#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3370,7 +3397,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 a107258662fb4bd4a9a3d8754e34d1e9 +#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3379,7 +3406,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 fc1a6502d831458ab8371a575cea47e2 +#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3387,11 +3414,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 2d10806bf1ce4e26b92adda61efc0862 +#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 046c5e134de94b629cc22d416f3c9182 +#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3402,7 +3429,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 52fa22d3277940049fbb589a3ea73433 +#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3410,23 +3437,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 6043beb96c2c49648011ec556aa9e986 +#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 5ac4310515124e2986724425bed5651f +#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 7958e91d5c2f4046aa9d2070a900f9ae +#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 2db234d776fe4fd38bab07245dcb783a +#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3434,7 +3461,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 7cfb17230e284ee7b6e2a00efe8eeb74 +#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3442,59 +3469,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 4311ac98544e4fb0b2f4b24985710a01 +#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 780f9c72e6c34c39918642c7e2477355 +#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 cc4a7316db644b438cbaa181ad9ef2d3 +#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 dfc461a03fe8487794837904febb8b63 +#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 1e83485b00b64dfaba897bd8d772e0f0 +#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 d0321d6805ec4d3abf3877d02a0a417f +#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 d7d77e807b3048c7bdf89558f76804cb +#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 8d9b8be147fc4a71922dde858842e543 +#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 34b7705416a745a6a42e6d402c0757ed +#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 257adcee9da64d5c987f3b64efd20ab0 +#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 fa6ed5d0c14f42f4aa3c5144648db22c +#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3512,7 +3539,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 333e8ce458d54de394526769f96d12d2 +#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3520,38 +3547,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 b819e8a5df6e4fa495924095709669ef +#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 f1955468a1364d44a930db77c9c4b495 +#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 8c3b9b645a204d02b2c73a205e8ec296 +#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 4d88b9c186cd4502adbf752e8a70b6ce +#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 9927673564024ba5833b5ac271737857 +#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 84f4ed7ce2004742b8db9087104a469a +#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 2b5f9757adca4490a149c7f45e14fcb5 +#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3560,7 +3587,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 0418de720813442f81ecff293c9448b5 +#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3568,62 +3595,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 524eec63be8248ae982939c975ef50a2 +#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 5e99f9912cc549a7890e2934425eb943 +#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 b0121ee087d6424fbb0ea5957a7b0b8c +#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 49e9f6b3a06840289decf3f557860f87 +#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 ed9eebec0b3d4b72ba65507d37757a37 +#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 bf9b255a24a84f3ba989a223492b8f41 +#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 e79fa0b7f8b14810a3a20908ef92bc55 +#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 290e2035f903417cbecb5dc5f09d6ebe +#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 d420730151534f1a89076588a3358f09 +#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 a6b5378bbe1e4bee9e37a765bddf75f7 +#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 6e4d9465dc2b454d96b02d7ad1817795 +#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 a649d4af5f434dac9395e013ec4836bb +#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 446190a298834b73bda068286e8490cf +#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3633,7 +3660,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 2f35c012ff174721bffe66a3f58a804f +#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3642,7 +3669,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 43127c98c9d94aedac61cee67929c1a6 +#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3653,28 +3680,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dc4fe561203c4c38a9caea5bd6eff2cd +#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 f924e4896db2424d99ce8c9da14c599a +#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 bf7646f5f925485c842a6d34140e40b8 +#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 c483e61dec8949fa96bb893d422888a0 +#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 85fcb523d0e34a499eae04d304887f7b +#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3685,7 +3712,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 83d47c8736a34f3cbf09e3997845e4f4 +#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3698,11 +3725,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 c698fb3d37bc403e9aeb679b8fc0e15e +#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 ae8af2f0eeda4aec97201211dfa965c7 +#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3713,26 +3740,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 2ee87aa465cd41fda16a61e242f8c9d0 +#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 0a6fd4469ff24b61b3ad001b09eead18 +#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 b96ba19bce9341d39c46054e1f10fe8f +#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 903f30af3d0c45cfb61063936a8097a7 +#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 ede8db7c0a58432e8a1c416e937a06d2 +#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3742,64 +3769,52 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 c8b53615476a4a1fbef2420d93bac94e +#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 ea03cb5525cc491f9feb5c4780b38fee +#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 92fd3a5e31714eab859dd630af2e78cf +#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 de660ecdb5b44c97a0e519d00b232497 +#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 5afc1e1288e74ed0985e61e5164479c7 +#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 862dc7ac81e54b1fb3d4c2f961b8810e +#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 e2c94c0e1c7048d38cd7aa2c465a859d +#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 b63253780f51467a95207d820d13ac39 +#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 6d06ca7ed5df4560aaed286f4fe33928 +#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 5448df4a6a8f431d80e269bcd480e19e +#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" -#~ msgid "" -#~ "Unless required by applicable law or " -#~ "agreed to in writing, software " -#~ "distributed under the License is " -#~ "distributed on an \"AS IS\" BASIS, " -#~ "WITHOUT WARRANTIES OR CONDITIONS OF ANY" -#~ " KIND, either express or implied. See" -#~ " the License for the specific " -#~ "language governing permissions and limitations" -#~ " under the License." -#~ msgstr "" - diff --git a/locales/user_guide.pot b/locales/user_guide.pot index a806cea1..0a669946 100644 --- a/locales/user_guide.pot +++ b/locales/user_guide.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 16:53+0100\n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -16,1273 +16,1273 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" -#: ../../LICENSE.rst:2 -#: 75de2be8809847b8bf1ccd42aa694a24 +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 msgid "Licenses" msgstr "" -#: ../../LICENSE.rst:5 -#: 2edd71801f6245ef821887a74f21b94c +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" msgstr "" -#: ../../LICENSE.rst:7 -#: 3c0a9704ed8f4367893242a4f75d703f -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." msgstr "" -#: ../../LICENSE.rst:12 -#: 90cc755d172e4c82b882b4ee620fe652 +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" msgstr "" -#: ../../LICENSE.rst:14 -#: e5246890525144bda8547106b6643382 -msgid "to **Share**—copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" -#: ../../LICENSE.rst:16 -#: 4d96baa7ca7a4240b75be213696558ba -msgid "to **Adapt**—remix, transform, and build upon the material" +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "" -#: ../../LICENSE.rst:18 -#: e19adbba09d14d069534251a7ef70993 +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." msgstr "" -#: ../../LICENSE.rst:20 -#: 8bc6672f4a33428296226112a1be6fbe +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" msgstr "" -#: ../../LICENSE.rst:23 -#: be38276e7b374f57b9997391bf898a62 -msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" -#: ../../LICENSE.rst:31 -#: f00d5c3846034c2ea116c2f74786d9fc -msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" -#: ../../LICENSE.rst:35 -#: 1798d65c10104040923c2fea2199bab2 +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." msgstr "" -#: ../../LICENSE.rst:38 -#: c65198b804f8436ba783643d51bc72d9 +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" -#: ../../LICENSE.rst:44 -#: 4777f6a958394b138c5b68eee0367734 +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea msgid "Software" msgstr "" -#: ../../LICENSE.rst:46 -#: 7dec2236137f4de5ac7df7a8c8eaf98b -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" -#: ../../LICENSE.rst:50 -#: 9c4d58a1129a4d4eb4db1bfabbeddb6e -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 #: ../../src/_includes/what-is-cwl.md:2 -#: bdd540403a5746ff99edf2dcad0e3122 -#: 5ad4be9b62d54c95a913795b514676fd -#: dfc7702e073140c985cf47272a20214d +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." msgstr "" #: ../../src/episodes.md:5 #: ../../src/setup.md:5 -#: f1b89ae4325343f783bce8b7c9971047 -#: 810c4e8dd79247d6a6fd51a8f65d3975 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f msgid "This page has moved" msgstr "" #: ../../src/episodes.md:9 -#: 3060770b3bef41d7bcfcdfb413d7689c +#: cc11f5d29206492d9f2f0922882b6159 msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." msgstr "" #: ../../src/faq.md:1 -#: 48bb9f628b344ba1a3b67ae1cb264e3c +#: e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" msgstr "" #: ../../src/faq.md:11 -#: 7e3684e9672643738846756e1ebafd18 +#: 61edb787dab04ca2ad3ed07616d878a0 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" #: ../../src/faq.md:41 -#: 187ceabb7fd9480bb8cf0f2da47f65ef +#: d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" msgstr "" #: ../../src/faq.md:43 -#: b548b76bcc85420a9b30792386105139 +#: fc62427c0a004810b055dee90ec5e2d9 msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." msgstr "" #: ../../src/faq.md:59 -#: 9ce692b78ead47e4b0f8cdae8837d35b +#: 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" msgstr "" #: ../../src/faq.md:61 -#: 6df1201c159343da9e7515379980d6a0 +#: bc7ad10c929848a3a9a240a3c501d299 msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" msgstr "" #: ../../src/faq.md:82 -#: f9ab1d0dc1c842b6abb5385268c1d3bd +#: 7225a993d281421b95c8e3df2846a0e3 msgid "Referencing a Local Script" msgstr "" #: ../../src/faq.md:84 -#: 9f6a84ab6a9343b6ad7db826f8964362 +#: 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" msgstr "" #: ../../src/faq.md:86 -#: fa50e4fa990b42d1ba4c0f4ae1e5caa1 +#: 450edf800a18423195bea4fe8793a2cb msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." msgstr "" #: ../../src/faq.md:89 -#: 3a871012fcfd4f3ebeca0cb86ec93435 +#: 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" #: ../../src/faq.md:95 -#: d954edfff2584288ac8c600733070d2e +#: a7d84f740a714ec588503ee084fbbc34 msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" msgstr "" #: ../../src/faq.md:97 -#: af6b1e37d6be4450a761854480ec9aab +#: 569d553abe85450c9d1c37456bf412f4 msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." msgstr "" #: ../../src/faq.md:104 -#: 31f4a2d43062493ca64c648f80afc8e9 +#: 95f5dbbd21084a318413b9528fb867be msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" #: ../../src/faq.md:113 -#: 41c54e71b6cd4f63b2a619a515240d34 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." msgstr "" #: ../../src/faq.md:115 -#: 8edc3541ad134ab5a1d23c724f1f0a4e +#: 8d86baa239364f799d4f9d5ea2b0e314 msgid "The second method involves including an input of `type: File` in the script itself:" msgstr "" #: ../../src/faq.md:135 -#: ac0ea81eba8842a18801ab03cbf80a57 +#: f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." msgstr "" #: ../../src/faq.md:138 -#: 52be1a5640234feabe958ff7ade33653 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" #: ../../src/faq.md:140 -#: c6db734d5aef4f4f99676bdebf9c83c9 +#: 2c38cc58cbb340bc935a5f00e96ba95c msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." msgstr "" #: ../../src/faq.md:165 -#: a9f7b47c0dd741739795da39bf114879 +#: ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" #: ../../src/faq.md:167 -#: e3fdd9228b924905a4a1f4b2b7ad7159 +#: d06cbf89028b4638ad54c2529bcbfa25 msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." msgstr "" #: ../../src/faq.md:188 -#: 3f7cda1437cc48f18745a827ebb74582 +#: d53fb28dcad04e7788cba9e280a2343c msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" #: ../../src/faq.md:190 -#: 5aeaba2cae64442e816bbd458aee833a +#: d9e30e11533b4d53a144f5df7041268d msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/faq.md:194 -#: 5af827a402834978addd82c70be6b5ab +#: 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" msgstr "" #: ../../src/faq.md:196 -#: 6d69e42bd8e443c4b19d80807c7efd6b +#: 937cb94a370640c788fbc3fe0b19f2e5 msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." msgstr "" #: ../../src/faq.md:199 -#: 404640397b6e40c2a2cd5cf85ab3b1c0 +#: a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" #: ../../src/faq.md:201 -#: 1682c2486e224770b62269709a8663cf +#: c8c235a9bf6240628f0b5493ffebf7e0 msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." msgstr "" #: ../../src/faq.md:229 -#: 9078fc009bc145808813c9cc2b734b58 +#: 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" msgstr "" #: ../../src/faq.md:231 -#: d4b5a54a400c409cb7984428f6a03ec8 +#: 89b90d3bf1ea4ebd88482d435241fac5 msgid "To make an input parameter optional, add a question mark to the type declaration." msgstr "" #: ../../src/faq.md:247 -#: 9e8dbee6e8f84d08b1a54fffa06394ef +#: a854006054ce4ffe94bbfa73bdbecbf2 msgid "" msgstr "" #: ../../src/faq.md:248 -#: 1d846bfb5f054d09a4afad1da8e4b642 +#: f80eb714e9df417fbba555b5dd5f4d8c msgid "Enum Inputs ⚜️" msgstr "" #: ../../src/faq.md:250 -#: 2d0e95fec8084787b734388d60188574 +#: 10af80fa13af4158aec7060550485350 msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" msgstr "" #: ../../src/faq.md:267 -#: eccc4a364330470fa474dcaaa3433390 +#: ad1c26711ccd4efd8fdb25f9293d33fd msgid "" msgstr "" #: ../../src/faq.md:268 -#: e945f6a337af4e4686bed482a4fe6c39 +#: 49e2095b51f84f609f5d4bc088ad9745 msgid "Record Inputs 📀" msgstr "" #: ../../src/faq.md:270 -#: 8a3efaa0ad1548428bcfd6e01d135cdc +#: 52b8538177c64090af51f5f6a696c28c msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." msgstr "" #: ../../src/faq.md:322 -#: cdab644adc5643708870fb08c06cbfca +#: f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" msgstr "" #: ../../src/faq.md:324 -#: 089a5a0b076b44aeaab4d69ee3c79f97 +#: 7dc0540508084a3495ff3b2ac90fd323 msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." msgstr "" #: ../../src/faq.md:342 -#: 561172559c6f41a68819608fd9e58bb0 +#: b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" msgstr "" #: ../../src/faq.md:344 -#: c5ee4946d2e840abaa3dc796a62652c7 +#: cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" msgstr "" #: ../../src/faq.md:349 -#: 4f2069a2113c414db18eca95550e9e09 +#: 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" msgstr "" #: ../../src/faq.md:351 -#: 31f3390e6771414ba7bf57c044c4b0c4 +#: 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." msgstr "" #: ../../src/faq.md:359 -#: 3b77ce4930ae46d5be9f6965e8c54727 +#: 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" #: ../../src/faq.md:361 -#: 06f36bbe4d3840229b7374f27b86ae80 +#: 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" #: ../../src/faq.md:363 -#: 3cb2f70d00274a4dafd972ccd8c519c2 +#: fdaec25650ab4b0fb1c527610e24ae5a msgid "For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" #: ../../src/faq.md:371 -#: 093a1529262043ef84a99675054938e0 +#: 182959fc9f4746d082994e07d05c8cde msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." msgstr "" #: ../../src/faq.md:373 -#: 45b6d9acbfaa47e5984184f7da554d0a +#: cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 -#: 5705c9bacca5405ca6f14315a5575db8 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" msgstr "" #: ../../src/faq.md:384 -#: 82bfc285b59a439ca97d3278997f0fce +#: 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" msgstr "" #: ../../src/faq.md:396 -#: 181d5130101d45ccb22aebae3d154c2f +#: ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" msgstr "" #: ../../src/faq.md:410 -#: e864390b5ddb423aaa10e9d33d257dc1 +#: e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." msgstr "" #: ../../src/faq.md:423 -#: fe637c32fb15427a9045679b5da42ec5 +#: f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" #: ../../src/faq.md:436 -#: 1f8004b9df8547029d82e57f9abdc979 +#: 190099a242a645c9b9f8bc3ce89d920d msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" msgstr "" #: ../../src/faq.md:442 -#: 70990dc5a0034099921ceb89c89e2dcc +#: 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" msgstr "" #: ../../src/faq.md:445 -#: f679e26f18d9455f945fd13361a9c906 +#: 1901c34201054a9cae199b0dbb8b945e msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." msgstr "" #: ../../src/faq.md:450 -#: fcd0273dbdd84e728cfd8fbe239f2a01 +#: 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" msgstr "" #: ../../src/faq.md:452 -#: 173ddbd1e7c64927a8dcb12a2a2140f8 +#: d7b044f5224a48eda09bc949cf645193 msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" #: ../../src/index.md:1 -#: 662fe273e2fb4042b688512955e450a1 +#: 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" msgstr "" #: ../../src/index.md:3 -#: a15b52205f0145feaac298510e4d678a +#: f8d6e4cd54cb42c88182a43171d97bab msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." msgstr "" #: ../../src/index.md:7 -#: 512aa0c7166b429e8116f71eef007f79 +#: 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" msgstr "" #: ../../src/index.md:9 -#: b1b19e17a18540939cb3bb7f8a700cab +#: 0f47157605a34ea58770ea898deebae4 msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" #: ../../src/index.md:16 -#: d58b36ac43ac44139897be752fbb1f87 +#: 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" msgstr "" #: ../../src/index.md:18 -#: 6726cf3585a646a8b4cbeb543cf84a38 +#: ed74c9a4b623464480e2c184668fcec0 msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." msgstr "" #: ../../src/index.md:23 -#: 2e504aa7c46a426fa959e7254e9a84a5 +#: cfa67cf5521b414da6f7d34cbed283f7 msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." msgstr "" #: ../../src/index.md:28 -#: e7be0df0838b432d9c7f296d777f120b +#: ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" msgstr "" #: ../../src/introduction/basic-concepts.md:1 -#: 173e0816db20432c8d9dba1de5393dee +#: e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" msgstr "" #: ../../src/introduction/basic-concepts.md:3 -#: 30eacc583f6841719e2142d283811d97 +#: ac62d326a68145b695e46b714d4e8156 msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." msgstr "" #: ../../src/introduction/basic-concepts.md:10 -#: 791b8f38a14147bbaa174c7eb595f17e +#: 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" msgstr "" #: ../../src/introduction/basic-concepts.md:21 -#: 1a3989dcbb9844b39d84bf6df6b352ed +#: cbe1d761da5b403d9605fa1fb8e62fdf msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." msgstr "" #: ../../src/introduction/basic-concepts.md:25 -#: db1bbc6e980f404f9f3fcd08e92ee9a3 +#: 3a71b269bd3c49eb913cf69b60373c24 msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." msgstr "" #: ../../src/introduction/basic-concepts.md:33 -#: acc7887c65974114996f700a38a7eccc +#: b171b72c48d44050a3416a7a42c4021d msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." msgstr "" #: ../../src/introduction/basic-concepts.md:37 -#: d2476d9bcff44f21b8d84a3a0d87a246 +#: b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" msgstr "" #: ../../src/introduction/basic-concepts.md:39 -#: f86415e4d78e48c4a8a76ced81221b98 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." msgstr "" #: ../../src/introduction/basic-concepts.md:44 -#: c5524d73708c4c779980528864506fd4 +#: c3869b4ec5ff47d99e8da79770722e04 msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." msgstr "" #: ../../src/introduction/basic-concepts.md:51 -#: ac46a9f8850a434bac5bc2b41ee6294e +#: 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: 9bba7c4f783942e4a299603430601363 +#: a5ebc727fb3443f78e81d6b7ed5ac750 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: e2140e0f0e7747ef8383887c20a7945a +#: 86e6a06992dc4228bfda7add48e28ca3 msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 15bf490724cd46dcbcfab44633c5a9a2 +#: 8c9772f96caf4169924d22eb929a4f0f msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 51d52d051e654a8395239f88df7c9d8c +#: 4fac209a62114798b79e4810f7a0148b msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: eb496cc818524fa7bae5a22ddd00a19c +#: b97ba368fd664caab0494e2392795697 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: c4a22d12e7f149ff901d27de32b9361d +#: 903a6796e3304a19ad885b2428b0e80f msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 7618de899a7043989d77baacf62eb7b2 +#: 6e352ac1f8e144c392ac5adf18c28298 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: 6f1544a220664b79b04bf008058b5a91 +#: cf2922f645904ac7955428ecddc37b8a msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: fbd14ac9a2f541478a320ed4cbc69e13 +#: 5f47aae608c041aeb4134d59dad314d2 msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: da4dba50d25d4533b3dbb92f54d32a30 +#: f6f589481d0c4891beaccb63160619ef msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: ce11c9f8d65c4268984d0384d95144cc +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 3a201aa497e84f70855bb2251e7e3281 +#: 4ace6b92f4e04a07aa202840ebe36417 msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: b78f7fa2be1c4bb090f6da895457ad1e +#: cc6cd8cb81564cadb8e6a4c49423b7f7 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: f7e95d264ffa4e2db0864faccd9e5a0e +#: 2d9f53b6ed5041dbb6c0b54835897856 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 3f1e5b01e49a4dc1b1c99936a4589afc +#: 907674a4ecff4826a2b880e28fc38f33 msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 03c3048f38ae4938a484cf02001877b3 +#: 037cd0e5ceda482eaeaca03d51745aee msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: f9715b5ec65c405c849bb030c1927060 +#: e4643938445b48cc80eb8973ceeb126e msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 442662f50e9e4620970ce32b1b127969 +#: c4c3315c96714e81b364f8cc003b87e6 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 2b34c786af3840e88f29d214e19dc837 +#: 3eb6a013a2a4478ca2ad134661f65c58 msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: dd6aadff8cf54ce78ea6b317afbaddb0 +#: 074af9633627470485e5225326d5f20a msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: fe7f1f0b28434f8aaf0f6ac6589a83f0 +#: 847951c055b94a83b1e081594cef22ee msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: d10cf45b3c7f49dc98bc0e5d1246f224 +#: 44bde1fae06b4678bcac4f3224601296 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 #: ../../src/introduction/quick-start.md:94 -#: ebf339ed376a4d3b89b15b4d5afe593b -#: 332b6e8b831e4bc5aed3745938230a57 -#: ce7fc63b808d4499b9bf9828c2dafe35 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 8badec9987ba40609cf1f626172b2b2d +#: 9d5100c7d0a040aea1020bf633ad17de msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: c75a8b4bf0e24781bf6713cf6f013cd1 +#: 36eb4b3b966640af90faa55db3789cb6 msgid "The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 79b146ffe6d74e1b8f6019251dc4b7c2 +#: 2ccb956baa6b4376a04ad9fcc4654631 msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 07cca9a33d8f4b77ac6ad35ca8b95655 +#: 72889b830c514afe9a7cb1e64b5666a0 msgid "The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: 31db11c8ddf2423192a8b2063b3e91c2 +#: e29bd7f973544600be589c3b3f84cf63 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: d81dd96143ea444aa78ff45cfa0584b3 +#: c377a7f5dbe645cebbb6c7eccf831a0b msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." msgstr "" #: ../../src/introduction/index.md:1 -#: c54984605872472190ae7771809a20db +#: 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" msgstr "" #: ../../src/introduction/index.md:3 -#: 01a237b8ec2f46c9acd31d142591ce75 +#: 950370f0a36048b38e1bde9b78f80816 msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." msgstr "" #: ../../src/introduction/prerequisites.md:1 -#: 3fb9888b666945eab1e3ff109646c574 +#: f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" msgstr "" #: ../../src/introduction/prerequisites.md:6 -#: 5fb0486762354f93853fff209f835c08 +#: 353b14f06ee845d0a06a829643e31534 msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." msgstr "" #: ../../src/introduction/prerequisites.md:12 -#: 5f1e7a608e0b455196d191c845a5c98e +#: b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" msgstr "" #: ../../src/introduction/prerequisites.md:14 -#: 7ba4b5c51be24f5392949d06ee42e018 +#: ff2bb4c6504b456bac7ca9c514414dbf msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." msgstr "" #: ../../src/introduction/prerequisites.md:19 -#: e2d3e6dd13b14d819a504c35da6fe8e7 +#: cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" msgstr "" #: ../../src/introduction/prerequisites.md:21 -#: 91251d1f0efb4d4cb083b4517ff3107a +#: 5089fdba8aed4113983fa86e698df98b msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" msgstr "" #: ../../src/introduction/prerequisites.md:24 -#: 6ad263e267514c5fb05794d3d76d418d +#: dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" msgstr "" #: ../../src/introduction/prerequisites.md:25 -#: 8a3bfd72dccf4a8c874a96aebcbe5cb7 +#: c05187af85be41b782678b79627f8fbf msgid "macOS" msgstr "" #: ../../src/introduction/prerequisites.md:26 -#: 5195706d9c6c4573aff135fd539759a2 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" msgstr "" #: ../../src/introduction/prerequisites.md:29 -#: 9c4506915e4c40599527bc1d2b18645b +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." msgstr "" #: ../../src/introduction/prerequisites.md:35 -#: 37d9eb784ec1425786158f98e3f63890 +#: 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" msgstr "" #: ../../src/introduction/prerequisites.md:41 -#: 572f493a985141a1b92dafbdba92790d +#: 0f2704bf1f7148be95e999e312899f11 msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." msgstr "" #: ../../src/introduction/prerequisites.md:46 -#: 9606d3c4849f4b17b2e55a298210f055 +#: 86264c9e56104ecea9146407c379aae2 msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" msgstr "" #: ../../src/introduction/prerequisites.md:51 -#: 754fc59967d94ffa935284676d55ffed +#: 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" #: ../../src/introduction/prerequisites.md:62 -#: 2905c6362d4146e8b35bc74744841972 +#: f7aaafeee230400da056464c853582c2 msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." msgstr "" #: ../../src/introduction/prerequisites.md:65 -#: 091278ece252483a9838fb771de3e04e +#: 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:67 -#: 0928a5c668c3414a945bc9eda147892c +#: 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:73 -#: 56f3c481762848298214a88e559fc0f9 +#: 6391e08e0bde49f4b21286d8fdb97433 msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" msgstr "" #: ../../src/introduction/prerequisites.md:79 -#: 710c266ab4a5477b84d6ea987420fa20 +#: cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:84 -#: cc353db5da2546bb88a77ce1a202ff9d +#: d41c4bc740aa474ea09a7cbd267c8840 msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" #: ../../src/introduction/prerequisites.md:86 -#: b62df08ec96f4cdb887600079856dd76 +#: 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:91 -#: 97e02557293440d1a58ba659dad21113 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" msgstr "" #: ../../src/introduction/prerequisites.md:93 -#: 0935c3ff01634c75b5c91546dc36c7b9 +#: 096d0a50f69e48bd9915238d1b4264c1 msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." msgstr "" #: ../../src/introduction/prerequisites.md:101 -#: cfb37fd605164a8d9cc75bf892ce97c0 +#: f9df974a8e2645a6918e67466bd1fdc2 msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" #: ../../src/introduction/prerequisites.md:104 -#: 5f06a7a6aae343d989a5b30979c600f6 +#: 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" #: ../../src/introduction/prerequisites.md:111 -#: 5f956260f3874b6dbeaf3ad7ecc09c9a +#: 746c6fc9c29d466494458a08d4c96672 msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." msgstr "" #: ../../src/introduction/prerequisites.md:115 -#: d35e4effec554a638d6c3047ef3fd05f +#: b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:120 -#: 15a1f944a0d642729d3736ed1c907074 +#: 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:125 -#: fa34c808bb494ddfa3f3926bc42e650c +#: 705807fae182425dbf4244dbf2be1226 msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" #: ../../src/introduction/prerequisites.md:129 -#: 0c15f62eb7534e809f625f3fa213e92d +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:135 -#: d67719a6f0ce4ba1bb6152a10507b729 +#: 164c438baab54ec19bbb4584a10dd411 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" #: ../../src/introduction/prerequisites.md:137 -#: 1c96e75281844bfab0578bab2e816854 +#: bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." msgstr "" #: ../../src/introduction/prerequisites.md:144 -#: bece1fc3c3f842b0b30d8f1b7fbfc200 +#: 695184d1b45a42f393e2da99c3721773 msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." msgstr "" #: ../../src/introduction/prerequisites.md:148 -#: a7caa36b0f83448b91ef2e76e30abc51 +#: 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" #: ../../src/introduction/prerequisites.md:154 -#: 39321e93e9994fcca20b425aa45c2894 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," msgstr "" #: ../../src/introduction/prerequisites.md:161 -#: 601cf500d76c4e0287af4429a46b36d2 +#: eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" msgstr "" #: ../../src/introduction/prerequisites.md:163 -#: b286d5359e184ef58054c72df4014629 +#: f6b39b12bd5c495cb53e2795bf9200ed msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" #: ../../src/introduction/prerequisites.md:167 -#: e14423edd829401faed0950772123240 +#: 2fdb62a13f9447bc89183426260ce781 msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" msgstr "" #: ../../src/introduction/prerequisites.md:171 -#: 889c44360bd54a0e85e7f0e61aa6593c +#: 1f07135156254f74a6b043bf33d00cc3 msgid "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" #: ../../src/introduction/prerequisites.md:172 -#: 7b9bff73624947ac90a99c7880e2e911 +#: de344f356b1c466d9131cdbd4d7353a3 msgid "cwl-plugin for IntelliJ - " msgstr "" #: ../../src/introduction/prerequisites.md:174 -#: c5ff687c86ef4ccaae25d8bcfbd5f873 +#: 3f9324ede11441f58d93875867034cf0 msgid "The CWL community also maintains a list of editors and viewers: " msgstr "" #: ../../src/introduction/prerequisites.md:177 -#: 0a610a9632064deb824afd0719429d3a +#: 6ce8b81560e341c580d316d69202b268 msgid "Docker" msgstr "" #: ../../src/introduction/prerequisites.md:181 -#: ec0c47438a5242cb99dffa7a4997e95a +#: 40cfd559d6a848d1aae354d3bdaa8e9c msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." msgstr "" #: ../../src/introduction/prerequisites.md:185 -#: aae94ac2114641f186eac0f4117223eb +#: 8a9a50b0ebe847ce90593881ffe0d69c msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." msgstr "" #: ../../src/introduction/prerequisites.md:191 -#: 209e072724ed4d27b37e9bff6d55d811 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." msgstr "" #: ../../src/introduction/prerequisites.md:198 -#: 3bf47876e3694e6cadb05123326459cb +#: 9390b03889de44638141d705e0ef8322 msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." msgstr "" #: ../../src/introduction/prerequisites.md:199 -#: 459a65b8e67c4a9aaa03138c1abe94ad +#: 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " msgstr "" #: ../../src/introduction/quick-start.md:1 -#: 898eb29ac7714c69840b795633953a05 +#: cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" msgstr "" #: ../../src/introduction/quick-start.md:3 -#: 2a658bd2d8ce4533ab7e056fc3a3ffcf +#: c43d9675ed134b78b02acb5a102a764a msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." msgstr "" #: ../../src/introduction/quick-start.md:7 -#: 32dd2e28cf0f40b6930750f0162355eb +#: 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" msgstr "" #: ../../src/introduction/quick-start.md:12 -#: 471c47d311074ecfac071b6d52d9cfb6 +#: cb203354977d42a58112d09357f62565 msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" msgstr "" #: ../../src/introduction/quick-start.md:16 -#: 5078140028ea4d04973cb9cd20f0607e +#: 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" msgstr "" #: ../../src/introduction/quick-start.md:22 -#: ab127d4ba0a44526ab129587a8160923 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." msgstr "" #: ../../src/introduction/quick-start.md:27 -#: d5cc6b4295a74f3586f022b0227759b3 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." msgstr "" #: ../../src/introduction/quick-start.md:32 -#: 585a4fe583ce44e180a062742b3b0849 +#: 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" msgstr "" #: ../../src/introduction/quick-start.md:34 -#: 0d81b0c9ea58420789d1d71cca32ce88 +#: f3e56aedd56b4b93bdc3894273e8c144 msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" msgstr "" #: ../../src/introduction/quick-start.md:39 -#: ea4ab0782d8049d8b1b89cea4ae60048 +#: 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." msgstr "" #: ../../src/introduction/quick-start.md:47 -#: f6f3b7453a254f828bd4c9e9fef92bed +#: a81342e756d24c40acc15835d0a768f2 msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." msgstr "" #: ../../src/introduction/quick-start.md:51 -#: 3bf9050175d4444ebbbabe219412574f +#: c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" msgstr "" #: ../../src/introduction/quick-start.md:53 -#: e03f72a14dcf4bf38ce8232598ca761d +#: 9b68bcb1a41849dc9601ab47c5bbb0fe msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" msgstr "" #: ../../src/introduction/quick-start.md:57 -#: 3dcfb2facd324dccb3084c02487625dc +#: ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:62 -#: b8531da183964b02bca19f818ec076d4 +#: 0d8a788402914ebd8f09a5ca80650011 msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" msgstr "" #: ../../src/introduction/quick-start.md:65 -#: 7ba1ddebeb2843179fe99fc410b193c6 +#: 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" #: ../../src/introduction/quick-start.md:70 -#: a6dc303e9d284b60bf1102212505ca27 +#: 2ea056ab04b6419a9faf350de22a17f2 msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" msgstr "" #: ../../src/introduction/quick-start.md:74 -#: 59ac7830ae3e4d7cb1bf503e8c90fe30 +#: 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" msgstr "" #: ../../src/introduction/quick-start.md:80 -#: 6d1d6f42ada2418ba0a1de1371825b9f +#: e76bfcc0c9f84bcdb3f6d5277869a88c msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" msgstr "" #: ../../src/introduction/quick-start.md:82 -#: 1cd924fe8ace4a82ad8701f37b5e7d84 +#: d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:88 -#: aa297c52cd964291a47bb91c0135156b +#: b6d59e4b9c854abab1b3f7a0fa26f504 msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." msgstr "" #: ../../src/introduction/quick-start.md:96 -#: 28b02c90397745bfbacc03c3b1034939 +#: 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" msgstr "" #: ../../src/introduction/quick-start.md:97 -#: ef2a4f39f01049b891868b84d968c0dd +#: 77e43c7117fd4c52b140f0dd52cc3963 msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" #: ../../src/introduction/quick-start.md:98 -#: 89e3fa8dceda4f0cb1cfdfd1f17fe4df +#: 7282abfa7155497ca47c30f9abfb6474 msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." msgstr "" #: ../../src/introduction/quick-start.md:99 -#: 7cd178223ba94d1ab3ee8cc5f13a8dcf +#: 176d8d47830f4031bb95dc231ebf1303 msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" #: ../../src/introduction/quick-start.md:100 -#: 46f6f8d050ce4f8c897056167d9707a7 +#: 82a7ca3703bc4f0daa18942a1ac8943b msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" #: ../../src/introduction/quick-start.md:101 -#: 5ee00ee409b746dc951ca1d4c360e624 +#: d039a9d6461c44628d4660c00d9ce6ff msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." msgstr "" #: ../../src/introduction/quick-start.md:102 -#: d4af972281174b8999eab55ee0ab1a0e +#: fbc3383d9e1c4eaca7931c3cc4f1752b msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" #: ../../src/setup.md:9 -#: 80401cfffae042ab9ec4b3754af04b25 +#: 1330bd38c4b5495f890b98c669f81a9d msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 32f86f911ebe4a4c94975f81742333f3 +#: 9c87c76c690948ac8e18088a0fffe679 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: d5f1ad2b95ad46d48f8f2ca5e357bb5d +#: ad00d94d4fb64bbdac356e64dd3803b9 msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: c53ceee943ad4acea779e072b9137889 +#: d8110ed19da94ad8a9f56e7006c4a2cf msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 7dfe9dffbf5744299bf232599644c7f6 +#: a74935dc31664e979ca8f90a6a4ba53c msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 -#: 00709fa451134ee09a0d808e101f28ed -#: 991172e201ec4796992a349dee44f090 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 1f3c23a4769043ca985b8ddfed19391d +#: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: f81b43c7cb194a1cad8672129223c833 +#: 9643449da1da46d7861866dce490cbcb msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: a20073a8f5374eb1bc8531ff33e622b6 +#: 713666580a0a4466b4ba6e3eb2b54f0a msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d08869beca3a4774baf1097b63e79474 +#: d50574c8b9694f83aa376d39b9a6fcd6 msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." msgstr "" #: ../../src/topics/best-practices.md:1 -#: 109b773789024b2b9c063a6169c6169f +#: 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "" #: ../../src/topics/best-practices.md:3 -#: 959fa04f88e54d42b9b774cc95d85ee0 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." msgstr "" #: ../../src/topics/best-practices.md:8 -#: 64674980c3f24c45bbfbf3f957dda55e +#: 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" #: ../../src/topics/best-practices.md:11 -#: 90f2e4265919446a902e17627f4420e2 +#: 4dee8504a8e5496081dadc386ab45540 msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." msgstr "" #: ../../src/topics/best-practices.md:20 -#: 6b5f91a749fd44b5acfd6071c9913342 +#: 674c238b25e240eda05e22e399f2f78f msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." msgstr "" #: ../../src/topics/best-practices.md:26 -#: 5fe2962837b14f0e9989063be4a506c3 +#: b651f80f47b4442fbf29454a233697fc msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" msgstr "" #: ../../src/topics/best-practices.md:28 -#: 4e1bdea962ed4618884cb9d1d59d7509 +#: 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" #: ../../src/topics/best-practices.md:37 -#: 37eff4ca02e843259f6ffa38e4a87a04 +#: 3a87a0fb2a364e3da5aaa4017e430b19 msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." msgstr "" #: ../../src/topics/best-practices.md:40 -#: ae47231c203d40a98c10045038ea9b65 +#: ecf2b9c0b1664afe9c4e180610610021 msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." msgstr "" #: ../../src/topics/best-practices.md:44 -#: 018a6d5dbf1044559b365c7b9017eb3f +#: e24cb13d98014e558b6a6946758359e0 msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:47 -#: e073d8f990c44b09a73d642cfe49bebd +#: f2b14a92374e449d9fb1e8c86ae0dd61 msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" #: ../../src/topics/best-practices.md:50 -#: e04fae88d9b64493ac69eaee24585098 +#: 928e3df7ca3e479ca6474a8e72cf36eb msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" #: ../../src/topics/best-practices.md:55 -#: b26b9c9b1c4346a297a31c9721f0172a +#: d355f035676446c88b028f327aeb4829 msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:58 -#: b50500c3c3f54b16a535a16175a44653 +#: 339b852df24242189d6efcd2898a3396 msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." msgstr "" #: ../../src/topics/best-practices.md:66 -#: 623f3a804199449bb85e23e00c8bb507 +#: 3ef57e6862f240bebcf193a52397af0a msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." msgstr "" #: ../../src/topics/best-practices.md:69 -#: effea0b1356447c0899ca0746667ea31 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." msgstr "" #: ../../src/topics/best-practices.md:73 -#: 00e8ef87864c4ca2b2c1c0548b02b38d +#: 1ac4c3d8c3e44bd1af3fc5df70051926 msgid "Custom types should be defined with one external YAML per type definition for re-use." msgstr "" #: ../../src/topics/best-practices.md:76 -#: 6e6f48d70b894a6c959ca30fe6bad772 +#: c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" #: ../../src/topics/best-practices.md:78 -#: 02fe08760a4a4ab49e96f4e51316a81d +#: fae385da16aa443da996fa23ac03d6ae msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." msgstr "" #: ../../src/topics/best-practices.md:82 -#: 172ed7915a654964ba63f860b2d65330 +#: 92430be71ecc40e18bbbb80d5576c613 msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." msgstr "" #: ../../src/topics/best-practices.md:85 -#: 4d0a2871a7484e21b3c39c4dbaaa63fc +#: 387d83db81024f65aa9a890c2d07874a msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." msgstr "" #: ../../src/topics/best-practices.md:90 -#: 1eea9f1e284447718141f5417b6bb433 +#: d8e2280a75a74916a1630afaa2fe2ae3 msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." msgstr "" #: ../../src/topics/best-practices.md:93 -#: 509411d353fe4314b087b81b09ea960b +#: f1c1340f9745458980e0fbd641738687 msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." msgstr "" #: ../../src/topics/best-practices.md:97 -#: a54bc80bf08243bba67d98dd682ee134 +#: 5424e5472c3d466fa2a3d2022c6cb475 msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." msgstr "" #: ../../src/topics/command-line-tool.md:1 -#: 69ecdaea24ef42eebef9d86e5d716b11 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" #: ../../src/topics/command-line-tool.md:3 -#: 3cc5847468d1478bb5589dee68147189 +#: 12f57b2ba76b492abe1816e06bfb1417 msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." msgstr "" #: ../../src/topics/command-line-tool.md:8 -#: 98c6bc409420485095ae65d6b0b9a3a0 +#: e1f657a46ce94a0d83671540e2cc2dab msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." msgstr "" #: ../../src/topics/command-line-tool.md:19 -#: ebe23e5378514f888a9ec32a2adb1e98 +#: abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" #: ../../src/topics/command-line-tool.md:50 -#: 387cfe85604f424f8d31c4a4c9c15edb +#: 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" #: ../../src/topics/command-line-tool.md:57 -#: 7b1d65754e854693bb60289c97d3fb5d +#: a5eacdbc9aa142c890b177869da4143d msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." msgstr "" #: ../../src/topics/command-line-tool.md:68 -#: f440cef729c8410281432307a4da8d55 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" #: ../../src/topics/command-line-tool.md:69 -#: 4fbb8ceb1b59480583ac611142167049 +#: e3bdaceae8784ab0807b2cf356a98580 msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." msgstr "" #: ../../src/topics/command-line-tool.md:83 -#: b87869204838415bbf694214e3680593 +#: ed521ac365db4a6ba5a1051fbaa2932e msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: 12cf5f2264504c44a2173e858bb2c283 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 7694f9cabfe04308bbddd2c88ae6d9b9 +#: 0cf51b6da6884065ae42032abc20eb0d msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: b557dc4f8ef549b98f59412a918643de +#: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 3011eb003c084285b30cfa56a8da45b6 +#: d3f74c3b094a427fbec831afab657d50 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 +#: cfffc518ba6e4ed1a80762ed6f7d25df msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: ce78b2d147054da895beba66d0ecdab4 +#: 9454a330b9324744b89448f2694b1b03 msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: a973846ec5a946eeaff02c5b00997da9 +#: 7f8d99a30b644457a62ac1523d0c72aa msgid "To test the above CWL tool, use this job to provide the input value `message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 #: ../../src/topics/outputs.md:77 -#: ccec7f73b9d948e79a6cdf32bc124092 -#: 9e8eb1542db640ff9e300649ce50dc9d -#: 294fd83a97a64249bac38f7482159372 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 22948f19cb78485f8f86244686a35c09 +#: 10d1373bb14a4a3cacd3b92a2f83382d msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 001d9579bfce438e865377fb9c2df776 +#: 70e257091bdb456e8957f90a8fa90e8c msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: e62618db8995428bb3f260e03ac8f459 +#: 1741804e33aa43ce88b4320c11ae5973 msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." msgstr "" @@ -1291,193 +1291,193 @@ msgstr "" #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 #: ../../src/topics/workflows.md:198 -#: 98e0548845fa447fb05a29c9fc2f17b5 -#: e9801b2142cd45368a73ef9b121c1d08 -#: 457756c4e9544f068af897113358cc89 -#: de5e8aad4e3046bf9bfc2ad8ccba17d0 -#: 6d5ae75431424ea788c3440606f22940 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/custom-types.md:1 -#: ee2bca9bdbb74b60a706c3118d6a17ba +#: cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" #: ../../src/topics/custom-types.md:3 -#: e63ae9694f40438d872d141ae824a42d +#: 67573252cc064b27ab13eebc468ac58a msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." msgstr "" #: ../../src/topics/custom-types.md:9 -#: 750fdd4c270e46a09f79e867358f7414 +#: 73e68b3af9cf41338d843c0c40e50cdc msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:12 -#: b3f688cc82444ef7a7a0aa63dac39cac +#: ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" #: ../../src/topics/custom-types.md:18 -#: 3638be18b4f64cf08053d512e590dda3 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" #: ../../src/topics/custom-types.md:24 -#: 7d5b9c21739c48f18c13614ca6967f6b +#: a999b1acda2641598086648c64aa3831 msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" #: ../../src/topics/custom-types.md:30 -#: 8fea29993f944d8d8d3181afa29bd0a6 +#: f8c12a58cb0b46a488823c6ae95f25ea msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" msgstr "" #: ../../src/topics/custom-types.md:46 -#: 02d0b648d70f49d7892f690be06df585 +#: f25a63e0926d4932bbe64b2e4bdabf9e msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:53 -#: 0743bef42b9a42328849c8c2f9da9eed +#: b0a4df0fd3ca42338cff4689235dcf4e msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" #: ../../src/topics/custom-types.md:55 -#: 85c5d0cbbc6243a6823f5eeac0f85dd9 +#: fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" #: ../../src/topics/custom-types.md:61 -#: be848f30769543eb9c0be55263e3f758 +#: d718630a296545f3a989c8c71e9ddc77 msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" msgstr "" #: ../../src/topics/custom-types.md:76 -#: cbff44a64ba4432cb59a82f82c2f0103 +#: 9a97acd430064710bcdf76edbd9f711c msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." msgstr "" #: ../../src/topics/environment-variables.md:1 -#: 617f1c0084cf42d9be4c7a8fa5a48432 +#: 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" #: ../../src/topics/environment-variables.md:3 -#: cee79afa3c6f43c29ef05e06b7843d35 +#: 3c821c9c46d841ec89b8a5b1018f3af8 msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." msgstr "" #: ../../src/topics/environment-variables.md:7 -#: 225903b11efa417989df42de86ad2451 +#: bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:1 -#: 1a5f058290064c1cad05e63eb127fcbb +#: 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" #: ../../src/topics/expression-tool.md:3 -#: 74ad8d69cf294ae880dbbe28e25b3545 +#: 48deb71f361a43e48a56ed483075bca8 msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." msgstr "" #: ../../src/topics/expression-tool.md:8 -#: 5293e8ee9b3b4f59947cfc164ef111c4 +#: 716b56506ca7470299899c5d820a9ea2 msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." msgstr "" #: ../../src/topics/expression-tool.md:17 -#: ffa1955c759942c68e7589429e5ea86b +#: b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" #: ../../src/topics/expression-tool.md:48 -#: 038bc0ba5f6a405a8255a7be76979baf +#: 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:67 -#: fae1c63de02e48c0969a98e4c49b2e06 +#: e3ecac0a8e604f2b98a2a12b0579990a msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." msgstr "" #: ../../src/topics/expressions.md:1 -#: 7093a94695524851a5463193f0701b78 +#: c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" #: ../../src/topics/expressions.md:3 -#: dc8274ecb15948c29a31db89b12a58bd +#: 007a345b4bad49cf996c4301b8386473 msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." msgstr "" #: ../../src/topics/expressions.md:9 -#: cec8eef8a5aa49778ecedd4195ab9f2c +#: 2edbd398eadb458b8eacd5fa5496f0a2 msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." msgstr "" #: ../../src/topics/expressions.md:16 -#: df100967597043c78112bf43b520cfab +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:22 -#: 59ccf4daba39406581a6bc2d9bb1b7d2 +#: efb5fd14988c4e2a8f834ee5369d4102 msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" msgstr "" #: ../../src/topics/expressions.md:25 -#: 570cc75699dd4e0a987fc9aca9a01ee4 +#: e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" #: ../../src/topics/expressions.md:31 -#: 9e123723048546d495ed5110d7177708 +#: 276f688ba7cc471a842f085ca852b1d9 msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." msgstr "" #: ../../src/topics/expressions.md:35 -#: 26543894f6e04270b89ab702451bcc89 +#: ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" #: ../../src/topics/expressions.md:37 -#: f403c1d4e43a4aa0aef8488d2b5a6262 +#: 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:47 -#: 249dffb569a944c897ce5862e5f28fad +#: 8b70a1ad70514039b97164fa630c12e4 msgid "Note that requirements can be provided with the map syntax, as in the example above:" msgstr "" #: ../../src/topics/expressions.md:54 -#: 1641c96aca2f4923885fe8a509eb3a49 +#: 2f28ab412d2843ffa5f14acdc01fc732 msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." msgstr "" #: ../../src/topics/expressions.md:62 -#: bc63405a0d964df2bd9493996abc48fe +#: d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" #: ../../src/topics/expressions.md:64 -#: 5c191d1420db4e26aca31c1b1e34cb75 +#: cbec9277b5004e50af2728cbda0df740 msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" msgstr "" #: ../../src/topics/expressions.md:66 -#: d6a5c65e824a4bbc94578df9597d4716 +#: e259f55f8000479bbd8009e25cf0ca6c msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 -#: a7ff51fe564748229a88a0d3044dbc17 -#: c12625211cc542b68cb51365a63eef00 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 msgid "`arguments`" msgstr "" @@ -1487,38 +1487,38 @@ msgstr "" #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 #: ../../src/topics/parameter-references.md:86 -#: 3a64ccbbf70447d1a813a725e528b6fe -#: 5fb932af34a54a0ea691260d43053eba -#: 2a2286a9c8494e3b88db35bf63230f33 -#: e7f1993580f0425098a719e83a64cc7f -#: 05c34a5a2e404a14b9d284a9d0c73bd3 -#: e5b0293e6fcd4e9b8d7be3fc9fc127d3 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 #: ../../src/topics/parameter-references.md:66 -#: 2fd5b42cafe34d3185888de041818dff -#: c158e9ee5fbf4e868b152a0a5880092f +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 #: ../../src/topics/parameter-references.md:67 -#: 92697d3179ec48898eaea9aba3c24dcd -#: 3f29e4a3087847e9af6f19166a8def9a +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 #: ../../src/topics/parameter-references.md:68 -#: d6722e3093884ad7b62696fbb2f48fdc -#: c0eaef93bc3743279549bcfb8b014ca3 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" #: ../../src/topics/expressions.md:72 -#: 37c493fdc2f0410a9748f8faf09ce5b5 +#: 8210b36347a749889450529ecdf4ff0e msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" @@ -1530,14 +1530,14 @@ msgstr "" #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 #: ../../src/topics/parameter-references.md:90 -#: 9cfb6ca1255241aa9e5928ea981286e9 -#: 4ff7326e660f42d8b45c3353005554f8 -#: 04e3eefe4ec445cb90c2fa42344aaed5 -#: 07611b01b06a4afb808322a0dccccf30 -#: 6020618711d449a48618c11215453487 -#: c358a25b1f9543598b90d3df7c012b85 -#: c610220d06484d589313dc29faf8222c -#: 7b132c6e720f4256859757778f5c4fef +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" @@ -1549,1574 +1549,1574 @@ msgstr "" #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 #: ../../src/topics/parameter-references.md:91 -#: e193aebe7124444c90be1f6cad81482a -#: 74652fdbeaf14d82b9c5053e322504da -#: 93d2b17bb236426286ffd51bbecda61d -#: a44c278bde5849aeac122c981294332c -#: 6dfc264200a9496f9d2458fc759993d8 -#: f71216a4b35e4157aece5ffa2602d8bf -#: 662b36e3505f4ac3bb5070bb6e055217 -#: ee3d416cc68c4f11a79849bb67395f1b +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae msgid "`secondaryFiles`" msgstr "" #: ../../src/topics/expressions.md:75 -#: a3c775a0f04b4541a9b712bfe2e4e69a +#: 23088850ad02459696f6bbd385109aac msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/expressions.md:77 -#: ef16c4a9a7ea415fa399297b63b9710c +#: f02257a822ad46ac93c5981531cc85d5 msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:80 -#: 2592e429c74c4ff5b8ba68a36f060c1a +#: 989a1c4aaa1143be9f53b90cd8b6d500 msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 -#: 5cca4c2ad617400eb6efad4066b1839b -#: ba1fff3ebb274dfba845b3ee20ebd71f +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 #: ../../src/topics/parameter-references.md:79 -#: 6914526c0a7c43a2a05438519508ee0f -#: 722d3bd7184841639b9f9a38914002da +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 -#: 737b0f9392154241ae5b56c6caa823f5 -#: 7b46d408e7e7481b91a950b2d4010c9a +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c msgid "From `Workflow`" msgstr "" #: ../../src/topics/expressions.md:84 -#: f09e7371708b4c0685eef2a314791ccd +#: d289541e460147aa933f7878996f8649 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 -#: aa6ca1def2024c98b9d5542de1a81425 -#: e9fc5f7fa4474dfc95039b94167fe894 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c msgid "From `steps`" msgstr "" #: ../../src/topics/expressions.md:88 -#: 6c37a1ff939748bf83a86c07c3d017fe +#: 81b4d1f23a3642bfa9bb395b94260cd1 msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 -#: 3a8126b0a0334df890b2be2c693ea5d5 -#: 61744122b7d7494890cbe6b2fb72b9f7 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 -#: 93cb9015dacc4b50a4ef177ce4ece2e7 -#: e0c7ccc8f8664cf794cbb7330355f3fe +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf msgid "`expression`" msgstr "" #: ../../src/topics/expressions.md:92 -#: 58a1773b1cf546d7890010fdebd47388 +#: f495da32f05a4a5ba9539be0a54c1a59 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:95 -#: 230f3227ed1144f7abe0f8c231bebbd5 +#: bdb4c68a175047ddbe141ca24960127f msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 -#: c9534670f5f04769aa3749c3778eb705 -#: 5c77dc9f8afe4dd88933943030e836f2 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 #: ../../src/topics/parameter-references.md:94 -#: 4ec8bbac5fb14371a6a4cd53d7cd6450 -#: 7b0887a8caed41b2acccf7021bb323d3 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 #: ../../src/topics/parameter-references.md:95 -#: aceedfb558b246bc87eb3eaedea187fd -#: e5e8b8c75f0f43cbb6e160e5bf810c6e +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 -#: fe3b9fb45e01490498c5a35c012b3de8 -#: 266dfb5fe6a842078baf66073cac9623 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 #: ../../src/topics/parameter-references.md:97 -#: 85f424cbfc85460f9da310aee1ff0b82 -#: ddf82b12b12d416fb65f3ce3f51bbdf0 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 -#: 966e88656ae5402a975022ee60646283 -#: af14fda3cca645fbb2f3c5825fe0788e +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 #: ../../src/topics/parameter-references.md:99 -#: fec70bb106ad4d95a2d55ebdcf711afc -#: 09120baec1464afb8aed4edd773bf509 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: c98db5b115ee4c4abb211481fe7214b0 -#: 2e128858cd06466680fc6bbfb577b818 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" #: ../../src/topics/expressions.md:104 -#: 1dc4148caef748428a7d13caff37b1b1 +#: 97b61352363f47cb890e8937c5613fa3 msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 8caf296626024598b4450311ade09e56 -#: 568406e34c8642578396177b40043014 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" #: ../../src/topics/expressions.md:106 -#: 947b1ca132a54ed39745cd12ebcd65e1 +#: 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 3af8e4ce750048e6b9de12d26b9647a6 -#: f56fb5fa08994fe08cc8ae8c193828d9 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: c6dbe0a66b9f47e5b4b47c44d9f54519 -#: 063e2ae9a0eb404e8c277ef7090eb6bc +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 72acfeef964841e7b65937b62b5850f0 -#: 39c6edc2866542cfa7da9f842fd3edd0 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" #: ../../src/topics/expressions.md:110 -#: 5fa512d352d945e7a3e0d59b0987cd1b +#: 0bc424ef2ca346099f29b937379908a0 msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 79755be159fb45b0ad06cecce623ce2c -#: 520bf799546b4700a4f38f950ffd913b +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" #: ../../src/topics/expressions.md:116 -#: 81e91df082834d2cab7ef1f62d8ba57a +#: 10d36a1adfd04144b401c993b12b4094 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" #: ../../src/topics/expressions.md:118 -#: e6bfd1dc2e324992b6c3332c11ae3445 +#: 29b73e1dd72744f68377f0a38c10f062 msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." msgstr "" #: ../../src/topics/expressions.md:122 -#: acf10261df2944ec890d754fd56c6b28 +#: 38a2afaf4a6c4d04909af22c93f2808d msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:128 -#: bda6b8f398554b0c946c2c7d96308a42 +#: cd74f34b21af4de9be96fd897efc469b msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" #: ../../src/topics/expressions.md:135 -#: 454c02c3918647039c90ae387005dea6 +#: f12e371f3f1a4b0cb2cff9800352d48c msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" msgstr "" #: ../../src/topics/expressions.md:139 -#: e1fad28bf9cb4c4c85eb74dd520ba107 +#: 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" #: ../../src/topics/expressions.md:146 -#: 9835d0b399b84a0084fe5a4d9e7e6405 +#: 8f0e8f050e334ac08334e9215e1dcf61 msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" msgstr "" #: ../../src/topics/expressions.md:149 -#: 410ba7a5ac6349a98460c6337ee5c4fb +#: 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" #: ../../src/topics/expressions.md:155 -#: d2daf50d7f3d4de18331c8fd2c8a5786 +#: 7a6be0005a6441feb67f036d005d7885 msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" msgstr "" #: ../../src/topics/expressions.md:158 -#: 8f2015c12b2b4d5d9a800ddeaf428f25 +#: ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" #: ../../src/topics/expressions.md:164 -#: f0ff919ffc12439d89d7b40f51ade84c +#: 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" #: ../../src/topics/expressions.md:171 -#: 307a17a893fc4dafaec2a63a95704644 +#: 06635145b441418aaae84dc804f3d6ac msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:175 -#: 7f393e86b114470f8dda47b2deec63aa +#: 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" #: ../../src/topics/expressions.md:181 -#: c3f459b87b96435583637b3f1573e658 +#: 04eaf1f7c630450db318dcd8b7626e15 msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." msgstr "" #: ../../src/topics/expressions.md:186 -#: 9f676022eb2744839ca2109920250cb6 +#: c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" #: ../../src/topics/expressions.md:193 -#: ede7285f77864fb0aee6cfecc2c97fa0 +#: 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" #: ../../src/topics/expressions.md:200 -#: c55fb184bc614ee2b6e5e64611e5df9b +#: fd4579a3c9844492b314b5c3c1775fc7 msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." msgstr "" #: ../../src/topics/file-formats.md:1 -#: 66b522f46ce242149386e79f63b32cf8 +#: 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" #: ../../src/topics/file-formats.md:3 -#: 64a20285785d48ca86227a0cf6353ad4 +#: e024bcb70e04412e90e1838426d1b69a msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." msgstr "" #: ../../src/topics/file-formats.md:8 -#: 5f71bbe2c74e4260b79d4d9230d35397 +#: a3db21c0b3114802a8a5b610e252ef13 msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" #: ../../src/topics/file-formats.md:14 -#: 63bfff437e3348428f7e33ece7ec55e7 +#: 0f5bc8520d6a4dafa37c65343da9702a msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." msgstr "" #: ../../src/topics/file-formats.md:17 -#: 6ce83d9c06e4436881aa47d94ef41e0b +#: 5cb830da47464a8b9c3950983fa4d56f msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." msgstr "" #: ../../src/topics/file-formats.md:20 -#: 55006c594abf4e70a38e979568fadcf4 +#: 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 12ba2083a9ae4c78bf502ab762a29c7d -#: 5c8f1709fe61423bba3ceaca2fc7cf09 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" #: ../../src/topics/file-formats.md:32 -#: 1a1905ff2d624eca952c8a53b3bee678 +#: 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" #: ../../src/topics/file-formats.md:34 -#: 368ff92476b14f5c8331260eafc5acb5 +#: a2ce43b391864e8bbde16328cc19b32b msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." msgstr "" #: ../../src/topics/file-formats.md:39 -#: 5d530afa23f349a79f54d51d40724747 +#: aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "" #: ../../src/topics/file-formats.md:45 -#: 16f965f86712483aa7f95dfa3f944a17 +#: 56ee4dcfff6141d5bef80eb96559876d msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" #: ../../src/topics/index.md:1 -#: dc629e2c90ed458b96107a6994676434 +#: 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" #: ../../src/topics/inputs.md:1 -#: cf2f077cf8044079a7005e6e508dcd8c +#: 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" #: ../../src/topics/inputs.md:3 -#: 129e1d2a71894d28b009f4846754a75d +#: d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" #: ../../src/topics/inputs.md:5 -#: d6791bbe575042b9a7282c69407dd907 +#: 96671c56523c4ea9992fb5dfcfa6490e msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/inputs.md:9 -#: e8da87f8bb664334adf831995601f462 +#: bcc6246742cb46bfb185e415c4a3431a msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." msgstr "" #: ../../src/topics/inputs.md:13 -#: de6c322618304207b6d1364d1ec2dc13 +#: 86dce36de687449c88fb5eb9d64eb045 msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." msgstr "" #: ../../src/topics/inputs.md:16 -#: 43bdcf6dc1b14030bff27fa53289c02c +#: cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" #: ../../src/topics/inputs.md:18 -#: 056510b42ea64717996ab49c307bda86 +#: 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" #: ../../src/topics/inputs.md:24 -#: 6852f5dbd9094c99bb68f2a88f76c9bc +#: c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" #: ../../src/topics/inputs.md:26 -#: f33b6800367248b7927d97ad7b4be5b5 +#: dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" #: ../../src/topics/inputs.md:33 -#: 8ad812d7e88f4cbba83228ffb1711576 +#: 36ab1d9edafc4831bb1bca5f123b04b0 msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" msgstr "" #: ../../src/topics/inputs.md:40 -#: cc680bbf091a46f8b4b3dbe6324c040a +#: 7dc630ea86464b1dba3a4e5079260b3b msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." msgstr "" #: ../../src/topics/inputs.md:44 -#: 446ac81f078d46289a18f494748f482c +#: ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." msgstr "" #: ../../src/topics/inputs.md:47 -#: 3d6d958d111943f3a2139b4dbb7810db +#: 651e032007ea4a119d20c820bb61f86b msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." msgstr "" #: ../../src/topics/inputs.md:53 -#: ba0ec9157709430c822f4e91459288e2 +#: 0b056dde9e87428996e47870b12119da msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" msgstr "" #: ../../src/topics/inputs.md:64 -#: 2565f8fd4a15429e887aeb71eacdff1e +#: 628124a1670b4b058bb0fb6e495a099c msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" msgstr "" #: ../../src/topics/inputs.md:70 -#: 659ed5c64fb546399b741553a347b8e8 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." msgstr "" #: ../../src/topics/inputs.md:83 -#: 3d87e69d41374fbab23b26d36c1aee03 +#: ec2adb3912bc46e28891229e9e0d9a1c msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." msgstr "" #: ../../src/topics/inputs.md:95 -#: 07bc81683e2c4ac68b379462bae95207 +#: a519be60726a44af9941fdce04735353 msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." msgstr "" #: ../../src/topics/inputs.md:109 -#: 3e304da2150f448d9e39715ac5f5deaa +#: cb8fc8c4c79e467eac5fab4ca685201e msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." msgstr "" #: ../../src/topics/inputs.md:124 -#: fd8a98686e3c4c609f79ae427f1558d3 +#: a26cc105716f47cb807174c9003153b0 msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." msgstr "" #: ../../src/topics/inputs.md:131 -#: f1a2e1bbb1104a4fab5a7f04cac845c7 +#: cc159dd5fe5748caac838862f5b8c4d1 msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." msgstr "" #: ../../src/topics/inputs.md:134 -#: 6a7f0ccd227e4f90a8c8ca96744bda68 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." msgstr "" #: ../../src/topics/inputs.md:142 -#: 1f79d115d8a145189638c68c3095396c +#: 6812698e9ad84d3385de5e88e9dde0b3 msgid "The `baseCommand` field will always appear in the final command line before the parameters." msgstr "" #: ../../src/topics/inputs.md:146 -#: 6e1b3e2d90184e34925891099d2b5cc1 +#: 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" #: ../../src/topics/inputs.md:148 -#: 4f6df7f13e42448eb4a53f03bc477b56 +#: d1f02be278754267893dfce5a940997d msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." msgstr "" #: ../../src/topics/inputs.md:154 -#: dbc0b52627514ad0908969d0b4ddfdf4 +#: 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" #: ../../src/topics/inputs.md:160 -#: f173dd96ad124470a53573c86a8df203 +#: 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 #: ../../src/topics/outputs.md:82 #: ../../src/topics/outputs.md:105 -#: e0098a77080d4349b05ceb7735a5fdf5 -#: af25945b530048b685891b1de4e35e72 -#: cb07caa4ff0149b3ae832be53f8d76f6 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/inputs.md:178 -#: 2445d2c7c2794fd3ad8b6ed8b4a9440b +#: 75d59e395c66416cae9b352db5081516 msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." msgstr "" #: ../../src/topics/inputs.md:185 -#: 4459819ba75647d185986a3386939494 +#: 874c6f19abbf45d7ab7d30a378c4048d msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." msgstr "" #: ../../src/topics/inputs.md:191 -#: 8f163bd34ded4785b6e28c8e2147e0dd +#: 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" #: ../../src/topics/inputs.md:193 -#: 1799e11a7b9c4929a3d1379d7ea45d03 +#: dea0d4b681f94e73b13965dcfe75cf7d msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." msgstr "" #: ../../src/topics/inputs.md:198 -#: 9510c0b431a44b5e84e0b583de7c5446 +#: ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" #: ../../src/topics/inputs.md:204 -#: efb4eb6f5e994b50a52fa2c707dad1ce +#: d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" #: ../../src/topics/inputs.md:215 -#: 34599c6f10ce4104be2359a1b37f91cb +#: 750474486a84482292eeba45f118287f msgid "In the first example, you can't provide `itemA` without also providing `itemB`." msgstr "" #: ../../src/topics/inputs.md:217 -#: 0663ea7918994d3f9c45c652a3ed12db +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" #: ../../src/topics/inputs.md:233 -#: a98dda6ca4b14edba467de638bba28fc +#: 1eb0e39bb6d04b8cab300f44a79f3add msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." msgstr "" #: ../../src/topics/inputs.md:236 -#: 10d0e9f8df8c47788703073b17529bc8 +#: bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" #: ../../src/topics/inputs.md:252 -#: 9a0e1a130fba4d24a9168ca3e455cd23 +#: 4b2ab812f62c4f949dd25c8527f2411c msgid "In the third example, only `itemD` is provided, so it appears on the command line." msgstr "" #: ../../src/topics/inputs.md:255 -#: 992a8c801ceb4233acf56b6bff315188 +#: b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" #: ../../src/topics/inputs.md:257 -#: 9027d23fa7074b789c3b86ca5ea17fa4 +#: 2c3b884cb1c54521900cc90782e8a58d msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." msgstr "" #: ../../src/topics/inputs.md:262 -#: 68b47710a8ea4b978428b42c627944e9 +#: a1073b6306044dffb414319ae01f68bb msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." msgstr "" #: ../../src/topics/inputs.md:265 -#: d33e4cac65d14111a89c838c4d1759b9 +#: 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" #: ../../src/topics/inputs.md:271 -#: 24cea1cf7d774b6ab56959f289cab39d +#: 9a1d92334685449386dfa3b3a899ed48 msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" msgstr "" #: ../../src/topics/inputs.md:280 -#: b866867d6f8e4d3999b62a85e6884ebc +#: fb623af4c480411b8fde28d01c981411 msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." msgstr "" #: ../../src/topics/inputs.md:289 -#: 80c49ed168b14d25b2f09b3b0186b44f +#: e98e165f6bba40809c90473d72f9d592 msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 71628ebe908b4cd28dd1fa17e3d2e2fb +#: d33aa2353ad44fb885d3a1ee48263dc4 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: f123ca244c23413c91405a4b84887525 +#: cd64d2d828834cbbb24ea5358caf5405 msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 23299ae1bec94b00a32a8af7eeac350f +#: 80af387fe3ff4e2da999903385bd602b msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 2495a9f2032a47c188338cb81ba429eb +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 3fd2f3cf7bdf44089df2ce3122534801 +#: d402bf528c7f4eb69aaaa275be2bf1d4 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: d5a5b8b490b640439db92da949266e4e +#: cb9980db4e5f4c74b01c2dec6d5e92d0 msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 5935ed94331d4b2f8ce597f31edea843 +#: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" msgstr "" #: ../../src/topics/operations.md:1 -#: 5feb559552194ba58da7206c601292fe +#: 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" #: ../../src/topics/operations.md:3 -#: b7124ba4df9042baadc1641ee09545d6 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." msgstr "" #: ../../src/topics/operations.md:7 -#: d34b698c62114041a64e0abce25ca935 +#: 5565c1b2d8a349169a305a9b26b4574d msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" msgstr "" #: ../../src/topics/operations.md:10 -#: cba2c31262bd450cbafc7ca77f4fb8fa +#: 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "" #: ../../src/topics/operations.md:16 -#: b01be5f632104096b5af6193aab34d90 +#: 88160cef4cfa4add9020aa89511a5749 msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" msgstr "" #: ../../src/topics/operations.md:24 -#: 60a6a02c1367403db6df3ec10f75eb69 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" msgstr "" #: ../../src/topics/operations.md:55 -#: 314ea7bc35154f41b2af5fa6683ca389 +#: 730ba1434a1445ae847ec6153b6a3b72 msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" msgstr "" #: ../../src/topics/operations.md:58 -#: d81e679b13474f74bc5e1ce1e31c2bc6 +#: 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" #: ../../src/topics/operations.md:66 -#: d7fb27131ee44bfc82f698ee44b2bae0 +#: a25d0b1e13324b40a6b8fcd227948c4f msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." msgstr "" #: ../../src/topics/outputs.md:1 -#: b8ef11eafd1d46e088f1277f4ac372bc +#: da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" #: ../../src/topics/outputs.md:3 -#: d2382ed1f644459594655d5b5b4d838a +#: 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" #: ../../src/topics/outputs.md:5 -#: 6651632d977b44479b721174fffeda2d +#: d661df070e3040869da412d07a71f716 msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/outputs.md:10 -#: bee5f532554241088764ac9e56abbe85 +#: a11585474d3849cca5467512ed964743 msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." msgstr "" #: ../../src/topics/outputs.md:16 -#: 0c7c506f38be421399073871f64e99b0 +#: 2682f9ca8e604a0c9986f7746fdec960 msgid "The following example demonstrates how to return a file that has been extracted from a tar file." msgstr "" #: ../../src/topics/outputs.md:19 -#: 8b60286e56cc42a8ab5f751a97adf771 +#: 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" #: ../../src/topics/outputs.md:21 -#: fa0ad674f15348339a1eee771a6ba9e2 +#: 22447a560f6f4317bf67bd7c4336126c msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" msgstr "" #: ../../src/topics/outputs.md:26 -#: 177b5f1b95a34fb9b2eb42f733d79ac8 +#: f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" #: ../../src/topics/outputs.md:32 -#: a08a6d8aca8e490482e127a8fd5e650e +#: ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" #: ../../src/topics/outputs.md:38 -#: c2c60f68b1e045f88844076e191fda9b +#: dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "" #: ../../src/topics/outputs.md:45 -#: 6d939f62526e4e6d95acb57d72f60a84 +#: 52703d6b7f914097934bfad13663abeb msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/outputs.md:51 -#: c48edd9034364b81ad42540a98b51d91 +#: 5e1c79df657d4a6e84e055dd6b300a5d msgid "The field `outputBinding` describes how to set the value of each output parameter." msgstr "" #: ../../src/topics/outputs.md:62 -#: 9ebe0186a7124dfaa30e558e8f59653a +#: 329d2809dfae4f90bc638f5f03a47ee3 msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." msgstr "" #: ../../src/topics/outputs.md:65 -#: 9381b7d7c9904df0a5e16dac29c2e08f +#: 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" #: ../../src/topics/outputs.md:67 -#: 2aa9c6916e3546b7b92fa64bb83275d1 +#: c6bcf7c6a8774dd6be41cc775848c3b8 msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." msgstr "" #: ../../src/topics/outputs.md:71 -#: 63afb7a597fc4e459b6a7dbd40bbf6ff +#: 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" #: ../../src/topics/outputs.md:89 -#: 7418915470f041c9af5bd39ea652de36 +#: 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" #: ../../src/topics/outputs.md:91 -#: f82db001b58c4969b2d8bc1dcbd7cf8a +#: 9647019d8c37466886e7aab6f176634d msgid "You can also capture multiple output files into an array of files using `glob`." msgstr "" #: ../../src/topics/outputs.md:93 -#: 26d9f0b28d384617a8e490c1f8e26e52 +#: b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" #: ../../src/topics/outputs.md:99 -#: cf46c971b31b4e10bf0fefb4cd028c2f +#: cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" #: ../../src/topics/outputs.md:112 -#: a4347983fb9945a4a2773af88e426dc9 +#: cc067051f22f433bbece08f60933e002 msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" #: ../../src/topics/parameter-references.md:1 -#: c5489e0633114372b273098ee2c9ffd9 +#: a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" #: ../../src/topics/parameter-references.md:3 -#: 75de9fd63393429daf1ca10a85339aa7 +#: dbfe2c1123144316aa026374b0f353d3 msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." msgstr "" #: ../../src/topics/parameter-references.md:13 -#: 8b5d0ada32d645be9359f43a431f5f91 +#: 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" #: ../../src/topics/parameter-references.md:19 -#: 2ed93dc8778e44209194f41b9ad193d5 +#: 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "" #: ../../src/topics/parameter-references.md:25 -#: a80dd6d9920540e9880514e04035af86 +#: 074cf5d912854d8c864607cc24b15302 msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/parameter-references.md:36 -#: 9de300f7b9da49f59d1c9fd96dec4a8b +#: 0290af3e3cbb4b32b0450c8771f3bf95 msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." msgstr "" #: ../../src/topics/parameter-references.md:47 -#: a61f52d3c1024c3692899e05fcea4bee +#: b54240bb94f746bba7511633aa969db0 msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." msgstr "" #: ../../src/topics/parameter-references.md:51 -#: dafc9ba578c14fd79d075160e6b7bd6b +#: 8b70a072aa87414c88e89a3e19af0a51 msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." msgstr "" #: ../../src/topics/parameter-references.md:54 -#: 28ca6cae42904559bcec98fb9d2b07cb +#: eea20f89c45f424a888178df53713b28 msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." msgstr "" #: ../../src/topics/parameter-references.md:59 -#: 616c9ff9fcae489285f0bbbc67f07d29 +#: cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" #: ../../src/topics/parameter-references.md:61 -#: ac17acd83ddb43dc9fb7a5e595ab1153 +#: 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" #: ../../src/topics/parameter-references.md:63 -#: 156573324cde41ee8b3c47deabf43db8 +#: 7647e0229a924f988cf02b7812a55c06 msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/parameter-references.md:69 -#: c9725be01e8a401fb3ad9ff01339f81e +#: 9d663249666045618a0d3acddb85a9a9 msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:72 -#: 6797335256e2412cbbe7636507931455 +#: 5fed4984f6784347b4cbe0630b1dd2c2 msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/parameter-references.md:74 -#: 05a5f0fcb7454cb697e3d810d55fac26 +#: dbf6153cd02542a6a01c172803122b7f msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:77 -#: 406e68280b5c4ee494632f94b635b7ad +#: b6250cf6fa8a4a0c94b33302e0decca5 msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/parameter-references.md:81 -#: 2d6e2a4ff391494591bbdf8dbcc4a6ae +#: fa6ca3bbc6784380a03a950a6f49a180 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:85 -#: e71a974b29624210a107fc2d097d4196 +#: b92b516e537a4773ad67b4af586e7a25 msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/parameter-references.md:89 -#: b59df98754e24654bfef0b1fe1d91660 +#: 467a701228504d06b971b79a59c69064 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:92 -#: d2bccbff1ce646348fe38c776ad183e1 +#: 2634f989eb304009a8568d70ed42786c msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 943ba46512ce48fe8c5b62327734c503 +#: 5d8bed66282c408695292ea92a03b2c4 msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: bbcd43d5af7d44108aeb65075a6bd2be +#: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 834295755af841a78e466eea43864861 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: a6b626489bfa468e8f059ab3aa669201 +#: aac74f957774479a83aab4c6ff1390ae msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: e1dbea105aa845c38cb1f90b43847271 +#: b75d29d1d55d44488338f9689f156855 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: e9640f47d40e45bca184eb30700df648 +#: 574d93d1d592458a985f259519c036cb msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 0456efb3718b4356ad2b277ee16de967 +#: 82e48b3e3c3f451480cc0b6a529271f6 msgid "In this example, the software requirement being described is InterProScan version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: f7e97f926505407f8f8e9a427e055e43 +#: 02e40154eac74ecc98d0447d03475b44 msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: ec597ff8f6ee47bc815b069335869f1f +#: 8cb1c5d9b1a54c40924099494eb766c6 msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." msgstr "" #: ../../src/topics/staging-input-files.md:1 -#: 7467a7f6f26a459ba4ce83e4e6dfcc2b +#: b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" #: ../../src/topics/staging-input-files.md:3 -#: 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." msgstr "" #: ../../src/topics/staging-input-files.md:9 -#: a03372581fa44f9b8e3e088a4099cdd9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:1 -#: 36e082be73464be0ad5d0b681cc510da +#: 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "" #: ../../src/topics/troubleshooting.md:3 -#: 4464455b51ad4873ac13c4a63ee5fb54 +#: fbe0c65b444441f785d0054176d036a6 msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." msgstr "" #: ../../src/topics/troubleshooting.md:6 -#: ed7ff0753d1743a995f4cfedd6e5dcc2 +#: 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" #: ../../src/topics/troubleshooting.md:8 -#: 4c2dd10dd66446058477a52fb8d2c602 +#: 9a710602e00c4934ae3a3b471aa68458 msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." msgstr "" #: ../../src/topics/troubleshooting.md:14 -#: 978b6a5fd5fa425fa9a18d9f0e8788da +#: 21b5be7270a14f0987240c81d1ec879b msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" #: ../../src/topics/troubleshooting.md:20 -#: 000c0d6ae8bf414d9293b9f13fd2e448 +#: 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:27 -#: 7e91b8811be14f8e80df39ac4c5bd316 +#: cfe9d8241fe84bd5b74042a5625d933f msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" msgstr "" #: ../../src/topics/troubleshooting.md:35 -#: d42799cc5bd4484bb6beb309a61e103e +#: 764d933cc4da446abd8dd8f913f05dac msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" msgstr "" #: ../../src/topics/troubleshooting.md:44 -#: 48bb0f6666ac48648c7d969608b3bd48 +#: c93efc6d4e004859981ee7f5fa28ed03 msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." msgstr "" #: ../../src/topics/troubleshooting.md:48 -#: f8876044db184cbaaca56579d0c773df +#: 546601da44cb49bd9611b1c85807fd90 msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." msgstr "" #: ../../src/topics/troubleshooting.md:59 -#: a5a3d408dbe34cfda4dd0b2abe67e7d7 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." msgstr "" #: ../../src/topics/using-containers.md:1 -#: 4c240a18c4e6441189489011242c1efd +#: eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "" #: ../../src/topics/using-containers.md:3 -#: e37e76ef376a4ee695e600998906ec1c +#: 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" #: ../../src/topics/using-containers.md:5 -#: 51a307b0ba7c4c1d89309ba8d2250471 +#: e07f33d01b804663a25ffb08aad74821 msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." msgstr "" #: ../../src/topics/using-containers.md:15 -#: 13cc38d72d34468fa4eb6d91f23ff105 +#: 7a644506619a4f08958ec7d4540cd557 msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." msgstr "" #: ../../src/topics/using-containers.md:18 -#: 42a48398d3ef4b03bd7395120f2cfb42 +#: b5195b7d8eaa419fb2b90cb33a57783a msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." msgstr "" #: ../../src/topics/using-containers.md:21 -#: d59387b433bc4ecfaf7e72026624db02 +#: 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" #: ../../src/topics/using-containers.md:27 -#: d963418ccc0b4803bbc758d718ccb5aa +#: 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" #: ../../src/topics/using-containers.md:33 -#: a224d1510c9e46aab23d8bdc03c349dd +#: 2713594c937d4c528fc8d04d9e9819ed msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." msgstr "" #: ../../src/topics/using-containers.md:44 -#: 0a82f8a45b0546aaac4c976dcc98014a +#: cf94c1424fc2413c85647fd1ee73d951 msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." msgstr "" #: ../../src/topics/using-containers.md:52 -#: bc418a2a535e49359c4cd44b373bbe02 +#: dc0452107c604e29bdf32bb289fe5db8 msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/using-containers.md:55 -#: a799fba2322944cea00e413c08066536 +#: 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" #: ../../src/topics/using-containers.md:69 -#: 35379c6b972940bd8451f10b74dd793e +#: 483181f498fc4d968b5fe6ef427709f7 msgid "Notice the CWL runner has constructed a Docker command line to run the script." msgstr "" #: ../../src/topics/using-containers.md:72 -#: 2d5265525ad544a0b64ad2cf07aacc26 +#: 7487485d6aa4458089a4b4bdf107ea64 msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." msgstr "" #: ../../src/topics/workflows.md:1 -#: e2521b89596d42f8a87a3207fd6c32f2 +#: 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" #: ../../src/topics/workflows.md:3 -#: 3676f23b63e142cb8e5715ae07216a47 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" #: ../../src/topics/workflows.md:13 -#: 00725aed13a440ca8b3c4f9155fbee99 +#: f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" #: ../../src/topics/workflows.md:41 -#: 2e38a4f9072b4ad9bbb74f943d22084d +#: 5870ac44e4c24b8daf5f06c49f95ce04 msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." msgstr "" #: ../../src/topics/workflows.md:51 -#: 2b9f4035ea864b6db50c861a1819289d +#: a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" #: ../../src/topics/workflows.md:81 -#: 28e9064780e7418a8e02a22f92e34404 +#: 93188ed43ee949cc98b3ea679ce14feb msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" msgstr "" #: ../../src/topics/workflows.md:91 -#: 66ce14a10d2d4dc497d3ed71e11ed8b8 +#: 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" #: ../../src/topics/workflows.md:150 -#: 8dc00528c3d2426c8a3492a8191f1d81 +#: 1cc17ad26e9c474b895ba5cd20c8b66a msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." msgstr "" #: ../../src/topics/workflows.md:160 -#: f9ef5e258f7c4971a8543d1dfed711a8 +#: 24aca0bea4d94e3593b844cf0586cffe msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." msgstr "" #: ../../src/topics/workflows.md:165 -#: 324bc51071d743ea80124c23880ddc0a +#: 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" #: ../../src/topics/workflows.md:167 -#: d8c13e01976b43a1af34c11a7bc36897 +#: 9c56528acd5f49deb139e034dfbfac7c msgid "This workflow extracts a java source file from a tar file and then compiles it." msgstr "" #: ../../src/topics/workflows.md:170 -#: 43910a8ab4484e529a17df418b1aedbb +#: 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 #: ../../src/topics/workflows.md:180 -#: eab3ac7490f24645bbf0babb20aa9df0 -#: 56917e39cfa34470a7a88b52b1f955d9 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" #: ../../src/topics/workflows.md:180 -#: 7ad12d67e815400c94080804b9285629 +#: a2dd833fdca4443181648e41051a5232 msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" #: ../../src/topics/workflows.md:183 -#: 457d5a31c79143acae2683d95d27f7a3 +#: 7e40cc9f9e1341c195e843c009575b94 msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" msgstr "" #: ../../src/topics/workflows.md:185 -#: a2a73901bf634547900d08b9a1ac8889 +#: 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "" #: ../../src/topics/workflows.md:191 -#: f347d80e62384b14acf6423675e5359a +#: 6fcf8ad3d1bd49afa4a105622437bd59 msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." msgstr "" #: ../../src/topics/workflows.md:205 -#: 2a845a4f3f98428fb82f3ca7ce038a6e +#: 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" #: ../../src/topics/workflows.md:212 -#: e2007c74d5f449a882809d6b91c010bf +#: def35d6021394def80a53ae49a2cdbde msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." msgstr "" #: ../../src/topics/workflows.md:221 -#: 7f5e53ee7cf94be2bff45ef64db28a24 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." msgstr "" #: ../../src/topics/workflows.md:233 -#: a0d076b7b8b048478580c99ef0c8429f +#: c84d4450bc6a475dbf34e0b22cea9130 msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." msgstr "" #: ../../src/topics/workflows.md:248 -#: 7fd926c18ad548e98845e9b5134dd6f2 +#: cca9665f6daa44b49233baf34ab9fcc7 msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." msgstr "" #: ../../src/topics/workflows.md:256 -#: 789fbd47f8564cceb430ef3c0bc90e9b +#: 547edbf5fa424b8286cc21674ff159b0 msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." msgstr "" #: ../../src/topics/workflows.md:261 -#: 45c4d0492d6143ca9cebe81e9b2cf3ae +#: 7ca248888b9d484cb544cd76ba538662 msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" #: ../../src/topics/workflows.md:267 -#: 73bd3da2af8545928d5ea71d0f7454f6 +#: ae6b240718104380b08db5552d7355ea msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." msgstr "" #: ../../src/topics/workflows.md:278 -#: 15ce3d2700424f0fbb280d602ccebcf6 +#: e5a8b7f84be64020b191099f3fad30ed msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." msgstr "" #: ../../src/topics/workflows.md:285 -#: af4268f19202436eb0a7e8c6bed5e386 +#: f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" #: ../../src/topics/workflows.md:287 -#: 94a4eadca6b949d79de2990a0150eee8 +#: 12a06d8358534102b202965d4258c18e msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" msgstr "" #: ../../src/topics/workflows.md:297 -#: 09c1619e8cbd4febbb637f7e99ad5890 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" msgstr "" #: ../../src/topics/workflows.md:300 -#: 677ea7a27eb64568ab3689142d6efe70 +#: 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "" #: ../../src/topics/workflows.md:309 -#: 097e6d47f9394e62b80110700492783a +#: b7f93705e5b8416696be01850072e8c0 msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" #: ../../src/topics/workflows.md:314 -#: e93affce8c104bf6977182047c1f1077 +#: e87045829b344089ab59dc27063ddd7a msgid "\"Visualization \"Visualization" msgstr "" #: ../../src/topics/workflows.md:322 -#: 06c9e04ba890473b851240a0fa9c3b12 +#: 42ef2f145b824d69b63abc1da175c216 msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." msgstr "" #: ../../src/topics/workflows.md:336 -#: 0380dc1fe3aa48e4b62283b7b2a611d8 +#: c61cedf543664d388183e04b3939cc39 msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." msgstr "" #: ../../src/topics/workflows.md:341 -#: 49b251f7a313492ea60504b00109e526 +#: 9e39e3f1501c4fcaab3e8962e090f6be msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." msgstr "" #: ../../src/topics/workflows.md:347 -#: 7ee55702d7dd4679a24ff052f6f0cbeb +#: 03e2f767c4da461982fc3c0f3ba94762 msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" #: ../../src/topics/workflows.md:366 -#: 85d7e2e270874aa6b9f477cec0f48154 +#: 3bea5822b8694e2aa32c446e1c54a045 msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" #: ../../src/topics/workflows.md:383 -#: 570e94513c984c09ad6aa255f534216d +#: 426023bd6e3a471cbb30dbda3d6f9e57 msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." msgstr "" #: ../../src/topics/workflows.md:389 -#: a107258662fb4bd4a9a3d8754e34d1e9 +#: 0d498cd4caf54c15891ca1afe58e2727 msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." msgstr "" #: ../../src/topics/workflows.md:394 -#: fc1a6502d831458ab8371a575cea47e2 +#: b2d75045e02741b4850f5ff1243f7858 msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." msgstr "" #: ../../src/topics/workflows.md:398 -#: 2d10806bf1ce4e26b92adda61efc0862 +#: cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" #: ../../src/topics/workflows.md:400 -#: 046c5e134de94b629cc22d416f3c9182 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." msgstr "" #: ../../src/topics/workflows.md:411 -#: 52fa22d3277940049fbb589a3ea73433 +#: 5fa79c62049a447c8328ebf9db54ebf4 msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" msgstr "" #: ../../src/topics/workflows.md:415 -#: 6043beb96c2c49648011ec556aa9e986 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:421 -#: 5ac4310515124e2986724425bed5651f +#: 3a67d77a2e7b4c0bb61cc3585ceae942 msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" msgstr "" #: ../../src/topics/workflows.md:429 -#: 7958e91d5c2f4046aa9d2070a900f9ae +#: f1cb55fc59824cc18a95fd6dcb32cf4c msgid "First of all, notice that the main workflow level input here requires an array of strings." msgstr "" #: ../../src/topics/workflows.md:441 -#: 2db234d776fe4fd38bab07245dcb783a +#: d947c54933d64aad90df392a1cedd63f msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." msgstr "" #: ../../src/topics/workflows.md:445 -#: 7cfb17230e284ee7b6e2a00efe8eeb74 +#: 651d35997332404186aa6d5711da4a3d msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" msgstr "" #: ../../src/topics/workflows.md:450 -#: 4311ac98544e4fb0b2f4b24985710a01 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "" #: ../../src/topics/workflows.md:452 -#: 780f9c72e6c34c39918642c7e2477355 +#: 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" #: ../../src/topics/workflows.md:458 -#: cc4a7316db644b438cbaa181ad9ef2d3 +#: b662c1a5a4424c8d8350a806356acc61 msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" msgstr "" #: ../../src/topics/workflows.md:466 -#: dfc461a03fe8487794837904febb8b63 +#: 04d6babfd87343d7a5f13867ea02b65f msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" msgstr "" #: ../../src/topics/workflows.md:469 -#: 1e83485b00b64dfaba897bd8d772e0f0 +#: 2eaacf1a90204a2b9bd621344560f2a1 msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" msgstr "" #: ../../src/topics/workflows.md:472 -#: d0321d6805ec4d3abf3877d02a0a417f +#: 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" #: ../../src/topics/workflows.md:480 -#: d7d77e807b3048c7bdf89558f76804cb +#: 4a94e5f7e1bc4d628702140e4e51d6d3 msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" msgstr "" #: ../../src/topics/workflows.md:483 -#: 8d9b8be147fc4a71922dde858842e543 +#: e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "" #: ../../src/topics/workflows.md:489 -#: 34b7705416a745a6a42e6d402c0757ed +#: e3a7182f00f440b8b5461da91194a64b msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" msgstr "" #: ../../src/topics/workflows.md:491 -#: 257adcee9da64d5c987f3b64efd20ab0 +#: 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" #: ../../src/topics/workflows.md:497 -#: fa6ed5d0c14f42f4aa3c5144648db22c +#: b5338f39e8c74ff28e139da68089a742 msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." msgstr "" #: ../../src/topics/workflows.md:509 -#: 333e8ce458d54de394526769f96d12d2 +#: f6d92156d67c4a339bcfd194cff897df msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" msgstr "" #: ../../src/topics/workflows.md:513 -#: b819e8a5df6e4fa495924095709669ef +#: 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:519 -#: f1955468a1364d44a930db77c9c4b495 +#: d80ab383eec9402faba997b548fe42eb msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." msgstr "" #: ../../src/topics/workflows.md:522 -#: 8c3b9b645a204d02b2c73a205e8ec296 +#: f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "" #: ../../src/topics/workflows.md:524 -#: 4d88b9c186cd4502adbf752e8a70b6ce +#: 49217c02f58c43ff9ec00f10da8d4e84 msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." msgstr "" #: ../../src/topics/workflows.md:527 -#: 9927673564024ba5833b5ac271737857 +#: 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:566 -#: 84f4ed7ce2004742b8db9087104a469a +#: 8dbd56473f8c40c0bb12a48be06117e3 msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." msgstr "" #: ../../src/topics/workflows.md:573 -#: 2b5f9757adca4490a149c7f45e14fcb5 +#: 78d7f3ede2c746d482042adef050b2c4 msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." msgstr "" #: ../../src/topics/workflows.md:587 -#: 0418de720813442f81ecff293c9448b5 +#: cbbf93c70fe04ba7932ba25758ddc611 msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" #: ../../src/topics/workflows.md:607 -#: 524eec63be8248ae982939c975ef50a2 +#: cfa1c1fde4454df283f87cc54a9c59ec msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" #: ../../src/topics/workflows.md:627 -#: 5e99f9912cc549a7890e2934425eb943 +#: 1a8be2950cbb475bbb2617e005f0fac9 msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." msgstr "" #: ../../src/topics/yaml-guide.md:1 -#: b0121ee087d6424fbb0ea5957a7b0b8c +#: 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "" #: ../../src/topics/yaml-guide.md:6 -#: 49e9f6b3a06840289decf3f557860f87 +#: 5d83c56102e141cc978500f678dd0c1c msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." msgstr "" #: ../../src/topics/yaml-guide.md:13 -#: ed9eebec0b3d4b72ba65507d37757a37 +#: c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" #: ../../src/topics/yaml-guide.md:16 -#: bf9b255a24a84f3ba989a223492b8f41 +#: fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "" #: ../../src/topics/yaml-guide.md:18 -#: e79fa0b7f8b14810a3a20908ef92bc55 +#: 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" #: ../../src/topics/yaml-guide.md:19 -#: 290e2035f903417cbecb5dc5f09d6ebe +#: b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" #: ../../src/topics/yaml-guide.md:20 -#: d420730151534f1a89076588a3358f09 +#: b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" #: ../../src/topics/yaml-guide.md:21 -#: a6b5378bbe1e4bee9e37a765bddf75f7 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" #: ../../src/topics/yaml-guide.md:22 -#: 6e4d9465dc2b454d96b02d7ad1817795 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "" #: ../../src/topics/yaml-guide.md:24 -#: a649d4af5f434dac9395e013ec4836bb +#: 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "" #: ../../src/topics/yaml-guide.md:26 -#: 446190a298834b73bda068286e8490cf +#: cda73485875d4c8e9464679a20558616 msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:42 -#: 2f35c012ff174721bffe66a3f58a804f +#: 98cae24919b74c088a5d89706aec581b msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" #: ../../src/topics/yaml-guide.md:51 -#: 43127c98c9d94aedac61cee67929c1a6 +#: b4b0940b4b5743c09637b36b964202d0 msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" #: ../../src/topics/yaml-guide.md:61 -#: dc4fe561203c4c38a9caea5bd6eff2cd +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" #: ../../src/topics/yaml-guide.md:63 -#: f924e4896db2424d99ce8c9da14c599a +#: 9ca3554d771d45998e88aaede525b227 msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:76 -#: bf7646f5f925485c842a6d34140e40b8 +#: 3fca839cede94cfd8e4f605c73ba699d msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" msgstr "" #: ../../src/topics/yaml-guide.md:79 -#: c483e61dec8949fa96bb893d422888a0 +#: da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "" #: ../../src/topics/yaml-guide.md:81 -#: 85fcb523d0e34a499eae04d304887f7b +#: 3ded0f125249485c921994b6e6b93ac9 msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" msgstr "" #: ../../src/topics/yaml-guide.md:104 -#: 83d47c8736a34f3cbf09e3997845e4f4 +#: 53ece35d309a4c8d99f1efb2122a7092 msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." msgstr "" #: ../../src/topics/yaml-guide.md:127 -#: c698fb3d37bc403e9aeb679b8fc0e15e +#: d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" #: ../../src/topics/yaml-guide.md:129 -#: ae8af2f0eeda4aec97201211dfa965c7 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:146 -#: 2ee87aa465cd41fda16a61e242f8c9d0 +#: fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" #: ../../src/topics/yaml-guide.md:167 -#: 0a6fd4469ff24b61b3ad001b09eead18 +#: 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "" #: ../../src/topics/yaml-guide.md:169 -#: b96ba19bce9341d39c46054e1f10fe8f +#: 87bafb845c714b109874f6137b84462d msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:177 -#: 903f30af3d0c45cfb61063936a8097a7 +#: 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "" #: ../../src/topics/yaml-guide.md:184 -#: ede8db7c0a58432e8a1c416e937a06d2 +#: fcd05b1ef31a4046946a2399c7fc5575 msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." msgstr "" #: ../../src/topics/yaml-guide.md:194 -#: c8b53615476a4a1fbef2420d93bac94e +#: f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "" #: ../../src/topics/yaml-guide.md:196 -#: ea03cb5525cc491f9feb5c4780b38fee +#: 859368c1f25c4a4aad57abfd046c63f5 msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." msgstr "" #: ../../src/tutorials.md:1 -#: 92fd3a5e31714eab859dd630af2e78cf +#: 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" msgstr "" #: ../../src/tutorials.md:5 -#: de660ecdb5b44c97a0e519d00b232497 +#: 5d92464923c245818c070fbef102be89 msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." msgstr "" #: ../../src/tutorials.md:7 -#: 5afc1e1288e74ed0985e61e5164479c7 +#: 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" msgstr "" #: ../../src/tutorials.md:9 -#: 862dc7ac81e54b1fb3d4c2f961b8810e +#: 13d7e2e92e96432787c712cf6a595424 msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" #: ../../src/tutorials.md:11 -#: e2c94c0e1c7048d38cd7aa2c465a859d +#: 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" msgstr "" #: ../../src/tutorials.md:13 -#: b63253780f51467a95207d820d13ac39 +#: 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" #: ../../src/tutorials.md:15 -#: 6d06ca7ed5df4560aaed286f4fe33928 +#: 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" msgstr "" #: ../../src/tutorials.md:17 -#: 5448df4a6a8f431d80e269bcd480e19e +#: a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" diff --git a/src/LICENSE.md b/src/LICENSE.md new file mode 100644 index 00000000..84798e58 --- /dev/null +++ b/src/LICENSE.md @@ -0,0 +1,2 @@ +```{include} ../LICENSE.md +``` diff --git a/src/LICENSE.rst b/src/LICENSE.rst deleted file mode 100644 index 68c5792f..00000000 --- a/src/LICENSE.rst +++ /dev/null @@ -1 +0,0 @@ -.. include:: ../LICENSE.rst diff --git a/src/index.md b/src/index.md index e1a0c0cb..8e10fa54 100644 --- a/src/index.md +++ b/src/index.md @@ -35,7 +35,7 @@ introduction/index.md topics/index.md tutorials.md faq.md -LICENSE.rst +LICENSE.md ``` [repo]: https://github.com/common-workflow-language/user_guide/issues From 3cf11ae4363e77095c9bb2a3c10355b71584b0f4 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 27 Jan 2023 13:44:54 +0100 Subject: [PATCH 046/179] Makefile: drop default turn warnings into errors option --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 81bc3c77..83ba9e13 100644 --- a/Makefile +++ b/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line, and also # from the environment for the first two. -SPHINXOPTS = "-W" +SPHINXOPTS = "" # was "-W" (turn warnings into errors) SPHINXBUILD = sphinx-build SOURCEDIR = src BUILDDIR = _build From 0efc0ad56cd7e96d32b5518b9fbdab291f528d8f Mon Sep 17 00:00:00 2001 From: Michael Crusoe Date: Fri, 27 Jan 2023 15:27:15 +0100 Subject: [PATCH 047/179] Translated using Weblate (Spanish) Currently translated at 3.4% (21 of 605 strings) Translated using Weblate (Portuguese) Currently translated at 2.1% (13 of 598 strings) Translated using Weblate (Spanish) Currently translated at 2.5% (15 of 598 strings) Translated using Weblate (Spanish) Currently translated at 100.0% (2 of 2 strings) Translated using Weblate (Portuguese) Currently translated at 100.0% (2 of 2 strings) Co-authored-by: Michael Crusoe Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-sphinx/es/ Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-sphinx/pt/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/es/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/pt/ Translation: Common Workflow Language/CWL User Guide Translation: Common Workflow Language/CWL User Guide: Sphinx --- locales/es/LC_MESSAGES/sphinx.po | 18 +- locales/es/LC_MESSAGES/user_guide.po | 2804 +++++++++++++++----------- locales/pt/LC_MESSAGES/sphinx.po | 18 +- locales/pt/LC_MESSAGES/user_guide.po | 2789 +++++++++++++++---------- 4 files changed, 3375 insertions(+), 2254 deletions(-) diff --git a/locales/es/LC_MESSAGES/sphinx.po b/locales/es/LC_MESSAGES/sphinx.po index 38526232..2bdf9af4 100644 --- a/locales/es/LC_MESSAGES/sphinx.po +++ b/locales/es/LC_MESSAGES/sphinx.po @@ -4,25 +4,27 @@ # Language User Guide package. # FIRST AUTHOR , 2023. # -#, fuzzy msgid "" msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" +"Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" +"PO-Revision-Date: 2023-01-26 13:55+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Spanish \n" +"Language: es\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" #: ../../src/_templates/sidebar-nav-bs.html:1 d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" -msgstr "" +msgstr "Navegación principal" #: ../../src/_templates/sidebar-nav-bs.html:3 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" -msgstr "" - +msgstr "Sección Navegación" diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index ba080ed4..b1952aae 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -4,16 +4,15 @@ # Language User Guide package. # FIRST AUTHOR , 2023. # -#, fuzzy msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-24 19:53+0100\n" -"PO-Revision-Date: 2023-01-25 13:37+0000\n" +"PO-Revision-Date: 2023-01-27 14:27+0000\n" "Last-Translator: Michael Crusoe \n" "Language-Team: Spanish \n" +"user-guide/es/>\n" "Language: es\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" @@ -22,21 +21,23 @@ msgstr "" "X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 ../../LICENSE.rst:2 +#: dcdc2e8da0ec4d9e9453601fdd83bac5 msgid "Licenses" msgstr "Licencias" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 ../../LICENSE.rst:5 +#: 3e165520ca56481b8f8d494a8d471de3 msgid "Instructional Material" msgstr "Material didáctico" #: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable " -"summary of (and not a substitute for) the [full legal text of the CC BY " -"4.0 license][cc-by-legal]." +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable summary " +"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" +"[cc-by-legal]." msgstr "" "Todo el material instructivo del proyecto Common Workflow Language y los " "cambios en la estructura también están disponibles bajo la [licencia " @@ -44,12 +45,14 @@ msgstr "" "legible por humanos (y no un sustituto) del [texto legal completo de la " "licencia CC BY 4.0][cc-by-legal]." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 ../../LICENSE.rst:12 +#: b7a7a0fb40344fe087c1cc3ec19308aa msgid "You are free:" msgstr "Usted es libre de:" #: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" +msgid "" +"to **Share**---copy and redistribute the material in any medium or format" msgstr "" "**Compartir**---copiar y redistribuir el material en cualquier medio o " "formato" @@ -58,90 +61,93 @@ msgstr "" msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 ../../LICENSE.rst:18 +#: 430ff4de74924bc3a3b2c7e809ea4456 msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e ../../LICENSE.rst:20 +#: 8bc6672f4a33428296226112a1be6fbe msgid "" -"The licensor cannot revoke these freedoms as long as you follow the " -"license terms:" +"The licensor cannot revoke these freedoms as long as you follow the license " +"terms:" msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " -"términos de la licencia." +"términos de la licencia:" #: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow " -"Language project, and, where practical, linking to " -"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" -"human], and indicate if changes were made. You may do so in any " -"reasonable manner, but not in any way that suggests the licensor endorses" -" you or your use." -msgstr "" -"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su " -"trabajo se deriva de un trabajo que tiene «Copyright © The Common Workflow " -"Language Project» y, cuando sea práctico, con un enlace a https://www." -"commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e indicar " -"si se han realizado cambios. Puede hacerlo en cualquier forma razonable, " -"pero no de forma tal que sugiera que usted o su uso tienen el apoyo de la " -"licenciante." +"work is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a [link to the license][cc-by-human], and indicate if changes were " +"made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." +msgstr "" +"**Atribución**---Usted debe dar crédito de manera adecuada(mencionando que " +"su trabajo se deriva de un trabajo que tiene «Copyright © The Common " +"Workflow Language Project» y, cuando sea práctico, con un enlace a " +"https://www.commonwl.org/%20),%20brindar%20un%20[enlace%20a%20la%20licencia][cc-by-human]," +"e indicar si se han realizado cambios. Puede hacerlo en cualquier forma " +"razonable, pero no de forma tal que sugiera que usted o su uso tienen el " +"apoyo de la licenciante." #: ../../LICENSE.md:32 8161753b7526445db319210044566200 msgid "" "**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything " -"the license permits. With the understanding that:" +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" msgstr "" "**No hay restricciones adicionales**---No puede aplicar términos legales ni " "medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " "permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 ../../LICENSE.rst:35 +#: 1798d65c10104040923c2fea2199bab2 msgid "" -"You do not have to comply with the license for elements of the material " -"in the public domain or where your use is permitted by an applicable " -"exception or limitation." +"You do not have to comply with the license for elements of the material in " +"the public domain or where your use is permitted by an applicable exception " +"or limitation." msgstr "" "No tiene que cumplir con la licencia para elementos del materiale en el " "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 ../../LICENSE.rst:38 +#: c65198b804f8436ba783643d51bc72d9 msgid "" -"No warranties are given. The license may not give you all of the " -"permissions necessary for your intended use. For example, other rights " -"such as publicity, privacy, or moral rights may limit how you use the " -"material." +"No warranties are given. The license may not give you all of the permissions " +"necessary for your intended use. For example, other rights such as " +"publicity, privacy, or moral rights may limit how you use the material." msgstr "" "No se dan garantías. La licencia podría no darle todos los permisos que " "necesita para el uso que tenga previsto. Por ejemplo, otros derechos como " "publicidad, privacidad, o derechos morales pueden limitar la forma en que " "utilice el material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea ../../LICENSE.rst:44 +#: 3d7ca3f2cede4d5f998bf014bd970748 msgid "Software" msgstr "Software" #: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 msgid "" "Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +"provided by Common Workflow Language project are made available under the " +"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Excepto cuando se indique lo contrario, los programas de ejemplo y otro " "software proporcionado por el proyecto Common Workflow Language están " "disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " -"la [OSI][Osi]." +"la [OSI][osi]." #: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, " -"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " -"See the License for the specific language governing permissions and " -"limitations under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." msgstr "" "Unless required by applicable law or agreed to in writing, software " "distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " @@ -151,82 +157,97 @@ msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 #: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 -#: eab02dc13915490bb3c9ba744d78b6a7 +#: eab02dc13915490bb3c9ba744d78b6a7 271049c39d294b11b9bd94cb6be2857f +#: 61af90891e2d4542b5f45fb3ec6480af bf309fa01bed4355bf052ae4afbf9a67 msgid "" "CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." +"create workflows. Because CWL is a specification and not a specific piece of " +"software, tools and workflows described using CWL are portable across a " +"variety of platforms that support the CWL standard." msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 #: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +#: 055f0e960450410585b59760ef3ad284 6294af2e32e04207a87399c7f0780011 msgid "This page has moved" msgstr "" #: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +#: 6428125fc43c43bba8518ece2f5d150f msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" #: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +#: ce8fade1e88e4b03ac0d3fc71d16f844 msgid "FAQ" msgstr "" #: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +#: 9e7483b53a984b689964c69afcaa7123 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" #: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 +#: 8c5a89257ef248cd99cba303713e5082 msgid "Rename an Input File" msgstr "" #: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +#: 9e80d8eeefcf4a9d95fd5fe9d9fa124a msgid "" -"This example demonstrates how to change the name of an input file as part" -" of a tool description. This could be useful when you are taking files " -"produced from another step in a workflow, and don't want to work with the" -" default names that these files were given when they were created." +"This example demonstrates how to change the name of an input file as part of " +"a tool description. This could be useful when you are taking files produced " +"from another step in a workflow, and don't want to work with the default " +"names that these files were given when they were created." msgstr "" #: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f +#: c2e5f62490f940aab19166403a840597 msgid "Rename an Output File" msgstr "" #: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +#: ffcffabdf25a4c398e8e53bc817ea769 msgid "" -"This example demonstrates how to change the name of an output file from " -"the default name given to it by a tool:" +"This example demonstrates how to change the name of an output file from the " +"default name given to it by a tool:" msgstr "" #: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 +#: c8a6b85cfca542ccb042a0269294e5e3 msgid "Referencing a Local Script" msgstr "" #: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +#: 98f583e5e36941c1856d719a16e58e4a msgid "There are two ways to reference a local script:" msgstr "" #: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +#: fb9cac0954474b5284793330b7424949 msgid "" -"The first method involves adding the folder containing your scripts to " -"the `PATH` environment variable. This allows you to run the shell script " +"The first method involves adding the folder containing your scripts to the " +"`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" #: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +#: cc45d609de1f423db86d58eea933e132 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" #: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +#: 27ee63895cb14321a1814f4372d3180f msgid "" -"After that, make the script executable with the command `chmod +x " -"scriptname.sh`" +"After that, make the script executable with the command `chmod +x scriptname." +"sh`" msgstr "" #: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +#: f1c841980f3d4364a2158a4eb2f0d257 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " @@ -234,117 +255,138 @@ msgid "" msgstr "" #: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +#: 6d53d38ddcf244fb997db37eae7fcf90 +msgid "" +"Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" #: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +#: b6d60d66f3744ab3aea1b175ecb23d4a msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" #: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +#: cf4fa3ae602841d393b4143e9f6f5e82 msgid "" -"The second method involves including an input of `type: File` in the " -"script itself:" +"The second method involves including an input of `type: File` in the script " +"itself:" msgstr "" #: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 +#: 41a3c9aa55c5406f9b52af2243c79ccc msgid "In CWL, everything must be directly stated." msgstr "" #: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +#: 3b8eb247425a4a708f51c08cf258e30a msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" #: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +#: 388a6e091a054dc48afc928f46dac7b7 msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their " -"input binding makes use of `self`. Below is an example workaround for " -"this, pending a more sophisticated fix." +"Currently, `cwltool` can't cope with missing optional inputs if their input " +"binding makes use of `self`. Below is an example workaround for this, " +"pending a more sophisticated fix." msgstr "" #: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 +#: 28c59d12156e44ea833822fd3ecaf824 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" #: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +#: 8267843ff5c940c590b10047455f2102 msgid "" -"Below is an example showing how to specify different strings to be added " -"to a command line, based on the value given to a Boolean parameter." +"Below is an example showing how to specify different strings to be added to " +"a command line, based on the value given to a Boolean parameter." msgstr "" #: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +#: 6e6f55bc915e4cceb8e360544d6b4ae5 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" #: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +#: 1bc80953bd60405082a10a7798c1413d msgid "" -"Using " -"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" -" along with [`linkMerge: " +"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +#: a6cd4bf4dc314e66a951f7f1227c7bb7 msgid "merge_nested" msgstr "" #: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +#: 7ab2440a92aa44b09e8a324cd67ca728 msgid "" -"The input must be an array consisting of exactly one entry for each input" -" link. If \"merge_nested\" is specified with a single link, the value " -"from the link must be wrapped in a single-item list." +"The input must be an array consisting of exactly one entry for each input " +"link. If \"merge_nested\" is specified with a single link, the value from " +"the link must be wrapped in a single-item list." msgstr "" #: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +#: 152a529dfa2c42c1b6f0083589fa5aeb msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" #: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +#: b278c137167d4b958c099c0509edb79c msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " -"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" -" destination step." +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " +"add `linkMerge: merge_nested` under the appropriate `in` entry of the " +"destination step." msgstr "" #: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd +#: f0b38723838f479d9db8eb5142d28a1e msgid "Optional Inputs 💯" msgstr "" #: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +#: fc1e4a808e85422cbb4d128c5a1f4d0c msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" #: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +#: d74964c9d19241848f4dd92a201e201f msgid "" msgstr "" #: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c +#: 859b8e18e05a4c3285fb20bbb44c1ed4 msgid "Enum Inputs ⚜️" msgstr "" #: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +#: eb6e932924a54afd9114c629b2d0e93b msgid "" -"For command line flags that require a specific input as the argument an " -"enum type can be declared in CWL. **Specifying null here is known as long" -" form style. It does the same thing as the question mark on the other " -"inputs.**" +"For command line flags that require a specific input as the argument an enum " +"type can be declared in CWL. **Specifying null here is known as long form " +"style. It does the same thing as the question mark on the other inputs.**" msgstr "" #: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +#: 31d70b41ddf042f6aa530b7bd6daae73 msgid "" msgstr "" #: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 +#: 9aa3ff8c957b42c8a30f37167a8177fd msgid "Record Inputs 📀" msgstr "" #: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +#: 777ac7f6bde2470b981efc91feb01c81 msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " @@ -352,117 +394,138 @@ msgid "" msgstr "" #: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 +#: 8647071efc0548a1807c03fe8a4ee54c msgid "Setting Mutually Exclusive Parameters" msgstr "" #: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +#: 4404233183124085990c44793a6b25f6 msgid "" -"To properly set fields in a record input type, you need to pass a " -"dictionary to the input to properly set the parameters. This is done by " -"using inline JavaScript and returning the dictionary with the key of the " -"field you want to set. The source field is set to indicate the input from" -" the workflow to be used as the value." +"To properly set fields in a record input type, you need to pass a dictionary " +"to the input to properly set the parameters. This is done by using inline " +"JavaScript and returning the dictionary with the key of the field you want " +"to set. The source field is set to indicate the input from the workflow to " +"be used as the value." msgstr "" #: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 +#: c5eecacfa07f47649f07ef9d888f4c5e msgid "Setting Booleans" msgstr "" #: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +#: 1efef04061fd48f1ab39a99508b5bc0b msgid "These can be set by using the default field" msgstr "" #: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 +#: 57e8ace8e8d64e7a90510e1ccea69612 msgid "Concatenating Strings in Inputs" msgstr "" #: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +#: 138606e8d7be40bb960f278977f9107f msgid "The valueFrom field must be used instead of default." msgstr "" #: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c +#: d0f668dc78464469a9f2bfc61a90aa76 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" #: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +#: f2a49a7663e1456cac6b2eac0c46c662 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" #: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +#: eefe4adebdba4063af0cac3ab5d46442 msgid "" -"For example, the filename `a space is here.txt` includes 3 space " -"characters." +"For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" #: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +#: 526f2816123a43ecbcf09c46904b4b5f msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" #: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +#: 0ecf267c5f4d4557ad0d7ddef2f4b5e6 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +#: 935a253376854d12928f00c2870ed4c0 msgid "If `cwltool --validate` returns valid" msgstr "" #: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +#: bc6c0bf679ae48e7822add7ab2cda220 msgid "But executing it causes an error like:" msgstr "" #: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +#: a63643806a2a4eee8ebd3502fd6ce2b5 msgid "The file is here" msgstr "" #: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +#: fc54964adcd648948d7baff02f47598e msgid "Problem caused by `-` (hyphen character)." msgstr "" #: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 +#: aabc495306a149fdb15835ae1df93c42 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" #: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +#: 2930faead8be45a6b9adbf51dcdfef6e msgid "" -"If it is not possible to change the input identifier, then you can use an" -" alternative CWL Parameter Reference syntax:" +"If it is not possible to change the input identifier, then you can use an " +"alternative CWL Parameter Reference syntax:" msgstr "" #: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 +#: f885e4716a8d4de0b25d2d3356789672 msgid "Use CWL and cwltool with Singularity" msgstr "" #: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +#: 6487ff3c19c944eb8257b2cf60d0aac7 msgid "" -"The CWL standards are built around (optional) Docker format containers. " -"The reference runner and several other CWL implementations support " -"running those Docker format containers using the Singularity engine. " -"Directly specifying a Singularity format container is not part of the CWL" -" standards." +"The CWL standards are built around (optional) Docker format containers. The " +"reference runner and several other CWL implementations support running those " +"Docker format containers using the Singularity engine. Directly specifying a " +"Singularity format container is not part of the CWL standards." msgstr "" #: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 +#: 4cbacce539ce4f6cb5bb8ccf1574640c msgid "Debug JavaScript Expressions" msgstr "" #: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +#: 27321576de714cd5b82c67f59b2e3e6f msgid "" -"You can use the --js-console option of cwltool," -" or you can try creating a JavaScript or TypeScript project for your " -"code, and load it using expressionLib, e.g.: " -"https://github.com/common-workflow-language/common-workflow-" -"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +"You can use the --js-console option of cwltool, or " +"you can try creating a JavaScript or TypeScript project for your code, and " +"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" #: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +#: 6afded7ba21247099c9bfcedf40c9171 msgid "Common Workflow Language User Guide" msgstr "" #: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +#: 17c386e7cd25496784207140f9876b90 msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " @@ -470,267 +533,275 @@ msgid "" msgstr "" #: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +#: 3bfd9bcf826a4400935dfad338612b12 msgid "Contributions and Feedback are Welcome!" msgstr "" #: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +#: 4b38f1439da44ebb967b5b1e3df8f78a msgid "" -"If you find that something is missing from this guide, or if you would " -"like to provide other feedback, file an Issue on the [project repository " -"for this guide][repo]. You can also suggest changes directly in a Pull " -"Request by clicking the \"Edit this page\" button at the right sidebar of" -" each page." +"If you find that something is missing from this guide, or if you would like " +"to provide other feedback, file an Issue on the [project repository for this " +"guide][repo]. You can also suggest changes directly in a Pull Request by " +"clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" #: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +#: a4a60a8d010448b0b8ad1e05cbc78f2b msgid "Navigating the User Guide" msgstr "" #: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +#: e23e00e89c81410ba8381fd81bc73b3c msgid "" -"If you are a beginner user get started with the " -"[Introduction](/introduction/index.md) section. For advanced users the " -"subsections of the [Topics](/topics/index.md) have detailed information " -"about the most common topics for CWL." +"If you are a beginner user get started with the [Introduction](/introduction/" +"index.md) section. For advanced users the subsections of the [Topics](/" +"topics/index.md) have detailed information about the most common topics for " +"CWL." msgstr "" #: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +#: 7274d92e678a440eb0d3ae3109f4157a msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " -"subsections. The right sidebar contains links to the sections of each " -"page, and the Search form is on the left sidebar." +"subsections. The right sidebar contains links to the sections of each page, " +"and the Search form is on the left sidebar." msgstr "" #: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +#: 6ad5f2d254a24ac1b3faf382d08b58aa msgid "Table of Contents" msgstr "" #: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +#: 7208cbccb84d45d58c7d5becec74b7d3 msgid "Basic Concepts" msgstr "" #: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +#: 8b9809abb49840b195a89943ba15f78a msgid "" "This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are " -"expected to be familiar with workflow managers, YAML, and comfortable " -"with following instructions for the command-line. The other sections of " -"the user guide cover the same concepts, but in more detail. If you are " -"already familiar with CWL or you are looking for more advanced content, " -"you may want to skip this section." +"working with Common Workflow Language (CWL) workflows. Readers are expected " +"to be familiar with workflow managers, YAML, and comfortable with following " +"instructions for the command-line. The other sections of the user guide " +"cover the same concepts, but in more detail. If you are already familiar " +"with CWL or you are looking for more advanced content, you may want to skip " +"this section." msgstr "" #: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +#: 9a934bf0848b438aaef7c4f00e0f2901 msgid "The CWL Specification" msgstr "" #: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +#: 5a299600dc304fd886b7153de1a706f7 msgid "" "The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered " -"in this user guide is the {{ cwl_version }}." +"community. The specification has different versions. The version covered in " +"this user guide is the {{ cwl_version }}." msgstr "" #: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +#: 55f7696f07d64277ad1b39d283175b37 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" "incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes " -"that are backward-compatible. The last number is used for bug fixes, like" -" typos and other corrections to the specification." +"number is the minor release, used for new features or smaller changes that " +"are backward-compatible. The last number is used for bug fixes, like typos " +"and other corrections to the specification." msgstr "" #: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +#: b854ca0af98347d2b66e74754eb92a50 msgid "" -"The model used for the specification version is called Semantic " -"Versioning. See the end of this section to [learn more](#learn-more) " -"about it." +"The model used for the specification version is called Semantic Versioning. " +"See the end of this section to [learn more](#learn-more) about it." msgstr "" #: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +#: d9785269c51e4902bf3a70e917d33238 msgid "Implementations" msgstr "" #: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +#: b57a31b8d26545d1823fcd1fa2c83316 msgid "" -"An implementation of the CWL specification is any software written " -"following what is defined in a version of the specification document. " -"However, implementations may not implement every aspect of the " -"specification. CWL implementations are licensed under both Open Source " -"and commercial licenses." +"An implementation of the CWL specification is any software written following " +"what is defined in a version of the specification document. However, " +"implementations may not implement every aspect of the specification. CWL " +"implementations are licensed under both Open Source and commercial licenses." msgstr "" #: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +#: 4e264b1a40bd4935abb5bdeb75fa5c64 msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud" -" and high performance computing environments where tasks are scheduled in" -" parallel across many nodes." +"CWL is well suited for describing large-scale workflows in cluster, cloud " +"and high performance computing environments where tasks are scheduled in " +"parallel across many nodes." msgstr "" #: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +#: 791b02bb1ee6459d8d8332fc2dee353c msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: a5ebc727fb3443f78e81d6b7ed5ac750 17300bbe695044e7b8917d23bd0aa597 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 +#: 86e6a06992dc4228bfda7add48e28ca3 526614f195614818a614fc9a576e7cb5 msgid "" -"A process is a computing unit that takes inputs and produces outputs. The" -" behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification" -" {{ cwl_version }}:" +"A process is a computing unit that takes inputs and produces outputs. The " +"behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification " +"{{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 8c9772f96caf4169924d22eb929a4f0f 7b47991653054f2d9f49a91720754abf msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 4fac209a62114798b79e4810f7a0148b aa8838c0ee0a4b4285cb1b5dc6eb5d31 msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: b97ba368fd664caab0494e2392795697 457c73a37cb143d98005ebf6e67f5bf1 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: 903a6796e3304a19ad885b2428b0e80f c28057f3b7814f8395dbc3ad54d5f6f9 msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 6e352ac1f8e144c392ac5adf18c28298 83afed0785cd4b0bb86863c2841ce982 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a +#: cf2922f645904ac7955428ecddc37b8a f332864bcc1e49d582a82f3d721ff3cf msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 +#: 5f47aae608c041aeb4134d59dad314d2 3005c6d669de412ab7f8e30d00752a20 msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be " -"used to simplify workflows and command-line tools, moving common parts of" -" a workflow execution into reusable JavaScript code that takes inputs and" -" produces outputs like a command-line tool." +"An expression tool is a wrapper for a JavaScript expression. It can be used " +"to simplify workflows and command-line tools, moving common parts of a " +"workflow execution into reusable JavaScript code that takes inputs and " +"produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef +#: f6f589481d0c4891beaccb63160619ef 2e4041cb402e4054a53ea5890b938ac1 msgid "" -"Operation is an abstract process that also takes inputs, produces " -"outputs, and can be used in a workflow. But it is a special operation not" -" so commonly used. It is discussed in the [Operations " -"section](../topics/operations.md) of this user guide." +"Operation is an abstract process that also takes inputs, produces outputs, " +"and can be used in a workflow. But it is a special operation not so commonly " +"used. It is discussed in the [Operations section](../topics/operations.md) " +"of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 972f9a1e64394a63be3258d3af0b1d79 msgid "" -"The workflow is a process that contains steps. Steps can be other " -"workflows (nested workflows), command-line tools, or expression tools. " -"The inputs of a workflow can be passed to any of its steps, while the " -"outputs produced by its steps can be used in the final output of the " -"workflow." +"The workflow is a process that contains steps. Steps can be other workflows " +"(nested workflows), command-line tools, or expression tools. The inputs of a " +"workflow can be passed to any of its steps, while the outputs produced by " +"its steps can be used in the final output of the workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 +#: 4ace6b92f4e04a07aa202840ebe36417 a572f0789084402fb2d216ac845bbfdb msgid "" "The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through " -"*requirements*. There are many requirements defined in the CWL " -"specification, for instance:" +"functionality and specify prerequisites to workflows through *requirements*. " +"There are many requirements defined in the CWL specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 c7c5c9a1e98e47c0a5a6dfa69e96f921 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 +#: 2d9f53b6ed5041dbb6c0b54835897856 357d42768e794286bf5463ca5850a7ed msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 +#: 907674a4ecff4826a2b880e28fc38f33 61966aab989744c1b9b93f7751f35ebc msgid "" -"`InitialWorkDirRequirement` - controls staging files in the input " -"directory." +"`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee +#: 037cd0e5ceda482eaeaca03d51745aee e14a2082d2c44f3690a07d3cee5b13d1 msgid "" -"Some CWL runners may provide requirements that are not in the " -"specification. For example, GPU requirements are supported in `cwltool` " -"through the `cwltool:CUDARequirement` requirement, but it is not part of " -"the {{ cwl_version }} specification and may not be supported by other CWL" -" runners." +"Some CWL runners may provide requirements that are not in the specification. " +"For example, GPU requirements are supported in `cwltool` through the " +"`cwltool:CUDARequirement` requirement, but it is not part of the " +"{{ cwl_version }} specification and may not be supported by other CWL " +"runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e +#: e4643938445b48cc80eb8973ceeb126e c128a76992e04d20bcc3edae8b6c0bc0 msgid "" -"Hints are similar to requirements, but while requirements list features " -"that are required, hints list optional features. Requirements are " -"explained in detail in the [Requirements](../topics/requirements-and-" -"hints.md) section." +"Hints are similar to requirements, but while requirements list features that " +"are required, hints list optional features. Requirements are explained in " +"detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: c4c3315c96714e81b364f8cc003b87e6 42953a3d591c48c6b4e80e9ea4b97bb3 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 +#: 3eb6a013a2a4478ca2ad134661f65c58 e3762a763ba24571a9627efafe172441 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " "machine accessibility and that all digital assets should be Findable, " "Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created." -" It is thus important that workflows support the creation of FAIR data " -"and adhere to the FAIR principles. — [FAIR Computational " -"Workflows](https://workflows.community/groups/fair/), Workflows Community" -" Initiative." +"which the scientific process is conducted and via which data are created. It " +"is thus important that workflows support the creation of FAIR data and " +"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" +"workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a +#: 074af9633627470485e5225326d5f20a be8e01a012ed45d6b7e4e6aab1afcc32 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\"," -" CWL tasks are isolated, and you must be explicit about your inputs and " +"execution, based on dependencies between tasks. However, unlike \"make\", " +"CWL tasks are isolated, and you must be explicit about your inputs and " "outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee +#: 847951c055b94a83b1e081594cef22ee cf31aca4294d486cb0e25c6436996d17 msgid "" -"The benefit of explicitness and isolation are flexibility, portability, " -"and scalability; tools and workflows described with CWL can transparently" -" leverage technologies such as Docker and be used with CWL " -"implementations from different vendors." +"The benefit of explicitness and isolation are flexibility, portability, and " +"scalability; tools and workflows described with CWL can transparently " +"leverage technologies such as Docker and be used with CWL implementations " +"from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: 44bde1fae06b4678bcac4f3224601296 cc7adbdc66df4aeaad1429f7268c90c0 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" @@ -738,264 +809,306 @@ msgstr "" #: ../../src/introduction/prerequisites.md:196 #: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 #: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf +#: 71beb059c9e54a9ab5430f0dc44e07ea 84679c5b03a3469294de849d9abe0a82 +#: fd690fdd46344e0e8d9fc546f6d4013b msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 9d5100c7d0a040aea1020bf633ad17de 89ddaddb64f64b0c86c7e89da0edfaae msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 +#: 36eb4b3b966640af90faa55db3789cb6 e920a824207746ffae63242d33137ac7 msgid "" -"The CWL Specification page in the CWL website: " -"" +"The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 +#: 2ccb956baa6b4376a04ad9fcc4654631 51d619152aa44651889ff2006c8f5800 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 +#: 72889b830c514afe9a7cb1e64b5666a0 88f3f5dd8aa6401793b89e8de3b8c7a7 msgid "" -"The list of Implementations in the CWL website: " -"" +"The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: e29bd7f973544600be589c3b3f84cf63 f1f9ee90d07c4381a8bb0851bdac231e msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b +#: c377a7f5dbe645cebbb6c7eccf831a0b e3b710dabec2482d8ec1072d64d4e1f8 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" #: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +#: 418699fcb6c241dcbeeed81d82e9f84f msgid "Introduction" msgstr "" #: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +#: 28b6521a55aa4ab190ca998a59c52609 msgid "" "This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that" -" are useful to know before reading the rest of the user guide." +"prerequisites for following this user guide, and some basic concepts that " +"are useful to know before reading the rest of the user guide." msgstr "" #: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +#: 0e4969399eda48b98d883a3fc1540633 msgid "Prerequisites" msgstr "" #: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +#: 6d59f082157b494ebcfff2f649abc524 msgid "" -"The software and configurations listed in this section are prerequisites " -"for following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements " -"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" -"compatible runner or workflow system, but the results and interface may " -"look different (though the exact workflow outputs should be identical)." +"The software and configurations listed in this section are prerequisites for " +"following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements focuses " +"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " +"runner or workflow system, but the results and interface may look different " +"(though the exact workflow outputs should be identical)." msgstr "" #: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +#: 2b83beccbc1b43969b705156b9c29482 msgid "CWL Implementations" msgstr "" #: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +#: 594fe5e0aaf0499ebfa9218aaad4d08d msgid "" -"There are many implementations of the CWL standards. Some are complete " -"CWL runners, while others could be plug-ins or extensions to workflow " -"engines. We have a better explanation in the [Implementations](basic-" -"concepts.md#implementations) section." +"There are many implementations of the CWL standards. Some are complete CWL " +"runners, while others could be plug-ins or extensions to workflow engines. " +"We have a better explanation in the [Implementations](basic-concepts." +"md#implementations) section." msgstr "" #: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +#: f69c7c75a36048f5af0ed1b56df9320d msgid "Operating System" msgstr "" #: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +#: f28638ffb8394ccead4ac52f30adc627 msgid "" -"We recommend using an up-to-date operating system. You can choose any of " -"the following options for your operating system:" +"We recommend using an up-to-date operating system. You can choose any of the " +"following options for your operating system:" msgstr "" #: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +#: 8993d7d5c8d24fc5a9c7005800c0a1f1 msgid "Linux" msgstr "" #: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +#: 2073109799e748d68304f5558c82b105 msgid "macOS" msgstr "" #: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +#: 9fb2c31bd36d495786397c7a7d6b3417 msgid "Windows" msgstr "" #: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +#: 43e1957537034c5886574118fc2533da msgid "" -"If you are using Windows, you will have to install the [Windows Subsystem" -" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " -"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" -"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " -"details on installing WSL2. Your operating system also needs internet " -"access and a recent version of Python (3.6+)." +"If you are using Windows, you will have to install the [Windows Subsystem " +"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " +"installing WSL2. Your operating system also needs internet access and a " +"recent version of Python (3.6+)." msgstr "" #: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +#: e3a3d9b94b1e44c48f298dfcdcd27104 msgid "CWL Runner" msgstr "" #: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +#: 8a385803ed3945ff81d38a3543a69d94 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL " -"community. It is also the CWL reference runner, which means it must " -"support everything in the current CWL specification, {{ cwl_version }}." +"`cwltool` is a Python Open Source project maintained by the CWL community. " +"It is also the CWL reference runner, which means it must support everything " +"in the current CWL specification, {{ cwl_version }}." msgstr "" #: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +#: bf56727d93994d3995b0af0c68c2c583 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " -"environment like `venv` or `conda`. The following commands will create " -"and activate a Python virtual environment using the `venv` module, and " -"install `cwltool` in that environment:" +"environment like `venv` or `conda`. The following commands will create and " +"activate a Python virtual environment using the `venv` module, and install " +"`cwltool` in that environment:" msgstr "" #: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +#: 9a959bd914d543b78f9625f03df95765 msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" #: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +#: 198ce7d893a04fcb806ec1671838d588 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool#install) for other ways to install `cwltool` with `apt` " -"and `conda`." +"language/cwltool#install) for other ways to install `cwltool` with `apt` and " +"`conda`." msgstr "" #: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +#: cc2be8feeab54a22a0b64a2a72991003 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +#: 749c672e8c234c1c9a5eb2cc9b77c4e3 msgid "`true.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +#: 29c64936318a4a2ba882e1eae8f03f57 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the " -"CWL standards. However, these actions will be performed without running " -"the document. To validate CWL workflows (or even a standalone command " -"line tool description like the above) pass the `--validate` option to the" -" `cwltool` command:" +"errors, and verify that the workflow descriptions are compliant with the CWL " +"standards. However, these actions will be performed without running the " +"document. To validate CWL workflows (or even a standalone command line tool " +"description like the above) pass the `--validate` option to the `cwltool` " +"command:" msgstr "" #: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +#: 44106744147f45bab675eb66148531c7 msgid "Validating `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 -msgid "You can run the CWL tool description by omitting the `--validate` option:" +#: 6d84c6890f564b4baf7b34f6a52cbfc4 +msgid "" +"You can run the CWL tool description by omitting the `--validate` option:" msgstr "" #: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +#: 7eb67993e8ca48dc929e1a992f78cb39 msgid "Running `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: 52886c54c3c54b83896c52ebd7d53fad msgid "Cwl-runner Python Module" msgstr "" #: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +#: 097945c33f7542e2bae2e9f7ba1cf84d msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be " -"invoked independently, and is not reliant on a particular CWL runner " -"program name. Users can invoke `cwl-runner` instead of invoking a CWL " -"runner like `cwltool` directly. The `cwl-runner` is installed by a system" -" administrator or user to point to the preferred CWL implementation. This" -" is convenient for environments with multiple CWL runners." +"runner. This simply means that the `cwl-runner` alias command can be invoked " +"independently, and is not reliant on a particular CWL runner program name. " +"Users can invoke `cwl-runner` instead of invoking a CWL runner like " +"`cwltool` directly. The `cwl-runner` is installed by a system administrator " +"or user to point to the preferred CWL implementation. This is convenient for " +"environments with multiple CWL runners." msgstr "" #: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +#: 3853bfc6a85747019c615a50c7ca6b40 msgid "" -"The CWL community publishes a Python package with the name `cwlref-" -"runner` that installs an alias for `cwltool` under the name `cwl-runner`" +"The CWL community publishes a Python package with the name `cwlref-runner` " +"that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" #: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +#: 662230f538504f44941c6f4801f6251c msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" #: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +#: 1c9eb9e2bb9e40a9985ada16c34eea2d msgid "" -"Now you can validate and run your workflow with the `cwl-runner` " -"executable, which will invoke `cwltool`. You should have the same results" -" and output as in the previous section." +"Now you can validate and run your workflow with the `cwl-runner` executable, " +"which will invoke `cwltool`. You should have the same results and output as " +"in the previous section." msgstr "" #: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +#: 7f53ba159979461393c0f278fe97fb30 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +#: 7e8077c2dd584eda89ead60ecc5eabf3 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +#: 1787a3c749ee48218b87c8401f6255d7 msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For" -" that, the first thing you need to do is copy `true.cwl` workflow into a " -"new file: `true_shebang.cwl`, and include a special first line, a " -"*shebang*:" +"Another way to execute `cwl-runner` is by invoking the file directly. For " +"that, the first thing you need to do is copy `true.cwl` workflow into a new " +"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" #: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: a52ca4ce9a184e938c3a5cac9cb882ca msgid "`true_shebang.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +#: 41d3287a9a774a73aefd49bd709764bf +msgid "" +"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" #: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +#: 3b9d30094611400b85b55db163cb303e msgid "Making `true.cwl` executable." msgstr "" #: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +#: b6ea77357b4f45528ed1379f8fe67cfd msgid "" -"And finally, you can execute it directly in the command-line. On " -"execution, the program specified in the shebang (`cwl-runner`) will be " -"used to execute the rest of the file." +"And finally, you can execute it directly in the command-line. On execution, " +"the program specified in the shebang (`cwl-runner`) will be used to execute " +"the rest of the file." msgstr "" #: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +#: 8797ce327d7443fdb3d4617d3fc2cf7f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" #: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +#: 896b6896b1e44d0cab5f35e7d0dd88e3 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute " -"the script using the executable specified after the shebang. It is " -"considered a good practice to use `/usr/bin/env ` rather than" -" using a hard-coded location, since `/usr/bin/env ` looks for" -" the `` program in the system `PATH`," +"script. When the script is executable, the operating system will execute the " +"script using the executable specified after the shebang. It is considered a " +"good practice to use `/usr/bin/env ` rather than using a hard-" +"coded location, since `/usr/bin/env ` looks for the " +"`` program in the system `PATH`," msgstr "" #: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +#: 4b839d23d72f4d3fbe4f1ce7e568b20b msgid "Text Editor" msgstr "" #: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +#: a42b9ab315b5402493e4ce0067d0a18e msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " @@ -1003,379 +1116,429 @@ msgid "" msgstr "" #: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +#: 2f63483960634a7782f95e9e2feaa5a6 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting" -" and better auto-complete:" +"integration with CWL, and features such as customized syntax highlighting " +"and better auto-complete:" msgstr "" #: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +#: 3471105073204d7998aaf790b73f785d msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " -"" +"Visual Studio Code with the Benten (CWL) plugin - " msgstr "" #: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +#: 0b8b47511b5e4296b7438be0ad2604ed msgid "" -"cwl-plugin for IntelliJ - " +"cwl-plugin for IntelliJ - " msgstr "" #: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +#: 3e3eec00f23f4f21873ddb005204a875 msgid "" -"The CWL community also maintains a list of editors and viewers: " -"" +"The CWL community also maintains a list of editors and viewers: " msgstr "" #: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +#: 2ceb25f2668442839e3e9f4512772a03 msgid "Docker" msgstr "" #: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +#: 20c753c5371b43ed834fa741b0ce7692 msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: " -"." +"documentation to install it for your operating system: ." msgstr "" #: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +#: a19c4fc9fa404912a0389337536d9c25 msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models " -"with and without containers." +"examples, and to clarify the differences between the execution models with " +"and without containers." msgstr "" #: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +#: a0f38c1e28ca4850b3986617625acbf2 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for " -"pulling images." +"Singularity. You can also use alternative container registries for pulling " +"images." msgstr "" #: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +#: 37e1162f30894a1ca7dada9870ffa3da msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the " -"next section, Basic Concepts." +"The [Implementations](basic-concepts.md#implementations) topic in the next " +"section, Basic Concepts." msgstr "" #: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +#: 1c25a51edf6f47c5979c721b19cf11b5 msgid "The Python `venv` module: " msgstr "" #: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +#: ace930cf878d45a99f12b71bf0987a87 msgid "Quick Start" msgstr "" #: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +#: 46587a5e0d534af5867ae4f70a116bee msgid "" -"This section will show you a brief overview of what CWL is, and where you" -" can learn more about it. No previous knowledge of CWL is required, but " -"you must be comfortable following instructions for the command-line." +"This section will show you a brief overview of what CWL is, and where you " +"can learn more about it. No previous knowledge of CWL is required, but you " +"must be comfortable following instructions for the command-line." msgstr "" #: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +#: a0774d4e779e46f7a983922425203066 msgid "“Hello World”" msgstr "" #: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +#: 1658ee6f3cac4d04afc732aa758b1f48 msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " -"The example below shows a simple CWL “Hello World” workflow annotated " -"with comments. Note that comments start with `#`:" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " +"example below shows a simple CWL “Hello World” workflow annotated with " +"comments. Note that comments start with `#`:" msgstr "" #: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +#: d8e2bc671b894f3fa8a091261754c728 msgid "`hello_world.cwl`" msgstr "" #: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +#: 683a469bf4824c64a8ea32e048d5df73 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the" -" same result as the command-line `echo \"Hello World\"`." +"Running the workflow above with the default input values will produce the " +"same result as the command-line `echo \"Hello World\"`." msgstr "" #: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +#: b7c50413f7864a86815f3b581561cdb5 msgid "" -"In CWL, there is a distinction between a command-line tool and a " -"workflow. But for the sake of simplicity, we are using the term " -"“workflow” here. You will learn more about this in the [basic concepts" -"](basic-concepts.md) section." +"In CWL, there is a distinction between a command-line tool and a workflow. " +"But for the sake of simplicity, we are using the term “workflow” here. You " +"will learn more about this in the [basic concepts](basic-concepts.md) " +"section." msgstr "" #: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +#: d2ed66bdfcab4f7dad95b00c95d4a3d6 msgid "Installing a CWL Runner" msgstr "" #: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +#: 4dcbe776a70645e5a6c7513348fa6bee msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the " -"CWL *Reference Runner* for the specification, and it is compliant with " -"the latest version of the specification: {{ cwl_version }}. You can " -"install `cwltool` using `pip`:" +"`cwltool` is an implementation of the CWL specification. It is also the CWL " +"*Reference Runner* for the specification, and it is compliant with the " +"latest version of the specification: {{ cwl_version }}. You can install " +"`cwltool` using `pip`:" msgstr "" #: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +#: bae5b03fb74541e6ad79277a576e0516 msgid "Installing `cwltool` with `pip`." msgstr "" #: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +#: 8ff0d7a8d37b48488e4504ff8e3adcc5 msgid "" -"If installing the cwltool using the pip command doesn't work for you, the" -" [prerequisites](prerequisites.md) section contains other ways to install" -" `cwltool` and a more detailed list of software and libraries used for " +"If installing the cwltool using the pip command doesn't work for you, the " +"[prerequisites](prerequisites.md) section contains other ways to install " +"`cwltool` and a more detailed list of software and libraries used for " "following the rest of this user guide." msgstr "" #: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +#: 6255b499b9b144128afaeed64fabe8e5 msgid "Running \"Hello World\"" msgstr "" #: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +#: e861db9c43ed4b8ba262af8e435a350a msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [INPUTS_OBJECT]`. You can run the " -"`hello_world.cwl` workflow without specifying any option:" +"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " +"workflow without specifying any option:" msgstr "" #: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +#: c6318f06bcd74cda8c1f0caef9452b51 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +#: c862e745217244d28cd4c2f0842e203f msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" #: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +#: eba007736b92434a9711f683e64bb153 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" #: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +#: aebc2caf5d1b47f1b7cc0aa53e5a684e msgid "" -"Another way of passing values to your workflow input parameters is via an" -" *Inputs Object*. This is a file containing the input fields with their " +"Another way of passing values to your workflow input parameters is via an " +"*Inputs Object*. This is a file containing the input fields with their " "corresponding values. The Inputs Objects file can be written in JSON or " "YAML. For example:" msgstr "" #: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +#: 1242171f8b854562bb7848b06d2d065d msgid "`hello_world-job.json`" msgstr "" #: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +#: 24e82ecf7926428386a89f18a34eb00c msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" #: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +#: 00e75efe03554835bc33ebaed0652626 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +#: 4ba34ec455704844a9cfcbac3522ea0c msgid "" "We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but " -"it is not a requirement. You can choose any name for your workflows and " -"Inputs Object files." +"files. The *-job.json* suffix is very common in Inputs Object files, but it " +"is not a requirement. You can choose any name for your workflows and Inputs " +"Object files." msgstr "" #: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +#: c0e9673440db454bb51af04432aeddbb msgid "Continue reading the next sections of this User Guide!" msgstr "" #: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +#: 39a23a9d02ab4bccb36d6a714639509b +msgid "" +"[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" #: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +#: 23a878e0166b40d78984a2263f63b760 msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" #: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +#: 5d9c435820674bf4b1c5d3fef5df736d msgid "" -"[Common Workflow Language at " -"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." msgstr "" #: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +#: e724ee53db1940b9b09a909f4db531a4 msgid "" -"[YAML.org](http://yaml.org/) and [YAML at " -"Wikipedia](https://en.wikipedia.org/wiki/YAML)." +"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." +"org/wiki/YAML)." msgstr "" #: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +#: 7820eb801a8145feb603145f153263b9 msgid "" -"The {{'[CWL Specification " -"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " -"cwl_version_text) }}." +"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." +"replace('VERSION', cwl_version_text) }}." msgstr "" #: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +#: e8db3f10be294f13abe3a4418bbae4b6 msgid "" -"[Workflow management system at " -"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." msgstr "" #: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +#: 95211ea6924148a6a1fa5ae8facc2c7b msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. The information on this page has been migrated to the " -"[FAQ](/faq.md) section of the new user guide." +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. The information on this page has been migrated to the [FAQ](/faq." +"md) section of the new user guide." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 9c87c76c690948ac8e18088a0fffe679 b742a74d586e42e6b0480b7af3e49c9e msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 +#: ad00d94d4fb64bbdac356e64dd3803b9 cd3da03d43044ec9843e476a54e704be msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf +#: d8110ed19da94ad8a9f56e7006c4a2cf 0d48e2f07d784504a17cad0ae20262c2 msgid "" "In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files " -"in the same directory as the source file. However, CWL input files (and " -"the directories in which they appear) may be read-only, so we need to " -"instruct \"javac\" to write the class file to the designated output " -"directory instead." +"file to a class file. By default, \"javac\" will create the class files in " +"the same directory as the source file. However, CWL input files (and the " +"directories in which they appear) may be read-only, so we need to instruct " +"\"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: a74935dc31664e979ca8f90a6a4ba53c 4d372b89f0ce451db2a505b1754b8356 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: f357755f6dcb4971bade8636064f8dd1 573e903ef3d34514ab7b20e79c446567 +#: cfb40fbe52174d3799a6bec175db60a5 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: 6359191b4f684d5aa3602e4aaf394883 95841b1c75c84f01bd5fcb7cf3afe78d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb +#: 9643449da1da46d7861866dce490cbcb c8bca3654ebb4b29bf3f028b4c65fa35 msgid "" -"And now invoke `cwltool` providing the tool description and the input " -"object on the command line:" +"And now invoke `cwltool` providing the tool description and the input object " +"on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a +#: 713666580a0a4466b4ba6e3eb2b54f0a 1432105e38014a6d9d0cf80007141007 msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 +#: d50574c8b9694f83aa376d39b9a6fcd6 bcad473b34ec43f7906253123a1661fa msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include " -"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " -"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " -"Environment][runtime] section of the CWL specification for details." +"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" +"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." +"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " +"specification for details." msgstr "" #: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +#: e1c8949e663b4debaf87735f1d62a2fc msgid "Best Practices" msgstr "" #: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +#: dcc991b647d34ffc8ea3bf9c3a38258d msgid "" -"The following are a set of recommended good practices to keep in mind " -"when writing a Common Workflow Language description for a tool or " -"workflow. These guidelines are presented for consideration on a scale of " -"usefulness: although more is better, not all are required." +"The following are a set of recommended good practices to keep in mind when " +"writing a Common Workflow Language description for a tool or workflow. These " +"guidelines are presented for consideration on a scale of usefulness: " +"although more is better, not all are required." msgstr "" #: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +#: f26c222638e54187b8bb62fe30b66bc3 msgid "" -"No `type: string` parameters for names of input or reference " -"files/directories; use `type: File` or `type: Directory` as appropriate." +"No `type: string` parameters for names of input or reference files/" +"directories; use `type: File` or `type: Directory` as appropriate." msgstr "" #: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +#: 23720e4ab3d1407597f1d1c2a4d4d90c msgid "" "A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that" -" the usual rules of software licensing apply to this document. For " -"example, if the workflow is shared publicly, licensing terms must be " -"clear so that a future user understands under what conditions they can " -"run the workflow, modify it and/or combine it with other workflows. For " -"this reason, please consider including a license field in the document. " -"The authors of this guide urge you to choose a pre-existing license " -"rather than trying to write your own (see the link below to learn more " -"about choosing a license), and our recommended practice is to choose a " -"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" -"license]." +"`Dockerfile`s) is software code. Workflow developers should be aware that " +"the usual rules of software licensing apply to this document. For example, " +"if the workflow is shared publicly, licensing terms must be clear so that a " +"future user understands under what conditions they can run the workflow, " +"modify it and/or combine it with other workflows. For this reason, please " +"consider including a license field in the document. The authors of this " +"guide urge you to choose a pre-existing license rather than trying to write " +"your own (see the link below to learn more about choosing a license), and " +"our recommended practice is to choose a license that allows for re-use by " +"anyone, e.g. [Apache 2.0][apache-license]." msgstr "" #: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +#: b3638183c59744c897246af7dab5d10e msgid "" -"If possible, the license should be specified with its corresponding [SPDX" -" identifier][spdx]. Construct the metadata field for the license by " -"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " -"`SPDX-ID` is taken from the list of identifiers linked above. See the " -"example snippet below for guidance. For non-standard licenses without an " -"SPDX identifier, provide a URL to the license." +"If possible, the license should be specified with its corresponding [SPDX " +"identifier][spdx]. Construct the metadata field for the license by providing " +"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " +"taken from the list of identifiers linked above. See the example snippet " +"below for guidance. For non-standard licenses without an SPDX identifier, " +"provide a URL to the license." msgstr "" #: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +#: 2c0291133b964ad8b751f8a8ed2338fc msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" #: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +#: 325c8c4058f045aa8fbd705238122798 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" #: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +#: 05333866485b43479352f7ee9326c7fd msgid "" -"For more examples of providing metadata within CWL descriptions, see " -"[the Metadata and Authorship section of this User Guide](../topics" -"/metadata-and-authorship.md)." +"For more examples of providing metadata within CWL descriptions, see [the " +"Metadata and Authorship section of this User Guide](../topics/metadata-and-" +"authorship.md)." msgstr "" #: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +#: f8140ec6e9cc41ee88ec4bde61a44d47 msgid "" -"Include [attribution information][license-example] for the author(s) of " -"the CWL tool or workflow description. Use unambiguous identifiers like " -"[ORCID][orcid]." +"Include [attribution information][license-example] for the author(s) of the " +"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" +"[orcid]." msgstr "" #: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +#: 1d68f50dafaf4cc1851e2d67b3e78603 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +#: b283942434c54456a3f29fbb0960b6c4 msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in " -"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" +"identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" #: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +#: 0b4477c5b0184e59aa0c07161008a7bf msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1384,24 +1547,26 @@ msgid "" msgstr "" #: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +#: 9741651d51f249ffba1820694ab78e92 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +#: 5e76d4a9708244ff91f2587350d684a4 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " -"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" -"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " -"types). For non-bioinformatics tools, use or build an appropriate " -"ontology/controlled vocabulary in the same way. Please edit this page to " -"let us know about it." +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" +"$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " +"[Full IANA media type list][iana-types] (also known as MIME types). For non-" +"bioinformatics tools, use or build an appropriate ontology/controlled " +"vocabulary in the same way. Please edit this page to let us know about it." msgstr "" #: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +#: 89e7028e55b54f968e87b9c1c3caeecf msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " @@ -1409,158 +1574,175 @@ msgid "" msgstr "" #: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +#: 88e2338fb2614ef29dc497d8c01a2f2f msgid "" -"Each `CommandLineTool` description should focus on a single operation " -"only, even if the (sub)command is capable of more. Don't overcomplicate " -"your tool descriptions with options that you don't need or use." +"Each `CommandLineTool` description should focus on a single operation only, " +"even if the (sub)command is capable of more. Don't overcomplicate your tool " +"descriptions with options that you don't need or use." msgstr "" #: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +#: 0f3aad35924344659eb5a6719ab2b8f0 msgid "" -"Custom types should be defined with one external YAML per type definition" -" for re-use." +"Custom types should be defined with one external YAML per type definition " +"for re-use." msgstr "" #: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +#: 877cbb1d537b46d3b6d05b2d8c025e70 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" #: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +#: 5c0debbc1c1b428ebb32b589b99fe17d msgid "" -"If useful, include a top-level `doc` as well. This should provide a " -"longer, more detailed description than was provided in the top-level " -"`label` (see above)." +"If useful, include a top-level `doc` as well. This should provide a longer, " +"more detailed description than was provided in the top-level `label` (see " +"above)." msgstr "" #: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +#: 1ff97183191240edb98f0cc365cc028b msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list" -" of valid values." +"Use `type: enum` instead of `type: string` for elements with a fixed list of " +"valid values." msgstr "" #: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +#: 22f7725deb07422fa0a7bc2e6f01e4d0 msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. " -"One common example: manipulating `File` names and paths? Consider whether" -" one of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc., could be used instead." +"Evaluate all use of JavaScript for possible elimination or replacement. One " +"common example: manipulating `File` names and paths? Consider whether one of " +"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc., could be used instead." msgstr "" #: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +#: 982313839ccc4f5a8527fe9a854c78eb msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" #: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +#: 267c9d10ab5e4b6c8a6104952deb1690 msgid "" -"Complex workflows with individual components which can be abstracted " -"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" -" their workflow modular and allow sections of them to be easily reused." +"Complex workflows with individual components which can be abstracted should " +"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " +"workflow modular and allow sections of them to be easily reused." msgstr "" #: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +#: 2eff0eec58c94f4d8986a4cb91b14b8e msgid "" "Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics" -" software\"][containers] (also useful to other disciplines)." +"[\"Recommendations for the packaging and containerizing of bioinformatics " +"software\"][containers] (also useful to other disciplines)." msgstr "" #: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +#: f38db701740b442c89ce58e937bd35c5 msgid "Command Line Tool" msgstr "" #: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +#: 034aac9e186645e384c28bb2a739cfff msgid "" -"A command-line tool is a type of Process object that can be run by itself" -" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " -"`tar`, etc. The command-line tool is defined in the `baseCommand` " -"attribute of the command-line tool CWL document." +"A command-line tool is a type of Process object that can be run by itself or " +"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " +"etc. The command-line tool is defined in the `baseCommand` attribute of the " +"command-line tool CWL document." msgstr "" #: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +#: 5f835cdfc0ae4f378d8dad6ae7ab1855 msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The " -"following example contains a minimal example of a CWL command-line tool " -"for the `echo` Linux command, using inputs and outputs." +"A CWL command-line tool must also have `inputs` and `outputs`. The following " +"example contains a minimal example of a CWL command-line tool for the `echo` " +"Linux command, using inputs and outputs." msgstr "" #: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +#: 02900cb8ae4c4da89d264b76a984d6cd msgid "CWL command-line tool." msgstr "" #: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +#: 753e48d6dfd54a88a12773b996f182d7 msgid "`echo.cwl`" msgstr "" #: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +#: c7ed6d1654c54bf390e933ef0f847b99 msgid "" -"The example above uses a simplified form to define inputs and outputs. " -"You will learn more about in the [Inputs](../topics/inputs.md) and in the" -" [Outputs](../topics/outputs.md) sections." +"The example above uses a simplified form to define inputs and outputs. You " +"will learn more about in the [Inputs](../topics/inputs.md) and in the " +"[Outputs](../topics/outputs.md) sections." msgstr "" #: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +#: 0a0f855ce34449a0a37c036105c65839 msgid "Network Access" msgstr "" #: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +#: c4300454f49548f49e4bd186192515a1 msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network " -"access. If a command-line tool is written manually in CWL v1.1+, there is" -" a need to specify when network access is required." +"This indicates whether a process requires outgoing IPv4/IPv6 network access. " +"If a command-line tool is written manually in CWL v1.1+, there is a need to " +"specify when network access is required." msgstr "" #: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +#: f985d58070de4c0fb5f5a491fd4dc31c msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " -"Network Access automatically." +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " +"Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b 2f4e2c85677a4e56a35b6bef36d67334 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d +#: 0cf51b6da6884065ae42032abc20eb0d 13c6d5600a30406c81ffa25ce42eb0c8 msgid "" -"Sometimes you need to create a file on the fly from input parameters, " -"such as tools that expect to read their input configuration from a file " -"rather than the command line parameters, or need a small wrapper shell " -"script." +"Sometimes you need to create a file on the fly from input parameters, such " +"as tools that expect to read their input configuration from a file rather " +"than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff +#: 2df3a3a9094d4b79b1d5dd99195f3bff 3bf773b8560e44a3a37c68b6fcdc6a23 msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: d3f74c3b094a427fbec831afab657d50 68b8578d2f6442929941ed2522b218ad msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df +#: cfffc518ba6e4ed1a80762ed6f7d25df 755149ed46c348c2b723b49c3b3152a8 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the " -"value at the input `message`." +"expanded by the CWL engine before creating the file. Here, insert the value " +"at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 +#: 9454a330b9324744b89448f2694b1b03 54b7ff590d52454eb87d9f23fca44501 msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later" -" during command line tool invocation. That means that any genuine need " -"for the character `$` must be **escaped** with `\\`. For instance, " -"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " -"be evaluated by the shell script instead of the CWL engine." +"The _CWL expressions_ are independent of any _shell variables_ used later " +"during command line tool invocation. That means that any genuine need for " +"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " +"above is expanded to `${PREFIX}` in the generated file to be evaluated by " +"the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa +#: 7f8d99a30b644457a62ac1523d0c72aa a7c74a4a74c9414e9f29fa20bab7e295 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1569,32 +1751,33 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 #: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb -#: ca03defa3ad14cf698171cb09e3055c1 +#: ca03defa3ad14cf698171cb09e3055c1 0cbf233379024800bcebb963e0a3eb6f +#: ae3bc02e4f3b404c89f3c461a62c5bc4 dc32a2bacf2d4c8cb841be6eb8b839ad msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d +#: 10d1373bb14a4a3cacd3b92a2f83382d 34a56bc23af44353a003ee295fb2c609 msgid "" -"Before we run this, let us look at each step in a little more detail. The" -" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"Before we run this, let us look at each step in a little more detail. The " +"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " "command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c +#: 70e257091bdb456e8957f90a8fa90e8c c7855ec1f09d4945afcb0aec22567b31 msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " -"YAML array, we need a `-` on the first line of each element of the array," -" in this case we have just one element. `entryname:` can have any value, " -"but it must match what was specified in the `baseCommand`. The final part" -" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " -"means that you are using a multiline string (without it, we would need to" -" write the whole script on one line)." +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " +"array, we need a `-` on the first line of each element of the array, in this " +"case we have just one element. `entryname:` can have any value, but it must " +"match what was specified in the `baseCommand`. The final part is `entry:`, " +"this is followed by `|-` which is YAML quoting syntax, and means that you " +"are using a multiline string (without it, we would need to write the whole " +"script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 +#: 1741804e33aa43ce88b4320c11ae5973 5c60492e27014735bb9a86307ee654d6 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1606,221 +1789,258 @@ msgstr "" #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 #: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f #: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 -#: f924d65fed0c4cb5b0a019b084a8b535 +#: f924d65fed0c4cb5b0a019b084a8b535 80a9c04358e64ca28ef4879ad74ef733 +#: a2b470f06ad94871970b7d95339fd369 dc65b4b5e48e48a6ada03da0fac18a51 +#: ea2360c5286b43ccabac202dfa97fbe7 ee4ca94dadf64ab69a70b6cd4eaf451a msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line:" msgstr "" #: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +#: 285d23ef9bbc46c9890ae7957d487c12 msgid "Custom Types" msgstr "" #: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +#: 3edd322daad940d8957f88a2637876b5 msgid "" -"Sometimes you may want to write your own custom types for use and reuse " -"in CWL descriptions. Use of such custom types can reduce redundancy " -"between multiple descriptions that all use the same type, and also allow " -"for additional customisation/configuration of a tool/analysis without the" -" need to fiddle with the CWL description directly." +"Sometimes you may want to write your own custom types for use and reuse in " +"CWL descriptions. Use of such custom types can reduce redundancy between " +"multiple descriptions that all use the same type, and also allow for " +"additional customisation/configuration of a tool/analysis without the need " +"to fiddle with the CWL description directly." msgstr "" #: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +#: a1bd9b0dfa234e6caa6a684e981d89b5 msgid "" -"The example below is a CWL description of the [biom convert format][biom]" -" tool for converting a standard biom table file to hdf5 format." +"The example below is a CWL description of the [biom convert format][biom] " +"tool for converting a standard biom table file to hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +#: 0aeacb6ac20f4ebca3600425ca32f5f4 msgid "`custom-types.cwl`" msgstr "" #: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +#: 1c813ebce2904f008b5b33656f673ebc msgid "`custom-types.yml`" msgstr "" #: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +#: cc36359e94c841d3aa5cbb26a094e1d5 msgid "" -"___Note:___ To follow the example below, you need to [download the " -"example input file](https://github.com/common-workflow-" -"language/user_guide/blob/main/src/_includes/cwl/custom-" -"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " -"`wget`:" +"___Note:___ To follow the example below, you need to [download the example " +"input file](https://github.com/common-workflow-language/user_guide/blob/main/" +"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " +"*rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" #: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +#: dc79668b05e8439591a0beb4b57acc66 msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to " -"be used in the table conversion are imported as a custom object:" +"On line 29, in `inputs:table_type`, a list of allowable table options to be " +"used in the table conversion are imported as a custom object:" msgstr "" #: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +#: 08aba4f77aa442d4a34aa1535f78c49e msgid "" -"The reference to a custom type is a combination of the name of the file " -"in which the object is defined (`biom-convert-table.yaml`) and the name " -"of the object within that file (`table_type`) that defines the custom " -"type. In this case the `symbols` array from the imported `biom-convert-" -"table.yaml` file define the allowable table options. For example, in " -"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" -" to create an OTU table in hdf5 format." +"The reference to a custom type is a combination of the name of the file in " +"which the object is defined (`biom-convert-table.yaml`) and the name of the " +"object within that file (`table_type`) that defines the custom type. In this " +"case the `symbols` array from the imported `biom-convert-table.yaml` file " +"define the allowable table options. For example, in `custom-types.yml`, we " +"pass `OTU table` as an `input` that tells the tool to create an OTU table in " +"hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e -msgid "The contents of the YAML file describing the custom type are given below:" +#: 63431a972f994bccacf55d5fac0d614e +msgid "" +"The contents of the YAML file describing the custom type are given below:" msgstr "" #: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +#: 55e7695aca4f4319b1cf7551105a8782 msgid "`biom-convert-table.yaml`" msgstr "" #: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +#: 0c5ab34ebbf54ff6940b8ce3f080d744 msgid "" -"In order for the custom type to be used in the CWL description, it must " -"be imported. Imports are described in " -"`requirements:SchemaDefRequirement`, as below in the example `custom-" -"types.cwl` description:" +"In order for the custom type to be used in the CWL description, it must be " +"imported. Imports are described in `requirements:SchemaDefRequirement`, as " +"below in the example `custom-types.cwl` description:" msgstr "" #: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +#: f97e18d2d3b946468c4fac227920e011 msgid "" "Note also that the author of this CWL description has also included " -"`ResourceRequirement`s, specifying the minimum amount of RAM and number " -"of cores required for the tool to run successfully, as well as details of" -" the version of the software that the description was written for and " -"other useful metadata. These features are discussed further in other " -"chapters of this user guide." +"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " +"cores required for the tool to run successfully, as well as details of the " +"version of the software that the description was written for and other " +"useful metadata. These features are discussed further in other chapters of " +"this user guide." msgstr "" #: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +#: 62644031403548898ff36addbc0b1f6f msgid "Environment Variables" msgstr "" #: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +#: 595630b0687c4467aa65bfed289281f4 msgid "" -"Tools run in a restricted environment and do not inherit most environment" -" variables from the parent process. You can set environment variables " -"for the tool using `EnvVarRequirement`." +"Tools run in a restricted environment and do not inherit most environment " +"variables from the parent process. You can set environment variables for " +"the tool using `EnvVarRequirement`." msgstr "" #: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +#: 34e005c135864a89a00e817d79118e2e msgid "`env.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +#: b624f9f99c294e6996f212c8b62f20b0 msgid "Expression Tool" msgstr "" #: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +#: 14df63ab847e4efca820f712548cd076 msgid "" -"An expression tool is a type of Process that can be run by itself or as a" -" Workflow step. It executes a pure JavaScript expression. It is meant to " -"be used as a way to isolate complex JavaScript expressions that need to " -"operate on input data and produce some result as output." +"An expression tool is a type of Process that can be run by itself or as a " +"Workflow step. It executes a pure JavaScript expression. It is meant to be " +"used as a way to isolate complex JavaScript expressions that need to operate " +"on input data and produce some result as output." msgstr "" #: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +#: 91d4224b41c6473f936c03bd0ab9d370 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" #: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +#: 519989399dab493ea41941ed85cb9670 msgid "CWL expression tool." msgstr "" #: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +#: 28dd1cf24309404eaf717d417272e094 msgid "`uppercase.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +#: 3f536ad8c86d442c8bbe61777dbb1a54 msgid "" -"We had to use an `InlineJavascriptRequirement` as our expression contains" -" a JavaScript call in `.toUpperCase()`. This means to tools using the " +"We had to use an `InlineJavascriptRequirement` as our expression contains a " +"JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" #: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +#: b9e9894c6d024e60929d020dbaa553f0 msgid "Expressions" msgstr "" #: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +#: 482debe1a40f490b90d4ece1b3f9d732 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " -"legal you can provide a fragment of Javascript that will be evaluated by " -"the CWL runner." +"legal you can provide a fragment of Javascript that will be evaluated by the " +"CWL runner." msgstr "" #: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +#: 708346038be745d097685970cc462f4a msgid "" -"JavaScript expressions should only be used when absolutely necessary. " -"When manipulating file names, extensions, paths etc, consider whether one" -" of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " -"practices](best-practices.md)." +"JavaScript expressions should only be used when absolutely necessary. When " +"manipulating file names, extensions, paths etc, consider whether one of the " +"[built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc, could be used instead. See the [list of best practices](best-" +"practices.md)." msgstr "" #: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: 99347b6b2c404a4b9bbcc96e0b4bd925 msgid "`expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +#: e6629f0914324c76a08fe179575b73d5 msgid "" -"As this tool does not require any `inputs` we can run it with an (almost)" -" empty job file:" +"As this tool does not require any `inputs` we can run it with an (almost) " +"empty job file:" msgstr "" #: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +#: 2287002a87184fb9b95d775a368f0e46 msgid "`empty.yml`" msgstr "" #: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +#: c23d4543d9f949a9a7015fdcbb40dcd0 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object" -" is represented simply by a set of empty brackets." +"descriptions are contained inside curly brackets `{}`, so an empty object is " +"represented simply by a set of empty brackets." msgstr "" #: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +#: c04a9dcc84b84f37bcf32c3790672038 msgid "We can then run `expression.cwl`:" msgstr "" #: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +#: 9f27c79365db455d9d31053576ebe05e msgid "Running `expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +#: a2b3ad1e2c884e24948a915c3305aee1 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" #: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +#: dd7665bbc5e9449588c9539e3c1910de msgid "" "Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" -" describe the additional command line arguments." +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " +"describe the additional command line arguments." msgstr "" #: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +#: 0972c757f7c74ea9beabf6b9ef9dbf4c msgid "Where are JavaScript expressions allowed?" msgstr "" #: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +#: 175de3b9854546568f60a20cc19887de msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" #: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +#: 0c286e5ba1714a059a95b566fe49be31 msgid "" -"From " -"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 -#: 1acb064f7a4a482aa0174bdc847c6382 +#: 1acb064f7a4a482aa0174bdc847c6382 3029c1dfe5424c2b812597b03ea76178 +#: a5503b6c524e4848aa308b0f4c26d774 msgid "`arguments`" msgstr "" @@ -1831,32 +2051,39 @@ msgstr "" #: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e #: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 #: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 0e03befa46c74dc2b09420e1eb2a6fbd +#: 50f81e7ab73a4713bbc60f6f5609b906 718dc3def33c462786174fb42097981f +#: 9c2acd930553458eb105f96213b5d7b0 d4bf86a995d546c0a9159b3f29a84125 +#: e98424244f554c7399e9e7ad560849a6 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 #: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: 17ac6d2c703b466f9720b7489209a2ff 2be930b5da674874a0b634eca3ad9346 +#: ce445ad0f00f403985eed1328103a500 msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 #: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 2fe48d6404864ea39ef0634169f67be1 +#: 43453d90db244c558a815ca872dc716c msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 #: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: 37392218309d4baebe62fc38bf50efe9 78eaa318ba81407e9ca9c2c1702ead11 +#: f5da7058f7f146d584314a5bf4de5498 msgid "`stderr`" msgstr "" #: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +#: 7189f4415d204fb388c4a7e927e15b71 msgid "" -"From " -"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" #: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 @@ -1868,7 +2095,11 @@ msgstr "" #: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd #: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 #: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb -#: ed875a006df64f9e8a55fa5e9fa87404 +#: ed875a006df64f9e8a55fa5e9fa87404 17a83cc91963434e89822a3e46df8401 +#: 194d3e48d38c476fa8f731e3bc2d8c7f 3a3000a6446b4ef4ac66a28acb13b136 +#: 5cc35210e95e4f2ba6a1a6f118926fdd 68b3d1481a4e4375b1b0c4fca8285374 +#: 94f2bc195bc0487da014bc3f4d2dc8fa b92b4eff2429437d9da911ca68cef954 +#: fc0a1353e87e479d8c8b6c973d547465 msgid "`format`" msgstr "" @@ -1881,800 +2112,914 @@ msgstr "" #: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d #: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f #: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c -#: f760465a49d64d4c8468ad9c4fea62b1 +#: f760465a49d64d4c8468ad9c4fea62b1 5478cbeadc64412bbb32619fae9b9958 +#: 6950cbe52d334fe58bf4fa20e5f1f8ca 6b5bda581d0047819c6d92edd8ac9045 +#: 8248329fbe504b3a96bcd890908b070f 978c0fea8ed1481a9f06b6abb31ebd21 +#: a24ba514d66d49cea281fd4c9c7a2b8d b6e2c8e7abf74d64b2915063dda8479b +#: bc184adfad0e4642bc864d367b8779b7 msgid "`secondaryFiles`" msgstr "" #: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +#: 5bba2d465e0a4c5d9575406d1294a225 msgid "" -"From " -"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" #: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +#: da385d3cde614749887e195ea6d95291 msgid "" -"From " -"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +#: 487c95417f8e48be8391163578ca9519 msgid "" -"From " -"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: d193ce0123db4535a4f0b11405ad0322 48437402c00147d4b4ca8bd6b38a5823 +#: bdcb3920048f4e578a4005fc2e30233b msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 #: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b -#: d555a3d991e344a5a8e1289168d7c6d1 +#: d555a3d991e344a5a8e1289168d7c6d1 121556d49d584cc491a15ef8404ce462 +#: 183ba52666744f7ca5772939db2efd6c msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c -#: e9fa9430535c424fa3e8be5d460d2ba4 +#: e9fa9430535c424fa3e8be5d460d2ba4 08ad064936d8406f8c3852526f4f863d +#: 30c927925c6b483b80b583ca7c735437 msgid "From `Workflow`" msgstr "" #: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +#: 32a26dd9c5f84e88995f093cda953ac9 msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c -#: b0290d1a477b48119e17cf1fed9d6dff +#: b0290d1a477b48119e17cf1fed9d6dff 05ee6df2f9b247629d148fd59c293660 +#: e7b7d782b6ac49b3aa0c8d8ce7ff04d1 msgid "From `steps`" msgstr "" #: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +#: b0cccc07e5bb4effb60424623351499e msgid "" -"From " -"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 -#: e1cde4aa32c041238ed2596173c6d824 +#: e1cde4aa32c041238ed2596173c6d824 4e5281c8663c4b6e8851be10f50143f1 +#: b5c22c66397e4268b4b3d53b9a253a3a msgid "" -"From " -"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." +"html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf -#: c2a92d3eca7f4ee39cec649170eeea53 +#: c2a92d3eca7f4ee39cec649170eeea53 98a28fec818e42af9e177e17fa12aa7a +#: c37d0b1fd75e44a28b3b6409f912e865 msgid "`expression`" msgstr "" #: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +#: dcc42c6c49964a4ca7bcf2124e26ebfd msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](https://www." +"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +#: d2ba352ac5fe427ea7ceb0bde01458ba msgid "" -"From " -"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: d0eec6969d174b258e0f010800884cc6 235cfd6e9baf48698102447fcb83e0e1 +#: 8aad01df8d8d4ab7905a5da7ce7f6bbf msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 #: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 -#: 718ceee9973240ec9c100977bbcc8921 +#: 718ceee9973240ec9c100977bbcc8921 058ba8c9c2da4ebf8b2291600dafd611 +#: cea47d3e10f641a2b64f08ee100ea6bf msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 #: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 -#: c07ab08eb75d4528949c56a3d7c12b28 +#: c07ab08eb75d4528949c56a3d7c12b28 3b039de5ad144207ae337aa88b3b1a1f +#: e0ecfe44b34e45dea513459b6b3e44a6 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: b885e108dced4981a445e5fa0a044394 1cfc6cb0be4e4ddd90f546adb796b805 +#: b62f6eaa7c394792929dda83a187c632 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 #: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: e9f5306ae6ea49bbb6801dcce9be2d67 8b13b0e4071444179b26401929de8a10 +#: 8ffb471129c04fc6bb52b782fbd09f9b msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: 58bf8016f5f04c26b645025f405e2288 331f58b998cd4d309940ebfcc60a44f8 +#: 5041700e6ccc48989e395a6dcb1be3c4 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 #: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: 7c817029d55b4700ae8e84be4d0f0ca0 14402b41c64548f8a9691c3b7ccaf3ac +#: cb4837a2b25343d2880a07143f85f40e msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 #: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +#: 1d1c2894600544b686a8ec3c36cdf767 eaa30e987ec543ef8d6f7171de5525f0 msgid "`outdirMax`" msgstr "" #: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +#: 065c97a553904db6ba61c20cf9d9939c msgid "" -"From " -"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 #: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +#: 36be05289972455ea4a60aa1f0b9cbdf 49e1ab5bc5734debb83060759d5c3236 msgid "`listing`" msgstr "" #: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +#: f8e37cd35aea4bbb92d28e8d7e803ebb msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 #: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b +#: de816d1dc9f24c0cbef86fd6a09eff6b e265df9d1cfe439bb798ab6cd32485af msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 #: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 +#: 0363e32e12604eb896f4bdf6bbefd550 8b5289393b7f477699d007ded45a4df1 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 #: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +#: 2c704cae43d64ecbbed33d18eb3f66f3 89acc8f8387d4643a844ac3efb186000 msgid "From `EnvVarRequirement`" msgstr "" #: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +#: 0597c6c214924e75ba2f212cd6b0c9f2 msgid "" -"From " -"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 #: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +#: 1eb1c2432dd943f6a27a1f8b92e3981b 5b9ba9380f10425b809c6157a1f0b052 msgid "`envValue`" msgstr "" #: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +#: b4cc7cc55cf04449b291a27514fc99ae +msgid "" +"Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" #: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +#: cdb48eff43e7459fbf3ed21eb7791d66 msgid "" -"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" -" attribute that allows users to load external JavaScript files, or to " -"provide inline JavaScript code." +"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " +"attribute that allows users to load external JavaScript files, or to provide " +"inline JavaScript code." msgstr "" #: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +#: 67a4dc675c0e444585d579954b99614e msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts" -" of the CWL document." +"files or to create JavaScript functions that can be called in other parts of " +"the CWL document." msgstr "" #: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +#: ea3238db48494ab7b044bab9f96590af msgid "" -"The CWL standards (versions 1.0 through 1.2) " -"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" -" that the only version of JavaScript valid in CWL expressions is " -"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " -"that any code that you include or write in your CWL Document must be " -"compliant with ECMAScript 5.1." +"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." +"org/v1.0/CommandLineTool.html#Expressions) that the only version of " +"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" +"international.org/5.1/). This means that any code that you include or write " +"in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" #: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +#: baf2f6ac8d514705a1f7bf7ea8c71d2e msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a " -"JavaScript function inline in `expressionLib`. That function can then be " -"used in other parts of the CWL document:" +"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " +"function inline in `expressionLib`. That function can then be used in other " +"parts of the CWL document:" msgstr "" #: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +#: ef45f4e14fb943cd9fbf179f5d3680e5 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" #: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +#: 030261615c38485d83ed986c9c98ce15 msgid "" -"Running this CWL workflow will invoke the JavaScript function and result " -"in the `echo` command printing the input message with capital initial " -"letters:" +"Running this CWL workflow will invoke the JavaScript function and result in " +"the `echo` command printing the input message with capital initial letters:" msgstr "" #: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +#: 1728e2370cbb49ab97bee4c2f74fff2d msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" #: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +#: 4514fc0c99ac4688a37bf30bffe139e8 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" #: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +#: 33804649720143e5a70e890af9ad9119 msgid "`custom-functions.js`" msgstr "" #: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +#: c114496be4c243d6834776e17bf15010 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" #: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +#: c784e86f14f54e4982db206741fbd96e msgid "" -"The `custom-functions.js` file is included in the CWL document with the " -"`$include: custom-functions.js` statement. That makes the functions and " +"The `custom-functions.js` file is included in the CWL document with the `" +"$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +#: f9de69aad9b44afabded71221c84adc2 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" #: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +#: b853c964611e45c2b37a8ac3c34a4133 msgid "" -"Finally, note that you can have both inline and external JavaScript code " -"in your CWL document. In this final example we have added another entry " -"to the `expressionLib` attribute with the new function " -"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" -" the external file `custom-functions.js`." +"Finally, note that you can have both inline and external JavaScript code in " +"your CWL document. In this final example we have added another entry to the " +"`expressionLib` attribute with the new function `createHelloWorldMessage`, " +"that calls the `capitalizeWords` function from the external file `custom-" +"functions.js`." msgstr "" #: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +#: a10d143210b94f83857f62e972d69134 msgid "`hello-world-expressionlib.cwl`" msgstr "" #: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +#: b07734b172664040aff04f83bd4395a5 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" #: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +#: 1f9a5377a1f04ee3b8a9ae22390e0cae msgid "" -"The `$include` statement can be used to include a file from the local " -"disk or from a remote location. It works with both relative and absolute " -"paths. Read the [text about " -"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " -"the CWL specification to learn more about it." +"The `$include` statement can be used to include a file from the local disk " +"or from a remote location. It works with both relative and absolute paths. " +"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." +"html#Include) from the CWL specification to learn more about it." msgstr "" #: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +#: 359bb6448aa140f8b940baf769c13db6 msgid "File Formats" msgstr "" #: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +#: c4aba730bee14931b051d6aead7c2dae msgid "" "Tools and workflows can take `File` types as input and produce them as " -"output. We also recommend indicating the format for `File` types. This " -"helps document for others how to use your tool while allowing you to do " -"some simple type-checking when creating parameter files." +"output. We also recommend indicating the format for `File` types. This helps " +"document for others how to use your tool while allowing you to do some " +"simple type-checking when creating parameter files." msgstr "" #: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +#: c4dfcff573424bccb97580fdd1ef27a1 msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM" -" in our example), reference a local ontology for your institution, or do " -"not add a file format initially for quick development before sharing your" -" tool with others. You can browse existing [IANA file format " -"listings][IANA] and [EDAM file format listings][EDAM] on their websites." +"For file formats, we recommend referencing existing ontologies (like EDAM in " +"our example), reference a local ontology for your institution, or do not add " +"a file format initially for quick development before sharing your tool with " +"others. You can browse existing [IANA file format listings][IANA] and [EDAM " +"file format listings][EDAM] on their websites." msgstr "" #: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +#: 1457fa489c894f1bae8a3949ef200527 msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` " -"section of the document in greater detail, so don't worry about these for" -" now." +"In the next tutorial, we explain the `$namespaces` and `$schemas` section " +"of the document in greater detail, so don't worry about these for now." msgstr "" #: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +#: cc4fa87d57b344ed8961c31bc4397e71 msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" #: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +#: 091815ab1d824787a1460ce11ffb834d msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 #: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +#: 414b68dac4654163b3dc13e140ffdbf8 96fad38b4aea461493bf0827476163bd msgid "The equivalent of this CWL description in command line format is:" msgstr "" #: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +#: 4f71de1140974e73ab033fe7dd9dc165 msgid "Sample Parameter Files" msgstr "" #: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +#: b84e3294c8f648aab634e59b6f58441e msgid "" -"Below is an example of a parameter file for the example above. We " -"encourage checking in working examples of parameter files for your tool. " -"This allows others to quickly work with your tool, starting from a " -"\"known good\" parameterization." +"Below is an example of a parameter file for the example above. We encourage " +"checking in working examples of parameter files for your tool. This allows " +"others to quickly work with your tool, starting from a \"known good\" " +"parameterization." msgstr "" #: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +#: 6d9ae44900d64532906532432881d29d msgid "`sample.yml`" msgstr "" #: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +#: 5b99384b3a854832bcca2fb02bdfc1b6 msgid "" -"___Note:___ To follow the example below, you need to download the example" -" input file, *file-formats.bam*. The file is available from " -" and can be downloaded e.g. via `wget`:" +"___Note:___ To follow the example below, you need to download the example " +"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" #: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +#: 3141fc6828024c3e8201e88ca10e19ee msgid "Topics" msgstr "" #: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +#: 5f8c8ea68d7f46fead000315226ec164 msgid "Inputs" msgstr "" #: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +#: 86c18e5105b1400d86d413e28ad72f48 msgid "Essential Input Parameters" msgstr "" #: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +#: fa15037f9b0b4a2c9a1f4cff9b8fde43 msgid "" -"The `inputs` of a tool is a list of input parameters that control how to " -"run the tool. Each parameter has an `id` for the name of parameter, and " -"`type` describing what types of values are valid for that parameter." +"The `inputs` of a tool is a list of input parameters that control how to run " +"the tool. Each parameter has an `id` for the name of parameter, and `type` " +"describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +#: fba6d2b7843e466abee33183103cf47d msgid "" -"Available primitive types are *string*, *int*, *long*, *float*, *double*," -" and *null*; complex types are *array* and *record*; in addition there " -"are special types *File*, *Directory* and *Any*." +"Available primitive types are *string*, *int*, *long*, *float*, *double*, " +"and *null*; complex types are *array* and *record*; in addition there are " +"special types *File*, *Directory* and *Any*." msgstr "" #: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +#: 09f5a55611d14e39b2266245b79ed763 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" #: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +#: bdfb39c2656040858616afe731111d1a msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" #: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +#: c306335ff07e4c03955fe87cad16efd1 msgid "`inp.cwl`" msgstr "" #: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +#: 50bd3db6bfb348eea13ba4714ecb2a20 msgid "Create a file called `inp-job.yml`:" msgstr "" #: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +#: 5d32cfb6f6ed4dd8b11ed316830edba8 msgid "`inp-job.yml`" msgstr "" #: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +#: b90fb1b2d38b42c1bad2d9667aaa22fd msgid "" -"You can use `cwltool` to create a template input object. That saves you " -"from having to type all the input parameters in a input object file:" +"You can use `cwltool` to create a template input object. That saves you from " +"having to type all the input parameters in a input object file:" msgstr "" #: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +#: 6029a96abf9c4d7295eb86d435a1f58d msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template " -"inp.cwl > inp-job.yml`, and then modify the default values with your " -"desired input values." +"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " +"> inp-job.yml`, and then modify the default values with your desired input " +"values." msgstr "" #: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +#: 902e9df74f78431ca9cf1421a26e097a msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" #: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +#: 9760d15bad144e70a86dc0a8da72363a msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" -" command line." +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " +"command line." msgstr "" #: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +#: 75bf3fae131049308441bc496f543f6e msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " -"following boxed text describes these two commands and the expected output" -" from the command line:" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " +"boxed text describes these two commands and the expected output from the " +"command line:" msgstr "" #: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +#: 38d8a9c157404bb496bc49f1e427bf99 msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not " -"explicitly specified" +"that the tools aren't accidentally accessing files that were not explicitly " +"specified" msgstr "" #: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +#: 502994ee84234f048e545633bb04cd3c msgid "" -"The field `inputBinding` is optional and indicates whether and how the " -"input parameter should appear on the tool's command line. If " -"`inputBinding` is missing, the parameter does not appear on the command " -"line. Let's look at each example in detail." +"The field `inputBinding` is optional and indicates whether and how the input " +"parameter should appear on the tool's command line. If `inputBinding` is " +"missing, the parameter does not appear on the command line. Let's look at " +"each example in detail." msgstr "" #: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +#: 551b06b8a3064bcd8d0f1693a4c0ee94 msgid "" -"Boolean types are treated as a flag. If the input parameter " -"\"example_flag\" is \"true\", then `prefix` will be added to the command " -"line. If false, no flag is added." +"Boolean types are treated as a flag. If the input parameter \"example_flag" +"\" is \"true\", then `prefix` will be added to the command line. If false, " +"no flag is added." msgstr "" #: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +#: 1838e7438be5449c91c6406a7e40d8cb msgid "" -"String types appear on the command line as literal values. The `prefix` " -"is optional, if provided, it appears as a separate argument on the " -"command line before the parameter . In the example above, this is " -"rendered as `--example-string hello`." +"String types appear on the command line as literal values. The `prefix` is " +"optional, if provided, it appears as a separate argument on the command line " +"before the parameter . In the example above, this is rendered as `--example-" +"string hello`." msgstr "" #: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +#: 098bb02c941a4bf2a8d4dd9ab3bf052e msgid "" -"Integer (and floating point) types appear on the command line with " -"decimal text representation. When the option `separate` is false (the " -"default value is true), the prefix and value are combined into a single " -"argument. In the example above, this is rendered as `-i42`." +"Integer (and floating point) types appear on the command line with decimal " +"text representation. When the option `separate` is false (the default value " +"is true), the prefix and value are combined into a single argument. In the " +"example above, this is rendered as `-i42`." msgstr "" #: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +#: b43194d2b3ef4fc6a8c4b58741317b29 msgid "" "File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the " -"parameter is optional. In the example above, this is rendered as " -"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " -"parameter were not provided in the input, nothing would appear on the " -"command line." +"parameter type ends with a question mark `?` it indicates that the parameter " +"is optional. In the example above, this is rendered as `--file=/tmp/random/" +"path/whale.txt`. However, if the \"example_file\" parameter were not " +"provided in the input, nothing would appear on the command line." msgstr "" #: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +#: e17c55c9ed034dd68f4d24272a61d2f1 msgid "" -"Input files are read-only. If you wish to update an input file, you must" -" [first copy it to the output directory](staging-input-files.md)." +"Input files are read-only. If you wish to update an input file, you must " +"[first copy it to the output directory](staging-input-files.md)." msgstr "" #: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +#: c97a6945e4bc49888d280bbc43c3c069 msgid "" -"The value of `position` is used to determine where parameter should " -"appear on the command line. Positions are relative to one another, not " -"absolute. As a result, positions do not have to be sequential, three " -"parameters with positions 1, 3, 5 will result in the same command line as" -" 1, 2, 3. More than one parameter can have the same position (ties are " -"broken using the parameter name), and the position field itself is " -"optional. The default position is 0." +"The value of `position` is used to determine where parameter should appear " +"on the command line. Positions are relative to one another, not absolute. " +"As a result, positions do not have to be sequential, three parameters with " +"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " +"than one parameter can have the same position (ties are broken using the " +"parameter name), and the position field itself is optional. The default " +"position is 0." msgstr "" #: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +#: 503666cda07b4d7397c65561714d8034 msgid "" -"The `baseCommand` field will always appear in the final command line " -"before the parameters." +"The `baseCommand` field will always appear in the final command line before " +"the parameters." msgstr "" #: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +#: e5463be0a00d42e386aa6fd3dfacaeaf msgid "Array Inputs" msgstr "" #: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +#: 14b98bd0ef4a4065a24e66443458d607 msgid "" "It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to " -"provide `type` field with `type: array` and `items` defining the valid " -"data types that may appear in the array. Alternatively, brackets `[]` may" -" be added after the type name to indicate that input parameter is array " -"of that type." +"line. There are two ways to specify an array parameter. First is to provide " +"`type` field with `type: array` and `items` defining the valid data types " +"that may appear in the array. Alternatively, brackets `[]` may be added " +"after the type name to indicate that input parameter is array of that type." msgstr "" #: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +#: 98fa5dab117e41d4a42da8d78c533c64 msgid "`array-inputs.cwl`" msgstr "" #: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +#: 116c212444da4488b32abdbd725db98a msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 #: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 #: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d +#: 065e556e01b34c35b6be4b54b7cc0203 4745f370dcbd4ee8bbf4b3a20ac5b9fe +#: d11761f2d576464f8a2c63bdec02d410 msgid "" -"Now invoke `cwltool` providing the tool description and the input object " -"on the command line:" +"Now invoke `cwltool` providing the tool description and the input object on " +"the command line:" msgstr "" #: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +#: b3bf1d7e95704682b1bae17472eaa4bc msgid "" -"The `inputBinding` can appear either on the outer array parameter " -"definition or the inner array element definition, and these produce " -"different behavior when constructing the command line, as shown above. In" -" addition, the `itemSeparator` field, if provided, specifies that array " -"values should be concatenated into a single argument separated by the " -"item separator string." +"The `inputBinding` can appear either on the outer array parameter definition " +"or the inner array element definition, and these produce different behavior " +"when constructing the command line, as shown above. In addition, the " +"`itemSeparator` field, if provided, specifies that array values should be " +"concatenated into a single argument separated by the item separator string." msgstr "" #: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +#: 04bc655130234786b06b2d5b9e693635 msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` " -"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " -"lines, where array values that are not defined with an associated key are" -" marked by a leading `-`. This will be demonstrated in the next lesson " -"and is discussed in more detail in the [YAML Guide](yaml-" -"guide.md#arrays). You can specify arrays of arrays, arrays of records, " -"and other complex types." +"Note that the arrays of inputs are specified inside square brackets `[]` in " +"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " +"where array values that are not defined with an associated key are marked by " +"a leading `-`. This will be demonstrated in the next lesson and is discussed " +"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " +"arrays of arrays, arrays of records, and other complex types." msgstr "" #: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +#: e2c18a43b2794448b45c489dd2fa951e msgid "Inclusive and Exclusive Inputs" msgstr "" #: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +#: 38968ed627514ef38e43b3d1e4a5e25f msgid "" "Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be " -"provided together (they are exclusive). You can use records and type " -"unions to group parameters together to describe these two conditions." +"together (they are dependent) or several arguments that cannot be provided " +"together (they are exclusive). You can use records and type unions to group " +"parameters together to describe these two conditions." msgstr "" #: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +#: 06aab84eceeb41d087b7e295ffa21586 msgid "`record.cwl`" msgstr "" #: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +#: a0317edb8b964cd2a36c59eaa6df302a msgid "`record-job1.yml`" msgstr "" #: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +#: 5a3d1b82c79c4ccdb7d06381f4d0acda msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" #: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: e1fc6c3a324a46ee84b0eb59f8396552 msgid "`record-job2.yml`" msgstr "" #: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +#: f22e7d9e23b541ef88f3254095147519 msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the " -"first matching item (`itemC`) is added to the command line and remaining " -"item (`itemD`) is ignored." +"In the second example, `itemC` and `itemD` are exclusive, so only the first " +"matching item (`itemC`) is added to the command line and remaining item " +"(`itemD`) is ignored." msgstr "" #: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +#: d473d2fa11f64e8fa86554b5777c98e4 msgid "`record-job3.yml`" msgstr "" #: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +#: 290461c321d14d23b39003b93008a7cb msgid "" -"In the third example, only `itemD` is provided, so it appears on the " -"command line." +"In the third example, only `itemD` is provided, so it appears on the command " +"line." msgstr "" #: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +#: add43f7531bb4c6988053ae799c366f0 msgid "Exclusive Input Parameters with Expressions" msgstr "" #: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +#: b12b6f5e34c14dbc9b40458d92e6797f msgid "" -"If you use exclusive input parameters combined with expressions, you need" -" to be aware that the `inputs` JavaScript object will contain one of the " +"If you use exclusive input parameters combined with expressions, you need to " +"be aware that the `inputs` JavaScript object will contain one of the " "exclusive input values. This means that you might need to use an **or** " "boolean operator to check which values are present." msgstr "" #: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +#: 4d8f38679952486095a77692387db2d3 msgid "" "Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from" -" an enum." +"parameter that accepts `null` (i.e. no value provided), or any value from an " +"enum." msgstr "" #: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +#: 47ec49759e274e59834192b794ec2d9b msgid "`exclusive-parameter-expressions.cwl`" msgstr "" #: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +#: 0657044c742348fe9e63f662692570a1 msgid "" "Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you " -"provide a valid value, such as “fasta” (one of the values of the enum), " -"your command should execute successfully:" +"parameter without taking into consideration a `null` value. If you provide a " +"valid value, such as “fasta” (one of the values of the enum), your command " +"should execute successfully:" msgstr "" #: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +#: 30c21cafda144f848bfe79d8e232296e msgid "" -"However, if you do not provide any input value, then `file_format` will " -"be evaluated to a `null` value, which does not match the expected type " -"for the output field (a `string`), resulting in failure when running your" -" workflow." +"However, if you do not provide any input value, then `file_format` will be " +"evaluated to a `null` value, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your workflow." msgstr "" #: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +#: 1cc8ea6abb684470b7790808acea2be1 msgid "" -"To correct it, you must remember to use an or operator in your JavaScript" -" expression when using exclusive parameters, or any parameter that allows" -" `null`. For example, the expression could be changed to " -"`$(inputs.file_format || 'auto')`, to have a default value if none was " -"provided in the command line or job input file." +"To correct it, you must remember to use an or operator in your JavaScript " +"expression when using exclusive parameters, or any parameter that allows " +"`null`. For example, the expression could be changed to `$(inputs." +"file_format || 'auto')`, to have a default value if none was provided in the " +"command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: d33aa2353ad44fb885d3a1ee48263dc4 c3b84742343449f9b3866285d98b53bb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 +#: cd64d2d828834cbbb24ea5358caf5405 0a1b08fe707c41089ad3d4895960ba17 msgid "" -"Implementation extensions not required for correct execution (for " -"example, fields related to GUI presentation) and metadata about the tool " -"or workflow itself (for example, authorship for use in citations) may be " -"provided as additional fields on any object. Such extensions fields (e.g." -" `format: edam:format_2572`) can use a namespace prefix listed in the " -"`$namespaces` section of the document (e.g. edam: " -"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" -"][schema-salad]. Once you add the namespace prefix, you can access it " -"anywhere in the document as shown below. Otherwise, one must use full " -"URLs: `format: http://edamontology.org/format_2572`." +"Implementation extensions not required for correct execution (for example, " +"fields related to GUI presentation) and metadata about the tool or workflow " +"itself (for example, authorship for use in citations) may be provided as " +"additional fields on any object. Such extensions fields (e.g. `format: edam:" +"format_2572`) can use a namespace prefix listed in the `$namespaces` section " +"of the document (e.g. edam: http://edamontology.org/) as described in the " +"[Schema Salad specification][schema-salad]. Once you add the namespace " +"prefix, you can access it anywhere in the document as shown below. " +"Otherwise, one must use full URLs: `format: http://edamontology.org/" +"format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b +#: 80af387fe3ff4e2da999903385bd602b 5bc4ef6584c74b948ffd5c0bddf8e569 msgid "" "For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to " -"cite your tool." +"tool and workflows. This example includes metadata allowing others to cite " +"your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 47ee25d60a4a4faa80476797954ec7a9 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: d402bf528c7f4eb69aaaa275be2bf1d4 195d4a8d5aad41159beffafd198d4640 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 b0c5946fbf79415aa74c8e72fa88cf85 msgid "" -"For those that are highly motivated, it is also possible to annotate your" -" tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints" -" at hardware requirements in order to use the tool, and a few more " -"metadata fields." +"For those that are highly motivated, it is also possible to annotate your " +"tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints at " +"hardware requirements in order to use the tool, and a few more metadata " +"fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: 2dfbd4d580044ed083992f3ceb1bc64e a98236fc1be745a69271855e1b5eecdb msgid "`metadata_example3.cwl`" msgstr "" #: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +#: 5f0da8d7e06a47fda38053dbadcbec18 msgid "Operations" msgstr "" #: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +#: 23d41792b0524742878a6ab8f3ff0fe1 msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-" -"line tool, or an expression tool. It is a step of a workflow that " -"specifies inputs and outputs, but it does not provide enough information " -"to be executed." +"An Operation is a type of CWL process, just like a workflow, a command-line " +"tool, or an expression tool. It is a step of a workflow that specifies " +"inputs and outputs, but it does not provide enough information to be " +"executed." msgstr "" #: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +#: c0f723242f11464392dfc32f67a3b67b msgid "" -"You can create operations to visualize a workflow during development, " -"before you are ready to submit the workflow to a CWL runner:" +"You can create operations to visualize a workflow during development, before " +"you are ready to submit the workflow to a CWL runner:" msgstr "" #: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +#: c9f3a48a3a064cb3b1759effe724301d msgid "`operations.cwl`" msgstr "" #: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +#: fbad0b0144984ae78b84307ea68d0a03 msgid "" -"The `uppercase` step of the workflow is an operation. It can be used like" -" a command line tool or an expression. You can also plot it with the CWL " -"Viewer or `cwltool`:" +"The `uppercase` step of the workflow is an operation. It can be used like a " +"command line tool or an expression. You can also plot it with the CWL Viewer " +"or `cwltool`:" msgstr "" #: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +#: 59e9ff3276454ff19eb351ff33737f12 msgid "" -"The output of the command above can be rendered with a Graphviz renderer." -" The following image is rendered with the Sphinx Graphviz directive (this" -" user guide is built with Sphinx):" +"The output of the command above can be rendered with a Graphviz renderer. " +"The following image is rendered with the Sphinx Graphviz directive (this " +"user guide is built with Sphinx):" msgstr "" #: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +#: ba74f2ab7f6d4c178f3c4c43c461afbd msgid "" -"If you try running it with `cwltool`, the command will fail since " -"`cwltool` does not have enough information to know how to execute it:" +"If you try running it with `cwltool`, the command will fail since `cwltool` " +"does not have enough information to know how to execute it:" msgstr "" #: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +#: 93c8b61a12134991ae9bb78223e2017e msgid "`cwltool` does not know how to run operations" msgstr "" #: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +#: cbbdba36dc3841f2b1d820f369a8c680 msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A" -" CWL runner could, for instance, use abstract operations with ID's that " +"CWL runners may come up with ways to bind operations to concrete steps. A " +"CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" #: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +#: 4649c8d743f448ab94ee589a1b3a342a msgid "Outputs" msgstr "" #: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +#: 1a9d6e2e33244d01b820cf11fe2beaff msgid "Returning Output Files" msgstr "" #: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +#: 233c8865faac4d6c8ec7704e9a997719 msgid "" "The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name" -" of parameter, and `type` describing what types of values are valid for " -"that parameter." +"returned after running the tool. Each parameter has an `id` for the name of " +"parameter, and `type` describing what types of values are valid for that " +"parameter." msgstr "" #: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +#: 5aab1c0db3d5449cbb4a0f0dad615d87 msgid "" -"When a tool runs under CWL, the starting working directory is the " -"designated output directory. The underlying tool or script must record " -"its results in the form of files created in the output directory. The " -"output parameters returned by the CWL tool are either the output files " -"themselves, or come from examining the content of those files." +"When a tool runs under CWL, the starting working directory is the designated " +"output directory. The underlying tool or script must record its results in " +"the form of files created in the output directory. The output parameters " +"returned by the CWL tool are either the output files themselves, or come " +"from examining the content of those files." msgstr "" #: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +#: 46b4eeb3ce8946dca0f8a94c399b4c96 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" #: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +#: 8d322609948a4d6e87d7962b3d29df2f msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" #: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +#: 9fdcb55e965444ee8b5d74a2a9870d27 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2683,464 +3028,520 @@ msgid "" msgstr "" #: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +#: e4c490f599a0469a821aa8e74f4ef0ef msgid "`tar.cwl`" msgstr "" #: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +#: b8ed6ebe6928455cb094ea430e21e5d4 msgid "`tar-job.yml`" msgstr "" #: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +#: 3e65c52d218946fc83b8c3e6adcb21fe msgid "Next, create a tar file for the example." msgstr "" #: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +#: 03751b45cdf647b689a3a69156989db5 msgid "" -"And now invoke `cwltool` with the tool description and the input object " -"on the command line:" +"And now invoke `cwltool` with the tool description and the input object on " +"the command line:" msgstr "" #: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +#: 1b6f59623f5d4cd984426da21b8438bf msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" #: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +#: 095902cca30944d19a0d5f17f582e3b0 msgid "" -"The `glob` field consists of the name of a file in the output directory. " -"If you don't know name of the file in advance, you can use a wildcard " -"pattern like `glob: '*.txt'`." +"The `glob` field consists of the name of a file in the output directory. If " +"you don't know name of the file in advance, you can use a wildcard pattern " +"like `glob: '*.txt'`." msgstr "" #: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +#: 6d95fbfa321144a9932f26ab5f9ddc74 msgid "Capturing Standard Output" msgstr "" #: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +#: 8be7ef160e8b421a89124a639dc7fd84 msgid "" -"To capture a tool's standard output stream, add the `stdout` field with " -"the name of the file where the output stream should go. Then add `type: " -"stdout` on the corresponding output parameter." +"To capture a tool's standard output stream, add the `stdout` field with the " +"name of the file where the output stream should go. Then add `type: stdout` " +"on the corresponding output parameter." msgstr "" #: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +#: fcf4490c351d4cd6a208345308168ef7 msgid "`stdout.cwl`" msgstr "" #: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +#: 00f1bb92a38b4f3a8c0065ac75530689 msgid "Array Outputs" msgstr "" #: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +#: 1477d0fc5c4c4f82bcc1c8e6ba8eed4d msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" #: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +#: dee904cb678d4eb49dc829d6590b267a msgid "`array-outputs.cwl`" msgstr "" #: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +#: a21c1fd3194a49ae992a743023653dc5 msgid "`array-outputs-job.yml`" msgstr "" #: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +#: e72c526da47a455da4b10e33938d1600 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions" -" to mark entries in arrays, as demonstrated in several of the upcoming " -"sections." +"marked by a leading `-`. This format can also be used in CWL descriptions to " +"mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" #: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +#: 6447f4b8bb5f4f93bd8ec2c7b1fb09cb msgid "Parameter References" msgstr "" #: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +#: 1faea30495a440a68dbd1647dacc404c msgid "" "In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file " -"we were interested in was called \"hello.txt\", and this was written into" -" the `.cwl` file. This is not the best way to do this, as the " -"\"hello.txt\" filename may vary or be dependent on the input file(s) " -"used. To avoid this we can specify the name of the file we want in the " -"job parameters file (`.yml`). In this example, you will see how to " -"reference the value of input parameters dynamically from other fields, " -"which will allow us to then specify the name of the file to extract." +"However, that example was very limited because it assumed that the file we " +"were interested in was called \"hello.txt\", and this was written into the `." +"cwl` file. This is not the best way to do this, as the \"hello.txt\" " +"filename may vary or be dependent on the input file(s) used. To avoid this " +"we can specify the name of the file we want in the job parameters file (`." +"yml`). In this example, you will see how to reference the value of input " +"parameters dynamically from other fields, which will allow us to then " +"specify the name of the file to extract." msgstr "" #: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +#: 0c0a3f58a93f492dbfca14523809aacc msgid "`tar-param.cwl`" msgstr "" #: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +#: 460842f202db493dbb901be73a02797f msgid "`tar-param-job.yml`" msgstr "" #: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +#: 2591c2cf9e5f402281031ea8dd41a251 msgid "" -"Create your input files and invoke `cwltool` with the tool description " -"and the input object on the command line:" +"Create your input files and invoke `cwltool` with the tool description and " +"the input object on the command line:" msgstr "" #: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +#: b093abbff3614b2ba0141f07376a5220 msgid "" -"Certain fields permit parameter references which are enclosed in " -"`$(...)`. These are evaluated and replaced with value being referenced." +"Certain fields permit parameter references which are enclosed in `$(...)`. " +"These are evaluated and replaced with value being referenced." msgstr "" #: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +#: fda3718113354215bd2ac212553fb2d4 msgid "" "References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " -"`$(inputs['extractfile'])` are equivalent." +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" +"$(inputs['extractfile'])` are equivalent." msgstr "" #: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +#: 271e78089c274154a0233289d705e628 msgid "" -"The value of the \"inputs\" variable is the input object provided when " -"the CWL tool was invoked." +"The value of the \"inputs\" variable is the input object provided when the " +"CWL tool was invoked." msgstr "" #: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +#: 29ab4fa0876b4c11a0c7482cca56ed80 msgid "" -"Note that because `File` parameters are objects, to get the path to an " -"input file you must reference the path field on a file object; to " -"reference the path to the tar file in the above example you would write " -"`$(inputs.tarfile.path)`." +"Note that because `File` parameters are objects, to get the path to an input " +"file you must reference the path field on a file object; to reference the " +"path to the tar file in the above example you would write `$(inputs.tarfile." +"path)`." msgstr "" #: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +#: 78e1857c5bd54af1b7ca4728879e6219 msgid "Where are parameter references allowed?" msgstr "" #: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +#: dae7873015254aa7874379164c90a8d0 msgid "You can only use parameter references in certain fields. These are:" msgstr "" #: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +#: 7a45deb4682b49fd86d62fae41831db8 msgid "" -"From " -"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" #: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +#: 442f77a69b314cba8e8857470263c706 msgid "" -"From " -"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +#: d4455241f14549b791e59fc1f942c8cb msgid "" -"From " -"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" #: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +#: ff4b1c05c5804ec7846043ae8814ad21 msgid "" -"From " -"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +#: 119e026b595f49c090d62aa7b7c77de4 msgid "" -"From " -"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" #: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +#: 5449d9c5687544a3bfbf8b2b25640a83 msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +#: b3191a7bd03d4ff18802ae0f5d419676 msgid "" -"From " -"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" #: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +#: ea9cfbbd4cbd4f26ba4b0cb50d58635b msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +#: 7d39ed2a3a724dc1a75e6b2cdf87d91d msgid "" -"From " -"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 +#: 5d8bed66282c408695292ea92a03b2c4 a1306ee650344278ae39d6086b1ed7d9 msgid "" -"From " -"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: 958178d1fa8843aaa0541e2bb115cfd4 21d76d22f3044460b925fee68ac74454 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 6b8a5c59217c4928874710ead1456622 msgid "" -"From " -"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: aac74f957774479a83aab4c6ff1390ae a9f6d09055c24029a5f85c3a663c4202 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: b75d29d1d55d44488338f9689f156855 d3948618f9274ad0a333722567efeea5 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb +#: 574d93d1d592458a985f259519c036cb 44623c81141345a0b0080e719e1418ab msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " -"include a `SoftwareRequirement` field in the `hints` section. This may " -"also help to avoid confusion about which version of a tool the " -"description was written for." +"include a `SoftwareRequirement` field in the `hints` section. This may also " +"help to avoid confusion about which version of a tool the description was " +"written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 +#: 82e48b3e3c3f451480cc0b6a529271f6 6e80d82ed57b441b8292961ec3163213 msgid "" -"In this example, the software requirement being described is InterProScan" -" version 5.21-60." +"In this example, the software requirement being described is InterProScan " +"version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 +#: 02e40154eac74ecc98d0447d03475b44 fc61f369e720463f8a5cd6c751d1d5e6 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the " -"[dependency resolvers configuration][dependencies]." +"enable these checks with the reference implementation, use the [dependency " +"resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 -msgid "" -"As well as a version number, a unique resource identifier (URI) for the " -"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" -" looked up in the [SciCrunch][scicrunch] registry, which provides a " -"portal for finding, tracking, and referring to scientific resources " -"consistently. If you want to specify a tool as a `SoftwareRequirement`, " -"search for the tool on SciCrunch and use the RRID that it has been " -"assigned in the registry. (Follow this [Adding a Resource Tutorial" -"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " -"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " -"field of your requirement description. Other good choices, in order of " -"preference, are to include the DOI for the main tool citation and the URL" -" to the tool." +#: 8cb1c5d9b1a54c40924099494eb766c6 f20aadbfc13243498ad199376c314e72 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the tool " +"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " +"up in the [SciCrunch][scicrunch] registry, which provides a portal for " +"finding, tracking, and referring to scientific resources consistently. If " +"you want to specify a tool as a `SoftwareRequirement`, search for the tool " +"on SciCrunch and use the RRID that it has been assigned in the registry. " +"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " +"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." +"org][identifiers]) in the `specs` field of your requirement description. " +"Other good choices, in order of preference, are to include the DOI for the " +"main tool citation and the URL to the tool." msgstr "" #: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +#: e66956313b8f4f02bb96cfb256e2a7d4 msgid "Staging Input Files" msgstr "" #: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +#: f18c5a8fcbe84135a6e06cbf8008cd63 msgid "" -"Normally, input files are located in a read-only directory separate from " -"the output directory. This causes problems if the underlying tool " -"expects to write its output files alongside the input file in the same " -"directory. You use `InitialWorkDirRequirement` to stage input files into" -" the output directory. In this example, we use a JavaScript expression to" -" extract the base name of the input file from its leading directory path." +"Normally, input files are located in a read-only directory separate from the " +"output directory. This causes problems if the underlying tool expects to " +"write its output files alongside the input file in the same directory. You " +"use `InitialWorkDirRequirement` to stage input files into the output " +"directory. In this example, we use a JavaScript expression to extract the " +"base name of the input file from its leading directory path." msgstr "" #: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: 87fe14c9a0594602aa56a7706e089458 msgid "`linkfile.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +#: 6e10063f55b747e1b07d6109ab7b046b msgid "Troubleshooting" msgstr "" #: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +#: e8831832b32449f4a8a3dde3c1b479cd msgid "" -"In this section you will find ways to troubleshoot when you have problems" -" executing CWL. We focus on `cwltool` here but some of these techniques " -"may apply to other CWL Runners." +"In this section you will find ways to troubleshoot when you have problems " +"executing CWL. We focus on `cwltool` here but some of these techniques may " +"apply to other CWL Runners." msgstr "" #: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +#: 9c86467137864626a2079cb6cecb71c0 msgid "Run `cwltool` with `cachedir`" msgstr "" #: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +#: 24b66a3e2e464ec6a85b5dfbaad1cbf4 msgid "" "You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor " -"output files, but created while your workflow is running). By default, " -"these files are created in a temporary directory but writing them to a " -"separate directory makes accessing them easier." +"`cwltool` to cache intermediate files (files that are not input nor output " +"files, but created while your workflow is running). By default, these files " +"are created in a temporary directory but writing them to a separate " +"directory makes accessing them easier." msgstr "" #: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +#: 6d28f1cd40c045f384313c4d74073ed2 msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " -"World\" | rev`, which would print the message \"Hello World\" reversed, " -"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," -" where instead of executing the `rev` command it tries to execute `revv`," -" which fails." +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " +"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " +"olleH\". However, the second step, `step_b`, **has a typo**, where instead " +"of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" #: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +#: 5235ff0c35c54396aceb799a65f6158e msgid "`troubleshooting-wf1.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +#: fc49344510594559b4f888bc45093b51 msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " -"value (`cwltool` will create the directory for you if it does not exist " -"already):" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " +"(`cwltool` will create the directory for you if it does not exist already):" msgstr "" #: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +#: 6e62be8d7d1344e8917904278b508518 msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. " -"You can inspect the intermediate files created:" +"successfully and its output has been cached in your `cachedir` location. You " +"can inspect the intermediate files created:" msgstr "" #: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +#: c91b3a2818b143f58bd37da63479c560 msgid "" -"Each workflow step has received a unique ID (the long value that looks " -"like a hash). The `${HASH}.status` files display the status of each step " -"executed by the workflow. And the `step_a` output file `stdout.txt` is " -"visible in the output of the command above." +"Each workflow step has received a unique ID (the long value that looks like " +"a hash). The `${HASH}.status` files display the status of each step executed " +"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " +"output of the command above." msgstr "" #: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +#: 86f283bc522c4be2adfac16256f01b0e msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" -" in the `step_b`). After fixing the typo, when you execute `cwltool` with" -" the same arguments as the previous time, note that now `cwltool` output " -"contains information about pre-cached outputs for `step_a`, and about a " -"new cache entry for the output of `step_b`. Also note that the status of " -"`step_b` is now of success." +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " +"the `step_b`). After fixing the typo, when you execute `cwltool` with the " +"same arguments as the previous time, note that now `cwltool` output contains " +"information about pre-cached outputs for `step_a`, and about a new cache " +"entry for the output of `step_b`. Also note that the status of `step_b` is " +"now of success." msgstr "" #: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +#: 5362aa1d28344968953ab9cb389ccd8e msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had" -" been cached, and there was no change in its execution or output. " +"In this example the workflow step `step_a` was not re-evaluated as it had " +"been cached, and there was no change in its execution or output. " "Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for" -" troubleshooting your CWL documents and also as a way to prevent " -"`cwltool` to re-evaluate steps unnecessarily." +"`step_b` after we fixed the executable name. This technique is useful for " +"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " +"re-evaluate steps unnecessarily." msgstr "" #: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +#: 4bb1aafde4f745a083d3a276497523dc msgid "Using Containers" msgstr "" #: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +#: b00987baf6974ff9b7e3b8cdfd7abd9a msgid "Running Tools Inside Docker" msgstr "" #: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +#: 9ac51c5a2a0a45859e14d9e388edd5f0 msgid "" -"[Docker][docker] containers simplify software installation by providing a" -" complete known-good runtime for software and its dependencies. However," -" containers are also purposefully isolated from the host system, so in " -"order to run a tool inside a Docker container there is additional work to" -" ensure that input files are available inside the container and output " -"files can be recovered from the container. A CWL runner can perform this" -" work automatically, allowing you to use Docker to simplify your software" -" management while avoiding the complexity of invoking and managing Docker" -" containers." +"[Docker][docker] containers simplify software installation by providing a " +"complete known-good runtime for software and its dependencies. However, " +"containers are also purposefully isolated from the host system, so in order " +"to run a tool inside a Docker container there is additional work to ensure " +"that input files are available inside the container and output files can be " +"recovered from the container. A CWL runner can perform this work " +"automatically, allowing you to use Docker to simplify your software " +"management while avoiding the complexity of invoking and managing Docker " +"containers." msgstr "" #: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +#: 5494ccdb1a354b2386c82bd9a6f0b6a9 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the " -"container." +"input files to reflect the location where they appear inside the container." msgstr "" #: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +#: 4cfa8fc2bb224883946d5f63b372de82 msgid "" -"This example runs a simple Node.js script inside a Docker container which" -" will then print \"Hello World\" to the standard output." +"This example runs a simple Node.js script inside a Docker container which " +"will then print \"Hello World\" to the standard output." msgstr "" #: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +#: e16c1922527a46e28bb5d933614cdaf7 msgid "`docker.cwl`" msgstr "" #: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +#: 7498a71704be462abef71c42e6b83d1b msgid "`docker-job.yml`" msgstr "" #: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +#: ac0689bff9db46ea8bff8cd35cde86f3 msgid "" "Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that " -"is really new is the `dockerRequirement` section." +"Most of this has been explained in previous sections, the only part that is " +"really new is the `dockerRequirement` section." msgstr "" #: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +#: c4b7da5575674ca3ae734424022ef090 msgid "" -"`baseCommand: node` tells CWL that we will be running this command using " -"the Node Js runtime that is meant for Javascript files. We then need to " -"specify some `hints` for how to find the container we want. In this case" -" we list just our requirements for the docker container in " -"`DockerRequirements`. The `dockerPull:` parameter takes the same value " -"that you would pass to a `docker pull` command. That is, the name of the " -"container image (you can even specify the tag, which is good idea for " -"best practices when using containers for reproducible research). In this " -"case we have used a container called `node:slim`." +"`baseCommand: node` tells CWL that we will be running this command using the " +"Node Js runtime that is meant for Javascript files. We then need to specify " +"some `hints` for how to find the container we want. In this case we list " +"just our requirements for the docker container in `DockerRequirements`. The " +"`dockerPull:` parameter takes the same value that you would pass to a " +"`docker pull` command. That is, the name of the container image (you can " +"even specify the tag, which is good idea for best practices when using " +"containers for reproducible research). In this case we have used a container " +"called `node:slim`." msgstr "" #: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +#: d24fcecc17d0461cbd8689067f770c0d msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` " -"providing the tool description and the input object on the command line:" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " +"the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +#: 833d4d3b3f0e4c7cb8b1d35cb9a78a7e msgid "`hello.js`" msgstr "" #: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +#: 50fc0573276e4dd4a47208ed81109991 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" #: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +#: f72e10e746604421904057ddf7078d3e msgid "" -"In this example, the path to the script `hello.js` is " -"`/home/me/cwl/user_guide/hello.js` outside the container but " -"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " -"reflected in the invocation of the `node` command." +"In this example, the path to the script `hello.js` is `/home/me/cwl/" +"user_guide/hello.js` outside the container but `/var/lib/cwl/" +"job369354770_examples/hello.js` inside the container, as reflected in the " +"invocation of the `node` command." msgstr "" #: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +#: ee126833f6014e378c7841c4048dae85 msgid "Workflows" msgstr "" #: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +#: 0325bd610aa747b0b657afa0c978a1eb msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " @@ -3148,239 +3549,265 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +#: 7c901105cf6949909d87be5681331368 msgid "CWL workflow." msgstr "" #: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +#: 74138d0c2ded4311bf688df4a28387b5 msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier " -"examples." +"command-line tool, and the expression tool showed in the earlier examples." msgstr "" #: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +#: 1ec4773e7319414b997d746d1965ff56 msgid "`echo-uppercase.cwl`" msgstr "" #: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +#: 5f860dd70e3b435188c61a538e5de0ef msgid "" -"A command-line tool or expression tool can also be written directly in " -"the same CWL document as the workflow. For example, we can rewrite the " -"`echo-uppercase.cwl` workflow as a single file:" +"A command-line tool or expression tool can also be written directly in the " +"same CWL document as the workflow. For example, we can rewrite the `echo-" +"uppercase.cwl` workflow as a single file:" msgstr "" #: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +#: a9c56df6dca441dfabda7fa54fbe56c6 msgid "`echo-uppercase-single-file.cwl`" msgstr "" #: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +#: 586d561ddf724319b3da9ae857828648 msgid "" -"Having separate files helps with modularity and code organization. But it" -" can be helpful writing everything in a single file for development. " -"There are other ways to combine multiple files into a single file (e.g. " -"`cwltool --pack`) discussed further in other sections of this user guide." +"Having separate files helps with modularity and code organization. But it " +"can be helpful writing everything in a single file for development. There " +"are other ways to combine multiple files into a single file (e.g. `cwltool --" +"pack`) discussed further in other sections of this user guide." msgstr "" #: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +#: f3e80b1903534065a30323611c267e9b msgid "" "For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this" -" user guide in more detail." +"`SubworkflowFeatureRequirement`. It is covered in another section of this " +"user guide in more detail." msgstr "" #: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +#: 6ed53c6f9fb94d4ab3d10532c605c46b msgid "Writing Workflows" msgstr "" #: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +#: 3fcfdf43b0a049388634625c45e0b1bb msgid "" -"This workflow extracts a java source file from a tar file and then " -"compiles it." +"This workflow extracts a java source file from a tar file and then compiles " +"it." msgstr "" #: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +#: 49415efafae64f94b66cb46ca2bbd40a msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 #: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +#: 4806a2ef982944e8b073fafd416d3d74 d45701eeaa6e42feb4ef79d2fc4af756 msgid "Visualization of 1st-workflow.cwl" msgstr "" #: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +#: 155cd684ff304258ae374b2e13090e5f msgid "" -"[![Visualization of 1st-" -"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-" +"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" "workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-workflow.cwl)" +"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" +"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" #: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +#: d8bdb44011274f94b606277799a6fa6f msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a" -" run:" +"Use a YAML or a JSON object in a separate file to describe the input of a " +"run:" msgstr "" #: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +#: 9e1d9bc2f83743ea9964ec418d225200 msgid "`1st-workflow-job.yml`" msgstr "" #: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +#: a1240eab3ef746cf82a2c5451042b888 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" #: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +#: a73cdc43a8e44973808027c29903afa3 msgid "What's going on here? Let's break it down:" msgstr "" #: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +#: 4277837a9fd443378d5ca3d9252993c9 msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a " -"workflow." +"document. The `class` field indicates this document describes a workflow." msgstr "" #: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#: 09b714af60ee4ecc8ab1b95eac8284dd msgid "" -"The `inputs` section describes the inputs of the workflow. This is a " -"list of input parameters where each parameter consists of an identifier " -"and a data type. These parameters can be used as sources for input to " -"specific workflows steps." +"The `inputs` section describes the inputs of the workflow. This is a list " +"of input parameters where each parameter consists of an identifier and a " +"data type. These parameters can be used as sources for input to specific " +"workflows steps." msgstr "" #: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +#: 3e99a3be9265463daf74b00a21d89cff msgid "" -"The `outputs` section describes the outputs of the workflow. This is a " -"list of output parameters where each parameter consists of an identifier " -"and a data type. The `outputSource` connects the output parameter " -"`classfile` of the `compile` step to the workflow output parameter " -"`compiled_class`." +"The `outputs` section describes the outputs of the workflow. This is a list " +"of output parameters where each parameter consists of an identifier and a " +"data type. The `outputSource` connects the output parameter `classfile` of " +"the `compile` step to the workflow output parameter `compiled_class`." msgstr "" #: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +#: 1c4a959d43b74686ab801a26ef412b3d msgid "" "The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second " -"step compiles the file from the first step using the java compiler. " -"Workflow steps are not necessarily run in the order they are listed, " -"instead the order is determined by the dependencies between steps (using " -"`source`). In addition, workflow steps which do not depend on one " -"another may run in parallel." +"example, the first step extracts a file from a tar file, and the second step " +"compiles the file from the first step using the java compiler. Workflow " +"steps are not necessarily run in the order they are listed, instead the " +"order is determined by the dependencies between steps (using `source`). In " +"addition, workflow steps which do not depend on one another may run in " +"parallel." msgstr "" #: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +#: 55daf180336d4045ac0cc4c14af98cfc msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input" -" parameters, `tarfile` and `extractfile` and one output parameter " +"[Parameter References](parameter-references.md)). This tool has two input " +"parameters, `tarfile` and `extractfile` and one output parameter " "`extracted_file`." msgstr "" #: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +#: 5ae40eb04d5440d5ba882a74aa5b9708 msgid "" -"The ``in`` section of the workflow step connects these two input " -"parameters to the inputs of the workflow, `tarball` and " -"`name_of_file_to_extract` using `source`. This means that when the " -"workflow step is executed, the values assigned to `tarball` and " -"`name_of_file_to_extract` will be used for the parameters `tarfile` and " -"`extractfile` in order to run the tool." +"The ``in`` section of the workflow step connects these two input parameters " +"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " +"`source`. This means that when the workflow step is executed, the values " +"assigned to `tarball` and `name_of_file_to_extract` will be used for the " +"parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" #: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +#: f93e9b776a4544018877b7a13399609b msgid "" -"The `out` section of the workflow step lists the output parameters that " -"are expected from the tool." +"The `out` section of the workflow step lists the output parameters that are " +"expected from the tool." msgstr "" #: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +#: 0e587435e3884334bc51a4abf4b4d785 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described " -"previously in [Additional Arguments and Parameters](additional-arguments-" -"and-parameters.md)). The output of this step `classfile` is connected to " -"the `outputs` section for the Workflow, described above." +"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " +"in [Additional Arguments and Parameters](additional-arguments-and-parameters." +"md)). The output of this step `classfile` is connected to the `outputs` " +"section for the Workflow, described above." msgstr "" #: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +#: 81b98764289245c79f18fcff478f4a9b msgid "Nested Workflows" msgstr "" #: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +#: 9baddec4015f40ad82ea2dee30305654 msgid "" -"Workflows are ways to combine multiple tools to perform a larger " -"operations. We can also think of a workflow as being a tool itself; a CWL" -" workflow can be used as a step in another CWL workflow, if the workflow " -"engine supports the `SubworkflowFeatureRequirement`:" +"Workflows are ways to combine multiple tools to perform a larger operations. " +"We can also think of a workflow as being a tool itself; a CWL workflow can " +"be used as a step in another CWL workflow, if the workflow engine supports " +"the `SubworkflowFeatureRequirement`:" msgstr "" #: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +#: 986c3dd9460b42b3b20e2d01ba1fbe51 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" #: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +#: 4558f174fea445fd97b80d963fc74f43 msgid "`nestedworkflows.cwl`" msgstr "" #: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +#: 532823a13154401090e9fee3e018fda9 msgid "" -"This two-step workflow starts with the `create-tar` step which is " -"connected to the `compile` step in orange; `compile` is another workflow," -" diagrammed on the right. In purple we see the fixed string " -"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +"This two-step workflow starts with the `create-tar` step which is connected " +"to the `compile` step in orange; `compile` is another workflow, diagrammed " +"on the right. In purple we see the fixed string `\"Hello.java\"` being " +"supplied as the `name_of_file_to_extract`." msgstr "" #: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +#: 7b6f46b70bac4f848a956ea160243621 msgid "" " \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/nestedworkflows.cwl" +"\"> \"Visualization" msgstr "" #: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +#: 3861b4a31f71471b97bf9dc18cc80594 msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " -"its CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " -"mapped to become the step's input/outputs." +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " +"CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " +"to become the step's input/outputs." msgstr "" #: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +#: a10c37f65ac14ef2a5971872bc9b8f9a msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and " -"`*.java` filename. This is generally best-practice, as it means it can be" -" reused in multiple parent workflows, or even in multiple steps within " -"the same workflow." +"running it we had to provide a job file to denote the tar file and `*.java` " +"filename. This is generally best-practice, as it means it can be reused in " +"multiple parent workflows, or even in multiple steps within the same " +"workflow." msgstr "" #: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +#: 34175f932716406f836840732618caee msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar" -" file at `tarball`, which we will prepare in the `create-tar` step. At " -"this point it is probably a good idea to refactor `1st-workflow.cwl` to " -"have more specific input/output names, as those also appear in its usage " -"as a tool." +"`name_of_file_to_extract` input, however our workflow also requires a tar " +"file at `tarball`, which we will prepare in the `create-tar` step. At this " +"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " +"specific input/output names, as those also appear in its usage as a tool." msgstr "" #: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +#: 0d132dc39cdf4818bc8e20132073f669 msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3389,186 +3816,212 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +#: 9f8c45f077974cf79612ee83df3d152b msgid "" -"In this case our step can assume `Hello.java` rather than be " -"parameterized, so we can use hardcoded values `hello.tar` and " -"`Hello.java` in a `baseCommand` and the resulting `outputs`:" +"In this case our step can assume `Hello.java` rather than be parameterized, " +"so we can use hardcoded values `hello.tar` and `Hello.java` in a " +"`baseCommand` and the resulting `outputs`:" msgstr "" #: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +#: 435f80d0599b4d93ae1339e8c7bc020a msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This " -"is generally not best practice, as the tool then can't be reused. The " -"reason for doing it in this case is because the command line is hard-" -"coded with filenames that only make sense within this workflow." +"separate file, but rather embedded it within the CWL Workflow file? This is " +"generally not best practice, as the tool then can't be reused. The reason " +"for doing it in this case is because the command line is hard-coded with " +"filenames that only make sense within this workflow." msgstr "" #: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +#: d39b024a1a8d4eae8d7fd3c929a782e9 msgid "" -"In this example we had to prepare a tar file outside, but only because " -"our inner workflow was designed to take that as an input. A better " -"refactoring of the inner workflow would be to take a list of Java files " -"to compile, which would simplify its usage as a tool step in other " -"workflows." +"In this example we had to prepare a tar file outside, but only because our " +"inner workflow was designed to take that as an input. A better refactoring " +"of the inner workflow would be to take a list of Java files to compile, " +"which would simplify its usage as a tool step in other workflows." msgstr "" #: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +#: 3cbbe074843d4306b762d2fbc6fe9850 msgid "" "Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL" -" Tool description, care must be taken to improve its usability in " -"multiple workflows." +"functional and reusable workflow units - but just like for creating a CWL " +"Tool description, care must be taken to improve its usability in multiple " +"workflows." msgstr "" #: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +#: 7118b6e09b9f44129c7d98d90570f2c2 msgid "Scattering Steps" msgstr "" #: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +#: 70f3e73ee3714f22ad6ee43dd5ece703 msgid "" "Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish " -"to run a tool or workflow multiple times over a list of inputs. The " -"workflow then takes the input(s) as an array and will run the specified " -"step(s) on each element of the array as if it were a single input. This " -"allows you to run the same workflow on multiple inputs without having to " -"generate many different commands or input yaml files." +"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " +"run a tool or workflow multiple times over a list of inputs. The workflow " +"then takes the input(s) as an array and will run the specified step(s) on " +"each element of the array as if it were a single input. This allows you to " +"run the same workflow on multiple inputs without having to generate many " +"different commands or input yaml files." msgstr "" #: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +#: 279495257ead4a4fa725c7d68c504162 msgid "" -"The most common reason a new user might want to use scatter is to perform" -" the same analysis on different samples. Let's start with a simple " -"workflow that calls our first example (`hello_world.cwl`) and takes an " -"array of strings as input to the workflow:" +"The most common reason a new user might want to use scatter is to perform " +"the same analysis on different samples. Let's start with a simple workflow " +"that calls our first example (`hello_world.cwl`) and takes an array of " +"strings as input to the workflow:" msgstr "" #: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: 86d1d742bb5c4a9898aa573ce648f0ec msgid "`scatter-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +#: f4987847f46e4a2db54127ec7ebcadf7 msgid "" -"Aside from the `requirements` section including " -"`ScatterFeatureRequirement`, what is going on here?" +"Aside from the `requirements` section including `ScatterFeatureRequirement`, " +"what is going on here?" msgstr "" #: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +#: 80e7c22dfe4d40749f2e9c3bf02bf8bc msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" #: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +#: e930bb5d430a41d9b5bf49e473dd2ed1 msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This " -"field tells the runner that we'd like to scatter over this input for this" -" particular step. Note that the input name listed after scatter is the " -"one of the step's input, not a workflow level input." +"Here we've added a new field to the step `echo` called `scatter`. This field " +"tells the runner that we'd like to scatter over this input for this " +"particular step. Note that the input name listed after scatter is the one of " +"the step's input, not a workflow level input." msgstr "" #: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +#: 4076e9eb67ed4bd5942f089e394bad26 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if " -"you expect that the final output of your workflow will now have multiple " -"outputs to collect, be sure to update that to an array type as well!" +"collect any outputs, we still use `outputs: []` in our workflow, but if you " +"expect that the final output of your workflow will now have multiple outputs " +"to collect, be sure to update that to an array type as well!" msgstr "" #: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: 1b44092e87b840de8f1d022676d0990d msgid "Using the following input file:" msgstr "" #: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +#: a8afac626f5d4240a57267085b9bef26 msgid "`scatter-job.yml`" msgstr "" #: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +#: 0896efc674bc402495c6e73c6c352523 msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" -" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " +"calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" #: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +#: 91a53d918d4b47bdbe0b0a6d4adfc0dc msgid "" -"You can see that the workflow calls echo multiple times on each element " -"of our `message_array`. Ok, so how about if we want to scatter over two " -"steps in a workflow?" +"You can see that the workflow calls echo multiple times on each element of " +"our `message_array`. Ok, so how about if we want to scatter over two steps " +"in a workflow?" msgstr "" #: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +#: 8325682d51d8421b9ea507f424f71e73 msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding " -"the following lines instead of `outputs: []`" +"Let's perform a simple echo like above, but capturing `stdout` by adding the " +"following lines instead of `outputs: []`" msgstr "" #: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +#: 503d068602d8477a820b91d835fa3f28 msgid "`hello_world_to_stdout.cwl`" msgstr "" #: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +#: 4e768b91eb274a5cb157f1e3fe2f85cd msgid "" -"And add a second step that uses `wc` to count the characters in each " -"file. See the tool below:" +"And add a second step that uses `wc` to count the characters in each file. " +"See the tool below:" msgstr "" #: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +#: 18ec5231b7bf4c9ea59361b325fcdd01 msgid "`wc-tool.cwl`" msgstr "" #: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +#: 87fd118dc2774cf08db0a3ba56520da5 msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under " -"each step:" +"Now, how do we incorporate scatter? Remember the scatter field is under each " +"step:" msgstr "" #: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +#: 8168ffcb23124b3f839a9862a7ec0958 msgid "`scatter-two-steps.cwl`" msgstr "" #: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 -msgid "" -"Here we have placed the scatter field under each step. This is fine for " -"this example since it runs quickly, but if you're running many samples " -"for a more complex workflow, you may wish to consider an alternative. " -"Here we are running scatter on each step independently, but since the " -"second step is not dependent on the first step completing all languages, " -"we aren't using the scatter functionality efficiently. The second step " -"expects an array as input from the first step, so it will wait until " -"everything in step one is finished before doing anything. Pretend that " -"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " -"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " -"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " -"could finish in 4 minutes, it will actually finish in 8 minutes because " -"the first step must wait on `echo Hallo welt!`. You can see how this " -"might not scale well." +#: 37c222ea14904fd4a8fa93a1e0103239 +msgid "" +"Here we have placed the scatter field under each step. This is fine for this " +"example since it runs quickly, but if you're running many samples for a more " +"complex workflow, you may wish to consider an alternative. Here we are " +"running scatter on each step independently, but since the second step is not " +"dependent on the first step completing all languages, we aren't using the " +"scatter functionality efficiently. The second step expects an array as input " +"from the first step, so it will wait until everything in step one is " +"finished before doing anything. Pretend that `echo Hello World!` takes 1 " +"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " +"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " +"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " +"actually finish in 8 minutes because the first step must wait on `echo Hallo " +"welt!`. You can see how this might not scale well." msgstr "" #: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +#: d392813fc6d14851a294a391426d41f6 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can" -" make an entire workflow a single step in another workflow! Convert our " -"two-step workflow to a single step subworkflow:" +"samples? Remember from [Nested Workflows](#nested-workflows), that we can " +"make an entire workflow a single step in another workflow! Convert our two-" +"step workflow to a single step subworkflow:" msgstr "" #: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +#: 652155460eaa42b6856c16cffdb845c0 msgid "`scatter-nested-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +#: 6313cb377dc249e0b2262a3fe732fe32 msgid "" -"Now the scatter acts on a single step, but that step consists of two " -"steps so each step is performed in parallel." +"Now the scatter acts on a single step, but that step consists of two steps " +"so each step is performed in parallel." msgstr "" #: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +#: 11f73cf24fb044e3a3afb3adb6137708 msgid "Conditional Workflows" msgstr "" #: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +#: def9e62bf73f49eebce09677954e2a92 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " @@ -3576,252 +4029,357 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +#: 200dfe47d09d4b0b9e4acf29b7e038da msgid "`conditional-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +#: 858bda7fb6524e9dbfb35596ce6a6d07 msgid "" -"The first thing you'll notice is that this workflow is only compatible " -"for version 1.2 or greater of the CWL standards." +"The first thing you'll notice is that this workflow is only compatible for " +"version 1.2 or greater of the CWL standards." msgstr "" #: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +#: 28897819504247a3a6cf9a9d9476b63b msgid "" "The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when`" -" is where the condition validation takes place. In this case only when " -"`in1` from the workflow contains a value `< 1` this step will be " -"executed." +"will execute foo.cwl when the conditions are met. The new property `when` is " +"where the condition validation takes place. In this case only when `in1` " +"from the workflow contains a value `< 1` this step will be executed." msgstr "" #: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +#: 4f8fd11e29b048e1851299002c3a48c4 msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" -" will pass the first conditional step and will therefore be executed and " -"is shown in the log by `INFO [step step1] start` whereas the second step " -"is skipped as indicated by `INFO [step step2] will be skipped`." +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " +"will pass the first conditional step and will therefore be executed and is " +"shown in the log by `INFO [step step1] start` whereas the second step is " +"skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" #: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +#: ed33196347d949eda752a081c7af4657 msgid "" -"When a value of 3 is given the first conditional step will not be " -"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +"When a value of 3 is given the first conditional step will not be executed " +"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" #: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +#: 738c67568dbb4f2bbb5756fc5e727c01 msgid "" -"If no conditions are met for example when using `--val 2` the workflow " -"will raise a permanentFail." +"If no conditions are met for example when using `--val 2` the workflow will " +"raise a permanentFail." msgstr "" #: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +#: 19b016a1fec14056a9812c1c195c7c90 msgid "YAML Guide" msgstr "" #: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +#: a513367d60a74f559339c05d8ef10eb7 msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers " -"and humans. This guide introduces the features of YAML that are relevant " -"when writing CWL descriptions and input parameter files." +"[YAML][yaml] is a file format designed to be readable by both computers and " +"humans. This guide introduces the features of YAML that are relevant when " +"writing CWL descriptions and input parameter files." msgstr "" #: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +#: 5e30680941164047a47f98417e916188 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" #: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +#: ca02f2bf1d754d5190f296674245b936 msgid "Contents" msgstr "" #: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +#: 466615194bb541fdbe2e6515b50531b3 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" #: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +#: 33e664d59a30407891336db290a8a5b2 msgid "[Comments](#comments)" msgstr "" #: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +#: 3e52ab079dcf4fc6a3f052a517f4d31b msgid "[Maps](#maps)" msgstr "" #: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: abcad6b7d37a4342a90c2d5952ea1232 msgid "[Arrays](#arrays)" msgstr "" #: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: 500a489e4fae4d1abaa8883f632d1a24 msgid "[JSON Style](#json-style)" msgstr "" #: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +#: 546c1ef51a63487c91c98059dd46b0cb msgid "Key-Value Pairs" msgstr "" #: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +#: 72b4262833054edd9efe6078381de654 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the " -"`:` is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have " -"special meaning in the CWL specification and underscored key names " -"otherwise. For example:" +"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " +"is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have special " +"meaning in the CWL specification and underscored key names otherwise. For " +"example:" msgstr "" #: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +#: 7b7e8242660744b791ba3868e4ed7e37 msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, " -"`age_years`, and `home` - with their four respective values. Values can " -"be character strings, numeric (integer, floating point, or scientific " -"representation), Boolean (`true` or `false`), or more complex nested " -"types (see below)." +"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " +"and `home` - with their four respective values. Values can be character " +"strings, numeric (integer, floating point, or scientific representation), " +"Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" #: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +#: 492d994a541c4c948fb5da9041153bcf msgid "" -"Values may be wrapped in quotation marks, but be aware that this may " -"change the way that they are interpreted i.e. `\"1234\"` will be treated " -"as a character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a" -" command: in CWL all parts of `baseCommand` must be strings so, if you " -"want to specify a fixed numeric value to a command, make sure that you " -"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +"Values may be wrapped in quotation marks, but be aware that this may change " +"the way that they are interpreted i.e. `\"1234\"` will be treated as a " +"character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a " +"command: in CWL all parts of `baseCommand` must be strings so, if you want " +"to specify a fixed numeric value to a command, make sure that you wrap that " +"numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" #: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: e2209269db394f3988f18b147a57677c msgid "Comments" msgstr "" #: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +#: e15c39c65aca47f690264d8008463bec msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program " -"interpreting the YAML. For example:" +"characters to the right of ` #` will be ignored by the program interpreting " +"the YAML. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +#: afa546fcb7fb447d939d4a167f206f79 msgid "" -"If there is anything on the line before the comment, be sure to add at " -"least one space before the `#`!" +"If there is anything on the line before the comment, be sure to add at least " +"one space before the `#`!" msgstr "" #: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +#: 7dd375e0fd964413af4957396d2a0474 msgid "Maps" msgstr "" #: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +#: af8ef039a64a4c0783d7229dbdac65ef msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, " -"these hierarchical structures are described in YAML by providing " -"additional key-value pairs as the value of any key. These pairs " -"(sometimes referred to as \"children\") are written on new lines under " -"the key to which they belong (the \"parent\"), and should be indented " -"with two spaces (⇥tab characters are not allowed). For example:" +"construct more complex, nested representations. Referred to as _maps_, these " +"hierarchical structures are described in YAML by providing additional key-" +"value pairs as the value of any key. These pairs (sometimes referred to as " +"\"children\") are written on new lines under the key to which they belong " +"(the \"parent\"), and should be indented with two spaces (⇥tab characters " +"are not allowed). For example:" msgstr "" #: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +#: 3ce968cb39a443059f6a828b3c8c2f33 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and " -"`inputBinding`, while one of these children, `inputBinding`, contains a " -"further two key-value pairs (`position` and `prefix`). See the " -"[Arrays](#arrays) section below for more information about providing " -"multiple values/key-value pairs for a single key. For comparison with the" -" example YAML above, here is a graphical representation of the `inputs` " -"object it describes." +"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " +"while one of these children, `inputBinding`, contains a further two key-" +"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " +"below for more information about providing multiple values/key-value pairs " +"for a single key. For comparison with the example YAML above, here is a " +"graphical representation of the `inputs` object it describes." msgstr "" #: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +#: 3c2f48a8e616400b9a8ffb4b6f7efc9b msgid "Arrays" msgstr "" #: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +#: c432b1656e0e49ef87aa3d6e42acad84 msgid "" "In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) " -"section above, more than one key-value pair can be mapped to a single " -"key. However, it is also possible to define multiple values for a key " -"without having to provide a unique key for each value. We can achieve " -"this with an _array_, where each value is defined on its own line and " -"preceded by `-`. For example:" +"objects for a single key. As we've already seen in the [Maps](#maps) section " +"above, more than one key-value pair can be mapped to a single key. However, " +"it is also possible to define multiple values for a key without having to " +"provide a unique key for each value. We can achieve this with an _array_, " +"where each value is defined on its own line and preceded by `-`. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +#: cac5e52767f74ce98693e2a19ee1eb0d msgid "and a more complex example combining maps and arrays:" msgstr "" #: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +#: 101666907f8b4fb994e25ceffcf04a13 msgid "JSON Style" msgstr "" #: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +#: 5461960a469042a487b89e440f856aea msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " -"arrays can also be defined in YAML using the native JSON syntax. For " -"example:" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " +"can also be defined in YAML using the native JSON syntax. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +#: e31349c164c84a9da46e2fb1861793df msgid "and:" msgstr "" #: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +#: 49a0b3dfdc9e4d58b6bc966db979ace8 msgid "" -"Native JSON can be useful in indicating where a field is intentionally " -"left empty (such as `[]` for an empty array), as well as where it makes " -"more sense for the values to be located on the same line (For example, " -"when providing option flags and their values in a shell command). " -"However, as the second example above shows, it can severely affect the " -"readability of a YAML file, and should be used sparingly." +"Native JSON can be useful in indicating where a field is intentionally left " +"empty (such as `[]` for an empty array), as well as where it makes more " +"sense for the values to be located on the same line (For example, when " +"providing option flags and their values in a shell command). However, as the " +"second example above shows, it can severely affect the readability of a YAML " +"file, and should be used sparingly." msgstr "" #: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +#: e08ec8c473e847f98e8a18b9ca0f2670 msgid "Reference" msgstr "" #: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +#: 6ee7bfb4a9e04dd19b5180bca5b02705 msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" -" us while we wrote this guide, though it also covers features that are " -"not valid in CWL." +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " +"while we wrote this guide, though it also covers features that are not valid " +"in CWL." msgstr "" #: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +#: 42614ab7ba1546f89abeb8f48991271c msgid "Tutorials" msgstr "" #: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +#: b8df5b8393ed4d869c066640fe83ec7b msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to " -"the list." +"this page` link in the menu if you would like to add another tutorial to the " +"list." msgstr "" #: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +#: 5b9aee5af41f438b9f4208294bf97f4a msgid "Beginner Tutorials" msgstr "" #: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +#: a71d3022dcfc44979cca4655ea51ad42 msgid "" -"[Introduction to Workflows with Common Workflow Language: For " -"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" -"tutorial/)" +"[Introduction to Workflows with Common Workflow Language: For Contributors.]" +"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" #: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +#: 42b5a982e86f46dfbfcd7bfcc99d72a5 msgid "Advanced Tutorials" msgstr "" #: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +#: 12dc402d053044b78d69927dd391fe9d msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" #: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +#: 687c20e2e4bc4f869c7ee9390e61476a msgid "Bioinformatics Tutorials" msgstr "" #: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +#: a975fbb3ea7d467881ce0245de538295 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" +#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee +msgid "" +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the `Creative Commons " +"Attribution license `_. The following is a human-readable " +"summary of (and not a substitute for) the `full legal text of the CC BY 4.0 " +"license `_." +msgstr "" +"Todo el material instructivo del proyecto Common Workflow Language y los " +"cambios en la estructura también están disponibles bajo la `licencia " +"Creative Commons Attribution `_. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del `texto legal completo de la " +"licencia CC BY 4.0 `_." + +#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 +msgid "to **Share**—copy and redistribute the material in any medium or format" +msgstr "" +"**Compartir**—copiar y redistribuir el material en cualquier medio o formato" + +#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 +msgid "to **Adapt**—remix, transform, and build upon the material" +msgstr "**Adaptar**—remezclar, transformar y construir a partir del material" + +#: ../../LICENSE.rst:23 be38276e7b374f57b9997391bf898a62 +msgid "" +"**Attribution**—You must give appropriate credit (mentioning that your work " +"is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a `link to the license `_, and indicate if changes " +"were made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." +msgstr "" +"**Atribución**---Usted debe dar crédito de manera adecuada(mencionando que " +"su trabajo se deriva de un trabajo que tiene «Copyright © The Common " +"Workflow Language Project» y, cuando sea práctico, con un enlace a " +"https://www.commonwl.org/%20),%20brindar%20un%20%60enlace%20a%20la%20licencia%20%3Ccc-by-human_%3E%60" +"_, e indicar si se han realizado cambios. Puede hacerlo en cualquier forma " +"razonable, pero no de forma tal que sugiera que usted o su uso tienen el " +"apoyo de la licenciante." + +#: ../../LICENSE.rst:31 f00d5c3846034c2ea116c2f74786d9fc +msgid "" +"**No additional restrictions**—You may not apply legal terms or " +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" +msgstr "" +"**No hay restricciones adicionales**---No puede aplicar términos legales ni " +"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " +"permitido por la licencia. Con el entendimiento de que:" + +#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the " +"`OSI`_-approved `Apache 2.0 license `_." +msgstr "" +"Excepto cuando se indique lo contrario, los programas de ejemplo y otro " +"software proporcionado por el proyecto Common Workflow Language están " +"disponibles bajo la `licencia Apache 2.0 `_ aprobada por la " +"`OSI`_." + +#: ../../LICENSE.rst:50 4ee4d68b90fe422880da856cd539b982 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." +msgstr "" diff --git a/locales/pt/LC_MESSAGES/sphinx.po b/locales/pt/LC_MESSAGES/sphinx.po index 38526232..fc56cb08 100644 --- a/locales/pt/LC_MESSAGES/sphinx.po +++ b/locales/pt/LC_MESSAGES/sphinx.po @@ -4,25 +4,27 @@ # Language User Guide package. # FIRST AUTHOR , 2023. # -#, fuzzy msgid "" msgstr "" -"Project-Id-Version: Common Workflow Language User Guide \n" +"Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: FULL NAME \n" -"Language-Team: LANGUAGE \n" +"PO-Revision-Date: 2023-01-26 13:55+0000\n" +"Last-Translator: Michael Crusoe \n" +"Language-Team: Portuguese \n" +"Language: pt\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" #: ../../src/_templates/sidebar-nav-bs.html:1 d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" -msgstr "" +msgstr "Navegação principal" #: ../../src/_templates/sidebar-nav-bs.html:3 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" -msgstr "" - +msgstr "Seção Navegação" diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po index 3584ce39..fd0da8d1 100644 --- a/locales/pt/LC_MESSAGES/user_guide.po +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -12,8 +12,8 @@ msgstr "" "POT-Creation-Date: 2023-01-24 17:23+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" -"Language-Team: Portuguese \n" +"Language-Team: Portuguese \n" "Language: pt\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" @@ -21,21 +21,23 @@ msgstr "" "Plural-Forms: nplurals=2; plural=n > 1;\n" "X-Generator: Weblate 4.16-dev\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 ../../LICENSE.rst:2 +#: 75de2be8809847b8bf1ccd42aa694a24 msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 ../../LICENSE.rst:5 +#: 2edd71801f6245ef821887a74f21b94c msgid "Instructional Material" msgstr "" #: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable " -"summary of (and not a substitute for) the [full legal text of the CC BY " -"4.0 license][cc-by-legal]." +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable summary " +"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" +"[cc-by-legal]." msgstr "" "Todo o material instrucional do projeto Common Workflow Language e " "alterações na estrutura também são disponibilizados sob a [licença Creative " @@ -43,12 +45,14 @@ msgstr "" "humanos de (e não um substituto para) o [texto legal completo da licença CC " "BY 4.0][cc-by-legal]." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 ../../LICENSE.rst:12 +#: 90cc755d172e4c82b882b4ee620fe652 msgid "You are free:" msgstr "Você tem o direito de:" #: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" +msgid "" +"to **Share**---copy and redistribute the material in any medium or format" msgstr "" "**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " "formato" @@ -57,27 +61,28 @@ msgstr "" msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 ../../LICENSE.rst:18 +#: 430ff4de74924bc3a3b2c7e809ea4456 msgid "for any purpose, even commercially." msgstr "para qualquer fim, mesmo que comercial." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e ../../LICENSE.rst:20 +#: 2173e2af49be41ee97a74c4e879faf25 msgid "" -"The licensor cannot revoke these freedoms as long as you follow the " -"license terms:" +"The licensor cannot revoke these freedoms as long as you follow the license " +"terms:" msgstr "" "O licenciante não pode revogar estes direitos desde que você respeite os " -"termos da licença." +"termos da licença:" #: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow " -"Language project, and, where practical, linking to " -"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" -"human], and indicate if changes were made. You may do so in any " -"reasonable manner, but not in any way that suggests the licensor endorses" -" you or your use." +"work is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a [link to the license][cc-by-human], and indicate if changes were " +"made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." msgstr "" "Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " "trabalho deriva de um trabalho que é «Copyright © The Common Workflow " @@ -90,136 +95,153 @@ msgstr "" #: ../../LICENSE.md:32 8161753b7526445db319210044566200 msgid "" "**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything " -"the license permits. With the understanding that:" +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" msgstr "" "**Sem restrições adicionais**---Você não pode aplicar termos jurídicos ou " "medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " "algo que a licença permita. Com o entendimento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 ../../LICENSE.rst:35 +#: f6aae4a5cd0547118c8a3240ca2b4be6 msgid "" -"You do not have to comply with the license for elements of the material " -"in the public domain or where your use is permitted by an applicable " -"exception or limitation." +"You do not have to comply with the license for elements of the material in " +"the public domain or where your use is permitted by an applicable exception " +"or limitation." msgstr "" "Não tem de cumprir com os termos da licença relativamente a elementos do " "material que estejam no domínio público ou cuja utilização seja permitida " "por uma exceção ou limitação que seja aplicável." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 ../../LICENSE.rst:38 +#: a40c173be35b4c1b92e83f42bfe2382c msgid "" -"No warranties are given. The license may not give you all of the " -"permissions necessary for your intended use. For example, other rights " -"such as publicity, privacy, or moral rights may limit how you use the " -"material." +"No warranties are given. The license may not give you all of the permissions " +"necessary for your intended use. For example, other rights such as " +"publicity, privacy, or moral rights may limit how you use the material." msgstr "" "Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " "autorizações necessárias para o uso pretendido. Por exemplo, outros " "direitos, tais como direitos de imagem, de privacidade ou direitos morais, " "podem limitar o uso do material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea ../../LICENSE.rst:44 +#: 3d7ca3f2cede4d5f998bf014bd970748 msgid "Software" msgstr "Software" #: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 msgid "" "Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +"provided by Common Workflow Language project are made available under the " +"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Salvo indicação em contrário, os programas de exemplo e outro software " -"fornecido pelo projecto Common Workflow Language são disponibilizados sob a [" -"licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a " +"[licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." #: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, " -"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " -"See the License for the specific language governing permissions and " -"limitations under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 #: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 -#: eab02dc13915490bb3c9ba744d78b6a7 +#: eab02dc13915490bb3c9ba744d78b6a7 5ad4be9b62d54c95a913795b514676fd +#: bdd540403a5746ff99edf2dcad0e3122 dfc7702e073140c985cf47272a20214d msgid "" "CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." +"create workflows. Because CWL is a specification and not a specific piece of " +"software, tools and workflows described using CWL are portable across a " +"variety of platforms that support the CWL standard." msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 #: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 msgid "This page has moved" msgstr "" #: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +#: 3060770b3bef41d7bcfcdfb413d7689c msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" #: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +#: 48bb9f628b344ba1a3b67ae1cb264e3c msgid "FAQ" msgstr "" #: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +#: 7e3684e9672643738846756e1ebafd18 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" #: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 +#: 187ceabb7fd9480bb8cf0f2da47f65ef msgid "Rename an Input File" msgstr "" #: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +#: b548b76bcc85420a9b30792386105139 msgid "" -"This example demonstrates how to change the name of an input file as part" -" of a tool description. This could be useful when you are taking files " -"produced from another step in a workflow, and don't want to work with the" -" default names that these files were given when they were created." +"This example demonstrates how to change the name of an input file as part of " +"a tool description. This could be useful when you are taking files produced " +"from another step in a workflow, and don't want to work with the default " +"names that these files were given when they were created." msgstr "" #: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f +#: 9ce692b78ead47e4b0f8cdae8837d35b msgid "Rename an Output File" msgstr "" #: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +#: 6df1201c159343da9e7515379980d6a0 msgid "" -"This example demonstrates how to change the name of an output file from " -"the default name given to it by a tool:" +"This example demonstrates how to change the name of an output file from the " +"default name given to it by a tool:" msgstr "" #: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 +#: f9ab1d0dc1c842b6abb5385268c1d3bd msgid "Referencing a Local Script" msgstr "" #: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +#: 9f6a84ab6a9343b6ad7db826f8964362 msgid "There are two ways to reference a local script:" msgstr "" #: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +#: fa50e4fa990b42d1ba4c0f4ae1e5caa1 msgid "" -"The first method involves adding the folder containing your scripts to " -"the `PATH` environment variable. This allows you to run the shell script " +"The first method involves adding the folder containing your scripts to the " +"`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" #: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +#: 3a871012fcfd4f3ebeca0cb86ec93435 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" #: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +#: d954edfff2584288ac8c600733070d2e msgid "" -"After that, make the script executable with the command `chmod +x " -"scriptname.sh`" +"After that, make the script executable with the command `chmod +x scriptname." +"sh`" msgstr "" #: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +#: af6b1e37d6be4450a761854480ec9aab msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " @@ -227,117 +249,138 @@ msgid "" msgstr "" #: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +#: 31f4a2d43062493ca64c648f80afc8e9 +msgid "" +"Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" #: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +#: 41c54e71b6cd4f63b2a619a515240d34 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" #: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +#: 8edc3541ad134ab5a1d23c724f1f0a4e msgid "" -"The second method involves including an input of `type: File` in the " -"script itself:" +"The second method involves including an input of `type: File` in the script " +"itself:" msgstr "" #: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 +#: ac0ea81eba8842a18801ab03cbf80a57 msgid "In CWL, everything must be directly stated." msgstr "" #: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +#: 52be1a5640234feabe958ff7ade33653 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" #: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +#: c6db734d5aef4f4f99676bdebf9c83c9 msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their " -"input binding makes use of `self`. Below is an example workaround for " -"this, pending a more sophisticated fix." +"Currently, `cwltool` can't cope with missing optional inputs if their input " +"binding makes use of `self`. Below is an example workaround for this, " +"pending a more sophisticated fix." msgstr "" #: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 +#: a9f7b47c0dd741739795da39bf114879 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" #: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +#: e3fdd9228b924905a4a1f4b2b7ad7159 msgid "" -"Below is an example showing how to specify different strings to be added " -"to a command line, based on the value given to a Boolean parameter." +"Below is an example showing how to specify different strings to be added to " +"a command line, based on the value given to a Boolean parameter." msgstr "" #: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +#: 3f7cda1437cc48f18745a827ebb74582 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" #: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +#: 5aeaba2cae64442e816bbd458aee833a msgid "" -"Using " -"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" -" along with [`linkMerge: " +"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +#: 5af827a402834978addd82c70be6b5ab msgid "merge_nested" msgstr "" #: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +#: 6d69e42bd8e443c4b19d80807c7efd6b msgid "" -"The input must be an array consisting of exactly one entry for each input" -" link. If \"merge_nested\" is specified with a single link, the value " -"from the link must be wrapped in a single-item list." +"The input must be an array consisting of exactly one entry for each input " +"link. If \"merge_nested\" is specified with a single link, the value from " +"the link must be wrapped in a single-item list." msgstr "" #: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +#: 404640397b6e40c2a2cd5cf85ab3b1c0 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" #: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +#: 1682c2486e224770b62269709a8663cf msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " -"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" -" destination step." +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " +"add `linkMerge: merge_nested` under the appropriate `in` entry of the " +"destination step." msgstr "" #: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd +#: 9078fc009bc145808813c9cc2b734b58 msgid "Optional Inputs 💯" msgstr "" #: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +#: d4b5a54a400c409cb7984428f6a03ec8 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" #: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +#: 9e8dbee6e8f84d08b1a54fffa06394ef msgid "" msgstr "" #: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c +#: 1d846bfb5f054d09a4afad1da8e4b642 msgid "Enum Inputs ⚜️" msgstr "" #: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +#: 2d0e95fec8084787b734388d60188574 msgid "" -"For command line flags that require a specific input as the argument an " -"enum type can be declared in CWL. **Specifying null here is known as long" -" form style. It does the same thing as the question mark on the other " -"inputs.**" +"For command line flags that require a specific input as the argument an enum " +"type can be declared in CWL. **Specifying null here is known as long form " +"style. It does the same thing as the question mark on the other inputs.**" msgstr "" #: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +#: eccc4a364330470fa474dcaaa3433390 msgid "" msgstr "" #: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 +#: e945f6a337af4e4686bed482a4fe6c39 msgid "Record Inputs 📀" msgstr "" #: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +#: 8a3efaa0ad1548428bcfd6e01d135cdc msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " @@ -345,117 +388,138 @@ msgid "" msgstr "" #: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 +#: cdab644adc5643708870fb08c06cbfca msgid "Setting Mutually Exclusive Parameters" msgstr "" #: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +#: 089a5a0b076b44aeaab4d69ee3c79f97 msgid "" -"To properly set fields in a record input type, you need to pass a " -"dictionary to the input to properly set the parameters. This is done by " -"using inline JavaScript and returning the dictionary with the key of the " -"field you want to set. The source field is set to indicate the input from" -" the workflow to be used as the value." +"To properly set fields in a record input type, you need to pass a dictionary " +"to the input to properly set the parameters. This is done by using inline " +"JavaScript and returning the dictionary with the key of the field you want " +"to set. The source field is set to indicate the input from the workflow to " +"be used as the value." msgstr "" #: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 +#: 561172559c6f41a68819608fd9e58bb0 msgid "Setting Booleans" msgstr "" #: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +#: c5ee4946d2e840abaa3dc796a62652c7 msgid "These can be set by using the default field" msgstr "" #: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 +#: 4f2069a2113c414db18eca95550e9e09 msgid "Concatenating Strings in Inputs" msgstr "" #: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +#: 31f3390e6771414ba7bf57c044c4b0c4 msgid "The valueFrom field must be used instead of default." msgstr "" #: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c +#: 3b77ce4930ae46d5be9f6965e8c54727 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" #: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +#: 06f36bbe4d3840229b7374f27b86ae80 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" #: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +#: 3cb2f70d00274a4dafd972ccd8c519c2 msgid "" -"For example, the filename `a space is here.txt` includes 3 space " -"characters." +"For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" #: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +#: 093a1529262043ef84a99675054938e0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" #: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +#: 45b6d9acbfaa47e5984184f7da554d0a msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +#: 5705c9bacca5405ca6f14315a5575db8 msgid "If `cwltool --validate` returns valid" msgstr "" #: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +#: 82bfc285b59a439ca97d3278997f0fce msgid "But executing it causes an error like:" msgstr "" #: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +#: 181d5130101d45ccb22aebae3d154c2f msgid "The file is here" msgstr "" #: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +#: e864390b5ddb423aaa10e9d33d257dc1 msgid "Problem caused by `-` (hyphen character)." msgstr "" #: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 +#: fe637c32fb15427a9045679b5da42ec5 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" #: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +#: 1f8004b9df8547029d82e57f9abdc979 msgid "" -"If it is not possible to change the input identifier, then you can use an" -" alternative CWL Parameter Reference syntax:" +"If it is not possible to change the input identifier, then you can use an " +"alternative CWL Parameter Reference syntax:" msgstr "" #: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 +#: 70990dc5a0034099921ceb89c89e2dcc msgid "Use CWL and cwltool with Singularity" msgstr "" #: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +#: f679e26f18d9455f945fd13361a9c906 msgid "" -"The CWL standards are built around (optional) Docker format containers. " -"The reference runner and several other CWL implementations support " -"running those Docker format containers using the Singularity engine. " -"Directly specifying a Singularity format container is not part of the CWL" -" standards." +"The CWL standards are built around (optional) Docker format containers. The " +"reference runner and several other CWL implementations support running those " +"Docker format containers using the Singularity engine. Directly specifying a " +"Singularity format container is not part of the CWL standards." msgstr "" #: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 +#: fcd0273dbdd84e728cfd8fbe239f2a01 msgid "Debug JavaScript Expressions" msgstr "" #: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +#: 173ddbd1e7c64927a8dcb12a2a2140f8 msgid "" -"You can use the --js-console option of cwltool," -" or you can try creating a JavaScript or TypeScript project for your " -"code, and load it using expressionLib, e.g.: " -"https://github.com/common-workflow-language/common-workflow-" -"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +"You can use the --js-console option of cwltool, or " +"you can try creating a JavaScript or TypeScript project for your code, and " +"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" #: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +#: 662fe273e2fb4042b688512955e450a1 msgid "Common Workflow Language User Guide" msgstr "" #: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +#: a15b52205f0145feaac298510e4d678a msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " @@ -463,267 +527,275 @@ msgid "" msgstr "" #: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +#: 512aa0c7166b429e8116f71eef007f79 msgid "Contributions and Feedback are Welcome!" msgstr "" #: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +#: b1b19e17a18540939cb3bb7f8a700cab msgid "" -"If you find that something is missing from this guide, or if you would " -"like to provide other feedback, file an Issue on the [project repository " -"for this guide][repo]. You can also suggest changes directly in a Pull " -"Request by clicking the \"Edit this page\" button at the right sidebar of" -" each page." +"If you find that something is missing from this guide, or if you would like " +"to provide other feedback, file an Issue on the [project repository for this " +"guide][repo]. You can also suggest changes directly in a Pull Request by " +"clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" #: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +#: d58b36ac43ac44139897be752fbb1f87 msgid "Navigating the User Guide" msgstr "" #: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +#: 6726cf3585a646a8b4cbeb543cf84a38 msgid "" -"If you are a beginner user get started with the " -"[Introduction](/introduction/index.md) section. For advanced users the " -"subsections of the [Topics](/topics/index.md) have detailed information " -"about the most common topics for CWL." +"If you are a beginner user get started with the [Introduction](/introduction/" +"index.md) section. For advanced users the subsections of the [Topics](/" +"topics/index.md) have detailed information about the most common topics for " +"CWL." msgstr "" #: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +#: 2e504aa7c46a426fa959e7254e9a84a5 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " -"subsections. The right sidebar contains links to the sections of each " -"page, and the Search form is on the left sidebar." +"subsections. The right sidebar contains links to the sections of each page, " +"and the Search form is on the left sidebar." msgstr "" #: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +#: e7be0df0838b432d9c7f296d777f120b msgid "Table of Contents" msgstr "" #: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +#: 173e0816db20432c8d9dba1de5393dee msgid "Basic Concepts" msgstr "" #: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +#: 30eacc583f6841719e2142d283811d97 msgid "" "This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are " -"expected to be familiar with workflow managers, YAML, and comfortable " -"with following instructions for the command-line. The other sections of " -"the user guide cover the same concepts, but in more detail. If you are " -"already familiar with CWL or you are looking for more advanced content, " -"you may want to skip this section." +"working with Common Workflow Language (CWL) workflows. Readers are expected " +"to be familiar with workflow managers, YAML, and comfortable with following " +"instructions for the command-line. The other sections of the user guide " +"cover the same concepts, but in more detail. If you are already familiar " +"with CWL or you are looking for more advanced content, you may want to skip " +"this section." msgstr "" #: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +#: 791b8f38a14147bbaa174c7eb595f17e msgid "The CWL Specification" msgstr "" #: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +#: 1a3989dcbb9844b39d84bf6df6b352ed msgid "" "The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered " -"in this user guide is the {{ cwl_version }}." +"community. The specification has different versions. The version covered in " +"this user guide is the {{ cwl_version }}." msgstr "" #: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +#: db1bbc6e980f404f9f3fcd08e92ee9a3 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" "incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes " -"that are backward-compatible. The last number is used for bug fixes, like" -" typos and other corrections to the specification." +"number is the minor release, used for new features or smaller changes that " +"are backward-compatible. The last number is used for bug fixes, like typos " +"and other corrections to the specification." msgstr "" #: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +#: acc7887c65974114996f700a38a7eccc msgid "" -"The model used for the specification version is called Semantic " -"Versioning. See the end of this section to [learn more](#learn-more) " -"about it." +"The model used for the specification version is called Semantic Versioning. " +"See the end of this section to [learn more](#learn-more) about it." msgstr "" #: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +#: d2476d9bcff44f21b8d84a3a0d87a246 msgid "Implementations" msgstr "" #: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +#: f86415e4d78e48c4a8a76ced81221b98 msgid "" -"An implementation of the CWL specification is any software written " -"following what is defined in a version of the specification document. " -"However, implementations may not implement every aspect of the " -"specification. CWL implementations are licensed under both Open Source " -"and commercial licenses." +"An implementation of the CWL specification is any software written following " +"what is defined in a version of the specification document. However, " +"implementations may not implement every aspect of the specification. CWL " +"implementations are licensed under both Open Source and commercial licenses." msgstr "" #: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +#: c5524d73708c4c779980528864506fd4 msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud" -" and high performance computing environments where tasks are scheduled in" -" parallel across many nodes." +"CWL is well suited for describing large-scale workflows in cluster, cloud " +"and high performance computing environments where tasks are scheduled in " +"parallel across many nodes." msgstr "" #: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +#: ac46a9f8850a434bac5bc2b41ee6294e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: a5ebc727fb3443f78e81d6b7ed5ac750 9bba7c4f783942e4a299603430601363 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 +#: 86e6a06992dc4228bfda7add48e28ca3 e2140e0f0e7747ef8383887c20a7945a msgid "" -"A process is a computing unit that takes inputs and produces outputs. The" -" behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification" -" {{ cwl_version }}:" +"A process is a computing unit that takes inputs and produces outputs. The " +"behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification " +"{{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 8c9772f96caf4169924d22eb929a4f0f 15bf490724cd46dcbcfab44633c5a9a2 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 4fac209a62114798b79e4810f7a0148b 51d52d051e654a8395239f88df7c9d8c msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: b97ba368fd664caab0494e2392795697 eb496cc818524fa7bae5a22ddd00a19c msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: 903a6796e3304a19ad885b2428b0e80f c4a22d12e7f149ff901d27de32b9361d msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 6e352ac1f8e144c392ac5adf18c28298 7618de899a7043989d77baacf62eb7b2 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a +#: cf2922f645904ac7955428ecddc37b8a 6f1544a220664b79b04bf008058b5a91 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 +#: 5f47aae608c041aeb4134d59dad314d2 fbd14ac9a2f541478a320ed4cbc69e13 msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be " -"used to simplify workflows and command-line tools, moving common parts of" -" a workflow execution into reusable JavaScript code that takes inputs and" -" produces outputs like a command-line tool." +"An expression tool is a wrapper for a JavaScript expression. It can be used " +"to simplify workflows and command-line tools, moving common parts of a " +"workflow execution into reusable JavaScript code that takes inputs and " +"produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef +#: f6f589481d0c4891beaccb63160619ef da4dba50d25d4533b3dbb92f54d32a30 msgid "" -"Operation is an abstract process that also takes inputs, produces " -"outputs, and can be used in a workflow. But it is a special operation not" -" so commonly used. It is discussed in the [Operations " -"section](../topics/operations.md) of this user guide." +"Operation is an abstract process that also takes inputs, produces outputs, " +"and can be used in a workflow. But it is a special operation not so commonly " +"used. It is discussed in the [Operations section](../topics/operations.md) " +"of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 ce11c9f8d65c4268984d0384d95144cc msgid "" -"The workflow is a process that contains steps. Steps can be other " -"workflows (nested workflows), command-line tools, or expression tools. " -"The inputs of a workflow can be passed to any of its steps, while the " -"outputs produced by its steps can be used in the final output of the " -"workflow." +"The workflow is a process that contains steps. Steps can be other workflows " +"(nested workflows), command-line tools, or expression tools. The inputs of a " +"workflow can be passed to any of its steps, while the outputs produced by " +"its steps can be used in the final output of the workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 +#: 4ace6b92f4e04a07aa202840ebe36417 3a201aa497e84f70855bb2251e7e3281 msgid "" "The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through " -"*requirements*. There are many requirements defined in the CWL " -"specification, for instance:" +"functionality and specify prerequisites to workflows through *requirements*. " +"There are many requirements defined in the CWL specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 b78f7fa2be1c4bb090f6da895457ad1e msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 +#: 2d9f53b6ed5041dbb6c0b54835897856 f7e95d264ffa4e2db0864faccd9e5a0e msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 +#: 907674a4ecff4826a2b880e28fc38f33 3f1e5b01e49a4dc1b1c99936a4589afc msgid "" -"`InitialWorkDirRequirement` - controls staging files in the input " -"directory." +"`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee +#: 037cd0e5ceda482eaeaca03d51745aee 03c3048f38ae4938a484cf02001877b3 msgid "" -"Some CWL runners may provide requirements that are not in the " -"specification. For example, GPU requirements are supported in `cwltool` " -"through the `cwltool:CUDARequirement` requirement, but it is not part of " -"the {{ cwl_version }} specification and may not be supported by other CWL" -" runners." +"Some CWL runners may provide requirements that are not in the specification. " +"For example, GPU requirements are supported in `cwltool` through the " +"`cwltool:CUDARequirement` requirement, but it is not part of the " +"{{ cwl_version }} specification and may not be supported by other CWL " +"runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e +#: e4643938445b48cc80eb8973ceeb126e f9715b5ec65c405c849bb030c1927060 msgid "" -"Hints are similar to requirements, but while requirements list features " -"that are required, hints list optional features. Requirements are " -"explained in detail in the [Requirements](../topics/requirements-and-" -"hints.md) section." +"Hints are similar to requirements, but while requirements list features that " +"are required, hints list optional features. Requirements are explained in " +"detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: c4c3315c96714e81b364f8cc003b87e6 442662f50e9e4620970ce32b1b127969 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 +#: 3eb6a013a2a4478ca2ad134661f65c58 2b34c786af3840e88f29d214e19dc837 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " "machine accessibility and that all digital assets should be Findable, " "Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created." -" It is thus important that workflows support the creation of FAIR data " -"and adhere to the FAIR principles. — [FAIR Computational " -"Workflows](https://workflows.community/groups/fair/), Workflows Community" -" Initiative." +"which the scientific process is conducted and via which data are created. It " +"is thus important that workflows support the creation of FAIR data and " +"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" +"workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a +#: 074af9633627470485e5225326d5f20a dd6aadff8cf54ce78ea6b317afbaddb0 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\"," -" CWL tasks are isolated, and you must be explicit about your inputs and " +"execution, based on dependencies between tasks. However, unlike \"make\", " +"CWL tasks are isolated, and you must be explicit about your inputs and " "outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee +#: 847951c055b94a83b1e081594cef22ee fe7f1f0b28434f8aaf0f6ac6589a83f0 msgid "" -"The benefit of explicitness and isolation are flexibility, portability, " -"and scalability; tools and workflows described with CWL can transparently" -" leverage technologies such as Docker and be used with CWL " -"implementations from different vendors." +"The benefit of explicitness and isolation are flexibility, portability, and " +"scalability; tools and workflows described with CWL can transparently " +"leverage technologies such as Docker and be used with CWL implementations " +"from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: 44bde1fae06b4678bcac4f3224601296 d10cf45b3c7f49dc98bc0e5d1246f224 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" @@ -731,264 +803,306 @@ msgstr "" #: ../../src/introduction/prerequisites.md:196 #: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 #: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf +#: 332b6e8b831e4bc5aed3745938230a57 ce7fc63b808d4499b9bf9828c2dafe35 +#: ebf339ed376a4d3b89b15b4d5afe593b msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 9d5100c7d0a040aea1020bf633ad17de 8badec9987ba40609cf1f626172b2b2d msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 +#: 36eb4b3b966640af90faa55db3789cb6 c75a8b4bf0e24781bf6713cf6f013cd1 msgid "" -"The CWL Specification page in the CWL website: " -"" +"The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 +#: 2ccb956baa6b4376a04ad9fcc4654631 79b146ffe6d74e1b8f6019251dc4b7c2 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 +#: 72889b830c514afe9a7cb1e64b5666a0 07cca9a33d8f4b77ac6ad35ca8b95655 msgid "" -"The list of Implementations in the CWL website: " -"" +"The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: e29bd7f973544600be589c3b3f84cf63 31db11c8ddf2423192a8b2063b3e91c2 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b +#: c377a7f5dbe645cebbb6c7eccf831a0b d81dd96143ea444aa78ff45cfa0584b3 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" #: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +#: c54984605872472190ae7771809a20db msgid "Introduction" msgstr "" #: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +#: 01a237b8ec2f46c9acd31d142591ce75 msgid "" "This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that" -" are useful to know before reading the rest of the user guide." +"prerequisites for following this user guide, and some basic concepts that " +"are useful to know before reading the rest of the user guide." msgstr "" #: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +#: 3fb9888b666945eab1e3ff109646c574 msgid "Prerequisites" msgstr "" #: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +#: 5fb0486762354f93853fff209f835c08 msgid "" -"The software and configurations listed in this section are prerequisites " -"for following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements " -"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" -"compatible runner or workflow system, but the results and interface may " -"look different (though the exact workflow outputs should be identical)." +"The software and configurations listed in this section are prerequisites for " +"following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements focuses " +"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " +"runner or workflow system, but the results and interface may look different " +"(though the exact workflow outputs should be identical)." msgstr "" #: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +#: 5f1e7a608e0b455196d191c845a5c98e msgid "CWL Implementations" msgstr "" #: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +#: 7ba4b5c51be24f5392949d06ee42e018 msgid "" -"There are many implementations of the CWL standards. Some are complete " -"CWL runners, while others could be plug-ins or extensions to workflow " -"engines. We have a better explanation in the [Implementations](basic-" -"concepts.md#implementations) section." +"There are many implementations of the CWL standards. Some are complete CWL " +"runners, while others could be plug-ins or extensions to workflow engines. " +"We have a better explanation in the [Implementations](basic-concepts." +"md#implementations) section." msgstr "" #: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +#: e2d3e6dd13b14d819a504c35da6fe8e7 msgid "Operating System" msgstr "" #: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +#: 91251d1f0efb4d4cb083b4517ff3107a msgid "" -"We recommend using an up-to-date operating system. You can choose any of " -"the following options for your operating system:" +"We recommend using an up-to-date operating system. You can choose any of the " +"following options for your operating system:" msgstr "" #: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +#: 6ad263e267514c5fb05794d3d76d418d msgid "Linux" msgstr "" #: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +#: 8a3bfd72dccf4a8c874a96aebcbe5cb7 msgid "macOS" msgstr "" #: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +#: 5195706d9c6c4573aff135fd539759a2 msgid "Windows" msgstr "" #: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +#: 9c4506915e4c40599527bc1d2b18645b msgid "" -"If you are using Windows, you will have to install the [Windows Subsystem" -" for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " -"(WSL2). Visit the `cwltool` [documentation](https://github.com/common-" -"workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for " -"details on installing WSL2. Your operating system also needs internet " -"access and a recent version of Python (3.6+)." +"If you are using Windows, you will have to install the [Windows Subsystem " +"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " +"installing WSL2. Your operating system also needs internet access and a " +"recent version of Python (3.6+)." msgstr "" #: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +#: 37d9eb784ec1425786158f98e3f63890 msgid "CWL Runner" msgstr "" #: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +#: 572f493a985141a1b92dafbdba92790d msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL " -"community. It is also the CWL reference runner, which means it must " -"support everything in the current CWL specification, {{ cwl_version }}." +"`cwltool` is a Python Open Source project maintained by the CWL community. " +"It is also the CWL reference runner, which means it must support everything " +"in the current CWL specification, {{ cwl_version }}." msgstr "" #: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +#: 9606d3c4849f4b17b2e55a298210f055 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " -"environment like `venv` or `conda`. The following commands will create " -"and activate a Python virtual environment using the `venv` module, and " -"install `cwltool` in that environment:" +"environment like `venv` or `conda`. The following commands will create and " +"activate a Python virtual environment using the `venv` module, and install " +"`cwltool` in that environment:" msgstr "" #: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +#: 754fc59967d94ffa935284676d55ffed msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" #: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +#: 2905c6362d4146e8b35bc74744841972 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool#install) for other ways to install `cwltool` with `apt` " -"and `conda`." +"language/cwltool#install) for other ways to install `cwltool` with `apt` and " +"`conda`." msgstr "" #: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +#: 091278ece252483a9838fb771de3e04e msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +#: 0928a5c668c3414a945bc9eda147892c msgid "`true.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +#: 56f3c481762848298214a88e559fc0f9 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the " -"CWL standards. However, these actions will be performed without running " -"the document. To validate CWL workflows (or even a standalone command " -"line tool description like the above) pass the `--validate` option to the" -" `cwltool` command:" +"errors, and verify that the workflow descriptions are compliant with the CWL " +"standards. However, these actions will be performed without running the " +"document. To validate CWL workflows (or even a standalone command line tool " +"description like the above) pass the `--validate` option to the `cwltool` " +"command:" msgstr "" #: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +#: 710c266ab4a5477b84d6ea987420fa20 msgid "Validating `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 -msgid "You can run the CWL tool description by omitting the `--validate` option:" +#: cc353db5da2546bb88a77ce1a202ff9d +msgid "" +"You can run the CWL tool description by omitting the `--validate` option:" msgstr "" #: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +#: b62df08ec96f4cdb887600079856dd76 msgid "Running `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: 97e02557293440d1a58ba659dad21113 msgid "Cwl-runner Python Module" msgstr "" #: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +#: 0935c3ff01634c75b5c91546dc36c7b9 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be " -"invoked independently, and is not reliant on a particular CWL runner " -"program name. Users can invoke `cwl-runner` instead of invoking a CWL " -"runner like `cwltool` directly. The `cwl-runner` is installed by a system" -" administrator or user to point to the preferred CWL implementation. This" -" is convenient for environments with multiple CWL runners." +"runner. This simply means that the `cwl-runner` alias command can be invoked " +"independently, and is not reliant on a particular CWL runner program name. " +"Users can invoke `cwl-runner` instead of invoking a CWL runner like " +"`cwltool` directly. The `cwl-runner` is installed by a system administrator " +"or user to point to the preferred CWL implementation. This is convenient for " +"environments with multiple CWL runners." msgstr "" #: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +#: cfb37fd605164a8d9cc75bf892ce97c0 msgid "" -"The CWL community publishes a Python package with the name `cwlref-" -"runner` that installs an alias for `cwltool` under the name `cwl-runner`" +"The CWL community publishes a Python package with the name `cwlref-runner` " +"that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" #: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +#: 5f06a7a6aae343d989a5b30979c600f6 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" #: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +#: 5f956260f3874b6dbeaf3ad7ecc09c9a msgid "" -"Now you can validate and run your workflow with the `cwl-runner` " -"executable, which will invoke `cwltool`. You should have the same results" -" and output as in the previous section." +"Now you can validate and run your workflow with the `cwl-runner` executable, " +"which will invoke `cwltool`. You should have the same results and output as " +"in the previous section." msgstr "" #: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +#: d35e4effec554a638d6c3047ef3fd05f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +#: 15a1f944a0d642729d3736ed1c907074 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +#: fa34c808bb494ddfa3f3926bc42e650c msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For" -" that, the first thing you need to do is copy `true.cwl` workflow into a " -"new file: `true_shebang.cwl`, and include a special first line, a " -"*shebang*:" +"Another way to execute `cwl-runner` is by invoking the file directly. For " +"that, the first thing you need to do is copy `true.cwl` workflow into a new " +"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" #: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: 0c15f62eb7534e809f625f3fa213e92d msgid "`true_shebang.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +#: d67719a6f0ce4ba1bb6152a10507b729 +msgid "" +"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" #: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +#: 1c96e75281844bfab0578bab2e816854 msgid "Making `true.cwl` executable." msgstr "" #: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +#: bece1fc3c3f842b0b30d8f1b7fbfc200 msgid "" -"And finally, you can execute it directly in the command-line. On " -"execution, the program specified in the shebang (`cwl-runner`) will be " -"used to execute the rest of the file." +"And finally, you can execute it directly in the command-line. On execution, " +"the program specified in the shebang (`cwl-runner`) will be used to execute " +"the rest of the file." msgstr "" #: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +#: a7caa36b0f83448b91ef2e76e30abc51 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" #: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +#: 39321e93e9994fcca20b425aa45c2894 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute " -"the script using the executable specified after the shebang. It is " -"considered a good practice to use `/usr/bin/env ` rather than" -" using a hard-coded location, since `/usr/bin/env ` looks for" -" the `` program in the system `PATH`," +"script. When the script is executable, the operating system will execute the " +"script using the executable specified after the shebang. It is considered a " +"good practice to use `/usr/bin/env ` rather than using a hard-" +"coded location, since `/usr/bin/env ` looks for the " +"`` program in the system `PATH`," msgstr "" #: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +#: 601cf500d76c4e0287af4429a46b36d2 msgid "Text Editor" msgstr "" #: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +#: b286d5359e184ef58054c72df4014629 msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " @@ -996,379 +1110,429 @@ msgid "" msgstr "" #: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +#: e14423edd829401faed0950772123240 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting" -" and better auto-complete:" +"integration with CWL, and features such as customized syntax highlighting " +"and better auto-complete:" msgstr "" #: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +#: 889c44360bd54a0e85e7f0e61aa6593c msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " -"" +"Visual Studio Code with the Benten (CWL) plugin - " msgstr "" #: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +#: 7b9bff73624947ac90a99c7880e2e911 msgid "" -"cwl-plugin for IntelliJ - " +"cwl-plugin for IntelliJ - " msgstr "" #: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +#: c5ff687c86ef4ccaae25d8bcfbd5f873 msgid "" -"The CWL community also maintains a list of editors and viewers: " -"" +"The CWL community also maintains a list of editors and viewers: " msgstr "" #: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +#: 0a610a9632064deb824afd0719429d3a msgid "Docker" msgstr "" #: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +#: ec0c47438a5242cb99dffa7a4997e95a msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: " -"." +"documentation to install it for your operating system: ." msgstr "" #: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +#: aae94ac2114641f186eac0f4117223eb msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models " -"with and without containers." +"examples, and to clarify the differences between the execution models with " +"and without containers." msgstr "" #: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +#: 209e072724ed4d27b37e9bff6d55d811 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for " -"pulling images." +"Singularity. You can also use alternative container registries for pulling " +"images." msgstr "" #: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +#: 3bf47876e3694e6cadb05123326459cb msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the " -"next section, Basic Concepts." +"The [Implementations](basic-concepts.md#implementations) topic in the next " +"section, Basic Concepts." msgstr "" #: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +#: 459a65b8e67c4a9aaa03138c1abe94ad msgid "The Python `venv` module: " msgstr "" #: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +#: 898eb29ac7714c69840b795633953a05 msgid "Quick Start" msgstr "" #: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +#: 2a658bd2d8ce4533ab7e056fc3a3ffcf msgid "" -"This section will show you a brief overview of what CWL is, and where you" -" can learn more about it. No previous knowledge of CWL is required, but " -"you must be comfortable following instructions for the command-line." +"This section will show you a brief overview of what CWL is, and where you " +"can learn more about it. No previous knowledge of CWL is required, but you " +"must be comfortable following instructions for the command-line." msgstr "" #: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +#: 32dd2e28cf0f40b6930750f0162355eb msgid "“Hello World”" msgstr "" #: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +#: 471c47d311074ecfac071b6d52d9cfb6 msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " -"The example below shows a simple CWL “Hello World” workflow annotated " -"with comments. Note that comments start with `#`:" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " +"example below shows a simple CWL “Hello World” workflow annotated with " +"comments. Note that comments start with `#`:" msgstr "" #: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +#: 5078140028ea4d04973cb9cd20f0607e msgid "`hello_world.cwl`" msgstr "" #: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +#: ab127d4ba0a44526ab129587a8160923 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the" -" same result as the command-line `echo \"Hello World\"`." +"Running the workflow above with the default input values will produce the " +"same result as the command-line `echo \"Hello World\"`." msgstr "" #: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +#: d5cc6b4295a74f3586f022b0227759b3 msgid "" -"In CWL, there is a distinction between a command-line tool and a " -"workflow. But for the sake of simplicity, we are using the term " -"“workflow” here. You will learn more about this in the [basic concepts" -"](basic-concepts.md) section." +"In CWL, there is a distinction between a command-line tool and a workflow. " +"But for the sake of simplicity, we are using the term “workflow” here. You " +"will learn more about this in the [basic concepts](basic-concepts.md) " +"section." msgstr "" #: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +#: 585a4fe583ce44e180a062742b3b0849 msgid "Installing a CWL Runner" msgstr "" #: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +#: 0d81b0c9ea58420789d1d71cca32ce88 msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the " -"CWL *Reference Runner* for the specification, and it is compliant with " -"the latest version of the specification: {{ cwl_version }}. You can " -"install `cwltool` using `pip`:" +"`cwltool` is an implementation of the CWL specification. It is also the CWL " +"*Reference Runner* for the specification, and it is compliant with the " +"latest version of the specification: {{ cwl_version }}. You can install " +"`cwltool` using `pip`:" msgstr "" #: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +#: ea4ab0782d8049d8b1b89cea4ae60048 msgid "Installing `cwltool` with `pip`." msgstr "" #: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +#: f6f3b7453a254f828bd4c9e9fef92bed msgid "" -"If installing the cwltool using the pip command doesn't work for you, the" -" [prerequisites](prerequisites.md) section contains other ways to install" -" `cwltool` and a more detailed list of software and libraries used for " +"If installing the cwltool using the pip command doesn't work for you, the " +"[prerequisites](prerequisites.md) section contains other ways to install " +"`cwltool` and a more detailed list of software and libraries used for " "following the rest of this user guide." msgstr "" #: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +#: 3bf9050175d4444ebbbabe219412574f msgid "Running \"Hello World\"" msgstr "" #: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +#: e03f72a14dcf4bf38ce8232598ca761d msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [INPUTS_OBJECT]`. You can run the " -"`hello_world.cwl` workflow without specifying any option:" +"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " +"workflow without specifying any option:" msgstr "" #: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +#: 3dcfb2facd324dccb3084c02487625dc msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +#: b8531da183964b02bca19f818ec076d4 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" #: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +#: 7ba1ddebeb2843179fe99fc410b193c6 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" #: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +#: a6dc303e9d284b60bf1102212505ca27 msgid "" -"Another way of passing values to your workflow input parameters is via an" -" *Inputs Object*. This is a file containing the input fields with their " +"Another way of passing values to your workflow input parameters is via an " +"*Inputs Object*. This is a file containing the input fields with their " "corresponding values. The Inputs Objects file can be written in JSON or " "YAML. For example:" msgstr "" #: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +#: 59ac7830ae3e4d7cb1bf503e8c90fe30 msgid "`hello_world-job.json`" msgstr "" #: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +#: 6d1d6f42ada2418ba0a1de1371825b9f msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" #: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +#: 1cd924fe8ace4a82ad8701f37b5e7d84 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +#: aa297c52cd964291a47bb91c0135156b msgid "" "We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but " -"it is not a requirement. You can choose any name for your workflows and " -"Inputs Object files." +"files. The *-job.json* suffix is very common in Inputs Object files, but it " +"is not a requirement. You can choose any name for your workflows and Inputs " +"Object files." msgstr "" #: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +#: 28b02c90397745bfbacc03c3b1034939 msgid "Continue reading the next sections of this User Guide!" msgstr "" #: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +#: ef2a4f39f01049b891868b84d968c0dd +msgid "" +"[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" #: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +#: 89e3fa8dceda4f0cb1cfdfd1f17fe4df msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" #: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +#: 7cd178223ba94d1ab3ee8cc5f13a8dcf msgid "" -"[Common Workflow Language at " -"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." msgstr "" #: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +#: 46f6f8d050ce4f8c897056167d9707a7 msgid "" -"[YAML.org](http://yaml.org/) and [YAML at " -"Wikipedia](https://en.wikipedia.org/wiki/YAML)." +"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." +"org/wiki/YAML)." msgstr "" #: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +#: 5ee00ee409b746dc951ca1d4c360e624 msgid "" -"The {{'[CWL Specification " -"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " -"cwl_version_text) }}." +"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." +"replace('VERSION', cwl_version_text) }}." msgstr "" #: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +#: d4af972281174b8999eab55ee0ab1a0e msgid "" -"[Workflow management system at " -"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." msgstr "" #: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +#: 80401cfffae042ab9ec4b3754af04b25 msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. The information on this page has been migrated to the " -"[FAQ](/faq.md) section of the new user guide." +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. The information on this page has been migrated to the [FAQ](/faq." +"md) section of the new user guide." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 9c87c76c690948ac8e18088a0fffe679 32f86f911ebe4a4c94975f81742333f3 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 +#: ad00d94d4fb64bbdac356e64dd3803b9 d5f1ad2b95ad46d48f8f2ca5e357bb5d msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf +#: d8110ed19da94ad8a9f56e7006c4a2cf c53ceee943ad4acea779e072b9137889 msgid "" "In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files " -"in the same directory as the source file. However, CWL input files (and " -"the directories in which they appear) may be read-only, so we need to " -"instruct \"javac\" to write the class file to the designated output " -"directory instead." +"file to a class file. By default, \"javac\" will create the class files in " +"the same directory as the source file. However, CWL input files (and the " +"directories in which they appear) may be read-only, so we need to instruct " +"\"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: a74935dc31664e979ca8f90a6a4ba53c 7dfe9dffbf5744299bf232599644c7f6 msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: f357755f6dcb4971bade8636064f8dd1 00709fa451134ee09a0d808e101f28ed +#: 991172e201ec4796992a349dee44f090 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: 6359191b4f684d5aa3602e4aaf394883 1f3c23a4769043ca985b8ddfed19391d msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb +#: 9643449da1da46d7861866dce490cbcb f81b43c7cb194a1cad8672129223c833 msgid "" -"And now invoke `cwltool` providing the tool description and the input " -"object on the command line:" +"And now invoke `cwltool` providing the tool description and the input object " +"on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a +#: 713666580a0a4466b4ba6e3eb2b54f0a a20073a8f5374eb1bc8531ff33e622b6 msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 +#: d50574c8b9694f83aa376d39b9a6fcd6 d08869beca3a4774baf1097b63e79474 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include " -"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " -"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " -"Environment][runtime] section of the CWL specification for details." +"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" +"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." +"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " +"specification for details." msgstr "" #: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +#: 109b773789024b2b9c063a6169c6169f msgid "Best Practices" msgstr "" #: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +#: 959fa04f88e54d42b9b774cc95d85ee0 msgid "" -"The following are a set of recommended good practices to keep in mind " -"when writing a Common Workflow Language description for a tool or " -"workflow. These guidelines are presented for consideration on a scale of " -"usefulness: although more is better, not all are required." +"The following are a set of recommended good practices to keep in mind when " +"writing a Common Workflow Language description for a tool or workflow. These " +"guidelines are presented for consideration on a scale of usefulness: " +"although more is better, not all are required." msgstr "" #: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +#: 64674980c3f24c45bbfbf3f957dda55e msgid "" -"No `type: string` parameters for names of input or reference " -"files/directories; use `type: File` or `type: Directory` as appropriate." +"No `type: string` parameters for names of input or reference files/" +"directories; use `type: File` or `type: Directory` as appropriate." msgstr "" #: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +#: 90f2e4265919446a902e17627f4420e2 msgid "" "A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that" -" the usual rules of software licensing apply to this document. For " -"example, if the workflow is shared publicly, licensing terms must be " -"clear so that a future user understands under what conditions they can " -"run the workflow, modify it and/or combine it with other workflows. For " -"this reason, please consider including a license field in the document. " -"The authors of this guide urge you to choose a pre-existing license " -"rather than trying to write your own (see the link below to learn more " -"about choosing a license), and our recommended practice is to choose a " -"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" -"license]." +"`Dockerfile`s) is software code. Workflow developers should be aware that " +"the usual rules of software licensing apply to this document. For example, " +"if the workflow is shared publicly, licensing terms must be clear so that a " +"future user understands under what conditions they can run the workflow, " +"modify it and/or combine it with other workflows. For this reason, please " +"consider including a license field in the document. The authors of this " +"guide urge you to choose a pre-existing license rather than trying to write " +"your own (see the link below to learn more about choosing a license), and " +"our recommended practice is to choose a license that allows for re-use by " +"anyone, e.g. [Apache 2.0][apache-license]." msgstr "" #: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +#: 6b5f91a749fd44b5acfd6071c9913342 msgid "" -"If possible, the license should be specified with its corresponding [SPDX" -" identifier][spdx]. Construct the metadata field for the license by " -"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " -"`SPDX-ID` is taken from the list of identifiers linked above. See the " -"example snippet below for guidance. For non-standard licenses without an " -"SPDX identifier, provide a URL to the license." +"If possible, the license should be specified with its corresponding [SPDX " +"identifier][spdx]. Construct the metadata field for the license by providing " +"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " +"taken from the list of identifiers linked above. See the example snippet " +"below for guidance. For non-standard licenses without an SPDX identifier, " +"provide a URL to the license." msgstr "" #: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +#: 5fe2962837b14f0e9989063be4a506c3 msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" #: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +#: 4e1bdea962ed4618884cb9d1d59d7509 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" #: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +#: 37eff4ca02e843259f6ffa38e4a87a04 msgid "" -"For more examples of providing metadata within CWL descriptions, see " -"[the Metadata and Authorship section of this User Guide](../topics" -"/metadata-and-authorship.md)." +"For more examples of providing metadata within CWL descriptions, see [the " +"Metadata and Authorship section of this User Guide](../topics/metadata-and-" +"authorship.md)." msgstr "" #: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +#: ae47231c203d40a98c10045038ea9b65 msgid "" -"Include [attribution information][license-example] for the author(s) of " -"the CWL tool or workflow description. Use unambiguous identifiers like " -"[ORCID][orcid]." +"Include [attribution information][license-example] for the author(s) of the " +"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" +"[orcid]." msgstr "" #: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +#: 018a6d5dbf1044559b365c7b9017eb3f msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +#: e073d8f990c44b09a73d642cfe49bebd msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in " -"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" +"identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" #: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +#: e04fae88d9b64493ac69eaee24585098 msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1377,24 +1541,26 @@ msgid "" msgstr "" #: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +#: b26b9c9b1c4346a297a31c9721f0172a msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +#: b50500c3c3f54b16a535a16175a44653 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " -"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" -"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " -"types). For non-bioinformatics tools, use or build an appropriate " -"ontology/controlled vocabulary in the same way. Please edit this page to " -"let us know about it." +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" +"$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " +"[Full IANA media type list][iana-types] (also known as MIME types). For non-" +"bioinformatics tools, use or build an appropriate ontology/controlled " +"vocabulary in the same way. Please edit this page to let us know about it." msgstr "" #: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +#: 623f3a804199449bb85e23e00c8bb507 msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " @@ -1402,158 +1568,175 @@ msgid "" msgstr "" #: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +#: effea0b1356447c0899ca0746667ea31 msgid "" -"Each `CommandLineTool` description should focus on a single operation " -"only, even if the (sub)command is capable of more. Don't overcomplicate " -"your tool descriptions with options that you don't need or use." +"Each `CommandLineTool` description should focus on a single operation only, " +"even if the (sub)command is capable of more. Don't overcomplicate your tool " +"descriptions with options that you don't need or use." msgstr "" #: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +#: 00e8ef87864c4ca2b2c1c0548b02b38d msgid "" -"Custom types should be defined with one external YAML per type definition" -" for re-use." +"Custom types should be defined with one external YAML per type definition " +"for re-use." msgstr "" #: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +#: 6e6f48d70b894a6c959ca30fe6bad772 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" #: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +#: 02fe08760a4a4ab49e96f4e51316a81d msgid "" -"If useful, include a top-level `doc` as well. This should provide a " -"longer, more detailed description than was provided in the top-level " -"`label` (see above)." +"If useful, include a top-level `doc` as well. This should provide a longer, " +"more detailed description than was provided in the top-level `label` (see " +"above)." msgstr "" #: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +#: 172ed7915a654964ba63f860b2d65330 msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list" -" of valid values." +"Use `type: enum` instead of `type: string` for elements with a fixed list of " +"valid values." msgstr "" #: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +#: 4d0a2871a7484e21b3c39c4dbaaa63fc msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. " -"One common example: manipulating `File` names and paths? Consider whether" -" one of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc., could be used instead." +"Evaluate all use of JavaScript for possible elimination or replacement. One " +"common example: manipulating `File` names and paths? Consider whether one of " +"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc., could be used instead." msgstr "" #: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +#: 1eea9f1e284447718141f5417b6bb433 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" #: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +#: 509411d353fe4314b087b81b09ea960b msgid "" -"Complex workflows with individual components which can be abstracted " -"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" -" their workflow modular and allow sections of them to be easily reused." +"Complex workflows with individual components which can be abstracted should " +"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " +"workflow modular and allow sections of them to be easily reused." msgstr "" #: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +#: a54bc80bf08243bba67d98dd682ee134 msgid "" "Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics" -" software\"][containers] (also useful to other disciplines)." +"[\"Recommendations for the packaging and containerizing of bioinformatics " +"software\"][containers] (also useful to other disciplines)." msgstr "" #: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +#: 69ecdaea24ef42eebef9d86e5d716b11 msgid "Command Line Tool" msgstr "" #: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +#: 3cc5847468d1478bb5589dee68147189 msgid "" -"A command-line tool is a type of Process object that can be run by itself" -" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " -"`tar`, etc. The command-line tool is defined in the `baseCommand` " -"attribute of the command-line tool CWL document." +"A command-line tool is a type of Process object that can be run by itself or " +"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " +"etc. The command-line tool is defined in the `baseCommand` attribute of the " +"command-line tool CWL document." msgstr "" #: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +#: 98c6bc409420485095ae65d6b0b9a3a0 msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The " -"following example contains a minimal example of a CWL command-line tool " -"for the `echo` Linux command, using inputs and outputs." +"A CWL command-line tool must also have `inputs` and `outputs`. The following " +"example contains a minimal example of a CWL command-line tool for the `echo` " +"Linux command, using inputs and outputs." msgstr "" #: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +#: ebe23e5378514f888a9ec32a2adb1e98 msgid "CWL command-line tool." msgstr "" #: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +#: 387cfe85604f424f8d31c4a4c9c15edb msgid "`echo.cwl`" msgstr "" #: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +#: 7b1d65754e854693bb60289c97d3fb5d msgid "" -"The example above uses a simplified form to define inputs and outputs. " -"You will learn more about in the [Inputs](../topics/inputs.md) and in the" -" [Outputs](../topics/outputs.md) sections." +"The example above uses a simplified form to define inputs and outputs. You " +"will learn more about in the [Inputs](../topics/inputs.md) and in the " +"[Outputs](../topics/outputs.md) sections." msgstr "" #: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +#: f440cef729c8410281432307a4da8d55 msgid "Network Access" msgstr "" #: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +#: 4fbb8ceb1b59480583ac611142167049 msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network " -"access. If a command-line tool is written manually in CWL v1.1+, there is" -" a need to specify when network access is required." +"This indicates whether a process requires outgoing IPv4/IPv6 network access. " +"If a command-line tool is written manually in CWL v1.1+, there is a need to " +"specify when network access is required." msgstr "" #: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +#: b87869204838415bbf694214e3680593 msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " -"Network Access automatically." +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " +"Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b 12cf5f2264504c44a2173e858bb2c283 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d +#: 0cf51b6da6884065ae42032abc20eb0d 7694f9cabfe04308bbddd2c88ae6d9b9 msgid "" -"Sometimes you need to create a file on the fly from input parameters, " -"such as tools that expect to read their input configuration from a file " -"rather than the command line parameters, or need a small wrapper shell " -"script." +"Sometimes you need to create a file on the fly from input parameters, such " +"as tools that expect to read their input configuration from a file rather " +"than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff +#: 2df3a3a9094d4b79b1d5dd99195f3bff b557dc4f8ef549b98f59412a918643de msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: d3f74c3b094a427fbec831afab657d50 3011eb003c084285b30cfa56a8da45b6 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df +#: cfffc518ba6e4ed1a80762ed6f7d25df 9f9c90a2bb4b4d3b8e99b63cb0e72f76 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the " -"value at the input `message`." +"expanded by the CWL engine before creating the file. Here, insert the value " +"at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 +#: 9454a330b9324744b89448f2694b1b03 ce78b2d147054da895beba66d0ecdab4 msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later" -" during command line tool invocation. That means that any genuine need " -"for the character `$` must be **escaped** with `\\`. For instance, " -"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " -"be evaluated by the shell script instead of the CWL engine." +"The _CWL expressions_ are independent of any _shell variables_ used later " +"during command line tool invocation. That means that any genuine need for " +"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " +"above is expanded to `${PREFIX}` in the generated file to be evaluated by " +"the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa +#: 7f8d99a30b644457a62ac1523d0c72aa a973846ec5a946eeaff02c5b00997da9 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1562,32 +1745,33 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 #: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb -#: ca03defa3ad14cf698171cb09e3055c1 +#: ca03defa3ad14cf698171cb09e3055c1 294fd83a97a64249bac38f7482159372 +#: 9e8eb1542db640ff9e300649ce50dc9d ccec7f73b9d948e79a6cdf32bc124092 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d +#: 10d1373bb14a4a3cacd3b92a2f83382d 22948f19cb78485f8f86244686a35c09 msgid "" -"Before we run this, let us look at each step in a little more detail. The" -" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"Before we run this, let us look at each step in a little more detail. The " +"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " "command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c +#: 70e257091bdb456e8957f90a8fa90e8c 001d9579bfce438e865377fb9c2df776 msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " -"YAML array, we need a `-` on the first line of each element of the array," -" in this case we have just one element. `entryname:` can have any value, " -"but it must match what was specified in the `baseCommand`. The final part" -" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " -"means that you are using a multiline string (without it, we would need to" -" write the whole script on one line)." +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " +"array, we need a `-` on the first line of each element of the array, in this " +"case we have just one element. `entryname:` can have any value, but it must " +"match what was specified in the `baseCommand`. The final part is `entry:`, " +"this is followed by `|-` which is YAML quoting syntax, and means that you " +"are using a multiline string (without it, we would need to write the whole " +"script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 +#: 1741804e33aa43ce88b4320c11ae5973 e62618db8995428bb3f260e03ac8f459 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1599,221 +1783,258 @@ msgstr "" #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 #: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f #: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 -#: f924d65fed0c4cb5b0a019b084a8b535 +#: f924d65fed0c4cb5b0a019b084a8b535 457756c4e9544f068af897113358cc89 +#: 6d5ae75431424ea788c3440606f22940 98e0548845fa447fb05a29c9fc2f17b5 +#: de5e8aad4e3046bf9bfc2ad8ccba17d0 e9801b2142cd45368a73ef9b121c1d08 msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line:" msgstr "" #: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +#: ee2bca9bdbb74b60a706c3118d6a17ba msgid "Custom Types" msgstr "" #: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +#: e63ae9694f40438d872d141ae824a42d msgid "" -"Sometimes you may want to write your own custom types for use and reuse " -"in CWL descriptions. Use of such custom types can reduce redundancy " -"between multiple descriptions that all use the same type, and also allow " -"for additional customisation/configuration of a tool/analysis without the" -" need to fiddle with the CWL description directly." +"Sometimes you may want to write your own custom types for use and reuse in " +"CWL descriptions. Use of such custom types can reduce redundancy between " +"multiple descriptions that all use the same type, and also allow for " +"additional customisation/configuration of a tool/analysis without the need " +"to fiddle with the CWL description directly." msgstr "" #: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +#: 750fdd4c270e46a09f79e867358f7414 msgid "" -"The example below is a CWL description of the [biom convert format][biom]" -" tool for converting a standard biom table file to hdf5 format." +"The example below is a CWL description of the [biom convert format][biom] " +"tool for converting a standard biom table file to hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +#: b3f688cc82444ef7a7a0aa63dac39cac msgid "`custom-types.cwl`" msgstr "" #: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +#: 3638be18b4f64cf08053d512e590dda3 msgid "`custom-types.yml`" msgstr "" #: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +#: 7d5b9c21739c48f18c13614ca6967f6b msgid "" -"___Note:___ To follow the example below, you need to [download the " -"example input file](https://github.com/common-workflow-" -"language/user_guide/blob/main/src/_includes/cwl/custom-" -"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " -"`wget`:" +"___Note:___ To follow the example below, you need to [download the example " +"input file](https://github.com/common-workflow-language/user_guide/blob/main/" +"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " +"*rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" #: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +#: 8fea29993f944d8d8d3181afa29bd0a6 msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to " -"be used in the table conversion are imported as a custom object:" +"On line 29, in `inputs:table_type`, a list of allowable table options to be " +"used in the table conversion are imported as a custom object:" msgstr "" #: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +#: 02d0b648d70f49d7892f690be06df585 msgid "" -"The reference to a custom type is a combination of the name of the file " -"in which the object is defined (`biom-convert-table.yaml`) and the name " -"of the object within that file (`table_type`) that defines the custom " -"type. In this case the `symbols` array from the imported `biom-convert-" -"table.yaml` file define the allowable table options. For example, in " -"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" -" to create an OTU table in hdf5 format." +"The reference to a custom type is a combination of the name of the file in " +"which the object is defined (`biom-convert-table.yaml`) and the name of the " +"object within that file (`table_type`) that defines the custom type. In this " +"case the `symbols` array from the imported `biom-convert-table.yaml` file " +"define the allowable table options. For example, in `custom-types.yml`, we " +"pass `OTU table` as an `input` that tells the tool to create an OTU table in " +"hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e -msgid "The contents of the YAML file describing the custom type are given below:" +#: 0743bef42b9a42328849c8c2f9da9eed +msgid "" +"The contents of the YAML file describing the custom type are given below:" msgstr "" #: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +#: 85c5d0cbbc6243a6823f5eeac0f85dd9 msgid "`biom-convert-table.yaml`" msgstr "" #: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +#: be848f30769543eb9c0be55263e3f758 msgid "" -"In order for the custom type to be used in the CWL description, it must " -"be imported. Imports are described in " -"`requirements:SchemaDefRequirement`, as below in the example `custom-" -"types.cwl` description:" +"In order for the custom type to be used in the CWL description, it must be " +"imported. Imports are described in `requirements:SchemaDefRequirement`, as " +"below in the example `custom-types.cwl` description:" msgstr "" #: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +#: cbff44a64ba4432cb59a82f82c2f0103 msgid "" "Note also that the author of this CWL description has also included " -"`ResourceRequirement`s, specifying the minimum amount of RAM and number " -"of cores required for the tool to run successfully, as well as details of" -" the version of the software that the description was written for and " -"other useful metadata. These features are discussed further in other " -"chapters of this user guide." +"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " +"cores required for the tool to run successfully, as well as details of the " +"version of the software that the description was written for and other " +"useful metadata. These features are discussed further in other chapters of " +"this user guide." msgstr "" #: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +#: 617f1c0084cf42d9be4c7a8fa5a48432 msgid "Environment Variables" msgstr "" #: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +#: cee79afa3c6f43c29ef05e06b7843d35 msgid "" -"Tools run in a restricted environment and do not inherit most environment" -" variables from the parent process. You can set environment variables " -"for the tool using `EnvVarRequirement`." +"Tools run in a restricted environment and do not inherit most environment " +"variables from the parent process. You can set environment variables for " +"the tool using `EnvVarRequirement`." msgstr "" #: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +#: 225903b11efa417989df42de86ad2451 msgid "`env.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +#: 1a5f058290064c1cad05e63eb127fcbb msgid "Expression Tool" msgstr "" #: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +#: 74ad8d69cf294ae880dbbe28e25b3545 msgid "" -"An expression tool is a type of Process that can be run by itself or as a" -" Workflow step. It executes a pure JavaScript expression. It is meant to " -"be used as a way to isolate complex JavaScript expressions that need to " -"operate on input data and produce some result as output." +"An expression tool is a type of Process that can be run by itself or as a " +"Workflow step. It executes a pure JavaScript expression. It is meant to be " +"used as a way to isolate complex JavaScript expressions that need to operate " +"on input data and produce some result as output." msgstr "" #: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +#: 5293e8ee9b3b4f59947cfc164ef111c4 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" #: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +#: ffa1955c759942c68e7589429e5ea86b msgid "CWL expression tool." msgstr "" #: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +#: 038bc0ba5f6a405a8255a7be76979baf msgid "`uppercase.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +#: fae1c63de02e48c0969a98e4c49b2e06 msgid "" -"We had to use an `InlineJavascriptRequirement` as our expression contains" -" a JavaScript call in `.toUpperCase()`. This means to tools using the " +"We had to use an `InlineJavascriptRequirement` as our expression contains a " +"JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" #: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +#: 7093a94695524851a5463193f0701b78 msgid "Expressions" msgstr "" #: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +#: dc8274ecb15948c29a31db89b12a58bd msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " -"legal you can provide a fragment of Javascript that will be evaluated by " -"the CWL runner." +"legal you can provide a fragment of Javascript that will be evaluated by the " +"CWL runner." msgstr "" #: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +#: cec8eef8a5aa49778ecedd4195ab9f2c msgid "" -"JavaScript expressions should only be used when absolutely necessary. " -"When manipulating file names, extensions, paths etc, consider whether one" -" of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " -"practices](best-practices.md)." +"JavaScript expressions should only be used when absolutely necessary. When " +"manipulating file names, extensions, paths etc, consider whether one of the " +"[built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc, could be used instead. See the [list of best practices](best-" +"practices.md)." msgstr "" #: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: df100967597043c78112bf43b520cfab msgid "`expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +#: 59ccf4daba39406581a6bc2d9bb1b7d2 msgid "" -"As this tool does not require any `inputs` we can run it with an (almost)" -" empty job file:" +"As this tool does not require any `inputs` we can run it with an (almost) " +"empty job file:" msgstr "" #: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +#: 570cc75699dd4e0a987fc9aca9a01ee4 msgid "`empty.yml`" msgstr "" #: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +#: 9e123723048546d495ed5110d7177708 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object" -" is represented simply by a set of empty brackets." +"descriptions are contained inside curly brackets `{}`, so an empty object is " +"represented simply by a set of empty brackets." msgstr "" #: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +#: 26543894f6e04270b89ab702451bcc89 msgid "We can then run `expression.cwl`:" msgstr "" #: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +#: f403c1d4e43a4aa0aef8488d2b5a6262 msgid "Running `expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +#: 249dffb569a944c897ce5862e5f28fad msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" #: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +#: 1641c96aca2f4923885fe8a509eb3a49 msgid "" "Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" -" describe the additional command line arguments." +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " +"describe the additional command line arguments." msgstr "" #: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +#: bc63405a0d964df2bd9493996abc48fe msgid "Where are JavaScript expressions allowed?" msgstr "" #: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +#: 5c191d1420db4e26aca31c1b1e34cb75 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" #: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +#: d6a5c65e824a4bbc94578df9597d4716 msgid "" -"From " -"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 -#: 1acb064f7a4a482aa0174bdc847c6382 +#: 1acb064f7a4a482aa0174bdc847c6382 a7ff51fe564748229a88a0d3044dbc17 +#: c12625211cc542b68cb51365a63eef00 msgid "`arguments`" msgstr "" @@ -1824,32 +2045,39 @@ msgstr "" #: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e #: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 #: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 05c34a5a2e404a14b9d284a9d0c73bd3 +#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe +#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 +#: e7f1993580f0425098a719e83a64cc7f msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 #: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: 17ac6d2c703b466f9720b7489209a2ff 2fd5b42cafe34d3185888de041818dff +#: c158e9ee5fbf4e868b152a0a5880092f msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 #: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 3f29e4a3087847e9af6f19166a8def9a +#: 92697d3179ec48898eaea9aba3c24dcd msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 #: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: 37392218309d4baebe62fc38bf50efe9 c0eaef93bc3743279549bcfb8b014ca3 +#: d6722e3093884ad7b62696fbb2f48fdc msgid "`stderr`" msgstr "" #: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +#: 37c493fdc2f0410a9748f8faf09ce5b5 msgid "" -"From " -"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" #: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 @@ -1861,7 +2089,11 @@ msgstr "" #: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd #: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 #: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb -#: ed875a006df64f9e8a55fa5e9fa87404 +#: ed875a006df64f9e8a55fa5e9fa87404 04e3eefe4ec445cb90c2fa42344aaed5 +#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 +#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef +#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 +#: c610220d06484d589313dc29faf8222c msgid "`format`" msgstr "" @@ -1874,800 +2106,914 @@ msgstr "" #: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d #: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f #: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c -#: f760465a49d64d4c8468ad9c4fea62b1 +#: f760465a49d64d4c8468ad9c4fea62b1 662b36e3505f4ac3bb5070bb6e055217 +#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da +#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c +#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b +#: f71216a4b35e4157aece5ffa2602d8bf msgid "`secondaryFiles`" msgstr "" #: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +#: a3c775a0f04b4541a9b712bfe2e4e69a msgid "" -"From " -"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" #: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +#: ef16c4a9a7ea415fa399297b63b9710c msgid "" -"From " -"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +#: 2592e429c74c4ff5b8ba68a36f060c1a msgid "" -"From " -"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: d193ce0123db4535a4f0b11405ad0322 5cca4c2ad617400eb6efad4066b1839b +#: ba1fff3ebb274dfba845b3ee20ebd71f msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 #: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b -#: d555a3d991e344a5a8e1289168d7c6d1 +#: d555a3d991e344a5a8e1289168d7c6d1 6914526c0a7c43a2a05438519508ee0f +#: 722d3bd7184841639b9f9a38914002da msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c -#: e9fa9430535c424fa3e8be5d460d2ba4 +#: e9fa9430535c424fa3e8be5d460d2ba4 737b0f9392154241ae5b56c6caa823f5 +#: 7b46d408e7e7481b91a950b2d4010c9a msgid "From `Workflow`" msgstr "" #: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +#: f09e7371708b4c0685eef2a314791ccd msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c -#: b0290d1a477b48119e17cf1fed9d6dff +#: b0290d1a477b48119e17cf1fed9d6dff aa6ca1def2024c98b9d5542de1a81425 +#: e9fc5f7fa4474dfc95039b94167fe894 msgid "From `steps`" msgstr "" #: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +#: 6c37a1ff939748bf83a86c07c3d017fe msgid "" -"From " -"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 -#: e1cde4aa32c041238ed2596173c6d824 +#: e1cde4aa32c041238ed2596173c6d824 3a8126b0a0334df890b2be2c693ea5d5 +#: 61744122b7d7494890cbe6b2fb72b9f7 msgid "" -"From " -"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." +"html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf -#: c2a92d3eca7f4ee39cec649170eeea53 +#: c2a92d3eca7f4ee39cec649170eeea53 93cb9015dacc4b50a4ef177ce4ece2e7 +#: e0c7ccc8f8664cf794cbb7330355f3fe msgid "`expression`" msgstr "" #: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +#: 58a1773b1cf546d7890010fdebd47388 msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](https://www." +"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +#: 230f3227ed1144f7abe0f8c231bebbd5 msgid "" -"From " -"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: d0eec6969d174b258e0f010800884cc6 5c77dc9f8afe4dd88933943030e836f2 +#: c9534670f5f04769aa3749c3778eb705 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 #: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 -#: 718ceee9973240ec9c100977bbcc8921 +#: 718ceee9973240ec9c100977bbcc8921 4ec8bbac5fb14371a6a4cd53d7cd6450 +#: 7b0887a8caed41b2acccf7021bb323d3 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 #: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 -#: c07ab08eb75d4528949c56a3d7c12b28 +#: c07ab08eb75d4528949c56a3d7c12b28 aceedfb558b246bc87eb3eaedea187fd +#: e5e8b8c75f0f43cbb6e160e5bf810c6e msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: b885e108dced4981a445e5fa0a044394 266dfb5fe6a842078baf66073cac9623 +#: fe3b9fb45e01490498c5a35c012b3de8 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 #: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: e9f5306ae6ea49bbb6801dcce9be2d67 85f424cbfc85460f9da310aee1ff0b82 +#: ddf82b12b12d416fb65f3ce3f51bbdf0 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: 58bf8016f5f04c26b645025f405e2288 966e88656ae5402a975022ee60646283 +#: af14fda3cca645fbb2f3c5825fe0788e msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 #: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: 7c817029d55b4700ae8e84be4d0f0ca0 09120baec1464afb8aed4edd773bf509 +#: fec70bb106ad4d95a2d55ebdcf711afc msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 #: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 msgid "`outdirMax`" msgstr "" #: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +#: 1dc4148caef748428a7d13caff37b1b1 msgid "" -"From " -"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 #: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 msgid "`listing`" msgstr "" #: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +#: 947b1ca132a54ed39745cd12ebcd65e1 msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 #: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b +#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 #: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 +#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 #: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 msgid "From `EnvVarRequirement`" msgstr "" #: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +#: 5fa512d352d945e7a3e0d59b0987cd1b msgid "" -"From " -"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 #: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c msgid "`envValue`" msgstr "" #: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +#: 81e91df082834d2cab7ef1f62d8ba57a +msgid "" +"Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" #: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +#: e6bfd1dc2e324992b6c3332c11ae3445 msgid "" -"The requirement `InlineJavascriptRequirement` supports an `expressionLib`" -" attribute that allows users to load external JavaScript files, or to " -"provide inline JavaScript code." +"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " +"attribute that allows users to load external JavaScript files, or to provide " +"inline JavaScript code." msgstr "" #: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +#: acf10261df2944ec890d754fd56c6b28 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts" -" of the CWL document." +"files or to create JavaScript functions that can be called in other parts of " +"the CWL document." msgstr "" #: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +#: bda6b8f398554b0c946c2c7d96308a42 msgid "" -"The CWL standards (versions 1.0 through 1.2) " -"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" -" that the only version of JavaScript valid in CWL expressions is " -"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " -"that any code that you include or write in your CWL Document must be " -"compliant with ECMAScript 5.1." +"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." +"org/v1.0/CommandLineTool.html#Expressions) that the only version of " +"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" +"international.org/5.1/). This means that any code that you include or write " +"in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" #: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +#: 454c02c3918647039c90ae387005dea6 msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a " -"JavaScript function inline in `expressionLib`. That function can then be " -"used in other parts of the CWL document:" +"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " +"function inline in `expressionLib`. That function can then be used in other " +"parts of the CWL document:" msgstr "" #: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +#: e1fad28bf9cb4c4c85eb74dd520ba107 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" #: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +#: 9835d0b399b84a0084fe5a4d9e7e6405 msgid "" -"Running this CWL workflow will invoke the JavaScript function and result " -"in the `echo` command printing the input message with capital initial " -"letters:" +"Running this CWL workflow will invoke the JavaScript function and result in " +"the `echo` command printing the input message with capital initial letters:" msgstr "" #: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +#: 410ba7a5ac6349a98460c6337ee5c4fb msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" #: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +#: d2daf50d7f3d4de18331c8fd2c8a5786 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" #: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +#: 8f2015c12b2b4d5d9a800ddeaf428f25 msgid "`custom-functions.js`" msgstr "" #: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +#: f0ff919ffc12439d89d7b40f51ade84c msgid "`hello-world-expressionlib-external.cwl`" msgstr "" #: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +#: 307a17a893fc4dafaec2a63a95704644 msgid "" -"The `custom-functions.js` file is included in the CWL document with the " -"`$include: custom-functions.js` statement. That makes the functions and " +"The `custom-functions.js` file is included in the CWL document with the `" +"$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +#: 7f393e86b114470f8dda47b2deec63aa msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" #: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +#: c3f459b87b96435583637b3f1573e658 msgid "" -"Finally, note that you can have both inline and external JavaScript code " -"in your CWL document. In this final example we have added another entry " -"to the `expressionLib` attribute with the new function " -"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" -" the external file `custom-functions.js`." +"Finally, note that you can have both inline and external JavaScript code in " +"your CWL document. In this final example we have added another entry to the " +"`expressionLib` attribute with the new function `createHelloWorldMessage`, " +"that calls the `capitalizeWords` function from the external file `custom-" +"functions.js`." msgstr "" #: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +#: 9f676022eb2744839ca2109920250cb6 msgid "`hello-world-expressionlib.cwl`" msgstr "" #: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +#: ede7285f77864fb0aee6cfecc2c97fa0 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" #: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +#: c55fb184bc614ee2b6e5e64611e5df9b msgid "" -"The `$include` statement can be used to include a file from the local " -"disk or from a remote location. It works with both relative and absolute " -"paths. Read the [text about " -"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " -"the CWL specification to learn more about it." +"The `$include` statement can be used to include a file from the local disk " +"or from a remote location. It works with both relative and absolute paths. " +"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." +"html#Include) from the CWL specification to learn more about it." msgstr "" #: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +#: 66b522f46ce242149386e79f63b32cf8 msgid "File Formats" msgstr "" #: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +#: 64a20285785d48ca86227a0cf6353ad4 msgid "" "Tools and workflows can take `File` types as input and produce them as " -"output. We also recommend indicating the format for `File` types. This " -"helps document for others how to use your tool while allowing you to do " -"some simple type-checking when creating parameter files." +"output. We also recommend indicating the format for `File` types. This helps " +"document for others how to use your tool while allowing you to do some " +"simple type-checking when creating parameter files." msgstr "" #: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +#: 5f71bbe2c74e4260b79d4d9230d35397 msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM" -" in our example), reference a local ontology for your institution, or do " -"not add a file format initially for quick development before sharing your" -" tool with others. You can browse existing [IANA file format " -"listings][IANA] and [EDAM file format listings][EDAM] on their websites." +"For file formats, we recommend referencing existing ontologies (like EDAM in " +"our example), reference a local ontology for your institution, or do not add " +"a file format initially for quick development before sharing your tool with " +"others. You can browse existing [IANA file format listings][IANA] and [EDAM " +"file format listings][EDAM] on their websites." msgstr "" #: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +#: 63bfff437e3348428f7e33ece7ec55e7 msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` " -"section of the document in greater detail, so don't worry about these for" -" now." +"In the next tutorial, we explain the `$namespaces` and `$schemas` section " +"of the document in greater detail, so don't worry about these for now." msgstr "" #: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +#: 6ce83d9c06e4436881aa47d94ef41e0b msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" #: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +#: 55006c594abf4e70a38e979568fadcf4 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 #: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 msgid "The equivalent of this CWL description in command line format is:" msgstr "" #: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +#: 1a1905ff2d624eca952c8a53b3bee678 msgid "Sample Parameter Files" msgstr "" #: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +#: 368ff92476b14f5c8331260eafc5acb5 msgid "" -"Below is an example of a parameter file for the example above. We " -"encourage checking in working examples of parameter files for your tool. " -"This allows others to quickly work with your tool, starting from a " -"\"known good\" parameterization." +"Below is an example of a parameter file for the example above. We encourage " +"checking in working examples of parameter files for your tool. This allows " +"others to quickly work with your tool, starting from a \"known good\" " +"parameterization." msgstr "" #: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +#: 5d530afa23f349a79f54d51d40724747 msgid "`sample.yml`" msgstr "" #: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +#: 16f965f86712483aa7f95dfa3f944a17 msgid "" -"___Note:___ To follow the example below, you need to download the example" -" input file, *file-formats.bam*. The file is available from " -" and can be downloaded e.g. via `wget`:" +"___Note:___ To follow the example below, you need to download the example " +"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" #: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +#: dc629e2c90ed458b96107a6994676434 msgid "Topics" msgstr "" #: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +#: cf2f077cf8044079a7005e6e508dcd8c msgid "Inputs" msgstr "" #: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +#: 129e1d2a71894d28b009f4846754a75d msgid "Essential Input Parameters" msgstr "" #: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +#: d6791bbe575042b9a7282c69407dd907 msgid "" -"The `inputs` of a tool is a list of input parameters that control how to " -"run the tool. Each parameter has an `id` for the name of parameter, and " -"`type` describing what types of values are valid for that parameter." +"The `inputs` of a tool is a list of input parameters that control how to run " +"the tool. Each parameter has an `id` for the name of parameter, and `type` " +"describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +#: e8da87f8bb664334adf831995601f462 msgid "" -"Available primitive types are *string*, *int*, *long*, *float*, *double*," -" and *null*; complex types are *array* and *record*; in addition there " -"are special types *File*, *Directory* and *Any*." +"Available primitive types are *string*, *int*, *long*, *float*, *double*, " +"and *null*; complex types are *array* and *record*; in addition there are " +"special types *File*, *Directory* and *Any*." msgstr "" #: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +#: de6c322618304207b6d1364d1ec2dc13 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" #: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +#: 43bdcf6dc1b14030bff27fa53289c02c msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" #: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +#: 056510b42ea64717996ab49c307bda86 msgid "`inp.cwl`" msgstr "" #: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +#: 6852f5dbd9094c99bb68f2a88f76c9bc msgid "Create a file called `inp-job.yml`:" msgstr "" #: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +#: f33b6800367248b7927d97ad7b4be5b5 msgid "`inp-job.yml`" msgstr "" #: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +#: 8ad812d7e88f4cbba83228ffb1711576 msgid "" -"You can use `cwltool` to create a template input object. That saves you " -"from having to type all the input parameters in a input object file:" +"You can use `cwltool` to create a template input object. That saves you from " +"having to type all the input parameters in a input object file:" msgstr "" #: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +#: cc680bbf091a46f8b4b3dbe6324c040a msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template " -"inp.cwl > inp-job.yml`, and then modify the default values with your " -"desired input values." +"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " +"> inp-job.yml`, and then modify the default values with your desired input " +"values." msgstr "" #: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +#: 446ac81f078d46289a18f494748f482c msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" #: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +#: 3d6d958d111943f3a2139b4dbb7810db msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" -" command line." +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " +"command line." msgstr "" #: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +#: ba0ec9157709430c822f4e91459288e2 msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " -"following boxed text describes these two commands and the expected output" -" from the command line:" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " +"boxed text describes these two commands and the expected output from the " +"command line:" msgstr "" #: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +#: 2565f8fd4a15429e887aeb71eacdff1e msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not " -"explicitly specified" +"that the tools aren't accidentally accessing files that were not explicitly " +"specified" msgstr "" #: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +#: 659ed5c64fb546399b741553a347b8e8 msgid "" -"The field `inputBinding` is optional and indicates whether and how the " -"input parameter should appear on the tool's command line. If " -"`inputBinding` is missing, the parameter does not appear on the command " -"line. Let's look at each example in detail." +"The field `inputBinding` is optional and indicates whether and how the input " +"parameter should appear on the tool's command line. If `inputBinding` is " +"missing, the parameter does not appear on the command line. Let's look at " +"each example in detail." msgstr "" #: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +#: 3d87e69d41374fbab23b26d36c1aee03 msgid "" -"Boolean types are treated as a flag. If the input parameter " -"\"example_flag\" is \"true\", then `prefix` will be added to the command " -"line. If false, no flag is added." +"Boolean types are treated as a flag. If the input parameter \"example_flag" +"\" is \"true\", then `prefix` will be added to the command line. If false, " +"no flag is added." msgstr "" #: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +#: 07bc81683e2c4ac68b379462bae95207 msgid "" -"String types appear on the command line as literal values. The `prefix` " -"is optional, if provided, it appears as a separate argument on the " -"command line before the parameter . In the example above, this is " -"rendered as `--example-string hello`." +"String types appear on the command line as literal values. The `prefix` is " +"optional, if provided, it appears as a separate argument on the command line " +"before the parameter . In the example above, this is rendered as `--example-" +"string hello`." msgstr "" #: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +#: 3e304da2150f448d9e39715ac5f5deaa msgid "" -"Integer (and floating point) types appear on the command line with " -"decimal text representation. When the option `separate` is false (the " -"default value is true), the prefix and value are combined into a single " -"argument. In the example above, this is rendered as `-i42`." +"Integer (and floating point) types appear on the command line with decimal " +"text representation. When the option `separate` is false (the default value " +"is true), the prefix and value are combined into a single argument. In the " +"example above, this is rendered as `-i42`." msgstr "" #: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +#: fd8a98686e3c4c609f79ae427f1558d3 msgid "" "File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the " -"parameter is optional. In the example above, this is rendered as " -"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " -"parameter were not provided in the input, nothing would appear on the " -"command line." +"parameter type ends with a question mark `?` it indicates that the parameter " +"is optional. In the example above, this is rendered as `--file=/tmp/random/" +"path/whale.txt`. However, if the \"example_file\" parameter were not " +"provided in the input, nothing would appear on the command line." msgstr "" #: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +#: f1a2e1bbb1104a4fab5a7f04cac845c7 msgid "" -"Input files are read-only. If you wish to update an input file, you must" -" [first copy it to the output directory](staging-input-files.md)." +"Input files are read-only. If you wish to update an input file, you must " +"[first copy it to the output directory](staging-input-files.md)." msgstr "" #: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +#: 6a7f0ccd227e4f90a8c8ca96744bda68 msgid "" -"The value of `position` is used to determine where parameter should " -"appear on the command line. Positions are relative to one another, not " -"absolute. As a result, positions do not have to be sequential, three " -"parameters with positions 1, 3, 5 will result in the same command line as" -" 1, 2, 3. More than one parameter can have the same position (ties are " -"broken using the parameter name), and the position field itself is " -"optional. The default position is 0." +"The value of `position` is used to determine where parameter should appear " +"on the command line. Positions are relative to one another, not absolute. " +"As a result, positions do not have to be sequential, three parameters with " +"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " +"than one parameter can have the same position (ties are broken using the " +"parameter name), and the position field itself is optional. The default " +"position is 0." msgstr "" #: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +#: 1f79d115d8a145189638c68c3095396c msgid "" -"The `baseCommand` field will always appear in the final command line " -"before the parameters." +"The `baseCommand` field will always appear in the final command line before " +"the parameters." msgstr "" #: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +#: 6e1b3e2d90184e34925891099d2b5cc1 msgid "Array Inputs" msgstr "" #: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +#: 4f6df7f13e42448eb4a53f03bc477b56 msgid "" "It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to " -"provide `type` field with `type: array` and `items` defining the valid " -"data types that may appear in the array. Alternatively, brackets `[]` may" -" be added after the type name to indicate that input parameter is array " -"of that type." +"line. There are two ways to specify an array parameter. First is to provide " +"`type` field with `type: array` and `items` defining the valid data types " +"that may appear in the array. Alternatively, brackets `[]` may be added " +"after the type name to indicate that input parameter is array of that type." msgstr "" #: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +#: dbc0b52627514ad0908969d0b4ddfdf4 msgid "`array-inputs.cwl`" msgstr "" #: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +#: f173dd96ad124470a53573c86a8df203 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 #: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 #: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d +#: af25945b530048b685891b1de4e35e72 cb07caa4ff0149b3ae832be53f8d76f6 +#: e0098a77080d4349b05ceb7735a5fdf5 msgid "" -"Now invoke `cwltool` providing the tool description and the input object " -"on the command line:" +"Now invoke `cwltool` providing the tool description and the input object on " +"the command line:" msgstr "" #: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +#: 2445d2c7c2794fd3ad8b6ed8b4a9440b msgid "" -"The `inputBinding` can appear either on the outer array parameter " -"definition or the inner array element definition, and these produce " -"different behavior when constructing the command line, as shown above. In" -" addition, the `itemSeparator` field, if provided, specifies that array " -"values should be concatenated into a single argument separated by the " -"item separator string." +"The `inputBinding` can appear either on the outer array parameter definition " +"or the inner array element definition, and these produce different behavior " +"when constructing the command line, as shown above. In addition, the " +"`itemSeparator` field, if provided, specifies that array values should be " +"concatenated into a single argument separated by the item separator string." msgstr "" #: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +#: 4459819ba75647d185986a3386939494 msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` " -"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " -"lines, where array values that are not defined with an associated key are" -" marked by a leading `-`. This will be demonstrated in the next lesson " -"and is discussed in more detail in the [YAML Guide](yaml-" -"guide.md#arrays). You can specify arrays of arrays, arrays of records, " -"and other complex types." +"Note that the arrays of inputs are specified inside square brackets `[]` in " +"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " +"where array values that are not defined with an associated key are marked by " +"a leading `-`. This will be demonstrated in the next lesson and is discussed " +"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " +"arrays of arrays, arrays of records, and other complex types." msgstr "" #: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +#: 8f163bd34ded4785b6e28c8e2147e0dd msgid "Inclusive and Exclusive Inputs" msgstr "" #: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +#: 1799e11a7b9c4929a3d1379d7ea45d03 msgid "" "Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be " -"provided together (they are exclusive). You can use records and type " -"unions to group parameters together to describe these two conditions." +"together (they are dependent) or several arguments that cannot be provided " +"together (they are exclusive). You can use records and type unions to group " +"parameters together to describe these two conditions." msgstr "" #: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +#: 9510c0b431a44b5e84e0b583de7c5446 msgid "`record.cwl`" msgstr "" #: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +#: efb4eb6f5e994b50a52fa2c707dad1ce msgid "`record-job1.yml`" msgstr "" #: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +#: 34599c6f10ce4104be2359a1b37f91cb msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" #: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: 0663ea7918994d3f9c45c652a3ed12db msgid "`record-job2.yml`" msgstr "" #: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +#: a98dda6ca4b14edba467de638bba28fc msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the " -"first matching item (`itemC`) is added to the command line and remaining " -"item (`itemD`) is ignored." +"In the second example, `itemC` and `itemD` are exclusive, so only the first " +"matching item (`itemC`) is added to the command line and remaining item " +"(`itemD`) is ignored." msgstr "" #: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +#: 10d0e9f8df8c47788703073b17529bc8 msgid "`record-job3.yml`" msgstr "" #: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +#: 9a0e1a130fba4d24a9168ca3e455cd23 msgid "" -"In the third example, only `itemD` is provided, so it appears on the " -"command line." +"In the third example, only `itemD` is provided, so it appears on the command " +"line." msgstr "" #: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +#: 992a8c801ceb4233acf56b6bff315188 msgid "Exclusive Input Parameters with Expressions" msgstr "" #: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +#: 9027d23fa7074b789c3b86ca5ea17fa4 msgid "" -"If you use exclusive input parameters combined with expressions, you need" -" to be aware that the `inputs` JavaScript object will contain one of the " +"If you use exclusive input parameters combined with expressions, you need to " +"be aware that the `inputs` JavaScript object will contain one of the " "exclusive input values. This means that you might need to use an **or** " "boolean operator to check which values are present." msgstr "" #: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +#: 68b47710a8ea4b978428b42c627944e9 msgid "" "Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from" -" an enum." +"parameter that accepts `null` (i.e. no value provided), or any value from an " +"enum." msgstr "" #: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +#: d33e4cac65d14111a89c838c4d1759b9 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" #: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +#: 24cea1cf7d774b6ab56959f289cab39d msgid "" "Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you " -"provide a valid value, such as “fasta” (one of the values of the enum), " -"your command should execute successfully:" +"parameter without taking into consideration a `null` value. If you provide a " +"valid value, such as “fasta” (one of the values of the enum), your command " +"should execute successfully:" msgstr "" #: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +#: b866867d6f8e4d3999b62a85e6884ebc msgid "" -"However, if you do not provide any input value, then `file_format` will " -"be evaluated to a `null` value, which does not match the expected type " -"for the output field (a `string`), resulting in failure when running your" -" workflow." +"However, if you do not provide any input value, then `file_format` will be " +"evaluated to a `null` value, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your workflow." msgstr "" #: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +#: 80c49ed168b14d25b2f09b3b0186b44f msgid "" -"To correct it, you must remember to use an or operator in your JavaScript" -" expression when using exclusive parameters, or any parameter that allows" -" `null`. For example, the expression could be changed to " -"`$(inputs.file_format || 'auto')`, to have a default value if none was " -"provided in the command line or job input file." +"To correct it, you must remember to use an or operator in your JavaScript " +"expression when using exclusive parameters, or any parameter that allows " +"`null`. For example, the expression could be changed to `$(inputs." +"file_format || 'auto')`, to have a default value if none was provided in the " +"command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: d33aa2353ad44fb885d3a1ee48263dc4 71628ebe908b4cd28dd1fa17e3d2e2fb msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 +#: cd64d2d828834cbbb24ea5358caf5405 f123ca244c23413c91405a4b84887525 msgid "" -"Implementation extensions not required for correct execution (for " -"example, fields related to GUI presentation) and metadata about the tool " -"or workflow itself (for example, authorship for use in citations) may be " -"provided as additional fields on any object. Such extensions fields (e.g." -" `format: edam:format_2572`) can use a namespace prefix listed in the " -"`$namespaces` section of the document (e.g. edam: " -"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" -"][schema-salad]. Once you add the namespace prefix, you can access it " -"anywhere in the document as shown below. Otherwise, one must use full " -"URLs: `format: http://edamontology.org/format_2572`." +"Implementation extensions not required for correct execution (for example, " +"fields related to GUI presentation) and metadata about the tool or workflow " +"itself (for example, authorship for use in citations) may be provided as " +"additional fields on any object. Such extensions fields (e.g. `format: edam:" +"format_2572`) can use a namespace prefix listed in the `$namespaces` section " +"of the document (e.g. edam: http://edamontology.org/) as described in the " +"[Schema Salad specification][schema-salad]. Once you add the namespace " +"prefix, you can access it anywhere in the document as shown below. " +"Otherwise, one must use full URLs: `format: http://edamontology.org/" +"format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b +#: 80af387fe3ff4e2da999903385bd602b 23299ae1bec94b00a32a8af7eeac350f msgid "" "For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to " -"cite your tool." +"tool and workflows. This example includes metadata allowing others to cite " +"your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 2495a9f2032a47c188338cb81ba429eb msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: d402bf528c7f4eb69aaaa275be2bf1d4 3fd2f3cf7bdf44089df2ce3122534801 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 d5a5b8b490b640439db92da949266e4e msgid "" -"For those that are highly motivated, it is also possible to annotate your" -" tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints" -" at hardware requirements in order to use the tool, and a few more " -"metadata fields." +"For those that are highly motivated, it is also possible to annotate your " +"tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints at " +"hardware requirements in order to use the tool, and a few more metadata " +"fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: 2dfbd4d580044ed083992f3ceb1bc64e 5935ed94331d4b2f8ce597f31edea843 msgid "`metadata_example3.cwl`" msgstr "" #: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +#: 5feb559552194ba58da7206c601292fe msgid "Operations" msgstr "" #: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +#: b7124ba4df9042baadc1641ee09545d6 msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-" -"line tool, or an expression tool. It is a step of a workflow that " -"specifies inputs and outputs, but it does not provide enough information " -"to be executed." +"An Operation is a type of CWL process, just like a workflow, a command-line " +"tool, or an expression tool. It is a step of a workflow that specifies " +"inputs and outputs, but it does not provide enough information to be " +"executed." msgstr "" #: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +#: d34b698c62114041a64e0abce25ca935 msgid "" -"You can create operations to visualize a workflow during development, " -"before you are ready to submit the workflow to a CWL runner:" +"You can create operations to visualize a workflow during development, before " +"you are ready to submit the workflow to a CWL runner:" msgstr "" #: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +#: cba2c31262bd450cbafc7ca77f4fb8fa msgid "`operations.cwl`" msgstr "" #: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +#: b01be5f632104096b5af6193aab34d90 msgid "" -"The `uppercase` step of the workflow is an operation. It can be used like" -" a command line tool or an expression. You can also plot it with the CWL " -"Viewer or `cwltool`:" +"The `uppercase` step of the workflow is an operation. It can be used like a " +"command line tool or an expression. You can also plot it with the CWL Viewer " +"or `cwltool`:" msgstr "" #: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +#: 60a6a02c1367403db6df3ec10f75eb69 msgid "" -"The output of the command above can be rendered with a Graphviz renderer." -" The following image is rendered with the Sphinx Graphviz directive (this" -" user guide is built with Sphinx):" +"The output of the command above can be rendered with a Graphviz renderer. " +"The following image is rendered with the Sphinx Graphviz directive (this " +"user guide is built with Sphinx):" msgstr "" #: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +#: 314ea7bc35154f41b2af5fa6683ca389 msgid "" -"If you try running it with `cwltool`, the command will fail since " -"`cwltool` does not have enough information to know how to execute it:" +"If you try running it with `cwltool`, the command will fail since `cwltool` " +"does not have enough information to know how to execute it:" msgstr "" #: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +#: d81e679b13474f74bc5e1ce1e31c2bc6 msgid "`cwltool` does not know how to run operations" msgstr "" #: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +#: d7fb27131ee44bfc82f698ee44b2bae0 msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A" -" CWL runner could, for instance, use abstract operations with ID's that " +"CWL runners may come up with ways to bind operations to concrete steps. A " +"CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" #: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +#: b8ef11eafd1d46e088f1277f4ac372bc msgid "Outputs" msgstr "" #: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +#: d2382ed1f644459594655d5b5b4d838a msgid "Returning Output Files" msgstr "" #: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +#: 6651632d977b44479b721174fffeda2d msgid "" "The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name" -" of parameter, and `type` describing what types of values are valid for " -"that parameter." +"returned after running the tool. Each parameter has an `id` for the name of " +"parameter, and `type` describing what types of values are valid for that " +"parameter." msgstr "" #: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +#: bee5f532554241088764ac9e56abbe85 msgid "" -"When a tool runs under CWL, the starting working directory is the " -"designated output directory. The underlying tool or script must record " -"its results in the form of files created in the output directory. The " -"output parameters returned by the CWL tool are either the output files " -"themselves, or come from examining the content of those files." +"When a tool runs under CWL, the starting working directory is the designated " +"output directory. The underlying tool or script must record its results in " +"the form of files created in the output directory. The output parameters " +"returned by the CWL tool are either the output files themselves, or come " +"from examining the content of those files." msgstr "" #: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +#: 0c7c506f38be421399073871f64e99b0 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" #: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +#: 8b60286e56cc42a8ab5f751a97adf771 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" #: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +#: fa0ad674f15348339a1eee771a6ba9e2 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2676,464 +3022,520 @@ msgid "" msgstr "" #: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +#: 177b5f1b95a34fb9b2eb42f733d79ac8 msgid "`tar.cwl`" msgstr "" #: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +#: a08a6d8aca8e490482e127a8fd5e650e msgid "`tar-job.yml`" msgstr "" #: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +#: c2c60f68b1e045f88844076e191fda9b msgid "Next, create a tar file for the example." msgstr "" #: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +#: 6d939f62526e4e6d95acb57d72f60a84 msgid "" -"And now invoke `cwltool` with the tool description and the input object " -"on the command line:" +"And now invoke `cwltool` with the tool description and the input object on " +"the command line:" msgstr "" #: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +#: c48edd9034364b81ad42540a98b51d91 msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" #: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +#: 9ebe0186a7124dfaa30e558e8f59653a msgid "" -"The `glob` field consists of the name of a file in the output directory. " -"If you don't know name of the file in advance, you can use a wildcard " -"pattern like `glob: '*.txt'`." +"The `glob` field consists of the name of a file in the output directory. If " +"you don't know name of the file in advance, you can use a wildcard pattern " +"like `glob: '*.txt'`." msgstr "" #: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +#: 9381b7d7c9904df0a5e16dac29c2e08f msgid "Capturing Standard Output" msgstr "" #: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +#: 2aa9c6916e3546b7b92fa64bb83275d1 msgid "" -"To capture a tool's standard output stream, add the `stdout` field with " -"the name of the file where the output stream should go. Then add `type: " -"stdout` on the corresponding output parameter." +"To capture a tool's standard output stream, add the `stdout` field with the " +"name of the file where the output stream should go. Then add `type: stdout` " +"on the corresponding output parameter." msgstr "" #: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +#: 63afb7a597fc4e459b6a7dbd40bbf6ff msgid "`stdout.cwl`" msgstr "" #: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +#: 7418915470f041c9af5bd39ea652de36 msgid "Array Outputs" msgstr "" #: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +#: f82db001b58c4969b2d8bc1dcbd7cf8a msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" #: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +#: 26d9f0b28d384617a8e490c1f8e26e52 msgid "`array-outputs.cwl`" msgstr "" #: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +#: cf46c971b31b4e10bf0fefb4cd028c2f msgid "`array-outputs-job.yml`" msgstr "" #: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +#: a4347983fb9945a4a2773af88e426dc9 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions" -" to mark entries in arrays, as demonstrated in several of the upcoming " -"sections." +"marked by a leading `-`. This format can also be used in CWL descriptions to " +"mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" #: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +#: c5489e0633114372b273098ee2c9ffd9 msgid "Parameter References" msgstr "" #: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +#: 75de9fd63393429daf1ca10a85339aa7 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file " -"we were interested in was called \"hello.txt\", and this was written into" -" the `.cwl` file. This is not the best way to do this, as the " -"\"hello.txt\" filename may vary or be dependent on the input file(s) " -"used. To avoid this we can specify the name of the file we want in the " -"job parameters file (`.yml`). In this example, you will see how to " -"reference the value of input parameters dynamically from other fields, " -"which will allow us to then specify the name of the file to extract." +"However, that example was very limited because it assumed that the file we " +"were interested in was called \"hello.txt\", and this was written into the `." +"cwl` file. This is not the best way to do this, as the \"hello.txt\" " +"filename may vary or be dependent on the input file(s) used. To avoid this " +"we can specify the name of the file we want in the job parameters file (`." +"yml`). In this example, you will see how to reference the value of input " +"parameters dynamically from other fields, which will allow us to then " +"specify the name of the file to extract." msgstr "" #: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +#: 8b5d0ada32d645be9359f43a431f5f91 msgid "`tar-param.cwl`" msgstr "" #: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +#: 2ed93dc8778e44209194f41b9ad193d5 msgid "`tar-param-job.yml`" msgstr "" #: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +#: a80dd6d9920540e9880514e04035af86 msgid "" -"Create your input files and invoke `cwltool` with the tool description " -"and the input object on the command line:" +"Create your input files and invoke `cwltool` with the tool description and " +"the input object on the command line:" msgstr "" #: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +#: 9de300f7b9da49f59d1c9fd96dec4a8b msgid "" -"Certain fields permit parameter references which are enclosed in " -"`$(...)`. These are evaluated and replaced with value being referenced." +"Certain fields permit parameter references which are enclosed in `$(...)`. " +"These are evaluated and replaced with value being referenced." msgstr "" #: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +#: a61f52d3c1024c3692899e05fcea4bee msgid "" "References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " -"`$(inputs['extractfile'])` are equivalent." +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" +"$(inputs['extractfile'])` are equivalent." msgstr "" #: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +#: dafc9ba578c14fd79d075160e6b7bd6b msgid "" -"The value of the \"inputs\" variable is the input object provided when " -"the CWL tool was invoked." +"The value of the \"inputs\" variable is the input object provided when the " +"CWL tool was invoked." msgstr "" #: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +#: 28ca6cae42904559bcec98fb9d2b07cb msgid "" -"Note that because `File` parameters are objects, to get the path to an " -"input file you must reference the path field on a file object; to " -"reference the path to the tar file in the above example you would write " -"`$(inputs.tarfile.path)`." +"Note that because `File` parameters are objects, to get the path to an input " +"file you must reference the path field on a file object; to reference the " +"path to the tar file in the above example you would write `$(inputs.tarfile." +"path)`." msgstr "" #: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +#: 616c9ff9fcae489285f0bbbc67f07d29 msgid "Where are parameter references allowed?" msgstr "" #: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +#: ac17acd83ddb43dc9fb7a5e595ab1153 msgid "You can only use parameter references in certain fields. These are:" msgstr "" #: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +#: 156573324cde41ee8b3c47deabf43db8 msgid "" -"From " -"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" #: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +#: c9725be01e8a401fb3ad9ff01339f81e msgid "" -"From " -"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +#: 6797335256e2412cbbe7636507931455 msgid "" -"From " -"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" #: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +#: 05a5f0fcb7454cb697e3d810d55fac26 msgid "" -"From " -"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +#: 406e68280b5c4ee494632f94b635b7ad msgid "" -"From " -"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" #: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +#: 2d6e2a4ff391494591bbdf8dbcc4a6ae msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +#: e71a974b29624210a107fc2d097d4196 msgid "" -"From " -"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" #: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +#: b59df98754e24654bfef0b1fe1d91660 msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +#: d2bccbff1ce646348fe38c776ad183e1 msgid "" -"From " -"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 +#: 5d8bed66282c408695292ea92a03b2c4 943ba46512ce48fe8c5b62327734c503 msgid "" -"From " -"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: 958178d1fa8843aaa0541e2bb115cfd4 bbcd43d5af7d44108aeb65075a6bd2be msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 834295755af841a78e466eea43864861 msgid "" -"From " -"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: aac74f957774479a83aab4c6ff1390ae a6b626489bfa468e8f059ab3aa669201 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: b75d29d1d55d44488338f9689f156855 e1dbea105aa845c38cb1f90b43847271 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb +#: 574d93d1d592458a985f259519c036cb e9640f47d40e45bca184eb30700df648 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " -"include a `SoftwareRequirement` field in the `hints` section. This may " -"also help to avoid confusion about which version of a tool the " -"description was written for." +"include a `SoftwareRequirement` field in the `hints` section. This may also " +"help to avoid confusion about which version of a tool the description was " +"written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 +#: 82e48b3e3c3f451480cc0b6a529271f6 0456efb3718b4356ad2b277ee16de967 msgid "" -"In this example, the software requirement being described is InterProScan" -" version 5.21-60." +"In this example, the software requirement being described is InterProScan " +"version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 +#: 02e40154eac74ecc98d0447d03475b44 f7e97f926505407f8f8e9a427e055e43 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the " -"[dependency resolvers configuration][dependencies]." +"enable these checks with the reference implementation, use the [dependency " +"resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 -msgid "" -"As well as a version number, a unique resource identifier (URI) for the " -"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" -" looked up in the [SciCrunch][scicrunch] registry, which provides a " -"portal for finding, tracking, and referring to scientific resources " -"consistently. If you want to specify a tool as a `SoftwareRequirement`, " -"search for the tool on SciCrunch and use the RRID that it has been " -"assigned in the registry. (Follow this [Adding a Resource Tutorial" -"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " -"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " -"field of your requirement description. Other good choices, in order of " -"preference, are to include the DOI for the main tool citation and the URL" -" to the tool." +#: 8cb1c5d9b1a54c40924099494eb766c6 ec597ff8f6ee47bc815b069335869f1f +msgid "" +"As well as a version number, a unique resource identifier (URI) for the tool " +"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " +"up in the [SciCrunch][scicrunch] registry, which provides a portal for " +"finding, tracking, and referring to scientific resources consistently. If " +"you want to specify a tool as a `SoftwareRequirement`, search for the tool " +"on SciCrunch and use the RRID that it has been assigned in the registry. " +"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " +"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." +"org][identifiers]) in the `specs` field of your requirement description. " +"Other good choices, in order of preference, are to include the DOI for the " +"main tool citation and the URL to the tool." msgstr "" #: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +#: 7467a7f6f26a459ba4ce83e4e6dfcc2b msgid "Staging Input Files" msgstr "" #: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +#: 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 msgid "" -"Normally, input files are located in a read-only directory separate from " -"the output directory. This causes problems if the underlying tool " -"expects to write its output files alongside the input file in the same " -"directory. You use `InitialWorkDirRequirement` to stage input files into" -" the output directory. In this example, we use a JavaScript expression to" -" extract the base name of the input file from its leading directory path." +"Normally, input files are located in a read-only directory separate from the " +"output directory. This causes problems if the underlying tool expects to " +"write its output files alongside the input file in the same directory. You " +"use `InitialWorkDirRequirement` to stage input files into the output " +"directory. In this example, we use a JavaScript expression to extract the " +"base name of the input file from its leading directory path." msgstr "" #: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: a03372581fa44f9b8e3e088a4099cdd9 msgid "`linkfile.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +#: 36e082be73464be0ad5d0b681cc510da msgid "Troubleshooting" msgstr "" #: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +#: 4464455b51ad4873ac13c4a63ee5fb54 msgid "" -"In this section you will find ways to troubleshoot when you have problems" -" executing CWL. We focus on `cwltool` here but some of these techniques " -"may apply to other CWL Runners." +"In this section you will find ways to troubleshoot when you have problems " +"executing CWL. We focus on `cwltool` here but some of these techniques may " +"apply to other CWL Runners." msgstr "" #: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +#: ed7ff0753d1743a995f4cfedd6e5dcc2 msgid "Run `cwltool` with `cachedir`" msgstr "" #: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +#: 4c2dd10dd66446058477a52fb8d2c602 msgid "" "You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor " -"output files, but created while your workflow is running). By default, " -"these files are created in a temporary directory but writing them to a " -"separate directory makes accessing them easier." +"`cwltool` to cache intermediate files (files that are not input nor output " +"files, but created while your workflow is running). By default, these files " +"are created in a temporary directory but writing them to a separate " +"directory makes accessing them easier." msgstr "" #: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +#: 978b6a5fd5fa425fa9a18d9f0e8788da msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " -"World\" | rev`, which would print the message \"Hello World\" reversed, " -"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," -" where instead of executing the `rev` command it tries to execute `revv`," -" which fails." +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " +"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " +"olleH\". However, the second step, `step_b`, **has a typo**, where instead " +"of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" #: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +#: 000c0d6ae8bf414d9293b9f13fd2e448 msgid "`troubleshooting-wf1.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +#: 7e91b8811be14f8e80df39ac4c5bd316 msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " -"value (`cwltool` will create the directory for you if it does not exist " -"already):" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " +"(`cwltool` will create the directory for you if it does not exist already):" msgstr "" #: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +#: d42799cc5bd4484bb6beb309a61e103e msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. " -"You can inspect the intermediate files created:" +"successfully and its output has been cached in your `cachedir` location. You " +"can inspect the intermediate files created:" msgstr "" #: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +#: 48bb0f6666ac48648c7d969608b3bd48 msgid "" -"Each workflow step has received a unique ID (the long value that looks " -"like a hash). The `${HASH}.status` files display the status of each step " -"executed by the workflow. And the `step_a` output file `stdout.txt` is " -"visible in the output of the command above." +"Each workflow step has received a unique ID (the long value that looks like " +"a hash). The `${HASH}.status` files display the status of each step executed " +"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " +"output of the command above." msgstr "" #: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +#: f8876044db184cbaaca56579d0c773df msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" -" in the `step_b`). After fixing the typo, when you execute `cwltool` with" -" the same arguments as the previous time, note that now `cwltool` output " -"contains information about pre-cached outputs for `step_a`, and about a " -"new cache entry for the output of `step_b`. Also note that the status of " -"`step_b` is now of success." +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " +"the `step_b`). After fixing the typo, when you execute `cwltool` with the " +"same arguments as the previous time, note that now `cwltool` output contains " +"information about pre-cached outputs for `step_a`, and about a new cache " +"entry for the output of `step_b`. Also note that the status of `step_b` is " +"now of success." msgstr "" #: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +#: a5a3d408dbe34cfda4dd0b2abe67e7d7 msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had" -" been cached, and there was no change in its execution or output. " +"In this example the workflow step `step_a` was not re-evaluated as it had " +"been cached, and there was no change in its execution or output. " "Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for" -" troubleshooting your CWL documents and also as a way to prevent " -"`cwltool` to re-evaluate steps unnecessarily." +"`step_b` after we fixed the executable name. This technique is useful for " +"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " +"re-evaluate steps unnecessarily." msgstr "" #: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +#: 4c240a18c4e6441189489011242c1efd msgid "Using Containers" msgstr "" #: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +#: e37e76ef376a4ee695e600998906ec1c msgid "Running Tools Inside Docker" msgstr "" #: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +#: 51a307b0ba7c4c1d89309ba8d2250471 msgid "" -"[Docker][docker] containers simplify software installation by providing a" -" complete known-good runtime for software and its dependencies. However," -" containers are also purposefully isolated from the host system, so in " -"order to run a tool inside a Docker container there is additional work to" -" ensure that input files are available inside the container and output " -"files can be recovered from the container. A CWL runner can perform this" -" work automatically, allowing you to use Docker to simplify your software" -" management while avoiding the complexity of invoking and managing Docker" -" containers." +"[Docker][docker] containers simplify software installation by providing a " +"complete known-good runtime for software and its dependencies. However, " +"containers are also purposefully isolated from the host system, so in order " +"to run a tool inside a Docker container there is additional work to ensure " +"that input files are available inside the container and output files can be " +"recovered from the container. A CWL runner can perform this work " +"automatically, allowing you to use Docker to simplify your software " +"management while avoiding the complexity of invoking and managing Docker " +"containers." msgstr "" #: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +#: 13cc38d72d34468fa4eb6d91f23ff105 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the " -"container." +"input files to reflect the location where they appear inside the container." msgstr "" #: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +#: 42a48398d3ef4b03bd7395120f2cfb42 msgid "" -"This example runs a simple Node.js script inside a Docker container which" -" will then print \"Hello World\" to the standard output." +"This example runs a simple Node.js script inside a Docker container which " +"will then print \"Hello World\" to the standard output." msgstr "" #: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +#: d59387b433bc4ecfaf7e72026624db02 msgid "`docker.cwl`" msgstr "" #: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +#: d963418ccc0b4803bbc758d718ccb5aa msgid "`docker-job.yml`" msgstr "" #: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +#: a224d1510c9e46aab23d8bdc03c349dd msgid "" "Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that " -"is really new is the `dockerRequirement` section." +"Most of this has been explained in previous sections, the only part that is " +"really new is the `dockerRequirement` section." msgstr "" #: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +#: 0a82f8a45b0546aaac4c976dcc98014a msgid "" -"`baseCommand: node` tells CWL that we will be running this command using " -"the Node Js runtime that is meant for Javascript files. We then need to " -"specify some `hints` for how to find the container we want. In this case" -" we list just our requirements for the docker container in " -"`DockerRequirements`. The `dockerPull:` parameter takes the same value " -"that you would pass to a `docker pull` command. That is, the name of the " -"container image (you can even specify the tag, which is good idea for " -"best practices when using containers for reproducible research). In this " -"case we have used a container called `node:slim`." +"`baseCommand: node` tells CWL that we will be running this command using the " +"Node Js runtime that is meant for Javascript files. We then need to specify " +"some `hints` for how to find the container we want. In this case we list " +"just our requirements for the docker container in `DockerRequirements`. The " +"`dockerPull:` parameter takes the same value that you would pass to a " +"`docker pull` command. That is, the name of the container image (you can " +"even specify the tag, which is good idea for best practices when using " +"containers for reproducible research). In this case we have used a container " +"called `node:slim`." msgstr "" #: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +#: bc418a2a535e49359c4cd44b373bbe02 msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` " -"providing the tool description and the input object on the command line:" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " +"the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +#: a799fba2322944cea00e413c08066536 msgid "`hello.js`" msgstr "" #: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +#: 35379c6b972940bd8451f10b74dd793e msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" #: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +#: 2d5265525ad544a0b64ad2cf07aacc26 msgid "" -"In this example, the path to the script `hello.js` is " -"`/home/me/cwl/user_guide/hello.js` outside the container but " -"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " -"reflected in the invocation of the `node` command." +"In this example, the path to the script `hello.js` is `/home/me/cwl/" +"user_guide/hello.js` outside the container but `/var/lib/cwl/" +"job369354770_examples/hello.js` inside the container, as reflected in the " +"invocation of the `node` command." msgstr "" #: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +#: e2521b89596d42f8a87a3207fd6c32f2 msgid "Workflows" msgstr "" #: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +#: 3676f23b63e142cb8e5715ae07216a47 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " @@ -3141,239 +3543,265 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +#: 00725aed13a440ca8b3c4f9155fbee99 msgid "CWL workflow." msgstr "" #: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +#: 2e38a4f9072b4ad9bbb74f943d22084d msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier " -"examples." +"command-line tool, and the expression tool showed in the earlier examples." msgstr "" #: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +#: 2b9f4035ea864b6db50c861a1819289d msgid "`echo-uppercase.cwl`" msgstr "" #: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +#: 28e9064780e7418a8e02a22f92e34404 msgid "" -"A command-line tool or expression tool can also be written directly in " -"the same CWL document as the workflow. For example, we can rewrite the " -"`echo-uppercase.cwl` workflow as a single file:" +"A command-line tool or expression tool can also be written directly in the " +"same CWL document as the workflow. For example, we can rewrite the `echo-" +"uppercase.cwl` workflow as a single file:" msgstr "" #: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +#: 66ce14a10d2d4dc497d3ed71e11ed8b8 msgid "`echo-uppercase-single-file.cwl`" msgstr "" #: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +#: 8dc00528c3d2426c8a3492a8191f1d81 msgid "" -"Having separate files helps with modularity and code organization. But it" -" can be helpful writing everything in a single file for development. " -"There are other ways to combine multiple files into a single file (e.g. " -"`cwltool --pack`) discussed further in other sections of this user guide." +"Having separate files helps with modularity and code organization. But it " +"can be helpful writing everything in a single file for development. There " +"are other ways to combine multiple files into a single file (e.g. `cwltool --" +"pack`) discussed further in other sections of this user guide." msgstr "" #: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +#: f9ef5e258f7c4971a8543d1dfed711a8 msgid "" "For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this" -" user guide in more detail." +"`SubworkflowFeatureRequirement`. It is covered in another section of this " +"user guide in more detail." msgstr "" #: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +#: 324bc51071d743ea80124c23880ddc0a msgid "Writing Workflows" msgstr "" #: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +#: d8c13e01976b43a1af34c11a7bc36897 msgid "" -"This workflow extracts a java source file from a tar file and then " -"compiles it." +"This workflow extracts a java source file from a tar file and then compiles " +"it." msgstr "" #: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +#: 43910a8ab4484e529a17df418b1aedbb msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 #: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 msgid "Visualization of 1st-workflow.cwl" msgstr "" #: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +#: 7ad12d67e815400c94080804b9285629 msgid "" -"[![Visualization of 1st-" -"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-" +"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" "workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-workflow.cwl)" +"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" +"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" #: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +#: 457d5a31c79143acae2683d95d27f7a3 msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a" -" run:" +"Use a YAML or a JSON object in a separate file to describe the input of a " +"run:" msgstr "" #: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +#: a2a73901bf634547900d08b9a1ac8889 msgid "`1st-workflow-job.yml`" msgstr "" #: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +#: f347d80e62384b14acf6423675e5359a msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" #: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +#: 2a845a4f3f98428fb82f3ca7ce038a6e msgid "What's going on here? Let's break it down:" msgstr "" #: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +#: e2007c74d5f449a882809d6b91c010bf msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a " -"workflow." +"document. The `class` field indicates this document describes a workflow." msgstr "" #: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#: 7f5e53ee7cf94be2bff45ef64db28a24 msgid "" -"The `inputs` section describes the inputs of the workflow. This is a " -"list of input parameters where each parameter consists of an identifier " -"and a data type. These parameters can be used as sources for input to " -"specific workflows steps." +"The `inputs` section describes the inputs of the workflow. This is a list " +"of input parameters where each parameter consists of an identifier and a " +"data type. These parameters can be used as sources for input to specific " +"workflows steps." msgstr "" #: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +#: a0d076b7b8b048478580c99ef0c8429f msgid "" -"The `outputs` section describes the outputs of the workflow. This is a " -"list of output parameters where each parameter consists of an identifier " -"and a data type. The `outputSource` connects the output parameter " -"`classfile` of the `compile` step to the workflow output parameter " -"`compiled_class`." +"The `outputs` section describes the outputs of the workflow. This is a list " +"of output parameters where each parameter consists of an identifier and a " +"data type. The `outputSource` connects the output parameter `classfile` of " +"the `compile` step to the workflow output parameter `compiled_class`." msgstr "" #: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +#: 7fd926c18ad548e98845e9b5134dd6f2 msgid "" "The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second " -"step compiles the file from the first step using the java compiler. " -"Workflow steps are not necessarily run in the order they are listed, " -"instead the order is determined by the dependencies between steps (using " -"`source`). In addition, workflow steps which do not depend on one " -"another may run in parallel." +"example, the first step extracts a file from a tar file, and the second step " +"compiles the file from the first step using the java compiler. Workflow " +"steps are not necessarily run in the order they are listed, instead the " +"order is determined by the dependencies between steps (using `source`). In " +"addition, workflow steps which do not depend on one another may run in " +"parallel." msgstr "" #: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +#: 789fbd47f8564cceb430ef3c0bc90e9b msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input" -" parameters, `tarfile` and `extractfile` and one output parameter " +"[Parameter References](parameter-references.md)). This tool has two input " +"parameters, `tarfile` and `extractfile` and one output parameter " "`extracted_file`." msgstr "" #: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +#: 45c4d0492d6143ca9cebe81e9b2cf3ae msgid "" -"The ``in`` section of the workflow step connects these two input " -"parameters to the inputs of the workflow, `tarball` and " -"`name_of_file_to_extract` using `source`. This means that when the " -"workflow step is executed, the values assigned to `tarball` and " -"`name_of_file_to_extract` will be used for the parameters `tarfile` and " -"`extractfile` in order to run the tool." +"The ``in`` section of the workflow step connects these two input parameters " +"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " +"`source`. This means that when the workflow step is executed, the values " +"assigned to `tarball` and `name_of_file_to_extract` will be used for the " +"parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" #: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +#: 73bd3da2af8545928d5ea71d0f7454f6 msgid "" -"The `out` section of the workflow step lists the output parameters that " -"are expected from the tool." +"The `out` section of the workflow step lists the output parameters that are " +"expected from the tool." msgstr "" #: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +#: 15ce3d2700424f0fbb280d602ccebcf6 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described " -"previously in [Additional Arguments and Parameters](additional-arguments-" -"and-parameters.md)). The output of this step `classfile` is connected to " -"the `outputs` section for the Workflow, described above." +"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " +"in [Additional Arguments and Parameters](additional-arguments-and-parameters." +"md)). The output of this step `classfile` is connected to the `outputs` " +"section for the Workflow, described above." msgstr "" #: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +#: af4268f19202436eb0a7e8c6bed5e386 msgid "Nested Workflows" msgstr "" #: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +#: 94a4eadca6b949d79de2990a0150eee8 msgid "" -"Workflows are ways to combine multiple tools to perform a larger " -"operations. We can also think of a workflow as being a tool itself; a CWL" -" workflow can be used as a step in another CWL workflow, if the workflow " -"engine supports the `SubworkflowFeatureRequirement`:" +"Workflows are ways to combine multiple tools to perform a larger operations. " +"We can also think of a workflow as being a tool itself; a CWL workflow can " +"be used as a step in another CWL workflow, if the workflow engine supports " +"the `SubworkflowFeatureRequirement`:" msgstr "" #: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +#: 09c1619e8cbd4febbb637f7e99ad5890 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" #: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +#: 677ea7a27eb64568ab3689142d6efe70 msgid "`nestedworkflows.cwl`" msgstr "" #: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +#: 097e6d47f9394e62b80110700492783a msgid "" -"This two-step workflow starts with the `create-tar` step which is " -"connected to the `compile` step in orange; `compile` is another workflow," -" diagrammed on the right. In purple we see the fixed string " -"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +"This two-step workflow starts with the `create-tar` step which is connected " +"to the `compile` step in orange; `compile` is another workflow, diagrammed " +"on the right. In purple we see the fixed string `\"Hello.java\"` being " +"supplied as the `name_of_file_to_extract`." msgstr "" #: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +#: e93affce8c104bf6977182047c1f1077 msgid "" " \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/nestedworkflows.cwl" +"\"> \"Visualization" msgstr "" #: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +#: 06c9e04ba890473b851240a0fa9c3b12 msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " -"its CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " -"mapped to become the step's input/outputs." +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " +"CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " +"to become the step's input/outputs." msgstr "" #: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +#: 0380dc1fe3aa48e4b62283b7b2a611d8 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and " -"`*.java` filename. This is generally best-practice, as it means it can be" -" reused in multiple parent workflows, or even in multiple steps within " -"the same workflow." +"running it we had to provide a job file to denote the tar file and `*.java` " +"filename. This is generally best-practice, as it means it can be reused in " +"multiple parent workflows, or even in multiple steps within the same " +"workflow." msgstr "" #: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +#: 49b251f7a313492ea60504b00109e526 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar" -" file at `tarball`, which we will prepare in the `create-tar` step. At " -"this point it is probably a good idea to refactor `1st-workflow.cwl` to " -"have more specific input/output names, as those also appear in its usage " -"as a tool." +"`name_of_file_to_extract` input, however our workflow also requires a tar " +"file at `tarball`, which we will prepare in the `create-tar` step. At this " +"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " +"specific input/output names, as those also appear in its usage as a tool." msgstr "" #: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +#: 7ee55702d7dd4679a24ff052f6f0cbeb msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3382,186 +3810,212 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +#: 85d7e2e270874aa6b9f477cec0f48154 msgid "" -"In this case our step can assume `Hello.java` rather than be " -"parameterized, so we can use hardcoded values `hello.tar` and " -"`Hello.java` in a `baseCommand` and the resulting `outputs`:" +"In this case our step can assume `Hello.java` rather than be parameterized, " +"so we can use hardcoded values `hello.tar` and `Hello.java` in a " +"`baseCommand` and the resulting `outputs`:" msgstr "" #: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +#: 570e94513c984c09ad6aa255f534216d msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This " -"is generally not best practice, as the tool then can't be reused. The " -"reason for doing it in this case is because the command line is hard-" -"coded with filenames that only make sense within this workflow." +"separate file, but rather embedded it within the CWL Workflow file? This is " +"generally not best practice, as the tool then can't be reused. The reason " +"for doing it in this case is because the command line is hard-coded with " +"filenames that only make sense within this workflow." msgstr "" #: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +#: a107258662fb4bd4a9a3d8754e34d1e9 msgid "" -"In this example we had to prepare a tar file outside, but only because " -"our inner workflow was designed to take that as an input. A better " -"refactoring of the inner workflow would be to take a list of Java files " -"to compile, which would simplify its usage as a tool step in other " -"workflows." +"In this example we had to prepare a tar file outside, but only because our " +"inner workflow was designed to take that as an input. A better refactoring " +"of the inner workflow would be to take a list of Java files to compile, " +"which would simplify its usage as a tool step in other workflows." msgstr "" #: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +#: fc1a6502d831458ab8371a575cea47e2 msgid "" "Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL" -" Tool description, care must be taken to improve its usability in " -"multiple workflows." +"functional and reusable workflow units - but just like for creating a CWL " +"Tool description, care must be taken to improve its usability in multiple " +"workflows." msgstr "" #: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +#: 2d10806bf1ce4e26b92adda61efc0862 msgid "Scattering Steps" msgstr "" #: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +#: 046c5e134de94b629cc22d416f3c9182 msgid "" "Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish " -"to run a tool or workflow multiple times over a list of inputs. The " -"workflow then takes the input(s) as an array and will run the specified " -"step(s) on each element of the array as if it were a single input. This " -"allows you to run the same workflow on multiple inputs without having to " -"generate many different commands or input yaml files." +"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " +"run a tool or workflow multiple times over a list of inputs. The workflow " +"then takes the input(s) as an array and will run the specified step(s) on " +"each element of the array as if it were a single input. This allows you to " +"run the same workflow on multiple inputs without having to generate many " +"different commands or input yaml files." msgstr "" #: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +#: 52fa22d3277940049fbb589a3ea73433 msgid "" -"The most common reason a new user might want to use scatter is to perform" -" the same analysis on different samples. Let's start with a simple " -"workflow that calls our first example (`hello_world.cwl`) and takes an " -"array of strings as input to the workflow:" +"The most common reason a new user might want to use scatter is to perform " +"the same analysis on different samples. Let's start with a simple workflow " +"that calls our first example (`hello_world.cwl`) and takes an array of " +"strings as input to the workflow:" msgstr "" #: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: 6043beb96c2c49648011ec556aa9e986 msgid "`scatter-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +#: 5ac4310515124e2986724425bed5651f msgid "" -"Aside from the `requirements` section including " -"`ScatterFeatureRequirement`, what is going on here?" +"Aside from the `requirements` section including `ScatterFeatureRequirement`, " +"what is going on here?" msgstr "" #: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +#: 7958e91d5c2f4046aa9d2070a900f9ae msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" #: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +#: 2db234d776fe4fd38bab07245dcb783a msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This " -"field tells the runner that we'd like to scatter over this input for this" -" particular step. Note that the input name listed after scatter is the " -"one of the step's input, not a workflow level input." +"Here we've added a new field to the step `echo` called `scatter`. This field " +"tells the runner that we'd like to scatter over this input for this " +"particular step. Note that the input name listed after scatter is the one of " +"the step's input, not a workflow level input." msgstr "" #: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +#: 7cfb17230e284ee7b6e2a00efe8eeb74 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if " -"you expect that the final output of your workflow will now have multiple " -"outputs to collect, be sure to update that to an array type as well!" +"collect any outputs, we still use `outputs: []` in our workflow, but if you " +"expect that the final output of your workflow will now have multiple outputs " +"to collect, be sure to update that to an array type as well!" msgstr "" #: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: 4311ac98544e4fb0b2f4b24985710a01 msgid "Using the following input file:" msgstr "" #: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +#: 780f9c72e6c34c39918642c7e2477355 msgid "`scatter-job.yml`" msgstr "" #: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +#: cc4a7316db644b438cbaa181ad9ef2d3 msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" -" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " +"calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" #: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +#: dfc461a03fe8487794837904febb8b63 msgid "" -"You can see that the workflow calls echo multiple times on each element " -"of our `message_array`. Ok, so how about if we want to scatter over two " -"steps in a workflow?" +"You can see that the workflow calls echo multiple times on each element of " +"our `message_array`. Ok, so how about if we want to scatter over two steps " +"in a workflow?" msgstr "" #: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +#: 1e83485b00b64dfaba897bd8d772e0f0 msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding " -"the following lines instead of `outputs: []`" +"Let's perform a simple echo like above, but capturing `stdout` by adding the " +"following lines instead of `outputs: []`" msgstr "" #: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +#: d0321d6805ec4d3abf3877d02a0a417f msgid "`hello_world_to_stdout.cwl`" msgstr "" #: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +#: d7d77e807b3048c7bdf89558f76804cb msgid "" -"And add a second step that uses `wc` to count the characters in each " -"file. See the tool below:" +"And add a second step that uses `wc` to count the characters in each file. " +"See the tool below:" msgstr "" #: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +#: 8d9b8be147fc4a71922dde858842e543 msgid "`wc-tool.cwl`" msgstr "" #: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +#: 34b7705416a745a6a42e6d402c0757ed msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under " -"each step:" +"Now, how do we incorporate scatter? Remember the scatter field is under each " +"step:" msgstr "" #: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +#: 257adcee9da64d5c987f3b64efd20ab0 msgid "`scatter-two-steps.cwl`" msgstr "" #: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 -msgid "" -"Here we have placed the scatter field under each step. This is fine for " -"this example since it runs quickly, but if you're running many samples " -"for a more complex workflow, you may wish to consider an alternative. " -"Here we are running scatter on each step independently, but since the " -"second step is not dependent on the first step completing all languages, " -"we aren't using the scatter functionality efficiently. The second step " -"expects an array as input from the first step, so it will wait until " -"everything in step one is finished before doing anything. Pretend that " -"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " -"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " -"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " -"could finish in 4 minutes, it will actually finish in 8 minutes because " -"the first step must wait on `echo Hallo welt!`. You can see how this " -"might not scale well." +#: fa6ed5d0c14f42f4aa3c5144648db22c +msgid "" +"Here we have placed the scatter field under each step. This is fine for this " +"example since it runs quickly, but if you're running many samples for a more " +"complex workflow, you may wish to consider an alternative. Here we are " +"running scatter on each step independently, but since the second step is not " +"dependent on the first step completing all languages, we aren't using the " +"scatter functionality efficiently. The second step expects an array as input " +"from the first step, so it will wait until everything in step one is " +"finished before doing anything. Pretend that `echo Hello World!` takes 1 " +"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " +"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " +"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " +"actually finish in 8 minutes because the first step must wait on `echo Hallo " +"welt!`. You can see how this might not scale well." msgstr "" #: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +#: 333e8ce458d54de394526769f96d12d2 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can" -" make an entire workflow a single step in another workflow! Convert our " -"two-step workflow to a single step subworkflow:" +"samples? Remember from [Nested Workflows](#nested-workflows), that we can " +"make an entire workflow a single step in another workflow! Convert our two-" +"step workflow to a single step subworkflow:" msgstr "" #: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +#: b819e8a5df6e4fa495924095709669ef msgid "`scatter-nested-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +#: f1955468a1364d44a930db77c9c4b495 msgid "" -"Now the scatter acts on a single step, but that step consists of two " -"steps so each step is performed in parallel." +"Now the scatter acts on a single step, but that step consists of two steps " +"so each step is performed in parallel." msgstr "" #: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +#: 8c3b9b645a204d02b2c73a205e8ec296 msgid "Conditional Workflows" msgstr "" #: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +#: 4d88b9c186cd4502adbf752e8a70b6ce msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " @@ -3569,252 +4023,357 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +#: 9927673564024ba5833b5ac271737857 msgid "`conditional-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +#: 84f4ed7ce2004742b8db9087104a469a msgid "" -"The first thing you'll notice is that this workflow is only compatible " -"for version 1.2 or greater of the CWL standards." +"The first thing you'll notice is that this workflow is only compatible for " +"version 1.2 or greater of the CWL standards." msgstr "" #: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +#: 2b5f9757adca4490a149c7f45e14fcb5 msgid "" "The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when`" -" is where the condition validation takes place. In this case only when " -"`in1` from the workflow contains a value `< 1` this step will be " -"executed." +"will execute foo.cwl when the conditions are met. The new property `when` is " +"where the condition validation takes place. In this case only when `in1` " +"from the workflow contains a value `< 1` this step will be executed." msgstr "" #: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +#: 0418de720813442f81ecff293c9448b5 msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" -" will pass the first conditional step and will therefore be executed and " -"is shown in the log by `INFO [step step1] start` whereas the second step " -"is skipped as indicated by `INFO [step step2] will be skipped`." +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " +"will pass the first conditional step and will therefore be executed and is " +"shown in the log by `INFO [step step1] start` whereas the second step is " +"skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" #: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +#: 524eec63be8248ae982939c975ef50a2 msgid "" -"When a value of 3 is given the first conditional step will not be " -"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +"When a value of 3 is given the first conditional step will not be executed " +"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" #: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +#: 5e99f9912cc549a7890e2934425eb943 msgid "" -"If no conditions are met for example when using `--val 2` the workflow " -"will raise a permanentFail." +"If no conditions are met for example when using `--val 2` the workflow will " +"raise a permanentFail." msgstr "" #: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +#: b0121ee087d6424fbb0ea5957a7b0b8c msgid "YAML Guide" msgstr "" #: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +#: 49e9f6b3a06840289decf3f557860f87 msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers " -"and humans. This guide introduces the features of YAML that are relevant " -"when writing CWL descriptions and input parameter files." +"[YAML][yaml] is a file format designed to be readable by both computers and " +"humans. This guide introduces the features of YAML that are relevant when " +"writing CWL descriptions and input parameter files." msgstr "" #: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +#: ed9eebec0b3d4b72ba65507d37757a37 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" #: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +#: bf9b255a24a84f3ba989a223492b8f41 msgid "Contents" msgstr "" #: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +#: e79fa0b7f8b14810a3a20908ef92bc55 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" #: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +#: 290e2035f903417cbecb5dc5f09d6ebe msgid "[Comments](#comments)" msgstr "" #: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +#: d420730151534f1a89076588a3358f09 msgid "[Maps](#maps)" msgstr "" #: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: a6b5378bbe1e4bee9e37a765bddf75f7 msgid "[Arrays](#arrays)" msgstr "" #: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: 6e4d9465dc2b454d96b02d7ad1817795 msgid "[JSON Style](#json-style)" msgstr "" #: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +#: a649d4af5f434dac9395e013ec4836bb msgid "Key-Value Pairs" msgstr "" #: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +#: 446190a298834b73bda068286e8490cf msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the " -"`:` is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have " -"special meaning in the CWL specification and underscored key names " -"otherwise. For example:" +"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " +"is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have special " +"meaning in the CWL specification and underscored key names otherwise. For " +"example:" msgstr "" #: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +#: 2f35c012ff174721bffe66a3f58a804f msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, " -"`age_years`, and `home` - with their four respective values. Values can " -"be character strings, numeric (integer, floating point, or scientific " -"representation), Boolean (`true` or `false`), or more complex nested " -"types (see below)." +"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " +"and `home` - with their four respective values. Values can be character " +"strings, numeric (integer, floating point, or scientific representation), " +"Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" #: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +#: 43127c98c9d94aedac61cee67929c1a6 msgid "" -"Values may be wrapped in quotation marks, but be aware that this may " -"change the way that they are interpreted i.e. `\"1234\"` will be treated " -"as a character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a" -" command: in CWL all parts of `baseCommand` must be strings so, if you " -"want to specify a fixed numeric value to a command, make sure that you " -"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +"Values may be wrapped in quotation marks, but be aware that this may change " +"the way that they are interpreted i.e. `\"1234\"` will be treated as a " +"character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a " +"command: in CWL all parts of `baseCommand` must be strings so, if you want " +"to specify a fixed numeric value to a command, make sure that you wrap that " +"numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" #: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: dc4fe561203c4c38a9caea5bd6eff2cd msgid "Comments" msgstr "" #: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +#: f924e4896db2424d99ce8c9da14c599a msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program " -"interpreting the YAML. For example:" +"characters to the right of ` #` will be ignored by the program interpreting " +"the YAML. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +#: bf7646f5f925485c842a6d34140e40b8 msgid "" -"If there is anything on the line before the comment, be sure to add at " -"least one space before the `#`!" +"If there is anything on the line before the comment, be sure to add at least " +"one space before the `#`!" msgstr "" #: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +#: c483e61dec8949fa96bb893d422888a0 msgid "Maps" msgstr "" #: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +#: 85fcb523d0e34a499eae04d304887f7b msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, " -"these hierarchical structures are described in YAML by providing " -"additional key-value pairs as the value of any key. These pairs " -"(sometimes referred to as \"children\") are written on new lines under " -"the key to which they belong (the \"parent\"), and should be indented " -"with two spaces (⇥tab characters are not allowed). For example:" +"construct more complex, nested representations. Referred to as _maps_, these " +"hierarchical structures are described in YAML by providing additional key-" +"value pairs as the value of any key. These pairs (sometimes referred to as " +"\"children\") are written on new lines under the key to which they belong " +"(the \"parent\"), and should be indented with two spaces (⇥tab characters " +"are not allowed). For example:" msgstr "" #: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +#: 83d47c8736a34f3cbf09e3997845e4f4 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and " -"`inputBinding`, while one of these children, `inputBinding`, contains a " -"further two key-value pairs (`position` and `prefix`). See the " -"[Arrays](#arrays) section below for more information about providing " -"multiple values/key-value pairs for a single key. For comparison with the" -" example YAML above, here is a graphical representation of the `inputs` " -"object it describes." +"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " +"while one of these children, `inputBinding`, contains a further two key-" +"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " +"below for more information about providing multiple values/key-value pairs " +"for a single key. For comparison with the example YAML above, here is a " +"graphical representation of the `inputs` object it describes." msgstr "" #: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +#: c698fb3d37bc403e9aeb679b8fc0e15e msgid "Arrays" msgstr "" #: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +#: ae8af2f0eeda4aec97201211dfa965c7 msgid "" "In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) " -"section above, more than one key-value pair can be mapped to a single " -"key. However, it is also possible to define multiple values for a key " -"without having to provide a unique key for each value. We can achieve " -"this with an _array_, where each value is defined on its own line and " -"preceded by `-`. For example:" +"objects for a single key. As we've already seen in the [Maps](#maps) section " +"above, more than one key-value pair can be mapped to a single key. However, " +"it is also possible to define multiple values for a key without having to " +"provide a unique key for each value. We can achieve this with an _array_, " +"where each value is defined on its own line and preceded by `-`. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +#: 2ee87aa465cd41fda16a61e242f8c9d0 msgid "and a more complex example combining maps and arrays:" msgstr "" #: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +#: 0a6fd4469ff24b61b3ad001b09eead18 msgid "JSON Style" msgstr "" #: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +#: b96ba19bce9341d39c46054e1f10fe8f msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " -"arrays can also be defined in YAML using the native JSON syntax. For " -"example:" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " +"can also be defined in YAML using the native JSON syntax. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +#: 903f30af3d0c45cfb61063936a8097a7 msgid "and:" msgstr "" #: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +#: ede8db7c0a58432e8a1c416e937a06d2 msgid "" -"Native JSON can be useful in indicating where a field is intentionally " -"left empty (such as `[]` for an empty array), as well as where it makes " -"more sense for the values to be located on the same line (For example, " -"when providing option flags and their values in a shell command). " -"However, as the second example above shows, it can severely affect the " -"readability of a YAML file, and should be used sparingly." +"Native JSON can be useful in indicating where a field is intentionally left " +"empty (such as `[]` for an empty array), as well as where it makes more " +"sense for the values to be located on the same line (For example, when " +"providing option flags and their values in a shell command). However, as the " +"second example above shows, it can severely affect the readability of a YAML " +"file, and should be used sparingly." msgstr "" #: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +#: c8b53615476a4a1fbef2420d93bac94e msgid "Reference" msgstr "" #: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +#: ea03cb5525cc491f9feb5c4780b38fee msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" -" us while we wrote this guide, though it also covers features that are " -"not valid in CWL." +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " +"while we wrote this guide, though it also covers features that are not valid " +"in CWL." msgstr "" #: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +#: 92fd3a5e31714eab859dd630af2e78cf msgid "Tutorials" msgstr "" #: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +#: de660ecdb5b44c97a0e519d00b232497 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to " -"the list." +"this page` link in the menu if you would like to add another tutorial to the " +"list." msgstr "" #: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +#: 5afc1e1288e74ed0985e61e5164479c7 msgid "Beginner Tutorials" msgstr "" #: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +#: 862dc7ac81e54b1fb3d4c2f961b8810e msgid "" -"[Introduction to Workflows with Common Workflow Language: For " -"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" -"tutorial/)" +"[Introduction to Workflows with Common Workflow Language: For Contributors.]" +"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" #: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +#: e2c94c0e1c7048d38cd7aa2c465a859d msgid "Advanced Tutorials" msgstr "" #: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +#: b63253780f51467a95207d820d13ac39 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" #: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +#: 6d06ca7ed5df4560aaed286f4fe33928 msgid "Bioinformatics Tutorials" msgstr "" #: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +#: 5448df4a6a8f431d80e269bcd480e19e msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" +#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee +msgid "" +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the `Creative Commons " +"Attribution license `_. The following is a human-readable " +"summary of (and not a substitute for) the `full legal text of the CC BY 4.0 " +"license `_." +msgstr "" +"Todo o material instrucional do projeto Common Workflow Language e " +"alterações na estrutura também são disponibilizados sob a `licença Creative " +"Commons Attribution `_. O seguinte é um resumo legível por " +"humanos de (e não um substituto para) o `texto legal completo da licença CC " +"BY 4.0 `_." + +#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 +msgid "to **Share**—copy and redistribute the material in any medium or format" +msgstr "" +"**Compartilhar**—copiar e redistribuir o material em qualquer suporte ou " +"formato" + +#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 +msgid "to **Adapt**—remix, transform, and build upon the material" +msgstr "**Adaptar**—remixar, transformar, e criar a partir do material" + +#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 +msgid "" +"**Attribution**—You must give appropriate credit (mentioning that your work " +"is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a `link to the license `_, and indicate if changes " +"were made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." +msgstr "" +"Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " +"trabalho deriva de um trabalho que é «Copyright © The Common Workflow " +"Language project», e, quando prático, criar uma ligação para https://www." +"commonwl.org/ ), fornecer um `link para a licença `_, e " +"indicar se foram feitas alterações. Você pode fazê-lo de qualquer forma " +"razoável, mas não de uma forma que sugira que o licenciante o apoia ou " +"aprova o seu uso." + +#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 +msgid "" +"**No additional restrictions**—You may not apply legal terms or " +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" +msgstr "" +"**Sem restrições adicionais**—Você não pode aplicar termos jurídicos ou " +"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " +"algo que a licença permita. Com o entendimento de que:" + +#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the " +"`OSI`_-approved `Apache 2.0 license `_." +msgstr "" +"Salvo indicação em contrário, os programas de exemplo e outro software " +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a " +"`licença Apache 2.0 `_ aprovada pela `OSI`_." + +#: ../../LICENSE.rst:50 9c4d58a1129a4d4eb4db1bfabbeddb6e +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." +msgstr "" From 761ad42bf4a9d7747a9170a77e764711bd1f1494 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 27 Jan 2023 16:14:13 +0100 Subject: [PATCH 048/179] remove obsolete .rst translations --- Makefile | 2 +- locales/es/LC_MESSAGES/user_guide.po | 1935 +++++++++----------------- locales/pt/LC_MESSAGES/user_guide.po | 1930 +++++++++---------------- 3 files changed, 1323 insertions(+), 2544 deletions(-) diff --git a/Makefile b/Makefile index 83ba9e13..c549b172 100644 --- a/Makefile +++ b/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line, and also # from the environment for the first two. -SPHINXOPTS = "" # was "-W" (turn warnings into errors) +#SPHINXOPTS = # was "-W" (turn warnings into errors) SPHINXBUILD = sphinx-build SOURCEDIR = src BUILDDIR = _build diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index b1952aae..ca09ccab 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -8,30 +8,27 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 19:53+0100\n" +"POT-Creation-Date: 2023-01-27 16:02+0100\n" "PO-Revision-Date: 2023-01-27 14:27+0000\n" "Last-Translator: Michael Crusoe \n" -"Language-Team: Spanish \n" "Language: es\n" +"Language-Team: Spanish \n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=2; plural=n != 1;\n" -"X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 ../../LICENSE.rst:2 -#: dcdc2e8da0ec4d9e9453601fdd83bac5 +#: ../../LICENSE.md:2 3eb955b4f3dd4c3188924b97ea6ab592 msgid "Licenses" msgstr "Licencias" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 ../../LICENSE.rst:5 -#: 3e165520ca56481b8f8d494a8d471de3 +#: ../../LICENSE.md:4 bf4480e7fff4460a87e8f43c11599f07 msgid "Instructional Material" msgstr "Material didáctico" -#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +#: ../../LICENSE.md:6 9e9eab12205d4e82b4fedca520370f4c msgid "" "All Common Workflow Language project instructional material and changes to " "the structure are also made available under the [Creative Commons " @@ -45,29 +42,26 @@ msgstr "" "legible por humanos (y no un sustituto) del [texto legal completo de la " "licencia CC BY 4.0][cc-by-legal]." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 ../../LICENSE.rst:12 -#: b7a7a0fb40344fe087c1cc3ec19308aa +#: ../../LICENSE.md:12 a8e98ad541c642e58e201afa625ec791 msgid "You are free:" msgstr "Usted es libre de:" -#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +#: ../../LICENSE.md:14 b4cb4bc4261347fcb0d2c8a93995ab76 msgid "" "to **Share**---copy and redistribute the material in any medium or format" msgstr "" "**Compartir**---copiar y redistribuir el material en cualquier medio o " "formato" -#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +#: ../../LICENSE.md:15 d66dcbf95ccc41aaa53be523487ec913 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 ../../LICENSE.rst:18 -#: 430ff4de74924bc3a3b2c7e809ea4456 +#: ../../LICENSE.md:17 ca1c299a1b834b868bcdd4ca9f244696 msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e ../../LICENSE.rst:20 -#: 8bc6672f4a33428296226112a1be6fbe +#: ../../LICENSE.md:19 6133f79f93be4991a6f5290f72d1a63d msgid "" "The licensor cannot revoke these freedoms as long as you follow the license " "terms:" @@ -75,7 +69,7 @@ msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " "términos de la licencia:" -#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +#: ../../LICENSE.md:24 2d6ce81add1043629b676187f890288c msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " "work is derived from work that is Copyright © the Common Workflow Language " @@ -86,13 +80,13 @@ msgid "" msgstr "" "**Atribución**---Usted debe dar crédito de manera adecuada(mencionando que " "su trabajo se deriva de un trabajo que tiene «Copyright © The Common " -"Workflow Language Project» y, cuando sea práctico, con un enlace a " -"https://www.commonwl.org/%20),%20brindar%20un%20[enlace%20a%20la%20licencia][cc-by-human]," -"e indicar si se han realizado cambios. Puede hacerlo en cualquier forma " +"Workflow Language Project» y, cuando sea práctico, con un enlace a https://" +"www.commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e " +"indicar si se han realizado cambios. Puede hacerlo en cualquier forma " "razonable, pero no de forma tal que sugiera que usted o su uso tienen el " "apoyo de la licenciante." -#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +#: ../../LICENSE.md:32 f3f22597b6f845208a0cce3b3b2c8f5d msgid "" "**No additional restrictions**---You may not apply legal terms or " "technological measures that legally restrict others from doing anything the " @@ -102,8 +96,7 @@ msgstr "" "medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " "permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 ../../LICENSE.rst:35 -#: 1798d65c10104040923c2fea2199bab2 +#: ../../LICENSE.md:36 3cfedee64d4e46098a159cb2acdba4ef msgid "" "You do not have to comply with the license for elements of the material in " "the public domain or where your use is permitted by an applicable exception " @@ -113,8 +106,7 @@ msgstr "" "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 ../../LICENSE.rst:38 -#: c65198b804f8436ba783643d51bc72d9 +#: ../../LICENSE.md:39 c836a570faaf449d9716da5f75556627 msgid "" "No warranties are given. The license may not give you all of the permissions " "necessary for your intended use. For example, other rights such as " @@ -125,12 +117,11 @@ msgstr "" "publicidad, privacidad, o derechos morales pueden limitar la forma en que " "utilice el material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea ../../LICENSE.rst:44 -#: 3d7ca3f2cede4d5f998bf014bd970748 +#: ../../LICENSE.md:44 896f9966e5014e8a88b060be3063fe09 msgid "Software" msgstr "Software" -#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +#: ../../LICENSE.md:46 007f8613dc234c3fa8d5d92b18af0eb1 msgid "" "Except where otherwise noted, the example programs and other software " "provided by Common Workflow Language project are made available under the " @@ -141,7 +132,7 @@ msgstr "" "disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " "la [OSI][osi]." -#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +#: ../../LICENSE.md:51 227bc635a06f49dbb771fd9b62157d00 msgid "" "Unless required by applicable law or agreed to in writing, software " "distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " @@ -156,9 +147,8 @@ msgstr "" "under the License." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 -#: eab02dc13915490bb3c9ba744d78b6a7 271049c39d294b11b9bd94cb6be2857f -#: 61af90891e2d4542b5f45fb3ec6480af bf309fa01bed4355bf052ae4afbf9a67 +#: 1861131d3df648ae9e74ce1c87f0be7b a2ffa927deb2451d95ec63528e8078dd +#: d6055d3f15604ce6940770c7b561d4c5 msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece of " @@ -167,36 +157,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f -#: 055f0e960450410585b59760ef3ad284 6294af2e32e04207a87399c7f0780011 +#: 38b062f219b34e08a46bd8f6525353ec 89e7e1dd05474344a1d929cb492e9caf msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 -#: 6428125fc43c43bba8518ece2f5d150f +#: ../../src/episodes.md:9 d3357ff3c8874e368aea0d6062ef6190 msgid "" "This page is out-of-date and was kept here to preserve the links of the old " "User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 -#: ce8fade1e88e4b03ac0d3fc71d16f844 +#: ../../src/faq.md:1 f2c4882e0e164c2b869e3eb969241061 msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 -#: 9e7483b53a984b689964c69afcaa7123 +#: ../../src/faq.md:11 41099ab64e0544d894bd9e3af2718bda msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 -#: 8c5a89257ef248cd99cba303713e5082 +#: ../../src/faq.md:41 bb6aff70534148fa8a4b01140f7be150 msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 -#: 9e80d8eeefcf4a9d95fd5fe9d9fa124a +#: ../../src/faq.md:43 70ebc653b0d54d60a866edc0dbf56b57 msgid "" "This example demonstrates how to change the name of an input file as part of " "a tool description. This could be useful when you are taking files produced " @@ -204,139 +188,117 @@ msgid "" "names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f -#: c2e5f62490f940aab19166403a840597 +#: ../../src/faq.md:59 38b687f707d2438b85df08a445ab816f msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 -#: ffcffabdf25a4c398e8e53bc817ea769 +#: ../../src/faq.md:61 d48422c020004ef084ca11e6229b5450 msgid "" "This example demonstrates how to change the name of an output file from the " "default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 -#: c8a6b85cfca542ccb042a0269294e5e3 +#: ../../src/faq.md:82 48765409ab9d48ccbcecceb46ddf2e91 msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 -#: 98f583e5e36941c1856d719a16e58e4a +#: ../../src/faq.md:84 a59b8acd72124e2c95d1905ae494d928 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb -#: fb9cac0954474b5284793330b7424949 +#: ../../src/faq.md:86 f36088ba90d24f9f9c7c1bd59deb6f49 msgid "" "The first method involves adding the folder containing your scripts to the " "`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 -#: cc45d609de1f423db86d58eea933e132 +#: ../../src/faq.md:89 45ee965ee4a7494a8354b82208e2ab45 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 -#: 27ee63895cb14321a1814f4372d3180f +#: ../../src/faq.md:95 734cc1abe1c841ffac8d0895463d91fc msgid "" "After that, make the script executable with the command `chmod +x scriptname." "sh`" msgstr "" -#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 -#: f1c841980f3d4364a2158a4eb2f0d257 +#: ../../src/faq.md:97 f01bc8c4d6134f0ea27dc7f5b39def24 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be -#: 6d53d38ddcf244fb997db37eae7fcf90 +#: ../../src/faq.md:104 dd6fc2a04e3b476892f05bc5b746d0fa msgid "" "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 -#: b6d60d66f3744ab3aea1b175ecb23d4a +#: ../../src/faq.md:113 e309eaad55144052866ce131eb80fd14 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 -#: cf4fa3ae602841d393b4143e9f6f5e82 +#: ../../src/faq.md:115 f0d649a60a13404ebecd540789202b87 msgid "" "The second method involves including an input of `type: File` in the script " "itself:" msgstr "" -#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 -#: 41a3c9aa55c5406f9b52af2243c79ccc +#: ../../src/faq.md:135 e2b782f88d494de398af0c9002a3ccdc msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 -#: 3b8eb247425a4a708f51c08cf258e30a +#: ../../src/faq.md:138 b4a033731fcd4322bd2bb71c609a4cb7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c -#: 388a6e091a054dc48afc928f46dac7b7 +#: ../../src/faq.md:140 43a64810b12b4c7d82a5803c3b910fe5 msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their input " "binding makes use of `self`. Below is an example workaround for this, " "pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 -#: 28c59d12156e44ea833822fd3ecaf824 +#: ../../src/faq.md:165 60f009e3714c405695da069204b196ea msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 -#: 8267843ff5c940c590b10047455f2102 +#: ../../src/faq.md:167 98916ed9355842e49bef073430e10675 msgid "" "Below is an example showing how to specify different strings to be added to " "a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c -#: 6e6f55bc915e4cceb8e360544d6b4ae5 +#: ../../src/faq.md:188 9b8f2d0b33db4bbc82aaf5836b6f7ed8 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d -#: 1bc80953bd60405082a10a7798c1413d +#: ../../src/faq.md:190 a251693354d24bf0bda4938c8890090a msgid "" "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" "Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 -#: a6cd4bf4dc314e66a951f7f1227c7bb7 +#: ../../src/faq.md:194 f46740ac0acb473583facb9f7528d03c msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 -#: 7ab2440a92aa44b09e8a324cd67ca728 +#: ../../src/faq.md:196 7de1f9e3175b4c2ab156192f28fd3535 msgid "" "The input must be an array consisting of exactly one entry for each input " "link. If \"merge_nested\" is specified with a single link, the value from " "the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 -#: 152a529dfa2c42c1b6f0083589fa5aeb +#: ../../src/faq.md:199 225c6f08068e41f58eb62f99dc06210f msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 -#: b278c137167d4b958c099c0509edb79c +#: ../../src/faq.md:201 4e741f4e3bc74e10bd9568826e81c478 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -345,61 +307,51 @@ msgid "" "destination step." msgstr "" -#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd -#: f0b38723838f479d9db8eb5142d28a1e +#: ../../src/faq.md:229 bfdb011cb81c4ef9b9e56b24f1e9ccd5 msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 -#: fc1e4a808e85422cbb4d128c5a1f4d0c +#: ../../src/faq.md:231 09f385e325f942afaa3dd195c16a18d2 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 -#: d74964c9d19241848f4dd92a201e201f +#: ../../src/faq.md:247 c5d087082bb2468483e7ccda3ca45a07 msgid "" msgstr "" -#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c -#: 859b8e18e05a4c3285fb20bbb44c1ed4 +#: ../../src/faq.md:248 41e30b0224a0492f9047b4f320f39a23 msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 -#: eb6e932924a54afd9114c629b2d0e93b +#: ../../src/faq.md:250 f06d073014a44f33a60d947a8c5b0e59 msgid "" "For command line flags that require a specific input as the argument an enum " "type can be declared in CWL. **Specifying null here is known as long form " "style. It does the same thing as the question mark on the other inputs.**" msgstr "" -#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd -#: 31d70b41ddf042f6aa530b7bd6daae73 +#: ../../src/faq.md:267 2fb74cd1b41e4fdb81a8f9b3b6c84373 msgid "" msgstr "" -#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 -#: 9aa3ff8c957b42c8a30f37167a8177fd +#: ../../src/faq.md:268 09e19f34d0fd4e388d4939cbc2be3436 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c -#: 777ac7f6bde2470b981efc91feb01c81 +#: ../../src/faq.md:270 1ecae448dfcf45a4ae0dd39bd011e449 msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 -#: 8647071efc0548a1807c03fe8a4ee54c +#: ../../src/faq.md:322 6df3d4e918cc4bccb823859ce07b197a msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 -#: 4404233183124085990c44793a6b25f6 +#: ../../src/faq.md:324 086db1a093e64caa88d958150accc19c msgid "" "To properly set fields in a record input type, you need to pass a dictionary " "to the input to properly set the parameters. This is done by using inline " @@ -408,93 +360,76 @@ msgid "" "be used as the value." msgstr "" -#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 -#: c5eecacfa07f47649f07ef9d888f4c5e +#: ../../src/faq.md:342 da77c818d8694ab99fb2eccf73083047 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 -#: 1efef04061fd48f1ab39a99508b5bc0b +#: ../../src/faq.md:344 254259509ed6462d8ebc296b5f811f44 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 -#: 57e8ace8e8d64e7a90510e1ccea69612 +#: ../../src/faq.md:349 f7a44f76579d4709a61d2d61bc352b76 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 -#: 138606e8d7be40bb960f278977f9107f +#: ../../src/faq.md:351 d67278e99c684f488f1e3418e1c8c207 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c -#: d0f668dc78464469a9f2bfc61a90aa76 +#: ../../src/faq.md:359 f5e35ee06cd24edf831589ebaa6193d2 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 -#: f2a49a7663e1456cac6b2eac0c46c662 +#: ../../src/faq.md:361 2ffb67e547c446499625a8db9a102da6 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a -#: eefe4adebdba4063af0cac3ab5d46442 +#: ../../src/faq.md:363 ee653ff9fefe4771b35e2e76199b536a msgid "" "For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" -#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde -#: 526f2816123a43ecbcf09c46904b4b5f +#: ../../src/faq.md:371 02b1eb159e934fd692929f7c30319ddd msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 -#: 0ecf267c5f4d4557ad0d7ddef2f4b5e6 +#: ../../src/faq.md:373 857024702f624885be706c405b7a088e msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 -#: 935a253376854d12928f00c2870ed4c0 +#: ../../src/faq.md:375 d664e30899bd463bb48d38adec318dd4 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 -#: bc6c0bf679ae48e7822add7ab2cda220 +#: ../../src/faq.md:384 9f3957bbe205454e8bffc4b5caac5970 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 -#: a63643806a2a4eee8ebd3502fd6ce2b5 +#: ../../src/faq.md:396 6ec3bbc6a1ca4e23b47f025f0732e609 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 -#: fc54964adcd648948d7baff02f47598e +#: ../../src/faq.md:410 3e727d79e65e4c6cb157550e80261c53 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 -#: aabc495306a149fdb15835ae1df93c42 +#: ../../src/faq.md:423 6e0705f4ab4b4e9093794cb4fccb6be9 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d -#: 2930faead8be45a6b9adbf51dcdfef6e +#: ../../src/faq.md:436 0047d039317349679fb6a66d18ec8487 msgid "" "If it is not possible to change the input identifier, then you can use an " "alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 -#: f885e4716a8d4de0b25d2d3356789672 +#: ../../src/faq.md:442 8c39608ad0494bee9a4a422cbeb34387 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e -#: 6487ff3c19c944eb8257b2cf60d0aac7 +#: ../../src/faq.md:445 7dac53bca8c14a3f9af75cb162cba4f9 msgid "" "The CWL standards are built around (optional) Docker format containers. The " "reference runner and several other CWL implementations support running those " @@ -502,13 +437,11 @@ msgid "" "Singularity format container is not part of the CWL standards." msgstr "" -#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 -#: 4cbacce539ce4f6cb5bb8ccf1574640c +#: ../../src/faq.md:450 ffcc38ff98324d71bfeb8d66d4901da7 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 -#: 27321576de714cd5b82c67f59b2e3e6f +#: ../../src/faq.md:452 0d7bf2cefe4a4e22b186bdf4d0ed793d msgid "" "You can use the --js-console option of cwltool, or " "you can try creating a JavaScript or TypeScript project for your code, and " @@ -519,26 +452,22 @@ msgid "" "dd>" msgstr "" -#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e -#: 6afded7ba21247099c9bfcedf40c9171 +#: ../../src/index.md:1 1506b4e7ee014a01bfdb067489501a9e msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab -#: 17c386e7cd25496784207140f9876b90 +#: ../../src/index.md:3 0ce058b5210d46a0b78eb78dbca07a9f msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 -#: 3bfd9bcf826a4400935dfad338612b12 +#: ../../src/index.md:7 3404c064950d453d8af446e8b6554cb6 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 -#: 4b38f1439da44ebb967b5b1e3df8f78a +#: ../../src/index.md:9 1e239cad669648e48694eaf91284766a msgid "" "If you find that something is missing from this guide, or if you would like " "to provide other feedback, file an Issue on the [project repository for this " @@ -546,13 +475,11 @@ msgid "" "clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" -#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f -#: a4a60a8d010448b0b8ad1e05cbc78f2b +#: ../../src/index.md:16 9dba2e06f1be4a50b1fabaaf216d02b4 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 -#: e23e00e89c81410ba8381fd81bc73b3c +#: ../../src/index.md:18 ba4074bbb69e4096a808001afaf2e0dc msgid "" "If you are a beginner user get started with the [Introduction](/introduction/" "index.md) section. For advanced users the subsections of the [Topics](/" @@ -560,8 +487,7 @@ msgid "" "CWL." msgstr "" -#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 -#: 7274d92e678a440eb0d3ae3109f4157a +#: ../../src/index.md:23 ad34a37bf4ec488bb825a34456f4fe8d msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -569,18 +495,15 @@ msgid "" "and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c -#: 6ad5f2d254a24ac1b3faf382d08b58aa +#: ../../src/index.md:28 2bd8eb5957ed40f4a72a6b7408044c78 msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 -#: 7208cbccb84d45d58c7d5becec74b7d3 +#: ../../src/introduction/basic-concepts.md:1 8bb0df5531474301a185f1ba375320df msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 -#: 8b9809abb49840b195a89943ba15f78a +#: ../../src/introduction/basic-concepts.md:3 653373e1f11e4f81ad561378854a71fc msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are expected " @@ -591,21 +514,18 @@ msgid "" "this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 -#: 9a934bf0848b438aaef7c4f00e0f2901 +#: ../../src/introduction/basic-concepts.md:10 7766227bf91b48b2b9752b625e5a9084 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf -#: 5a299600dc304fd886b7153de1a706f7 +#: ../../src/introduction/basic-concepts.md:21 032d414ac29740aa9041d89d0ebf70e6 msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered in " "this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 -#: 55f7696f07d64277ad1b39d283175b37 +#: ../../src/introduction/basic-concepts.md:25 74e92eb0a4e64098b5aaf08d043e0641 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -615,20 +535,17 @@ msgid "" "and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d -#: b854ca0af98347d2b66e74754eb92a50 +#: ../../src/introduction/basic-concepts.md:33 baa40b445f3c409b9a3e10a85fa38bfd msgid "" "The model used for the specification version is called Semantic Versioning. " "See the end of this section to [learn more](#learn-more) about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d -#: d9785269c51e4902bf3a70e917d33238 +#: ../../src/introduction/basic-concepts.md:37 648e94a9d368450dbdac706445254c9f msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 -#: b57a31b8d26545d1823fcd1fa2c83316 +#: ../../src/introduction/basic-concepts.md:39 e9ae15124dcd408395fc67e16b50696a msgid "" "An implementation of the CWL specification is any software written following " "what is defined in a version of the specification document. However, " @@ -636,26 +553,24 @@ msgid "" "implementations are licensed under both Open Source and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 -#: 4e264b1a40bd4935abb5bdeb75fa5c64 +#: ../../src/introduction/basic-concepts.md:44 b1c864d6775048cab01eb3de641f6475 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud " "and high performance computing environments where tasks are scheduled in " "parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf -#: 791b02bb1ee6459d8d8332fc2dee353c +#: ../../src/introduction/basic-concepts.md:51 a05d24121e534d65947eb26e4dada5b7 msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 17300bbe695044e7b8917d23bd0aa597 +#: ace0388fd04845e79d31ec99a48a8a3f msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 526614f195614818a614fc9a576e7cb5 +#: 70ecd37237e14ae19539f2bf692882ed msgid "" "A process is a computing unit that takes inputs and produces outputs. The " "behavior of a process can be affected by the inputs, requirements, and " @@ -664,39 +579,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f 7b47991653054f2d9f49a91720754abf +#: 38121b4b00324bebb6499184b3dcb5c1 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b aa8838c0ee0a4b4285cb1b5dc6eb5d31 +#: e0c278f52e824673ac708885d985b7d2 msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 457c73a37cb143d98005ebf6e67f5bf1 +#: 6b4d0f0651cc46f5abf195b281967913 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f c28057f3b7814f8395dbc3ad54d5f6f9 +#: 88bdc9e046e4487cb0eee3f1d4819e57 msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 83afed0785cd4b0bb86863c2841ce982 +#: 12eed3ef7d444585b150bbdab0665bc8 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a f332864bcc1e49d582a82f3d721ff3cf +#: dfc85226313d46f9868dc4de53546a69 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 3005c6d669de412ab7f8e30d00752a20 +#: f636b10c47734e589291de95443d8115 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be used " "to simplify workflows and command-line tools, moving common parts of a " @@ -705,7 +620,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef 2e4041cb402e4054a53ea5890b938ac1 +#: bb51025d04444dd5b16000d5d6a3f41a msgid "" "Operation is an abstract process that also takes inputs, produces outputs, " "and can be used in a workflow. But it is a special operation not so commonly " @@ -714,7 +629,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 972f9a1e64394a63be3258d3af0b1d79 +#: 93dbaa0aa2c6493ab22a937c6861fac4 msgid "" "The workflow is a process that contains steps. Steps can be other workflows " "(nested workflows), command-line tools, or expression tools. The inputs of a " @@ -723,7 +638,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 a572f0789084402fb2d216ac845bbfdb +#: fcde5ef65ebf45a3b4b67eec993a1729 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through *requirements*. " @@ -731,23 +646,23 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 c7c5c9a1e98e47c0a5a6dfa69e96f921 +#: c8ff34ff5d3b4a508e8c291196d08067 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 357d42768e794286bf5463ca5850a7ed +#: fe25f15fc11c49ab827b884d081c3df0 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 61966aab989744c1b9b93f7751f35ebc +#: 2b93b6219142431ca748a404a56ced5d msgid "" "`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee e14a2082d2c44f3690a07d3cee5b13d1 +#: 0094b13b26014ba3be61769b422802f5 msgid "" "Some CWL runners may provide requirements that are not in the specification. " "For example, GPU requirements are supported in `cwltool` through the " @@ -757,7 +672,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e c128a76992e04d20bcc3edae8b6c0bc0 +#: 576a0778d3dd44f68cb241346f441660 msgid "" "Hints are similar to requirements, but while requirements list features that " "are required, hints list optional features. Requirements are explained in " @@ -765,12 +680,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 42953a3d591c48c6b4e80e9ea4b97bb3 +#: 7d98949fe97744158fad81f41d780de9 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 e3762a763ba24571a9627efafe172441 +#: fc142b791aa1434aa75b0782248de988 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -783,7 +698,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a be8e01a012ed45d6b7e4e6aab1afcc32 +#: c3fc91ae3bae4e3db60e8271e95135a2 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\", " @@ -792,7 +707,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee cf31aca4294d486cb0e25c6436996d17 +#: 8f097ae5ff6a4be0b7428345362dc55e msgid "" "The benefit of explicitness and isolation are flexibility, portability, and " "scalability; tools and workflows described with CWL can transparently " @@ -801,77 +716,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 cc7adbdc66df4aeaad1429f7268c90c0 +#: 60c56fa6a67346d6966f0d841213e11b msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 -#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf -#: 71beb059c9e54a9ab5430f0dc44e07ea 84679c5b03a3469294de849d9abe0a82 -#: fd690fdd46344e0e8d9fc546f6d4013b +#: ../../src/introduction/quick-start.md:94 7377b155e8694798994bbc911a3f3152 +#: 7699685836064bd89db530a9c1918865 7d187a209ebd4e3ba6c6aeb05743041a msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de 89ddaddb64f64b0c86c7e89da0edfaae +#: 3fcbf810c86f4cf7b8499de88147aa95 msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 e920a824207746ffae63242d33137ac7 +#: e242228b6b3d440cbca8418050220267 msgid "" "The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 51d619152aa44651889ff2006c8f5800 +#: 6e01963a01cb49e39692455256679bfc msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 88f3f5dd8aa6401793b89e8de3b8c7a7 +#: ed81ea2234b041c79449dcd20f886cb6 msgid "" "The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 f1f9ee90d07c4381a8bb0851bdac231e +#: e8e3996f6a894b4f9cc266b46cb8d756 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b e3b710dabec2482d8ec1072d64d4e1f8 +#: 085e4d1a7a9744d2884f3003c64ca174 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 -#: 418699fcb6c241dcbeeed81d82e9f84f +#: ../../src/introduction/index.md:1 dcd96950854f47a6ad4169320c1dab34 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 -#: 28b6521a55aa4ab190ca998a59c52609 +#: ../../src/introduction/index.md:3 c4d17eec31874bf1ae9b49d73537d86c msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that " "are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 -#: 0e4969399eda48b98d883a3fc1540633 +#: ../../src/introduction/prerequisites.md:1 98a8bdfc7c91436d9cb46abbb7c19c57 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 -#: 6d59f082157b494ebcfff2f649abc524 +#: ../../src/introduction/prerequisites.md:6 244a716e267540c782e627adaea3a413 msgid "" "The software and configurations listed in this section are prerequisites for " "following this user guide. The CWL standards are implemented by many " @@ -881,13 +790,11 @@ msgid "" "(though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 -#: 2b83beccbc1b43969b705156b9c29482 +#: ../../src/introduction/prerequisites.md:12 2cdf453d2c8b4e2ea50555ef0b7364e5 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf -#: 594fe5e0aaf0499ebfa9218aaad4d08d +#: ../../src/introduction/prerequisites.md:14 53643a4f190c412d9552d1908f408318 msgid "" "There are many implementations of the CWL standards. Some are complete CWL " "runners, while others could be plug-ins or extensions to workflow engines. " @@ -895,35 +802,29 @@ msgid "" "md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 -#: f69c7c75a36048f5af0ed1b56df9320d +#: ../../src/introduction/prerequisites.md:19 1df6c63de3914af68f758054fe6955f4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b -#: f28638ffb8394ccead4ac52f30adc627 +#: ../../src/introduction/prerequisites.md:21 ceaa3a6bebab45a0907ee0cad01429a2 msgid "" "We recommend using an up-to-date operating system. You can choose any of the " "following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 -#: 8993d7d5c8d24fc5a9c7005800c0a1f1 +#: ../../src/introduction/prerequisites.md:24 1506ac904c6345c5806704a0ccf235aa msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf -#: 2073109799e748d68304f5558c82b105 +#: ../../src/introduction/prerequisites.md:25 a616213ed24e427bb91ee33cb21ec131 msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 -#: 9fb2c31bd36d495786397c7a7d6b3417 +#: ../../src/introduction/prerequisites.md:26 a4e9ae38103843739f13c62befd21f3e msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 -#: 43e1957537034c5886574118fc2533da +#: ../../src/introduction/prerequisites.md:29 2cd231aac42c4a69a925cea369999a8b msgid "" "If you are using Windows, you will have to install the [Windows Subsystem " "for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " @@ -933,13 +834,11 @@ msgid "" "recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 -#: e3a3d9b94b1e44c48f298dfcdcd27104 +#: ../../src/introduction/prerequisites.md:35 051d7cd7d3a94baa865d180afdd71688 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 -#: 8a385803ed3945ff81d38a3543a69d94 +#: ../../src/introduction/prerequisites.md:41 1a93aaf5bd5e4862b15e0636b4478640 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL community. " @@ -947,8 +846,7 @@ msgid "" "in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 -#: bf56727d93994d3995b0af0c68c2c583 +#: ../../src/introduction/prerequisites.md:46 edd0613118a2493c876652bdcb9e0fbf msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create and " @@ -956,31 +854,26 @@ msgid "" "`cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d -#: 9a959bd914d543b78f9625f03df95765 +#: ../../src/introduction/prerequisites.md:51 3448d215c2434866b8a4b340872ba81e msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 -#: 198ce7d893a04fcb806ec1671838d588 +#: ../../src/introduction/prerequisites.md:62 4c24d05f65794735b816024c78b63f1c msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` and " "`conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 -#: cc2be8feeab54a22a0b64a2a72991003 +#: ../../src/introduction/prerequisites.md:65 3167f4a2a8394feda1f848334be62022 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b -#: 749c672e8c234c1c9a5eb2cc9b77c4e3 +#: ../../src/introduction/prerequisites.md:67 3c4b67d62c9c4d658ccaafcd1977ec08 msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 -#: 29c64936318a4a2ba882e1eae8f03f57 +#: ../../src/introduction/prerequisites.md:73 30792f78348942e0acdde411342e8830 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -991,29 +884,24 @@ msgid "" "command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 -#: 44106744147f45bab675eb66148531c7 +#: ../../src/introduction/prerequisites.md:79 4473e41281fb4e738e4eb26c2d178934 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 -#: 6d84c6890f564b4baf7b34f6a52cbfc4 +#: ../../src/introduction/prerequisites.md:84 548393974d4d4acc91738f9bc13a3a48 msgid "" "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 -#: 7eb67993e8ca48dc929e1a992f78cb39 +#: ../../src/introduction/prerequisites.md:86 2ab3963cf9504ec097eda2b14f3448c4 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 -#: 52886c54c3c54b83896c52ebd7d53fad +#: ../../src/introduction/prerequisites.md:91 690882dcc29c48acbeb215a8be52eb9e msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 -#: 097945c33f7542e2bae2e9f7ba1cf84d +#: ../../src/introduction/prerequisites.md:93 6c3ba51b1e9a4add9203d62cec6ebae9 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be invoked " @@ -1024,75 +912,63 @@ msgid "" "environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 -#: 3853bfc6a85747019c615a50c7ca6b40 +#: ../../src/introduction/prerequisites.md:101 b2360ef646854422ad6c0f90fa49306f msgid "" "The CWL community publishes a Python package with the name `cwlref-runner` " "that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 -#: 662230f538504f44941c6f4801f6251c +#: ../../src/introduction/prerequisites.md:104 c9fadfa85a2641378e99a462e8e8d940 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 -#: 1c9eb9e2bb9e40a9985ada16c34eea2d +#: ../../src/introduction/prerequisites.md:111 abb8993ede4d4e479d88d2e848546f68 msgid "" "Now you can validate and run your workflow with the `cwl-runner` executable, " "which will invoke `cwltool`. You should have the same results and output as " "in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 -#: 7f53ba159979461393c0f278fe97fb30 +#: ../../src/introduction/prerequisites.md:115 ba0f7606e6174e53a8bf23c1ccd99250 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 -#: 7e8077c2dd584eda89ead60ecc5eabf3 +#: ../../src/introduction/prerequisites.md:120 dd2e10f43e8f498cb01de5faa4fccb70 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 -#: 1787a3c749ee48218b87c8401f6255d7 +#: ../../src/introduction/prerequisites.md:125 e500e9c71c7042169c25b31f21a09142 msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For " "that, the first thing you need to do is copy `true.cwl` workflow into a new " "file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a -#: a52ca4ce9a184e938c3a5cac9cb882ca +#: ../../src/introduction/prerequisites.md:129 d989516c873f4446bba005f42796b8b9 msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 -#: 41d3287a9a774a73aefd49bd709764bf +#: ../../src/introduction/prerequisites.md:135 e9d8610478094a98b5b5a0f568a315de msgid "" "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 -#: 3b9d30094611400b85b55db163cb303e +#: ../../src/introduction/prerequisites.md:137 d6d8131f91b740189e56ab9d90bee55a msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 -#: b6ea77357b4f45528ed1379f8fe67cfd +#: ../../src/introduction/prerequisites.md:144 def7400a00e84070a4bd80c2367d3bde msgid "" "And finally, you can execute it directly in the command-line. On execution, " "the program specified in the shebang (`cwl-runner`) will be used to execute " "the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f -#: 8797ce327d7443fdb3d4617d3fc2cf7f +#: ../../src/introduction/prerequisites.md:148 564e7be94d254e52a6c44b234d6ddc63 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 -#: 896b6896b1e44d0cab5f35e7d0dd88e3 +#: ../../src/introduction/prerequisites.md:154 bb5fe42ddd814ad4ac1071c0b18f24c2 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute the " @@ -1102,55 +978,47 @@ msgid "" "`` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 -#: 4b839d23d72f4d3fbe4f1ce7e568b20b +#: ../../src/introduction/prerequisites.md:161 53bb712a68cd49fca4db11e9e507c9a4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed -#: a42b9ab315b5402493e4ce0067d0a18e +#: ../../src/introduction/prerequisites.md:163 bdcf61cce5294e45a9f964628a8a66bd msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 -#: 2f63483960634a7782f95e9e2feaa5a6 +#: ../../src/introduction/prerequisites.md:167 28d33daee6e246c8a6d1382208e19c39 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting " "and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 -#: 3471105073204d7998aaf790b73f785d +#: ../../src/introduction/prerequisites.md:171 b071d7c87b7a4817b871085a652cd580 msgid "" "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" -#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 -#: 0b8b47511b5e4296b7438be0ad2604ed +#: ../../src/introduction/prerequisites.md:172 97658a1b16874ba8b0bb748242d0da64 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 -#: 3e3eec00f23f4f21873ddb005204a875 +#: ../../src/introduction/prerequisites.md:174 6198aa6769b74ef0a2a1ba539789f3ee msgid "" "The CWL community also maintains a list of editors and viewers: " msgstr "" -#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 -#: 2ceb25f2668442839e3e9f4512772a03 +#: ../../src/introduction/prerequisites.md:177 0c17235a374e40099be37b9b8ac8f1f0 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c -#: 20c753c5371b43ed834fa741b0ce7692 +#: ../../src/introduction/prerequisites.md:181 e3690e656b5a4348845c654689935a88 msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1158,8 +1026,7 @@ msgid "" "com/>." msgstr "" -#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c -#: a19c4fc9fa404912a0389337536d9c25 +#: ../../src/introduction/prerequisites.md:185 2db34e925a81422986ccb868463a7a42 msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1167,67 +1034,57 @@ msgid "" "and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 -#: a0f38c1e28ca4850b3986617625acbf2 +#: ../../src/introduction/prerequisites.md:191 d677fb155b0343ba8771398cca967fed msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for pulling " "images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 -#: 37e1162f30894a1ca7dada9870ffa3da +#: ../../src/introduction/prerequisites.md:198 22ed0b55de38408393af4a8309a995ea msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the next " "section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 -#: 1c25a51edf6f47c5979c721b19cf11b5 +#: ../../src/introduction/prerequisites.md:199 5ded73cae5db40ad840c3022e7cd447f msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 -#: ace930cf878d45a99f12b71bf0987a87 +#: ../../src/introduction/quick-start.md:1 23e5613df7c94e5f938c85b14f5441e4 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a -#: 46587a5e0d534af5867ae4f70a116bee +#: ../../src/introduction/quick-start.md:3 3b425afc63d841d4be57c92b25b4ed2d msgid "" "This section will show you a brief overview of what CWL is, and where you " "can learn more about it. No previous knowledge of CWL is required, but you " "must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee -#: a0774d4e779e46f7a983922425203066 +#: ../../src/introduction/quick-start.md:7 75a26c48d3e04e24abb96d81cb31c94e msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 -#: 1658ee6f3cac4d04afc732aa758b1f48 +#: ../../src/introduction/quick-start.md:12 88b4ecd45ea44dd4befe3ce89b30f6c2 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " "example below shows a simple CWL “Hello World” workflow annotated with " "comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb -#: d8e2bc671b894f3fa8a091261754c728 +#: ../../src/introduction/quick-start.md:16 e1789ef78bd64332a18d8601094a0f72 msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 -#: 683a469bf4824c64a8ea32e048d5df73 +#: ../../src/introduction/quick-start.md:22 196ceef96c27434eb4b0b7222c2fe73c msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the " "same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 -#: b7c50413f7864a86815f3b581561cdb5 +#: ../../src/introduction/quick-start.md:27 e6a44130c6b44d5bb6451a147f28dd8c msgid "" "In CWL, there is a distinction between a command-line tool and a workflow. " "But for the sake of simplicity, we are using the term “workflow” here. You " @@ -1235,13 +1092,11 @@ msgid "" "section." msgstr "" -#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 -#: d2ed66bdfcab4f7dad95b00c95d4a3d6 +#: ../../src/introduction/quick-start.md:32 340b46acc7a34b7b978f5a734f529553 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 -#: 4dcbe776a70645e5a6c7513348fa6bee +#: ../../src/introduction/quick-start.md:34 139e48dcf0474fea932ca07a0001d208 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the CWL " "*Reference Runner* for the specification, and it is compliant with the " @@ -1249,13 +1104,11 @@ msgid "" "`cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 -#: bae5b03fb74541e6ad79277a576e0516 +#: ../../src/introduction/quick-start.md:39 d6f6e061c0f4434eb6d70f9d84759042 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 -#: 8ff0d7a8d37b48488e4504ff8e3adcc5 +#: ../../src/introduction/quick-start.md:47 cb2b548489df45ee9d49b36116440eea msgid "" "If installing the cwltool using the pip command doesn't work for you, the " "[prerequisites](prerequisites.md) section contains other ways to install " @@ -1263,38 +1116,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 -#: 6255b499b9b144128afaeed64fabe8e5 +#: ../../src/introduction/quick-start.md:51 aa751bda67ec44ba988642b061e2a094 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe -#: e861db9c43ed4b8ba262af8e435a350a +#: ../../src/introduction/quick-start.md:53 a7e0209af0544b0ab31012864a43886c msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " "workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 -#: c6318f06bcd74cda8c1f0caef9452b51 +#: ../../src/introduction/quick-start.md:57 d0f424f0041c4635a0559fa32a76c86f msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 -#: c862e745217244d28cd4c2f0842e203f +#: ../../src/introduction/quick-start.md:62 eeee96c4e59447aea6b239c63e4bb3e5 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 -#: eba007736b92434a9711f683e64bb153 +#: ../../src/introduction/quick-start.md:65 961a385b340141e980aa4f8791fa2f12 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 -#: aebc2caf5d1b47f1b7cc0aa53e5a684e +#: ../../src/introduction/quick-start.md:70 c48cd1be543d4ccbab964b28c2e08584 msgid "" "Another way of passing values to your workflow input parameters is via an " "*Inputs Object*. This is a file containing the input fields with their " @@ -1302,25 +1149,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 -#: 1242171f8b854562bb7848b06d2d065d +#: ../../src/introduction/quick-start.md:74 e5619164bdf242f0b09cac668adc0ef7 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c -#: 24e82ecf7926428386a89f18a34eb00c +#: ../../src/introduction/quick-start.md:80 9f80772a53154bbeb27895d35435de10 msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 -#: 00e75efe03554835bc33ebaed0652626 +#: ../../src/introduction/quick-start.md:82 98b6d400cb274d08ad6489adbef08c4b msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 -#: 4ba34ec455704844a9cfcbac3522ea0c +#: ../../src/introduction/quick-start.md:88 4faabaab56f1444da290cf64cc389f37 msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but it " @@ -1328,54 +1171,46 @@ msgid "" "Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 -#: c0e9673440db454bb51af04432aeddbb +#: ../../src/introduction/quick-start.md:96 48beaccb16a24427bd015c63f9e06d37 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 -#: 39a23a9d02ab4bccb36d6a714639509b +#: ../../src/introduction/quick-start.md:97 68035ead1c6844128011ca32c04fd20f msgid "" "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 -#: 23a878e0166b40d78984a2263f63b760 +#: ../../src/introduction/quick-start.md:98 8fc1ebf21a6f4894a4acfba74a80602b msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 -#: 5d9c435820674bf4b1c5d3fef5df736d +#: ../../src/introduction/quick-start.md:99 27fbad579d8b4ebeacc6fd3ef7e85a39 msgid "" "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" "Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b -#: e724ee53db1940b9b09a909f4db531a4 +#: ../../src/introduction/quick-start.md:100 a8791b670848474da292a467f01f8c45 msgid "" "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." "org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff -#: 7820eb801a8145feb603145f153263b9 +#: ../../src/introduction/quick-start.md:101 fc20fa4c04104417b541a67ada2ab9a9 msgid "" "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." "replace('VERSION', cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b -#: e8db3f10be294f13abe3a4418bbae4b6 +#: ../../src/introduction/quick-start.md:102 a93a7797a12b48dfa5bc3a7c50ab88e7 msgid "" "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" "Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d -#: 95211ea6924148a6a1fa5ae8facc2c7b +#: ../../src/setup.md:9 6f02fa47aca14c59a35b3ab750f5f236 msgid "" "This page is out-of-date and was kept here to preserve the links of the old " "User Guide. The information on this page has been migrated to the [FAQ](/faq." @@ -1383,19 +1218,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 b742a74d586e42e6b0480b7af3e49c9e +#: 3821c2d16b254672a494522e47386cb0 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 cd3da03d43044ec9843e476a54e704be +#: 412a05f3492349a7bd26ea0c30e9bd80 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf 0d48e2f07d784504a17cad0ae20262c2 +#: 1232f6c81da141cb8482294eee5955dc msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files in " @@ -1405,55 +1240,52 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c 4d372b89f0ce451db2a505b1754b8356 +#: 485bb71673144e3f90f05b420b7079ac msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 573e903ef3d34514ab7b20e79c446567 -#: cfb40fbe52174d3799a6bec175db60a5 +#: ../../src/topics/staging-input-files.md:15 0beb10c3133643f6b62c7d4aeec33709 +#: 5d48d9a2e977431f9a3625abaa466f5f msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 95841b1c75c84f01bd5fcb7cf3afe78d +#: fcc1151a2e8b4a84b8595c7f913781a1 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb c8bca3654ebb4b29bf3f028b4c65fa35 +#: 4a291c7ac7c84257b7402567d8364a36 msgid "" "And now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a 1432105e38014a6d9d0cf80007141007 +#: 3b1ae26038fd498ca0ae23aa70a35d3f msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 bcad473b34ec43f7906253123a1661fa +#: 40388ebefb6947089c4a0f6d5d6e92e8 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" -"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." -"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " -"specification for details." +"designated output directory. Other parameters include `$(runtime.tmpdir)`, " +"`$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and " +"`$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of " +"the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 -#: e1c8949e663b4debaf87735f1d62a2fc +#: ../../src/topics/best-practices.md:1 a417fdd330db47a3aac07f7006c83ca9 msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 -#: dcc991b647d34ffc8ea3bf9c3a38258d +#: ../../src/topics/best-practices.md:3 99bad0fd9bee428a8d936d5a8e84d97d msgid "" "The following are a set of recommended good practices to keep in mind when " "writing a Common Workflow Language description for a tool or workflow. These " @@ -1461,15 +1293,13 @@ msgid "" "although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 -#: f26c222638e54187b8bb62fe30b66bc3 +#: ../../src/topics/best-practices.md:8 935500b0e6e249eba585644cddbd0253 msgid "" "No `type: string` parameters for names of input or reference files/" "directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 -#: 23720e4ab3d1407597f1d1c2a4d4d90c +#: ../../src/topics/best-practices.md:11 96f924d6e02f4005b35d463e49be2982 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that " @@ -1484,8 +1314,7 @@ msgid "" "anyone, e.g. [Apache 2.0][apache-license]." msgstr "" -#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f -#: b3638183c59744c897246af7dab5d10e +#: ../../src/topics/best-practices.md:20 25e0a5c93ccc49bc8b6206c7c2e3de5c msgid "" "If possible, the license should be specified with its corresponding [SPDX " "identifier][spdx]. Construct the metadata field for the license by providing " @@ -1495,50 +1324,43 @@ msgid "" "provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc -#: 2c0291133b964ad8b751f8a8ed2338fc +#: ../../src/topics/best-practices.md:26 34ad53bc5a40446daa0dac4571600d1e msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 -#: 325c8c4058f045aa8fbd705238122798 +#: ../../src/topics/best-practices.md:28 4c397ffd2e9148e39bdd614683a98a78 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 -#: 05333866485b43479352f7ee9326c7fd +#: ../../src/topics/best-practices.md:37 1ed7f7e73afb4bd2ad2e29b65d020ff1 msgid "" "For more examples of providing metadata within CWL descriptions, see [the " "Metadata and Authorship section of this User Guide](../topics/metadata-and-" "authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 -#: f8140ec6e9cc41ee88ec4bde61a44d47 +#: ../../src/topics/best-practices.md:40 13b058dfa3cd4bbea54ae7d5a56c4c50 msgid "" "Include [attribution information][license-example] for the author(s) of the " "CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" "[orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 -#: 1d68f50dafaf4cc1851e2d67b3e78603 +#: ../../src/topics/best-practices.md:44 69369b917c1a45199343266650b1b220 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 -#: b283942434c54456a3f29fbb0960b6c4 +#: ../../src/topics/best-practices.md:47 0245a61fd2ef4fb69cbb8d732086fb8f msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" "identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb -#: 0b4477c5b0184e59aa0c07161008a7bf +#: ../../src/topics/best-practices.md:50 e9a56e3634a042279cae1745b7820658 msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1546,70 +1368,61 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 -#: 9741651d51f249ffba1820694ab78e92 +#: ../../src/topics/best-practices.md:55 8a180861a66c4aaa9e8fdefd929ed829 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 -#: 5e76d4a9708244ff91f2587350d684a4 +#: ../../src/topics/best-practices.md:58 00f333a383b64578b32c687b42924a77 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" -"$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with " +"`$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " "[Full IANA media type list][iana-types] (also known as MIME types). For non-" "bioinformatics tools, use or build an appropriate ontology/controlled " "vocabulary in the same way. Please edit this page to let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a -#: 89e7028e55b54f968e87b9c1c3caeecf +#: ../../src/topics/best-practices.md:66 6b960d362bb540299f0560c14c5f2d8c msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c -#: 88e2338fb2614ef29dc497d8c01a2f2f +#: ../../src/topics/best-practices.md:69 9cf9342bf0864e87b495913d8e06d021 msgid "" "Each `CommandLineTool` description should focus on a single operation only, " "even if the (sub)command is capable of more. Don't overcomplicate your tool " "descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 -#: 0f3aad35924344659eb5a6719ab2b8f0 +#: ../../src/topics/best-practices.md:73 587b048324e447cb85844d8c64ae9a1e msgid "" "Custom types should be defined with one external YAML per type definition " "for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 -#: 877cbb1d537b46d3b6d05b2d8c025e70 +#: ../../src/topics/best-practices.md:76 d8df6bbd5d324f7c9f48edb33e113b75 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae -#: 5c0debbc1c1b428ebb32b589b99fe17d +#: ../../src/topics/best-practices.md:78 2235174088ad48a89d4fc21223e627b7 msgid "" "If useful, include a top-level `doc` as well. This should provide a longer, " "more detailed description than was provided in the top-level `label` (see " "above)." msgstr "" -#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 -#: 1ff97183191240edb98f0cc365cc028b +#: ../../src/topics/best-practices.md:82 a0f0953a1a9f40cebd4dbe028784ff96 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list of " "valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a -#: 22f7725deb07422fa0a7bc2e6f01e4d0 +#: ../../src/topics/best-practices.md:85 0ec380c683534892b6b8b8fcea84f765 msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. One " "common example: manipulating `File` names and paths? Consider whether one of " @@ -1617,36 +1430,31 @@ msgid "" "`nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 -#: 982313839ccc4f5a8527fe9a854c78eb +#: ../../src/topics/best-practices.md:90 65f23741db4e4a6abda8e5f7e036753a msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 -#: 267c9d10ab5e4b6c8a6104952deb1690 +#: ../../src/topics/best-practices.md:93 34c2caee8eb84e01a37033b67eb4aaba msgid "" "Complex workflows with individual components which can be abstracted should " "utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " "workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 -#: 2eff0eec58c94f4d8986a4cb91b14b8e +#: ../../src/topics/best-practices.md:97 d7c7484b2f1048aea9802400410f0858 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics " "software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 -#: f38db701740b442c89ce58e937bd35c5 +#: ../../src/topics/command-line-tool.md:1 a905abc2eead4dbaa035235936025499 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 -#: 034aac9e186645e384c28bb2a739cfff +#: ../../src/topics/command-line-tool.md:3 eb91b6dab34d4d5f9854ac580a6cbde2 msgid "" "A command-line tool is a type of Process object that can be run by itself or " "as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " @@ -1654,59 +1462,52 @@ msgid "" "command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab -#: 5f835cdfc0ae4f378d8dad6ae7ab1855 +#: ../../src/topics/command-line-tool.md:8 7caeb91564634091a932f1270c4f5ef9 msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The following " "example contains a minimal example of a CWL command-line tool for the `echo` " "Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 -#: 02900cb8ae4c4da89d264b76a984d6cd +#: ../../src/topics/command-line-tool.md:19 c6ac4a60d102407991f40b892fb60560 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 -#: 753e48d6dfd54a88a12773b996f182d7 +#: ../../src/topics/command-line-tool.md:50 51d3ce421db345f5ab19e02fbbc51df2 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d -#: c7ed6d1654c54bf390e933ef0f847b99 +#: ../../src/topics/command-line-tool.md:57 8311d1430e624435b7b04bf2574a90c5 msgid "" "The example above uses a simplified form to define inputs and outputs. You " "will learn more about in the [Inputs](../topics/inputs.md) and in the " "[Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e -#: 0a0f855ce34449a0a37c036105c65839 +#: ../../src/topics/command-line-tool.md:68 d1c03e5f19d64ea89276d126de6e4bda msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 -#: c4300454f49548f49e4bd186192515a1 +#: ../../src/topics/command-line-tool.md:69 8494b43e98dd424db7d57aa1d731f7b4 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network access. " "If a command-line tool is written manually in CWL v1.1+, there is a need to " "specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e -#: f985d58070de4c0fb5f5a491fd4dc31c +#: ../../src/topics/command-line-tool.md:83 8c4573fb120149269a0fe3a1ba6c9ef8 msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " "Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b 2f4e2c85677a4e56a35b6bef36d67334 +#: e1c709ac0fb249928d14aeced6551ae0 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d 13c6d5600a30406c81ffa25ce42eb0c8 +#: c26c9c640e0747c8b2c2977c860c9d82 msgid "" "Sometimes you need to create a file on the fly from input parameters, such " "as tools that expect to read their input configuration from a file rather " @@ -1714,17 +1515,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff 3bf773b8560e44a3a37c68b6fcdc6a23 +#: edbe918d7df14cafb440e171e46c6de3 msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 68b8578d2f6442929941ed2522b218ad +#: 6d457d9b4ae746d384e65d9a37ca3591 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df 755149ed46c348c2b723b49c3b3152a8 +#: 868394c1b8374ee6bbd43463e73d7edc msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the value " @@ -1732,7 +1533,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 54b7ff590d52454eb87d9f23fca44501 +#: 08a9e08cba674db09c9bfbef37e9579f msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later " "during command line tool invocation. That means that any genuine need for " @@ -1742,7 +1543,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa a7c74a4a74c9414e9f29fa20bab7e295 +#: 6f6f437753dd4eddae0b2ea62046fe39 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1750,14 +1551,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb -#: ca03defa3ad14cf698171cb09e3055c1 0cbf233379024800bcebb963e0a3eb6f -#: ae3bc02e4f3b404c89f3c461a62c5bc4 dc32a2bacf2d4c8cb841be6eb8b839ad +#: 096b17907bc3452d9927ef2fb6f5c11f 78ed5d8fb9bd4e068023d2c717e20f62 +#: c3a2e9e6b4414597a17db6d55d98e9d1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d 34a56bc23af44353a003ee295fb2c609 +#: ac783e6415a44cb59d4b425bac5087b7 msgid "" "Before we run this, let us look at each step in a little more detail. The " "base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1765,7 +1565,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c c7855ec1f09d4945afcb0aec22567b31 +#: b9e6e15b541149c6a2d3922c11405267 msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " "array, we need a `-` on the first line of each element of the array, in this " @@ -1777,7 +1577,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 5c60492e27014735bb9a86307ee654d6 +#: 87088899567a4402aeb34605d3c6b06b msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1787,23 +1587,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f -#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 -#: f924d65fed0c4cb5b0a019b084a8b535 80a9c04358e64ca28ef4879ad74ef733 -#: a2b470f06ad94871970b7d95339fd369 dc65b4b5e48e48a6ada03da0fac18a51 -#: ea2360c5286b43ccabac202dfa97fbe7 ee4ca94dadf64ab69a70b6cd4eaf451a +#: 304c1bfe5ecd4d26b5dfaf9ad2e2c7f8 3ef7f0e3099147d78fd2d30bfa73cc6b +#: 4fef79a30282456eb9b5dd34a5eec0b1 afe775762ed348e5982b99bcf1451606 +#: f0689cd0e5b34414b6693331186ee4a3 msgid "" "Now invoke `cwltool` with the tool description and the input object on the " "command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 -#: 285d23ef9bbc46c9890ae7957d487c12 +#: ../../src/topics/custom-types.md:1 9f1967411aa7497fa43a4851f0645d6e msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a -#: 3edd322daad940d8957f88a2637876b5 +#: ../../src/topics/custom-types.md:3 90bd62e4ef8b41e398a5c9b31f132774 msgid "" "Sometimes you may want to write your own custom types for use and reuse in " "CWL descriptions. Use of such custom types can reduce redundancy between " @@ -1812,25 +1608,21 @@ msgid "" "to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc -#: a1bd9b0dfa234e6caa6a684e981d89b5 +#: ../../src/topics/custom-types.md:9 3465527b8ff4407587f7c46fa9fa2a98 msgid "" "The example below is a CWL description of the [biom convert format][biom] " "tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 -#: 0aeacb6ac20f4ebca3600425ca32f5f4 +#: ../../src/topics/custom-types.md:12 c0cc869690804ada96a5c1813d17b895 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c -#: 1c813ebce2904f008b5b33656f673ebc +#: ../../src/topics/custom-types.md:18 01f369931c8142c08fe821a0ca31bf92 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 -#: cc36359e94c841d3aa5cbb26a094e1d5 +#: ../../src/topics/custom-types.md:24 0b3ff704cdea44e28aee3c704ca98e27 msgid "" "___Note:___ To follow the example below, you need to [download the example " "input file](https://github.com/common-workflow-language/user_guide/blob/main/" @@ -1838,15 +1630,13 @@ msgid "" "*rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea -#: dc79668b05e8439591a0beb4b57acc66 +#: ../../src/topics/custom-types.md:30 cb456bcae0dd41ffbc514eeea283e130 msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to be " "used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e -#: 08aba4f77aa442d4a34aa1535f78c49e +#: ../../src/topics/custom-types.md:46 c610173365d04c57900b22f4024b47b4 msgid "" "The reference to a custom type is a combination of the name of the file in " "which the object is defined (`biom-convert-table.yaml`) and the name of the " @@ -1857,27 +1647,23 @@ msgid "" "hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e -#: 63431a972f994bccacf55d5fac0d614e +#: ../../src/topics/custom-types.md:53 c2b2e18d55c94721812431583cfc4725 msgid "" "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 -#: 55e7695aca4f4319b1cf7551105a8782 +#: ../../src/topics/custom-types.md:55 3e61c3920a7a45db8917c348bd44384d msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 -#: 0c5ab34ebbf54ff6940b8ce3f080d744 +#: ../../src/topics/custom-types.md:61 cd87d210b03c4da2a7608b40a6bbcca0 msgid "" "In order for the custom type to be used in the CWL description, it must be " "imported. Imports are described in `requirements:SchemaDefRequirement`, as " "below in the example `custom-types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c -#: f97e18d2d3b946468c4fac227920e011 +#: ../../src/topics/custom-types.md:76 7af9ba3219e44ed49b8da781db5d6fb5 msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number of " @@ -1887,31 +1673,26 @@ msgid "" "this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 -#: 62644031403548898ff36addbc0b1f6f +#: ../../src/topics/environment-variables.md:1 eae1994f3a4d481b863b5125c7f4a383 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 -#: 595630b0687c4467aa65bfed289281f4 +#: ../../src/topics/environment-variables.md:3 8bd8c06d416740b69d126eb9f5f24ad3 msgid "" "Tools run in a restricted environment and do not inherit most environment " "variables from the parent process. You can set environment variables for " "the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 -#: 34e005c135864a89a00e817d79118e2e +#: ../../src/topics/environment-variables.md:7 11c6bffc620b4c789b29ab4034a8bfbd msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 -#: b624f9f99c294e6996f212c8b62f20b0 +#: ../../src/topics/expression-tool.md:1 89888b1b994546ce8a93f9630b4bb07e msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 -#: 14df63ab847e4efca820f712548cd076 +#: ../../src/topics/expression-tool.md:3 191d3010b9244b39bc3bc50246ac7ad7 msgid "" "An expression tool is a type of Process that can be run by itself or as a " "Workflow step. It executes a pure JavaScript expression. It is meant to be " @@ -1919,38 +1700,32 @@ msgid "" "on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 -#: 91d4224b41c6473f936c03bd0ab9d370 +#: ../../src/topics/expression-tool.md:8 3437ed6e184748e4af1ef62f32c8cef1 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe -#: 519989399dab493ea41941ed85cb9670 +#: ../../src/topics/expression-tool.md:17 c3ae1ef318bb4e0fada76c353dd5f6f1 msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 -#: 28dd1cf24309404eaf717d417272e094 +#: ../../src/topics/expression-tool.md:48 a7f5e04d242c48a7b3deffb5ff6528be msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a -#: 3f536ad8c86d442c8bbe61777dbb1a54 +#: ../../src/topics/expression-tool.md:67 32b6841faed044409bc618cba54a22f0 msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains a " "JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 -#: b9e9894c6d024e60929d020dbaa553f0 +#: ../../src/topics/expressions.md:1 6821ba7a84a44d309d245c429948ad09 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 -#: 482debe1a40f490b90d4ece1b3f9d732 +#: ../../src/topics/expressions.md:3 8167269bc3a64c72bd6c909362350a15 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1958,8 +1733,7 @@ msgid "" "CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 -#: 708346038be745d097685970cc462f4a +#: ../../src/topics/expressions.md:9 c0f75603a6024063a6911f17c70908cc msgid "" "JavaScript expressions should only be used when absolutely necessary. When " "manipulating file names, extensions, paths etc, consider whether one of the " @@ -1968,79 +1742,67 @@ msgid "" "practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 -#: 99347b6b2c404a4b9bbcc96e0b4bd925 +#: ../../src/topics/expressions.md:16 7faec63b389a4c07b6929b7a78f0cc70 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 -#: e6629f0914324c76a08fe179575b73d5 +#: ../../src/topics/expressions.md:22 d7dca89942f949d58cb18cb94bb7de72 msgid "" "As this tool does not require any `inputs` we can run it with an (almost) " "empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 -#: 2287002a87184fb9b95d775a368f0e46 +#: ../../src/topics/expressions.md:25 1abc1a21c0764415b138099e0e21432b msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 -#: c23d4543d9f949a9a7015fdcbb40dcd0 +#: ../../src/topics/expressions.md:31 b8b5a50a82e44e49a37c6396f1ff9464 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object is " "represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d -#: c04a9dcc84b84f37bcf32c3790672038 +#: ../../src/topics/expressions.md:35 b38d66c12ab74dfc9395e69d9c04bbf5 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc -#: 9f27c79365db455d9d31053576ebe05e +#: ../../src/topics/expressions.md:37 8417aa7a9d034361a41def6b71e93413 msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 -#: a2b3ad1e2c884e24948a915c3305aee1 +#: ../../src/topics/expressions.md:47 c1f672b377da4605b9c5098ebb6e1147 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 -#: dd7665bbc5e9449588c9539e3c1910de +#: ../../src/topics/expressions.md:54 af52f5197e8545d2be22cc0f7f03648c msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " "describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 -#: 0972c757f7c74ea9beabf6b9ef9dbf4c +#: ../../src/topics/expressions.md:62 5e12ce15018942bf9010ce6519c17b00 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 -#: 175de3b9854546568f60a20cc19887de +#: ../../src/topics/expressions.md:64 e2e9c5f7b681427a9589476649e5a9d8 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c -#: 0c286e5ba1714a059a95b566fe49be31 +#: ../../src/topics/expressions.md:66 8a74763ead0147bbaf3892e552fad546 msgid "" "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 -#: 1acb064f7a4a482aa0174bdc847c6382 3029c1dfe5424c2b812597b03ea76178 -#: a5503b6c524e4848aa308b0f4c26d774 +#: ../../src/topics/parameter-references.md:64 0aab7de8d69f49438d4eeed17316df68 +#: 75f90cb870d14d0dbb4c4ee80d32a65e msgid "`arguments`" msgstr "" @@ -2048,39 +1810,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e -#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 -#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 0e03befa46c74dc2b09420e1eb2a6fbd -#: 50f81e7ab73a4713bbc60f6f5609b906 718dc3def33c462786174fb42097981f -#: 9c2acd930553458eb105f96213b5d7b0 d4bf86a995d546c0a9159b3f29a84125 -#: e98424244f554c7399e9e7ad560849a6 +#: ../../src/topics/parameter-references.md:86 0b9d8268c177489b86b8eaa638dfa063 +#: 204cd6d8375a4462a8247863a96df906 2b7e56ceb4ad49a8b29a58b10bad7c0a +#: 81f15c64379941d8ac2a681b3879761c f11ae7d801db45989b598864dc6291c9 +#: fc4534b475334f7281d1740c9a78f640 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff 2be930b5da674874a0b634eca3ad9346 -#: ce445ad0f00f403985eed1328103a500 +#: ../../src/topics/parameter-references.md:66 70e9085b21f640d6893309a3375c0511 +#: f529003dd7a64bc7be0ccef8dbfa84b3 msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 2fe48d6404864ea39ef0634169f67be1 -#: 43453d90db244c558a815ca872dc716c +#: ../../src/topics/parameter-references.md:67 3fceb522ba6245129b826c342eaf31b4 +#: a5f71add5b8345a4bfa02853ef8a6d35 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 78eaa318ba81407e9ca9c2c1702ead11 -#: f5da7058f7f146d584314a5bf4de5498 +#: ../../src/topics/parameter-references.md:68 018300196ea24550988a0156894b5e85 +#: 2c799286e8204ed9a83c3fc006988139 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e -#: 7189f4415d204fb388c4a7e927e15b71 +#: ../../src/topics/expressions.md:72 25d91d6624bd42e7948e29c684e8e441 msgid "" "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandInputParameter)" @@ -2091,15 +1846,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc -#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd -#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 -#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb -#: ed875a006df64f9e8a55fa5e9fa87404 17a83cc91963434e89822a3e46df8401 -#: 194d3e48d38c476fa8f731e3bc2d8c7f 3a3000a6446b4ef4ac66a28acb13b136 -#: 5cc35210e95e4f2ba6a1a6f118926fdd 68b3d1481a4e4375b1b0c4fca8285374 -#: 94f2bc195bc0487da014bc3f4d2dc8fa b92b4eff2429437d9da911ca68cef954 -#: fc0a1353e87e479d8c8b6c973d547465 +#: ../../src/topics/parameter-references.md:90 0944d6525c3c460aa4b5a0e72552ca4d +#: 1187b0d330cb470fbea82a8b8c95aa28 265602307ccd42458ba47ac1b689242c +#: 2febce1b1ad74b18af3a9b3fa137c780 3215ee41f96541cbbda60a1167386c2f +#: 80efeab6ec0e447bbe158cbaa57f83d8 8d2bbd91b4ab4faa923fc1a14ec49dd5 +#: b4a6e640275b4fc7a18e3083e86b72a1 msgid "`format`" msgstr "" @@ -2108,62 +1859,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 -#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d -#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f -#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c -#: f760465a49d64d4c8468ad9c4fea62b1 5478cbeadc64412bbb32619fae9b9958 -#: 6950cbe52d334fe58bf4fa20e5f1f8ca 6b5bda581d0047819c6d92edd8ac9045 -#: 8248329fbe504b3a96bcd890908b070f 978c0fea8ed1481a9f06b6abb31ebd21 -#: a24ba514d66d49cea281fd4c9c7a2b8d b6e2c8e7abf74d64b2915063dda8479b -#: bc184adfad0e4642bc864d367b8779b7 +#: ../../src/topics/parameter-references.md:91 480b2e4207574b27b8d33dfe5e9ab64e +#: 4b4149a3b97a4de5b2d7fd84bd547ffe 7af1a82df41e40d0a430babafe1bc5e2 +#: be01787b66e34074af32bb45dcce8657 be099ab533504a7596fd56ec1ce7ca5d +#: c8b96271665444608f601a460dd28fb3 cb6dfa7bc68b41929a5247d929c2f94a +#: f7f452e92f6d4a14ba3912c62699019a msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac -#: 5bba2d465e0a4c5d9575406d1294a225 +#: ../../src/topics/expressions.md:75 4811c1b9867b44caa70dec4b91970484 msgid "" "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 -#: da385d3cde614749887e195ea6d95291 +#: ../../src/topics/expressions.md:77 0b1f2a8986e0419a90e484d3a945a037 msgid "" "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 -#: 487c95417f8e48be8391163578ca9519 +#: ../../src/topics/expressions.md:80 dbc02876870d49d2b9e39db4133a0f62 msgid "" "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 48437402c00147d4b4ca8bd6b38a5823 -#: bdcb3920048f4e578a4005fc2e30233b +#: ../../src/topics/parameter-references.md:78 97339a3fa43849f7b292f4643b5fe35c +#: da8b81b1e1884406a188fb04825ef90e msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b -#: d555a3d991e344a5a8e1289168d7c6d1 121556d49d584cc491a15ef8404ce462 -#: 183ba52666744f7ca5772939db2efd6c +#: ../../src/topics/parameter-references.md:79 077e7b0d2dde443699050af8c63ab912 +#: c8cbe3dfd0984221ae72012ea26edc6f msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c -#: e9fa9430535c424fa3e8be5d460d2ba4 08ad064936d8406f8c3852526f4f863d -#: 30c927925c6b483b80b583ca7c735437 +#: ../../src/topics/parameter-references.md:80 3f07f4a8594640c2b2da4da521872b59 +#: 573f7e4b72ec4c47ab2e54e2c4877d9c msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 -#: 32a26dd9c5f84e88995f093cda953ac9 +#: ../../src/topics/expressions.md:84 f03011b3479b47c690604c508d95c263 msgid "" "From [InputParameter](https://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" @@ -2171,108 +1911,93 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c -#: b0290d1a477b48119e17cf1fed9d6dff 05ee6df2f9b247629d148fd59c293660 -#: e7b7d782b6ac49b3aa0c8d8ce7ff04d1 +#: ../../src/topics/parameter-references.md:84 1ec3f913909b4e04bb602767d23bd85d +#: 2f7130500b8c450fa4af226b18e38407 msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 -#: b0cccc07e5bb4effb60424623351499e +#: ../../src/topics/expressions.md:88 a5849a856a374cda807ecf48034af915 msgid "" "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." "html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 -#: e1cde4aa32c041238ed2596173c6d824 4e5281c8663c4b6e8851be10f50143f1 -#: b5c22c66397e4268b4b3d53b9a253a3a +#: ../../src/topics/parameter-references.md:87 bd8bbd60aaff4e7aacec91bcbad500f4 +#: f0c99004211e4adf8c0b524d5bbcc12b msgid "" "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." "html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf -#: c2a92d3eca7f4ee39cec649170eeea53 98a28fec818e42af9e177e17fa12aa7a -#: c37d0b1fd75e44a28b3b6409f912e865 +#: ../../src/topics/parameter-references.md:88 96c544cf213245cfb3d1f5196223c6cc +#: c6a04d4f3ef24104b0a86f9093935c13 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 -#: dcc42c6c49964a4ca7bcf2124e26ebfd +#: ../../src/topics/expressions.md:92 946e0437a48b4d5da2a29d489250cbaa msgid "" "From [InputParameter](https://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [ExpressionToolOutputParameter](https://www." "commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f -#: d2ba352ac5fe427ea7ceb0bde01458ba +#: ../../src/topics/expressions.md:95 1f287ebf87ae4e93bd1ac65cc1d01bf4 msgid "" "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." "html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 235cfd6e9baf48698102447fcb83e0e1 -#: 8aad01df8d8d4ab7905a5da7ce7f6bbf +#: ../../src/topics/parameter-references.md:93 0d0f4f0e12174d588c131afef70efc5f +#: a74e0e3499d644b4a9d999d3555f03de msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 -#: 718ceee9973240ec9c100977bbcc8921 058ba8c9c2da4ebf8b2291600dafd611 -#: cea47d3e10f641a2b64f08ee100ea6bf +#: ../../src/topics/parameter-references.md:94 b2e31c38f7cb4ecabd6b9b89ef051c0e +#: ddc9d9ae72a64a76a2a8e2bba22584ee msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 -#: c07ab08eb75d4528949c56a3d7c12b28 3b039de5ad144207ae337aa88b3b1a1f -#: e0ecfe44b34e45dea513459b6b3e44a6 +#: ../../src/topics/parameter-references.md:95 12f86817dfc14f2bb39509886d56017f +#: 8a94f2c3b1674162a268f67935a3025b msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 1cfc6cb0be4e4ddd90f546adb796b805 -#: b62f6eaa7c394792929dda83a187c632 +#: ../../src/topics/parameter-references.md:96 a800acfefb3f433fae2cdda9ac4a795a +#: bcb58fc2447a4472b86913871b8c12ee msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 8b13b0e4071444179b26401929de8a10 -#: 8ffb471129c04fc6bb52b782fbd09f9b +#: ../../src/topics/parameter-references.md:97 5be337d412ba4d48877e991d535e810c +#: e6cf2f8498db4f549193be20d87e16f9 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 331f58b998cd4d309940ebfcc60a44f8 -#: 5041700e6ccc48989e395a6dcb1be3c4 +#: ../../src/topics/parameter-references.md:98 3bc61c8197664f12a98d1ac38b421b38 +#: 9973a87f747445ad89ce959420cac5fd msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 14402b41c64548f8a9691c3b7ccaf3ac -#: cb4837a2b25343d2880a07143f85f40e +#: ../../src/topics/parameter-references.md:99 0f5dc4f5a4c64f818e2e22f20472ae84 +#: 2ec9d1f191f44686b1cb8622336d6b92 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 -#: 1d1c2894600544b686a8ec3c36cdf767 eaa30e987ec543ef8d6f7171de5525f0 +#: 5382ff97ad2f419dbe1bed266997aa84 74406f77013443f28d4d6306c54b0df1 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 -#: 065c97a553904db6ba61c20cf9d9939c +#: ../../src/topics/expressions.md:104 f594a20dc038457e815dc17bae6e031d msgid "" "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" "CommandLineTool.html#InitialWorkDirRequirement)" @@ -2280,39 +2005,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 -#: 36be05289972455ea4a60aa1f0b9cbdf 49e1ab5bc5734debb83060759d5c3236 +#: 5814f96ee4ec4822aecad33c8eda0473 c46c44268b2a4b96b1df13e53e82e54c msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce -#: f8e37cd35aea4bbb92d28e8d7e803ebb +#: ../../src/topics/expressions.md:106 b9824103ef8745bab30b65887c82f62f msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b -#: de816d1dc9f24c0cbef86fd6a09eff6b e265df9d1cfe439bb798ab6cd32485af +#: 28b23f84c64549e7a0fe444ccc3e1b05 fdd5d742a6764e5db2281ed844bf3475 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 -#: 0363e32e12604eb896f4bdf6bbefd550 8b5289393b7f477699d007ded45a4df1 +#: b6123c911c804f3c8cb596d2aa495b2b d81a7d8b7db444409b286e5f1d863968 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 -#: 2c704cae43d64ecbbed33d18eb3f66f3 89acc8f8387d4643a844ac3efb186000 +#: eb6255a0f8d748588d87e7ad38e507bd fffc5a80bd68495396d32b7a1821eb4e msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 -#: 0597c6c214924e75ba2f212cd6b0c9f2 +#: ../../src/topics/expressions.md:110 b00a8a2a572742e0929470550433e929 msgid "" "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." "html#EnvironmentDef)" @@ -2320,27 +2039,23 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 -#: 1eb1c2432dd943f6a27a1f8b92e3981b 5b9ba9380f10425b809c6157a1f0b052 +#: 9b34c95e483e47f3828e79bf929a23b4 c968eebaf0114b23b789e9ce68e7588d msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 -#: b4cc7cc55cf04449b291a27514fc99ae +#: ../../src/topics/expressions.md:116 7c8fb996d1af4cfdb0d49d8ed2696745 msgid "" "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 -#: cdb48eff43e7459fbf3ed21eb7791d66 +#: ../../src/topics/expressions.md:118 75a29e9ff2cf4b5bb6afa87a741a111b msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib` " "attribute that allows users to load external JavaScript files, or to provide " "inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d -#: 67a4dc675c0e444585d579954b99614e +#: ../../src/topics/expressions.md:122 5233d8baa8b74391bf8fee5ae2324234 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2348,8 +2063,7 @@ msgid "" "the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b -#: ea3238db48494ab7b044bab9f96590af +#: ../../src/topics/expressions.md:128 343e8b78a1f94b8cbafac05212e5a333 msgid "" "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." "org/v1.0/CommandLineTool.html#Expressions) that the only version of " @@ -2358,63 +2072,53 @@ msgid "" "in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c -#: baf2f6ac8d514705a1f7bf7ea8c71d2e +#: ../../src/topics/expressions.md:135 0657ee8f03d8462ca6ca6fc538386b0d msgid "" "For example, we can use `InlineJavascriptRequirement` and write a JavaScript " "function inline in `expressionLib`. That function can then be used in other " "parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e -#: ef45f4e14fb943cd9fbf179f5d3680e5 +#: ../../src/topics/expressions.md:139 e3c593cf50da426f8d9df215c7db0bc9 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 -#: 030261615c38485d83ed986c9c98ce15 +#: ../../src/topics/expressions.md:146 b971e53c3ed847f1b7c7a6d50e344baf msgid "" "Running this CWL workflow will invoke the JavaScript function and result in " "the `echo` command printing the input message with capital initial letters:" msgstr "" -#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 -#: 1728e2370cbb49ab97bee4c2f74fff2d +#: ../../src/topics/expressions.md:149 d2315d46369f4e9d9c871d7f88f7006e msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 -#: 4514fc0c99ac4688a37bf30bffe139e8 +#: ../../src/topics/expressions.md:155 04fdaa45a7ed47d5830181611bda924e msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db -#: 33804649720143e5a70e890af9ad9119 +#: ../../src/topics/expressions.md:158 8d7686f62f314d98aae8c262befd5283 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 -#: c114496be4c243d6834776e17bf15010 +#: ../../src/topics/expressions.md:164 e68ee17607be4a06a66f9fc67624aff5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac -#: c784e86f14f54e4982db206741fbd96e +#: ../../src/topics/expressions.md:171 76b85d3729274fc08adfadcbf1172650 msgid "" -"The `custom-functions.js` file is included in the CWL document with the `" -"$include: custom-functions.js` statement. That makes the functions and " +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 -#: f9de69aad9b44afabded71221c84adc2 +#: ../../src/topics/expressions.md:175 29f334957fa940c289f385160cca6d63 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 -#: b853c964611e45c2b37a8ac3c34a4133 +#: ../../src/topics/expressions.md:181 6d255ae6b92a48fa9b7b98443cc2f5bb msgid "" "Finally, note that you can have both inline and external JavaScript code in " "your CWL document. In this final example we have added another entry to the " @@ -2423,18 +2127,15 @@ msgid "" "functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b -#: a10d143210b94f83857f62e972d69134 +#: ../../src/topics/expressions.md:186 89734e7855654b2e8bfddeea96241539 msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f -#: b07734b172664040aff04f83bd4395a5 +#: ../../src/topics/expressions.md:193 1915f8e68f624027827d28f8e17d2dec msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 -#: 1f9a5377a1f04ee3b8a9ae22390e0cae +#: ../../src/topics/expressions.md:200 750f94edb4f84e45a276f6ab28fad95e msgid "" "The `$include` statement can be used to include a file from the local disk " "or from a remote location. It works with both relative and absolute paths. " @@ -2442,13 +2143,11 @@ msgid "" "html#Include) from the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 -#: 359bb6448aa140f8b940baf769c13db6 +#: ../../src/topics/file-formats.md:1 2e9e8cfaf48a43a88c31a855dac4f748 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a -#: c4aba730bee14931b051d6aead7c2dae +#: ../../src/topics/file-formats.md:3 c574b54d998243f28d2caa91434968a7 msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This helps " @@ -2456,8 +2155,7 @@ msgid "" "simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 -#: c4dfcff573424bccb97580fdd1ef27a1 +#: ../../src/topics/file-formats.md:8 b0ec34507eea473c91d6ada09a1c5c09 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM in " "our example), reference a local ontology for your institution, or do not add " @@ -2466,39 +2164,33 @@ msgid "" "file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a -#: 1457fa489c894f1bae8a3949ef200527 +#: ../../src/topics/file-formats.md:14 a688e39859734a518c0fcc19f532a432 msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` section " "of the document in greater detail, so don't worry about these for now." msgstr "" -#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f -#: cc4fa87d57b344ed8961c31bc4397e71 +#: ../../src/topics/file-formats.md:17 e068422ad9b84ca1b27008127928cc0f msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 -#: 091815ab1d824787a1460ce11ffb834d +#: ../../src/topics/file-formats.md:20 8c3ef5e145b14299bf3671add0da56ac msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 -#: 414b68dac4654163b3dc13e140ffdbf8 96fad38b4aea461493bf0827476163bd +#: 0d92f1c0f1ce448fb698e9b390b45c15 fc4773204ebc4e3789bb076dff0d0393 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e -#: 4f71de1140974e73ab033fe7dd9dc165 +#: ../../src/topics/file-formats.md:32 900abc5aa6a940f48f9c93e79cd1c47f msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b -#: b84e3294c8f648aab634e59b6f58441e +#: ../../src/topics/file-formats.md:34 0390555b96c84aadbd9325c152972087 msgid "" "Below is an example of a parameter file for the example above. We encourage " "checking in working examples of parameter files for your tool. This allows " @@ -2506,13 +2198,11 @@ msgid "" "parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc -#: 6d9ae44900d64532906532432881d29d +#: ../../src/topics/file-formats.md:39 d5752ee5437b496ca10f4f12b76fc5dc msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d -#: 5b99384b3a854832bcca2fb02bdfc1b6 +#: ../../src/topics/file-formats.md:45 91dc76bb4565473ab948eecf628a405c msgid "" "___Note:___ To follow the example below, you need to download the example " "input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff -#: 3141fc6828024c3e8201e88ca10e19ee +#: ../../src/topics/index.md:1 0b8b9b7f533543a49f876421ce6057d9 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 -#: 5f8c8ea68d7f46fead000315226ec164 +#: ../../src/topics/inputs.md:1 1b6cfac3a92347d4b98bb54de1e26870 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea -#: 86c18e5105b1400d86d413e28ad72f48 +#: ../../src/topics/inputs.md:3 53dd5f476f064cbf9b9826d1e80eb830 msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e -#: fa15037f9b0b4a2c9a1f4cff9b8fde43 +#: ../../src/topics/inputs.md:5 420b33d143fc44d1b237bc678f0af663 msgid "" "The `inputs` of a tool is a list of input parameters that control how to run " "the tool. Each parameter has an `id` for the name of parameter, and `type` " "describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a -#: fba6d2b7843e466abee33183103cf47d +#: ../../src/topics/inputs.md:9 55136332e3bb48f892cf6a74c67a4ac6 msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*, " "and *null*; complex types are *array* and *record*; in addition there are " "special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 -#: 09f5a55611d14e39b2266245b79ed763 +#: ../../src/topics/inputs.md:13 cb2527899cc04b6d8060c4d57883beb5 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed -#: bdfb39c2656040858616afe731111d1a +#: ../../src/topics/inputs.md:16 c79668b856b14243b4fad0f46dc5d6d7 msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d -#: c306335ff07e4c03955fe87cad16efd1 +#: ../../src/topics/inputs.md:18 ed6f3e5c7b3f403a9a94359983107645 msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e -#: 50bd3db6bfb348eea13ba4714ecb2a20 +#: ../../src/topics/inputs.md:24 034075eb09db4897a96d3332408427db msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 -#: 5d32cfb6f6ed4dd8b11ed316830edba8 +#: ../../src/topics/inputs.md:26 08181d391cc543a5a81d3257654df213 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 -#: b90fb1b2d38b42c1bad2d9667aaa22fd +#: ../../src/topics/inputs.md:33 15215522e38242c4b17ec3aa089269d4 msgid "" "You can use `cwltool` to create a template input object. That saves you from " "having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b -#: 6029a96abf9c4d7295eb86d435a1f58d +#: ../../src/topics/inputs.md:40 64bd3382ec234ec8a50217b794b96916 msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " "> inp-job.yml`, and then modify the default values with your desired input " "values." msgstr "" -#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 -#: 902e9df74f78431ca9cf1421a26e097a +#: ../../src/topics/inputs.md:44 3611c1ca498a4197a4a6612c60f5f565 msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b -#: 9760d15bad144e70a86dc0a8da72363a +#: ../../src/topics/inputs.md:47 da924e8142d34e86bcb5de1cd1da71ca msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da -#: 75bf3fae131049308441bc496f543f6e +#: ../../src/topics/inputs.md:53 13c97256a5ee49c99f4010edf9dbc9bf msgid "" "Now invoke `cwltool` with the tool description and the input object on the " "command line, using the command `cwltool inp.cwl inp-job.yml`. The following " @@ -2616,8 +2291,7 @@ msgid "" "command line:" msgstr "" -#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c -#: 38d8a9c157404bb496bc49f1e427bf99 +#: ../../src/topics/inputs.md:64 dcc3f2a47a6449efb857af63ed4b65d0 msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2625,8 +2299,7 @@ msgid "" "specified" msgstr "" -#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 -#: 502994ee84234f048e545633bb04cd3c +#: ../../src/topics/inputs.md:70 cf54a30ae24f4013bb19f379a7ca67be msgid "" "The field `inputBinding` is optional and indicates whether and how the input " "parameter should appear on the tool's command line. If `inputBinding` is " @@ -2634,16 +2307,14 @@ msgid "" "each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c -#: 551b06b8a3064bcd8d0f1693a4c0ee94 +#: ../../src/topics/inputs.md:83 ff75644bae9c46af8379d78360d4c696 msgid "" -"Boolean types are treated as a flag. If the input parameter \"example_flag" -"\" is \"true\", then `prefix` will be added to the command line. If false, " -"no flag is added." +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 -#: 1838e7438be5449c91c6406a7e40d8cb +#: ../../src/topics/inputs.md:95 e90abe59a84e48d4b8d6caa737e087aa msgid "" "String types appear on the command line as literal values. The `prefix` is " "optional, if provided, it appears as a separate argument on the command line " @@ -2651,8 +2322,7 @@ msgid "" "string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e -#: 098bb02c941a4bf2a8d4dd9ab3bf052e +#: ../../src/topics/inputs.md:109 9275236d87b646cab1058dd750e11a50 msgid "" "Integer (and floating point) types appear on the command line with decimal " "text representation. When the option `separate` is false (the default value " @@ -2660,8 +2330,7 @@ msgid "" "example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 -#: b43194d2b3ef4fc6a8c4b58741317b29 +#: ../../src/topics/inputs.md:124 6a39929af73f4ba9b6455ed9fd287e08 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the parameter " @@ -2670,15 +2339,13 @@ msgid "" "provided in the input, nothing would appear on the command line." msgstr "" -#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 -#: e17c55c9ed034dd68f4d24272a61d2f1 +#: ../../src/topics/inputs.md:131 44ce716561cc4dff8fef1ca59f816c7c msgid "" "Input files are read-only. If you wish to update an input file, you must " "[first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 -#: c97a6945e4bc49888d280bbc43c3c069 +#: ../../src/topics/inputs.md:134 9f1da592350f40ee88920465e2004148 msgid "" "The value of `position` is used to determine where parameter should appear " "on the command line. Positions are relative to one another, not absolute. " @@ -2689,20 +2356,17 @@ msgid "" "position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 -#: 503666cda07b4d7397c65561714d8034 +#: ../../src/topics/inputs.md:142 5116d91f247f44518eb21840415f6eaa msgid "" "The `baseCommand` field will always appear in the final command line before " "the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 -#: e5463be0a00d42e386aa6fd3dfacaeaf +#: ../../src/topics/inputs.md:146 08b26d1688e3470288e73d587f052d88 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d -#: 14b98bd0ef4a4065a24e66443458d607 +#: ../../src/topics/inputs.md:148 f91994a4279a41bda3de41fe79008c62 msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to provide " @@ -2711,28 +2375,23 @@ msgid "" "after the type name to indicate that input parameter is array of that type." msgstr "" -#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 -#: 98fa5dab117e41d4a42da8d78c533c64 +#: ../../src/topics/inputs.md:154 4b93a4f980634e88a8f34a38703fc906 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 -#: 116c212444da4488b32abdbd725db98a +#: ../../src/topics/inputs.md:160 de3e760ebb0e4ae099deddb978046a2c msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 -#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d -#: 065e556e01b34c35b6be4b54b7cc0203 4745f370dcbd4ee8bbf4b3a20ac5b9fe -#: d11761f2d576464f8a2c63bdec02d410 +#: ../../src/topics/outputs.md:105 06ec811e8f0e43b8b929198533ac8082 +#: 797c06f0605d4e4ba306c2803a7834f9 d76d42c490a24b6daed944f45fe7a351 msgid "" "Now invoke `cwltool` providing the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 -#: b3bf1d7e95704682b1bae17472eaa4bc +#: ../../src/topics/inputs.md:178 49406f30f62346968bb1250efc940f70 msgid "" "The `inputBinding` can appear either on the outer array parameter definition " "or the inner array element definition, and these produce different behavior " @@ -2741,8 +2400,7 @@ msgid "" "concatenated into a single argument separated by the item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d -#: 04bc655130234786b06b2d5b9e693635 +#: ../../src/topics/inputs.md:185 3d8711f0135e4ab1b59fce94c83b97c0 msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` in " "`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " @@ -2752,13 +2410,11 @@ msgid "" "arrays of arrays, arrays of records, and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 -#: e2c18a43b2794448b45c489dd2fa951e +#: ../../src/topics/inputs.md:191 6f146779d6a84888948751b8b1fd0515 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d -#: 38968ed627514ef38e43b3d1e4a5e25f +#: ../../src/topics/inputs.md:193 e5970a83876e4b5e9a02f2ab0030eb83 msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be provided " @@ -2766,55 +2422,46 @@ msgid "" "parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 -#: 06aab84eceeb41d087b7e295ffa21586 +#: ../../src/topics/inputs.md:198 0db71b22173846d7b8d4aeb66d2ed8ed msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 -#: a0317edb8b964cd2a36c59eaa6df302a +#: ../../src/topics/inputs.md:204 f90fd48656a7424aac304987adf1b068 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f -#: 5a3d1b82c79c4ccdb7d06381f4d0acda +#: ../../src/topics/inputs.md:215 3c8bd9134a1c4bda9461362df3257d6b msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b -#: e1fc6c3a324a46ee84b0eb59f8396552 +#: ../../src/topics/inputs.md:217 63bd06780bb949e5b1a1d10389c8c23f msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add -#: f22e7d9e23b541ef88f3254095147519 +#: ../../src/topics/inputs.md:233 0d448baa57f14e7783d3167611e8c659 msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the first " "matching item (`itemC`) is added to the command line and remaining item " "(`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea -#: d473d2fa11f64e8fa86554b5777c98e4 +#: ../../src/topics/inputs.md:236 202239a6e90044e39b676d641aa6d58a msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c -#: 290461c321d14d23b39003b93008a7cb +#: ../../src/topics/inputs.md:252 512ecb3349b0450cb741de4ed2d2e850 msgid "" "In the third example, only `itemD` is provided, so it appears on the command " "line." msgstr "" -#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 -#: add43f7531bb4c6988053ae799c366f0 +#: ../../src/topics/inputs.md:255 185ff0bb49e841c592b29112eb171bdc msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d -#: b12b6f5e34c14dbc9b40458d92e6797f +#: ../../src/topics/inputs.md:257 6cd5df09e4594d78a526f199ac577881 msgid "" "If you use exclusive input parameters combined with expressions, you need to " "be aware that the `inputs` JavaScript object will contain one of the " @@ -2822,21 +2469,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb -#: 4d8f38679952486095a77692387db2d3 +#: ../../src/topics/inputs.md:262 9db9f784a5cd4ca5b90691d1e2e827ea msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from an " "enum." msgstr "" -#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 -#: 47ec49759e274e59834192b794ec2d9b +#: ../../src/topics/inputs.md:265 09b1db3cc6c845058cf0ad4c24d71733 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 -#: 0657044c742348fe9e63f662692570a1 +#: ../../src/topics/inputs.md:271 84aa6e0c479f4528836691005129056e msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you provide a " @@ -2844,16 +2488,14 @@ msgid "" "should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 -#: 30c21cafda144f848bfe79d8e232296e +#: ../../src/topics/inputs.md:280 76611ebb19764bdc8a1f6eacfb76138f msgid "" "However, if you do not provide any input value, then `file_format` will be " "evaluated to a `null` value, which does not match the expected type for the " "output field (a `string`), resulting in failure when running your workflow." msgstr "" -#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 -#: 1cc8ea6abb684470b7790808acea2be1 +#: ../../src/topics/inputs.md:289 bf9750d215be4294b1cf1e0490a0796a msgid "" "To correct it, you must remember to use an or operator in your JavaScript " "expression when using exclusive parameters, or any parameter that allows " @@ -2863,12 +2505,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 c3b84742343449f9b3866285d98b53bb +#: 612f9efa0ed04559a174c37958def6f7 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 0a1b08fe707c41089ad3d4895960ba17 +#: 57eb990c11f044dfb60c012a92a30eb1 msgid "" "Implementation extensions not required for correct execution (for example, " "fields related to GUI presentation) and metadata about the tool or workflow " @@ -2883,7 +2525,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b 5bc4ef6584c74b948ffd5c0bddf8e569 +#: a6e6155cb8ff40fb9d8b1fff3e94fb02 msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to cite " @@ -2891,17 +2533,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 47ee25d60a4a4faa80476797954ec7a9 +#: 063c28fc9e654dfd91c66da164ac1d3d msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 195d4a8d5aad41159beffafd198d4640 +#: 8fcd2ae1ce8d4c7f951281ced81ab32d msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 b0c5946fbf79415aa74c8e72fa88cf85 +#: 639533652456427480fa311da7beb4f0 msgid "" "For those that are highly motivated, it is also possible to annotate your " "tool with a much larger amount of metadata. This example includes EDAM " @@ -2911,17 +2553,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e a98236fc1be745a69271855e1b5eecdb +#: 266808daf2004bbd9830045fbc67a541 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f -#: 5f0da8d7e06a47fda38053dbadcbec18 +#: ../../src/topics/operations.md:1 fd9b715bfa3243b19a919ad19843232d msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 -#: 23d41792b0524742878a6ab8f3ff0fe1 +#: ../../src/topics/operations.md:3 fb568063fa7a4cbe83c271772d3d62bc msgid "" "An Operation is a type of CWL process, just like a workflow, a command-line " "tool, or an expression tool. It is a step of a workflow that specifies " @@ -2929,66 +2569,56 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d -#: c0f723242f11464392dfc32f67a3b67b +#: ../../src/topics/operations.md:7 981486166754435cbcd8152e93679405 msgid "" "You can create operations to visualize a workflow during development, before " "you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf -#: c9f3a48a3a064cb3b1759effe724301d +#: ../../src/topics/operations.md:10 7b165718ffeb42e793c97fad807f216f msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 -#: fbad0b0144984ae78b84307ea68d0a03 +#: ../../src/topics/operations.md:16 5e31cddd14414d31b7bd0a6c2745d272 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like a " "command line tool or an expression. You can also plot it with the CWL Viewer " "or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 -#: 59e9ff3276454ff19eb351ff33737f12 +#: ../../src/topics/operations.md:24 02c372245dc9453ea0841026335e405b msgid "" "The output of the command above can be rendered with a Graphviz renderer. " "The following image is rendered with the Sphinx Graphviz directive (this " "user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 -#: ba74f2ab7f6d4c178f3c4c43c461afbd +#: ../../src/topics/operations.md:55 d331327285d1434e8c17187737345919 msgid "" "If you try running it with `cwltool`, the command will fail since `cwltool` " "does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb -#: 93c8b61a12134991ae9bb78223e2017e +#: ../../src/topics/operations.md:58 72705f8940bb4194bc5554fcc29eed49 msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f -#: cbbdba36dc3841f2b1d820f369a8c680 +#: ../../src/topics/operations.md:66 76b7c63107e94323859904415d07d31c msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A " "CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de -#: 4649c8d743f448ab94ee589a1b3a342a +#: ../../src/topics/outputs.md:1 ebf56d267612461799bf801136e61b69 msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d -#: 1a9d6e2e33244d01b820cf11fe2beaff +#: ../../src/topics/outputs.md:3 f9cff6b272a24ef6ada90e263c1b1784 msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 -#: 233c8865faac4d6c8ec7704e9a997719 +#: ../../src/topics/outputs.md:5 e482821911004cdd8c3ff1539c69368a msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name of " @@ -2996,8 +2626,7 @@ msgid "" "parameter." msgstr "" -#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 -#: 5aab1c0db3d5449cbb4a0f0dad615d87 +#: ../../src/topics/outputs.md:10 e11fcfe1e84b476ea879810b76ff2cb8 msgid "" "When a tool runs under CWL, the starting working directory is the designated " "output directory. The underlying tool or script must record its results in " @@ -3006,20 +2635,17 @@ msgid "" "from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 -#: 46b4eeb3ce8946dca0f8a94c399b4c96 +#: ../../src/topics/outputs.md:16 65c73a37f06a4782bf43f4acf4f1c77e msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 -#: 8d322609948a4d6e87d7962b3d29df2f +#: ../../src/topics/outputs.md:19 e172dde545164fefac826d910ddd399e msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c -#: 9fdcb55e965444ee8b5d74a2a9870d27 +#: ../../src/topics/outputs.md:21 225f4d04c28149898f06bd771f741358 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -3027,85 +2653,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f -#: e4c490f599a0469a821aa8e74f4ef0ef +#: ../../src/topics/outputs.md:26 14e9e446768a454ea786b3256b49632e msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a -#: b8ed6ebe6928455cb094ea430e21e5d4 +#: ../../src/topics/outputs.md:32 4bd659cee1904868a7c33345f94f1300 msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 -#: 3e65c52d218946fc83b8c3e6adcb21fe +#: ../../src/topics/outputs.md:38 8803a28ccff846eea7d06f4bd908c763 msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb -#: 03751b45cdf647b689a3a69156989db5 +#: ../../src/topics/outputs.md:45 661b62e554d64e449c69e475e5188f99 msgid "" "And now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d -#: 1b6f59623f5d4cd984426da21b8438bf +#: ../../src/topics/outputs.md:51 44cdca5b777441baa246c87940df7264 msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 -#: 095902cca30944d19a0d5f17f582e3b0 +#: ../../src/topics/outputs.md:62 edb34af3b22d418d9a6178c0ecbb8b80 msgid "" "The `glob` field consists of the name of a file in the output directory. If " "you don't know name of the file in advance, you can use a wildcard pattern " "like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 -#: 6d95fbfa321144a9932f26ab5f9ddc74 +#: ../../src/topics/outputs.md:65 10e68fad866f4187981f0b365b957b03 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 -#: 8be7ef160e8b421a89124a639dc7fd84 +#: ../../src/topics/outputs.md:67 77e1261484964ba9ac67d9fc9139a1d6 msgid "" "To capture a tool's standard output stream, add the `stdout` field with the " "name of the file where the output stream should go. Then add `type: stdout` " "on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 -#: fcf4490c351d4cd6a208345308168ef7 +#: ../../src/topics/outputs.md:71 c66bd08354d54ccb9e3e1da89634a816 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 -#: 00f1bb92a38b4f3a8c0065ac75530689 +#: ../../src/topics/outputs.md:89 7d4056355da1451dbed6733fba8c3c38 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d -#: 1477d0fc5c4c4f82bcc1c8e6ba8eed4d +#: ../../src/topics/outputs.md:91 8fed80f9633a4e87a67c651dc3160ce6 msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 -#: dee904cb678d4eb49dc829d6590b267a +#: ../../src/topics/outputs.md:93 6cba36e037d54f93add05fb16d2359bd msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae -#: a21c1fd3194a49ae992a743023653dc5 +#: ../../src/topics/outputs.md:99 08862892ecf849a1ba2f25ecc9e98227 msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 -#: e72c526da47a455da4b10e33938d1600 +#: ../../src/topics/outputs.md:112 c5dcc68bb28041b3b96ac1af716b0db8 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -3113,13 +2725,11 @@ msgid "" "mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 -#: 6447f4b8bb5f4f93bd8ec2c7b1fb09cb +#: ../../src/topics/parameter-references.md:1 53b95fd10d61462daf153d45e5517dad msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 -#: 1faea30495a440a68dbd1647dacc404c +#: ../../src/topics/parameter-references.md:3 0702e71de81e493dac08a91d667569e3 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file we " @@ -3132,47 +2742,40 @@ msgid "" "specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 -#: 0c0a3f58a93f492dbfca14523809aacc +#: ../../src/topics/parameter-references.md:13 a1703da32ad64fd2b8bdd423605b50bd msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 -#: 460842f202db493dbb901be73a02797f +#: ../../src/topics/parameter-references.md:19 2f32531e47b4465594d41ddd218fb2fd msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 -#: 2591c2cf9e5f402281031ea8dd41a251 +#: ../../src/topics/parameter-references.md:25 501dd6f9dbb1438f9a59f6a025639f35 msgid "" "Create your input files and invoke `cwltool` with the tool description and " "the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 -#: b093abbff3614b2ba0141f07376a5220 +#: ../../src/topics/parameter-references.md:36 1bcdd99111bd4bc5b75a8297bb61d9bb msgid "" "Certain fields permit parameter references which are enclosed in `$(...)`. " "These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 -#: fda3718113354215bd2ac212553fb2d4 +#: ../../src/topics/parameter-references.md:47 32eae36c593e43a9a6b4e103a0c2028a msgid "" "References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" -"$(inputs['extractfile'])` are equivalent." +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 -#: 271e78089c274154a0233289d705e628 +#: ../../src/topics/parameter-references.md:51 1d785e8a450140a982142aa0fa906257 msgid "" "The value of the \"inputs\" variable is the input object provided when the " "CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 -#: 29ab4fa0876b4c11a0c7482cca56ed80 +#: ../../src/topics/parameter-references.md:54 e862bb8bc3e84e24a2aa5ec34298cfd5 msgid "" "Note that because `File` parameters are objects, to get the path to an input " "file you must reference the path field on a file object; to reference the " @@ -3180,112 +2783,101 @@ msgid "" "path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 -#: 78e1857c5bd54af1b7ca4728879e6219 +#: ../../src/topics/parameter-references.md:59 46ffaab11be040cea96a294d9a814738 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad -#: dae7873015254aa7874379164c90a8d0 +#: ../../src/topics/parameter-references.md:61 890d619c415741179c83ffcd56833fbe msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 -#: 7a45deb4682b49fd86d62fae41831db8 +#: ../../src/topics/parameter-references.md:63 373e1847d9f745d7a749928642c8e0e3 msgid "" "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 -#: 442f77a69b314cba8e8857470263c706 +#: ../../src/topics/parameter-references.md:69 90d3624e062c41c7a6d1a9824515d0df msgid "" "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 -#: d4455241f14549b791e59fc1f942c8cb +#: ../../src/topics/parameter-references.md:72 76d09490bd464b708c28991dbff0104e msgid "" "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f -#: ff4b1c05c5804ec7846043ae8814ad21 +#: ../../src/topics/parameter-references.md:74 f33c76e590dd4feaac1e3cf568069d33 msgid "" "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 -#: 119e026b595f49c090d62aa7b7c77de4 +#: ../../src/topics/parameter-references.md:77 74ed4a06c1984c58826ddceb1a45a4ea msgid "" "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 -#: 5449d9c5687544a3bfbf8b2b25640a83 +#: ../../src/topics/parameter-references.md:81 eba3362d34354daa89dc516722c6fbd0 msgid "" "From [InputParameter](http://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" "v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 -#: b3191a7bd03d4ff18802ae0f5d419676 +#: ../../src/topics/parameter-references.md:85 e924874af32d4be19c5e8446768226dd msgid "" "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." "html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 -#: ea9cfbbd4cbd4f26ba4b0cb50d58635b +#: ../../src/topics/parameter-references.md:89 b162113f364445af9ff1bfc8a6610e13 msgid "" "From [InputParameter](http://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." "org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c -#: 7d39ed2a3a724dc1a75e6b2cdf87d91d +#: ../../src/topics/parameter-references.md:92 aa721077e16948c3a5bb8ef5bd7aff04 msgid "" "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." "html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 a1306ee650344278ae39d6086b1ed7d9 +#: 2fad0c2bc2834350826b22c454d33cf0 msgid "" "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" "CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 21d76d22f3044460b925fee68ac74454 +#: 9e303aa89a9b4447b0dbdc5ac0a0eb9e msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 6b8a5c59217c4928874710ead1456622 +#: 7a4eb47c25a54d11a00eb73e9333ad1c msgid "" "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." "html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae a9f6d09055c24029a5f85c3a663c4202 +#: 8a957bc8e577476bb59647661b3c0990 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 d3948618f9274ad0a333722567efeea5 +#: 2b31f1dec3f5498e9e363a4f1f50dc8d msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb 44623c81141345a0b0080e719e1418ab +#: 5a5f84ecc2f449bf9f037dc9da0ac670 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -3295,14 +2887,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 6e80d82ed57b441b8292961ec3163213 +#: ee89f1526c1f4452b4e36ba67bb59747 msgid "" "In this example, the software requirement being described is InterProScan " "version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 fc61f369e720463f8a5cd6c751d1d5e6 +#: c76cec44f5424f6087df28aa33c521a2 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -3311,7 +2903,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 f20aadbfc13243498ad199376c314e72 +#: 072d7b3ce3284ed994ff0736b43bbb86 msgid "" "As well as a version number, a unique resource identifier (URI) for the tool " "is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " @@ -3326,13 +2918,11 @@ msgid "" "main tool citation and the URL to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 -#: e66956313b8f4f02bb96cfb256e2a7d4 +#: ../../src/topics/staging-input-files.md:1 395d611104604a28b78e11b112a95027 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 -#: f18c5a8fcbe84135a6e06cbf8008cd63 +#: ../../src/topics/staging-input-files.md:3 811b4db0b1794fa89dc870f6cb59a3cd msgid "" "Normally, input files are located in a read-only directory separate from the " "output directory. This causes problems if the underlying tool expects to " @@ -3342,31 +2932,26 @@ msgid "" "base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 -#: 87fe14c9a0594602aa56a7706e089458 +#: ../../src/topics/staging-input-files.md:9 7159b5c5023c47128057c4116cce69f4 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 -#: 6e10063f55b747e1b07d6109ab7b046b +#: ../../src/topics/troubleshooting.md:1 3bfa6791d78f43629de90345f4441ebb msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 -#: e8831832b32449f4a8a3dde3c1b479cd +#: ../../src/topics/troubleshooting.md:3 9a6bd5b684a740ed9e8993d9f8607774 msgid "" "In this section you will find ways to troubleshoot when you have problems " "executing CWL. We focus on `cwltool` here but some of these techniques may " "apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da -#: 9c86467137864626a2079cb6cecb71c0 +#: ../../src/topics/troubleshooting.md:6 6db8a02139644598894220d538c590b9 msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 -#: 24b66a3e2e464ec6a85b5dfbaad1cbf4 +#: ../../src/topics/troubleshooting.md:8 f0da0f6283d44bcc95224eb9fe2d1764 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor output " @@ -3375,8 +2960,7 @@ msgid "" "directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b -#: 6d28f1cd40c045f384313c4d74073ed2 +#: ../../src/topics/troubleshooting.md:14 e2fc28b44ffe4254892a7c7973dc80c4 msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " @@ -3385,20 +2969,17 @@ msgid "" "of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b -#: 5235ff0c35c54396aceb799a65f6158e +#: ../../src/topics/troubleshooting.md:20 505c7cf9ee9c4af1aeed29002eed1b33 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f -#: fc49344510594559b4f888bc45093b51 +#: ../../src/topics/troubleshooting.md:27 4c31fd11a28943538690d04baa2b5dd0 msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " "(`cwltool` will create the directory for you if it does not exist already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac -#: 6e62be8d7d1344e8917904278b508518 +#: ../../src/topics/troubleshooting.md:35 a8532ac700014db4bd8ef690a27fb844 msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -3406,8 +2987,7 @@ msgid "" "can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 -#: c91b3a2818b143f58bd37da63479c560 +#: ../../src/topics/troubleshooting.md:44 94a6148512b24b90b87fd1312a926d75 msgid "" "Each workflow step has received a unique ID (the long value that looks like " "a hash). The `${HASH}.status` files display the status of each step executed " @@ -3415,8 +2995,7 @@ msgid "" "output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 -#: 86f283bc522c4be2adfac16256f01b0e +#: ../../src/topics/troubleshooting.md:48 ec4165b7c25c449db6a8804161805e80 msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " "the `step_b`). After fixing the typo, when you execute `cwltool` with the " @@ -3426,8 +3005,7 @@ msgid "" "now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 -#: 5362aa1d28344968953ab9cb389ccd8e +#: ../../src/topics/troubleshooting.md:59 5c0b71a6376848d4aa491854ea2d185d msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had " "been cached, and there was no change in its execution or output. " @@ -3437,18 +3015,15 @@ msgid "" "re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 -#: 4bb1aafde4f745a083d3a276497523dc +#: ../../src/topics/using-containers.md:1 95b832552e8443ea9c652f8c95afc01e msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 -#: b00987baf6974ff9b7e3b8cdfd7abd9a +#: ../../src/topics/using-containers.md:3 561fc9c561bc492ea82c17784dfd439c msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 -#: 9ac51c5a2a0a45859e14d9e388edd5f0 +#: ../../src/topics/using-containers.md:5 2420b16855cf4b25af5bcb87413f6dd9 msgid "" "[Docker][docker] containers simplify software installation by providing a " "complete known-good runtime for software and its dependencies. However, " @@ -3461,40 +3036,34 @@ msgid "" "containers." msgstr "" -#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 -#: 5494ccdb1a354b2386c82bd9a6f0b6a9 +#: ../../src/topics/using-containers.md:15 f5266ee2c2b34170bc89cb501b869893 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the container." msgstr "" -#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a -#: 4cfa8fc2bb224883946d5f63b372de82 +#: ../../src/topics/using-containers.md:18 728166bf41504e1d89b755400742a1b4 msgid "" "This example runs a simple Node.js script inside a Docker container which " "will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 -#: e16c1922527a46e28bb5d933614cdaf7 +#: ../../src/topics/using-containers.md:21 104351ac29d247cb8e017228e2c9b3d8 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 -#: 7498a71704be462abef71c42e6b83d1b +#: ../../src/topics/using-containers.md:27 e11a38bfb30b404c99d223647960cb16 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed -#: ac0689bff9db46ea8bff8cd35cde86f3 +#: ../../src/topics/using-containers.md:33 7ed0bd21e998417cb02fdcb8e44734b6 msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that is " "really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 -#: c4b7da5575674ca3ae734424022ef090 +#: ../../src/topics/using-containers.md:44 9dcddf6812ba4bc2a7d6c5fcdb978a68 msgid "" "`baseCommand: node` tells CWL that we will be running this command using the " "Node Js runtime that is meant for Javascript files. We then need to specify " @@ -3507,27 +3076,23 @@ msgid "" "called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 -#: d24fcecc17d0461cbd8689067f770c0d +#: ../../src/topics/using-containers.md:52 bc1a09475f154562a4db445bf81ac92f msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " "the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 -#: 833d4d3b3f0e4c7cb8b1d35cb9a78a7e +#: ../../src/topics/using-containers.md:55 2e117019ace84604a8ed5a31214c2587 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 -#: 50fc0573276e4dd4a47208ed81109991 +#: ../../src/topics/using-containers.md:69 d0d5b2a1a008411e92859a72101088c1 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 -#: f72e10e746604421904057ddf7078d3e +#: ../../src/topics/using-containers.md:72 591d1cd0282b4095a267b44da7d59804 msgid "" "In this example, the path to the script `hello.js` is `/home/me/cwl/" "user_guide/hello.js` outside the container but `/var/lib/cwl/" @@ -3535,51 +3100,43 @@ msgid "" "invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 -#: ee126833f6014e378c7841c4048dae85 +#: ../../src/topics/workflows.md:1 9f989fff165448ecbcaad6adc0f58d6b msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 -#: 0325bd610aa747b0b657afa0c978a1eb +#: ../../src/topics/workflows.md:3 212c82dca23645e89d8b5bb7599f2d25 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 -#: 7c901105cf6949909d87be5681331368 +#: ../../src/topics/workflows.md:13 7530029ec04746f2a888dcbc10aa5ce4 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 -#: 74138d0c2ded4311bf688df4a28387b5 +#: ../../src/topics/workflows.md:41 c1f1d644b37b4f018b87e15249d8758d msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier examples." msgstr "" -#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 -#: 1ec4773e7319414b997d746d1965ff56 +#: ../../src/topics/workflows.md:51 2d07232b7d9c415b8ad971e8cbcd9577 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb -#: 5f860dd70e3b435188c61a538e5de0ef +#: ../../src/topics/workflows.md:81 fa1f770ffeba4b74bcb200cd3949e070 msgid "" "A command-line tool or expression tool can also be written directly in the " "same CWL document as the workflow. For example, we can rewrite the `echo-" "uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa -#: a9c56df6dca441dfabda7fa54fbe56c6 +#: ../../src/topics/workflows.md:91 570020792e824c2ba732bcc2c0134aa1 msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a -#: 586d561ddf724319b3da9ae857828648 +#: ../../src/topics/workflows.md:150 8a50c511004941d0917a8f0d471467f0 msgid "" "Having separate files helps with modularity and code organization. But it " "can be helpful writing everything in a single file for development. There " @@ -3587,39 +3144,33 @@ msgid "" "pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe -#: f3e80b1903534065a30323611c267e9b +#: ../../src/topics/workflows.md:160 4d2bf0341836405d9729c47d8020faea msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this " "user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 -#: 6ed53c6f9fb94d4ab3d10532c605c46b +#: ../../src/topics/workflows.md:165 dd6fc85f74984517b284853a0d46c122 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c -#: 3fcfdf43b0a049388634625c45e0b1bb +#: ../../src/topics/workflows.md:167 f857d80cd5d84622a560c895ab260a92 msgid "" "This workflow extracts a java source file from a tar file and then compiles " "it." msgstr "" -#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 -#: 49415efafae64f94b66cb46ca2bbd40a +#: ../../src/topics/workflows.md:170 02e7e81cdf7e4226973f910cd57b8ccf msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 -#: 4806a2ef982944e8b073fafd416d3d74 d45701eeaa6e42feb4ef79d2fc4af756 +#: 3a88d92f41aa4daaad4f4cc6829184b3 646367f222ea41e5987561941d17c4f9 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 -#: 155cd684ff304258ae374b2e13090e5f +#: ../../src/topics/workflows.md:180 aaba75eb272245db82d072fed97b311c msgid "" "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" "github.com/common-workflow-language/user_guide/blob/" @@ -3629,39 +3180,33 @@ msgid "" "_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 -#: d8bdb44011274f94b606277799a6fa6f +#: ../../src/topics/workflows.md:183 f8a6e1af5f0349a5a384be0629c37ac8 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a " "run:" msgstr "" -#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda -#: 9e1d9bc2f83743ea9964ec418d225200 +#: ../../src/topics/workflows.md:185 c4f854c7a279404da3688bdf424c7c5e msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 -#: a1240eab3ef746cf82a2c5451042b888 +#: ../../src/topics/workflows.md:191 d383ce45139944cb85768627965d9467 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 -#: a73cdc43a8e44973808027c29903afa3 +#: ../../src/topics/workflows.md:205 84293afa7a6c40f2af0b980c89581fc7 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde -#: 4277837a9fd443378d5ca3d9252993c9 +#: ../../src/topics/workflows.md:212 e66daf8af53849109936c36ca7d2b2c9 msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a workflow." msgstr "" -#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 -#: 09b714af60ee4ecc8ab1b95eac8284dd +#: ../../src/topics/workflows.md:221 8fbfbb587b264dcf98a3cea16dd36ef3 msgid "" "The `inputs` section describes the inputs of the workflow. This is a list " "of input parameters where each parameter consists of an identifier and a " @@ -3669,8 +3214,7 @@ msgid "" "workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 -#: 3e99a3be9265463daf74b00a21d89cff +#: ../../src/topics/workflows.md:233 5cdbc4771ea841b4960362b930de2af6 msgid "" "The `outputs` section describes the outputs of the workflow. This is a list " "of output parameters where each parameter consists of an identifier and a " @@ -3678,8 +3222,7 @@ msgid "" "the `compile` step to the workflow output parameter `compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 -#: 1c4a959d43b74686ab801a26ef412b3d +#: ../../src/topics/workflows.md:248 2e8a41fe43984dc6b4cf430e1ff66b28 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second step " @@ -3690,8 +3233,7 @@ msgid "" "parallel." msgstr "" -#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 -#: 55daf180336d4045ac0cc4c14af98cfc +#: ../../src/topics/workflows.md:256 78c20aa5a5724da6a4c908849c571334 msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input " @@ -3699,8 +3241,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 -#: 5ae40eb04d5440d5ba882a74aa5b9708 +#: ../../src/topics/workflows.md:261 1606a2f059eb4b0c9e90f2f0cbbe779b msgid "" "The ``in`` section of the workflow step connects these two input parameters " "to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " @@ -3709,15 +3250,13 @@ msgid "" "parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea -#: f93e9b776a4544018877b7a13399609b +#: ../../src/topics/workflows.md:267 b456b11e2760479bbf81a773a3e1f8ee msgid "" "The `out` section of the workflow step lists the output parameters that are " "expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed -#: 0e587435e3884334bc51a4abf4b4d785 +#: ../../src/topics/workflows.md:278 0fa01fcec32049c989ad1d68841c74de msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3727,13 +3266,11 @@ msgid "" "section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 -#: 81b98764289245c79f18fcff478f4a9b +#: ../../src/topics/workflows.md:285 2bc9829f95584a269eb577c610b2a80c msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e -#: 9baddec4015f40ad82ea2dee30305654 +#: ../../src/topics/workflows.md:287 0e5e6445bfcb42a4bd03612316dd7225 msgid "" "Workflows are ways to combine multiple tools to perform a larger operations. " "We can also think of a workflow as being a tool itself; a CWL workflow can " @@ -3741,20 +3278,17 @@ msgid "" "the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 -#: 986c3dd9460b42b3b20e2d01ba1fbe51 +#: ../../src/topics/workflows.md:297 0b83c1028b0e43ba972609e4302bc8a2 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 -#: 4558f174fea445fd97b80d963fc74f43 +#: ../../src/topics/workflows.md:300 cbe1ef068b0c417b953655e132333447 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 -#: 532823a13154401090e9fee3e018fda9 +#: ../../src/topics/workflows.md:309 a691c36a15044b11a6d037d16f818a6d msgid "" "This two-step workflow starts with the `create-tar` step which is connected " "to the `compile` step in orange; `compile` is another workflow, diagrammed " @@ -3762,23 +3296,21 @@ msgid "" "supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a -#: 7b6f46b70bac4f848a956ea160243621 +#: ../../src/topics/workflows.md:314 2e9797fcd4f04f56b5d2b2f1a3e306d5 msgid "" " \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/nestedworkflows." +"cwl\">\"Visualization \"Visualization" msgstr "" -#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 -#: 3861b4a31f71471b97bf9dc18cc80594 +#: ../../src/topics/workflows.md:322 28f4139911b44eeeb7afd31e9f7cae7b msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " "CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3786,8 +3318,7 @@ msgid "" "to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 -#: a10c37f65ac14ef2a5971872bc9b8f9a +#: ../../src/topics/workflows.md:336 4a6cb397a20241beab24d956920a8379 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and `*.java` " @@ -3796,8 +3327,7 @@ msgid "" "workflow." msgstr "" -#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be -#: 34175f932716406f836840732618caee +#: ../../src/topics/workflows.md:341 dccb5472a5dc42b7946dd9245a71ecf0 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar " @@ -3806,8 +3336,7 @@ msgid "" "specific input/output names, as those also appear in its usage as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 -#: 0d132dc39cdf4818bc8e20132073f669 +#: ../../src/topics/workflows.md:347 de1e18b69f654cabb75e52b47058030a msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3815,16 +3344,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 -#: 9f8c45f077974cf79612ee83df3d152b +#: ../../src/topics/workflows.md:366 b947e62f4b3b4c10b95737f1839bcc5a msgid "" "In this case our step can assume `Hello.java` rather than be parameterized, " "so we can use hardcoded values `hello.tar` and `Hello.java` in a " "`baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 -#: 435f80d0599b4d93ae1339e8c7bc020a +#: ../../src/topics/workflows.md:383 2ed0258a3a104ed5ba3b6b95ad998839 msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This is " @@ -3833,8 +3360,7 @@ msgid "" "filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 -#: d39b024a1a8d4eae8d7fd3c929a782e9 +#: ../../src/topics/workflows.md:389 6584c0995288450b8a01c35fa231afb6 msgid "" "In this example we had to prepare a tar file outside, but only because our " "inner workflow was designed to take that as an input. A better refactoring " @@ -3842,8 +3368,7 @@ msgid "" "which would simplify its usage as a tool step in other workflows." msgstr "" -#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 -#: 3cbbe074843d4306b762d2fbc6fe9850 +#: ../../src/topics/workflows.md:394 19237513fd134c33801a7af08f74e70c msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL " @@ -3851,13 +3376,11 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 -#: 7118b6e09b9f44129c7d98d90570f2c2 +#: ../../src/topics/workflows.md:398 b66e0d0a36994b3182a3784bda8ffc19 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 -#: 70f3e73ee3714f22ad6ee43dd5ece703 +#: ../../src/topics/workflows.md:400 3bfb9851302248568bb4535ddc87a27f msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish to " @@ -3868,8 +3391,7 @@ msgid "" "different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 -#: 279495257ead4a4fa725c7d68c504162 +#: ../../src/topics/workflows.md:411 78a5a600f8cc49ce8055c77a596ad833 msgid "" "The most common reason a new user might want to use scatter is to perform " "the same analysis on different samples. Let's start with a simple workflow " @@ -3877,27 +3399,23 @@ msgid "" "strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd -#: 86d1d742bb5c4a9898aa573ce648f0ec +#: ../../src/topics/workflows.md:415 f9618882e0a14a0b84ff9751346dc291 msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 -#: f4987847f46e4a2db54127ec7ebcadf7 +#: ../../src/topics/workflows.md:421 4fe03daddd304a9b828fdd1c29f0d072 msgid "" "Aside from the `requirements` section including `ScatterFeatureRequirement`, " "what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c -#: 80e7c22dfe4d40749f2e9c3bf02bf8bc +#: ../../src/topics/workflows.md:429 7ab022708a9642ab8aa2e79ea7810381 msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f -#: e930bb5d430a41d9b5bf49e473dd2ed1 +#: ../../src/topics/workflows.md:441 fe144641fc8040b283f15b2b99ecb5a2 msgid "" "Here we've added a new field to the step `echo` called `scatter`. This field " "tells the runner that we'd like to scatter over this input for this " @@ -3905,8 +3423,7 @@ msgid "" "the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d -#: 4076e9eb67ed4bd5942f089e394bad26 +#: ../../src/topics/workflows.md:445 f13d1b071a7f4a75a4cdee40ecef14fa msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if you " @@ -3914,70 +3431,59 @@ msgid "" "to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 -#: 1b44092e87b840de8f1d022676d0990d +#: ../../src/topics/workflows.md:450 b0b2e63d2b8a4fd0983e976c16440da4 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be -#: a8afac626f5d4240a57267085b9bef26 +#: ../../src/topics/workflows.md:452 47ac993a90fe46ca92e97d6b67b3276b msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 -#: 0896efc674bc402495c6e73c6c352523 +#: ../../src/topics/workflows.md:458 f5b8681b3c3b4890a86d7b9fb812d958 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " "calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f -#: 91a53d918d4b47bdbe0b0a6d4adfc0dc +#: ../../src/topics/workflows.md:466 74e70fec6d2447bbbd2a5bc8af1fa58c msgid "" "You can see that the workflow calls echo multiple times on each element of " "our `message_array`. Ok, so how about if we want to scatter over two steps " "in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 -#: 8325682d51d8421b9ea507f424f71e73 +#: ../../src/topics/workflows.md:469 76fed9e7ad1d4792b7bb364bb684eeb2 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding the " "following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de -#: 503d068602d8477a820b91d835fa3f28 +#: ../../src/topics/workflows.md:472 bef387d9be1f4ca19a97023cfdd1c910 msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 -#: 4e768b91eb274a5cb157f1e3fe2f85cd +#: ../../src/topics/workflows.md:480 eea1be83da574f39914566d835701b4a msgid "" "And add a second step that uses `wc` to count the characters in each file. " "See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a -#: 18ec5231b7bf4c9ea59361b325fcdd01 +#: ../../src/topics/workflows.md:483 2043f12eb2ce4424b133e0dc0b62aafc msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b -#: 87fd118dc2774cf08db0a3ba56520da5 +#: ../../src/topics/workflows.md:489 87ba95507fc44dbca4cb6c5283ce50f9 msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under each " "step:" msgstr "" -#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d -#: 8168ffcb23124b3f839a9862a7ec0958 +#: ../../src/topics/workflows.md:491 e6e1a79638d74547b00c64e3c8b05710 msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 -#: 37c222ea14904fd4a8fa93a1e0103239 +#: ../../src/topics/workflows.md:497 03fb16e74bf14c49b43e35ef6cb45030 msgid "" "Here we have placed the scatter field under each step. This is fine for this " "example since it runs quickly, but if you're running many samples for a more " @@ -3994,8 +3500,7 @@ msgid "" "welt!`. You can see how this might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df -#: d392813fc6d14851a294a391426d41f6 +#: ../../src/topics/workflows.md:509 eca3380c60094df2b91b44b5f7718fae msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can " @@ -4003,45 +3508,38 @@ msgid "" "step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b -#: 652155460eaa42b6856c16cffdb845c0 +#: ../../src/topics/workflows.md:513 6c61733fe4284f51a6b46e89cafe78c4 msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb -#: 6313cb377dc249e0b2262a3fe732fe32 +#: ../../src/topics/workflows.md:519 0585f83162c349969391c9456a884f28 msgid "" "Now the scatter acts on a single step, but that step consists of two steps " "so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 -#: 11f73cf24fb044e3a3afb3adb6137708 +#: ../../src/topics/workflows.md:522 f209343966db4d46b4611d3620c3b496 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 -#: def9e62bf73f49eebce09677954e2a92 +#: ../../src/topics/workflows.md:524 5a2661ce35dc4d79a15da1e17c0a95ec msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 -#: 200dfe47d09d4b0b9e4acf29b7e038da +#: ../../src/topics/workflows.md:527 8f7ee09c9d6b491195e2d80315dae398 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 -#: 858bda7fb6524e9dbfb35596ce6a6d07 +#: ../../src/topics/workflows.md:566 966acff0d3d24104ae9673df8a790fb1 msgid "" "The first thing you'll notice is that this workflow is only compatible for " "version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 -#: 28897819504247a3a6cf9a9d9476b63b +#: ../../src/topics/workflows.md:573 d60e1df759654f1b873276cf0296f234 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when` is " @@ -4049,8 +3547,7 @@ msgid "" "from the workflow contains a value `< 1` this step will be executed." msgstr "" -#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 -#: 4f8fd11e29b048e1851299002c3a48c4 +#: ../../src/topics/workflows.md:587 69aa8d3c9d9a4fe4a62875827648d95f msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " "will pass the first conditional step and will therefore be executed and is " @@ -4058,75 +3555,62 @@ msgid "" "skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec -#: ed33196347d949eda752a081c7af4657 +#: ../../src/topics/workflows.md:607 fee34c880e964e08b040adf2d3831803 msgid "" "When a value of 3 is given the first conditional step will not be executed " "but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 -#: 738c67568dbb4f2bbb5756fc5e727c01 +#: ../../src/topics/workflows.md:627 cb9e82cf4b484ca7be19612b14fbdf33 msgid "" "If no conditions are met for example when using `--val 2` the workflow will " "raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e -#: 19b016a1fec14056a9812c1c195c7c90 +#: ../../src/topics/yaml-guide.md:1 8e7c3365f0f94038930f71666f05170f msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c -#: a513367d60a74f559339c05d8ef10eb7 +#: ../../src/topics/yaml-guide.md:6 cbe6f35c21044054a010767f2f0cae46 msgid "" "[YAML][yaml] is a file format designed to be readable by both computers and " "humans. This guide introduces the features of YAML that are relevant when " "writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 -#: 5e30680941164047a47f98417e916188 +#: ../../src/topics/yaml-guide.md:13 2cc21093311548cd837aa7b3f0939093 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea -#: ca02f2bf1d754d5190f296674245b936 +#: ../../src/topics/yaml-guide.md:16 6e7ea76e8aeb477cbb8197efed33e53d msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee -#: 466615194bb541fdbe2e6515b50531b3 +#: ../../src/topics/yaml-guide.md:18 482e121a6e74428dbe6ad1f772f14684 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a -#: 33e664d59a30407891336db290a8a5b2 +#: ../../src/topics/yaml-guide.md:19 179290eee12343dd9aa4d49207cf7c68 msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c -#: 3e52ab079dcf4fc6a3f052a517f4d31b +#: ../../src/topics/yaml-guide.md:20 7880db40e98e4aaabdc96def3d9f515d msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc -#: abcad6b7d37a4342a90c2d5952ea1232 +#: ../../src/topics/yaml-guide.md:21 75f3b499494b445f9f9a532d178cbc10 msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 -#: 500a489e4fae4d1abaa8883f632d1a24 +#: ../../src/topics/yaml-guide.md:22 2b900b2779c84de5bbd3c933c56e5922 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 -#: 546c1ef51a63487c91c98059dd46b0cb +#: ../../src/topics/yaml-guide.md:24 189db6d0e54a400eb5615e259354827e msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 -#: 72b4262833054edd9efe6078381de654 +#: ../../src/topics/yaml-guide.md:26 e689c0e1dcd645348ceed51e91eb9ad0 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the `:` " @@ -4136,8 +3620,7 @@ msgid "" "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b -#: 7b7e8242660744b791ba3868e4ed7e37 +#: ../../src/topics/yaml-guide.md:42 9532ac8e1dda479e890bf970323a0a32 msgid "" "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " "and `home` - with their four respective values. Values can be character " @@ -4145,8 +3628,7 @@ msgid "" "Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 -#: 492d994a541c4c948fb5da9041153bcf +#: ../../src/topics/yaml-guide.md:51 91a057a7d10f438fad10338dd44c013c msgid "" "Values may be wrapped in quotation marks, but be aware that this may change " "the way that they are interpreted i.e. `\"1234\"` will be treated as a " @@ -4157,33 +3639,28 @@ msgid "" "numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 -#: e2209269db394f3988f18b147a57677c +#: ../../src/topics/yaml-guide.md:61 d18c1f5ef55d4bb6b8334438fcbc96b8 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 -#: e15c39c65aca47f690264d8008463bec +#: ../../src/topics/yaml-guide.md:63 dc6869049fc143b4af91d172a419a125 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program interpreting " "the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d -#: afa546fcb7fb447d939d4a167f206f79 +#: ../../src/topics/yaml-guide.md:76 c3c7f5ecfedb4884ad5e91bb79ba2a7c msgid "" "If there is anything on the line before the comment, be sure to add at least " "one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf -#: 7dd375e0fd964413af4957396d2a0474 +#: ../../src/topics/yaml-guide.md:79 84f16419237a4789ac0f3c682b3a11ee msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 -#: af8ef039a64a4c0783d7229dbdac65ef +#: ../../src/topics/yaml-guide.md:81 269ca8e05ce14e899fc8b2a00b1e458e msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, these " @@ -4194,8 +3671,7 @@ msgid "" "are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 -#: 3ce968cb39a443059f6a828b3c8c2f33 +#: ../../src/topics/yaml-guide.md:104 ce790af50da540eb9108ad89eae037cf msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -4207,13 +3683,11 @@ msgid "" "graphical representation of the `inputs` object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 -#: 3c2f48a8e616400b9a8ffb4b6f7efc9b +#: ../../src/topics/yaml-guide.md:127 c3c9ef616b5d472a894ad6330267bcd2 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 -#: c432b1656e0e49ef87aa3d6e42acad84 +#: ../../src/topics/yaml-guide.md:129 b8a7360f6e0640aa9a2c4907c1ba3fe8 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) section " @@ -4223,30 +3697,25 @@ msgid "" "where each value is defined on its own line and preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 -#: cac5e52767f74ce98693e2a19ee1eb0d +#: ../../src/topics/yaml-guide.md:146 363da878600a4d229efe0ba79835d73c msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d -#: 101666907f8b4fb994e25ceffcf04a13 +#: ../../src/topics/yaml-guide.md:167 209dfb0d0a1148ed962dbb33890a3160 msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d -#: 5461960a469042a487b89e440f856aea +#: ../../src/topics/yaml-guide.md:169 cd3a174dae334d0d977a3234e258bd25 msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " "can also be defined in YAML using the native JSON syntax. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc -#: e31349c164c84a9da46e2fb1861793df +#: ../../src/topics/yaml-guide.md:177 b0f0b10de8f54e1e951e480f696976f1 msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 -#: 49a0b3dfdc9e4d58b6bc966db979ace8 +#: ../../src/topics/yaml-guide.md:184 b5597e8984ad4e0bad33433c1dab89bd msgid "" "Native JSON can be useful in indicating where a field is intentionally left " "empty (such as `[]` for an empty array), as well as where it makes more " @@ -4256,130 +3725,50 @@ msgid "" "file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d -#: e08ec8c473e847f98e8a18b9ca0f2670 +#: ../../src/topics/yaml-guide.md:194 5ad7d551d3d347a097508a8488f9d15c msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 -#: 6ee7bfb4a9e04dd19b5180bca5b02705 +#: ../../src/topics/yaml-guide.md:196 58f80e6944f9402a810b9b02ba3ad917 msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " "while we wrote this guide, though it also covers features that are not valid " "in CWL." msgstr "" -#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 -#: 42614ab7ba1546f89abeb8f48991271c +#: ../../src/tutorials.md:1 8fdcc745f4684fa7816c62782507438e msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 -#: b8df5b8393ed4d869c066640fe83ec7b +#: ../../src/tutorials.md:5 3c933ac074ee4d94b7aeacb7abeaf388 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to the " "list." msgstr "" -#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c -#: 5b9aee5af41f438b9f4208294bf97f4a +#: ../../src/tutorials.md:7 1d6cdf13aa834cb4a682553227d9f725 msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 -#: a71d3022dcfc44979cca4655ea51ad42 +#: ../../src/tutorials.md:9 606cc939c5014e2abdab163e4d726f1b msgid "" "[Introduction to Workflows with Common Workflow Language: For Contributors.]" "(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f -#: 42b5a982e86f46dfbfcd7bfcc99d72a5 +#: ../../src/tutorials.md:11 3505468d39c34a20bc55f431a3c697f7 msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f -#: 12dc402d053044b78d69927dd391fe9d +#: ../../src/tutorials.md:13 e5731a11b89e492d8d751100a46c5226 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f -#: 687c20e2e4bc4f869c7ee9390e61476a +#: ../../src/tutorials.md:15 cdfeabb88f6245d9a687197d242ed3f9 msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 -#: a975fbb3ea7d467881ce0245de538295 +#: ../../src/tutorials.md:17 997679b781a84add9b6d8b1900deec35 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" - -#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee -msgid "" -"All Common Workflow Language project instructional material and changes to " -"the structure are also made available under the `Creative Commons " -"Attribution license `_. The following is a human-readable " -"summary of (and not a substitute for) the `full legal text of the CC BY 4.0 " -"license `_." -msgstr "" -"Todo el material instructivo del proyecto Common Workflow Language y los " -"cambios en la estructura también están disponibles bajo la `licencia " -"Creative Commons Attribution `_. Lo que sigue es un resumen " -"legible por humanos (y no un sustituto) del `texto legal completo de la " -"licencia CC BY 4.0 `_." - -#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 -msgid "to **Share**—copy and redistribute the material in any medium or format" -msgstr "" -"**Compartir**—copiar y redistribuir el material en cualquier medio o formato" - -#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 -msgid "to **Adapt**—remix, transform, and build upon the material" -msgstr "**Adaptar**—remezclar, transformar y construir a partir del material" - -#: ../../LICENSE.rst:23 be38276e7b374f57b9997391bf898a62 -msgid "" -"**Attribution**—You must give appropriate credit (mentioning that your work " -"is derived from work that is Copyright © the Common Workflow Language " -"project, and, where practical, linking to https://www.commonwl.org/ ), " -"provide a `link to the license `_, and indicate if changes " -"were made. You may do so in any reasonable manner, but not in any way that " -"suggests the licensor endorses you or your use." -msgstr "" -"**Atribución**---Usted debe dar crédito de manera adecuada(mencionando que " -"su trabajo se deriva de un trabajo que tiene «Copyright © The Common " -"Workflow Language Project» y, cuando sea práctico, con un enlace a " -"https://www.commonwl.org/%20),%20brindar%20un%20%60enlace%20a%20la%20licencia%20%3Ccc-by-human_%3E%60" -"_, e indicar si se han realizado cambios. Puede hacerlo en cualquier forma " -"razonable, pero no de forma tal que sugiera que usted o su uso tienen el " -"apoyo de la licenciante." - -#: ../../LICENSE.rst:31 f00d5c3846034c2ea116c2f74786d9fc -msgid "" -"**No additional restrictions**—You may not apply legal terms or " -"technological measures that legally restrict others from doing anything the " -"license permits. With the understanding that:" -msgstr "" -"**No hay restricciones adicionales**---No puede aplicar términos legales ni " -"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " -"permitido por la licencia. Con el entendimiento de que:" - -#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the " -"`OSI`_-approved `Apache 2.0 license `_." -msgstr "" -"Excepto cuando se indique lo contrario, los programas de ejemplo y otro " -"software proporcionado por el proyecto Common Workflow Language están " -"disponibles bajo la `licencia Apache 2.0 `_ aprobada por la " -"`OSI`_." - -#: ../../LICENSE.rst:50 4ee4d68b90fe422880da856cd539b982 -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." -msgstr "" diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po index fd0da8d1..b49c961f 100644 --- a/locales/pt/LC_MESSAGES/user_guide.po +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -9,29 +9,27 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-24 17:23+0100\n" +"POT-Creation-Date: 2023-01-27 16:02+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" +"Language: pt\n" "Language-Team: Portuguese \n" -"Language: pt\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" +"Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=2; plural=n > 1;\n" -"X-Generator: Weblate 4.16-dev\n" +"Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 ../../LICENSE.rst:2 -#: 75de2be8809847b8bf1ccd42aa694a24 +#: ../../LICENSE.md:2 3eb955b4f3dd4c3188924b97ea6ab592 msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 ../../LICENSE.rst:5 -#: 2edd71801f6245ef821887a74f21b94c +#: ../../LICENSE.md:4 bf4480e7fff4460a87e8f43c11599f07 msgid "Instructional Material" msgstr "" -#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +#: ../../LICENSE.md:6 9e9eab12205d4e82b4fedca520370f4c msgid "" "All Common Workflow Language project instructional material and changes to " "the structure are also made available under the [Creative Commons " @@ -45,29 +43,26 @@ msgstr "" "humanos de (e não um substituto para) o [texto legal completo da licença CC " "BY 4.0][cc-by-legal]." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 ../../LICENSE.rst:12 -#: 90cc755d172e4c82b882b4ee620fe652 +#: ../../LICENSE.md:12 a8e98ad541c642e58e201afa625ec791 msgid "You are free:" msgstr "Você tem o direito de:" -#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +#: ../../LICENSE.md:14 b4cb4bc4261347fcb0d2c8a93995ab76 msgid "" "to **Share**---copy and redistribute the material in any medium or format" msgstr "" "**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " "formato" -#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +#: ../../LICENSE.md:15 d66dcbf95ccc41aaa53be523487ec913 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 ../../LICENSE.rst:18 -#: 430ff4de74924bc3a3b2c7e809ea4456 +#: ../../LICENSE.md:17 ca1c299a1b834b868bcdd4ca9f244696 msgid "for any purpose, even commercially." msgstr "para qualquer fim, mesmo que comercial." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e ../../LICENSE.rst:20 -#: 2173e2af49be41ee97a74c4e879faf25 +#: ../../LICENSE.md:19 6133f79f93be4991a6f5290f72d1a63d msgid "" "The licensor cannot revoke these freedoms as long as you follow the license " "terms:" @@ -75,7 +70,7 @@ msgstr "" "O licenciante não pode revogar estes direitos desde que você respeite os " "termos da licença:" -#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +#: ../../LICENSE.md:24 2d6ce81add1043629b676187f890288c msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " "work is derived from work that is Copyright © the Common Workflow Language " @@ -92,7 +87,7 @@ msgstr "" "mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " "uso." -#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +#: ../../LICENSE.md:32 f3f22597b6f845208a0cce3b3b2c8f5d msgid "" "**No additional restrictions**---You may not apply legal terms or " "technological measures that legally restrict others from doing anything the " @@ -102,8 +97,7 @@ msgstr "" "medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " "algo que a licença permita. Com o entendimento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 ../../LICENSE.rst:35 -#: f6aae4a5cd0547118c8a3240ca2b4be6 +#: ../../LICENSE.md:36 3cfedee64d4e46098a159cb2acdba4ef msgid "" "You do not have to comply with the license for elements of the material in " "the public domain or where your use is permitted by an applicable exception " @@ -113,8 +107,7 @@ msgstr "" "material que estejam no domínio público ou cuja utilização seja permitida " "por uma exceção ou limitação que seja aplicável." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 ../../LICENSE.rst:38 -#: a40c173be35b4c1b92e83f42bfe2382c +#: ../../LICENSE.md:39 c836a570faaf449d9716da5f75556627 msgid "" "No warranties are given. The license may not give you all of the permissions " "necessary for your intended use. For example, other rights such as " @@ -125,12 +118,11 @@ msgstr "" "direitos, tais como direitos de imagem, de privacidade ou direitos morais, " "podem limitar o uso do material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea ../../LICENSE.rst:44 -#: 3d7ca3f2cede4d5f998bf014bd970748 +#: ../../LICENSE.md:44 896f9966e5014e8a88b060be3063fe09 msgid "Software" msgstr "Software" -#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +#: ../../LICENSE.md:46 007f8613dc234c3fa8d5d92b18af0eb1 msgid "" "Except where otherwise noted, the example programs and other software " "provided by Common Workflow Language project are made available under the " @@ -140,7 +132,7 @@ msgstr "" "fornecido pelo projecto Common Workflow Language são disponibilizados sob a " "[licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." -#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +#: ../../LICENSE.md:51 227bc635a06f49dbb771fd9b62157d00 msgid "" "Unless required by applicable law or agreed to in writing, software " "distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " @@ -150,9 +142,8 @@ msgid "" msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 -#: eab02dc13915490bb3c9ba744d78b6a7 5ad4be9b62d54c95a913795b514676fd -#: bdd540403a5746ff99edf2dcad0e3122 dfc7702e073140c985cf47272a20214d +#: 1861131d3df648ae9e74ce1c87f0be7b a2ffa927deb2451d95ec63528e8078dd +#: d6055d3f15604ce6940770c7b561d4c5 msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece of " @@ -161,36 +152,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f -#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 +#: 38b062f219b34e08a46bd8f6525353ec 89e7e1dd05474344a1d929cb492e9caf msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 -#: 3060770b3bef41d7bcfcdfb413d7689c +#: ../../src/episodes.md:9 d3357ff3c8874e368aea0d6062ef6190 msgid "" "This page is out-of-date and was kept here to preserve the links of the old " "User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 -#: 48bb9f628b344ba1a3b67ae1cb264e3c +#: ../../src/faq.md:1 f2c4882e0e164c2b869e3eb969241061 msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 -#: 7e3684e9672643738846756e1ebafd18 +#: ../../src/faq.md:11 41099ab64e0544d894bd9e3af2718bda msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 -#: 187ceabb7fd9480bb8cf0f2da47f65ef +#: ../../src/faq.md:41 bb6aff70534148fa8a4b01140f7be150 msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 -#: b548b76bcc85420a9b30792386105139 +#: ../../src/faq.md:43 70ebc653b0d54d60a866edc0dbf56b57 msgid "" "This example demonstrates how to change the name of an input file as part of " "a tool description. This could be useful when you are taking files produced " @@ -198,139 +183,117 @@ msgid "" "names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f -#: 9ce692b78ead47e4b0f8cdae8837d35b +#: ../../src/faq.md:59 38b687f707d2438b85df08a445ab816f msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 -#: 6df1201c159343da9e7515379980d6a0 +#: ../../src/faq.md:61 d48422c020004ef084ca11e6229b5450 msgid "" "This example demonstrates how to change the name of an output file from the " "default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 -#: f9ab1d0dc1c842b6abb5385268c1d3bd +#: ../../src/faq.md:82 48765409ab9d48ccbcecceb46ddf2e91 msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 -#: 9f6a84ab6a9343b6ad7db826f8964362 +#: ../../src/faq.md:84 a59b8acd72124e2c95d1905ae494d928 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb -#: fa50e4fa990b42d1ba4c0f4ae1e5caa1 +#: ../../src/faq.md:86 f36088ba90d24f9f9c7c1bd59deb6f49 msgid "" "The first method involves adding the folder containing your scripts to the " "`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 -#: 3a871012fcfd4f3ebeca0cb86ec93435 +#: ../../src/faq.md:89 45ee965ee4a7494a8354b82208e2ab45 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 -#: d954edfff2584288ac8c600733070d2e +#: ../../src/faq.md:95 734cc1abe1c841ffac8d0895463d91fc msgid "" "After that, make the script executable with the command `chmod +x scriptname." "sh`" msgstr "" -#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 -#: af6b1e37d6be4450a761854480ec9aab +#: ../../src/faq.md:97 f01bc8c4d6134f0ea27dc7f5b39def24 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be -#: 31f4a2d43062493ca64c648f80afc8e9 +#: ../../src/faq.md:104 dd6fc2a04e3b476892f05bc5b746d0fa msgid "" "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 -#: 41c54e71b6cd4f63b2a619a515240d34 +#: ../../src/faq.md:113 e309eaad55144052866ce131eb80fd14 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 -#: 8edc3541ad134ab5a1d23c724f1f0a4e +#: ../../src/faq.md:115 f0d649a60a13404ebecd540789202b87 msgid "" "The second method involves including an input of `type: File` in the script " "itself:" msgstr "" -#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 -#: ac0ea81eba8842a18801ab03cbf80a57 +#: ../../src/faq.md:135 e2b782f88d494de398af0c9002a3ccdc msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 -#: 52be1a5640234feabe958ff7ade33653 +#: ../../src/faq.md:138 b4a033731fcd4322bd2bb71c609a4cb7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c -#: c6db734d5aef4f4f99676bdebf9c83c9 +#: ../../src/faq.md:140 43a64810b12b4c7d82a5803c3b910fe5 msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their input " "binding makes use of `self`. Below is an example workaround for this, " "pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 -#: a9f7b47c0dd741739795da39bf114879 +#: ../../src/faq.md:165 60f009e3714c405695da069204b196ea msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 -#: e3fdd9228b924905a4a1f4b2b7ad7159 +#: ../../src/faq.md:167 98916ed9355842e49bef073430e10675 msgid "" "Below is an example showing how to specify different strings to be added to " "a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c -#: 3f7cda1437cc48f18745a827ebb74582 +#: ../../src/faq.md:188 9b8f2d0b33db4bbc82aaf5836b6f7ed8 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d -#: 5aeaba2cae64442e816bbd458aee833a +#: ../../src/faq.md:190 a251693354d24bf0bda4938c8890090a msgid "" "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" "Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 -#: 5af827a402834978addd82c70be6b5ab +#: ../../src/faq.md:194 f46740ac0acb473583facb9f7528d03c msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 -#: 6d69e42bd8e443c4b19d80807c7efd6b +#: ../../src/faq.md:196 7de1f9e3175b4c2ab156192f28fd3535 msgid "" "The input must be an array consisting of exactly one entry for each input " "link. If \"merge_nested\" is specified with a single link, the value from " "the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 -#: 404640397b6e40c2a2cd5cf85ab3b1c0 +#: ../../src/faq.md:199 225c6f08068e41f58eb62f99dc06210f msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 -#: 1682c2486e224770b62269709a8663cf +#: ../../src/faq.md:201 4e741f4e3bc74e10bd9568826e81c478 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -339,61 +302,51 @@ msgid "" "destination step." msgstr "" -#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd -#: 9078fc009bc145808813c9cc2b734b58 +#: ../../src/faq.md:229 bfdb011cb81c4ef9b9e56b24f1e9ccd5 msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 -#: d4b5a54a400c409cb7984428f6a03ec8 +#: ../../src/faq.md:231 09f385e325f942afaa3dd195c16a18d2 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 -#: 9e8dbee6e8f84d08b1a54fffa06394ef +#: ../../src/faq.md:247 c5d087082bb2468483e7ccda3ca45a07 msgid "" msgstr "" -#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c -#: 1d846bfb5f054d09a4afad1da8e4b642 +#: ../../src/faq.md:248 41e30b0224a0492f9047b4f320f39a23 msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 -#: 2d0e95fec8084787b734388d60188574 +#: ../../src/faq.md:250 f06d073014a44f33a60d947a8c5b0e59 msgid "" "For command line flags that require a specific input as the argument an enum " "type can be declared in CWL. **Specifying null here is known as long form " "style. It does the same thing as the question mark on the other inputs.**" msgstr "" -#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd -#: eccc4a364330470fa474dcaaa3433390 +#: ../../src/faq.md:267 2fb74cd1b41e4fdb81a8f9b3b6c84373 msgid "" msgstr "" -#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 -#: e945f6a337af4e4686bed482a4fe6c39 +#: ../../src/faq.md:268 09e19f34d0fd4e388d4939cbc2be3436 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c -#: 8a3efaa0ad1548428bcfd6e01d135cdc +#: ../../src/faq.md:270 1ecae448dfcf45a4ae0dd39bd011e449 msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 -#: cdab644adc5643708870fb08c06cbfca +#: ../../src/faq.md:322 6df3d4e918cc4bccb823859ce07b197a msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 -#: 089a5a0b076b44aeaab4d69ee3c79f97 +#: ../../src/faq.md:324 086db1a093e64caa88d958150accc19c msgid "" "To properly set fields in a record input type, you need to pass a dictionary " "to the input to properly set the parameters. This is done by using inline " @@ -402,93 +355,76 @@ msgid "" "be used as the value." msgstr "" -#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 -#: 561172559c6f41a68819608fd9e58bb0 +#: ../../src/faq.md:342 da77c818d8694ab99fb2eccf73083047 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 -#: c5ee4946d2e840abaa3dc796a62652c7 +#: ../../src/faq.md:344 254259509ed6462d8ebc296b5f811f44 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 -#: 4f2069a2113c414db18eca95550e9e09 +#: ../../src/faq.md:349 f7a44f76579d4709a61d2d61bc352b76 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 -#: 31f3390e6771414ba7bf57c044c4b0c4 +#: ../../src/faq.md:351 d67278e99c684f488f1e3418e1c8c207 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c -#: 3b77ce4930ae46d5be9f6965e8c54727 +#: ../../src/faq.md:359 f5e35ee06cd24edf831589ebaa6193d2 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 -#: 06f36bbe4d3840229b7374f27b86ae80 +#: ../../src/faq.md:361 2ffb67e547c446499625a8db9a102da6 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a -#: 3cb2f70d00274a4dafd972ccd8c519c2 +#: ../../src/faq.md:363 ee653ff9fefe4771b35e2e76199b536a msgid "" "For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" -#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde -#: 093a1529262043ef84a99675054938e0 +#: ../../src/faq.md:371 02b1eb159e934fd692929f7c30319ddd msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 -#: 45b6d9acbfaa47e5984184f7da554d0a +#: ../../src/faq.md:373 857024702f624885be706c405b7a088e msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 -#: 5705c9bacca5405ca6f14315a5575db8 +#: ../../src/faq.md:375 d664e30899bd463bb48d38adec318dd4 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 -#: 82bfc285b59a439ca97d3278997f0fce +#: ../../src/faq.md:384 9f3957bbe205454e8bffc4b5caac5970 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 -#: 181d5130101d45ccb22aebae3d154c2f +#: ../../src/faq.md:396 6ec3bbc6a1ca4e23b47f025f0732e609 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 -#: e864390b5ddb423aaa10e9d33d257dc1 +#: ../../src/faq.md:410 3e727d79e65e4c6cb157550e80261c53 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 -#: fe637c32fb15427a9045679b5da42ec5 +#: ../../src/faq.md:423 6e0705f4ab4b4e9093794cb4fccb6be9 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d -#: 1f8004b9df8547029d82e57f9abdc979 +#: ../../src/faq.md:436 0047d039317349679fb6a66d18ec8487 msgid "" "If it is not possible to change the input identifier, then you can use an " "alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 -#: 70990dc5a0034099921ceb89c89e2dcc +#: ../../src/faq.md:442 8c39608ad0494bee9a4a422cbeb34387 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e -#: f679e26f18d9455f945fd13361a9c906 +#: ../../src/faq.md:445 7dac53bca8c14a3f9af75cb162cba4f9 msgid "" "The CWL standards are built around (optional) Docker format containers. The " "reference runner and several other CWL implementations support running those " @@ -496,13 +432,11 @@ msgid "" "Singularity format container is not part of the CWL standards." msgstr "" -#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 -#: fcd0273dbdd84e728cfd8fbe239f2a01 +#: ../../src/faq.md:450 ffcc38ff98324d71bfeb8d66d4901da7 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 -#: 173ddbd1e7c64927a8dcb12a2a2140f8 +#: ../../src/faq.md:452 0d7bf2cefe4a4e22b186bdf4d0ed793d msgid "" "You can use the --js-console option of cwltool, or " "you can try creating a JavaScript or TypeScript project for your code, and " @@ -513,26 +447,22 @@ msgid "" "dd>" msgstr "" -#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e -#: 662fe273e2fb4042b688512955e450a1 +#: ../../src/index.md:1 1506b4e7ee014a01bfdb067489501a9e msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab -#: a15b52205f0145feaac298510e4d678a +#: ../../src/index.md:3 0ce058b5210d46a0b78eb78dbca07a9f msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 -#: 512aa0c7166b429e8116f71eef007f79 +#: ../../src/index.md:7 3404c064950d453d8af446e8b6554cb6 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 -#: b1b19e17a18540939cb3bb7f8a700cab +#: ../../src/index.md:9 1e239cad669648e48694eaf91284766a msgid "" "If you find that something is missing from this guide, or if you would like " "to provide other feedback, file an Issue on the [project repository for this " @@ -540,13 +470,11 @@ msgid "" "clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" -#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f -#: d58b36ac43ac44139897be752fbb1f87 +#: ../../src/index.md:16 9dba2e06f1be4a50b1fabaaf216d02b4 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 -#: 6726cf3585a646a8b4cbeb543cf84a38 +#: ../../src/index.md:18 ba4074bbb69e4096a808001afaf2e0dc msgid "" "If you are a beginner user get started with the [Introduction](/introduction/" "index.md) section. For advanced users the subsections of the [Topics](/" @@ -554,8 +482,7 @@ msgid "" "CWL." msgstr "" -#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 -#: 2e504aa7c46a426fa959e7254e9a84a5 +#: ../../src/index.md:23 ad34a37bf4ec488bb825a34456f4fe8d msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -563,18 +490,15 @@ msgid "" "and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c -#: e7be0df0838b432d9c7f296d777f120b +#: ../../src/index.md:28 2bd8eb5957ed40f4a72a6b7408044c78 msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 -#: 173e0816db20432c8d9dba1de5393dee +#: ../../src/introduction/basic-concepts.md:1 8bb0df5531474301a185f1ba375320df msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 -#: 30eacc583f6841719e2142d283811d97 +#: ../../src/introduction/basic-concepts.md:3 653373e1f11e4f81ad561378854a71fc msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are expected " @@ -585,21 +509,18 @@ msgid "" "this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 -#: 791b8f38a14147bbaa174c7eb595f17e +#: ../../src/introduction/basic-concepts.md:10 7766227bf91b48b2b9752b625e5a9084 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf -#: 1a3989dcbb9844b39d84bf6df6b352ed +#: ../../src/introduction/basic-concepts.md:21 032d414ac29740aa9041d89d0ebf70e6 msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered in " "this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 -#: db1bbc6e980f404f9f3fcd08e92ee9a3 +#: ../../src/introduction/basic-concepts.md:25 74e92eb0a4e64098b5aaf08d043e0641 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -609,20 +530,17 @@ msgid "" "and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d -#: acc7887c65974114996f700a38a7eccc +#: ../../src/introduction/basic-concepts.md:33 baa40b445f3c409b9a3e10a85fa38bfd msgid "" "The model used for the specification version is called Semantic Versioning. " "See the end of this section to [learn more](#learn-more) about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d -#: d2476d9bcff44f21b8d84a3a0d87a246 +#: ../../src/introduction/basic-concepts.md:37 648e94a9d368450dbdac706445254c9f msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 -#: f86415e4d78e48c4a8a76ced81221b98 +#: ../../src/introduction/basic-concepts.md:39 e9ae15124dcd408395fc67e16b50696a msgid "" "An implementation of the CWL specification is any software written following " "what is defined in a version of the specification document. However, " @@ -630,26 +548,24 @@ msgid "" "implementations are licensed under both Open Source and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 -#: c5524d73708c4c779980528864506fd4 +#: ../../src/introduction/basic-concepts.md:44 b1c864d6775048cab01eb3de641f6475 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud " "and high performance computing environments where tasks are scheduled in " "parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf -#: ac46a9f8850a434bac5bc2b41ee6294e +#: ../../src/introduction/basic-concepts.md:51 a05d24121e534d65947eb26e4dada5b7 msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 9bba7c4f783942e4a299603430601363 +#: ace0388fd04845e79d31ec99a48a8a3f msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 e2140e0f0e7747ef8383887c20a7945a +#: 70ecd37237e14ae19539f2bf692882ed msgid "" "A process is a computing unit that takes inputs and produces outputs. The " "behavior of a process can be affected by the inputs, requirements, and " @@ -658,39 +574,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f 15bf490724cd46dcbcfab44633c5a9a2 +#: 38121b4b00324bebb6499184b3dcb5c1 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b 51d52d051e654a8395239f88df7c9d8c +#: e0c278f52e824673ac708885d985b7d2 msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 eb496cc818524fa7bae5a22ddd00a19c +#: 6b4d0f0651cc46f5abf195b281967913 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f c4a22d12e7f149ff901d27de32b9361d +#: 88bdc9e046e4487cb0eee3f1d4819e57 msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 7618de899a7043989d77baacf62eb7b2 +#: 12eed3ef7d444585b150bbdab0665bc8 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a 6f1544a220664b79b04bf008058b5a91 +#: dfc85226313d46f9868dc4de53546a69 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 fbd14ac9a2f541478a320ed4cbc69e13 +#: f636b10c47734e589291de95443d8115 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be used " "to simplify workflows and command-line tools, moving common parts of a " @@ -699,7 +615,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef da4dba50d25d4533b3dbb92f54d32a30 +#: bb51025d04444dd5b16000d5d6a3f41a msgid "" "Operation is an abstract process that also takes inputs, produces outputs, " "and can be used in a workflow. But it is a special operation not so commonly " @@ -708,7 +624,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 ce11c9f8d65c4268984d0384d95144cc +#: 93dbaa0aa2c6493ab22a937c6861fac4 msgid "" "The workflow is a process that contains steps. Steps can be other workflows " "(nested workflows), command-line tools, or expression tools. The inputs of a " @@ -717,7 +633,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 3a201aa497e84f70855bb2251e7e3281 +#: fcde5ef65ebf45a3b4b67eec993a1729 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through *requirements*. " @@ -725,23 +641,23 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 b78f7fa2be1c4bb090f6da895457ad1e +#: c8ff34ff5d3b4a508e8c291196d08067 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 f7e95d264ffa4e2db0864faccd9e5a0e +#: fe25f15fc11c49ab827b884d081c3df0 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 3f1e5b01e49a4dc1b1c99936a4589afc +#: 2b93b6219142431ca748a404a56ced5d msgid "" "`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee 03c3048f38ae4938a484cf02001877b3 +#: 0094b13b26014ba3be61769b422802f5 msgid "" "Some CWL runners may provide requirements that are not in the specification. " "For example, GPU requirements are supported in `cwltool` through the " @@ -751,7 +667,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e f9715b5ec65c405c849bb030c1927060 +#: 576a0778d3dd44f68cb241346f441660 msgid "" "Hints are similar to requirements, but while requirements list features that " "are required, hints list optional features. Requirements are explained in " @@ -759,12 +675,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 442662f50e9e4620970ce32b1b127969 +#: 7d98949fe97744158fad81f41d780de9 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 2b34c786af3840e88f29d214e19dc837 +#: fc142b791aa1434aa75b0782248de988 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -777,7 +693,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a dd6aadff8cf54ce78ea6b317afbaddb0 +#: c3fc91ae3bae4e3db60e8271e95135a2 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\", " @@ -786,7 +702,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee fe7f1f0b28434f8aaf0f6ac6589a83f0 +#: 8f097ae5ff6a4be0b7428345362dc55e msgid "" "The benefit of explicitness and isolation are flexibility, portability, and " "scalability; tools and workflows described with CWL can transparently " @@ -795,77 +711,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 d10cf45b3c7f49dc98bc0e5d1246f224 +#: 60c56fa6a67346d6966f0d841213e11b msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 -#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf -#: 332b6e8b831e4bc5aed3745938230a57 ce7fc63b808d4499b9bf9828c2dafe35 -#: ebf339ed376a4d3b89b15b4d5afe593b +#: ../../src/introduction/quick-start.md:94 7377b155e8694798994bbc911a3f3152 +#: 7699685836064bd89db530a9c1918865 7d187a209ebd4e3ba6c6aeb05743041a msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de 8badec9987ba40609cf1f626172b2b2d +#: 3fcbf810c86f4cf7b8499de88147aa95 msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 c75a8b4bf0e24781bf6713cf6f013cd1 +#: e242228b6b3d440cbca8418050220267 msgid "" "The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 79b146ffe6d74e1b8f6019251dc4b7c2 +#: 6e01963a01cb49e39692455256679bfc msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 07cca9a33d8f4b77ac6ad35ca8b95655 +#: ed81ea2234b041c79449dcd20f886cb6 msgid "" "The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 31db11c8ddf2423192a8b2063b3e91c2 +#: e8e3996f6a894b4f9cc266b46cb8d756 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b d81dd96143ea444aa78ff45cfa0584b3 +#: 085e4d1a7a9744d2884f3003c64ca174 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 -#: c54984605872472190ae7771809a20db +#: ../../src/introduction/index.md:1 dcd96950854f47a6ad4169320c1dab34 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 -#: 01a237b8ec2f46c9acd31d142591ce75 +#: ../../src/introduction/index.md:3 c4d17eec31874bf1ae9b49d73537d86c msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that " "are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 -#: 3fb9888b666945eab1e3ff109646c574 +#: ../../src/introduction/prerequisites.md:1 98a8bdfc7c91436d9cb46abbb7c19c57 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 -#: 5fb0486762354f93853fff209f835c08 +#: ../../src/introduction/prerequisites.md:6 244a716e267540c782e627adaea3a413 msgid "" "The software and configurations listed in this section are prerequisites for " "following this user guide. The CWL standards are implemented by many " @@ -875,13 +785,11 @@ msgid "" "(though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 -#: 5f1e7a608e0b455196d191c845a5c98e +#: ../../src/introduction/prerequisites.md:12 2cdf453d2c8b4e2ea50555ef0b7364e5 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf -#: 7ba4b5c51be24f5392949d06ee42e018 +#: ../../src/introduction/prerequisites.md:14 53643a4f190c412d9552d1908f408318 msgid "" "There are many implementations of the CWL standards. Some are complete CWL " "runners, while others could be plug-ins or extensions to workflow engines. " @@ -889,35 +797,29 @@ msgid "" "md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 -#: e2d3e6dd13b14d819a504c35da6fe8e7 +#: ../../src/introduction/prerequisites.md:19 1df6c63de3914af68f758054fe6955f4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b -#: 91251d1f0efb4d4cb083b4517ff3107a +#: ../../src/introduction/prerequisites.md:21 ceaa3a6bebab45a0907ee0cad01429a2 msgid "" "We recommend using an up-to-date operating system. You can choose any of the " "following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 -#: 6ad263e267514c5fb05794d3d76d418d +#: ../../src/introduction/prerequisites.md:24 1506ac904c6345c5806704a0ccf235aa msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf -#: 8a3bfd72dccf4a8c874a96aebcbe5cb7 +#: ../../src/introduction/prerequisites.md:25 a616213ed24e427bb91ee33cb21ec131 msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 -#: 5195706d9c6c4573aff135fd539759a2 +#: ../../src/introduction/prerequisites.md:26 a4e9ae38103843739f13c62befd21f3e msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 -#: 9c4506915e4c40599527bc1d2b18645b +#: ../../src/introduction/prerequisites.md:29 2cd231aac42c4a69a925cea369999a8b msgid "" "If you are using Windows, you will have to install the [Windows Subsystem " "for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " @@ -927,13 +829,11 @@ msgid "" "recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 -#: 37d9eb784ec1425786158f98e3f63890 +#: ../../src/introduction/prerequisites.md:35 051d7cd7d3a94baa865d180afdd71688 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 -#: 572f493a985141a1b92dafbdba92790d +#: ../../src/introduction/prerequisites.md:41 1a93aaf5bd5e4862b15e0636b4478640 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL community. " @@ -941,8 +841,7 @@ msgid "" "in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 -#: 9606d3c4849f4b17b2e55a298210f055 +#: ../../src/introduction/prerequisites.md:46 edd0613118a2493c876652bdcb9e0fbf msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create and " @@ -950,31 +849,26 @@ msgid "" "`cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d -#: 754fc59967d94ffa935284676d55ffed +#: ../../src/introduction/prerequisites.md:51 3448d215c2434866b8a4b340872ba81e msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 -#: 2905c6362d4146e8b35bc74744841972 +#: ../../src/introduction/prerequisites.md:62 4c24d05f65794735b816024c78b63f1c msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` and " "`conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 -#: 091278ece252483a9838fb771de3e04e +#: ../../src/introduction/prerequisites.md:65 3167f4a2a8394feda1f848334be62022 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b -#: 0928a5c668c3414a945bc9eda147892c +#: ../../src/introduction/prerequisites.md:67 3c4b67d62c9c4d658ccaafcd1977ec08 msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 -#: 56f3c481762848298214a88e559fc0f9 +#: ../../src/introduction/prerequisites.md:73 30792f78348942e0acdde411342e8830 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -985,29 +879,24 @@ msgid "" "command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 -#: 710c266ab4a5477b84d6ea987420fa20 +#: ../../src/introduction/prerequisites.md:79 4473e41281fb4e738e4eb26c2d178934 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 -#: cc353db5da2546bb88a77ce1a202ff9d +#: ../../src/introduction/prerequisites.md:84 548393974d4d4acc91738f9bc13a3a48 msgid "" "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 -#: b62df08ec96f4cdb887600079856dd76 +#: ../../src/introduction/prerequisites.md:86 2ab3963cf9504ec097eda2b14f3448c4 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 -#: 97e02557293440d1a58ba659dad21113 +#: ../../src/introduction/prerequisites.md:91 690882dcc29c48acbeb215a8be52eb9e msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 -#: 0935c3ff01634c75b5c91546dc36c7b9 +#: ../../src/introduction/prerequisites.md:93 6c3ba51b1e9a4add9203d62cec6ebae9 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be invoked " @@ -1018,75 +907,63 @@ msgid "" "environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 -#: cfb37fd605164a8d9cc75bf892ce97c0 +#: ../../src/introduction/prerequisites.md:101 b2360ef646854422ad6c0f90fa49306f msgid "" "The CWL community publishes a Python package with the name `cwlref-runner` " "that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 -#: 5f06a7a6aae343d989a5b30979c600f6 +#: ../../src/introduction/prerequisites.md:104 c9fadfa85a2641378e99a462e8e8d940 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 -#: 5f956260f3874b6dbeaf3ad7ecc09c9a +#: ../../src/introduction/prerequisites.md:111 abb8993ede4d4e479d88d2e848546f68 msgid "" "Now you can validate and run your workflow with the `cwl-runner` executable, " "which will invoke `cwltool`. You should have the same results and output as " "in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 -#: d35e4effec554a638d6c3047ef3fd05f +#: ../../src/introduction/prerequisites.md:115 ba0f7606e6174e53a8bf23c1ccd99250 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 -#: 15a1f944a0d642729d3736ed1c907074 +#: ../../src/introduction/prerequisites.md:120 dd2e10f43e8f498cb01de5faa4fccb70 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 -#: fa34c808bb494ddfa3f3926bc42e650c +#: ../../src/introduction/prerequisites.md:125 e500e9c71c7042169c25b31f21a09142 msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For " "that, the first thing you need to do is copy `true.cwl` workflow into a new " "file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a -#: 0c15f62eb7534e809f625f3fa213e92d +#: ../../src/introduction/prerequisites.md:129 d989516c873f4446bba005f42796b8b9 msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 -#: d67719a6f0ce4ba1bb6152a10507b729 +#: ../../src/introduction/prerequisites.md:135 e9d8610478094a98b5b5a0f568a315de msgid "" "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 -#: 1c96e75281844bfab0578bab2e816854 +#: ../../src/introduction/prerequisites.md:137 d6d8131f91b740189e56ab9d90bee55a msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 -#: bece1fc3c3f842b0b30d8f1b7fbfc200 +#: ../../src/introduction/prerequisites.md:144 def7400a00e84070a4bd80c2367d3bde msgid "" "And finally, you can execute it directly in the command-line. On execution, " "the program specified in the shebang (`cwl-runner`) will be used to execute " "the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f -#: a7caa36b0f83448b91ef2e76e30abc51 +#: ../../src/introduction/prerequisites.md:148 564e7be94d254e52a6c44b234d6ddc63 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 -#: 39321e93e9994fcca20b425aa45c2894 +#: ../../src/introduction/prerequisites.md:154 bb5fe42ddd814ad4ac1071c0b18f24c2 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute the " @@ -1096,55 +973,47 @@ msgid "" "`` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 -#: 601cf500d76c4e0287af4429a46b36d2 +#: ../../src/introduction/prerequisites.md:161 53bb712a68cd49fca4db11e9e507c9a4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed -#: b286d5359e184ef58054c72df4014629 +#: ../../src/introduction/prerequisites.md:163 bdcf61cce5294e45a9f964628a8a66bd msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 -#: e14423edd829401faed0950772123240 +#: ../../src/introduction/prerequisites.md:167 28d33daee6e246c8a6d1382208e19c39 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting " "and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 -#: 889c44360bd54a0e85e7f0e61aa6593c +#: ../../src/introduction/prerequisites.md:171 b071d7c87b7a4817b871085a652cd580 msgid "" "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" -#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 -#: 7b9bff73624947ac90a99c7880e2e911 +#: ../../src/introduction/prerequisites.md:172 97658a1b16874ba8b0bb748242d0da64 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 -#: c5ff687c86ef4ccaae25d8bcfbd5f873 +#: ../../src/introduction/prerequisites.md:174 6198aa6769b74ef0a2a1ba539789f3ee msgid "" "The CWL community also maintains a list of editors and viewers: " msgstr "" -#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 -#: 0a610a9632064deb824afd0719429d3a +#: ../../src/introduction/prerequisites.md:177 0c17235a374e40099be37b9b8ac8f1f0 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c -#: ec0c47438a5242cb99dffa7a4997e95a +#: ../../src/introduction/prerequisites.md:181 e3690e656b5a4348845c654689935a88 msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1152,8 +1021,7 @@ msgid "" "com/>." msgstr "" -#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c -#: aae94ac2114641f186eac0f4117223eb +#: ../../src/introduction/prerequisites.md:185 2db34e925a81422986ccb868463a7a42 msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1161,67 +1029,57 @@ msgid "" "and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 -#: 209e072724ed4d27b37e9bff6d55d811 +#: ../../src/introduction/prerequisites.md:191 d677fb155b0343ba8771398cca967fed msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for pulling " "images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 -#: 3bf47876e3694e6cadb05123326459cb +#: ../../src/introduction/prerequisites.md:198 22ed0b55de38408393af4a8309a995ea msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the next " "section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 -#: 459a65b8e67c4a9aaa03138c1abe94ad +#: ../../src/introduction/prerequisites.md:199 5ded73cae5db40ad840c3022e7cd447f msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 -#: 898eb29ac7714c69840b795633953a05 +#: ../../src/introduction/quick-start.md:1 23e5613df7c94e5f938c85b14f5441e4 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a -#: 2a658bd2d8ce4533ab7e056fc3a3ffcf +#: ../../src/introduction/quick-start.md:3 3b425afc63d841d4be57c92b25b4ed2d msgid "" "This section will show you a brief overview of what CWL is, and where you " "can learn more about it. No previous knowledge of CWL is required, but you " "must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee -#: 32dd2e28cf0f40b6930750f0162355eb +#: ../../src/introduction/quick-start.md:7 75a26c48d3e04e24abb96d81cb31c94e msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 -#: 471c47d311074ecfac071b6d52d9cfb6 +#: ../../src/introduction/quick-start.md:12 88b4ecd45ea44dd4befe3ce89b30f6c2 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " "example below shows a simple CWL “Hello World” workflow annotated with " "comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb -#: 5078140028ea4d04973cb9cd20f0607e +#: ../../src/introduction/quick-start.md:16 e1789ef78bd64332a18d8601094a0f72 msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 -#: ab127d4ba0a44526ab129587a8160923 +#: ../../src/introduction/quick-start.md:22 196ceef96c27434eb4b0b7222c2fe73c msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the " "same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 -#: d5cc6b4295a74f3586f022b0227759b3 +#: ../../src/introduction/quick-start.md:27 e6a44130c6b44d5bb6451a147f28dd8c msgid "" "In CWL, there is a distinction between a command-line tool and a workflow. " "But for the sake of simplicity, we are using the term “workflow” here. You " @@ -1229,13 +1087,11 @@ msgid "" "section." msgstr "" -#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 -#: 585a4fe583ce44e180a062742b3b0849 +#: ../../src/introduction/quick-start.md:32 340b46acc7a34b7b978f5a734f529553 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 -#: 0d81b0c9ea58420789d1d71cca32ce88 +#: ../../src/introduction/quick-start.md:34 139e48dcf0474fea932ca07a0001d208 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the CWL " "*Reference Runner* for the specification, and it is compliant with the " @@ -1243,13 +1099,11 @@ msgid "" "`cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 -#: ea4ab0782d8049d8b1b89cea4ae60048 +#: ../../src/introduction/quick-start.md:39 d6f6e061c0f4434eb6d70f9d84759042 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 -#: f6f3b7453a254f828bd4c9e9fef92bed +#: ../../src/introduction/quick-start.md:47 cb2b548489df45ee9d49b36116440eea msgid "" "If installing the cwltool using the pip command doesn't work for you, the " "[prerequisites](prerequisites.md) section contains other ways to install " @@ -1257,38 +1111,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 -#: 3bf9050175d4444ebbbabe219412574f +#: ../../src/introduction/quick-start.md:51 aa751bda67ec44ba988642b061e2a094 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe -#: e03f72a14dcf4bf38ce8232598ca761d +#: ../../src/introduction/quick-start.md:53 a7e0209af0544b0ab31012864a43886c msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " "workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 -#: 3dcfb2facd324dccb3084c02487625dc +#: ../../src/introduction/quick-start.md:57 d0f424f0041c4635a0559fa32a76c86f msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 -#: b8531da183964b02bca19f818ec076d4 +#: ../../src/introduction/quick-start.md:62 eeee96c4e59447aea6b239c63e4bb3e5 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 -#: 7ba1ddebeb2843179fe99fc410b193c6 +#: ../../src/introduction/quick-start.md:65 961a385b340141e980aa4f8791fa2f12 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 -#: a6dc303e9d284b60bf1102212505ca27 +#: ../../src/introduction/quick-start.md:70 c48cd1be543d4ccbab964b28c2e08584 msgid "" "Another way of passing values to your workflow input parameters is via an " "*Inputs Object*. This is a file containing the input fields with their " @@ -1296,25 +1144,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 -#: 59ac7830ae3e4d7cb1bf503e8c90fe30 +#: ../../src/introduction/quick-start.md:74 e5619164bdf242f0b09cac668adc0ef7 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c -#: 6d1d6f42ada2418ba0a1de1371825b9f +#: ../../src/introduction/quick-start.md:80 9f80772a53154bbeb27895d35435de10 msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 -#: 1cd924fe8ace4a82ad8701f37b5e7d84 +#: ../../src/introduction/quick-start.md:82 98b6d400cb274d08ad6489adbef08c4b msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 -#: aa297c52cd964291a47bb91c0135156b +#: ../../src/introduction/quick-start.md:88 4faabaab56f1444da290cf64cc389f37 msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but it " @@ -1322,54 +1166,46 @@ msgid "" "Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 -#: 28b02c90397745bfbacc03c3b1034939 +#: ../../src/introduction/quick-start.md:96 48beaccb16a24427bd015c63f9e06d37 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 -#: ef2a4f39f01049b891868b84d968c0dd +#: ../../src/introduction/quick-start.md:97 68035ead1c6844128011ca32c04fd20f msgid "" "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 -#: 89e3fa8dceda4f0cb1cfdfd1f17fe4df +#: ../../src/introduction/quick-start.md:98 8fc1ebf21a6f4894a4acfba74a80602b msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 -#: 7cd178223ba94d1ab3ee8cc5f13a8dcf +#: ../../src/introduction/quick-start.md:99 27fbad579d8b4ebeacc6fd3ef7e85a39 msgid "" "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" "Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b -#: 46f6f8d050ce4f8c897056167d9707a7 +#: ../../src/introduction/quick-start.md:100 a8791b670848474da292a467f01f8c45 msgid "" "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." "org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff -#: 5ee00ee409b746dc951ca1d4c360e624 +#: ../../src/introduction/quick-start.md:101 fc20fa4c04104417b541a67ada2ab9a9 msgid "" "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." "replace('VERSION', cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b -#: d4af972281174b8999eab55ee0ab1a0e +#: ../../src/introduction/quick-start.md:102 a93a7797a12b48dfa5bc3a7c50ab88e7 msgid "" "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" "Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d -#: 80401cfffae042ab9ec4b3754af04b25 +#: ../../src/setup.md:9 6f02fa47aca14c59a35b3ab750f5f236 msgid "" "This page is out-of-date and was kept here to preserve the links of the old " "User Guide. The information on this page has been migrated to the [FAQ](/faq." @@ -1377,19 +1213,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 32f86f911ebe4a4c94975f81742333f3 +#: 3821c2d16b254672a494522e47386cb0 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 d5f1ad2b95ad46d48f8f2ca5e357bb5d +#: 412a05f3492349a7bd26ea0c30e9bd80 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf c53ceee943ad4acea779e072b9137889 +#: 1232f6c81da141cb8482294eee5955dc msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files in " @@ -1399,55 +1235,52 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c 7dfe9dffbf5744299bf232599644c7f6 +#: 485bb71673144e3f90f05b420b7079ac msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 00709fa451134ee09a0d808e101f28ed -#: 991172e201ec4796992a349dee44f090 +#: ../../src/topics/staging-input-files.md:15 0beb10c3133643f6b62c7d4aeec33709 +#: 5d48d9a2e977431f9a3625abaa466f5f msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 1f3c23a4769043ca985b8ddfed19391d +#: fcc1151a2e8b4a84b8595c7f913781a1 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb f81b43c7cb194a1cad8672129223c833 +#: 4a291c7ac7c84257b7402567d8364a36 msgid "" "And now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a a20073a8f5374eb1bc8531ff33e622b6 +#: 3b1ae26038fd498ca0ae23aa70a35d3f msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 d08869beca3a4774baf1097b63e79474 +#: 40388ebefb6947089c4a0f6d5d6e92e8 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" -"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." -"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " -"specification for details." +"designated output directory. Other parameters include `$(runtime.tmpdir)`, " +"`$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and " +"`$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of " +"the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 -#: 109b773789024b2b9c063a6169c6169f +#: ../../src/topics/best-practices.md:1 a417fdd330db47a3aac07f7006c83ca9 msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 -#: 959fa04f88e54d42b9b774cc95d85ee0 +#: ../../src/topics/best-practices.md:3 99bad0fd9bee428a8d936d5a8e84d97d msgid "" "The following are a set of recommended good practices to keep in mind when " "writing a Common Workflow Language description for a tool or workflow. These " @@ -1455,15 +1288,13 @@ msgid "" "although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 -#: 64674980c3f24c45bbfbf3f957dda55e +#: ../../src/topics/best-practices.md:8 935500b0e6e249eba585644cddbd0253 msgid "" "No `type: string` parameters for names of input or reference files/" "directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 -#: 90f2e4265919446a902e17627f4420e2 +#: ../../src/topics/best-practices.md:11 96f924d6e02f4005b35d463e49be2982 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that " @@ -1478,8 +1309,7 @@ msgid "" "anyone, e.g. [Apache 2.0][apache-license]." msgstr "" -#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f -#: 6b5f91a749fd44b5acfd6071c9913342 +#: ../../src/topics/best-practices.md:20 25e0a5c93ccc49bc8b6206c7c2e3de5c msgid "" "If possible, the license should be specified with its corresponding [SPDX " "identifier][spdx]. Construct the metadata field for the license by providing " @@ -1489,50 +1319,43 @@ msgid "" "provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc -#: 5fe2962837b14f0e9989063be4a506c3 +#: ../../src/topics/best-practices.md:26 34ad53bc5a40446daa0dac4571600d1e msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 -#: 4e1bdea962ed4618884cb9d1d59d7509 +#: ../../src/topics/best-practices.md:28 4c397ffd2e9148e39bdd614683a98a78 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 -#: 37eff4ca02e843259f6ffa38e4a87a04 +#: ../../src/topics/best-practices.md:37 1ed7f7e73afb4bd2ad2e29b65d020ff1 msgid "" "For more examples of providing metadata within CWL descriptions, see [the " "Metadata and Authorship section of this User Guide](../topics/metadata-and-" "authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 -#: ae47231c203d40a98c10045038ea9b65 +#: ../../src/topics/best-practices.md:40 13b058dfa3cd4bbea54ae7d5a56c4c50 msgid "" "Include [attribution information][license-example] for the author(s) of the " "CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" "[orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 -#: 018a6d5dbf1044559b365c7b9017eb3f +#: ../../src/topics/best-practices.md:44 69369b917c1a45199343266650b1b220 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 -#: e073d8f990c44b09a73d642cfe49bebd +#: ../../src/topics/best-practices.md:47 0245a61fd2ef4fb69cbb8d732086fb8f msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" "identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb -#: e04fae88d9b64493ac69eaee24585098 +#: ../../src/topics/best-practices.md:50 e9a56e3634a042279cae1745b7820658 msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1540,70 +1363,61 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 -#: b26b9c9b1c4346a297a31c9721f0172a +#: ../../src/topics/best-practices.md:55 8a180861a66c4aaa9e8fdefd929ed829 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 -#: b50500c3c3f54b16a535a16175a44653 +#: ../../src/topics/best-practices.md:58 00f333a383b64578b32c687b42924a77 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" -"$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with " +"`$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " "[Full IANA media type list][iana-types] (also known as MIME types). For non-" "bioinformatics tools, use or build an appropriate ontology/controlled " "vocabulary in the same way. Please edit this page to let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a -#: 623f3a804199449bb85e23e00c8bb507 +#: ../../src/topics/best-practices.md:66 6b960d362bb540299f0560c14c5f2d8c msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c -#: effea0b1356447c0899ca0746667ea31 +#: ../../src/topics/best-practices.md:69 9cf9342bf0864e87b495913d8e06d021 msgid "" "Each `CommandLineTool` description should focus on a single operation only, " "even if the (sub)command is capable of more. Don't overcomplicate your tool " "descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 -#: 00e8ef87864c4ca2b2c1c0548b02b38d +#: ../../src/topics/best-practices.md:73 587b048324e447cb85844d8c64ae9a1e msgid "" "Custom types should be defined with one external YAML per type definition " "for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 -#: 6e6f48d70b894a6c959ca30fe6bad772 +#: ../../src/topics/best-practices.md:76 d8df6bbd5d324f7c9f48edb33e113b75 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae -#: 02fe08760a4a4ab49e96f4e51316a81d +#: ../../src/topics/best-practices.md:78 2235174088ad48a89d4fc21223e627b7 msgid "" "If useful, include a top-level `doc` as well. This should provide a longer, " "more detailed description than was provided in the top-level `label` (see " "above)." msgstr "" -#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 -#: 172ed7915a654964ba63f860b2d65330 +#: ../../src/topics/best-practices.md:82 a0f0953a1a9f40cebd4dbe028784ff96 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list of " "valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a -#: 4d0a2871a7484e21b3c39c4dbaaa63fc +#: ../../src/topics/best-practices.md:85 0ec380c683534892b6b8b8fcea84f765 msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. One " "common example: manipulating `File` names and paths? Consider whether one of " @@ -1611,36 +1425,31 @@ msgid "" "`nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 -#: 1eea9f1e284447718141f5417b6bb433 +#: ../../src/topics/best-practices.md:90 65f23741db4e4a6abda8e5f7e036753a msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 -#: 509411d353fe4314b087b81b09ea960b +#: ../../src/topics/best-practices.md:93 34c2caee8eb84e01a37033b67eb4aaba msgid "" "Complex workflows with individual components which can be abstracted should " "utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " "workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 -#: a54bc80bf08243bba67d98dd682ee134 +#: ../../src/topics/best-practices.md:97 d7c7484b2f1048aea9802400410f0858 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics " "software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 -#: 69ecdaea24ef42eebef9d86e5d716b11 +#: ../../src/topics/command-line-tool.md:1 a905abc2eead4dbaa035235936025499 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 -#: 3cc5847468d1478bb5589dee68147189 +#: ../../src/topics/command-line-tool.md:3 eb91b6dab34d4d5f9854ac580a6cbde2 msgid "" "A command-line tool is a type of Process object that can be run by itself or " "as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " @@ -1648,59 +1457,52 @@ msgid "" "command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab -#: 98c6bc409420485095ae65d6b0b9a3a0 +#: ../../src/topics/command-line-tool.md:8 7caeb91564634091a932f1270c4f5ef9 msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The following " "example contains a minimal example of a CWL command-line tool for the `echo` " "Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 -#: ebe23e5378514f888a9ec32a2adb1e98 +#: ../../src/topics/command-line-tool.md:19 c6ac4a60d102407991f40b892fb60560 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 -#: 387cfe85604f424f8d31c4a4c9c15edb +#: ../../src/topics/command-line-tool.md:50 51d3ce421db345f5ab19e02fbbc51df2 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d -#: 7b1d65754e854693bb60289c97d3fb5d +#: ../../src/topics/command-line-tool.md:57 8311d1430e624435b7b04bf2574a90c5 msgid "" "The example above uses a simplified form to define inputs and outputs. You " "will learn more about in the [Inputs](../topics/inputs.md) and in the " "[Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e -#: f440cef729c8410281432307a4da8d55 +#: ../../src/topics/command-line-tool.md:68 d1c03e5f19d64ea89276d126de6e4bda msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 -#: 4fbb8ceb1b59480583ac611142167049 +#: ../../src/topics/command-line-tool.md:69 8494b43e98dd424db7d57aa1d731f7b4 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network access. " "If a command-line tool is written manually in CWL v1.1+, there is a need to " "specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e -#: b87869204838415bbf694214e3680593 +#: ../../src/topics/command-line-tool.md:83 8c4573fb120149269a0fe3a1ba6c9ef8 msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " "Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b 12cf5f2264504c44a2173e858bb2c283 +#: e1c709ac0fb249928d14aeced6551ae0 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d 7694f9cabfe04308bbddd2c88ae6d9b9 +#: c26c9c640e0747c8b2c2977c860c9d82 msgid "" "Sometimes you need to create a file on the fly from input parameters, such " "as tools that expect to read their input configuration from a file rather " @@ -1708,17 +1510,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff b557dc4f8ef549b98f59412a918643de +#: edbe918d7df14cafb440e171e46c6de3 msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 3011eb003c084285b30cfa56a8da45b6 +#: 6d457d9b4ae746d384e65d9a37ca3591 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df 9f9c90a2bb4b4d3b8e99b63cb0e72f76 +#: 868394c1b8374ee6bbd43463e73d7edc msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the value " @@ -1726,7 +1528,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 ce78b2d147054da895beba66d0ecdab4 +#: 08a9e08cba674db09c9bfbef37e9579f msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later " "during command line tool invocation. That means that any genuine need for " @@ -1736,7 +1538,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa a973846ec5a946eeaff02c5b00997da9 +#: 6f6f437753dd4eddae0b2ea62046fe39 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1744,14 +1546,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb -#: ca03defa3ad14cf698171cb09e3055c1 294fd83a97a64249bac38f7482159372 -#: 9e8eb1542db640ff9e300649ce50dc9d ccec7f73b9d948e79a6cdf32bc124092 +#: 096b17907bc3452d9927ef2fb6f5c11f 78ed5d8fb9bd4e068023d2c717e20f62 +#: c3a2e9e6b4414597a17db6d55d98e9d1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d 22948f19cb78485f8f86244686a35c09 +#: ac783e6415a44cb59d4b425bac5087b7 msgid "" "Before we run this, let us look at each step in a little more detail. The " "base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1759,7 +1560,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c 001d9579bfce438e865377fb9c2df776 +#: b9e6e15b541149c6a2d3922c11405267 msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " "array, we need a `-` on the first line of each element of the array, in this " @@ -1771,7 +1572,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 e62618db8995428bb3f260e03ac8f459 +#: 87088899567a4402aeb34605d3c6b06b msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1781,23 +1582,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f -#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 -#: f924d65fed0c4cb5b0a019b084a8b535 457756c4e9544f068af897113358cc89 -#: 6d5ae75431424ea788c3440606f22940 98e0548845fa447fb05a29c9fc2f17b5 -#: de5e8aad4e3046bf9bfc2ad8ccba17d0 e9801b2142cd45368a73ef9b121c1d08 +#: 304c1bfe5ecd4d26b5dfaf9ad2e2c7f8 3ef7f0e3099147d78fd2d30bfa73cc6b +#: 4fef79a30282456eb9b5dd34a5eec0b1 afe775762ed348e5982b99bcf1451606 +#: f0689cd0e5b34414b6693331186ee4a3 msgid "" "Now invoke `cwltool` with the tool description and the input object on the " "command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 -#: ee2bca9bdbb74b60a706c3118d6a17ba +#: ../../src/topics/custom-types.md:1 9f1967411aa7497fa43a4851f0645d6e msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a -#: e63ae9694f40438d872d141ae824a42d +#: ../../src/topics/custom-types.md:3 90bd62e4ef8b41e398a5c9b31f132774 msgid "" "Sometimes you may want to write your own custom types for use and reuse in " "CWL descriptions. Use of such custom types can reduce redundancy between " @@ -1806,25 +1603,21 @@ msgid "" "to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc -#: 750fdd4c270e46a09f79e867358f7414 +#: ../../src/topics/custom-types.md:9 3465527b8ff4407587f7c46fa9fa2a98 msgid "" "The example below is a CWL description of the [biom convert format][biom] " "tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 -#: b3f688cc82444ef7a7a0aa63dac39cac +#: ../../src/topics/custom-types.md:12 c0cc869690804ada96a5c1813d17b895 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c -#: 3638be18b4f64cf08053d512e590dda3 +#: ../../src/topics/custom-types.md:18 01f369931c8142c08fe821a0ca31bf92 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 -#: 7d5b9c21739c48f18c13614ca6967f6b +#: ../../src/topics/custom-types.md:24 0b3ff704cdea44e28aee3c704ca98e27 msgid "" "___Note:___ To follow the example below, you need to [download the example " "input file](https://github.com/common-workflow-language/user_guide/blob/main/" @@ -1832,15 +1625,13 @@ msgid "" "*rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea -#: 8fea29993f944d8d8d3181afa29bd0a6 +#: ../../src/topics/custom-types.md:30 cb456bcae0dd41ffbc514eeea283e130 msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to be " "used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e -#: 02d0b648d70f49d7892f690be06df585 +#: ../../src/topics/custom-types.md:46 c610173365d04c57900b22f4024b47b4 msgid "" "The reference to a custom type is a combination of the name of the file in " "which the object is defined (`biom-convert-table.yaml`) and the name of the " @@ -1851,27 +1642,23 @@ msgid "" "hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e -#: 0743bef42b9a42328849c8c2f9da9eed +#: ../../src/topics/custom-types.md:53 c2b2e18d55c94721812431583cfc4725 msgid "" "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 -#: 85c5d0cbbc6243a6823f5eeac0f85dd9 +#: ../../src/topics/custom-types.md:55 3e61c3920a7a45db8917c348bd44384d msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 -#: be848f30769543eb9c0be55263e3f758 +#: ../../src/topics/custom-types.md:61 cd87d210b03c4da2a7608b40a6bbcca0 msgid "" "In order for the custom type to be used in the CWL description, it must be " "imported. Imports are described in `requirements:SchemaDefRequirement`, as " "below in the example `custom-types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c -#: cbff44a64ba4432cb59a82f82c2f0103 +#: ../../src/topics/custom-types.md:76 7af9ba3219e44ed49b8da781db5d6fb5 msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number of " @@ -1881,31 +1668,26 @@ msgid "" "this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 -#: 617f1c0084cf42d9be4c7a8fa5a48432 +#: ../../src/topics/environment-variables.md:1 eae1994f3a4d481b863b5125c7f4a383 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 -#: cee79afa3c6f43c29ef05e06b7843d35 +#: ../../src/topics/environment-variables.md:3 8bd8c06d416740b69d126eb9f5f24ad3 msgid "" "Tools run in a restricted environment and do not inherit most environment " "variables from the parent process. You can set environment variables for " "the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 -#: 225903b11efa417989df42de86ad2451 +#: ../../src/topics/environment-variables.md:7 11c6bffc620b4c789b29ab4034a8bfbd msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 -#: 1a5f058290064c1cad05e63eb127fcbb +#: ../../src/topics/expression-tool.md:1 89888b1b994546ce8a93f9630b4bb07e msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 -#: 74ad8d69cf294ae880dbbe28e25b3545 +#: ../../src/topics/expression-tool.md:3 191d3010b9244b39bc3bc50246ac7ad7 msgid "" "An expression tool is a type of Process that can be run by itself or as a " "Workflow step. It executes a pure JavaScript expression. It is meant to be " @@ -1913,38 +1695,32 @@ msgid "" "on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 -#: 5293e8ee9b3b4f59947cfc164ef111c4 +#: ../../src/topics/expression-tool.md:8 3437ed6e184748e4af1ef62f32c8cef1 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe -#: ffa1955c759942c68e7589429e5ea86b +#: ../../src/topics/expression-tool.md:17 c3ae1ef318bb4e0fada76c353dd5f6f1 msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 -#: 038bc0ba5f6a405a8255a7be76979baf +#: ../../src/topics/expression-tool.md:48 a7f5e04d242c48a7b3deffb5ff6528be msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a -#: fae1c63de02e48c0969a98e4c49b2e06 +#: ../../src/topics/expression-tool.md:67 32b6841faed044409bc618cba54a22f0 msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains a " "JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 -#: 7093a94695524851a5463193f0701b78 +#: ../../src/topics/expressions.md:1 6821ba7a84a44d309d245c429948ad09 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 -#: dc8274ecb15948c29a31db89b12a58bd +#: ../../src/topics/expressions.md:3 8167269bc3a64c72bd6c909362350a15 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1952,8 +1728,7 @@ msgid "" "CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 -#: cec8eef8a5aa49778ecedd4195ab9f2c +#: ../../src/topics/expressions.md:9 c0f75603a6024063a6911f17c70908cc msgid "" "JavaScript expressions should only be used when absolutely necessary. When " "manipulating file names, extensions, paths etc, consider whether one of the " @@ -1962,79 +1737,67 @@ msgid "" "practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 -#: df100967597043c78112bf43b520cfab +#: ../../src/topics/expressions.md:16 7faec63b389a4c07b6929b7a78f0cc70 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 -#: 59ccf4daba39406581a6bc2d9bb1b7d2 +#: ../../src/topics/expressions.md:22 d7dca89942f949d58cb18cb94bb7de72 msgid "" "As this tool does not require any `inputs` we can run it with an (almost) " "empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 -#: 570cc75699dd4e0a987fc9aca9a01ee4 +#: ../../src/topics/expressions.md:25 1abc1a21c0764415b138099e0e21432b msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 -#: 9e123723048546d495ed5110d7177708 +#: ../../src/topics/expressions.md:31 b8b5a50a82e44e49a37c6396f1ff9464 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object is " "represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d -#: 26543894f6e04270b89ab702451bcc89 +#: ../../src/topics/expressions.md:35 b38d66c12ab74dfc9395e69d9c04bbf5 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc -#: f403c1d4e43a4aa0aef8488d2b5a6262 +#: ../../src/topics/expressions.md:37 8417aa7a9d034361a41def6b71e93413 msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 -#: 249dffb569a944c897ce5862e5f28fad +#: ../../src/topics/expressions.md:47 c1f672b377da4605b9c5098ebb6e1147 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 -#: 1641c96aca2f4923885fe8a509eb3a49 +#: ../../src/topics/expressions.md:54 af52f5197e8545d2be22cc0f7f03648c msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " "describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 -#: bc63405a0d964df2bd9493996abc48fe +#: ../../src/topics/expressions.md:62 5e12ce15018942bf9010ce6519c17b00 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 -#: 5c191d1420db4e26aca31c1b1e34cb75 +#: ../../src/topics/expressions.md:64 e2e9c5f7b681427a9589476649e5a9d8 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c -#: d6a5c65e824a4bbc94578df9597d4716 +#: ../../src/topics/expressions.md:66 8a74763ead0147bbaf3892e552fad546 msgid "" "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 -#: 1acb064f7a4a482aa0174bdc847c6382 a7ff51fe564748229a88a0d3044dbc17 -#: c12625211cc542b68cb51365a63eef00 +#: ../../src/topics/parameter-references.md:64 0aab7de8d69f49438d4eeed17316df68 +#: 75f90cb870d14d0dbb4c4ee80d32a65e msgid "`arguments`" msgstr "" @@ -2042,39 +1805,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e -#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 -#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 05c34a5a2e404a14b9d284a9d0c73bd3 -#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe -#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 -#: e7f1993580f0425098a719e83a64cc7f +#: ../../src/topics/parameter-references.md:86 0b9d8268c177489b86b8eaa638dfa063 +#: 204cd6d8375a4462a8247863a96df906 2b7e56ceb4ad49a8b29a58b10bad7c0a +#: 81f15c64379941d8ac2a681b3879761c f11ae7d801db45989b598864dc6291c9 +#: fc4534b475334f7281d1740c9a78f640 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff 2fd5b42cafe34d3185888de041818dff -#: c158e9ee5fbf4e868b152a0a5880092f +#: ../../src/topics/parameter-references.md:66 70e9085b21f640d6893309a3375c0511 +#: f529003dd7a64bc7be0ccef8dbfa84b3 msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 3f29e4a3087847e9af6f19166a8def9a -#: 92697d3179ec48898eaea9aba3c24dcd +#: ../../src/topics/parameter-references.md:67 3fceb522ba6245129b826c342eaf31b4 +#: a5f71add5b8345a4bfa02853ef8a6d35 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 c0eaef93bc3743279549bcfb8b014ca3 -#: d6722e3093884ad7b62696fbb2f48fdc +#: ../../src/topics/parameter-references.md:68 018300196ea24550988a0156894b5e85 +#: 2c799286e8204ed9a83c3fc006988139 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e -#: 37c493fdc2f0410a9748f8faf09ce5b5 +#: ../../src/topics/expressions.md:72 25d91d6624bd42e7948e29c684e8e441 msgid "" "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandInputParameter)" @@ -2085,15 +1841,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc -#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd -#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 -#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb -#: ed875a006df64f9e8a55fa5e9fa87404 04e3eefe4ec445cb90c2fa42344aaed5 -#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 -#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef -#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 -#: c610220d06484d589313dc29faf8222c +#: ../../src/topics/parameter-references.md:90 0944d6525c3c460aa4b5a0e72552ca4d +#: 1187b0d330cb470fbea82a8b8c95aa28 265602307ccd42458ba47ac1b689242c +#: 2febce1b1ad74b18af3a9b3fa137c780 3215ee41f96541cbbda60a1167386c2f +#: 80efeab6ec0e447bbe158cbaa57f83d8 8d2bbd91b4ab4faa923fc1a14ec49dd5 +#: b4a6e640275b4fc7a18e3083e86b72a1 msgid "`format`" msgstr "" @@ -2102,62 +1854,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 -#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d -#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f -#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c -#: f760465a49d64d4c8468ad9c4fea62b1 662b36e3505f4ac3bb5070bb6e055217 -#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da -#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c -#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b -#: f71216a4b35e4157aece5ffa2602d8bf +#: ../../src/topics/parameter-references.md:91 480b2e4207574b27b8d33dfe5e9ab64e +#: 4b4149a3b97a4de5b2d7fd84bd547ffe 7af1a82df41e40d0a430babafe1bc5e2 +#: be01787b66e34074af32bb45dcce8657 be099ab533504a7596fd56ec1ce7ca5d +#: c8b96271665444608f601a460dd28fb3 cb6dfa7bc68b41929a5247d929c2f94a +#: f7f452e92f6d4a14ba3912c62699019a msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac -#: a3c775a0f04b4541a9b712bfe2e4e69a +#: ../../src/topics/expressions.md:75 4811c1b9867b44caa70dec4b91970484 msgid "" "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 -#: ef16c4a9a7ea415fa399297b63b9710c +#: ../../src/topics/expressions.md:77 0b1f2a8986e0419a90e484d3a945a037 msgid "" "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 -#: 2592e429c74c4ff5b8ba68a36f060c1a +#: ../../src/topics/expressions.md:80 dbc02876870d49d2b9e39db4133a0f62 msgid "" "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 5cca4c2ad617400eb6efad4066b1839b -#: ba1fff3ebb274dfba845b3ee20ebd71f +#: ../../src/topics/parameter-references.md:78 97339a3fa43849f7b292f4643b5fe35c +#: da8b81b1e1884406a188fb04825ef90e msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b -#: d555a3d991e344a5a8e1289168d7c6d1 6914526c0a7c43a2a05438519508ee0f -#: 722d3bd7184841639b9f9a38914002da +#: ../../src/topics/parameter-references.md:79 077e7b0d2dde443699050af8c63ab912 +#: c8cbe3dfd0984221ae72012ea26edc6f msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c -#: e9fa9430535c424fa3e8be5d460d2ba4 737b0f9392154241ae5b56c6caa823f5 -#: 7b46d408e7e7481b91a950b2d4010c9a +#: ../../src/topics/parameter-references.md:80 3f07f4a8594640c2b2da4da521872b59 +#: 573f7e4b72ec4c47ab2e54e2c4877d9c msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 -#: f09e7371708b4c0685eef2a314791ccd +#: ../../src/topics/expressions.md:84 f03011b3479b47c690604c508d95c263 msgid "" "From [InputParameter](https://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" @@ -2165,108 +1906,93 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c -#: b0290d1a477b48119e17cf1fed9d6dff aa6ca1def2024c98b9d5542de1a81425 -#: e9fc5f7fa4474dfc95039b94167fe894 +#: ../../src/topics/parameter-references.md:84 1ec3f913909b4e04bb602767d23bd85d +#: 2f7130500b8c450fa4af226b18e38407 msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 -#: 6c37a1ff939748bf83a86c07c3d017fe +#: ../../src/topics/expressions.md:88 a5849a856a374cda807ecf48034af915 msgid "" "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." "html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 -#: e1cde4aa32c041238ed2596173c6d824 3a8126b0a0334df890b2be2c693ea5d5 -#: 61744122b7d7494890cbe6b2fb72b9f7 +#: ../../src/topics/parameter-references.md:87 bd8bbd60aaff4e7aacec91bcbad500f4 +#: f0c99004211e4adf8c0b524d5bbcc12b msgid "" "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." "html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf -#: c2a92d3eca7f4ee39cec649170eeea53 93cb9015dacc4b50a4ef177ce4ece2e7 -#: e0c7ccc8f8664cf794cbb7330355f3fe +#: ../../src/topics/parameter-references.md:88 96c544cf213245cfb3d1f5196223c6cc +#: c6a04d4f3ef24104b0a86f9093935c13 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 -#: 58a1773b1cf546d7890010fdebd47388 +#: ../../src/topics/expressions.md:92 946e0437a48b4d5da2a29d489250cbaa msgid "" "From [InputParameter](https://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [ExpressionToolOutputParameter](https://www." "commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f -#: 230f3227ed1144f7abe0f8c231bebbd5 +#: ../../src/topics/expressions.md:95 1f287ebf87ae4e93bd1ac65cc1d01bf4 msgid "" "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." "html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 5c77dc9f8afe4dd88933943030e836f2 -#: c9534670f5f04769aa3749c3778eb705 +#: ../../src/topics/parameter-references.md:93 0d0f4f0e12174d588c131afef70efc5f +#: a74e0e3499d644b4a9d999d3555f03de msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 -#: 718ceee9973240ec9c100977bbcc8921 4ec8bbac5fb14371a6a4cd53d7cd6450 -#: 7b0887a8caed41b2acccf7021bb323d3 +#: ../../src/topics/parameter-references.md:94 b2e31c38f7cb4ecabd6b9b89ef051c0e +#: ddc9d9ae72a64a76a2a8e2bba22584ee msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 -#: c07ab08eb75d4528949c56a3d7c12b28 aceedfb558b246bc87eb3eaedea187fd -#: e5e8b8c75f0f43cbb6e160e5bf810c6e +#: ../../src/topics/parameter-references.md:95 12f86817dfc14f2bb39509886d56017f +#: 8a94f2c3b1674162a268f67935a3025b msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 266dfb5fe6a842078baf66073cac9623 -#: fe3b9fb45e01490498c5a35c012b3de8 +#: ../../src/topics/parameter-references.md:96 a800acfefb3f433fae2cdda9ac4a795a +#: bcb58fc2447a4472b86913871b8c12ee msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 85f424cbfc85460f9da310aee1ff0b82 -#: ddf82b12b12d416fb65f3ce3f51bbdf0 +#: ../../src/topics/parameter-references.md:97 5be337d412ba4d48877e991d535e810c +#: e6cf2f8498db4f549193be20d87e16f9 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 966e88656ae5402a975022ee60646283 -#: af14fda3cca645fbb2f3c5825fe0788e +#: ../../src/topics/parameter-references.md:98 3bc61c8197664f12a98d1ac38b421b38 +#: 9973a87f747445ad89ce959420cac5fd msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 09120baec1464afb8aed4edd773bf509 -#: fec70bb106ad4d95a2d55ebdcf711afc +#: ../../src/topics/parameter-references.md:99 0f5dc4f5a4c64f818e2e22f20472ae84 +#: 2ec9d1f191f44686b1cb8622336d6b92 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 -#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 +#: 5382ff97ad2f419dbe1bed266997aa84 74406f77013443f28d4d6306c54b0df1 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 -#: 1dc4148caef748428a7d13caff37b1b1 +#: ../../src/topics/expressions.md:104 f594a20dc038457e815dc17bae6e031d msgid "" "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" "CommandLineTool.html#InitialWorkDirRequirement)" @@ -2274,39 +2000,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 -#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 +#: 5814f96ee4ec4822aecad33c8eda0473 c46c44268b2a4b96b1df13e53e82e54c msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce -#: 947b1ca132a54ed39745cd12ebcd65e1 +#: ../../src/topics/expressions.md:106 b9824103ef8745bab30b65887c82f62f msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b -#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 +#: 28b23f84c64549e7a0fe444ccc3e1b05 fdd5d742a6764e5db2281ed844bf3475 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 -#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 +#: b6123c911c804f3c8cb596d2aa495b2b d81a7d8b7db444409b286e5f1d863968 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 -#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 +#: eb6255a0f8d748588d87e7ad38e507bd fffc5a80bd68495396d32b7a1821eb4e msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 -#: 5fa512d352d945e7a3e0d59b0987cd1b +#: ../../src/topics/expressions.md:110 b00a8a2a572742e0929470550433e929 msgid "" "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." "html#EnvironmentDef)" @@ -2314,27 +2034,23 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 -#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c +#: 9b34c95e483e47f3828e79bf929a23b4 c968eebaf0114b23b789e9ce68e7588d msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 -#: 81e91df082834d2cab7ef1f62d8ba57a +#: ../../src/topics/expressions.md:116 7c8fb996d1af4cfdb0d49d8ed2696745 msgid "" "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 -#: e6bfd1dc2e324992b6c3332c11ae3445 +#: ../../src/topics/expressions.md:118 75a29e9ff2cf4b5bb6afa87a741a111b msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib` " "attribute that allows users to load external JavaScript files, or to provide " "inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d -#: acf10261df2944ec890d754fd56c6b28 +#: ../../src/topics/expressions.md:122 5233d8baa8b74391bf8fee5ae2324234 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2342,8 +2058,7 @@ msgid "" "the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b -#: bda6b8f398554b0c946c2c7d96308a42 +#: ../../src/topics/expressions.md:128 343e8b78a1f94b8cbafac05212e5a333 msgid "" "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." "org/v1.0/CommandLineTool.html#Expressions) that the only version of " @@ -2352,63 +2067,53 @@ msgid "" "in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c -#: 454c02c3918647039c90ae387005dea6 +#: ../../src/topics/expressions.md:135 0657ee8f03d8462ca6ca6fc538386b0d msgid "" "For example, we can use `InlineJavascriptRequirement` and write a JavaScript " "function inline in `expressionLib`. That function can then be used in other " "parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e -#: e1fad28bf9cb4c4c85eb74dd520ba107 +#: ../../src/topics/expressions.md:139 e3c593cf50da426f8d9df215c7db0bc9 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 -#: 9835d0b399b84a0084fe5a4d9e7e6405 +#: ../../src/topics/expressions.md:146 b971e53c3ed847f1b7c7a6d50e344baf msgid "" "Running this CWL workflow will invoke the JavaScript function and result in " "the `echo` command printing the input message with capital initial letters:" msgstr "" -#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 -#: 410ba7a5ac6349a98460c6337ee5c4fb +#: ../../src/topics/expressions.md:149 d2315d46369f4e9d9c871d7f88f7006e msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 -#: d2daf50d7f3d4de18331c8fd2c8a5786 +#: ../../src/topics/expressions.md:155 04fdaa45a7ed47d5830181611bda924e msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db -#: 8f2015c12b2b4d5d9a800ddeaf428f25 +#: ../../src/topics/expressions.md:158 8d7686f62f314d98aae8c262befd5283 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 -#: f0ff919ffc12439d89d7b40f51ade84c +#: ../../src/topics/expressions.md:164 e68ee17607be4a06a66f9fc67624aff5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac -#: 307a17a893fc4dafaec2a63a95704644 +#: ../../src/topics/expressions.md:171 76b85d3729274fc08adfadcbf1172650 msgid "" -"The `custom-functions.js` file is included in the CWL document with the `" -"$include: custom-functions.js` statement. That makes the functions and " +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 -#: 7f393e86b114470f8dda47b2deec63aa +#: ../../src/topics/expressions.md:175 29f334957fa940c289f385160cca6d63 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 -#: c3f459b87b96435583637b3f1573e658 +#: ../../src/topics/expressions.md:181 6d255ae6b92a48fa9b7b98443cc2f5bb msgid "" "Finally, note that you can have both inline and external JavaScript code in " "your CWL document. In this final example we have added another entry to the " @@ -2417,18 +2122,15 @@ msgid "" "functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b -#: 9f676022eb2744839ca2109920250cb6 +#: ../../src/topics/expressions.md:186 89734e7855654b2e8bfddeea96241539 msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f -#: ede7285f77864fb0aee6cfecc2c97fa0 +#: ../../src/topics/expressions.md:193 1915f8e68f624027827d28f8e17d2dec msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 -#: c55fb184bc614ee2b6e5e64611e5df9b +#: ../../src/topics/expressions.md:200 750f94edb4f84e45a276f6ab28fad95e msgid "" "The `$include` statement can be used to include a file from the local disk " "or from a remote location. It works with both relative and absolute paths. " @@ -2436,13 +2138,11 @@ msgid "" "html#Include) from the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 -#: 66b522f46ce242149386e79f63b32cf8 +#: ../../src/topics/file-formats.md:1 2e9e8cfaf48a43a88c31a855dac4f748 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a -#: 64a20285785d48ca86227a0cf6353ad4 +#: ../../src/topics/file-formats.md:3 c574b54d998243f28d2caa91434968a7 msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This helps " @@ -2450,8 +2150,7 @@ msgid "" "simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 -#: 5f71bbe2c74e4260b79d4d9230d35397 +#: ../../src/topics/file-formats.md:8 b0ec34507eea473c91d6ada09a1c5c09 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM in " "our example), reference a local ontology for your institution, or do not add " @@ -2460,39 +2159,33 @@ msgid "" "file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a -#: 63bfff437e3348428f7e33ece7ec55e7 +#: ../../src/topics/file-formats.md:14 a688e39859734a518c0fcc19f532a432 msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` section " "of the document in greater detail, so don't worry about these for now." msgstr "" -#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f -#: 6ce83d9c06e4436881aa47d94ef41e0b +#: ../../src/topics/file-formats.md:17 e068422ad9b84ca1b27008127928cc0f msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 -#: 55006c594abf4e70a38e979568fadcf4 +#: ../../src/topics/file-formats.md:20 8c3ef5e145b14299bf3671add0da56ac msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 -#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 +#: 0d92f1c0f1ce448fb698e9b390b45c15 fc4773204ebc4e3789bb076dff0d0393 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e -#: 1a1905ff2d624eca952c8a53b3bee678 +#: ../../src/topics/file-formats.md:32 900abc5aa6a940f48f9c93e79cd1c47f msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b -#: 368ff92476b14f5c8331260eafc5acb5 +#: ../../src/topics/file-formats.md:34 0390555b96c84aadbd9325c152972087 msgid "" "Below is an example of a parameter file for the example above. We encourage " "checking in working examples of parameter files for your tool. This allows " @@ -2500,13 +2193,11 @@ msgid "" "parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc -#: 5d530afa23f349a79f54d51d40724747 +#: ../../src/topics/file-formats.md:39 d5752ee5437b496ca10f4f12b76fc5dc msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d -#: 16f965f86712483aa7f95dfa3f944a17 +#: ../../src/topics/file-formats.md:45 91dc76bb4565473ab948eecf628a405c msgid "" "___Note:___ To follow the example below, you need to download the example " "input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff -#: dc629e2c90ed458b96107a6994676434 +#: ../../src/topics/index.md:1 0b8b9b7f533543a49f876421ce6057d9 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 -#: cf2f077cf8044079a7005e6e508dcd8c +#: ../../src/topics/inputs.md:1 1b6cfac3a92347d4b98bb54de1e26870 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea -#: 129e1d2a71894d28b009f4846754a75d +#: ../../src/topics/inputs.md:3 53dd5f476f064cbf9b9826d1e80eb830 msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e -#: d6791bbe575042b9a7282c69407dd907 +#: ../../src/topics/inputs.md:5 420b33d143fc44d1b237bc678f0af663 msgid "" "The `inputs` of a tool is a list of input parameters that control how to run " "the tool. Each parameter has an `id` for the name of parameter, and `type` " "describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a -#: e8da87f8bb664334adf831995601f462 +#: ../../src/topics/inputs.md:9 55136332e3bb48f892cf6a74c67a4ac6 msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*, " "and *null*; complex types are *array* and *record*; in addition there are " "special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 -#: de6c322618304207b6d1364d1ec2dc13 +#: ../../src/topics/inputs.md:13 cb2527899cc04b6d8060c4d57883beb5 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed -#: 43bdcf6dc1b14030bff27fa53289c02c +#: ../../src/topics/inputs.md:16 c79668b856b14243b4fad0f46dc5d6d7 msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d -#: 056510b42ea64717996ab49c307bda86 +#: ../../src/topics/inputs.md:18 ed6f3e5c7b3f403a9a94359983107645 msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e -#: 6852f5dbd9094c99bb68f2a88f76c9bc +#: ../../src/topics/inputs.md:24 034075eb09db4897a96d3332408427db msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 -#: f33b6800367248b7927d97ad7b4be5b5 +#: ../../src/topics/inputs.md:26 08181d391cc543a5a81d3257654df213 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 -#: 8ad812d7e88f4cbba83228ffb1711576 +#: ../../src/topics/inputs.md:33 15215522e38242c4b17ec3aa089269d4 msgid "" "You can use `cwltool` to create a template input object. That saves you from " "having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b -#: cc680bbf091a46f8b4b3dbe6324c040a +#: ../../src/topics/inputs.md:40 64bd3382ec234ec8a50217b794b96916 msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " "> inp-job.yml`, and then modify the default values with your desired input " "values." msgstr "" -#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 -#: 446ac81f078d46289a18f494748f482c +#: ../../src/topics/inputs.md:44 3611c1ca498a4197a4a6612c60f5f565 msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b -#: 3d6d958d111943f3a2139b4dbb7810db +#: ../../src/topics/inputs.md:47 da924e8142d34e86bcb5de1cd1da71ca msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da -#: ba0ec9157709430c822f4e91459288e2 +#: ../../src/topics/inputs.md:53 13c97256a5ee49c99f4010edf9dbc9bf msgid "" "Now invoke `cwltool` with the tool description and the input object on the " "command line, using the command `cwltool inp.cwl inp-job.yml`. The following " @@ -2610,8 +2286,7 @@ msgid "" "command line:" msgstr "" -#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c -#: 2565f8fd4a15429e887aeb71eacdff1e +#: ../../src/topics/inputs.md:64 dcc3f2a47a6449efb857af63ed4b65d0 msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2619,8 +2294,7 @@ msgid "" "specified" msgstr "" -#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 -#: 659ed5c64fb546399b741553a347b8e8 +#: ../../src/topics/inputs.md:70 cf54a30ae24f4013bb19f379a7ca67be msgid "" "The field `inputBinding` is optional and indicates whether and how the input " "parameter should appear on the tool's command line. If `inputBinding` is " @@ -2628,16 +2302,14 @@ msgid "" "each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c -#: 3d87e69d41374fbab23b26d36c1aee03 +#: ../../src/topics/inputs.md:83 ff75644bae9c46af8379d78360d4c696 msgid "" -"Boolean types are treated as a flag. If the input parameter \"example_flag" -"\" is \"true\", then `prefix` will be added to the command line. If false, " -"no flag is added." +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 -#: 07bc81683e2c4ac68b379462bae95207 +#: ../../src/topics/inputs.md:95 e90abe59a84e48d4b8d6caa737e087aa msgid "" "String types appear on the command line as literal values. The `prefix` is " "optional, if provided, it appears as a separate argument on the command line " @@ -2645,8 +2317,7 @@ msgid "" "string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e -#: 3e304da2150f448d9e39715ac5f5deaa +#: ../../src/topics/inputs.md:109 9275236d87b646cab1058dd750e11a50 msgid "" "Integer (and floating point) types appear on the command line with decimal " "text representation. When the option `separate` is false (the default value " @@ -2654,8 +2325,7 @@ msgid "" "example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 -#: fd8a98686e3c4c609f79ae427f1558d3 +#: ../../src/topics/inputs.md:124 6a39929af73f4ba9b6455ed9fd287e08 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the parameter " @@ -2664,15 +2334,13 @@ msgid "" "provided in the input, nothing would appear on the command line." msgstr "" -#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 -#: f1a2e1bbb1104a4fab5a7f04cac845c7 +#: ../../src/topics/inputs.md:131 44ce716561cc4dff8fef1ca59f816c7c msgid "" "Input files are read-only. If you wish to update an input file, you must " "[first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 -#: 6a7f0ccd227e4f90a8c8ca96744bda68 +#: ../../src/topics/inputs.md:134 9f1da592350f40ee88920465e2004148 msgid "" "The value of `position` is used to determine where parameter should appear " "on the command line. Positions are relative to one another, not absolute. " @@ -2683,20 +2351,17 @@ msgid "" "position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 -#: 1f79d115d8a145189638c68c3095396c +#: ../../src/topics/inputs.md:142 5116d91f247f44518eb21840415f6eaa msgid "" "The `baseCommand` field will always appear in the final command line before " "the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 -#: 6e1b3e2d90184e34925891099d2b5cc1 +#: ../../src/topics/inputs.md:146 08b26d1688e3470288e73d587f052d88 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d -#: 4f6df7f13e42448eb4a53f03bc477b56 +#: ../../src/topics/inputs.md:148 f91994a4279a41bda3de41fe79008c62 msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to provide " @@ -2705,28 +2370,23 @@ msgid "" "after the type name to indicate that input parameter is array of that type." msgstr "" -#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 -#: dbc0b52627514ad0908969d0b4ddfdf4 +#: ../../src/topics/inputs.md:154 4b93a4f980634e88a8f34a38703fc906 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 -#: f173dd96ad124470a53573c86a8df203 +#: ../../src/topics/inputs.md:160 de3e760ebb0e4ae099deddb978046a2c msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 -#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d -#: af25945b530048b685891b1de4e35e72 cb07caa4ff0149b3ae832be53f8d76f6 -#: e0098a77080d4349b05ceb7735a5fdf5 +#: ../../src/topics/outputs.md:105 06ec811e8f0e43b8b929198533ac8082 +#: 797c06f0605d4e4ba306c2803a7834f9 d76d42c490a24b6daed944f45fe7a351 msgid "" "Now invoke `cwltool` providing the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 -#: 2445d2c7c2794fd3ad8b6ed8b4a9440b +#: ../../src/topics/inputs.md:178 49406f30f62346968bb1250efc940f70 msgid "" "The `inputBinding` can appear either on the outer array parameter definition " "or the inner array element definition, and these produce different behavior " @@ -2735,8 +2395,7 @@ msgid "" "concatenated into a single argument separated by the item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d -#: 4459819ba75647d185986a3386939494 +#: ../../src/topics/inputs.md:185 3d8711f0135e4ab1b59fce94c83b97c0 msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` in " "`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " @@ -2746,13 +2405,11 @@ msgid "" "arrays of arrays, arrays of records, and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 -#: 8f163bd34ded4785b6e28c8e2147e0dd +#: ../../src/topics/inputs.md:191 6f146779d6a84888948751b8b1fd0515 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d -#: 1799e11a7b9c4929a3d1379d7ea45d03 +#: ../../src/topics/inputs.md:193 e5970a83876e4b5e9a02f2ab0030eb83 msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be provided " @@ -2760,55 +2417,46 @@ msgid "" "parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 -#: 9510c0b431a44b5e84e0b583de7c5446 +#: ../../src/topics/inputs.md:198 0db71b22173846d7b8d4aeb66d2ed8ed msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 -#: efb4eb6f5e994b50a52fa2c707dad1ce +#: ../../src/topics/inputs.md:204 f90fd48656a7424aac304987adf1b068 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f -#: 34599c6f10ce4104be2359a1b37f91cb +#: ../../src/topics/inputs.md:215 3c8bd9134a1c4bda9461362df3257d6b msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b -#: 0663ea7918994d3f9c45c652a3ed12db +#: ../../src/topics/inputs.md:217 63bd06780bb949e5b1a1d10389c8c23f msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add -#: a98dda6ca4b14edba467de638bba28fc +#: ../../src/topics/inputs.md:233 0d448baa57f14e7783d3167611e8c659 msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the first " "matching item (`itemC`) is added to the command line and remaining item " "(`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea -#: 10d0e9f8df8c47788703073b17529bc8 +#: ../../src/topics/inputs.md:236 202239a6e90044e39b676d641aa6d58a msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c -#: 9a0e1a130fba4d24a9168ca3e455cd23 +#: ../../src/topics/inputs.md:252 512ecb3349b0450cb741de4ed2d2e850 msgid "" "In the third example, only `itemD` is provided, so it appears on the command " "line." msgstr "" -#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 -#: 992a8c801ceb4233acf56b6bff315188 +#: ../../src/topics/inputs.md:255 185ff0bb49e841c592b29112eb171bdc msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d -#: 9027d23fa7074b789c3b86ca5ea17fa4 +#: ../../src/topics/inputs.md:257 6cd5df09e4594d78a526f199ac577881 msgid "" "If you use exclusive input parameters combined with expressions, you need to " "be aware that the `inputs` JavaScript object will contain one of the " @@ -2816,21 +2464,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb -#: 68b47710a8ea4b978428b42c627944e9 +#: ../../src/topics/inputs.md:262 9db9f784a5cd4ca5b90691d1e2e827ea msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from an " "enum." msgstr "" -#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 -#: d33e4cac65d14111a89c838c4d1759b9 +#: ../../src/topics/inputs.md:265 09b1db3cc6c845058cf0ad4c24d71733 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 -#: 24cea1cf7d774b6ab56959f289cab39d +#: ../../src/topics/inputs.md:271 84aa6e0c479f4528836691005129056e msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you provide a " @@ -2838,16 +2483,14 @@ msgid "" "should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 -#: b866867d6f8e4d3999b62a85e6884ebc +#: ../../src/topics/inputs.md:280 76611ebb19764bdc8a1f6eacfb76138f msgid "" "However, if you do not provide any input value, then `file_format` will be " "evaluated to a `null` value, which does not match the expected type for the " "output field (a `string`), resulting in failure when running your workflow." msgstr "" -#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 -#: 80c49ed168b14d25b2f09b3b0186b44f +#: ../../src/topics/inputs.md:289 bf9750d215be4294b1cf1e0490a0796a msgid "" "To correct it, you must remember to use an or operator in your JavaScript " "expression when using exclusive parameters, or any parameter that allows " @@ -2857,12 +2500,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 71628ebe908b4cd28dd1fa17e3d2e2fb +#: 612f9efa0ed04559a174c37958def6f7 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 f123ca244c23413c91405a4b84887525 +#: 57eb990c11f044dfb60c012a92a30eb1 msgid "" "Implementation extensions not required for correct execution (for example, " "fields related to GUI presentation) and metadata about the tool or workflow " @@ -2877,7 +2520,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b 23299ae1bec94b00a32a8af7eeac350f +#: a6e6155cb8ff40fb9d8b1fff3e94fb02 msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to cite " @@ -2885,17 +2528,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 2495a9f2032a47c188338cb81ba429eb +#: 063c28fc9e654dfd91c66da164ac1d3d msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 3fd2f3cf7bdf44089df2ce3122534801 +#: 8fcd2ae1ce8d4c7f951281ced81ab32d msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 d5a5b8b490b640439db92da949266e4e +#: 639533652456427480fa311da7beb4f0 msgid "" "For those that are highly motivated, it is also possible to annotate your " "tool with a much larger amount of metadata. This example includes EDAM " @@ -2905,17 +2548,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e 5935ed94331d4b2f8ce597f31edea843 +#: 266808daf2004bbd9830045fbc67a541 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f -#: 5feb559552194ba58da7206c601292fe +#: ../../src/topics/operations.md:1 fd9b715bfa3243b19a919ad19843232d msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 -#: b7124ba4df9042baadc1641ee09545d6 +#: ../../src/topics/operations.md:3 fb568063fa7a4cbe83c271772d3d62bc msgid "" "An Operation is a type of CWL process, just like a workflow, a command-line " "tool, or an expression tool. It is a step of a workflow that specifies " @@ -2923,66 +2564,56 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d -#: d34b698c62114041a64e0abce25ca935 +#: ../../src/topics/operations.md:7 981486166754435cbcd8152e93679405 msgid "" "You can create operations to visualize a workflow during development, before " "you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf -#: cba2c31262bd450cbafc7ca77f4fb8fa +#: ../../src/topics/operations.md:10 7b165718ffeb42e793c97fad807f216f msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 -#: b01be5f632104096b5af6193aab34d90 +#: ../../src/topics/operations.md:16 5e31cddd14414d31b7bd0a6c2745d272 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like a " "command line tool or an expression. You can also plot it with the CWL Viewer " "or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 -#: 60a6a02c1367403db6df3ec10f75eb69 +#: ../../src/topics/operations.md:24 02c372245dc9453ea0841026335e405b msgid "" "The output of the command above can be rendered with a Graphviz renderer. " "The following image is rendered with the Sphinx Graphviz directive (this " "user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 -#: 314ea7bc35154f41b2af5fa6683ca389 +#: ../../src/topics/operations.md:55 d331327285d1434e8c17187737345919 msgid "" "If you try running it with `cwltool`, the command will fail since `cwltool` " "does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb -#: d81e679b13474f74bc5e1ce1e31c2bc6 +#: ../../src/topics/operations.md:58 72705f8940bb4194bc5554fcc29eed49 msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f -#: d7fb27131ee44bfc82f698ee44b2bae0 +#: ../../src/topics/operations.md:66 76b7c63107e94323859904415d07d31c msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A " "CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de -#: b8ef11eafd1d46e088f1277f4ac372bc +#: ../../src/topics/outputs.md:1 ebf56d267612461799bf801136e61b69 msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d -#: d2382ed1f644459594655d5b5b4d838a +#: ../../src/topics/outputs.md:3 f9cff6b272a24ef6ada90e263c1b1784 msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 -#: 6651632d977b44479b721174fffeda2d +#: ../../src/topics/outputs.md:5 e482821911004cdd8c3ff1539c69368a msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name of " @@ -2990,8 +2621,7 @@ msgid "" "parameter." msgstr "" -#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 -#: bee5f532554241088764ac9e56abbe85 +#: ../../src/topics/outputs.md:10 e11fcfe1e84b476ea879810b76ff2cb8 msgid "" "When a tool runs under CWL, the starting working directory is the designated " "output directory. The underlying tool or script must record its results in " @@ -3000,20 +2630,17 @@ msgid "" "from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 -#: 0c7c506f38be421399073871f64e99b0 +#: ../../src/topics/outputs.md:16 65c73a37f06a4782bf43f4acf4f1c77e msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 -#: 8b60286e56cc42a8ab5f751a97adf771 +#: ../../src/topics/outputs.md:19 e172dde545164fefac826d910ddd399e msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c -#: fa0ad674f15348339a1eee771a6ba9e2 +#: ../../src/topics/outputs.md:21 225f4d04c28149898f06bd771f741358 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -3021,85 +2648,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f -#: 177b5f1b95a34fb9b2eb42f733d79ac8 +#: ../../src/topics/outputs.md:26 14e9e446768a454ea786b3256b49632e msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a -#: a08a6d8aca8e490482e127a8fd5e650e +#: ../../src/topics/outputs.md:32 4bd659cee1904868a7c33345f94f1300 msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 -#: c2c60f68b1e045f88844076e191fda9b +#: ../../src/topics/outputs.md:38 8803a28ccff846eea7d06f4bd908c763 msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb -#: 6d939f62526e4e6d95acb57d72f60a84 +#: ../../src/topics/outputs.md:45 661b62e554d64e449c69e475e5188f99 msgid "" "And now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d -#: c48edd9034364b81ad42540a98b51d91 +#: ../../src/topics/outputs.md:51 44cdca5b777441baa246c87940df7264 msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 -#: 9ebe0186a7124dfaa30e558e8f59653a +#: ../../src/topics/outputs.md:62 edb34af3b22d418d9a6178c0ecbb8b80 msgid "" "The `glob` field consists of the name of a file in the output directory. If " "you don't know name of the file in advance, you can use a wildcard pattern " "like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 -#: 9381b7d7c9904df0a5e16dac29c2e08f +#: ../../src/topics/outputs.md:65 10e68fad866f4187981f0b365b957b03 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 -#: 2aa9c6916e3546b7b92fa64bb83275d1 +#: ../../src/topics/outputs.md:67 77e1261484964ba9ac67d9fc9139a1d6 msgid "" "To capture a tool's standard output stream, add the `stdout` field with the " "name of the file where the output stream should go. Then add `type: stdout` " "on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 -#: 63afb7a597fc4e459b6a7dbd40bbf6ff +#: ../../src/topics/outputs.md:71 c66bd08354d54ccb9e3e1da89634a816 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 -#: 7418915470f041c9af5bd39ea652de36 +#: ../../src/topics/outputs.md:89 7d4056355da1451dbed6733fba8c3c38 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d -#: f82db001b58c4969b2d8bc1dcbd7cf8a +#: ../../src/topics/outputs.md:91 8fed80f9633a4e87a67c651dc3160ce6 msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 -#: 26d9f0b28d384617a8e490c1f8e26e52 +#: ../../src/topics/outputs.md:93 6cba36e037d54f93add05fb16d2359bd msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae -#: cf46c971b31b4e10bf0fefb4cd028c2f +#: ../../src/topics/outputs.md:99 08862892ecf849a1ba2f25ecc9e98227 msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 -#: a4347983fb9945a4a2773af88e426dc9 +#: ../../src/topics/outputs.md:112 c5dcc68bb28041b3b96ac1af716b0db8 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -3107,13 +2720,11 @@ msgid "" "mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 -#: c5489e0633114372b273098ee2c9ffd9 +#: ../../src/topics/parameter-references.md:1 53b95fd10d61462daf153d45e5517dad msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 -#: 75de9fd63393429daf1ca10a85339aa7 +#: ../../src/topics/parameter-references.md:3 0702e71de81e493dac08a91d667569e3 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file we " @@ -3126,47 +2737,40 @@ msgid "" "specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 -#: 8b5d0ada32d645be9359f43a431f5f91 +#: ../../src/topics/parameter-references.md:13 a1703da32ad64fd2b8bdd423605b50bd msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 -#: 2ed93dc8778e44209194f41b9ad193d5 +#: ../../src/topics/parameter-references.md:19 2f32531e47b4465594d41ddd218fb2fd msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 -#: a80dd6d9920540e9880514e04035af86 +#: ../../src/topics/parameter-references.md:25 501dd6f9dbb1438f9a59f6a025639f35 msgid "" "Create your input files and invoke `cwltool` with the tool description and " "the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 -#: 9de300f7b9da49f59d1c9fd96dec4a8b +#: ../../src/topics/parameter-references.md:36 1bcdd99111bd4bc5b75a8297bb61d9bb msgid "" "Certain fields permit parameter references which are enclosed in `$(...)`. " "These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 -#: a61f52d3c1024c3692899e05fcea4bee +#: ../../src/topics/parameter-references.md:47 32eae36c593e43a9a6b4e103a0c2028a msgid "" "References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" -"$(inputs['extractfile'])` are equivalent." +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 -#: dafc9ba578c14fd79d075160e6b7bd6b +#: ../../src/topics/parameter-references.md:51 1d785e8a450140a982142aa0fa906257 msgid "" "The value of the \"inputs\" variable is the input object provided when the " "CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 -#: 28ca6cae42904559bcec98fb9d2b07cb +#: ../../src/topics/parameter-references.md:54 e862bb8bc3e84e24a2aa5ec34298cfd5 msgid "" "Note that because `File` parameters are objects, to get the path to an input " "file you must reference the path field on a file object; to reference the " @@ -3174,112 +2778,101 @@ msgid "" "path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 -#: 616c9ff9fcae489285f0bbbc67f07d29 +#: ../../src/topics/parameter-references.md:59 46ffaab11be040cea96a294d9a814738 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad -#: ac17acd83ddb43dc9fb7a5e595ab1153 +#: ../../src/topics/parameter-references.md:61 890d619c415741179c83ffcd56833fbe msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 -#: 156573324cde41ee8b3c47deabf43db8 +#: ../../src/topics/parameter-references.md:63 373e1847d9f745d7a749928642c8e0e3 msgid "" "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 -#: c9725be01e8a401fb3ad9ff01339f81e +#: ../../src/topics/parameter-references.md:69 90d3624e062c41c7a6d1a9824515d0df msgid "" "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 -#: 6797335256e2412cbbe7636507931455 +#: ../../src/topics/parameter-references.md:72 76d09490bd464b708c28991dbff0104e msgid "" "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f -#: 05a5f0fcb7454cb697e3d810d55fac26 +#: ../../src/topics/parameter-references.md:74 f33c76e590dd4feaac1e3cf568069d33 msgid "" "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 -#: 406e68280b5c4ee494632f94b635b7ad +#: ../../src/topics/parameter-references.md:77 74ed4a06c1984c58826ddceb1a45a4ea msgid "" "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 -#: 2d6e2a4ff391494591bbdf8dbcc4a6ae +#: ../../src/topics/parameter-references.md:81 eba3362d34354daa89dc516722c6fbd0 msgid "" "From [InputParameter](http://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" "v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 -#: e71a974b29624210a107fc2d097d4196 +#: ../../src/topics/parameter-references.md:85 e924874af32d4be19c5e8446768226dd msgid "" "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." "html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 -#: b59df98754e24654bfef0b1fe1d91660 +#: ../../src/topics/parameter-references.md:89 b162113f364445af9ff1bfc8a6610e13 msgid "" "From [InputParameter](http://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." "org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c -#: d2bccbff1ce646348fe38c776ad183e1 +#: ../../src/topics/parameter-references.md:92 aa721077e16948c3a5bb8ef5bd7aff04 msgid "" "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." "html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 943ba46512ce48fe8c5b62327734c503 +#: 2fad0c2bc2834350826b22c454d33cf0 msgid "" "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" "CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 bbcd43d5af7d44108aeb65075a6bd2be +#: 9e303aa89a9b4447b0dbdc5ac0a0eb9e msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 834295755af841a78e466eea43864861 +#: 7a4eb47c25a54d11a00eb73e9333ad1c msgid "" "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." "html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae a6b626489bfa468e8f059ab3aa669201 +#: 8a957bc8e577476bb59647661b3c0990 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 e1dbea105aa845c38cb1f90b43847271 +#: 2b31f1dec3f5498e9e363a4f1f50dc8d msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb e9640f47d40e45bca184eb30700df648 +#: 5a5f84ecc2f449bf9f037dc9da0ac670 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -3289,14 +2882,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 0456efb3718b4356ad2b277ee16de967 +#: ee89f1526c1f4452b4e36ba67bb59747 msgid "" "In this example, the software requirement being described is InterProScan " "version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 f7e97f926505407f8f8e9a427e055e43 +#: c76cec44f5424f6087df28aa33c521a2 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -3305,7 +2898,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 ec597ff8f6ee47bc815b069335869f1f +#: 072d7b3ce3284ed994ff0736b43bbb86 msgid "" "As well as a version number, a unique resource identifier (URI) for the tool " "is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " @@ -3320,13 +2913,11 @@ msgid "" "main tool citation and the URL to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 -#: 7467a7f6f26a459ba4ce83e4e6dfcc2b +#: ../../src/topics/staging-input-files.md:1 395d611104604a28b78e11b112a95027 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 -#: 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 +#: ../../src/topics/staging-input-files.md:3 811b4db0b1794fa89dc870f6cb59a3cd msgid "" "Normally, input files are located in a read-only directory separate from the " "output directory. This causes problems if the underlying tool expects to " @@ -3336,31 +2927,26 @@ msgid "" "base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 -#: a03372581fa44f9b8e3e088a4099cdd9 +#: ../../src/topics/staging-input-files.md:9 7159b5c5023c47128057c4116cce69f4 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 -#: 36e082be73464be0ad5d0b681cc510da +#: ../../src/topics/troubleshooting.md:1 3bfa6791d78f43629de90345f4441ebb msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 -#: 4464455b51ad4873ac13c4a63ee5fb54 +#: ../../src/topics/troubleshooting.md:3 9a6bd5b684a740ed9e8993d9f8607774 msgid "" "In this section you will find ways to troubleshoot when you have problems " "executing CWL. We focus on `cwltool` here but some of these techniques may " "apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da -#: ed7ff0753d1743a995f4cfedd6e5dcc2 +#: ../../src/topics/troubleshooting.md:6 6db8a02139644598894220d538c590b9 msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 -#: 4c2dd10dd66446058477a52fb8d2c602 +#: ../../src/topics/troubleshooting.md:8 f0da0f6283d44bcc95224eb9fe2d1764 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor output " @@ -3369,8 +2955,7 @@ msgid "" "directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b -#: 978b6a5fd5fa425fa9a18d9f0e8788da +#: ../../src/topics/troubleshooting.md:14 e2fc28b44ffe4254892a7c7973dc80c4 msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " @@ -3379,20 +2964,17 @@ msgid "" "of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b -#: 000c0d6ae8bf414d9293b9f13fd2e448 +#: ../../src/topics/troubleshooting.md:20 505c7cf9ee9c4af1aeed29002eed1b33 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f -#: 7e91b8811be14f8e80df39ac4c5bd316 +#: ../../src/topics/troubleshooting.md:27 4c31fd11a28943538690d04baa2b5dd0 msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " "(`cwltool` will create the directory for you if it does not exist already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac -#: d42799cc5bd4484bb6beb309a61e103e +#: ../../src/topics/troubleshooting.md:35 a8532ac700014db4bd8ef690a27fb844 msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -3400,8 +2982,7 @@ msgid "" "can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 -#: 48bb0f6666ac48648c7d969608b3bd48 +#: ../../src/topics/troubleshooting.md:44 94a6148512b24b90b87fd1312a926d75 msgid "" "Each workflow step has received a unique ID (the long value that looks like " "a hash). The `${HASH}.status` files display the status of each step executed " @@ -3409,8 +2990,7 @@ msgid "" "output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 -#: f8876044db184cbaaca56579d0c773df +#: ../../src/topics/troubleshooting.md:48 ec4165b7c25c449db6a8804161805e80 msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " "the `step_b`). After fixing the typo, when you execute `cwltool` with the " @@ -3420,8 +3000,7 @@ msgid "" "now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 -#: a5a3d408dbe34cfda4dd0b2abe67e7d7 +#: ../../src/topics/troubleshooting.md:59 5c0b71a6376848d4aa491854ea2d185d msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had " "been cached, and there was no change in its execution or output. " @@ -3431,18 +3010,15 @@ msgid "" "re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 -#: 4c240a18c4e6441189489011242c1efd +#: ../../src/topics/using-containers.md:1 95b832552e8443ea9c652f8c95afc01e msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 -#: e37e76ef376a4ee695e600998906ec1c +#: ../../src/topics/using-containers.md:3 561fc9c561bc492ea82c17784dfd439c msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 -#: 51a307b0ba7c4c1d89309ba8d2250471 +#: ../../src/topics/using-containers.md:5 2420b16855cf4b25af5bcb87413f6dd9 msgid "" "[Docker][docker] containers simplify software installation by providing a " "complete known-good runtime for software and its dependencies. However, " @@ -3455,40 +3031,34 @@ msgid "" "containers." msgstr "" -#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 -#: 13cc38d72d34468fa4eb6d91f23ff105 +#: ../../src/topics/using-containers.md:15 f5266ee2c2b34170bc89cb501b869893 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the container." msgstr "" -#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a -#: 42a48398d3ef4b03bd7395120f2cfb42 +#: ../../src/topics/using-containers.md:18 728166bf41504e1d89b755400742a1b4 msgid "" "This example runs a simple Node.js script inside a Docker container which " "will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 -#: d59387b433bc4ecfaf7e72026624db02 +#: ../../src/topics/using-containers.md:21 104351ac29d247cb8e017228e2c9b3d8 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 -#: d963418ccc0b4803bbc758d718ccb5aa +#: ../../src/topics/using-containers.md:27 e11a38bfb30b404c99d223647960cb16 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed -#: a224d1510c9e46aab23d8bdc03c349dd +#: ../../src/topics/using-containers.md:33 7ed0bd21e998417cb02fdcb8e44734b6 msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that is " "really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 -#: 0a82f8a45b0546aaac4c976dcc98014a +#: ../../src/topics/using-containers.md:44 9dcddf6812ba4bc2a7d6c5fcdb978a68 msgid "" "`baseCommand: node` tells CWL that we will be running this command using the " "Node Js runtime that is meant for Javascript files. We then need to specify " @@ -3501,27 +3071,23 @@ msgid "" "called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 -#: bc418a2a535e49359c4cd44b373bbe02 +#: ../../src/topics/using-containers.md:52 bc1a09475f154562a4db445bf81ac92f msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " "the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 -#: a799fba2322944cea00e413c08066536 +#: ../../src/topics/using-containers.md:55 2e117019ace84604a8ed5a31214c2587 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 -#: 35379c6b972940bd8451f10b74dd793e +#: ../../src/topics/using-containers.md:69 d0d5b2a1a008411e92859a72101088c1 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 -#: 2d5265525ad544a0b64ad2cf07aacc26 +#: ../../src/topics/using-containers.md:72 591d1cd0282b4095a267b44da7d59804 msgid "" "In this example, the path to the script `hello.js` is `/home/me/cwl/" "user_guide/hello.js` outside the container but `/var/lib/cwl/" @@ -3529,51 +3095,43 @@ msgid "" "invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 -#: e2521b89596d42f8a87a3207fd6c32f2 +#: ../../src/topics/workflows.md:1 9f989fff165448ecbcaad6adc0f58d6b msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 -#: 3676f23b63e142cb8e5715ae07216a47 +#: ../../src/topics/workflows.md:3 212c82dca23645e89d8b5bb7599f2d25 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 -#: 00725aed13a440ca8b3c4f9155fbee99 +#: ../../src/topics/workflows.md:13 7530029ec04746f2a888dcbc10aa5ce4 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 -#: 2e38a4f9072b4ad9bbb74f943d22084d +#: ../../src/topics/workflows.md:41 c1f1d644b37b4f018b87e15249d8758d msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier examples." msgstr "" -#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 -#: 2b9f4035ea864b6db50c861a1819289d +#: ../../src/topics/workflows.md:51 2d07232b7d9c415b8ad971e8cbcd9577 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb -#: 28e9064780e7418a8e02a22f92e34404 +#: ../../src/topics/workflows.md:81 fa1f770ffeba4b74bcb200cd3949e070 msgid "" "A command-line tool or expression tool can also be written directly in the " "same CWL document as the workflow. For example, we can rewrite the `echo-" "uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa -#: 66ce14a10d2d4dc497d3ed71e11ed8b8 +#: ../../src/topics/workflows.md:91 570020792e824c2ba732bcc2c0134aa1 msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a -#: 8dc00528c3d2426c8a3492a8191f1d81 +#: ../../src/topics/workflows.md:150 8a50c511004941d0917a8f0d471467f0 msgid "" "Having separate files helps with modularity and code organization. But it " "can be helpful writing everything in a single file for development. There " @@ -3581,39 +3139,33 @@ msgid "" "pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe -#: f9ef5e258f7c4971a8543d1dfed711a8 +#: ../../src/topics/workflows.md:160 4d2bf0341836405d9729c47d8020faea msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this " "user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 -#: 324bc51071d743ea80124c23880ddc0a +#: ../../src/topics/workflows.md:165 dd6fc85f74984517b284853a0d46c122 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c -#: d8c13e01976b43a1af34c11a7bc36897 +#: ../../src/topics/workflows.md:167 f857d80cd5d84622a560c895ab260a92 msgid "" "This workflow extracts a java source file from a tar file and then compiles " "it." msgstr "" -#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 -#: 43910a8ab4484e529a17df418b1aedbb +#: ../../src/topics/workflows.md:170 02e7e81cdf7e4226973f910cd57b8ccf msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 -#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 +#: 3a88d92f41aa4daaad4f4cc6829184b3 646367f222ea41e5987561941d17c4f9 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 -#: 7ad12d67e815400c94080804b9285629 +#: ../../src/topics/workflows.md:180 aaba75eb272245db82d072fed97b311c msgid "" "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" "github.com/common-workflow-language/user_guide/blob/" @@ -3623,39 +3175,33 @@ msgid "" "_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 -#: 457d5a31c79143acae2683d95d27f7a3 +#: ../../src/topics/workflows.md:183 f8a6e1af5f0349a5a384be0629c37ac8 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a " "run:" msgstr "" -#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda -#: a2a73901bf634547900d08b9a1ac8889 +#: ../../src/topics/workflows.md:185 c4f854c7a279404da3688bdf424c7c5e msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 -#: f347d80e62384b14acf6423675e5359a +#: ../../src/topics/workflows.md:191 d383ce45139944cb85768627965d9467 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 -#: 2a845a4f3f98428fb82f3ca7ce038a6e +#: ../../src/topics/workflows.md:205 84293afa7a6c40f2af0b980c89581fc7 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde -#: e2007c74d5f449a882809d6b91c010bf +#: ../../src/topics/workflows.md:212 e66daf8af53849109936c36ca7d2b2c9 msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a workflow." msgstr "" -#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 -#: 7f5e53ee7cf94be2bff45ef64db28a24 +#: ../../src/topics/workflows.md:221 8fbfbb587b264dcf98a3cea16dd36ef3 msgid "" "The `inputs` section describes the inputs of the workflow. This is a list " "of input parameters where each parameter consists of an identifier and a " @@ -3663,8 +3209,7 @@ msgid "" "workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 -#: a0d076b7b8b048478580c99ef0c8429f +#: ../../src/topics/workflows.md:233 5cdbc4771ea841b4960362b930de2af6 msgid "" "The `outputs` section describes the outputs of the workflow. This is a list " "of output parameters where each parameter consists of an identifier and a " @@ -3672,8 +3217,7 @@ msgid "" "the `compile` step to the workflow output parameter `compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 -#: 7fd926c18ad548e98845e9b5134dd6f2 +#: ../../src/topics/workflows.md:248 2e8a41fe43984dc6b4cf430e1ff66b28 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second step " @@ -3684,8 +3228,7 @@ msgid "" "parallel." msgstr "" -#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 -#: 789fbd47f8564cceb430ef3c0bc90e9b +#: ../../src/topics/workflows.md:256 78c20aa5a5724da6a4c908849c571334 msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input " @@ -3693,8 +3236,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 -#: 45c4d0492d6143ca9cebe81e9b2cf3ae +#: ../../src/topics/workflows.md:261 1606a2f059eb4b0c9e90f2f0cbbe779b msgid "" "The ``in`` section of the workflow step connects these two input parameters " "to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " @@ -3703,15 +3245,13 @@ msgid "" "parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea -#: 73bd3da2af8545928d5ea71d0f7454f6 +#: ../../src/topics/workflows.md:267 b456b11e2760479bbf81a773a3e1f8ee msgid "" "The `out` section of the workflow step lists the output parameters that are " "expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed -#: 15ce3d2700424f0fbb280d602ccebcf6 +#: ../../src/topics/workflows.md:278 0fa01fcec32049c989ad1d68841c74de msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3721,13 +3261,11 @@ msgid "" "section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 -#: af4268f19202436eb0a7e8c6bed5e386 +#: ../../src/topics/workflows.md:285 2bc9829f95584a269eb577c610b2a80c msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e -#: 94a4eadca6b949d79de2990a0150eee8 +#: ../../src/topics/workflows.md:287 0e5e6445bfcb42a4bd03612316dd7225 msgid "" "Workflows are ways to combine multiple tools to perform a larger operations. " "We can also think of a workflow as being a tool itself; a CWL workflow can " @@ -3735,20 +3273,17 @@ msgid "" "the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 -#: 09c1619e8cbd4febbb637f7e99ad5890 +#: ../../src/topics/workflows.md:297 0b83c1028b0e43ba972609e4302bc8a2 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 -#: 677ea7a27eb64568ab3689142d6efe70 +#: ../../src/topics/workflows.md:300 cbe1ef068b0c417b953655e132333447 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 -#: 097e6d47f9394e62b80110700492783a +#: ../../src/topics/workflows.md:309 a691c36a15044b11a6d037d16f818a6d msgid "" "This two-step workflow starts with the `create-tar` step which is connected " "to the `compile` step in orange; `compile` is another workflow, diagrammed " @@ -3756,23 +3291,21 @@ msgid "" "supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a -#: e93affce8c104bf6977182047c1f1077 +#: ../../src/topics/workflows.md:314 2e9797fcd4f04f56b5d2b2f1a3e306d5 msgid "" " \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/nestedworkflows." +"cwl\">\"Visualization \"Visualization" msgstr "" -#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 -#: 06c9e04ba890473b851240a0fa9c3b12 +#: ../../src/topics/workflows.md:322 28f4139911b44eeeb7afd31e9f7cae7b msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " "CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3780,8 +3313,7 @@ msgid "" "to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 -#: 0380dc1fe3aa48e4b62283b7b2a611d8 +#: ../../src/topics/workflows.md:336 4a6cb397a20241beab24d956920a8379 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and `*.java` " @@ -3790,8 +3322,7 @@ msgid "" "workflow." msgstr "" -#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be -#: 49b251f7a313492ea60504b00109e526 +#: ../../src/topics/workflows.md:341 dccb5472a5dc42b7946dd9245a71ecf0 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar " @@ -3800,8 +3331,7 @@ msgid "" "specific input/output names, as those also appear in its usage as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 -#: 7ee55702d7dd4679a24ff052f6f0cbeb +#: ../../src/topics/workflows.md:347 de1e18b69f654cabb75e52b47058030a msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3809,16 +3339,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 -#: 85d7e2e270874aa6b9f477cec0f48154 +#: ../../src/topics/workflows.md:366 b947e62f4b3b4c10b95737f1839bcc5a msgid "" "In this case our step can assume `Hello.java` rather than be parameterized, " "so we can use hardcoded values `hello.tar` and `Hello.java` in a " "`baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 -#: 570e94513c984c09ad6aa255f534216d +#: ../../src/topics/workflows.md:383 2ed0258a3a104ed5ba3b6b95ad998839 msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This is " @@ -3827,8 +3355,7 @@ msgid "" "filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 -#: a107258662fb4bd4a9a3d8754e34d1e9 +#: ../../src/topics/workflows.md:389 6584c0995288450b8a01c35fa231afb6 msgid "" "In this example we had to prepare a tar file outside, but only because our " "inner workflow was designed to take that as an input. A better refactoring " @@ -3836,8 +3363,7 @@ msgid "" "which would simplify its usage as a tool step in other workflows." msgstr "" -#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 -#: fc1a6502d831458ab8371a575cea47e2 +#: ../../src/topics/workflows.md:394 19237513fd134c33801a7af08f74e70c msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL " @@ -3845,13 +3371,11 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 -#: 2d10806bf1ce4e26b92adda61efc0862 +#: ../../src/topics/workflows.md:398 b66e0d0a36994b3182a3784bda8ffc19 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 -#: 046c5e134de94b629cc22d416f3c9182 +#: ../../src/topics/workflows.md:400 3bfb9851302248568bb4535ddc87a27f msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish to " @@ -3862,8 +3386,7 @@ msgid "" "different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 -#: 52fa22d3277940049fbb589a3ea73433 +#: ../../src/topics/workflows.md:411 78a5a600f8cc49ce8055c77a596ad833 msgid "" "The most common reason a new user might want to use scatter is to perform " "the same analysis on different samples. Let's start with a simple workflow " @@ -3871,27 +3394,23 @@ msgid "" "strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd -#: 6043beb96c2c49648011ec556aa9e986 +#: ../../src/topics/workflows.md:415 f9618882e0a14a0b84ff9751346dc291 msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 -#: 5ac4310515124e2986724425bed5651f +#: ../../src/topics/workflows.md:421 4fe03daddd304a9b828fdd1c29f0d072 msgid "" "Aside from the `requirements` section including `ScatterFeatureRequirement`, " "what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c -#: 7958e91d5c2f4046aa9d2070a900f9ae +#: ../../src/topics/workflows.md:429 7ab022708a9642ab8aa2e79ea7810381 msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f -#: 2db234d776fe4fd38bab07245dcb783a +#: ../../src/topics/workflows.md:441 fe144641fc8040b283f15b2b99ecb5a2 msgid "" "Here we've added a new field to the step `echo` called `scatter`. This field " "tells the runner that we'd like to scatter over this input for this " @@ -3899,8 +3418,7 @@ msgid "" "the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d -#: 7cfb17230e284ee7b6e2a00efe8eeb74 +#: ../../src/topics/workflows.md:445 f13d1b071a7f4a75a4cdee40ecef14fa msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if you " @@ -3908,70 +3426,59 @@ msgid "" "to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 -#: 4311ac98544e4fb0b2f4b24985710a01 +#: ../../src/topics/workflows.md:450 b0b2e63d2b8a4fd0983e976c16440da4 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be -#: 780f9c72e6c34c39918642c7e2477355 +#: ../../src/topics/workflows.md:452 47ac993a90fe46ca92e97d6b67b3276b msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 -#: cc4a7316db644b438cbaa181ad9ef2d3 +#: ../../src/topics/workflows.md:458 f5b8681b3c3b4890a86d7b9fb812d958 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " "calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f -#: dfc461a03fe8487794837904febb8b63 +#: ../../src/topics/workflows.md:466 74e70fec6d2447bbbd2a5bc8af1fa58c msgid "" "You can see that the workflow calls echo multiple times on each element of " "our `message_array`. Ok, so how about if we want to scatter over two steps " "in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 -#: 1e83485b00b64dfaba897bd8d772e0f0 +#: ../../src/topics/workflows.md:469 76fed9e7ad1d4792b7bb364bb684eeb2 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding the " "following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de -#: d0321d6805ec4d3abf3877d02a0a417f +#: ../../src/topics/workflows.md:472 bef387d9be1f4ca19a97023cfdd1c910 msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 -#: d7d77e807b3048c7bdf89558f76804cb +#: ../../src/topics/workflows.md:480 eea1be83da574f39914566d835701b4a msgid "" "And add a second step that uses `wc` to count the characters in each file. " "See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a -#: 8d9b8be147fc4a71922dde858842e543 +#: ../../src/topics/workflows.md:483 2043f12eb2ce4424b133e0dc0b62aafc msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b -#: 34b7705416a745a6a42e6d402c0757ed +#: ../../src/topics/workflows.md:489 87ba95507fc44dbca4cb6c5283ce50f9 msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under each " "step:" msgstr "" -#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d -#: 257adcee9da64d5c987f3b64efd20ab0 +#: ../../src/topics/workflows.md:491 e6e1a79638d74547b00c64e3c8b05710 msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 -#: fa6ed5d0c14f42f4aa3c5144648db22c +#: ../../src/topics/workflows.md:497 03fb16e74bf14c49b43e35ef6cb45030 msgid "" "Here we have placed the scatter field under each step. This is fine for this " "example since it runs quickly, but if you're running many samples for a more " @@ -3988,8 +3495,7 @@ msgid "" "welt!`. You can see how this might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df -#: 333e8ce458d54de394526769f96d12d2 +#: ../../src/topics/workflows.md:509 eca3380c60094df2b91b44b5f7718fae msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can " @@ -3997,45 +3503,38 @@ msgid "" "step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b -#: b819e8a5df6e4fa495924095709669ef +#: ../../src/topics/workflows.md:513 6c61733fe4284f51a6b46e89cafe78c4 msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb -#: f1955468a1364d44a930db77c9c4b495 +#: ../../src/topics/workflows.md:519 0585f83162c349969391c9456a884f28 msgid "" "Now the scatter acts on a single step, but that step consists of two steps " "so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 -#: 8c3b9b645a204d02b2c73a205e8ec296 +#: ../../src/topics/workflows.md:522 f209343966db4d46b4611d3620c3b496 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 -#: 4d88b9c186cd4502adbf752e8a70b6ce +#: ../../src/topics/workflows.md:524 5a2661ce35dc4d79a15da1e17c0a95ec msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 -#: 9927673564024ba5833b5ac271737857 +#: ../../src/topics/workflows.md:527 8f7ee09c9d6b491195e2d80315dae398 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 -#: 84f4ed7ce2004742b8db9087104a469a +#: ../../src/topics/workflows.md:566 966acff0d3d24104ae9673df8a790fb1 msgid "" "The first thing you'll notice is that this workflow is only compatible for " "version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 -#: 2b5f9757adca4490a149c7f45e14fcb5 +#: ../../src/topics/workflows.md:573 d60e1df759654f1b873276cf0296f234 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when` is " @@ -4043,8 +3542,7 @@ msgid "" "from the workflow contains a value `< 1` this step will be executed." msgstr "" -#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 -#: 0418de720813442f81ecff293c9448b5 +#: ../../src/topics/workflows.md:587 69aa8d3c9d9a4fe4a62875827648d95f msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " "will pass the first conditional step and will therefore be executed and is " @@ -4052,75 +3550,62 @@ msgid "" "skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec -#: 524eec63be8248ae982939c975ef50a2 +#: ../../src/topics/workflows.md:607 fee34c880e964e08b040adf2d3831803 msgid "" "When a value of 3 is given the first conditional step will not be executed " "but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 -#: 5e99f9912cc549a7890e2934425eb943 +#: ../../src/topics/workflows.md:627 cb9e82cf4b484ca7be19612b14fbdf33 msgid "" "If no conditions are met for example when using `--val 2` the workflow will " "raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e -#: b0121ee087d6424fbb0ea5957a7b0b8c +#: ../../src/topics/yaml-guide.md:1 8e7c3365f0f94038930f71666f05170f msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c -#: 49e9f6b3a06840289decf3f557860f87 +#: ../../src/topics/yaml-guide.md:6 cbe6f35c21044054a010767f2f0cae46 msgid "" "[YAML][yaml] is a file format designed to be readable by both computers and " "humans. This guide introduces the features of YAML that are relevant when " "writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 -#: ed9eebec0b3d4b72ba65507d37757a37 +#: ../../src/topics/yaml-guide.md:13 2cc21093311548cd837aa7b3f0939093 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea -#: bf9b255a24a84f3ba989a223492b8f41 +#: ../../src/topics/yaml-guide.md:16 6e7ea76e8aeb477cbb8197efed33e53d msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee -#: e79fa0b7f8b14810a3a20908ef92bc55 +#: ../../src/topics/yaml-guide.md:18 482e121a6e74428dbe6ad1f772f14684 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a -#: 290e2035f903417cbecb5dc5f09d6ebe +#: ../../src/topics/yaml-guide.md:19 179290eee12343dd9aa4d49207cf7c68 msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c -#: d420730151534f1a89076588a3358f09 +#: ../../src/topics/yaml-guide.md:20 7880db40e98e4aaabdc96def3d9f515d msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc -#: a6b5378bbe1e4bee9e37a765bddf75f7 +#: ../../src/topics/yaml-guide.md:21 75f3b499494b445f9f9a532d178cbc10 msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 -#: 6e4d9465dc2b454d96b02d7ad1817795 +#: ../../src/topics/yaml-guide.md:22 2b900b2779c84de5bbd3c933c56e5922 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 -#: a649d4af5f434dac9395e013ec4836bb +#: ../../src/topics/yaml-guide.md:24 189db6d0e54a400eb5615e259354827e msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 -#: 446190a298834b73bda068286e8490cf +#: ../../src/topics/yaml-guide.md:26 e689c0e1dcd645348ceed51e91eb9ad0 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the `:` " @@ -4130,8 +3615,7 @@ msgid "" "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b -#: 2f35c012ff174721bffe66a3f58a804f +#: ../../src/topics/yaml-guide.md:42 9532ac8e1dda479e890bf970323a0a32 msgid "" "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " "and `home` - with their four respective values. Values can be character " @@ -4139,8 +3623,7 @@ msgid "" "Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 -#: 43127c98c9d94aedac61cee67929c1a6 +#: ../../src/topics/yaml-guide.md:51 91a057a7d10f438fad10338dd44c013c msgid "" "Values may be wrapped in quotation marks, but be aware that this may change " "the way that they are interpreted i.e. `\"1234\"` will be treated as a " @@ -4151,33 +3634,28 @@ msgid "" "numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 -#: dc4fe561203c4c38a9caea5bd6eff2cd +#: ../../src/topics/yaml-guide.md:61 d18c1f5ef55d4bb6b8334438fcbc96b8 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 -#: f924e4896db2424d99ce8c9da14c599a +#: ../../src/topics/yaml-guide.md:63 dc6869049fc143b4af91d172a419a125 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program interpreting " "the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d -#: bf7646f5f925485c842a6d34140e40b8 +#: ../../src/topics/yaml-guide.md:76 c3c7f5ecfedb4884ad5e91bb79ba2a7c msgid "" "If there is anything on the line before the comment, be sure to add at least " "one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf -#: c483e61dec8949fa96bb893d422888a0 +#: ../../src/topics/yaml-guide.md:79 84f16419237a4789ac0f3c682b3a11ee msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 -#: 85fcb523d0e34a499eae04d304887f7b +#: ../../src/topics/yaml-guide.md:81 269ca8e05ce14e899fc8b2a00b1e458e msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, these " @@ -4188,8 +3666,7 @@ msgid "" "are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 -#: 83d47c8736a34f3cbf09e3997845e4f4 +#: ../../src/topics/yaml-guide.md:104 ce790af50da540eb9108ad89eae037cf msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -4201,13 +3678,11 @@ msgid "" "graphical representation of the `inputs` object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 -#: c698fb3d37bc403e9aeb679b8fc0e15e +#: ../../src/topics/yaml-guide.md:127 c3c9ef616b5d472a894ad6330267bcd2 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 -#: ae8af2f0eeda4aec97201211dfa965c7 +#: ../../src/topics/yaml-guide.md:129 b8a7360f6e0640aa9a2c4907c1ba3fe8 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) section " @@ -4217,30 +3692,25 @@ msgid "" "where each value is defined on its own line and preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 -#: 2ee87aa465cd41fda16a61e242f8c9d0 +#: ../../src/topics/yaml-guide.md:146 363da878600a4d229efe0ba79835d73c msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d -#: 0a6fd4469ff24b61b3ad001b09eead18 +#: ../../src/topics/yaml-guide.md:167 209dfb0d0a1148ed962dbb33890a3160 msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d -#: b96ba19bce9341d39c46054e1f10fe8f +#: ../../src/topics/yaml-guide.md:169 cd3a174dae334d0d977a3234e258bd25 msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " "can also be defined in YAML using the native JSON syntax. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc -#: 903f30af3d0c45cfb61063936a8097a7 +#: ../../src/topics/yaml-guide.md:177 b0f0b10de8f54e1e951e480f696976f1 msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 -#: ede8db7c0a58432e8a1c416e937a06d2 +#: ../../src/topics/yaml-guide.md:184 b5597e8984ad4e0bad33433c1dab89bd msgid "" "Native JSON can be useful in indicating where a field is intentionally left " "empty (such as `[]` for an empty array), as well as where it makes more " @@ -4250,130 +3720,50 @@ msgid "" "file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d -#: c8b53615476a4a1fbef2420d93bac94e +#: ../../src/topics/yaml-guide.md:194 5ad7d551d3d347a097508a8488f9d15c msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 -#: ea03cb5525cc491f9feb5c4780b38fee +#: ../../src/topics/yaml-guide.md:196 58f80e6944f9402a810b9b02ba3ad917 msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " "while we wrote this guide, though it also covers features that are not valid " "in CWL." msgstr "" -#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 -#: 92fd3a5e31714eab859dd630af2e78cf +#: ../../src/tutorials.md:1 8fdcc745f4684fa7816c62782507438e msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 -#: de660ecdb5b44c97a0e519d00b232497 +#: ../../src/tutorials.md:5 3c933ac074ee4d94b7aeacb7abeaf388 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to the " "list." msgstr "" -#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c -#: 5afc1e1288e74ed0985e61e5164479c7 +#: ../../src/tutorials.md:7 1d6cdf13aa834cb4a682553227d9f725 msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 -#: 862dc7ac81e54b1fb3d4c2f961b8810e +#: ../../src/tutorials.md:9 606cc939c5014e2abdab163e4d726f1b msgid "" "[Introduction to Workflows with Common Workflow Language: For Contributors.]" "(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f -#: e2c94c0e1c7048d38cd7aa2c465a859d +#: ../../src/tutorials.md:11 3505468d39c34a20bc55f431a3c697f7 msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f -#: b63253780f51467a95207d820d13ac39 +#: ../../src/tutorials.md:13 e5731a11b89e492d8d751100a46c5226 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f -#: 6d06ca7ed5df4560aaed286f4fe33928 +#: ../../src/tutorials.md:15 cdfeabb88f6245d9a687197d242ed3f9 msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 -#: 5448df4a6a8f431d80e269bcd480e19e +#: ../../src/tutorials.md:17 997679b781a84add9b6d8b1900deec35 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" - -#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee -msgid "" -"All Common Workflow Language project instructional material and changes to " -"the structure are also made available under the `Creative Commons " -"Attribution license `_. The following is a human-readable " -"summary of (and not a substitute for) the `full legal text of the CC BY 4.0 " -"license `_." -msgstr "" -"Todo o material instrucional do projeto Common Workflow Language e " -"alterações na estrutura também são disponibilizados sob a `licença Creative " -"Commons Attribution `_. O seguinte é um resumo legível por " -"humanos de (e não um substituto para) o `texto legal completo da licença CC " -"BY 4.0 `_." - -#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 -msgid "to **Share**—copy and redistribute the material in any medium or format" -msgstr "" -"**Compartilhar**—copiar e redistribuir o material em qualquer suporte ou " -"formato" - -#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 -msgid "to **Adapt**—remix, transform, and build upon the material" -msgstr "**Adaptar**—remixar, transformar, e criar a partir do material" - -#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 -msgid "" -"**Attribution**—You must give appropriate credit (mentioning that your work " -"is derived from work that is Copyright © the Common Workflow Language " -"project, and, where practical, linking to https://www.commonwl.org/ ), " -"provide a `link to the license `_, and indicate if changes " -"were made. You may do so in any reasonable manner, but not in any way that " -"suggests the licensor endorses you or your use." -msgstr "" -"Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " -"trabalho deriva de um trabalho que é «Copyright © The Common Workflow " -"Language project», e, quando prático, criar uma ligação para https://www." -"commonwl.org/ ), fornecer um `link para a licença `_, e " -"indicar se foram feitas alterações. Você pode fazê-lo de qualquer forma " -"razoável, mas não de uma forma que sugira que o licenciante o apoia ou " -"aprova o seu uso." - -#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 -msgid "" -"**No additional restrictions**—You may not apply legal terms or " -"technological measures that legally restrict others from doing anything the " -"license permits. With the understanding that:" -msgstr "" -"**Sem restrições adicionais**—Você não pode aplicar termos jurídicos ou " -"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " -"algo que a licença permita. Com o entendimento de que:" - -#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the " -"`OSI`_-approved `Apache 2.0 license `_." -msgstr "" -"Salvo indicação em contrário, os programas de exemplo e outro software " -"fornecido pelo projecto Common Workflow Language são disponibilizados sob a " -"`licença Apache 2.0 `_ aprovada pela `OSI`_." - -#: ../../LICENSE.rst:50 9c4d58a1129a4d4eb4db1bfabbeddb6e -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." -msgstr "" From 6b74133f5986eb2364e88ee9642d688ca4a98d49 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 27 Jan 2023 16:17:18 +0100 Subject: [PATCH 049/179] add command to update translations --- Makefile | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/Makefile b/Makefile index c549b172..c4627689 100644 --- a/Makefile +++ b/Makefile @@ -42,6 +42,10 @@ check-json: container-pull: for container in $$(git grep dockerPull $$(git ls-files *.cwl) | awk '-F: ' '{print $$3}'); do docker pull $${container}; done +update_translations: gettext + sphinx-intl update -p _build/gettext + + .PHONY: help clean watch unittest-examples check-json Makefile # Catch-all target : route all unknown targets to Sphinx using the new From 8bc1400208c390e18c872896fca4f5d4b4ac8a42 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Fri, 27 Jan 2023 14:22:02 -0500 Subject: [PATCH 050/179] Apply suggestions made on #337 --- src/faq.md | 4 ++-- src/introduction/prerequisites.md | 7 +++---- src/topics/command-line-tool.md | 11 ++++++----- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/src/faq.md b/src/faq.md index 50843d6a..9e1cd870 100644 --- a/src/faq.md +++ b/src/faq.md @@ -83,8 +83,8 @@ outputs: There are two ways to reference a local script: -The first method involves adding the folder containing your scripts to the `PATH` environment variable. -This allows you to run the shell script directly without using `sh` or `bash` commands. +The first method involves adding the path to a folder containing your scripts to the `PATH` environment variable. This +allows you to execute the shell script directly (without explicitly using the `sh` or `bash` commands). Start with adding a _shebang_ at the top of your file: diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index afd26dd1..60947b0c 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -26,9 +26,8 @@ of the following options for your operating system: - Windows ```{note} -If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). -Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) -for details on installing WSL2. +If you are using Windows, you will have to install the Windows Subsystem for Linux 2 as documented in the +[`cwltool` documentation for Microsoft Windows users](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users). Your operating system also needs internet access and a recent version of Python (3.6+). ``` @@ -88,7 +87,7 @@ You can run the CWL tool description by omitting the `--validate` option: :caption: Running `true.cwl` with `cwltool`. ``` -### Cwl-runner Python Module +### Generic ``cwl-runner`` alias `cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular diff --git a/src/topics/command-line-tool.md b/src/topics/command-line-tool.md index 1aea6311..c4391994 100644 --- a/src/topics/command-line-tool.md +++ b/src/topics/command-line-tool.md @@ -66,9 +66,10 @@ and in the [Outputs](../topics/outputs.md) sections. ## Network Access -This indicates whether a process requires outgoing IPv4/IPv6 network access. -If a command-line tool is written manually in CWL v1.1+, there is a need to -specify when network access is required. +This indicates whether a process requires outgoing IPv4/IPv6 network +access. Starting with CWL v1.1, programs are not granted network +access by default, so you must include the requirement for network +access in the specification of your tool. ```cwl cwlVersion: v1.2 @@ -80,6 +81,6 @@ requirements: ``` ```{note} -CWL v1.0 command-line tools that are upgraded to v1.1 -or v1.2 get Network Access automatically. +CWL v1.0 command-line tools that are upgraded to v1.1 +or v1.2 or v1.2 will have `networkAccess: true` set automatically. ``` From ab019e0a0425064377e690c694f3e8123195ceee Mon Sep 17 00:00:00 2001 From: "Bruno P. Kinoshita" Date: Wed, 8 Feb 2023 14:53:49 +0100 Subject: [PATCH 051/179] Replace Travis by GH Actions --- .github/workflows/ci-tests.yml | 44 ++++++++++++++++++++++++++++++++++ .travis.yml | 21 ---------------- README.md | 2 +- 3 files changed, 45 insertions(+), 22 deletions(-) create mode 100644 .github/workflows/ci-tests.yml delete mode 100644 .travis.yml diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml new file mode 100644 index 00000000..9cb2de82 --- /dev/null +++ b/.github/workflows/ci-tests.yml @@ -0,0 +1,44 @@ +name: CI Tests + +# Migrated from .travis.yml, based on cwltool's ci-tests.yml. +# See .travis.yml in git history for previous changes and configurations. + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + workflow_dispatch: + +concurrency: + group: build-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +jobs: + + ci_tests: + name: CI Tests + runs-on: ubuntu-latest + strategy: + matrix: + py-ver-major: [ 3 ] + py-ver-minor: [ 9, 10, 11 ] + + env: + py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }} + + steps: + - uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: ${{ env.py-semver }} + cache: pip + cache-dependency-path: | + **/setup.cfg + + - run: pip install -U pip setuptools wheel typing + - run: pip install -e .[all] + + - run: make RUNNER=cwltool unittest-examples diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index d8ff220f..00000000 --- a/.travis.yml +++ /dev/null @@ -1,21 +0,0 @@ -services: - - docker - -language: python -python: - - 3.8 - -cache: - pip: true - -branches: - only: - - main - - /.*/ - -install: - - pip install -U pip setuptools wheel typing - - pip install -e .[all] - -script: - - make RUNNER=cwltool unittest-examples diff --git a/README.md b/README.md index d6817cc9..833d3bce 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ [![DOI for the latest version](https://zenodo.org/badge/89621457.svg)](https://zenodo.org/badge/latestdoi/89621457) -[![Syntax Check](https://app.travis-ci.com/common-workflow-language/user_guide.svg?branch=main)](https://app.travis-ci.com/common-workflow-language/user_guide) +[![CI Tests](https://github.com/common-workflow-language/user_guide/actions/workflows/ci-tests.yml/badge.svg?branch=main)](https://github.com/common-workflow-language/user_guide/actions/workflows/ci-tests.yml) [![Translation status](https://hosted.weblate.org/widgets/commonwl/-/user-guide/svg-badge.svg)](https://hosted.weblate.org/engage/commonwl/) From b22539f4e60db357752ad0a7bae00f671ce6b71c Mon Sep 17 00:00:00 2001 From: "Bruno P. Kinoshita" Date: Wed, 1 Feb 2023 19:31:46 +0100 Subject: [PATCH 052/179] Add SPHINXOPTS to the make watch build --- Makefile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Makefile b/Makefile index c4627689..183468f2 100644 --- a/Makefile +++ b/Makefile @@ -25,11 +25,13 @@ watch: clean @echo @echo "Building and watching for changes in the documentation." sphinx-autobuild "$(SOURCEDIR)" "$(BUILDDIR)" \ + -b html \ --ignore='**venv' \ --ignore='**.github' \ --ignore='*.egg-info' \ --ignore='**_includes/**/*.txt' \ - --watch='cwl' + --watch='cwl' \ + $(SPHINXOPTS) $(O) ## unittest-examples : unittest-examples: From 22547897830185fb3290cc777e368d1812727937 Mon Sep 17 00:00:00 2001 From: Ngumih Fien <72187339+Fienne@users.noreply.github.com> Date: Thu, 16 Feb 2023 16:27:38 +0100 Subject: [PATCH 053/179] update links to specifications in Introduction and Topics sections (#377) * update links to specifications in Introduction and Topics sections * update links from http to https --- src/introduction/basic-concepts.md | 6 +++--- src/topics/best-practices.md | 8 ++++---- src/topics/creating-files-at-runtime.md | 2 +- src/topics/custom-types.md | 2 +- src/topics/expression-tool.md | 4 ++-- src/topics/expressions.md | 6 +++--- src/topics/file-formats.md | 4 ++-- src/topics/inputs.md | 2 +- src/topics/outputs.md | 6 +++--- src/topics/parameter-references.md | 2 +- src/topics/specifying-software-requirements.md | 4 ++-- src/topics/staging-input-files.md | 2 +- src/topics/using-containers.md | 2 +- 13 files changed, 25 insertions(+), 25 deletions(-) diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index 33f1ced7..f6fd2819 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -138,9 +138,9 @@ The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance: -- `InlineJavascriptWorkflow` - enables JavaScript in expressions. -- `SubworkflowFeatureRequirement` - enables nested workflows. -- `InitialWorkDirRequirement` - controls staging files in the input directory. +- [`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement) - enables JavaScript in expressions. +- [`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow.html#SubworkflowFeatureRequirement) - enables nested workflows. +- [`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow.html#InitialWorkDirRequirement) - controls staging files in the input directory. Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the diff --git a/src/topics/best-practices.md b/src/topics/best-practices.md index 4c2e18ab..52bb5097 100644 --- a/src/topics/best-practices.md +++ b/src/topics/best-practices.md @@ -34,7 +34,7 @@ all are required. # other s: declarations ``` - For more examples of providing metadata within CWL descriptions, see + For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md). - Include [attribution information][license-example] for the author(s) of @@ -42,7 +42,7 @@ all are required. [ORCID][orcid]. - In tool descriptions, list dependencies using short name(s) under - `SoftwareRequirement`. + [`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement). - Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format. @@ -53,7 +53,7 @@ all are required. `result`, `input`, `output`, and so forth. - In tool descriptions, include a list of version(s) of the tool that are - known to work with this description under `SoftwareRequirement`. + known to work with this description under [`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement). - `format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. @@ -66,7 +66,7 @@ all are required. - Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`. -- Each `CommandLineTool` description should focus on a single operation +- Each [`CommandLineTool`](https://w3id.org/cwl/CommandLineTool.html#CommandLineTool) description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use. diff --git a/src/topics/creating-files-at-runtime.md b/src/topics/creating-files-at-runtime.md index 9a652b62..b2929e2e 100644 --- a/src/topics/creating-files-at-runtime.md +++ b/src/topics/creating-files-at-runtime.md @@ -4,7 +4,7 @@ Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script. -To generate such files, we can use the `InitialWorkDirRequirement`. +To generate such files, we can use the [`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement). ```{literalinclude} /_includes/cwl/creating-files-at-runtime/createfile.cwl :language: cwl diff --git a/src/topics/custom-types.md b/src/topics/custom-types.md index e4c47a59..1dca7d44 100644 --- a/src/topics/custom-types.md +++ b/src/topics/custom-types.md @@ -74,7 +74,7 @@ requirements: ``` Note also that the author of this CWL description has also included -`ResourceRequirement`s, specifying the minimum amount of RAM and number of cores +[`ResourceRequirement`](https://w3id.org/cwl/CommandLineTool.html#ResourceRequirement)s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide. diff --git a/src/topics/expression-tool.md b/src/topics/expression-tool.md index e9de8a9c..85cdce3a 100644 --- a/src/topics/expression-tool.md +++ b/src/topics/expression-tool.md @@ -6,7 +6,7 @@ meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output. Similar to the command-line tool it requires `inputs` and `outputs`. -But instead of `baseCommand`, it requires an `expression` attribute. +But instead of `baseCommand`, it requires an [`expression`](https://w3id.org/cwl/CommandLineTool.html#Expressions_(Optional)) attribute. % TODO: Fix the missing link the graph below. We cannot have % it here as this file is included in two other files. @@ -64,7 +64,7 @@ expression: | ```{note} -We had to use an `InlineJavascriptRequirement` as our expression +We had to use an [`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement) as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement. ``` diff --git a/src/topics/expressions.md b/src/topics/expressions.md index 4c034a7f..a2dc79ae 100644 --- a/src/topics/expressions.md +++ b/src/topics/expressions.md @@ -1,7 +1,7 @@ # Expressions If you need to manipulate input parameters, include the requirement -`InlineJavascriptRequirement` and then anywhere a parameter reference is +[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement) and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner. @@ -80,7 +80,7 @@ only in certain fields. These are: - From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding) - `glob` - `outputEval` -- From `Workflow` +- From [`Workflow`](https://w3id.org/cwl/Workflow.html) - From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter) - `format` - `secondaryFiles` @@ -115,7 +115,7 @@ only in certain fields. These are: ## Using External Libraries and Inline JavaScript Code with `expressionLib` -The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute +The requirement [`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement) supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code. diff --git a/src/topics/file-formats.md b/src/topics/file-formats.md index 54dee779..e1d0f5fa 100644 --- a/src/topics/file-formats.md +++ b/src/topics/file-formats.md @@ -1,7 +1,7 @@ # File Formats -Tools and workflows can take `File` types as input and produce them as output. -We also recommend indicating the format for `File` types. This helps document +Tools and workflows can take [`File`](https://w3id.org/cwl/CommandLineTool.html#File) types as input and produce them as output. +We also recommend indicating the format for [`File`](https://w3id.org/cwl/CommandLineTool.html#File) types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files. diff --git a/src/topics/inputs.md b/src/topics/inputs.md index 6733f47f..646098f5 100644 --- a/src/topics/inputs.md +++ b/src/topics/inputs.md @@ -67,7 +67,7 @@ the tools aren't accidentally accessing files that were not explicitly specified ``` -The field `inputBinding` is optional and indicates whether and how the +The field [`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding) is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail. diff --git a/src/topics/outputs.md b/src/topics/outputs.md index accf5caf..5de5639f 100644 --- a/src/topics/outputs.md +++ b/src/topics/outputs.md @@ -48,7 +48,7 @@ And now invoke `cwltool` with the tool description and the input object on the c :working-directory: src/_includes/cwl/outputs/ ``` -The field `outputBinding` describes how to set the value of each +The field [`outputBinding`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) describes how to set the value of each output parameter. ```cwl @@ -59,12 +59,12 @@ outputs: glob: hello.txt ``` -The `glob` field consists of the name of a file in the output directory. +The [`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`. ## Capturing Standard Output -To capture a tool's standard output stream, add the `stdout` field with +To capture a tool's standard output stream, add the [`stdout`](https://w3id.org/cwl/CommandLineTool.html#stdout) field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter. diff --git a/src/topics/parameter-references.md b/src/topics/parameter-references.md index c007b37f..d901029e 100644 --- a/src/topics/parameter-references.md +++ b/src/topics/parameter-references.md @@ -77,7 +77,7 @@ You can only use parameter references in certain fields. These are: - From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding) - `glob` - `outputEval` -- From `Workflow` +- From [`Workflow`](https://w3id.org/cwl/Workflow.html) - From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter) - `format` - `secondaryFiles` diff --git a/src/topics/specifying-software-requirements.md b/src/topics/specifying-software-requirements.md index c90a5ac5..bebd3596 100644 --- a/src/topics/specifying-software-requirements.md +++ b/src/topics/specifying-software-requirements.md @@ -2,7 +2,7 @@ Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a -`SoftwareRequirement` field in the `hints` section. +[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement) field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for. @@ -30,7 +30,7 @@ As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a -tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the +tool as a [`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement), search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to diff --git a/src/topics/staging-input-files.md b/src/topics/staging-input-files.md index 87d28c0f..8d4812b2 100644 --- a/src/topics/staging-input-files.md +++ b/src/topics/staging-input-files.md @@ -2,7 +2,7 @@ Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to -write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. +write its output files alongside the input file in the same directory. You use [`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement) to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path. diff --git a/src/topics/using-containers.md b/src/topics/using-containers.md index 90a3f0bb..5b47df68 100644 --- a/src/topics/using-containers.md +++ b/src/topics/using-containers.md @@ -31,7 +31,7 @@ then print "Hello World" to the standard output. ``` Before we run this, let's just break it down and see what some bits do. Most of this -has been explained in previous sections, the only part that is really new is the `dockerRequirement` +has been explained in previous sections, the only part that is really new is the [`dockerRequirement`](https://w3id.org/cwl/CommandLineTool.html#DockerRequirement) section. ```cwl From 36a4e83682f247b1e97f427721634364a5aec40d Mon Sep 17 00:00:00 2001 From: Ngumih Fien <72187339+Fienne@users.noreply.github.com> Date: Fri, 17 Feb 2023 15:17:36 +0100 Subject: [PATCH 054/179] Update Command line tool link (#379) * src/introduction/basic-concepts.md * chore:Updated version specification list item-command line tool description * chore: version link update * Update command line tool link --------- Co-authored-by: Buduzz Co-authored-by: Bruno P. Kinoshita Co-authored-by: Peter Amstutz --- src/introduction/basic-concepts.md | 1 + 1 file changed, 1 insertion(+) diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index f6fd2819..ec76882a 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -179,6 +179,7 @@ vendors. - Semantic Versioning - - The CWL Specification page in the CWL website: +- The Command Line Tool Description Standard: <[https://www.commonwl.org/v1.2/CommandLineTool.html](https://w3id.org/cwl/CommandLineTool.html)> - The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }} - The list of Implementations in the CWL website: - PROV-O: The PROV Ontology - From 5ffb52fc8581cfd52a3a83a1d6320bf1fd092252 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Levai=20Mackenzie=20=C3=81gb=C3=A0r=C3=A0?= <97461848+Mackenzie-OO7@users.noreply.github.com> Date: Fri, 17 Feb 2023 15:20:15 +0100 Subject: [PATCH 055/179] link to cwltool.readthedocs (#369) Co-authored-by: Peter Amstutz --- src/introduction/prerequisites.md | 24 ++++++------------------ 1 file changed, 6 insertions(+), 18 deletions(-) diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index afd26dd1..4ec6e183 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -27,7 +27,7 @@ of the following options for your operating system: ```{note} If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). -Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) +Visit the `cwltool` [documentation](https://cwltool.readthedocs.io/en/latest/#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+). ``` @@ -35,7 +35,6 @@ Your operating system also needs internet access and a recent version of Python ## CWL Runner % https://github.com/common-workflow-language/user_guide/issues/166 -% https://github.com/common-workflow-language/user_guide/issues/64 % https://www.synapse.org/#!Synapse:syn2813589/wiki/401462 The first thing you will need for running CWL workflows is a CWL runner. @@ -43,25 +42,14 @@ The first thing you will need for running CWL workflows is a CWL runner. is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}. -`cwltool` can be installed with `pip`. We recommend using a virtual environment -like `venv` or `conda`. The following commands will create and activate a Python -virtual environment using the `venv` module, and install `cwltool` in that -environment: - -```{code-block} console -:name: installing-cwltool-with-pip-and-venv -:caption: Installing `cwltool` with `pip` and `venv`. - -$ python3 -m venv venv -$ source venv/bin/activate -$ (venv) pip install -U pip setuptools wheel -$ (venv) pip install cwltool -``` +`cwltool` can be installed with `pip`, `apt`, or `conda`. We recommend using a virtual environment +like `venv` or `conda`. ```{note} -Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) -for other ways to install `cwltool` with `apt` and `conda`. +Visit the `cwltool` [documentation](https://cwltool.readthedocs.io/en/latest/#install) +for details on installing `cwltool`. ``` + Let's use a simple CWL tool description `true.cwl` with `cwltool`. ```{literalinclude} /_includes/cwl/true.cwl From 1a18cc1d484a611fccb3b24ba2b1c5b3aa0d8243 Mon Sep 17 00:00:00 2001 From: Ngumih Fien <72187339+Fienne@users.noreply.github.com> Date: Fri, 17 Feb 2023 18:41:39 +0100 Subject: [PATCH 056/179] Convert faq headings to questions (#358) * change FAQ heading 3 to question * change FAQ heading 4 to question * change FAQ heading 5 to question * change faq 6 to heading * change faq 7 to heading * change faq 8 to heading * change faq 9 to heading * change faq 10 to heading * modify faq 9 * change faq 11 heading to question * change faq 12 heading to question * change faq 13 heading to question * change faq 14 & 15 headings to questions * change faq 16 heading to question * change faq 1 heading to question * adust punctuation and capitalisation * updates from review --------- Co-authored-by: Peter Amstutz --- src/faq.md | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/src/faq.md b/src/faq.md index 50843d6a..91c234f7 100644 --- a/src/faq.md +++ b/src/faq.md @@ -8,7 +8,7 @@ :backlinks: "top" ``` -## Non "`File`" Types Using `evalFrom` +## How do I create non "`File`" types using `evalFrom`? ```yaml cwlVersion: v1.0 # or v1.1 @@ -38,7 +38,7 @@ outputs: outputEval: $(self[0].contents) ``` -## Rename an Input File +## How do I rename an input file? This example demonstrates how to change the name of an input file as part of a tool description. @@ -56,7 +56,7 @@ requirements: entryName: $(inputs.src1.basename)_custom_extension ``` -## Rename an Output File +## How do I rename an output file? This example demonstrates how to change the name of an output file from the default name given to it by a tool: @@ -79,7 +79,7 @@ outputs: outputEval: ${self[0].basename=inputs.otu_table_name; return self;} ``` -## Referencing a Local Script +## How do I reference a local script? There are two ways to reference a local script: @@ -135,7 +135,7 @@ outputs: [] In CWL, everything must be directly stated. ``` -## Setting `self`-based Input Bindings for Optional Inputs +## How can I set `self`-based input bindings for optional inputs? Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. @@ -162,7 +162,7 @@ baseCommand: echo outputs: [] ``` -## Model a "one-or-the-other" Parameter +## How can I model a "one-or-the-other" parameter? Below is an example showing how to specify different strings to be added to a command line, @@ -185,7 +185,7 @@ baseCommand: echo outputs: [] ``` -## Connect a Solo Value to an Input that Expects an Array of that Type +## How do I connect a solo value to an input that expects an array of that type? Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with @@ -226,7 +226,7 @@ outputs: type: File outputSource: first/txt ``` -## Optional Inputs 💯 +## How do make an input optional? 💯 To make an input parameter optional, add a question mark to the type declaration. @@ -245,7 +245,7 @@ inputs: prefix: "--casava" ``` -## Enum Inputs ⚜️ +## How do I specify an input that must come from a list of predefined values (i.e. How do I use enum inputs) ? For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.** @@ -265,7 +265,7 @@ Format: prefix: "--format" ``` -## Record Inputs 📀 +## How do I describe dependent or exclusive input parameters(e.g. How do I use record inputs)? For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs. @@ -319,7 +319,7 @@ For commandline flags that are either **mutually exclusive** or **dependent** a inputBinding: prefix: "--chromosomes" ``` -## Setting Mutually Exclusive Parameters +## How do I set mutually exclusive parameters? To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value. @@ -339,14 +339,14 @@ steps: out: [indexes] ``` -## Setting Booleans +## How can I set Booleans? These can be set by using the default field ```yaml input: default:true ``` -## Concatenating Strings in Inputs +## What should I do when concatenating strings in inputs? The valueFrom field must be used instead of default. @@ -356,7 +356,7 @@ input: My String: $(input.stringvalue) ``` -## `cwltool` Errors due to Filenames with Space Characters Inside +## I get `cwltool` errors due to filenames with space characters inside. What should I do? `cwltool` does not allow some characters in filenames by default. @@ -370,7 +370,7 @@ Invalid filename: 'a space is here.txt' contains illegal characters If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`. -## CWL Parameter Reference Error due to Hyphen in Input Identifier +## What should I do when I get CWL Parameter Reference error due to hyphen in an input identifier? If `cwltool --validate` returns valid @@ -439,7 +439,7 @@ If it is not possible to change the input identifier, then you can use an altern valueFrom: $(inputs["sample-input"]) ``` -## Use CWL and cwltool with Singularity +## How do I use CWL and cwltool with Singularity? The CWL standards are built around (optional) Docker format containers. @@ -447,7 +447,7 @@ The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards. -## Debug JavaScript Expressions +## How do I debug the JavaScript in my CWL tool? You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it From 65e84383ef244fc16b8b5c4621bb9cdbabfbbcdb Mon Sep 17 00:00:00 2001 From: Rhea-Xiao Date: Wed, 1 Mar 2023 06:35:33 +0100 Subject: [PATCH 057/179] Translated using Weblate (Chinese (Simplified)) Currently translated at 9.8% (59 of 598 strings) Added translation using Weblate (Chinese (Simplified)) Co-authored-by: Rhea-Xiao Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide --- locales/zh_Hans/LC_MESSAGES/user_guide.po | 3166 +++++++++++++++++++++ 1 file changed, 3166 insertions(+) create mode 100644 locales/zh_Hans/LC_MESSAGES/user_guide.po diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..786a7fd6 --- /dev/null +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -0,0 +1,3166 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: 2023-02-19 06:59+0000\n" +"Last-Translator: Rhea-Xiao \n" +"Language-Team: Chinese (Simplified) \n" +"Language: zh_Hans\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=1; plural=0;\n" +"X-Generator: Weblate 4.16-dev\n" + +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "许可证" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "指导材料" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" +"所有通用工作流语言项目的指导材料及结构变更信息均可在[知识共享署名许可][cc-by-" +"human]下查阅。以下是[CC BY 4.0许可的完整法律文本][cc-by-" +"legal]的可读摘要（不能替代原文本）。" + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "您可随时/自由执行以下操作：" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "**共享**——通过任何媒介或以任何格式复制和重新分发材料" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**改编**——调整、大幅修改及在原有材料基础上编写新材料" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "出于任何目的，甚至是商业目的。" + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "只要遵守以下许可条款，许可方便无法阻止您的自由操作：" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" +"**归属**——您必须进行适当说明（提及您的作品源自版权属于 Common Workflow " +"Language 项目的作品，更明确地说，源自官网 https://www.commonwl.org/" +"），并提供[许可链接][cc-by-human]。如有改动，也请指明。您可通过任何合理的方式" +"进行操作，但不能以任何方式暗示许可方支持您/您的使用。" + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "**无额外限制**——您可能未运用法律条款，或未采用可合法限制他人执行许可操作的技" +"术手段。这点可以理解为：" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "若材料内容衍自公有领域，或所采用部分为适用例外或限制所许可，您无需遵循许可条" +"款。" + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" +"未提供任何担保。许可证可能未赋予所有必要的许可，无法满足您出于特定用途使用材" +"料的需求。比如，出版权、隐私权或道德权等其他权利可能限制您使用材料的方式。" + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "软件" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" +"除非其他地方已注明，所有Common Workflow " +"Language项目提供的示例程序及其他软件均可从 [OSI][osi]-已批准 [Apache 2.0 " +"license][apache-2.0-license]下方获取。" + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" +"除非受适用法律要求或者书面同意，软件均根据在\"AS IS\" 基础上分发的许可证进行" +"发布，不提供任何形式的担保或条件，明示或默示。请查阅许可证，了解有关许可项下" +"管理许可和限制的特定语言。" + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" +"CWL是一种描述命令行工具的方式，并连接这些工具以创建工作流。由于CWL是一种规范" +"，而不是一个具体的软件，使用CWL描述的工具和工作流可在支持CWL标准的各种平台上" +"移植。" + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "本页已被移除" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" +"本页已过时，仍然保留是为了保存旧版《用户指南》的链接，请使用新链接 " +"[内容目录](index.md#table-of-contents)浏览《用户指南》。" + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "最常见问题" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "使用 `evalFrom` 的非“`文件`”类型" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "重命名“输入文件”" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" +"本例展示了如何更改“输入文件”名称，属于工具描述的内容。在打开创建于工作流其他" +"步骤的文件后，若您不想保留默认文件名（文件创建时的命名），此时该工具可为您提" +"供帮助。" + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "重命名“输出文件”" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "本例展示了如何通过以下工具更改“输出文件”名称：" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "引用本地脚本" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "可通过两种方法引用本地脚本:" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "第一种方法是将包含相关脚本的文件夹添加至`PATH`环境变量中，便可直接运行shell " +"脚本，无需使用`sh` 或 `bash`命令。" + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "首先，在文件顶部添加一个 _shebang_ ：" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "然后，使用 `chmod +x scriptname.sh`命令执行脚本" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "最后，修改`PATH`以添加脚本所在目录。（最好使用 `$HOME/bin`存储脚本）。" + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "现在，您可使用 `baseCommand: scriptname.sh` 直接运行脚本。" + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "若想稍后共享您的工作，您可将脚本放在一个Docker格式的软件容器中。" + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "第二种方法是将 `type: File` 输入内容编写进脚本：" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "在CWL中，一切都必须直接说明。" + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "为可选输入设置`self`的输入绑定" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "现在，如果`cwltool`的输入绑定采用`self`，则无法处理缺少的可选输入。下方是一个" +"示例解决方法，等待更复杂的修复。" + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "对“非此即彼”参数进行建模" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "下方示例演示了如何根据给定的布尔参数值，来指定要添加至命令行的不同字符串。" + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "将一个单独的值连接到一个期望有该类型数组的输入上" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" +"使用 [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement)及 [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "merge_nested" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "输入必须是一个数组，每个输入链接只包含一个条目。如果使用单个链接指定“merge_ne" +"sted”，则链接中的值必须包含在单项列表中。" + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "这意味着“创建一个将这些源作为元素的列表”" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" +"换言之：如果目标类型为 `文件[]`（`File ` 的数组），并且源类型为单个 `文件 `，" +"则将 `MultipleInputFeatureRequirements` 添加到工作流级别 `requirements`，" +"并在目标步骤的相应 `` 条目下添加 `linkMerge： merge_nested`。" + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "可选输入💯" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "若要使输入参数可选，请在类型声明中添加问号。" + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "枚举输入 ⚜️" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" +"对于需要特定输入作为参数的命令行标志，可以在 CWL 中声明枚举类型。**" +"在此处指定 null 称为长格式样式。它与其他输入上的问号执行相同的操作。**" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "记录输入 📀" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "对于 ** 互斥 ** 或 ** 依赖 ** 的命令行标志，可以定义特殊的记录类型。" +"您还可以在此处指定 null 以创建可选输入。" + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "设置互斥参数" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" +"要在记录输入类型中正确设置字段，您需要将字典传递给输入，以正确设置参数。" +"此操作通过使用内联 JavaScript 并返回包含欲设置字段键的字典来完成。源字段应设" +"置为指示工作流中要充当值的输入。" + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +#, fuzzy +msgid "Setting Booleans" +msgstr "设置布尔运算" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "可使用默认字段进行设置" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "在输入中连接字符串" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "必须使用 valueFrom 字段，而不是默认值。" + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "由于文件名包含空格字符，显示`cwltool`错误" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "在默认情况下，`cwltool`不允许在文件名中使用某些字符。" + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "例如，文件名 `a space is here.txt`中包含了3个空格字符。" + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 4dee8504a8e5496081dadc386ab45540 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 674c238b25e240eda05e22e399f2f78f +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: b651f80f47b4442fbf29454a233697fc +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: ecf2b9c0b1664afe9c4e180610610021 +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: e24cb13d98014e558b6a6946758359e0 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: 928e3df7ca3e479ca6474a8e72cf36eb +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: d355f035676446c88b028f327aeb4829 +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 339b852df24242189d6efcd2898a3396 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: 3ef57e6862f240bebcf193a52397af0a +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: fae385da16aa443da996fa23ac03d6ae +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: 92430be71ecc40e18bbbb80d5576c613 +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 387d83db81024f65aa9a890c2d07874a +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: d8e2280a75a74916a1630afaa2fe2ae3 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: f1c1340f9745458980e0fbd641738687 +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 5424e5472c3d466fa2a3d2022c6cb475 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: 12f57b2ba76b492abe1816e06bfb1417 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: e1f657a46ce94a0d83671540e2cc2dab +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a5eacdbc9aa142c890b177869da4143d +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: e3bdaceae8784ab0807b2cf356a98580 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: ed521ac365db4a6ba5a1051fbaa2932e +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 67573252cc064b27ab13eebc468ac58a +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 73e68b3af9cf41338d843c0c40e50cdc +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: a999b1acda2641598086648c64aa3831 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: f8c12a58cb0b46a488823c6ae95f25ea +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: f25a63e0926d4932bbe64b2e4bdabf9e +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: d718630a296545f3a989c8c71e9ddc77 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 9a97acd430064710bcdf76edbd9f711c +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: 48deb71f361a43e48a56ed483075bca8 +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 716b56506ca7470299899c5d820a9ea2 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: e3ecac0a8e604f2b98a2a12b0579990a +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 007a345b4bad49cf996c4301b8386473 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: efb5fd14988c4e2a8f834ee5369d4102 +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: 276f688ba7cc471a842f085ca852b1d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 8b70a1ad70514039b97164fa630c12e4 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 2f28ab412d2843ffa5f14acdc01fc732 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: cbec9277b5004e50af2728cbda0df740 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: e259f55f8000479bbd8009e25cf0ca6c +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 8210b36347a749889450529ecdf4ff0e +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 23088850ad02459696f6bbd385109aac +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: f02257a822ad46ac93c5981531cc85d5 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: d289541e460147aa933f7878996f8649 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: f495da32f05a4a5ba9539be0a54c1a59 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: bdb4c68a175047ddbe141ca24960127f +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 97b61352363f47cb890e8937c5613fa3 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: 0bc424ef2ca346099f29b937379908a0 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 29b73e1dd72744f68377f0a38c10f062 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 38a2afaf4a6c4d04909af22c93f2808d +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: cd74f34b21af4de9be96fd897efc469b +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: f12e371f3f1a4b0cb2cff9800352d48c +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 8f0e8f050e334ac08334e9215e1dcf61 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 7a6be0005a6441feb67f036d005d7885 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 06635145b441418aaae84dc804f3d6ac +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 04eaf1f7c630450db318dcd8b7626e15 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: fd4579a3c9844492b314b5c3c1775fc7 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: e024bcb70e04412e90e1838426d1b69a +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: a3db21c0b3114802a8a5b610e252ef13 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 0f5bc8520d6a4dafa37c65343da9702a +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 5cb830da47464a8b9c3950983fa4d56f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: a2ce43b391864e8bbde16328cc19b32b +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 56ee4dcfff6141d5bef80eb96559876d +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 96671c56523c4ea9992fb5dfcfa6490e +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: bcc6246742cb46bfb185e415c4a3431a +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 86dce36de687449c88fb5eb9d64eb045 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 7dc630ea86464b1dba3a4e5079260b3b +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: 651e032007ea4a119d20c820bb61f86b +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 0b056dde9e87428996e47870b12119da +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 628124a1670b4b058bb0fb6e495a099c +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: ec2adb3912bc46e28891229e9e0d9a1c +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: a519be60726a44af9941fdce04735353 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: cb8fc8c4c79e467eac5fab4ca685201e +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: a26cc105716f47cb807174c9003153b0 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: cc159dd5fe5748caac838862f5b8c4d1 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 6812698e9ad84d3385de5e88e9dde0b3 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: d1f02be278754267893dfce5a940997d +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: 75d59e395c66416cae9b352db5081516 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 874c6f19abbf45d7ab7d30a378c4048d +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: dea0d4b681f94e73b13965dcfe75cf7d +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: 750474486a84482292eeba45f118287f +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 1eb0e39bb6d04b8cab300f44a79f3add +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 4b2ab812f62c4f949dd25c8527f2411c +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 2c3b884cb1c54521900cc90782e8a58d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: a1073b6306044dffb414319ae01f68bb +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: 9a1d92334685449386dfa3b3a899ed48 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: fb623af4c480411b8fde28d01c981411 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: e98e165f6bba40809c90473d72f9d592 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 5565c1b2d8a349169a305a9b26b4574d +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: 88160cef4cfa4add9020aa89511a5749 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 730ba1434a1445ae847ec6153b6a3b72 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: a25d0b1e13324b40a6b8fcd227948c4f +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: d661df070e3040869da412d07a71f716 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: a11585474d3849cca5467512ed964743 +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 2682f9ca8e604a0c9986f7746fdec960 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 22447a560f6f4317bf67bd7c4336126c +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 52703d6b7f914097934bfad13663abeb +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 5e1c79df657d4a6e84e055dd6b300a5d +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 329d2809dfae4f90bc638f5f03a47ee3 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 9647019d8c37466886e7aab6f176634d +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: cc067051f22f433bbece08f60933e002 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: dbfe2c1123144316aa026374b0f353d3 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: 074cf5d912854d8c864607cc24b15302 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: b54240bb94f746bba7511633aa969db0 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 8b70a072aa87414c88e89a3e19af0a51 +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: eea20f89c45f424a888178df53713b28 +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7647e0229a924f988cf02b7812a55c06 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 9d663249666045618a0d3acddb85a9a9 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: dbf6153cd02542a6a01c172803122b7f +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: b6250cf6fa8a4a0c94b33302e0decca5 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: fa6ca3bbc6784380a03a950a6f49a180 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: b92b516e537a4773ad67b4af586e7a25 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: 467a701228504d06b971b79a59c69064 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: 2634f989eb304009a8568d70ed42786c +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: fbe0c65b444441f785d0054176d036a6 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 9a710602e00c4934ae3a3b471aa68458 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: 21b5be7270a14f0987240c81d1ec879b +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: cfe9d8241fe84bd5b74042a5625d933f +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 764d933cc4da446abd8dd8f913f05dac +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: c93efc6d4e004859981ee7f5fa28ed03 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: 546601da44cb49bd9611b1c85807fd90 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: e07f33d01b804663a25ffb08aad74821 +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: 7a644506619a4f08958ec7d4540cd557 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: b5195b7d8eaa419fb2b90cb33a57783a +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: 2713594c937d4c528fc8d04d9e9819ed +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: cf94c1424fc2413c85647fd1ee73d951 +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: dc0452107c604e29bdf32bb289fe5db8 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 483181f498fc4d968b5fe6ef427709f7 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 7487485d6aa4458089a4b4bdf107ea64 +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 93188ed43ee949cc98b3ea679ce14feb +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 24aca0bea4d94e3593b844cf0586cffe +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 9c56528acd5f49deb139e034dfbfac7c +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: a2dd833fdca4443181648e41051a5232 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: 7e40cc9f9e1341c195e843c009575b94 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: def35d6021394def80a53ae49a2cdbde +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: c84d4450bc6a475dbf34e0b22cea9130 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: cca9665f6daa44b49233baf34ab9fcc7 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: 547edbf5fa424b8286cc21674ff159b0 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 7ca248888b9d484cb544cd76ba538662 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: ae6b240718104380b08db5552d7355ea +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: e5a8b7f84be64020b191099f3fad30ed +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 12a06d8358534102b202965d4258c18e +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: b7f93705e5b8416696be01850072e8c0 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: e87045829b344089ab59dc27063ddd7a +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: 42ef2f145b824d69b63abc1da175c216 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: c61cedf543664d388183e04b3939cc39 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: 9e39e3f1501c4fcaab3e8962e090f6be +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: 03e2f767c4da461982fc3c0f3ba94762 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 3bea5822b8694e2aa32c446e1c54a045 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: 0d498cd4caf54c15891ca1afe58e2727 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: b2d75045e02741b4850f5ff1243f7858 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: 5fa79c62049a447c8328ebf9db54ebf4 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: d947c54933d64aad90df392a1cedd63f +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 651d35997332404186aa6d5711da4a3d +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: b662c1a5a4424c8d8350a806356acc61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 04d6babfd87343d7a5f13867ea02b65f +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 2eaacf1a90204a2b9bd621344560f2a1 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: e3a7182f00f440b8b5461da91194a64b +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: b5338f39e8c74ff28e139da68089a742 +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: f6d92156d67c4a339bcfd194cff897df +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: d80ab383eec9402faba997b548fe42eb +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: 49217c02f58c43ff9ec00f10da8d4e84 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 8dbd56473f8c40c0bb12a48be06117e3 +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 78d7f3ede2c746d482042adef050b2c4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: cbbf93c70fe04ba7932ba25758ddc611 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: cfa1c1fde4454df283f87cc54a9c59ec +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 1a8be2950cbb475bbb2617e005f0fac9 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: 5d83c56102e141cc978500f678dd0c1c +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: cda73485875d4c8e9464679a20558616 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 98cae24919b74c088a5d89706aec581b +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: b4b0940b4b5743c09637b36b964202d0 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 9ca3554d771d45998e88aaede525b227 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 3fca839cede94cfd8e4f605c73ba699d +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: 3ded0f125249485c921994b6e6b93ac9 +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 53ece35d309a4c8d99f1efb2122a7092 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 87bafb845c714b109874f6137b84462d +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: fcd05b1ef31a4046946a2399c7fc5575 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: 859368c1f25c4a4aad57abfd046c63f5 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" From fc85e3d7f6a10b52d7932d9db304074fd918cb5b Mon Sep 17 00:00:00 2001 From: Weblate Date: Wed, 1 Mar 2023 06:35:33 +0100 Subject: [PATCH 058/179] Added translation using Weblate (Chinese (Simplified)) Co-authored-by: Weblate --- locales/zh_Hans/LC_MESSAGES/sphinx.po | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 locales/zh_Hans/LC_MESSAGES/sphinx.po diff --git a/locales/zh_Hans/LC_MESSAGES/sphinx.po b/locales/zh_Hans/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..7a53375b --- /dev/null +++ b/locales/zh_Hans/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: zh_Hans\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "" From d4622471c3edef2cfe2cea31b4032cd3937f38ce Mon Sep 17 00:00:00 2001 From: Rhea-Xiao Date: Wed, 1 Mar 2023 06:35:34 +0100 Subject: [PATCH 059/179] Translated using Weblate (Chinese (Simplified)) Currently translated at 66.7% (399 of 598 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 40.3% (241 of 598 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 36.7% (220 of 598 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 33.4% (200 of 598 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 100.0% (2 of 2 strings) Co-authored-by: Rhea-Xiao Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-sphinx/zh_Hans/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide Translation: Common Workflow Language/CWL User Guide: Sphinx --- locales/zh_Hans/LC_MESSAGES/sphinx.po | 13 +- locales/zh_Hans/LC_MESSAGES/user_guide.po | 904 +++++++++++++++++----- 2 files changed, 699 insertions(+), 218 deletions(-) diff --git a/locales/zh_Hans/LC_MESSAGES/sphinx.po b/locales/zh_Hans/LC_MESSAGES/sphinx.po index 7a53375b..e402725a 100644 --- a/locales/zh_Hans/LC_MESSAGES/sphinx.po +++ b/locales/zh_Hans/LC_MESSAGES/sphinx.po @@ -8,20 +8,23 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" +"PO-Revision-Date: 2023-02-19 06:59+0000\n" +"Last-Translator: Rhea-Xiao \n" +"Language-Team: Chinese (Simplified) \n" "Language: zh_Hans\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=1; plural=0;\n" +"X-Generator: Weblate 4.16-dev\n" #: ../../src/_templates/sidebar-nav-bs.html:1 #: d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" -msgstr "" +msgstr "主导航" #: ../../src/_templates/sidebar-nav-bs.html:3 #: 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" -msgstr "" +msgstr "部分导航" diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 786a7fd6..2955f3b6 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-02-19 06:59+0000\n" +"PO-Revision-Date: 2023-03-01 05:35+0000\n" "Last-Translator: Rhea-Xiao \n" "Language-Team: Chinese (Simplified) \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 4.16-dev\n" +"X-Generator: Weblate 4.16-rc\n" #: ../../LICENSE.md:2 #: 4e203044f0464fd5a3256430391dde12 @@ -133,8 +133,8 @@ msgstr "本页已被移除" #: cc11f5d29206492d9f2f0922882b6159 msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." msgstr "" -"本页已过时，仍然保留是为了保存旧版《用户指南》的链接，请使用新链接 " -"[内容目录](index.md#table-of-contents)浏览《用户指南》。" +"此页面已过时，保留在此以保留旧用户指南链接，请使用新链接 [内容目录](index.md" +"#table-of-contents)浏览《用户指南》。" #: ../../src/faq.md:1 #: e2ed894d325a4f50a5e2dc69da5531a1 @@ -144,7 +144,7 @@ msgstr "最常见问题" #: ../../src/faq.md:11 #: 61edb787dab04ca2ad3ed07616d878a0 msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "使用 `evalFrom` 的非“`文件`”类型" +msgstr "使用 `evalFrom` 的非“`File`”类型" #: ../../src/faq.md:41 #: d5321589e7ed4f0db3c630cc39800791 @@ -155,9 +155,9 @@ msgstr "重命名“输入文件”" #: fc62427c0a004810b055dee90ec5e2d9 msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." msgstr "" -"本例展示了如何更改“输入文件”名称，属于工具描述的内容。在打开创建于工作流其他" -"步骤的文件后，若您不想保留默认文件名（文件创建时的命名），此时该工具可为您提" -"供帮助。" +"本示例演示了如何更改“输入文件”名称，属于工具描述的内容。在打开创建于工作流其" +"他步骤的文件后，若您不想保留默认文件名（文件创建时的命名），此时该工具可为您" +"提供帮助。" #: ../../src/faq.md:59 #: 1c6b8a4194a14611b4061b1540c3807f @@ -167,7 +167,7 @@ msgstr "重命名“输出文件”" #: ../../src/faq.md:61 #: bc7ad10c929848a3a9a240a3c501d299 msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" -msgstr "本例展示了如何通过以下工具更改“输出文件”名称：" +msgstr "本示例演示了如何通过以下工具更改“输出文件”名称：" #: ../../src/faq.md:82 #: 7225a993d281421b95c8e3df2846a0e3 @@ -233,8 +233,9 @@ msgstr "现在，如果`cwltool`的输入绑定采用`self`，则无法处理缺 #: ../../src/faq.md:165 #: ce6db54bd0f54839a5beb948530a21f0 +#, fuzzy msgid "Model a \"one-or-the-other\" Parameter" -msgstr "对“非此即彼”参数进行建模" +msgstr "对一个“非此即彼”参数进行建模" #: ../../src/faq.md:167 #: d06cbf89028b4638ad54c2529bcbfa25 @@ -257,7 +258,7 @@ msgstr "" #: ../../src/faq.md:194 #: 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" -msgstr "merge_nested" +msgstr "" #: ../../src/faq.md:196 #: 937cb94a370640c788fbc3fe0b19f2e5 @@ -336,7 +337,6 @@ msgstr "" #: ../../src/faq.md:342 #: b53dc77466b24a67b52b8aadf4fab724 -#, fuzzy msgid "Setting Booleans" msgstr "设置布尔运算" @@ -373,262 +373,322 @@ msgstr "例如，文件名 `a space is here.txt`中包含了3个空格字符。" #: ../../src/faq.md:371 #: 182959fc9f4746d082994e07d05c8cde msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." -msgstr "" +msgstr "如果无法避开这些危险的字符，您可以将 `--relax-path-checks`传送至 `cwltool`。" #: ../../src/faq.md:373 #: cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -msgstr "" +msgstr "由于输入标识符中包含连字符，显示CWL参数引用错误" #: ../../src/faq.md:375 #: 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" -msgstr "" +msgstr "如`cwltool --validate`返回有效" #: ../../src/faq.md:384 #: 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" -msgstr "" +msgstr "但执行时显示如下错误：" #: ../../src/faq.md:396 #: ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" -msgstr "" +msgstr "文件在此处" #: ../../src/faq.md:410 #: e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." -msgstr "" +msgstr "由`-`（连字符）引发的问题。" #: ../../src/faq.md:423 #: f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" +msgstr "要修复该错误，需将`-`（连字符）更改为`_` （下划线）" #: ../../src/faq.md:436 #: 190099a242a645c9b9f8bc3ce89d920d msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" -msgstr "" +msgstr "如无法更改输入标识符，您可使用另一种CWL参数引用语法：" #: ../../src/faq.md:442 #: 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" -msgstr "" +msgstr "将CWL和cwltool与Singularity一起使用" #: ../../src/faq.md:445 #: 1901c34201054a9cae199b0dbb8b945e msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." msgstr "" +"CWL标准是围绕（可选）Docker格式容器建立的，且引用运行程序和其他几种CWL执行均" +"支持通过Singularity引擎运行Docker格式容器，但直接指定一个Singularity " +"格式容器不属于CWL标准的内容。" #: ../../src/faq.md:450 #: 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" -msgstr "" +msgstr "调试 JavaScript 表达式" #: ../../src/faq.md:452 #: d7b044f5224a48eda09bc949cf645193 msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" +"您可使用 --js-console option of cwltool，" +"或尝试为代码创建一个JavaScript 或 " +"TypeScript项目，并使用expressionLib进行加载， 比如： https://github.com/" +"common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/" +"template-tool.cwl#L6-L8" #: ../../src/index.md:1 #: 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" -msgstr "" +msgstr "《通用工作流语言用户指南》" #: ../../src/index.md:3 #: f8d6e4cd54cb42c88182a43171d97bab msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." msgstr "" +"本指南将指导您使用[Common Workflow Language](https://www.commonwl.org/) (CWL)" +" 开放标准编写工作流，并介绍了最新规范 {{ cwl_version }}。" #: ../../src/index.md:7 #: 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" -msgstr "" +msgstr "欢迎投稿和反馈！" #: ../../src/index.md:9 #: 0f47157605a34ea58770ea898deebae4 msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" +"如您发现本指南存在内容缺失，或想提供其他反馈，请在[project repository for " +"this guide][repo]上提交问题。您也可单击页面右侧边栏的 “Edit this " +"page（编辑本页）”按钮，直接在Pull Request（拉取请求）中提交修改建议。" #: ../../src/index.md:16 #: 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" -msgstr "" +msgstr "浏览《用户指南》" #: ../../src/index.md:18 #: ed74c9a4b623464480e2c184668fcec0 msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." msgstr "" +"如您是初级用户，请查阅 [Introduction（介绍）](/introduction/index.md) " +"章节。而对于高级用户而言， [Topics主题](/topics/index." +"md)子章节则详细介绍了关于CWL的最常见主题。" #: ../../src/index.md:23 #: cfa67cf5521b414da6f7d34cbed283f7 msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." -msgstr "" +msgstr "目录显示在菜单顶部和左侧边栏，也出现在本页的下方（但也附带子章节的链接）。每" +"页所在章节的链接显示在右侧边栏，而搜索窗口则显示在左侧边栏。" #: ../../src/index.md:28 #: ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" -msgstr "" +msgstr "目录" #: ../../src/introduction/basic-concepts.md:1 #: e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" -msgstr "" +msgstr "基本概念" #: ../../src/introduction/basic-concepts.md:3 #: ac62d326a68145b695e46b714d4e8156 msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." msgstr "" +"本章节介绍了一些基本概念，以帮助用户更顺利地开始使用通用工作流语言（CWL）工作" +"。我们相信读者已经非常熟悉工作流管理工具YAML，且能熟练地按照命令行说明进行操" +"作。用户指南另一章节也介绍了相同的概念，但内容更为详细。如果您已经十分熟悉CWL" +"或正在寻找更高级的内容，可能需要跳过本章节。" #: ../../src/introduction/basic-concepts.md:10 #: 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" -msgstr "" +msgstr "CWL规范" #: ../../src/introduction/basic-concepts.md:21 #: cbe1d761da5b403d9605fa1fb8e62fdf msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." -msgstr "" +msgstr "CWL规范文档由CWL社区撰写并维护，此规范有不同版本，本用户指南所用版本为 {{ " +"cwl_version }}。" #: ../../src/introduction/basic-concepts.md:25 #: 3a71b269bd3c49eb913cf69b60373c24 msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." msgstr "" +"规范的版本最多包含三个数字，以 `.`（圆点）分隔。第一个数字说明主要版本，用于" +"标注删除弃用功能等向后不可兼容的更改。第二个数字说明次要版本，用于标注增添新" +"功能或小幅调整等向后兼容的更改。最后一个数字说明错误修复，用于标注拼写错误更" +"正或对规范的其他修正。" #: ../../src/introduction/basic-concepts.md:33 #: b171b72c48d44050a3416a7a42c4021d msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." -msgstr "" +msgstr "用于规范版本的模型称为“语义版本控制”，请参阅本章节末尾以[了解更多](#learn-" +"more)有关信息。" #: ../../src/introduction/basic-concepts.md:37 #: b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" -msgstr "" +msgstr "实现" #: ../../src/introduction/basic-concepts.md:39 #: 078b58ffc1cc4d25a7c4eea3bb76e025 msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." msgstr "" +"CWL规范的实现意味着所有软件的编写均需遵循规范文档中所定义版本的要求。但是，在" +"实现过程中可能无法满足规范的所有方面。目前，CWL规范已同时获取开源和商业许可的" +"授权。" #: ../../src/introduction/basic-concepts.md:44 #: c3869b4ec5ff47d99e8da79770722e04 msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." -msgstr "" +msgstr "CWL非常适用于描述集群、云和高性能计算环境中的大规模工作流情况，因为其中可以跨" +"节点并行调度任务。" #: ../../src/introduction/basic-concepts.md:51 #: 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." -msgstr "" +msgstr "CWL规范、实现及其他工具。" #: ../../src/introduction/basic-concepts.md:105 #: a5ebc727fb3443f78e81d6b7ed5ac750 msgid "Processes and Requirements" -msgstr "" +msgstr "流程和要求" #: ../../src/introduction/basic-concepts.md:107 #: 86e6a06992dc4228bfda7add48e28ca3 msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" msgstr "" +"流程是指接收输入并产生输出的计算单元，流程的行为可能受到输入、要求及提示的影" +"响。CWL规范{{ cwl_version }}定义的流程包括如下四种：" #: ../../src/introduction/basic-concepts.md:112 #: 8c9772f96caf4169924d22eb929a4f0f msgid "A command-line tool." -msgstr "" +msgstr "命令行工具。" #: ../../src/introduction/basic-concepts.md:113 #: 4fac209a62114798b79e4810f7a0148b msgid "An expression tool." -msgstr "" +msgstr "表达式工具。" #: ../../src/introduction/basic-concepts.md:114 #: b97ba368fd664caab0494e2392795697 msgid "An operation." -msgstr "" +msgstr "操作。" #: ../../src/introduction/basic-concepts.md:115 #: 903a6796e3304a19ad885b2428b0e80f msgid "A workflow." -msgstr "" +msgstr "工作流。" #: ../../src/introduction/basic-concepts.md:118 #: 6e352ac1f8e144c392ac5adf18c28298 msgid "The processing units available in the CWL objects model." -msgstr "" +msgstr "CWL对象模型中可用的处理单元。" #: ../../src/introduction/basic-concepts.md:119 #: cf2922f645904ac7955428ecddc37b8a msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" +msgstr "命令行工具是 `echo`、`ls` 及 `tar` " +"等命令行实用程序的包装器。可从工作流中调用命令行工具。" #: ../../src/introduction/basic-concepts.md:122 #: 5f47aae608c041aeb4134d59dad314d2 msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." msgstr "" +"表达式工具是 JavaScript 表达式的包装器，可用于简化工作流和命令行工具，" +"将工作流执行的常见部分移动到可重用的 JavaScript " +"代码中，这些代码像命令行工具一样接受输入并生成输出。" #: ../../src/introduction/basic-concepts.md:127 #: f6f589481d0c4891beaccb63160619ef msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." msgstr "" +"操作是一个抽象的流程，同样可接受输入并生成输出，且可用于工作流中。但是，这是" +"一种特殊的操作，并不十分常用。在本用户指南的 [操作章节](../topics/operations." +"md)中，我们对它进行了相关讨论。" #: ../../src/introduction/basic-concepts.md:131 #: 73b0c1ccb18c4b74a2c0fdf9706eca85 msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." msgstr "" +"工作流是包含步骤的流程。步骤可以是其他工作流（嵌套工作流）、命令行工具或表达" +"式工具。工作流的输入可以传送到其他任何步骤，而步骤生成的输出可用作工作流的最" +"终输出。" #: ../../src/introduction/basic-concepts.md:137 #: 4ace6b92f4e04a07aa202840ebe36417 msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" -msgstr "" +msgstr "CWL规范允许实现提供额外的功能或通过 " +"*requirements*指定工作流的先决条件。CWL规范中定义了很多要求，比如：" #: ../../src/introduction/basic-concepts.md:141 #: cc6cd8cb81564cadb8e6a4c49423b7f7 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" +msgstr "`InlineJavascriptWorkflow`——在表达式中启用JavaScript。" #: ../../src/introduction/basic-concepts.md:142 #: 2d9f53b6ed5041dbb6c0b54835897856 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" +msgstr "`SubworkflowFeatureRequirement` ——启用嵌套工作流。" #: ../../src/introduction/basic-concepts.md:143 #: 907674a4ecff4826a2b880e28fc38f33 msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." -msgstr "" +msgstr "`InitialWorkDirRequirement`——控制输入目录中的暂存文件。" #: ../../src/introduction/basic-concepts.md:145 #: 037cd0e5ceda482eaeaca03d51745aee msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." msgstr "" +"某些CWL运行程序可能提供规范之外的需求，比如`cwltool` 通过 " +"`cwltool:CUDARequirement` 需求来支持GPU需求，但这不属于 {{ cwl_version " +"}}版本规范的内容，可能不受其他CWL运行程序支持。" #: ../../src/introduction/basic-concepts.md:151 #: e4643938445b48cc80eb8973ceeb126e msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" +"提示类似于需求。但是，需求列出必需功能，而提示仅列出可选功能。[需求](../" +"topics/requirements-and-hints.md)章节对需求进行了详细介绍。" #: ../../src/introduction/basic-concepts.md:155 #: c4c3315c96714e81b364f8cc003b87e6 msgid "FAIR Workflows" -msgstr "" +msgstr "FAIR 工作流" #: ../../src/introduction/basic-concepts.md:157 #: 3eb6a013a2a4478ca2ad134661f65c58 msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" +"FAIR 原则为共享和公开数字资产（尤其是数据）提供了基础。FAIR 原则强调访问计算" +"机的重要性，且所有数字资产都应是可发现、可访问、可互操及可重用的。工作流解码" +"了执行科学流程的方法，并利用该方法来创建数据。因此，工作流必须支持FAIR数据的" +"创建且始终坚持FAIR原则。—— [FAIRFAIR计算工作流](https://workflows.community/" +"groups/fair/)，工作流社区协议。" #: ../../src/introduction/basic-concepts.md:167 #: 074af9633627470485e5225326d5f20a msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." msgstr "" +"CWL源于\"make\"，且拥有很多类似的工具，可基于任务间的依赖关系决定执行顺序。" +"但不同于\"make\"的是，CWL任务是独立的，您必须明确输入和输出。" #: ../../src/introduction/basic-concepts.md:171 #: 847951c055b94a83b1e081594cef22ee msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." msgstr "" +"任务明确且独立的好处在于灵活、可移植及可拓展。使用CWL描述的工具和工作流可公开" +"透明地使用Docker等技术，并与来自不同供应商的CWL实现一起使用。" #: ../../src/introduction/basic-concepts.md:176 #: 44bde1fae06b4678bcac4f3224601296 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" +msgstr "`cwltool` 也使用PROV-O标准本体来追溯数据来源。" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 @@ -637,302 +697,368 @@ msgstr "" #: f059896039524095b4deb65d693f8ddf #: 3439764fab0e49d2bcb7c9fbae556e65 msgid "Learn More" -msgstr "" +msgstr "了解更多信息" #: ../../src/introduction/basic-concepts.md:180 #: 9d5100c7d0a040aea1020bf633ad17de msgid "Semantic Versioning - " -msgstr "" +msgstr "语义版本控制 —— " #: ../../src/introduction/basic-concepts.md:181 #: 36eb4b3b966640af90faa55db3789cb6 msgid "The CWL Specification page in the CWL website: " -msgstr "" +msgstr "在CWL网站上查阅CWL规范页面，请前往： " #: ../../src/introduction/basic-concepts.md:182 #: 2ccb956baa6b4376a04ad9fcc4654631 msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" +"在Github上查阅当前版本CWL规范，请前往： {{ ''.format(cwl_version_text) }}" #: ../../src/introduction/basic-concepts.md:183 #: 72889b830c514afe9a7cb1e64b5666a0 msgid "The list of Implementations in the CWL website: " -msgstr "" +msgstr "在CWL网站上查阅实现列表，请前往：" #: ../../src/introduction/basic-concepts.md:184 #: e29bd7f973544600be589c3b3f84cf63 msgid "PROV-O: The PROV Ontology - " -msgstr "" +msgstr "PROV-O：PROV 本体——" #: ../../src/introduction/basic-concepts.md:185 #: c377a7f5dbe645cebbb6c7eccf831a0b msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." -msgstr "" +msgstr "本用户指南的[操作](../topics/operations.md)章节详细介绍了CWL操作。" #: ../../src/introduction/index.md:1 #: 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" -msgstr "" +msgstr "介绍" #: ../../src/introduction/index.md:3 #: 950370f0a36048b38e1bde9b78f80816 msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." -msgstr "" +msgstr "本章节将简要介绍CWL、遵循本用户指南的先决条件及一些基本概念，这些概念有助于阅" +"读（理解）用户指南的其他内容。" #: ../../src/introduction/prerequisites.md:1 #: f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" -msgstr "" +msgstr "先决条件" #: ../../src/introduction/prerequisites.md:6 #: 353b14f06ee845d0a06a829643e31534 msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." msgstr "" +"本章节所列的软件和配置是遵循本用户指南的先决条件。CWL标准通过不同的工作流运行" +"程序和平台实现。需求列表的重点在于CWL引用运行程序`cwltool`。您也可使用其他的" +"兼容CWL的运行程序或工作流系统，但结果和界面可能看上去不同（尽管精确的工作流输" +"出应该相同）。" #: ../../src/introduction/prerequisites.md:12 #: b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" -msgstr "" +msgstr "CWL实现" #: ../../src/introduction/prerequisites.md:14 #: ff2bb4c6504b456bac7ca9c514414dbf msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." msgstr "" +"CWL标准有很多种实现形式，可能是完整的CWL运行程序，或者是工作流引擎的插件或拓" +"展程序。 [实现](basic-concepts.md#implementations)章节对此提供了更好的解释。" #: ../../src/introduction/prerequisites.md:19 #: cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" -msgstr "" +msgstr "操作系统" #: ../../src/introduction/prerequisites.md:21 #: 5089fdba8aed4113983fa86e698df98b msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" -msgstr "" +msgstr "建议使用最新的操作系统，您可从下选项选择合适的操作系统：" #: ../../src/introduction/prerequisites.md:24 #: dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" -msgstr "" +msgstr "Linux操作系统" #: ../../src/introduction/prerequisites.md:25 #: c05187af85be41b782678b79627f8fbf msgid "macOS" -msgstr "" +msgstr "macOS操作系统" #: ../../src/introduction/prerequisites.md:26 #: beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" -msgstr "" +msgstr "Windows操作系统" #: ../../src/introduction/prerequisites.md:29 #: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." msgstr "" +"如您使用的是Windows操作系统，必须安装 [适用于 Linux " +"2的Windows子系统](https://learn.microsoft.com/en-us/windows/wsl/install) " +"(WSL2)。请参阅 `cwltool` [documentation](https://github.com/" +"common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) ，了" +"解更多关于安装WSL2的信息。同时，您的操作系统需要网络访问及最新版本的Python(3." +"56+)。" #: ../../src/introduction/prerequisites.md:35 #: 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" -msgstr "" +msgstr "CWL运行程序" #: ../../src/introduction/prerequisites.md:41 #: 0f2704bf1f7148be95e999e312899f11 msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." msgstr "" +"要运行CWL工作流，首先需要一个CWL运行程序。`cwltool`是由CWL社区维护的Python开" +"源项目，也是CWL引用运行程序，这意味着其必须支持当前版本CWL规范{{ cwl_version " +"}}的所有规定。" #: ../../src/introduction/prerequisites.md:46 #: 86264c9e56104ecea9146407c379aae2 msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" msgstr "" +"可通过`pip`安装`cwltool` ，建议您使用`venv` 或 " +"`conda`等虚拟环境进行安装。以下命令将使用`venv`模块创建和激活Python虚拟环境，" +"并在该环境中安装 `cwltool`：" #: ../../src/introduction/prerequisites.md:51 #: 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" +msgstr "使用 `pip` 和 `venv`安装`cwltool`。" #: ../../src/introduction/prerequisites.md:62 #: f7aaafeee230400da056464c853582c2 msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." msgstr "" +"请参阅`cwltool` [documentation](https://github.com/common-workflow-language/" +"cwltool#install)，了解使用 `apt` 和 `conda`安装`cwltool`的其他方法。" #: ../../src/introduction/prerequisites.md:65 #: 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" +msgstr "让我们使用`cwltool` 来执行一个简单的CWL工具描述`true.cwl`。" #: ../../src/introduction/prerequisites.md:67 #: 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" -msgstr "" +msgstr "`true.cwl`" #: ../../src/introduction/prerequisites.md:73 #: 6391e08e0bde49f4b21286d8fdb97433 msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" msgstr "" +"`cwltool` 命令具有验证 CWL 工具和工作流描述的选项，此选项将解析 CWL " +"文档，查找语法错误，并验证工作流描述是否符合 CWL " +"标准。但是，这些操作将在不运行文档的情况下执行。要验证 CWL " +"工作流（甚至是像上面这样的独立命令行工具描述），请将 `--validate` 选项传递给 " +"`cwltool` 命令：" #: ../../src/introduction/prerequisites.md:79 #: cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." -msgstr "" +msgstr "使用 `cwltool`验证 `true.cwl` 。" #: ../../src/introduction/prerequisites.md:84 #: d41c4bc740aa474ea09a7cbd267c8840 msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" +msgstr "您也可以通过省略`--validate`选项来运行CWL工具描述：" #: ../../src/introduction/prerequisites.md:86 #: 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." -msgstr "" +msgstr "使用 `cwltool` 运行 `true.cwl`。" #: ../../src/introduction/prerequisites.md:91 #: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" -msgstr "" +msgstr "Cwl-runner Python 模块" #: ../../src/introduction/prerequisites.md:93 #: 096d0a50f69e48bd9915238d1b4264c1 msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." msgstr "" +"`cwl-runner` 是任何符合标准的CWL运行程序的别名，其与实现无关。这仅仅意味着" +"`cwl-runner` 别名命令可独立调用，且不依赖于特定CWL运行程序名。用户可调用`cwl-" +"runner` ，而无需直接调用诸如 `cwltool`的CWL运行程序。 `cwl-" +"runner`由系统管理员安装，或用户通过指定偏好CWL实现来安装， " +"这对于拥有多个CWL运行程序的环境而言十分方便。" #: ../../src/introduction/prerequisites.md:101 #: f9df974a8e2645a6918e67466bd1fdc2 msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" +"CWL 社区发布了一个名为 `cwlref-runner` 的 Python 包，该软件包以 `cwl-" +"runner`作为`cwltool` 的别名" #: ../../src/introduction/prerequisites.md:104 #: 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" +msgstr "使用 `pip`为cwltool安装`cwl-runner`别名。" #: ../../src/introduction/prerequisites.md:111 #: 746c6fc9c29d466494458a08d4c96672 msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." msgstr "" +"现在，执行 `cwl-runner` 以调用 `cwltool`，便可验证和运行您的工作流。执行此操" +"作后，您应该得到与上一章节相同的结果和输出。" #: ../../src/introduction/prerequisites.md:115 #: b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" +msgstr "使用 `cwl-runner`验证 `true.cwl`。" #: ../../src/introduction/prerequisites.md:120 #: 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" +msgstr "使用 `cwl-runner` 运行 `true.cwl`。" #: ../../src/introduction/prerequisites.md:125 #: 705807fae182425dbf4244dbf2be1226 msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" +"执行 `cwl-runner` 的另一种方法是直接调用文件。为此，首先您需要将`true.cwl` " +"工作流复制到一个新文件中：`true_shebang.cwl`，并添加特殊的首行，即*shebang*：" #: ../../src/introduction/prerequisites.md:129 #: f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" -msgstr "" +msgstr "`true_shebang.cwl`" #: ../../src/introduction/prerequisites.md:135 #: 164c438baab54ec19bbb4584a10dd411 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" +msgstr "现在，您可使用 `chmod u+x` 执行 `true_shebang.cwl` 文件。" #: ../../src/introduction/prerequisites.md:137 #: bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." -msgstr "" +msgstr "执行 `true.cwl`文件。" #: ../../src/introduction/prerequisites.md:144 #: 695184d1b45a42f393e2da99c3721773 msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." -msgstr "" +msgstr "最后，您可直接在命令行执行此文件。在执行时，shebang （`cwl-runner`） " +"中指定的程序将用于执行文件的其余部分。" #: ../../src/introduction/prerequisites.md:148 #: 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" +msgstr "使用 shebang 运行 `true_shebang.cwl`。" #: ../../src/introduction/prerequisites.md:154 #: 3ba23b4ea01c46848e4e43bbeff5f5a1 msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," msgstr "" +"*shebang*是以`#！`两个字符序列开头的脚本。执行脚本时，" +"操作系统将使用在shebang 之后指定的可执行文件来执行脚本。最好使用 `/usr/bin/" +"env `， 而不是硬编码位置，因为/usr/bin/env 可在系统 " +"`PATH`中寻找``程序，" #: ../../src/introduction/prerequisites.md:161 #: eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" -msgstr "" +msgstr "文本编辑器" #: ../../src/introduction/prerequisites.md:163 #: f6b39b12bd5c495cb53e2795bf9200ed msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" +"您可使用任何带有CWL " +"的文本编辑器，但对于语法高亮而言，建议使用YAML支持的编辑器。" +"流行的编辑器包括Visual Studio Code、Sublime、WebStorm、vim / " +"neovim以及Emacs。" #: ../../src/introduction/prerequisites.md:167 #: 2fdb62a13f9447bc89183426260ce781 msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" -msgstr "" +msgstr "以下Visual Studio Code和WebStorm的拓展程序支持与CWL集成，且具备自定义语法高亮" +"及更好的自动补全等功能：" #: ../../src/introduction/prerequisites.md:171 #: 1f07135156254f74a6b043bf33d00cc3 msgid "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" +"带有 Benten (CWL) 插件的 Visual Studio Code —— " #: ../../src/introduction/prerequisites.md:172 #: de344f356b1c466d9131cdbd4d7353a3 msgid "cwl-plugin for IntelliJ - " msgstr "" +"IntelliJ支持的cwl插件 —— " #: ../../src/introduction/prerequisites.md:174 #: 3f9324ede11441f58d93875867034cf0 msgid "The CWL community also maintains a list of editors and viewers: " -msgstr "" +msgstr "CWL社区也在维护一个编辑器和阅读器清单：" #: ../../src/introduction/prerequisites.md:177 #: 6ce8b81560e341c580d316d69202b268 msgid "Docker" -msgstr "" +msgstr "Docker" #: ../../src/introduction/prerequisites.md:181 #: 40cfd559d6a848d1aae354d3bdaa8e9c msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." msgstr "" +"`cwltool` 使用 Docker 运行指定软件容器的工具、工作流及工作流步骤。" +"请按照Docker 文档中的说明，为您的操作系统安装Docker：。" #: ../../src/introduction/prerequisites.md:185 #: 8a9a50b0ebe847ce90593881ffe0d69c msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." msgstr "" +"您无需了解如何编写和构建 Docker 容器。在用户指南的其余部分，我们将使用现有的 " +"Docker 镜像来运行示例，并解释带容器和不带容器的执行模型之间的差异。" #: ../../src/introduction/prerequisites.md:191 #: 923cf9dd6d6c417aabe42f9fa62ffa35 msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." msgstr "" +"`cwltool` 支持使用 Docker、Podman、udocker 和 Singularity " +"运行容器，您也可使用其他容器注册表来拉取镜像。" #: ../../src/introduction/prerequisites.md:198 #: 9390b03889de44638141d705e0ef8322 msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." -msgstr "" +msgstr "下一章节（基本概念）中的 [实现](basic-concepts.md#implementations)主题。" #: ../../src/introduction/prerequisites.md:199 #: 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " -msgstr "" +msgstr "Python`venv`模块：" #: ../../src/introduction/quick-start.md:1 #: cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" -msgstr "" +msgstr "快速入门" #: ../../src/introduction/quick-start.md:3 #: c43d9675ed134b78b02acb5a102a764a msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." -msgstr "" +msgstr "本章节将向您简要介绍 CWL的定义以及您可以在哪里了解更多信息。不需要先前的 CWL " +"知识，但您必须能够熟练地按照命令行说明进行操作。" #: ../../src/introduction/quick-start.md:7 #: 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" -msgstr "" +msgstr "“Hello World”" #: ../../src/introduction/quick-start.md:12 #: cb203354977d42a58112d09357f62565 msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" msgstr "" +"CWL 文档是[YAML](../topics/index.md) (and/or JSON)中编写的。" +"下方例子演示了一个简单的 CWL“Hello World”工作流程，并带有注释。请注意，" +"注释以 `#` 开头：" #: ../../src/introduction/quick-start.md:16 #: 9e51962a7e5c47248f3e20703ae101eb @@ -943,61 +1069,77 @@ msgstr "" #: 7e475e3f3c4a4404bb0236124c0f7ce7 msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." msgstr "" +"上面的示例只是 `echo` 命令行工具的包装器。" +"使用默认输入值运行上述工作流将生成与命令行 `echo “Hello World”` 相同的结果。" #: ../../src/introduction/quick-start.md:27 #: 82613ca4e32b4ccab1b7735f5ba2d5a1 msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." msgstr "" +"在 CWL 中，命令行工具和工作流之间是有区别的。但为了简单起见，我们在这里使用术" +"语“工作流”。您将在[基本概念ba](basic-concepts.md)章节了解更多有关信息。" #: ../../src/introduction/quick-start.md:32 #: 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" -msgstr "" +msgstr "安装 CWL 运行程序" #: ../../src/introduction/quick-start.md:34 #: f3e56aedd56b4b93bdc3894273e8c144 msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" msgstr "" +"`cwltool` 是 CWL 规范的实现，也是符合规范的 CWL " +"*引用程序*，且符合最新版本的规范：{{ cwl_version }}。您可使用 `pip` 安装 " +"`cwltool`：" #: ../../src/introduction/quick-start.md:39 #: 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." -msgstr "" +msgstr "使用 `pip` 安装 `cwltool`。" #: ../../src/introduction/quick-start.md:47 #: a81342e756d24c40acc15835d0a768f2 msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." msgstr "" +"如您无法使用 pip 命令安装 cwltool，请参阅[先决条件p](prerequisites.md) 章节，" +"了解安装 `cwltool` " +"的其他方法，以及了解助于遵循用户指南其余内容的软件和库详细清单。" #: ../../src/introduction/quick-start.md:51 #: c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" -msgstr "" +msgstr "运行 “Hello World”" #: ../../src/introduction/quick-start.md:53 #: 9b68bcb1a41849dc9601ab47c5bbb0fe msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" msgstr "" +"执行 `cwltool`命令行的流程大致是 `cwltool [OPTIONS] " +"[INPUTS_OBJECT]`，因此您可直接运行 `hello_world." +"cwl`工作流，无需指定以下任何选项：" #: ../../src/introduction/quick-start.md:57 #: ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" +msgstr "使用 `cwltool` 运行 `hello_world.cwl`。" #: ../../src/introduction/quick-start.md:62 #: 0d8a788402914ebd8f09a5ca80650011 msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" -msgstr "" +msgstr "或者，您可替换输入参数 `message` 的默认值，方法类似于更改 `echo` " +"基本命令的参数：" #: ../../src/introduction/quick-start.md:65 #: 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" +msgstr "使用传递输入参数的 `cwltool` 运行 `hello_world.cwl`。" #: ../../src/introduction/quick-start.md:70 #: 2ea056ab04b6419a9faf350de22a17f2 msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" msgstr "" +"将值传递给工作流输入参数的另一种方法是通过*Inputs Object* " +"实现，这是一个包含对应值输入字段的文件，可使用 JSON 或 YAML 编写。例如：" #: ../../src/introduction/quick-start.md:74 #: 1a44a545434b448aa956005deeed90a8 @@ -1007,72 +1149,89 @@ msgstr "" #: ../../src/introduction/quick-start.md:80 #: e76bfcc0c9f84bcdb3f6d5277869a88c msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" -msgstr "" +msgstr "您现在可以使用此输入对象文件来执行“Hello World”工作流：" #: ../../src/introduction/quick-start.md:82 #: d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" +msgstr "将输入对象文件传递给 `cwltool`。" #: ../../src/introduction/quick-start.md:88 #: b6d59e4b9c854abab1b3f7a0fa26f504 msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." msgstr "" +"我们为工作流和输入对象文件使用了类似的文件名。*-job.json* 后缀在输入对象文件" +"中很常见，但非必需要求，您可为工作流和输入对象文件选择任何名称。" #: ../../src/introduction/quick-start.md:96 #: 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" -msgstr "" +msgstr "继续阅读本用户指南的下一章节！" #: ../../src/introduction/quick-start.md:97 #: 77e43c7117fd4c52b140f0dd52cc3963 msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" +msgstr "[ CWL 实现清单](https://www.commonwl.org/implementations)。" #: ../../src/introduction/quick-start.md:98 #: 7282abfa7155497ca47c30f9abfb6474 msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." msgstr "" +"在Github上访问 [`common-workflow-language` 组织](https://github.com/common-" +"workflow-language)。" #: ../../src/introduction/quick-start.md:99 #: 176d8d47830f4031bb95dc231ebf1303 msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" +"[在Wikipedia上查阅Common Workflow Language ](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)。" #: ../../src/introduction/quick-start.md:100 #: 82a7ca3703bc4f0daa18942a1ac8943b msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" +"访问[YAML.org](http://yaml.org/) 网站和[ 在Wikipedia上查阅YAML](https://en." +"wikipedia.org/wiki/YAML)." #: ../../src/introduction/quick-start.md:101 #: d039a9d6461c44628d4660c00d9ce6ff msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." msgstr "" +"{{'[CWL 规范版本](https://www.commonwl.org/VERSION)'.替代('VERSION', " +"cwl_version_text) }}。" #: ../../src/introduction/quick-start.md:102 #: fbc3383d9e1c4eaca7931c3cc4f1752b msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" +"[在 Wikipedia上查阅工作流管理系统 ](https://en.wikipedia.org/wiki/" +"Workflow_management_system)。" #: ../../src/setup.md:9 #: 1330bd38c4b5495f890b98c669f81a9d msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." -msgstr "" +msgstr "此页面已过时，保留在此以保留旧用户指南链接。此页面上的信息已迁移到新用户指南" +"的[最常见问题](/faq.md)章节。" #: ../../src/topics/additional-arguments-and-parameters.md:1 #: 9c87c76c690948ac8e18088a0fffe679 msgid "Additional Arguments and Parameters" -msgstr "" +msgstr "额外参数和指定参数" #: ../../src/topics/additional-arguments-and-parameters.md:3 #: ad00d94d4fb64bbdac356e64dd3803b9 msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." -msgstr "" +msgstr "有时工具需要额外的命令行选项，这些选项并不完全对应于输入参数。" #: ../../src/topics/additional-arguments-and-parameters.md:6 #: d8110ed19da94ad8a9f56e7006c4a2cf msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." msgstr "" +"在此示例中，我们将包装 Java 编译器，以将 java 源文件编译为类文件。 " +"默认情况下，“javac”将在与源文件相同的目录中创建类文件。 但是，CWL " +"输入文件（以及它们所在的目录）可能是只读的，因此我们需要指示 “javac” " +"将类文件写入指定的输出目录。" #: ../../src/topics/additional-arguments-and-parameters.md:13 #: a74935dc31664e979ca8f90a6a4ba53c @@ -1089,162 +1248,213 @@ msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 #: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "" +msgstr "接下来，创建一个用于命令行工具的示例 Java 文件。" #: ../../src/topics/additional-arguments-and-parameters.md:30 #: 9643449da1da46d7861866dce490cbcb msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" +msgstr "现在，调用在命令行上提供工具描述和输入对象的 `cwltool`：" #: ../../src/topics/additional-arguments-and-parameters.md:36 #: 713666580a0a4466b4ba6e3eb2b54f0a msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." -msgstr "" +msgstr "此处我们使用`arguments`字段将一个额外的参数添加至命令行，此参数与指定输出参数" +"无关。" #: ../../src/topics/additional-arguments-and-parameters.md:43 #: d50574c8b9694f83aa376d39b9a6fcd6 msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." msgstr "" +"此示例引用了运行时参数。运行时参数提供有关工具实际执行时硬件或软件环境的信息" +"。 `$(runtime.outdir)`参数是指定输出目录的路径。其他参数包括 `$(runtime." +"tmpdir)`、 `$(runtime.ram)`、`$(runtime.cores)`、 `$(runtime." +"outdirSize)`,以及`$(runtime.tmpdirSize)`。有关详细信息，请参阅 CWL 规范的 " +"[运行时环境][运行时] 章节。" #: ../../src/topics/best-practices.md:1 #: 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" -msgstr "" +msgstr "最佳实践" #: ../../src/topics/best-practices.md:3 #: 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." msgstr "" +"以下提供了一些关于为工具或工作流编写通用语言描述的建议，请牢记在心。此处仅基" +"于有用性量表提供部分指导原则：虽然越多越好，但并非所有原则都是必需的。" #: ../../src/topics/best-practices.md:8 #: 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" +"无用于输入名称或引用文件/目录的`type: string`参数，请根据需要使用 `type: " +"File`或`type: Directory`。" #: ../../src/topics/best-practices.md:11 #: 4dee8504a8e5496081dadc386ab45540 msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." msgstr "" +"CWL 文档（结合 `Dockerfile`等外部组件）是软件代码。工作流开发人员应注意，软件" +"许可的常规规则适用于本文档。例如，如果工作流是公开共享的，则许可条款必须明确" +"，以便将来的用户了解在什么条件下可以运行工作流、修改工作流和/或将其与其他工作" +"流组合。因此，请考虑在文档中包含许可证字段。本指南的作者敦促您选择预先存在的" +"许可证，而不是尝试编写自己的许可证（请访问下方链接，了解有关选择许可证的更多" +"信息），我们建议您选择允许任何人重复使用的许可证，例如 [Apache 2.0][apache-" +"license]。" #: ../../src/topics/best-practices.md:20 #: 674c238b25e240eda05e22e399f2f78f msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." msgstr "" +"如可能，请使用相应的 [SPDX 标识符][spdx] 指定许可证。通过提供 `https://spdx." +"org/licenses/[SPDX-ID]` 形式的URL构建许可证的元数据字段，其中 `SPDX-ID` " +"取自上方链接的标识符列表。有关指导，请参阅下方的示例代码段。对于没有 SPDX " +"标识符的非标准许可证，请提供许可证的 URL。" #: ../../src/topics/best-practices.md:26 #: b651f80f47b4442fbf29454a233697fc msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" -msgstr "" +msgstr "有用的阅读材料：“[A Quick科学家－程序员的软件许可快速入门指南 ][sci-license]”" #: ../../src/topics/best-practices.md:28 #: 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" +msgstr "_带有SPDX识别符的许可证元数据字段示例：_" #: ../../src/topics/best-practices.md:37 #: 3a87a0fb2a364e3da5aaa4017e430b19 msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." msgstr "" +"有关在CWL描述中提供更多元数据的示例，请查阅[本用户指南中的元数据和作者授权章" +"节](../topics/metadata-and-authorship.md)。" #: ../../src/topics/best-practices.md:40 #: ecf2b9c0b1664afe9c4e180610610021 msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." -msgstr "" +msgstr "包括CWL工具或工作流描述作者的 " +"[归属信息][许可证示例]。请使用明确的标识符，比如[ORCID][orcid]。" #: ../../src/topics/best-practices.md:44 #: e24cb13d98014e558b6a6946758359e0 msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." -msgstr "" +msgstr "在工具需求中，使用 `SoftwareRequirement`下方的短命名列出依赖关系。" #: ../../src/topics/best-practices.md:47 #: f2b14a92374e449d9fb1e8c86ae0dd61 msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" +"包括表示依赖关系的[SciCrunch][scicrunch]识别符，其格式为`https://identifiers." +"org/rrid/RRID:SCR_NNNNNN`。" #: ../../src/topics/best-practices.md:50 #: 928e3df7ca3e479ca6474a8e72cf36eb msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" +"所有`输入` 和`输出` " +"的标识符均应反映其概念特性，请使用`unaligned_sequences`、`reference_genome`、" +" `phylogeny`、或 `aligned_sequences` 等信息性名称，而不是`foo_input`、`foo_fi" +"le`、`result`、`input`及`output`等非信息性名称。" #: ../../src/topics/best-practices.md:55 #: d355f035676446c88b028f327aeb4829 msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." -msgstr "" +msgstr "在工具描述中， `SoftwareRequirement` 下方包含已知可使用此描述的工具版本列表。" #: ../../src/topics/best-practices.md:58 #: 339b852df24242189d6efcd2898a3396 msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." msgstr "" +"应为所有输入和输出 `文件` 指定`格式` 。生物信息学工具应使用来自 [EDAM][edam-" +"example] 的格式标识符。另请参阅 `iana:text/plain`、`iana:text/tab-separated-" +"values` 和 `$namespaces: { iana: \"https://www.iana.org/assignments/" +"media-types/\" }。[完整的 IANA 媒体列表][iana类型] (（也称为 MIME 类型）。对" +"于非生物信息学工具，请以相同的方式使用或创建适当的本体/受控词汇表。请编辑此页" +"面，让告知我们。" #: ../../src/topics/best-practices.md:66 #: 3ef57e6862f240bebcf193a52397af0a msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." -msgstr "" +msgstr "将所有以流式兼容方式读取或编写的输入和输出 `文件`（仅一次，无随机访问）" +"标记为 `流式传输：true`。" #: ../../src/topics/best-practices.md:69 #: f1a7c4f896a04a80b0c5f6a1db61ff8c msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." msgstr "" +"每个 `CommandLineTool` 描述应仅关注单个操作，即使 （子） " +"命令能够执行更多操作。请勿选择非必需或不使用的选项，以免工作描述过于复杂。" #: ../../src/topics/best-practices.md:73 #: 1ac4c3d8c3e44bd1af3fc5df70051926 msgid "Custom types should be defined with one external YAML per type definition for re-use." -msgstr "" +msgstr "为了方便重复使用，每个类型定义都应使用一个外部 YAML 来定义自定义的类型。" #: ../../src/topics/best-practices.md:76 #: c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "" +msgstr "包括总结工具/工作流的顶级短 ` 标签 `。" #: ../../src/topics/best-practices.md:78 #: fae385da16aa443da996fa23ac03d6ae msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." -msgstr "" +msgstr "如有需要，也可增加一个顶级`doc`。相比顶级 " +"`label`（见上方），此标签应长度更长且内容更详细。" #: ../../src/topics/best-practices.md:82 #: 92430be71ecc40e18bbbb80d5576c613 msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." -msgstr "" +msgstr "对于带有固定有效值列表的元素，请使用 `type： enum` ，而不是 `type： string`。" #: ../../src/topics/best-practices.md:85 #: 387d83db81024f65aa9a890c2d07874a msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." msgstr "" +"评估所有 JavaScript 的使用，以了解可能的消除或替代情况。一个常见示例：操作 `" +"文件 ` 名称和路径？考虑是否可使用 [内置 `文件` 属性][file-" +"prop]中的其中一种（如`basename`、`nameroot`和`nameext`等）来替代。" #: ../../src/topics/best-practices.md:90 #: d8e2280a75a74916a1630afaa2fe2ae3 msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." -msgstr "" +msgstr "邀请同事（最好来自其他公司）对工作描述进行测试并提供反馈。" #: ../../src/topics/best-practices.md:93 #: f1c1340f9745458980e0fbd641738687 msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." msgstr "" +"具有可抽象的单个组件的复杂工作流应利用 [`SubworkflowFeatureRequirement`][子工" +"作流]使其工作流模块化，并允许轻松重用工作流的各个部分。" #: ../../src/topics/best-practices.md:97 #: 5424e5472c3d466fa2a3d2022c6cb475 msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." -msgstr "" +msgstr "软件容器应符合[“生物信息学软件封装和容器化建议”][容器] （其他学科也适用）。" #: ../../src/topics/command-line-tool.md:1 #: 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" -msgstr "" +msgstr "命令行工具" #: ../../src/topics/command-line-tool.md:3 #: 12f57b2ba76b492abe1816e06bfb1417 msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." msgstr "" +"命令行工具是一种流程对象，可以单独运行或作为工作流步骤运行，它是 " +"`ls`、`echo`、`tar` 等命令的包装器。命令行工具 CWL " +"文档的`baseCommand`属性对命令行工具进行了定义。" #: ../../src/topics/command-line-tool.md:8 #: e1f657a46ce94a0d83671540e2cc2dab +#, fuzzy msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." msgstr "" +"CWL 命令行工具还必具有 ` 输入 ` 和 ` 输出 `。以下示例包含一个最小示例，演示了" +"支持`echo`Linux命令的CWL命令行工具如何使用输入和输出。" #: ../../src/topics/command-line-tool.md:19 #: abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." -msgstr "" +msgstr "CWL命令行工具。" #: ../../src/topics/command-line-tool.md:50 #: 3b1a9ae3412f4d6e96a39b9a16934232 @@ -1255,36 +1465,40 @@ msgstr "" #: a5eacdbc9aa142c890b177869da4143d msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." msgstr "" +"上方示例仅使用简化形式来定义输入和输出。了解更多有关信息，请查阅[输入](../" +"topics/inputs.md) 和 [输出](../topics/outputs.md) 章节。" #: ../../src/topics/command-line-tool.md:68 #: 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" -msgstr "" +msgstr "网络访问" #: ../../src/topics/command-line-tool.md:69 #: e3bdaceae8784ab0807b2cf356a98580 msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." -msgstr "" +msgstr "这指示进程是否需要传出 IPv4/IPv6 网络访问。如果在 CWL v1.1+ " +"中手动编写命令行工具，则需指定何时需要网络访问。" #: ../../src/topics/command-line-tool.md:83 #: ed521ac365db4a6ba5a1051fbaa2932e msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." -msgstr "" +msgstr "升级到至版本1.1或 1.2的 CWL v1.0 命令行工具将自动获取网络访问权限。" #: ../../src/topics/creating-files-at-runtime.md:1 #: a2a0f0eb0f404eb3aaf19cfd3cdb559b msgid "Creating Files at Runtime" -msgstr "" +msgstr "在运行时创建文件" #: ../../src/topics/creating-files-at-runtime.md:3 #: 0cf51b6da6884065ae42032abc20eb0d msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." -msgstr "" +msgstr "有时，您需要从输入参数动态创建文件，例如需要可从文件（而不是命令行参数）中读" +"取输入配置的工具，或者需要一个小型包装器的 shell 脚本。" #: ../../src/topics/creating-files-at-runtime.md:7 #: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "" +msgstr "要生成此类文件，我们可使用 `InitialWorkDirRequirements`。" #: ../../src/topics/creating-files-at-runtime.md:9 #: d3f74c3b094a427fbec831afab657d50 @@ -1295,16 +1509,23 @@ msgstr "" #: cfffc518ba6e4ed1a80762ed6f7d25df msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." msgstr "" +"在创建文件之前，CWL引擎将拓展所有诸如 `$(inputs.message)`的 [表达式](../" +"topics/expressions.md)。此处，应在输入`消息`中插入值。" #: ../../src/topics/creating-files-at-runtime.md:20 #: 9454a330b9324744b89448f2694b1b03 +#, fuzzy msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." msgstr "" +"_CWL 表达式 _ 独立于稍后在命令行工具调用期间使用的所有 _shell 变量 _，" +"这意味着字符 `$` 的所有真实需要必须** 删除 ** `\\` 。例如，上面的 `\\" +"${PREFIX}` 在生成的文件中扩展为 `${PREFIX}`，以供 shell 脚本（而不是 CWL " +"引擎）评估。" #: ../../src/topics/creating-files-at-runtime.md:27 #: 7f8d99a30b644457a62ac1523d0c72aa msgid "To test the above CWL tool, use this job to provide the input value `message`:" -msgstr "" +msgstr "若要测试上述 CWL 工具，请使用此作业提供输入值 `消息`：" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 @@ -1319,16 +1540,25 @@ msgstr "" #: 10d1373bb14a4a3cacd3b92a2f83382d msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." msgstr "" +"在运行此步骤之前，让我们详细地看一下每个步骤。基本命令 `baseCommand： [“sh”，" +" “example.sh”]` 将执行命令 `sh example.sh`，此步骤将运行我们在 shell " +"中创建的文件。" #: ../../src/topics/creating-files-at-runtime.md:40 #: 70e257091bdb456e8957f90a8fa90e8c msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." msgstr "" +"`InitialWorkDirRequirements` 需要 `列表 `。由于 `列表` 是一个 YAML 数组，" +"我们需要在数组每个元素的首行添加一个 " +"`-`，而在本示例中我们只有一个元素。`entryname:` 可以具有任何值，但它必须与 " +"`baseCommand` 中指定的值相匹配。最后一个步骤是 `entry：`，后面跟着 `|-`，" +"这是 YAML 引用语法，意味着正在使用多行字符串（没有它，我们则需要在一行上编写" +"整个脚本）。" #: ../../src/topics/creating-files-at-runtime.md:51 #: 1741804e33aa43ce88b4320c11ae5973 msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." -msgstr "" +msgstr "参阅 [YAML指南 ](../topics/yaml-guide.md#maps) ，了解更多有关格式的信息。" #: ../../src/topics/creating-files-at-runtime.md:54 #: ../../src/topics/environment-variables.md:18 @@ -1341,22 +1571,26 @@ msgstr "" #: d6255506eebe44be94c5ce703c44a513 #: 7bbd2d738fc54649aeb10f8d2bc38b6f msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" +msgstr "现在，通过命令行上的工具描述和输入对象调用 `cwltool`：" #: ../../src/topics/custom-types.md:1 #: cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" -msgstr "" +msgstr "自定义类型" #: ../../src/topics/custom-types.md:3 #: 67573252cc064b27ab13eebc468ac58a msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." msgstr "" +"有时您可能希望编写自己的自定义类型，以便在 CWL 描述中使用和重用。使用此类自定" +"义类型可以减少全部使用相同类型的多个描述之间的冗余工作，并且还允许对工具/分析" +"进行额外的自定义/配置，而无需直接修改 CWL 描述。" #: ../../src/topics/custom-types.md:9 #: 73e68b3af9cf41338d843c0c40e50cdc msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." -msgstr "" +msgstr "下方示例为 [biom 转换格式][biom] 工具的 CWL 描述，该工具可将标准 biom " +"表格文件转换为 hdf5 格式。" #: ../../src/topics/custom-types.md:12 #: ef5f35acb97f4ddfad7b688712f53484 @@ -1372,21 +1606,30 @@ msgstr "" #: a999b1acda2641598086648c64aa3831 msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" +"___注意：___要访问下方示例，您需要 [下载示例输入文件](https://github.com/" +"common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/" +"rich_sparse_otu_table.biom)， *rich_sparse_otu_table.biom* 比如通过 `wget`：" #: ../../src/topics/custom-types.md:30 #: f8c12a58cb0b46a488823c6ae95f25ea msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" -msgstr "" +msgstr "在29行的`inputs:table_type`中，可用于表格转换的表选项列表以自定义对象形式导入" +"：" #: ../../src/topics/custom-types.md:46 #: f25a63e0926d4932bbe64b2e4bdabf9e msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." msgstr "" +"自定义类型的引用是采用定义对象的文件名（`biom-convert-table.yaml` " +"）和该文件中定义自定义类型的对象名（`table_type` ）的组合。在本示例中，导入的" +"`biom-convert-table.yaml` 文件中的`符号` 数组定义了允许的表选项。例如，在 " +"`custom-types.yml` ，我们把`OTU表` " +"作为一个`输入`进行传递，告诉工具创建一个hdf5格式的OTU表。" #: ../../src/topics/custom-types.md:53 #: b0a4df0fd3ca42338cff4689235dcf4e msgid "The contents of the YAML file describing the custom type are given below:" -msgstr "" +msgstr "描述自定义类型的 YAML 文件的内容如下所示：" #: ../../src/topics/custom-types.md:55 #: fecfbb44456640d8ba05e519bf2ff564 @@ -1397,21 +1640,28 @@ msgstr "" #: d718630a296545f3a989c8c71e9ddc77 msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" msgstr "" +"为了在 CWL 描述中使用自定义类型，必须导入该类型。 " +"`requirements：SchemaDefRequirements` 对导入进行了描述，如下方示例 `custom-" +"types.cwl` 的描述所示：" #: ../../src/topics/custom-types.md:76 #: 9a97acd430064710bcdf76edbd9f711c msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." msgstr "" +"另请注意，此 CWL 描述的作者还增添了 `ResourceRequirement`，其指定了工具成功运" +"行所需的最小内存量和内核数、编写描述的软件版本的详细信息以及其他有用的元数据" +"。这些功能将在本用户指南的其他章节中进一步讨论。" #: ../../src/topics/environment-variables.md:1 #: 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" -msgstr "" +msgstr "环境变量" #: ../../src/topics/environment-variables.md:3 #: 3c821c9c46d841ec89b8a5b1018f3af8 msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." -msgstr "" +msgstr "工具在受限环境中运行，不会从父进程继承大多数环境变量。 您可以使用 " +"`EnvVarRequirements` 为该工具设置环境变量。" #: ../../src/topics/environment-variables.md:7 #: bfdebb32440a4034beb42135e38884e8 @@ -1421,22 +1671,26 @@ msgstr "" #: ../../src/topics/expression-tool.md:1 #: 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" -msgstr "" +msgstr "表达式工具" #: ../../src/topics/expression-tool.md:3 #: 48deb71f361a43e48a56ed483075bca8 msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." msgstr "" +"表达式工具是一种流程类型，可单独运行，或作为工作流的一个步骤运行。" +"其执行一个纯 JavaScript 表达式，旨在隔离复杂的 JavaScript " +"表达式，这些表达式需要对输入数据进行操作并产生一些结果作为输出。" #: ../../src/topics/expression-tool.md:8 #: 716b56506ca7470299899c5d820a9ea2 msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." -msgstr "" +msgstr "与命令行工具类似，其需要 ` 输入 ` 和 ` 输出 `，但需要的是`表达式 ` 属性，" +"而不是 `baseCommand`。" #: ../../src/topics/expression-tool.md:17 #: b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." -msgstr "" +msgstr "CWL 表达式工具。" #: ../../src/topics/expression-tool.md:48 #: 39727e9058f24b62b8746a46d3f812c2 @@ -1447,21 +1701,29 @@ msgstr "" #: e3ecac0a8e604f2b98a2a12b0579990a msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." msgstr "" +"我们必须使用 `InlineJavascriptRequirements`，因为我们的表达式包含 `." +"toUpperCase（）` 中的 JavaScript " +"调用，这意味着使用表达式工具必须调用JavaScript。" #: ../../src/topics/expressions.md:1 #: c8d648b765ec499a8e9c464590838492 msgid "Expressions" -msgstr "" +msgstr "表达式" #: ../../src/topics/expressions.md:3 #: 007a345b4bad49cf996c4301b8386473 msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." msgstr "" +"如果需要操作输入参数，请添加需求 `InlineJavascriptRequirement`，" +"然后在参数引用合法的任何地方提供将由 CWL 运行程序评估的 Javascript 片段。" #: ../../src/topics/expressions.md:9 #: 2edbd398eadb458b8eacd5fa5496f0a2 msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." msgstr "" +"只能在绝对必要时使用JavaScript表达式。操作文件名、扩展名、路径等时，请优先考" +"虑能否使用`basename`、`nameroot`、`nameext`等 [内置 `文件` 属性][file-" +"prop]。相关详细信息，请参阅[最佳实践列表]（bestpractice.md）。" #: ../../src/topics/expressions.md:16 #: 7fdbfd1c937b4991bf4a2fa26ea310e4 @@ -1471,7 +1733,8 @@ msgstr "" #: ../../src/topics/expressions.md:22 #: efb5fd14988c4e2a8f834ee5369d4102 msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" -msgstr "" +msgstr "由于此工具不需要任何 ` 输入 " +"`，因此我们可以使用一个（几乎）空的作业文件运行它：" #: ../../src/topics/expressions.md:25 #: e833649b951841c49397796f996d29f3 @@ -1481,42 +1744,49 @@ msgstr "" #: ../../src/topics/expressions.md:31 #: 276f688ba7cc471a842f085ca852b1d9 msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." -msgstr "" +msgstr "`empty.yml` 包含一个空 JSON 对象的描述。JSON 对象描述包含在大括号 `{}` " +"内，因此空对象仅由一组空括号表示。" #: ../../src/topics/expressions.md:35 #: ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" -msgstr "" +msgstr "然后我们可以运行 `expression.cwl`：" #: ../../src/topics/expressions.md:37 #: 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" -msgstr "" +msgstr "运行 `expression.cwl`" #: ../../src/topics/expressions.md:47 #: 8b70a1ad70514039b97164fa630c12e4 msgid "Note that requirements can be provided with the map syntax, as in the example above:" -msgstr "" +msgstr "请注意，如上例所示，可通过映射语法来提供要求：" #: ../../src/topics/expressions.md:54 #: 2f28ab412d2843ffa5f14acdc01fc732 msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." msgstr "" +"或者作为一个数组，每个条目（在本示例中，只有`class: " +"InlineJavascriptRequirement` ）均用 `-` " +"标记，便可使用相同的语法描述其他命令行参数。" #: ../../src/topics/expressions.md:62 #: d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" -msgstr "" +msgstr "哪里允许使用 JavaScript 表达式？" #: ../../src/topics/expressions.md:64 #: cbec9277b5004e50af2728cbda0df740 msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" -msgstr "" +msgstr "和 [参数引用](parameter-references.md)一样，只能在某些字段中使用 JavaScript " +"表达式。 这些字段是：" #: ../../src/topics/expressions.md:66 #: e259f55f8000479bbd8009e25cf0ca6c msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" +"来自[`CommandLineTool`] （https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool）" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 @@ -1565,6 +1835,8 @@ msgstr "" #: 8210b36347a749889450529ecdf4ff0e msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" +"来自 [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" #: ../../src/topics/expressions.md:73 #: ../../src/topics/expressions.md:78 @@ -1608,16 +1880,22 @@ msgstr "" #: 23088850ad02459696f6bbd385109aac msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" +"来自[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" #: ../../src/topics/expressions.md:77 #: f02257a822ad46ac93c5981531cc85d5 msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" +"来自 [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)的" #: ../../src/topics/expressions.md:80 #: 989a1c4aaa1143be9f53b90cd8b6d500 msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" +"来自[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 @@ -1638,24 +1916,29 @@ msgstr "" #: e9fa9430535c424fa3e8be5d460d2ba4 #: 0e306cc923974d1db83fdfb45105a11c msgid "From `Workflow`" -msgstr "" +msgstr "来自`Workflow`" #: ../../src/topics/expressions.md:84 #: d289541e460147aa933f7878996f8649 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" +"来自 [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) 和 [WorkflowOutputParameter](https://www.commonwl.org/v1" +".0/Workflow.html#WorkflowOutputParameter)" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 #: b0290d1a477b48119e17cf1fed9d6dff #: 446f1190af7a40a0913ff04ce7aa938c msgid "From `steps`" -msgstr "" +msgstr "来自`steps`" #: ../../src/topics/expressions.md:88 #: 81b4d1f23a3642bfa9bb395b94260cd1 msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" +"来自 [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 @@ -1663,6 +1946,8 @@ msgstr "" #: 557694f82e314baa9ccafba14d6ff2c9 msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" +"来自 [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." +"html#ExpressionTool)" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 @@ -1675,11 +1960,16 @@ msgstr "" #: f495da32f05a4a5ba9539be0a54c1a59 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" +"来自 [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) 和 [ExpressionToolOutputParameter](https://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" #: ../../src/topics/expressions.md:95 #: bdb4c68a175047ddbe141ca24960127f msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" +"来自[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 @@ -1741,6 +2031,8 @@ msgstr "" #: 97b61352363f47cb890e8937c5613fa3 msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" +"来自 [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 @@ -1752,7 +2044,7 @@ msgstr "" #: ../../src/topics/expressions.md:106 #: 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" +msgstr "在 [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)中" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 @@ -1773,12 +2065,14 @@ msgstr "" #: 2183ac54ae10428388649daa57b6a7f4 #: 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" -msgstr "" +msgstr "来自 `EnvVarRequirement`" #: ../../src/topics/expressions.md:110 #: 0bc424ef2ca346099f29b937379908a0 msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" +"来自 [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 @@ -1790,27 +2084,37 @@ msgstr "" #: ../../src/topics/expressions.md:116 #: 10d36a1adfd04144b401c993b12b4094 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" +msgstr "通过 `expressionLib` 使用外部库和内联 JavaScript 代码" #: ../../src/topics/expressions.md:118 #: 29b73e1dd72744f68377f0a38c10f062 msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." msgstr "" +"需求 `InlineJavascriptRequirements` 支持 `expressionLib` 属性，" +"该属性允许用户加载外部 JavaScript 文件或提供内联 JavaScript 代码。" #: ../../src/topics/expressions.md:122 #: 38a2afaf4a6c4d04909af22c93f2808d msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." msgstr "" +"添加到 `expressionLib`属性的条目通过CWL运行程序的JavaScript引擎进行解析，可用" +"于增添内部文件或创建可在CWL文档其他部分调用的JavaScript函数。" #: ../../src/topics/expressions.md:128 #: cd74f34b21af4de9be96fd897efc469b msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" +"CWL 标准（版本 1.0 到 1.2）[声明](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#Expressions)在 CWL 表达式中唯一有效的 JavaScript 版本是[" +"ECMAScript 5.1](https://262.ecma-international.org/5.1/) ，这意味着在 CWL " +"文档中添加或编写的所有代码都必须符合此版本。" #: ../../src/topics/expressions.md:135 #: f12e371f3f1a4b0cb2cff9800352d48c msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" msgstr "" +"例如，我们可以使用 `InlineJavascriptRequirements` 并在 `expressionLib` " +"中编写一个 内联JavaScript 函数，便可在 CWL 文档其他部分调用此函数：" #: ../../src/topics/expressions.md:139 #: 49d0fda2fc144e0b8b7c92afc1d8945e @@ -1820,17 +2124,19 @@ msgstr "" #: ../../src/topics/expressions.md:146 #: 8f0e8f050e334ac08334e9215e1dcf61 msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" -msgstr "" +msgstr "运行此CWL工作流，将调用JavaScript函数并生成`echo` " +"命令，以用大写首字母打印输入信息：" #: ../../src/topics/expressions.md:149 #: 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "" +msgstr "运行 `hello-world-expressionlib-inline.cwl`。" #: ../../src/topics/expressions.md:155 #: 7a6be0005a6441feb67f036d005d7885 msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" -msgstr "" +msgstr "让我们将 `capitalizeWords` 函数移动到外部文件 `custom-functions.js`，" +"并将其导入CWL 文档中：" #: ../../src/topics/expressions.md:158 #: ed590f9e6f4f425da886b110295c45db @@ -1846,16 +2152,21 @@ msgstr "" #: 06635145b441418aaae84dc804f3d6ac msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." msgstr "" +"已通过 `$include: custom-functions.js`语句将`custom-functions." +"js`文件添加至CWL文档，因此可在CWL文档其他部分调用相关函数和 变量。" #: ../../src/topics/expressions.md:175 #: 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "" +msgstr "运行 `hello-world-expressionlib-external.cwl`。" #: ../../src/topics/expressions.md:181 #: 04eaf1f7c630450db318dcd8b7626e15 msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." msgstr "" +"最后，请注意可在CWL文档中同时拥有内联和外部JavaScript代码。在最后一个示例中，" +"通过新建函数`createHelloWorldMessage`调用外部文件`custom-functions." +"js`中的`capitalizeWords` 函数，我们将其他条目添加至expressionLib`属性。" #: ../../src/topics/expressions.md:186 #: c4098489fbb049789f022cd3e5c3d49b @@ -1865,37 +2176,49 @@ msgstr "" #: ../../src/topics/expressions.md:193 #: 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" +msgstr "运行 `hello-world-expressionlib.cwl`。" #: ../../src/topics/expressions.md:200 #: fd4579a3c9844492b314b5c3c1775fc7 msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." msgstr "" +"可使用`$include` 语句添加本地磁盘或远程位置的文件。相对路径和绝对路径均可用。" +"了解更多相关信息，请查阅 CWL 规范中关于 `$include`](https://www.commonwl.org/" +"v1.0/SchemaSalad.html#Include) 的文本。" #: ../../src/topics/file-formats.md:1 #: 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" -msgstr "" +msgstr "文件格式" #: ../../src/topics/file-formats.md:3 #: e024bcb70e04412e90e1838426d1b69a msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." msgstr "" +"工具和工作流可将 `File` 类型作为输入，并将其生成为输出。同时，我们建议指定 `" +"文件 ` 类型的格式，这有助于其他人记录如何使用您的工具，同时允许您在创建参数文" +"件时执行一些简单的类型检查。" #: ../../src/topics/file-formats.md:8 #: a3db21c0b3114802a8a5b610e252ef13 msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" +"对于文件格式，我们建议引用现有本体（如示例中的 EDAM），引用您所在机构的本地本" +"体，或者在与他人共享工具之前不要添加文件格式以便快速开发。" +"您可以在其网站上浏览现有的 [IANA 文件格式列表][IANA] 和 [EDAM " +"文件格式列表][EDAM]。" #: ../../src/topics/file-formats.md:14 #: 0f5bc8520d6a4dafa37c65343da9702a msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." -msgstr "" +msgstr "在下一个教程中，我们将更详细地解释文档的 `$namespaces` 和 `$schemas` " +"章节，因此暂时不必担心这些。" #: ../../src/topics/file-formats.md:17 #: 5cb830da47464a8b9c3950983fa4d56f msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." -msgstr "" +msgstr "请注意，对于附加值而言， `cwltool` " +"可以根据文件格式进行一些基本推理，并在出现一些明显的不匹配时发出警告。" #: ../../src/topics/file-formats.md:20 #: 0535d5de416b4ea3b2f5996583deecc1 @@ -1906,18 +2229,21 @@ msgstr "" #: ../../src/topics/metadata-and-authorship.md:22 #: f558bcf2a993482195cd418b37761809 #: fb47f73c38cf4ec59bd3021866a631f8 +#, fuzzy msgid "The equivalent of this CWL description in command line format is:" -msgstr "" +msgstr "CWL描述的等效项在命令行的格式是：" #: ../../src/topics/file-formats.md:32 #: 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" -msgstr "" +msgstr "样本参数文件" #: ../../src/topics/file-formats.md:34 #: a2ce43b391864e8bbde16328cc19b32b msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." msgstr "" +"下方是一个样本参数文件的示例。我们鼓励您检查自己工具中的参数文件作业示例，这" +"将帮助其他人从一个“已知良好的”参数文件入手，更快地上手使用您的工具。" #: ../../src/topics/file-formats.md:39 #: aebee48b742c4145a600fd2daf8c75dc @@ -1928,41 +2254,49 @@ msgstr "" #: 56ee4dcfff6141d5bef80eb96559876d msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" +"___注意：___ 要查阅以下示例，您需要下载示例输入文件*file-formats.bam*，" +"该文件可从 获取，且可通过 " +"`wget`等工具下载：" #: ../../src/topics/index.md:1 #: 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" -msgstr "" +msgstr "主题" #: ../../src/topics/inputs.md:1 #: 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" -msgstr "" +msgstr "输入" #: ../../src/topics/inputs.md:3 #: d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" -msgstr "" +msgstr "基本输入参数" #: ../../src/topics/inputs.md:5 #: 96671c56523c4ea9992fb5dfcfa6490e msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "" +msgstr "工具`输入`是一张控制工具运行方式的输入参数列表。" +"每个参数都包含一个表示参数名称的 `id`和用于描述参数有效值类型的`type`。" #: ../../src/topics/inputs.md:9 #: bcc6246742cb46bfb185e415c4a3431a msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." msgstr "" +"可用的基元类型包括*string*、 *int*、*long*、 *float*、*double*以及 " +"*null*；复杂类型包括*array* 和*record* ；此外还有*File*、*Directory* 以及 " +"*Any*等特殊类型。" #: ../../src/topics/inputs.md:13 #: 86dce36de687449c88fb5eb9d64eb045 msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." -msgstr "" +msgstr "下面的示例演示了一些不同类型的输入参数，并以不同的方式显示在命令行上。" #: ../../src/topics/inputs.md:16 #: cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "" +msgstr "首先，新建一个名为 `inp.cwl` 的文件，包含以下内容：" #: ../../src/topics/inputs.md:18 #: 8bdb875b63104f699efe28ea0abb1e3d @@ -1972,7 +2306,7 @@ msgstr "" #: ../../src/topics/inputs.md:24 #: c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" -msgstr "" +msgstr "新建一个名为`inp-job.yml`的文件：" #: ../../src/topics/inputs.md:26 #: dc5e6b5e01d64226bd5dbbf3175fe010 @@ -1982,82 +2316,112 @@ msgstr "" #: ../../src/topics/inputs.md:33 #: 36ab1d9edafc4831bb1bca5f123b04b0 msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" -msgstr "" +msgstr "您可以使用 `cwltool` " +"创建模板输入对象，便无需在输入对象文件中键入所有输入参数：" #: ../../src/topics/inputs.md:40 #: 7dc630ea86464b1dba3a4e5079260b3b msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." msgstr "" +"您可将输出重定向到一个文件，即`cwltool --make-template inp.cwl > inp-job." +"yml`，然后将默认值更改为预期输入值。" #: ../../src/topics/inputs.md:44 #: ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." -msgstr "" +msgstr "注意: \"example_file\"是一种`文件` 类型，必须作为一个带有字段`class: File`和 " +"`path`的对象提供。" #: ../../src/topics/inputs.md:47 #: 651e032007ea4a119d20c820bb61f86b msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." -msgstr "" +msgstr "然后，在命令行键入 `touch whale.txt`，以使用[touch]新建一个whale.txt 。" #: ../../src/topics/inputs.md:53 #: 0b056dde9e87428996e47870b12119da msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" msgstr "" +"现在，使用`cwltool inp.cwl inp-job.yml`命令，以通过命令行上的工具描述和输入对" +"象调用`cwltool`。下方方框内文本描述了这两个命令及命令行的预期输出：" #: ../../src/topics/inputs.md:64 #: 628124a1670b4b058bb0fb6e495a099c msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" -msgstr "" +msgstr "CWL 引用运行程序 （cwltool） 和其他运行程序通过输入文件符号（“软”）链接创建临" +"时目录，以确保工具不会意外访问未明确指定的文件" #: ../../src/topics/inputs.md:70 #: 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." msgstr "" +"字段 `inputBinding` " +"为可选项，指示输入参数是否应显示在工具的命令行上以及以何种方式显示。 " +"如果`inputBinding`缺失 ，则该参数不会出现在命令行上。 " +"让我们来详细看看每个示例。" #: ../../src/topics/inputs.md:83 #: ec2adb3912bc46e28891229e9e0d9a1c msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." -msgstr "" +msgstr "布尔类型充当一种标志。如果输入参数“example_flag”为“真”，则命令行会添加`前缀`" +"。如果为假，则不添加任何标志。" #: ../../src/topics/inputs.md:95 #: a519be60726a44af9941fdce04735353 msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." msgstr "" +"字符串类型在命令行上显示为文本值。 `前缀`是可选的，如果提供，它将在命令行上作" +"为单独的参数出现，且位于指定参数之前。 在上面的示例中，其显示为 `--example-" +"string hello`。" #: ../../src/topics/inputs.md:109 #: cb8fc8c4c79e467eac5fab4ca685201e msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." msgstr "" +"整数（和浮点）类型在命令行中以十进制文本显示。 若选项 `separate`为假（默认值" +"为真），前缀和值被合并为一个参数。在上方的示例中，其显示为`-i42` 。" #: ../../src/topics/inputs.md:124 #: a26cc105716f47cb807174c9003153b0 msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." msgstr "" +"文件类型在命令行中显示为文件路径。若参数类型以问号 `?` " +"结尾，表示该参数为可选。在上方的示例中，其呈现为 `--file=/tmp/random/path/" +"whale." +"txt`。但是，如果输入中未提供“example_file”参数，则命令行上不会出现任何内容。" #: ../../src/topics/inputs.md:131 #: cc159dd5fe5748caac838862f5b8c4d1 msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." -msgstr "" +msgstr "输入文件为只读。 如果要更新输入文件，必须 [首先将其复制到输出目录](staging-" +"input-files.md)。" #: ../../src/topics/inputs.md:134 #: 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." msgstr "" +"`位置` 的值用于确定参数在命令行中应出现的位置。 位置是相对的，不是绝对的。 因" +"此，位置不一定是连续的，位置1、3、5的三个参数会生成与位置1、2、3相同的命令行" +"。 多个参数可以有相同的位置（使用参数名称断开连接），而位置字段本身是可选的。" +" 默认的位置是0。" #: ../../src/topics/inputs.md:142 #: 6812698e9ad84d3385de5e88e9dde0b3 msgid "The `baseCommand` field will always appear in the final command line before the parameters." -msgstr "" +msgstr "`baseCommand` 字段将始终出现在最后的命令行中，且位于指定参数之前。" #: ../../src/topics/inputs.md:146 #: 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" -msgstr "" +msgstr "数组输入" #: ../../src/topics/inputs.md:148 #: d1f02be278754267893dfce5a940997d msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." msgstr "" +"将显示的输入参数数组添加至命令行很简单。可通过两种方法指定数组参数。首先，" +"可提供带有 `type： array` 和 `items`的 `type` " +"字段，以定义数组中可能出现的有效数据类型。或者，可以在类型名称后添加方括号 " +"`[]`，以指示输入参数为此类型的数组。" #: ../../src/topics/inputs.md:154 #: 01f30e38dfdd452dba3a996073936e16 @@ -2076,27 +2440,38 @@ msgstr "" #: 02adef8ee8204842b5b4a0408f3bac33 #: 9db68837918a4a349f32f15f12697a1d msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" +msgstr "现在，调用在命令行上提供工具描述和输入对象的 `cwltool`：" #: ../../src/topics/inputs.md:178 #: 75d59e395c66416cae9b352db5081516 msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." msgstr "" +"`inputBinding` 可以出现在外部数组参数定义或内部数组元素定义中，如上所示，它们" +"在构造命令行时会产生不同的行为。此外，`itemSeparator` " +"字段（如提供的话）指明数组值应合并成一个独立参数，并以项目分隔符字符串分隔。" #: ../../src/topics/inputs.md:185 #: 874c6f19abbf45d7ab7d30a378c4048d msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." msgstr "" +"请注意，输入数组在 `array-inputs-job.yml` 的方括号 `[]` " +"内指定。数组也可以用多行表示，其中未使用关联键定义的数组值由前导 `-` " +"标记。这将在下一课中演示，并在 [YAML 指南]（yaml-guide.md#arrays） " +"中详细讨论。你可以指定数组的数组、记录的数组及其他复杂类型的数组。" #: ../../src/topics/inputs.md:191 #: 5d7d7a28cc5d4862803032aec78174d9 +#, fuzzy msgid "Inclusive and Exclusive Inputs" -msgstr "" +msgstr "包容性和互斥性输入" #: ../../src/topics/inputs.md:193 #: dea0d4b681f94e73b13965dcfe75cf7d msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." msgstr "" +"有时，基础工具具有多个必须一起提供的参数（它们是相互依赖的）或多个不能一起提" +"供的参数（它们是互斥的）。 " +"您可以使用记录和类型联合将参数组合在一起，以描述这两种情况。" #: ../../src/topics/inputs.md:198 #: ddf598abf4f34aca9fffa045860fbf96 @@ -2111,7 +2486,7 @@ msgstr "" #: ../../src/topics/inputs.md:215 #: 750474486a84482292eeba45f118287f msgid "In the first example, you can't provide `itemA` without also providing `itemB`." -msgstr "" +msgstr "在第一个示例中，如果不同时提供 `itemB`，则无法提供 `itemA`。" #: ../../src/topics/inputs.md:217 #: 9a5cf1d76fc84c1f9b0d123a3a2a480b @@ -2122,6 +2497,8 @@ msgstr "" #: 1eb0e39bb6d04b8cab300f44a79f3add msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." msgstr "" +"在第二个示例中，`itemC` 和 `itemD` 是互斥的，因此只有第一个匹配的项 " +"（`itemC`） 被添加到命令行，其余项 （`itemD`） 将被忽略。" #: ../../src/topics/inputs.md:236 #: bc21ee10bff843689cc98ac6630edcea @@ -2131,22 +2508,25 @@ msgstr "" #: ../../src/topics/inputs.md:252 #: 4b2ab812f62c4f949dd25c8527f2411c msgid "In the third example, only `itemD` is provided, so it appears on the command line." -msgstr "" +msgstr "在第三个示例中，仅提供了 `itemD`，因此它显示在命令行上。" #: ../../src/topics/inputs.md:255 #: b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" -msgstr "" +msgstr "带有表达式的互斥输入参数" #: ../../src/topics/inputs.md:257 #: 2c3b884cb1c54521900cc90782e8a58d msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." msgstr "" +"若要将互斥的输入参数与表达式结合，需意识到`inputs`JavaScript对象将包含互斥输" +"入值中的一个，这意味着你可能需要使用一个**or**布尔运算符来检查存在哪些值。" #: ../../src/topics/inputs.md:262 #: a1073b6306044dffb414319ae01f68bb msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." -msgstr "" +msgstr "让我们来一个示例，其包含了一个互斥的 `file_format`输入参数，该参数接受 " +"`null`（即未提供任何值）或任何枚举的值。" #: ../../src/topics/inputs.md:265 #: 4a31c733092142b1af834eab1747c224 @@ -2157,31 +2537,48 @@ msgstr "" #: 9a1d92334685449386dfa3b3a899ed48 msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" msgstr "" +"请留意，在不考虑`null`值的情况下，JavaScript表达式如何使用互斥输入参数的值。" +"如果提供一个有效值，比如 “fasta” （其中一个枚举的值），命令将成功执行：" #: ../../src/topics/inputs.md:280 #: fb623af4c480411b8fde28d01c981411 msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." msgstr "" +"但是，如果未提供任何输入值，则 `file_format` 将被评估为 `null` " +"值。由于该值与输出字段的预期类型（`字符串`）不匹配，工作流将运行失败。" #: ../../src/topics/inputs.md:289 #: e98e165f6bba40809c90473d72f9d592 msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." msgstr "" +"要进行纠正，请务必记住在使用互斥参数或任何允许 `null` 的参数时，应在 " +"JavaScript 表达式中采用 or 运算符。例如，表达式可以更改为 `$（" +"inputs.file_format " +"||'auto'）`，如果命令行或作业输入文件中未提供默认值，则表达式具有默认值。" #: ../../src/topics/metadata-and-authorship.md:1 #: d33aa2353ad44fb885d3a1ee48263dc4 +#, fuzzy msgid "Metadata and Authorship" -msgstr "" +msgstr "元数据和授权" #: ../../src/topics/metadata-and-authorship.md:3 #: cd64d2d828834cbbb24ea5358caf5405 msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." msgstr "" +"正确执行不需要的实现扩展（例如，与 GUI 表示相关的字段）和有关工具或工作流本身" +"的元数据（例如，用于引文的作者身份）可以作为任何对象的附加字段提供。正如 [" +"Schema Salad 规范][schema-salad]中所述，此类扩展字段（例如 `format: " +"edam:format_2572`）可以使用文档的 `$namespaces` 章节中所列的命名空间前缀（" +"例如 edam：http://edamontology.org/" +"）。如下所示，添加命名空间前缀后，便可在文档的任何位置访问该字段。否则，" +"必须使用完整的 URL：`格式：http://edamontology.org/format_2572`。" #: ../../src/topics/metadata-and-authorship.md:13 #: 80af387fe3ff4e2da999903385bd602b msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." -msgstr "" +msgstr "对于所有的开发人员，我们建议为你的工具和工作流程提供以下最小元数据。本示例包" +"含允许他人引用您工具的元数据。" #: ../../src/topics/metadata-and-authorship.md:16 #: 0d5200bbbfdc43e6a78b4e4c3096ebd7 @@ -2191,12 +2588,15 @@ msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 #: d402bf528c7f4eb69aaaa275be2bf1d4 msgid "Extended Example" -msgstr "" +msgstr "扩展示例" #: ../../src/topics/metadata-and-authorship.md:30 #: cb9980db4e5f4c74b01c2dec6d5e92d0 msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." msgstr "" +"对于积极性高的人而言，也可使用更多的元数据来注释工具。此示例包括作为关键字的 " +"EDAM 本体标记（允许对相关工具进行分组）、使用该工具所需的硬件要求的提示以及更" +"多元数据字段。" #: ../../src/topics/metadata-and-authorship.md:35 #: 2dfbd4d580044ed083992f3ceb1bc64e @@ -2206,17 +2606,19 @@ msgstr "" #: ../../src/topics/operations.md:1 #: 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" -msgstr "" +msgstr "操作" #: ../../src/topics/operations.md:3 #: 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." -msgstr "" +msgstr "操作是一种 CWL 流程，与工作流、命令行工具或表达式工具类似。操作是工作流的一个" +"步骤，用于指定输入和输出，但没有提供足够的信息来执行。" #: ../../src/topics/operations.md:7 #: 5565c1b2d8a349169a305a9b26b4574d msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" -msgstr "" +msgstr "在准备将工作流提交至 CWL " +"运行程序之前，您可以在开发期间创建操作以可视化工作流：" #: ../../src/topics/operations.md:10 #: 49cf614893d8438299b3bca384eb40cf @@ -2226,62 +2628,76 @@ msgstr "" #: ../../src/topics/operations.md:16 #: 88160cef4cfa4add9020aa89511a5749 msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" -msgstr "" +msgstr "工作流中的 `uppercase`步骤是一个操作，可以像命令行工具或表达式一样使用，" +"也可以使用 CWL 查看器或 `cwltool`进行绘制：" #: ../../src/topics/operations.md:24 #: 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" msgstr "" +"上述命令的输出可使用Graphviz渲染器进行渲染。下面的图片是使用Sphinx " +"Graphviz指令来渲染的（本用户指南是使用Sphinx构建的）：" #: ../../src/topics/operations.md:55 #: 730ba1434a1445ae847ec6153b6a3b72 msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" -msgstr "" +msgstr "如果您尝试通过`cwltool`来运行，命令将运行失败，因为`cwltool`缺少足够信息来了" +"解执行的方法：" #: ../../src/topics/operations.md:58 #: 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" -msgstr "" +msgstr "`cwltool`不知道如何运行操作" #: ../../src/topics/operations.md:66 #: a25d0b1e13324b40a6b8fcd227948c4f msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." msgstr "" +"CWL 运行程序可能会提出将操作绑定到具体步骤的方法。例如，CWL " +"运行程序可以使用带有 ID " +"的抽象操作，而这些操作对应于不同工作流引擎执行的步骤。" #: ../../src/topics/outputs.md:1 #: da077da5eb8a4ffebfde041fc16300de msgid "Outputs" -msgstr "" +msgstr "输出" #: ../../src/topics/outputs.md:3 #: 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" -msgstr "" +msgstr "返回输出文件" #: ../../src/topics/outputs.md:5 #: d661df070e3040869da412d07a71f716 msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "" +msgstr "工具的 ` 输出 ` 是运行工具后应返回的输出参数列表。 " +"每个参数都有一个代表其名称的 `id`以及描述其有效值类型的 `type`。" #: ../../src/topics/outputs.md:10 #: a11585474d3849cca5467512ed964743 msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." msgstr "" +"工具在 CWL 下运行时，起始工作目录即为指定的输出目录。 " +"基础工具或脚本必须以在输出目录中创建的文件形式记录其结果。 CWL " +"工具返回的输出参数要么是输出文件本身，要么来自检查这些文件的内容。" #: ../../src/topics/outputs.md:16 #: 2682f9ca8e604a0c9986f7746fdec960 msgid "The following example demonstrates how to return a file that has been extracted from a tar file." -msgstr "" +msgstr "下面的示例演示了如何返回已从 tar 文件中提取的文件。" #: ../../src/topics/outputs.md:19 #: 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "" +msgstr "将强制参数传递至 `baseCommand`" #: ../../src/topics/outputs.md:21 #: 22447a560f6f4317bf67bd7c4336126c msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" msgstr "" +"在前面的示例中，`baseCommand` 只是一个字符串，任何参数都作为 CWL 输入传递。" +"我们可以使用 _ 字符串数组 _ ，而不是单个字符串。 " +"第一个元素是要运行的命令，所有后续元素均为强制命令行参数" #: ../../src/topics/outputs.md:26 #: f1ee2e00b0cc4112b51c9df3a919b73f @@ -2296,32 +2712,36 @@ msgstr "" #: ../../src/topics/outputs.md:38 #: dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." -msgstr "" +msgstr "接下来，为此示例新建一个 tar 文件。" #: ../../src/topics/outputs.md:45 #: 52703d6b7f914097934bfad13663abeb msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" +msgstr "现在，通过命令行上的工具描述和输入对象调用 `cwltool`：" #: ../../src/topics/outputs.md:51 #: 5e1c79df657d4a6e84e055dd6b300a5d msgid "The field `outputBinding` describes how to set the value of each output parameter." -msgstr "" +msgstr "`outputBinding` 字段描述了如何设置每个输出参数的值。" #: ../../src/topics/outputs.md:62 #: 329d2809dfae4f90bc638f5f03a47ee3 msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." -msgstr "" +msgstr "`glob` " +"字段由输出目录中的文件名称组成。如果事先不知道文件名，可以使用通配符模式，" +"例如 `glob：“*.txt”`。" #: ../../src/topics/outputs.md:65 #: 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" -msgstr "" +msgstr "捕获标准输出" #: ../../src/topics/outputs.md:67 #: c6bcf7c6a8774dd6be41cc775848c3b8 msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." msgstr "" +"要捕获工具的标准输出流，请添加 `stdout` 字段及文件名（即输出流目标位置）。 " +"然后，在相应的输出参数上添加 `type： stdout`。" #: ../../src/topics/outputs.md:71 #: 9d86c03ab44841c785b924cc44727e31 @@ -2331,12 +2751,12 @@ msgstr "" #: ../../src/topics/outputs.md:89 #: 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" -msgstr "" +msgstr "数组输出" #: ../../src/topics/outputs.md:91 #: 9647019d8c37466886e7aab6f176634d msgid "You can also capture multiple output files into an array of files using `glob`." -msgstr "" +msgstr "您也可使用`glob`捕获多个输出文件，并将其保存为一个文件数组。" #: ../../src/topics/outputs.md:93 #: b9eaf21f5e014eefaae301c47dafd144 @@ -2352,16 +2772,25 @@ msgstr "" #: cc067051f22f433bbece08f60933e002 msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" +"如 [YAML 指南](yaml-guide.md#arrays)中所述，预期输出数组在 `array-outputs-job" +".yml` 中指定，每个条目均以前导符 `-`标记。这种格式也可以在 CWL " +"描述中用于标记数组中的条目，这将在接下来几个章节中进行演示。" #: ../../src/topics/parameter-references.md:1 #: a190a6440ec34898990cdac05d809f22 msgid "Parameter References" -msgstr "" +msgstr "参数引用" #: ../../src/topics/parameter-references.md:3 #: dbfe2c1123144316aa026374b0f353d3 msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." msgstr "" +"在前面的示例中，我们使用“tar”程序提取了一个文件。但是，该示例非常有限，因为它" +"假定我们感兴趣的文件称为“hello.txt”，并将其写入 `.cwl` " +"文件中。这不是执行此操作的最佳方法，因为“hello." +"txt”文件名可能会有所不同或取决于所使用的输入文件。 为了避免这种情况，" +"我们可以在作业参数文件 （`.yml`） 中指定文件名称。本示例将演示如何从其他字段" +"动态引用输入参数值，这将允许我们指定要提取的文件名称。" #: ../../src/topics/parameter-references.md:13 #: 280f1a07d0ae41d7a4674504f832fcf0 @@ -2376,137 +2805,186 @@ msgstr "" #: ../../src/topics/parameter-references.md:25 #: 074cf5d912854d8c864607cc24b15302 msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" +msgstr "新建输入文件，并使用命令行上的工具描述和输入对象调用 `cwltool`：" #: ../../src/topics/parameter-references.md:36 #: 0290af3e3cbb4b32b0450c8771f3bf95 msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." -msgstr "" +msgstr "某些字段允许 `$（...） " +"中所列的参数引用`，将对这些字段进行评估并替换为被引用的值。" #: ../../src/topics/parameter-references.md:47 #: b54240bb94f746bba7511633aa969db0 msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." msgstr "" +"需使用Javascript语法的子集编写引用。 在此示例中，`$（inputs." +"extractfile）`、`$（inputs[“extractfile”]）` 以及 " +"`$（inputs['extractfile']）` 为等效项。" #: ../../src/topics/parameter-references.md:51 #: 8b70a072aa87414c88e89a3e19af0a51 msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." -msgstr "" +msgstr "“输入”变量的值是调用 CWL 工具时提供的输入对象。" #: ../../src/topics/parameter-references.md:54 #: eea20f89c45f424a888178df53713b28 msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." msgstr "" +"请注意，由于 `File` " +"参数是对象，要获取输入文件的路径，必须引用文件对象上的路径字段；" +"若要引用上方示例中 tar 文件的路径，您需要编写 `$（inputs.tarfile.path）`。" #: ../../src/topics/parameter-references.md:59 #: cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" -msgstr "" +msgstr "哪里允许参数引用？" #: ../../src/topics/parameter-references.md:61 #: 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" -msgstr "" +msgstr "您只能在某些字段中使用参数引用。 这些字段是：" #: ../../src/topics/parameter-references.md:63 #: 7647e0229a924f988cf02b7812a55c06 msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" +"来自 [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" #: ../../src/topics/parameter-references.md:69 #: 9d663249666045618a0d3acddb85a9a9 msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" +"来自 [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" #: ../../src/topics/parameter-references.md:72 #: 5fed4984f6784347b4cbe0630b1dd2c2 msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" +"来自 [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" #: ../../src/topics/parameter-references.md:74 #: dbf6153cd02542a6a01c172803122b7f msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" +"来自 [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" #: ../../src/topics/parameter-references.md:77 #: b6250cf6fa8a4a0c94b33302e0decca5 msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" +"来自 [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" #: ../../src/topics/parameter-references.md:81 #: fa6ca3bbc6784380a03a950a6f49a180 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" +"来自[InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) 和 [WorkflowOutputParameter](http://www.commonwl.org/v1." +"0/Workflow.html#WorkflowOutputParameter)" #: ../../src/topics/parameter-references.md:85 #: b92b516e537a4773ad67b4af586e7a25 msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" +"来自 [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" #: ../../src/topics/parameter-references.md:89 #: 467a701228504d06b971b79a59c69064 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" +"来自 [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) 和 [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" #: ../../src/topics/parameter-references.md:92 #: 2634f989eb304009a8568d70ed42786c msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" +"来自 [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" #: ../../src/topics/parameter-references.md:101 #: 5d8bed66282c408695292ea92a03b2c4 msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" +"来自 [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" #: ../../src/topics/parameter-references.md:103 #: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" +msgstr "位于 [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" #: ../../src/topics/parameter-references.md:107 #: 9a6b311ded8d4e43ae635b1b927dbdf2 msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" +"来自 [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" #: ../../src/topics/requirements-and-hints.md:5 #: aac74f957774479a83aab4c6ff1390ae msgid "Requirements and Hints" -msgstr "" +msgstr "需求和提示" #: ../../src/topics/specifying-software-requirements.md:1 #: b75d29d1d55d44488338f9689f156855 msgid "Specifying Software Requirements" -msgstr "" +msgstr "指定软件需求" #: ../../src/topics/specifying-software-requirements.md:3 #: 574d93d1d592458a985f259519c036cb msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." msgstr "" +"通常，工具描述将针对特定版本的软件编写。为了方便其他人使用您的描述，您可以在 " +"`提示 ` 部分添加`SoftwareRequirement` " +"字段，这也可能有助于他人了解此描述所适用的工具版本。" #: ../../src/topics/specifying-software-requirements.md:13 #: 82e48b3e3c3f451480cc0b6a529271f6 msgid "In this example, the software requirement being described is InterProScan version 5.21-60." -msgstr "" +msgstr "在本示例中，所描述的软件要求是InterProScan版本5.21-60。" #: ../../src/topics/specifying-software-requirements.md:25 #: 02e40154eac74ecc98d0447d03475b44 msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." msgstr "" +"根据您的 CWL 运行程序，可在运行作业之前使用这些提示检查所需软件是否已安装且可" +"用。要使用参考实现启用这些检查，请使用 [依赖项解析程序配置][依赖项]。" #: ../../src/topics/specifying-software-requirements.md:29 #: 8cb1c5d9b1a54c40924099494eb766c6 msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." msgstr "" +"除了版本号之外，该工具的唯一资源标识符 (URI) 以 [RRID][rrid] 的形式给出。" +"可以在 [SciCrunch][scicrunch] 注册表中查找具有 RRID " +"的资源，该注册表提供了一个用于查找、跟踪和一致引用科学资源的门户。" +"如果要将工具指定为 `SoftwareRequirement`，请在 SciCrunch " +"上搜索该工具并使用在注册表中分配的 RRID。 （按照 [添加资源教程][scicrunch-" +"add-tool] 将工具添加到 SciCrunch）。您可以使用此 RRID 在需求描述的 `specs` " +"字段中引用该工具（通过 [identifiers." +"org][identifiers]）。其他不错的选择（按优先顺序）包括主要工具引用的 DOI " +"和工具的 URL。" #: ../../src/topics/staging-input-files.md:1 #: b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" -msgstr "" +msgstr "暂存输入文件" #: ../../src/topics/staging-input-files.md:3 #: 35f97d37492b4c7ca3ad6cfc1e6fa366 msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." msgstr "" +"通常，输入文件位于独立于输出目录的只读目录中。 " +"如果基础工具希望将其输出文件与输入文件一起写入同一目录中，则会导致问题。 " +"使用 `InitialWorkDirRequirement` 将输入文件暂存到输出目录中。在此示例中，" +"我们使用 JavaScript 表达式从输入文件的前导目录路径中提取该文件的基本名称。" #: ../../src/topics/staging-input-files.md:9 #: c8159d0cb2ab452a9ce8e8d2adbaaa94 @@ -2516,7 +2994,7 @@ msgstr "" #: ../../src/topics/troubleshooting.md:1 #: 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" -msgstr "" +msgstr "疑难解答" #: ../../src/topics/troubleshooting.md:3 #: fbe0c65b444441f785d0054176d036a6 From dd897f448ef3db0d4528c4e67b387a2cc04752a1 Mon Sep 17 00:00:00 2001 From: "Bruno P. Kinoshita" Date: Wed, 1 Mar 2023 06:35:35 +0100 Subject: [PATCH 060/179] Translated using Weblate (Portuguese) Currently translated at 23.4% (140 of 598 strings) Translated using Weblate (Portuguese) Currently translated at 14.0% (84 of 598 strings) Co-authored-by: Bruno P. Kinoshita Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/pt/ Translation: Common Workflow Language/CWL User Guide --- locales/pt/LC_MESSAGES/user_guide.po | 289 ++++++++++++++++++--------- 1 file changed, 197 insertions(+), 92 deletions(-) diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po index b49c961f..97ae0c66 100644 --- a/locales/pt/LC_MESSAGES/user_guide.po +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -4,21 +4,21 @@ # Language User Guide package. # FIRST AUTHOR , 2023. # -#, fuzzy msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-27 16:02+0100\n" -"PO-Revision-Date: 2023-01-25 13:37+0000\n" -"Last-Translator: Michael Crusoe \n" +"PO-Revision-Date: 2023-03-01 05:35+0000\n" +"Last-Translator: \"Bruno P. Kinoshita\" \n" +"Language-Team: Portuguese \n" "Language: pt\n" -"Language-Team: Portuguese \n" -"Plural-Forms: nplurals=2; plural=n > 1;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.16-rc\n" "Generated-By: Babel 2.10.3\n" #: ../../LICENSE.md:2 3eb955b4f3dd4c3188924b97ea6ab592 @@ -27,7 +27,7 @@ msgstr "Licenças" #: ../../LICENSE.md:4 bf4480e7fff4460a87e8f43c11599f07 msgid "Instructional Material" -msgstr "" +msgstr "Material Instrucional" #: ../../LICENSE.md:6 9e9eab12205d4e82b4fedca520370f4c msgid "" @@ -140,6 +140,10 @@ msgid "" "License for the specific language governing permissions and limitations " "under the License." msgstr "" +"A menos que exigido pela lei aplicável ou acordado por escrito, o software " +"distribuído sob a Licença é distribuído \"COMO ESTÁ\", SEM GARANTIAS OU " +"CONDIÇÕES DE QUALQUER TIPO, expressas ou implícitas. Consulte a Licença para " +"obter o texto específico sobre as permissões e limitações sob a Licença." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 #: 1861131d3df648ae9e74ce1c87f0be7b a2ffa927deb2451d95ec63528e8078dd @@ -150,11 +154,15 @@ msgid "" "software, tools and workflows described using CWL are portable across a " "variety of platforms that support the CWL standard." msgstr "" +"CWL é uma maneira de descrever ferramentas de linha de comando e de conectá-" +"las formando workflows. Como a CWL é uma especificação e não um software, " +"ferramentas e workflows descritos com a CWL são portáveis entre uma " +"variedade de plataformas que suportam o padrão CWL." #: ../../src/episodes.md:5 ../../src/setup.md:5 #: 38b062f219b34e08a46bd8f6525353ec 89e7e1dd05474344a1d929cb492e9caf msgid "This page has moved" -msgstr "" +msgstr "Esta página foi movida" #: ../../src/episodes.md:9 d3357ff3c8874e368aea0d6062ef6190 msgid "" @@ -162,18 +170,21 @@ msgid "" "User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" +"O conteúdo desta página está desatualizado e foi mantido para preservar os " +"links do antigo Guia do Usuário. Por favor, use o novo [Índice](index.md" +"#table-of-contents) para navegar o Guia do Usuário." #: ../../src/faq.md:1 f2c4882e0e164c2b869e3eb969241061 msgid "FAQ" -msgstr "" +msgstr "Perguntas Frequentes (FAQ)" #: ../../src/faq.md:11 41099ab64e0544d894bd9e3af2718bda msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "" +msgstr "Usando `evalFrom` para Tipos Diferentes de \"`File`\"" #: ../../src/faq.md:41 bb6aff70534148fa8a4b01140f7be150 msgid "Rename an Input File" -msgstr "" +msgstr "Renomear um Arquivo de Entrada" #: ../../src/faq.md:43 70ebc653b0d54d60a866edc0dbf56b57 msgid "" @@ -182,24 +193,30 @@ msgid "" "from another step in a workflow, and don't want to work with the default " "names that these files were given when they were created." msgstr "" +"Este exemplo demonstra como mudar o nome de um arquivo de entrada como parte " +"da descrição da ferramenta. Isso pode ser útil quando você tem arquivos " +"produzidos em outro passo de um workflow, mas prefere não utilizar os nomes " +"dados por padrão quando estes arquivos foram criados." #: ../../src/faq.md:59 38b687f707d2438b85df08a445ab816f msgid "Rename an Output File" -msgstr "" +msgstr "Renomear um Arquivo de Saída" #: ../../src/faq.md:61 d48422c020004ef084ca11e6229b5450 msgid "" "This example demonstrates how to change the name of an output file from the " "default name given to it by a tool:" msgstr "" +"Este exemplo demonstra como escolher o nome para um arquivo de saída " +"diferente do nome padrão criado por uma ferramenta:" #: ../../src/faq.md:82 48765409ab9d48ccbcecceb46ddf2e91 msgid "Referencing a Local Script" -msgstr "" +msgstr "Como Fazer Referência a um Script Local" #: ../../src/faq.md:84 a59b8acd72124e2c95d1905ae494d928 msgid "There are two ways to reference a local script:" -msgstr "" +msgstr "Há duas maneiras de fazer uma referência a um script local:" #: ../../src/faq.md:86 f36088ba90d24f9f9c7c1bd59deb6f49 msgid "" @@ -207,16 +224,21 @@ msgid "" "`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" +"A primeira maneira é adicionando o arquivo que contém os seus scripts para a " +"variável de ambiente `PATH`. Desta maneira você pode executar o shell script " +"diretamente sem utilizar comandos via `sh` ou `bash`." #: ../../src/faq.md:89 45ee965ee4a7494a8354b82208e2ab45 msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" +msgstr "Comece adicionando a _shebang_ no topo do seu arquivo:" #: ../../src/faq.md:95 734cc1abe1c841ffac8d0895463d91fc msgid "" "After that, make the script executable with the command `chmod +x scriptname." "sh`" msgstr "" +"Em seguida faça o seu script executável com o comando `chmod +x scriptname." +"sh`" #: ../../src/faq.md:97 f01bc8c4d6134f0ea27dc7f5b39def24 msgid "" @@ -224,31 +246,37 @@ msgid "" "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" +"E finalmente, modifique o seu `PATH` para adicionar o diretório que contém o " +"seu script. (É boa prática usar `$HOME/bin` para scripts do usuário local)." #: ../../src/faq.md:104 dd6fc2a04e3b476892f05bc5b746d0fa msgid "" "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" +"Agora você pode utilizar `baseCommand: scriptname.sh` para rodar o script " +"diretamente." #: ../../src/faq.md:113 e309eaad55144052866ce131eb80fd14 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" +"Depois quando você quiser compartilhar o seu trabalho, é possível utilizar " +"um container de software com ferramentas como Docker." #: ../../src/faq.md:115 f0d649a60a13404ebecd540789202b87 msgid "" "The second method involves including an input of `type: File` in the script " "itself:" -msgstr "" +msgstr "O segundo método utiliza um input `type: File` diretamente no script:" #: ../../src/faq.md:135 e2b782f88d494de398af0c9002a3ccdc msgid "In CWL, everything must be directly stated." -msgstr "" +msgstr "Em CWL tudo deve ser declarado diretamente." #: ../../src/faq.md:138 b4a033731fcd4322bd2bb71c609a4cb7 msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "" +msgstr "Definindo Bindings de Inputs utilizando `self` para Inputs Opcionais" #: ../../src/faq.md:140 43a64810b12b4c7d82a5803c3b910fe5 msgid "" @@ -256,20 +284,26 @@ msgid "" "binding makes use of `self`. Below is an example workaround for this, " "pending a more sophisticated fix." msgstr "" +"No momento `cwltool` não funciona quando inputs opcionais não estão " +"presentes se o binding de input deles utilizar `self`. O exemplo abaixo " +"contém uma solução alternativa para este problema, até que haja uma solução " +"mais elegante para este problema." #: ../../src/faq.md:165 60f009e3714c405695da069204b196ea msgid "Model a \"one-or-the-other\" Parameter" -msgstr "" +msgstr "Modelar um Parâmetro do tipo \"um-ou-o-outro\"" #: ../../src/faq.md:167 98916ed9355842e49bef073430e10675 msgid "" "Below is an example showing how to specify different strings to be added to " "a command line, based on the value given to a Boolean parameter." msgstr "" +"O exemplo abaixo demonstra como especificar diferentes strings que serão " +"adicionadas à linha de comando, dependendo do valor de um parâmetro Boolean." #: ../../src/faq.md:188 9b8f2d0b33db4bbc82aaf5836b6f7ed8 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "" +msgstr "Conectar um Único valor a um Input que Espera uma Lista daquele Tipo" #: ../../src/faq.md:190 a251693354d24bf0bda4938c8890090a msgid "" @@ -280,7 +314,7 @@ msgstr "" #: ../../src/faq.md:194 f46740ac0acb473583facb9f7528d03c msgid "merge_nested" -msgstr "" +msgstr "merge_nested" #: ../../src/faq.md:196 7de1f9e3175b4c2ab156192f28fd3535 msgid "" @@ -292,6 +326,7 @@ msgstr "" #: ../../src/faq.md:199 225c6f08068e41f58eb62f99dc06210f msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" +"Que significa \"criar uma lista com exatamente estes sources como elementos\"" #: ../../src/faq.md:201 4e741f4e3bc74e10bd9568826e81c478 msgid "" @@ -301,24 +336,31 @@ msgid "" "add `linkMerge: merge_nested` under the appropriate `in` entry of the " "destination step." msgstr "" +"Ou em outras palavras: se o parâmetro destino for do tipo `File[]` (uma " +"lista de `File`s) e a fonte é um único `File`, adicione então " +"`MultipleInputFeatureRequirement` ao `requirements` no nível do Workflow e " +"adicione `linkMerge: merge_nested` sob a entrada apropriada `in` ao step que " +"receberá o parâmetro (target)." #: ../../src/faq.md:229 bfdb011cb81c4ef9b9e56b24f1e9ccd5 msgid "Optional Inputs 💯" -msgstr "" +msgstr "Inputs Opcionais 💯" #: ../../src/faq.md:231 09f385e325f942afaa3dd195c16a18d2 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" +"Para fazer um parâmetro de entrada opcional, adicione um ponto de " +"interrogação à declaração do tipo." #: ../../src/faq.md:247 c5d087082bb2468483e7ccda3ca45a07 msgid "" -msgstr "" +msgstr "" #: ../../src/faq.md:248 41e30b0224a0492f9047b4f320f39a23 msgid "Enum Inputs ⚜️" -msgstr "" +msgstr "Inputs Enum ⚜️" #: ../../src/faq.md:250 f06d073014a44f33a60d947a8c5b0e59 msgid "" @@ -326,14 +368,18 @@ msgid "" "type can be declared in CWL. **Specifying null here is known as long form " "style. It does the same thing as the question mark on the other inputs.**" msgstr "" +"O tipo enum por ser utilizado em CWL para flags de linha de comando que " +"requerem um tipo de input específico como argumento. **Especificar null aqui " +"é tido como forma estendida. O resultado é o mesmo que o uso do ponto de " +"interrogação nos outros inputs.**" #: ../../src/faq.md:267 2fb74cd1b41e4fdb81a8f9b3b6c84373 msgid "" -msgstr "" +msgstr "" #: ../../src/faq.md:268 09e19f34d0fd4e388d4939cbc2be3436 msgid "Record Inputs 📀" -msgstr "" +msgstr "Inputs do tipo Record" #: ../../src/faq.md:270 1ecae448dfcf45a4ae0dd39bd011e449 msgid "" @@ -344,7 +390,7 @@ msgstr "" #: ../../src/faq.md:322 6df3d4e918cc4bccb823859ce07b197a msgid "Setting Mutually Exclusive Parameters" -msgstr "" +msgstr "Definindo Parâmetros Mutualmente Exclusivos" #: ../../src/faq.md:324 086db1a093e64caa88d958150accc19c msgid "" @@ -357,72 +403,80 @@ msgstr "" #: ../../src/faq.md:342 da77c818d8694ab99fb2eccf73083047 msgid "Setting Booleans" -msgstr "" +msgstr "Utilizando Booleans" #: ../../src/faq.md:344 254259509ed6462d8ebc296b5f811f44 msgid "These can be set by using the default field" -msgstr "" +msgstr "Estes são definidos através do campo padrão" #: ../../src/faq.md:349 f7a44f76579d4709a61d2d61bc352b76 msgid "Concatenating Strings in Inputs" -msgstr "" +msgstr "Concatenando Strings em Inputs" #: ../../src/faq.md:351 d67278e99c684f488f1e3418e1c8c207 msgid "The valueFrom field must be used instead of default." -msgstr "" +msgstr "O campo valueFrom deve ser utilizado ao invés do valor padrão." #: ../../src/faq.md:359 f5e35ee06cd24edf831589ebaa6193d2 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "" +msgstr "Erros do `cwltool` devido a Nomes de Arquivos com Espaços" #: ../../src/faq.md:361 2ffb67e547c446499625a8db9a102da6 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" +"O `cwltool` não permite alguns caracteres em nomes de arquivos por padrão." #: ../../src/faq.md:363 ee653ff9fefe4771b35e2e76199b536a msgid "" "For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" +"Por exemplo, o nome de arquivo `um espaco vai aqui.txt` inclui 3 espaços.." #: ../../src/faq.md:371 02b1eb159e934fd692929f7c30319ddd msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" +"Se você não tem opção e precisa utilizar estes caracteres apesar do risco, " +"você deve então passar `--relax-path-checks` ao chamar o `cwltool`." #: ../../src/faq.md:373 857024702f624885be706c405b7a088e msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" +"Erro de Referência em Parâmetro CWL devido a Hífen no Identificador de " +"Entrada" #: ../../src/faq.md:375 d664e30899bd463bb48d38adec318dd4 msgid "If `cwltool --validate` returns valid" -msgstr "" +msgstr "Se `cwltool --validate` valida com sucesso" #: ../../src/faq.md:384 9f3957bbe205454e8bffc4b5caac5970 msgid "But executing it causes an error like:" -msgstr "" +msgstr "Mas ao executar o workflow um erro como o seguinte aparece:" #: ../../src/faq.md:396 6ec3bbc6a1ca4e23b47f025f0732e609 msgid "The file is here" -msgstr "" +msgstr "Este é o arquivo" #: ../../src/faq.md:410 3e727d79e65e4c6cb157550e80261c53 msgid "Problem caused by `-` (hyphen character)." -msgstr "" +msgstr "O problema é causado pelo `-` (hífen)." #: ../../src/faq.md:423 6e0705f4ab4b4e9093794cb4fccb6be9 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" +msgstr "Para corrigir este erro, substitua o `-` (hífen) por `_` (sublinhado)" #: ../../src/faq.md:436 0047d039317349679fb6a66d18ec8487 msgid "" "If it is not possible to change the input identifier, then you can use an " "alternative CWL Parameter Reference syntax:" msgstr "" +"Se não for possível mudar o identificador do input, você pode reescrever " +"utilizando uma sintaxe alternativa para Referências de Parâmetros CWL:" #: ../../src/faq.md:442 8c39608ad0494bee9a4a422cbeb34387 msgid "Use CWL and cwltool with Singularity" -msgstr "" +msgstr "Utilizar CWL e cwltool com Singularity" #: ../../src/faq.md:445 7dac53bca8c14a3f9af75cb162cba4f9 msgid "" @@ -434,7 +488,7 @@ msgstr "" #: ../../src/faq.md:450 ffcc38ff98324d71bfeb8d66d4901da7 msgid "Debug JavaScript Expressions" -msgstr "" +msgstr "Depurar Expressões JavaScript" #: ../../src/faq.md:452 0d7bf2cefe4a4e22b186bdf4d0ed793d msgid "" @@ -511,7 +565,7 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:10 7766227bf91b48b2b9752b625e5a9084 msgid "The CWL Specification" -msgstr "" +msgstr "A Especificação CWL" #: ../../src/introduction/basic-concepts.md:21 032d414ac29740aa9041d89d0ebf70e6 msgid "" @@ -538,7 +592,7 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:37 648e94a9d368450dbdac706445254c9f msgid "Implementations" -msgstr "" +msgstr "Implementações" #: ../../src/introduction/basic-concepts.md:39 e9ae15124dcd408395fc67e16b50696a msgid "" @@ -720,12 +774,12 @@ msgstr "" #: ../../src/introduction/quick-start.md:94 7377b155e8694798994bbc911a3f3152 #: 7699685836064bd89db530a9c1918865 7d187a209ebd4e3ba6c6aeb05743041a msgid "Learn More" -msgstr "" +msgstr "Saiba Mais" #: ../../src/introduction/basic-concepts.md:180 #: 3fcbf810c86f4cf7b8499de88147aa95 msgid "Semantic Versioning - " -msgstr "" +msgstr "Versionamento Semântico - " #: ../../src/introduction/basic-concepts.md:181 #: e242228b6b3d440cbca8418050220267 @@ -733,6 +787,7 @@ msgid "" "The CWL Specification page in the CWL website: " msgstr "" +"A página web da Especificação CWL: " #: ../../src/introduction/basic-concepts.md:182 #: 6e01963a01cb49e39692455256679bfc @@ -740,6 +795,8 @@ msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" +"A especificação CWL atual no GitHub: {{ ''.format(cwl_version_text) }}" #: ../../src/introduction/basic-concepts.md:183 #: ed81ea2234b041c79449dcd20f886cb6 @@ -747,11 +804,13 @@ msgid "" "The list of Implementations in the CWL website: " msgstr "" +"A lista de Implementações na página web da CWL: " #: ../../src/introduction/basic-concepts.md:184 #: e8e3996f6a894b4f9cc266b46cb8d756 msgid "PROV-O: The PROV Ontology - " -msgstr "" +msgstr "PROV-O: A Ontologia PROV - " #: ../../src/introduction/basic-concepts.md:185 #: 085e4d1a7a9744d2884f3003c64ca174 @@ -762,7 +821,7 @@ msgstr "" #: ../../src/introduction/index.md:1 dcd96950854f47a6ad4169320c1dab34 msgid "Introduction" -msgstr "" +msgstr "Introdução" #: ../../src/introduction/index.md:3 c4d17eec31874bf1ae9b49d73537d86c msgid "" @@ -773,7 +832,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:1 98a8bdfc7c91436d9cb46abbb7c19c57 msgid "Prerequisites" -msgstr "" +msgstr "Pré-requisitos" #: ../../src/introduction/prerequisites.md:6 244a716e267540c782e627adaea3a413 msgid "" @@ -787,7 +846,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:12 2cdf453d2c8b4e2ea50555ef0b7364e5 msgid "CWL Implementations" -msgstr "" +msgstr "Implementações da CWL" #: ../../src/introduction/prerequisites.md:14 53643a4f190c412d9552d1908f408318 msgid "" @@ -809,15 +868,15 @@ msgstr "" #: ../../src/introduction/prerequisites.md:24 1506ac904c6345c5806704a0ccf235aa msgid "Linux" -msgstr "" +msgstr "Linux" #: ../../src/introduction/prerequisites.md:25 a616213ed24e427bb91ee33cb21ec131 msgid "macOS" -msgstr "" +msgstr "macOS" #: ../../src/introduction/prerequisites.md:26 a4e9ae38103843739f13c62befd21f3e msgid "Windows" -msgstr "" +msgstr "Windows" #: ../../src/introduction/prerequisites.md:29 2cd231aac42c4a69a925cea369999a8b msgid "" @@ -851,7 +910,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:51 3448d215c2434866b8a4b340872ba81e msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" +msgstr "Instalando `cwltool` com `pip` e `venv`." #: ../../src/introduction/prerequisites.md:62 4c24d05f65794735b816024c78b63f1c msgid "" @@ -859,14 +918,18 @@ msgid "" "language/cwltool#install) for other ways to install `cwltool` with `apt` and " "`conda`." msgstr "" +"Visite a [documentação](https://github.com/common-workflow-language/" +"cwltool#install) do `cwltool` para outras opções para instalar `cwltool` com " +"`apt` e `conda`." #: ../../src/introduction/prerequisites.md:65 3167f4a2a8394feda1f848334be62022 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" +"Vamos usar uma simples descrição de ferramenta CWL `true.cwl` com `cwltool`." #: ../../src/introduction/prerequisites.md:67 3c4b67d62c9c4d658ccaafcd1977ec08 msgid "`true.cwl`" -msgstr "" +msgstr "`true.cwl`" #: ../../src/introduction/prerequisites.md:73 30792f78348942e0acdde411342e8830 msgid "" @@ -894,7 +957,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:91 690882dcc29c48acbeb215a8be52eb9e msgid "Cwl-runner Python Module" -msgstr "" +msgstr "Módulo Python cwl-runner" #: ../../src/introduction/prerequisites.md:93 6c3ba51b1e9a4add9203d62cec6ebae9 msgid "" @@ -930,7 +993,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:120 dd2e10f43e8f498cb01de5faa4fccb70 msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" +msgstr "Executando `true.cwl` com `cwl-runner`." #: ../../src/introduction/prerequisites.md:125 e500e9c71c7042169c25b31f21a09142 msgid "" @@ -975,7 +1038,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:161 53bb712a68cd49fca4db11e9e507c9a4 msgid "Text Editor" -msgstr "" +msgstr "Editor de Texto" #: ../../src/introduction/prerequisites.md:163 bdcf61cce5294e45a9f964628a8a66bd msgid "" @@ -1011,7 +1074,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:177 0c17235a374e40099be37b9b8ac8f1f0 msgid "Docker" -msgstr "" +msgstr "Docker" #: ../../src/introduction/prerequisites.md:181 e3690e656b5a4348845c654689935a88 msgid "" @@ -1101,7 +1164,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:39 d6f6e061c0f4434eb6d70f9d84759042 msgid "Installing `cwltool` with `pip`." -msgstr "" +msgstr "Instalando `cwltool` com `pip`." #: ../../src/introduction/quick-start.md:47 cb2b548489df45ee9d49b36116440eea msgid "" @@ -1113,7 +1176,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:51 aa751bda67ec44ba988642b061e2a094 msgid "Running \"Hello World\"" -msgstr "" +msgstr "Executando \"Hello World\"" #: ../../src/introduction/quick-start.md:53 a7e0209af0544b0ab31012864a43886c msgid "" @@ -1124,7 +1187,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:57 d0f424f0041c4635a0559fa32a76c86f msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" +msgstr "Executando `hello_world.cwl` com `cwltool`." #: ../../src/introduction/quick-start.md:62 eeee96c4e59447aea6b239c63e4bb3e5 msgid "" @@ -1146,17 +1209,19 @@ msgstr "" #: ../../src/introduction/quick-start.md:74 e5619164bdf242f0b09cac668adc0ef7 msgid "`hello_world-job.json`" -msgstr "" +msgstr "`hello_world-job.json`" #: ../../src/introduction/quick-start.md:80 9f80772a53154bbeb27895d35435de10 msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" +"Você pode utilizar este arquivo de Objetos de Inputs agora para executar o " +"workflow “Hello World”:" #: ../../src/introduction/quick-start.md:82 98b6d400cb274d08ad6489adbef08c4b msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" +msgstr "Passando um arquivo de Objeto de Inputs para o `cwltool`." #: ../../src/introduction/quick-start.md:88 4faabaab56f1444da290cf64cc389f37 msgid "" @@ -1168,42 +1233,53 @@ msgstr "" #: ../../src/introduction/quick-start.md:96 48beaccb16a24427bd015c63f9e06d37 msgid "Continue reading the next sections of this User Guide!" -msgstr "" +msgstr "Continue lendo as seções seguintes deste Guia do Usuário!" #: ../../src/introduction/quick-start.md:97 68035ead1c6844128011ca32c04fd20f msgid "" "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" +"[Lista das Implementações da CWL](https://www.commonwl.org/implementations)." #: ../../src/introduction/quick-start.md:98 8fc1ebf21a6f4894a4acfba74a80602b msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" +"A [organização`common-workflow-language`](https://github.com/common-workflow-" +"language) no GitHub." #: ../../src/introduction/quick-start.md:99 27fbad579d8b4ebeacc6fd3ef7e85a39 msgid "" "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" "Common_Workflow_Language)." msgstr "" +"[Common Workflow Language na Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." #: ../../src/introduction/quick-start.md:100 a8791b670848474da292a467f01f8c45 msgid "" "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." "org/wiki/YAML)." msgstr "" +"[YAML.org](http://yaml.org/) e [YAML at Wikipedia](https://en.wikipedia.org/" +"wiki/YAML)." #: ../../src/introduction/quick-start.md:101 fc20fa4c04104417b541a67ada2ab9a9 msgid "" "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." "replace('VERSION', cwl_version_text) }}." msgstr "" +"A {{'[Especificação CWL VERSION](https://www.commonwl.org/VERSION)'.replace(" +"'VERSION', cwl_version_text) }}." #: ../../src/introduction/quick-start.md:102 a93a7797a12b48dfa5bc3a7c50ab88e7 msgid "" "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" "Workflow_management_system)." msgstr "" +"[Workflow management system na Wikipedia](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." #: ../../src/setup.md:9 6f02fa47aca14c59a35b3ab750f5f236 msgid "" @@ -1211,11 +1287,14 @@ msgid "" "User Guide. The information on this page has been migrated to the [FAQ](/faq." "md) section of the new user guide." msgstr "" +"O conteúdo desta página está desatualizado mas foi mantido aqui para " +"preservar os links do antigo Guia do Usuário. A informação desta página foi " +"migrada para a seção [FAQ](/faq.md) do novo guia do usuário." #: ../../src/topics/additional-arguments-and-parameters.md:1 #: 3821c2d16b254672a494522e47386cb0 msgid "Additional Arguments and Parameters" -msgstr "" +msgstr "Argumentos e Parâmetros Adicionais" #: ../../src/topics/additional-arguments-and-parameters.md:3 #: 412a05f3492349a7bd26ea0c30e9bd80 @@ -1237,18 +1316,20 @@ msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 #: 485bb71673144e3f90f05b420b7079ac msgid "`arguments.cwl`" -msgstr "" +msgstr "`arguments.cwl`" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 0beb10c3133643f6b62c7d4aeec33709 #: 5d48d9a2e977431f9a3625abaa466f5f msgid "`arguments-job.yml`" -msgstr "" +msgstr "`arguments-job.yml`" #: ../../src/topics/additional-arguments-and-parameters.md:24 #: fcc1151a2e8b4a84b8595c7f913781a1 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" +"Em seguida, crie um arquivo Java de exemplo para usar com a ferramenta de " +"linha de comando." #: ../../src/topics/additional-arguments-and-parameters.md:30 #: 4a291c7ac7c84257b7402567d8364a36 @@ -1256,6 +1337,8 @@ msgid "" "And now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" +"E agora execute `cwltool` utilizando a descrição de ferramenta e o objeto de " +"input na linha de comando:" #: ../../src/topics/additional-arguments-and-parameters.md:36 #: 3b1ae26038fd498ca0ae23aa70a35d3f @@ -1278,7 +1361,7 @@ msgstr "" #: ../../src/topics/best-practices.md:1 a417fdd330db47a3aac07f7006c83ca9 msgid "Best Practices" -msgstr "" +msgstr "Melhores Práticas" #: ../../src/topics/best-practices.md:3 99bad0fd9bee428a8d936d5a8e84d97d msgid "" @@ -2195,7 +2278,7 @@ msgstr "" #: ../../src/topics/file-formats.md:39 d5752ee5437b496ca10f4f12b76fc5dc msgid "`sample.yml`" -msgstr "" +msgstr "`sample.yml`" #: ../../src/topics/file-formats.md:45 91dc76bb4565473ab948eecf628a405c msgid "" @@ -2277,6 +2360,8 @@ msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " "command line." msgstr "" +"Em sequência, cria um arquivo chamado whale.txt utilizando [touch] digitando " +"`touch whale.txt` na linha de comando." #: ../../src/topics/inputs.md:53 13c97256a5ee49c99f4010edf9dbc9bf msgid "" @@ -2385,6 +2470,8 @@ msgid "" "Now invoke `cwltool` providing the tool description and the input object on " "the command line:" msgstr "" +"Agora chame o `cwltool` passando a descrição da ferramenta e o objeto de " +"entrada na linha de comando:" #: ../../src/topics/inputs.md:178 49406f30f62346968bb1250efc940f70 msgid "" @@ -2473,7 +2560,7 @@ msgstr "" #: ../../src/topics/inputs.md:265 09b1db3cc6c845058cf0ad4c24d71733 msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" +msgstr "`exclusive-parameter-expressions.cwl`" #: ../../src/topics/inputs.md:271 84aa6e0c479f4528836691005129056e msgid "" @@ -2572,7 +2659,7 @@ msgstr "" #: ../../src/topics/operations.md:10 7b165718ffeb42e793c97fad807f216f msgid "`operations.cwl`" -msgstr "" +msgstr "`operations.cwl`" #: ../../src/topics/operations.md:16 5e31cddd14414d31b7bd0a6c2745d272 msgid "" @@ -2658,7 +2745,7 @@ msgstr "" #: ../../src/topics/outputs.md:38 8803a28ccff846eea7d06f4bd908c763 msgid "Next, create a tar file for the example." -msgstr "" +msgstr "Agora, crie um arquivo tar para o exemplo." #: ../../src/topics/outputs.md:45 661b62e554d64e449c69e475e5188f99 msgid "" @@ -2743,7 +2830,7 @@ msgstr "" #: ../../src/topics/parameter-references.md:19 2f32531e47b4465594d41ddd218fb2fd msgid "`tar-param-job.yml`" -msgstr "" +msgstr "`tar-param-job.yml`" #: ../../src/topics/parameter-references.md:25 501dd6f9dbb1438f9a59f6a025639f35 msgid "" @@ -2824,10 +2911,13 @@ msgid "" msgstr "" #: ../../src/topics/parameter-references.md:85 e924874af32d4be19c5e8446768226dd +#, fuzzy msgid "" "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." "html#WorkflowStepInput)" msgstr "" +"De [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" #: ../../src/topics/parameter-references.md:89 b162113f364445af9ff1bfc8a6610e13 msgid "" @@ -2835,6 +2925,9 @@ msgid "" "html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." "org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" +"De [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) e [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" #: ../../src/topics/parameter-references.md:92 aa721077e16948c3a5bb8ef5bd7aff04 msgid "" @@ -2929,11 +3022,11 @@ msgstr "" #: ../../src/topics/staging-input-files.md:9 7159b5c5023c47128057c4116cce69f4 msgid "`linkfile.cwl`" -msgstr "" +msgstr "`linkfile.cwl`" #: ../../src/topics/troubleshooting.md:1 3bfa6791d78f43629de90345f4441ebb msgid "Troubleshooting" -msgstr "" +msgstr "Solucionando Problemas" #: ../../src/topics/troubleshooting.md:3 9a6bd5b684a740ed9e8993d9f8607774 msgid "" @@ -3012,7 +3105,7 @@ msgstr "" #: ../../src/topics/using-containers.md:1 95b832552e8443ea9c652f8c95afc01e msgid "Using Containers" -msgstr "" +msgstr "Utilizando Containers" #: ../../src/topics/using-containers.md:3 561fc9c561bc492ea82c17784dfd439c msgid "Running Tools Inside Docker" @@ -3097,7 +3190,7 @@ msgstr "" #: ../../src/topics/workflows.md:1 9f989fff165448ecbcaad6adc0f58d6b msgid "Workflows" -msgstr "" +msgstr "Workflows" #: ../../src/topics/workflows.md:3 212c82dca23645e89d8b5bb7599f2d25 msgid "" @@ -3183,7 +3276,7 @@ msgstr "" #: ../../src/topics/workflows.md:185 c4f854c7a279404da3688bdf424c7c5e msgid "`1st-workflow-job.yml`" -msgstr "" +msgstr "`1st-workflow-job.yml`" #: ../../src/topics/workflows.md:191 d383ce45139944cb85768627965d9467 msgid "" @@ -3281,7 +3374,7 @@ msgstr "" #: ../../src/topics/workflows.md:300 cbe1ef068b0c417b953655e132333447 msgid "`nestedworkflows.cwl`" -msgstr "" +msgstr "`nestedworkflows.cwl`" #: ../../src/topics/workflows.md:309 a691c36a15044b11a6d037d16f818a6d msgid "" @@ -3396,7 +3489,7 @@ msgstr "" #: ../../src/topics/workflows.md:415 f9618882e0a14a0b84ff9751346dc291 msgid "`scatter-workflow.cwl`" -msgstr "" +msgstr "`scatter-workflow.cwl`" #: ../../src/topics/workflows.md:421 4fe03daddd304a9b828fdd1c29f0d072 msgid "" @@ -3428,7 +3521,7 @@ msgstr "" #: ../../src/topics/workflows.md:450 b0b2e63d2b8a4fd0983e976c16440da4 msgid "Using the following input file:" -msgstr "" +msgstr "Usando o seguinte arquivo de entrada:" #: ../../src/topics/workflows.md:452 47ac993a90fe46ca92e97d6b67b3276b msgid "`scatter-job.yml`" @@ -3466,7 +3559,7 @@ msgstr "" #: ../../src/topics/workflows.md:483 2043f12eb2ce4424b133e0dc0b62aafc msgid "`wc-tool.cwl`" -msgstr "" +msgstr "`wc-tool.cwl`" #: ../../src/topics/workflows.md:489 87ba95507fc44dbca4cb6c5283ce50f9 msgid "" @@ -3505,7 +3598,7 @@ msgstr "" #: ../../src/topics/workflows.md:513 6c61733fe4284f51a6b46e89cafe78c4 msgid "`scatter-nested-workflow.cwl`" -msgstr "" +msgstr "`scatter-nested-workflow.cwl`" #: ../../src/topics/workflows.md:519 0585f83162c349969391c9456a884f28 msgid "" @@ -3515,7 +3608,7 @@ msgstr "" #: ../../src/topics/workflows.md:522 f209343966db4d46b4611d3620c3b496 msgid "Conditional Workflows" -msgstr "" +msgstr "Workflows Condicionais" #: ../../src/topics/workflows.md:524 5a2661ce35dc4d79a15da1e17c0a95ec msgid "" @@ -3564,7 +3657,7 @@ msgstr "" #: ../../src/topics/yaml-guide.md:1 8e7c3365f0f94038930f71666f05170f msgid "YAML Guide" -msgstr "" +msgstr "Guia de YAML" #: ../../src/topics/yaml-guide.md:6 cbe6f35c21044054a010767f2f0cae46 msgid "" @@ -3579,7 +3672,7 @@ msgstr "" #: ../../src/topics/yaml-guide.md:16 6e7ea76e8aeb477cbb8197efed33e53d msgid "Contents" -msgstr "" +msgstr "Conteúdo" #: ../../src/topics/yaml-guide.md:18 482e121a6e74428dbe6ad1f772f14684 msgid "[Key-Value Pairs](#key-value-pairs)" @@ -3599,11 +3692,11 @@ msgstr "" #: ../../src/topics/yaml-guide.md:22 2b900b2779c84de5bbd3c933c56e5922 msgid "[JSON Style](#json-style)" -msgstr "" +msgstr "[Estilo JSON](#json-style)" #: ../../src/topics/yaml-guide.md:24 189db6d0e54a400eb5615e259354827e msgid "Key-Value Pairs" -msgstr "" +msgstr "Pares de Chave-Valor" #: ../../src/topics/yaml-guide.md:26 e689c0e1dcd645348ceed51e91eb9ad0 msgid "" @@ -3614,6 +3707,13 @@ msgid "" "meaning in the CWL specification and underscored key names otherwise. For " "example:" msgstr "" +"Em princípio, um arquivo escrito em YAML consiste de uma série de _pares de " +"chave-valor`. Cada par é escrito como `chave: valor`, onde o espaço em " +"branco entre o `:` é um requisito. Os nomes das chaves em arquivos CWL não " +"devem conter espaços em branco - [_camelCase_][camelCase] é usado para " +"valores de chaves que contém múltiplas palavras e possuem um valor especial " +"na especificação CWL, caso contrário os valores dos nomes de chaves aparecem " +"sublinhados. For exemplo:" #: ../../src/topics/yaml-guide.md:42 9532ac8e1dda479e890bf970323a0a32 msgid "" @@ -3622,6 +3722,11 @@ msgid "" "strings, numeric (integer, floating point, or scientific representation), " "Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" +"O YAML acima define quatro chaves - `first_name`, `last_name`, `age_years`, " +"e `home` - com quatro valores respectivos. Os valores podem ser strings de " +"caracteres, númericos (integer, floating point, ou representação científica)" +", Boolean (`true` ou `false`), ou valores mais complexos com tipos aninhados " +"(veja abaixo)." #: ../../src/topics/yaml-guide.md:51 91a057a7d10f438fad10338dd44c013c msgid "" @@ -3653,7 +3758,7 @@ msgstr "" #: ../../src/topics/yaml-guide.md:79 84f16419237a4789ac0f3c682b3a11ee msgid "Maps" -msgstr "" +msgstr "Dicionários" #: ../../src/topics/yaml-guide.md:81 269ca8e05ce14e899fc8b2a00b1e458e msgid "" @@ -3698,7 +3803,7 @@ msgstr "" #: ../../src/topics/yaml-guide.md:167 209dfb0d0a1148ed962dbb33890a3160 msgid "JSON Style" -msgstr "" +msgstr "Estilo JSON" #: ../../src/topics/yaml-guide.md:169 cd3a174dae334d0d977a3234e258bd25 msgid "" @@ -3708,7 +3813,7 @@ msgstr "" #: ../../src/topics/yaml-guide.md:177 b0f0b10de8f54e1e951e480f696976f1 msgid "and:" -msgstr "" +msgstr "e:" #: ../../src/topics/yaml-guide.md:184 b5597e8984ad4e0bad33433c1dab89bd msgid "" @@ -3722,7 +3827,7 @@ msgstr "" #: ../../src/topics/yaml-guide.md:194 5ad7d551d3d347a097508a8488f9d15c msgid "Reference" -msgstr "" +msgstr "Referencia" #: ../../src/topics/yaml-guide.md:196 58f80e6944f9402a810b9b02ba3ad917 msgid "" @@ -3733,7 +3838,7 @@ msgstr "" #: ../../src/tutorials.md:1 8fdcc745f4684fa7816c62782507438e msgid "Tutorials" -msgstr "" +msgstr "Tutoriais" #: ../../src/tutorials.md:5 3c933ac074ee4d94b7aeacb7abeaf388 msgid "" @@ -3744,7 +3849,7 @@ msgstr "" #: ../../src/tutorials.md:7 1d6cdf13aa834cb4a682553227d9f725 msgid "Beginner Tutorials" -msgstr "" +msgstr "Tutoriais para Iniciantes" #: ../../src/tutorials.md:9 606cc939c5014e2abdab163e4d726f1b msgid "" From f940a62fdc9f4381cb88288b6ea02acdd970960f Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Wed, 26 Apr 2023 13:57:41 +0200 Subject: [PATCH 061/179] sphinx: support newer myst_parser --- src/conf.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/conf.py b/src/conf.py index bcfe20a8..dd428640 100644 --- a/src/conf.py +++ b/src/conf.py @@ -254,7 +254,8 @@ merge_file_level, read_topmatter, ) -from myst_parser.mdit_to_docutils.sphinx_ import SphinxRenderer, create_warning +from myst_parser.mdit_to_docutils.sphinx_ import SphinxRenderer +from myst_parser.warnings_ import create_warning from myst_parser.parsers.mdit import create_md_parser SPHINX_LOGGER = logging.getLogger(__name__) From 1c54d806fec8117be57b40cf4507dd506dc3cfea Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Wed, 26 Apr 2023 14:06:40 +0200 Subject: [PATCH 062/179] Translations update from Hosted Weblate (#383) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Added translation using Weblate (Portuguese (Portugal)) Added translation using Weblate (Portuguese (Brazil)) Co-authored-by: Michael Crusoe * Added translation using Weblate (Portuguese (Portugal)) Added translation using Weblate (Portuguese (Brazil)) Co-authored-by: Weblate * Translated using Weblate (Portuguese (Brazil)) Currently translated at 0.3% (2 of 598 strings) Co-authored-by: Bruno P. Kinoshita Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/pt_BR/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Portuguese (Portugal)) Currently translated at 22.5% (135 of 598 strings) Translated using Weblate (Portuguese) Currently translated at 23.4% (140 of 598 strings) Co-authored-by: ssantos Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/pt/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/pt_PT/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Chinese (Simplified)) Currently translated at 100.0% (2 of 2 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 68.2% (408 of 598 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 67.0% (401 of 598 strings) Co-authored-by: Zoë Ma Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-sphinx/zh_Hans/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide Translation: Common Workflow Language/CWL User Guide: Sphinx --------- Co-authored-by: Michael Crusoe Co-authored-by: Bruno P. Kinoshita Co-authored-by: ssantos Co-authored-by: Zoë Ma --- locales/pt/LC_MESSAGES/user_guide.po | 31 +- locales/pt_BR/LC_MESSAGES/sphinx.po | 27 + locales/pt_BR/LC_MESSAGES/user_guide.po | 3125 ++++++++++++++++++++ locales/pt_PT/LC_MESSAGES/sphinx.po | 27 + locales/pt_PT/LC_MESSAGES/user_guide.po | 3250 +++++++++++++++++++++ locales/zh_Hans/LC_MESSAGES/sphinx.po | 8 +- locales/zh_Hans/LC_MESSAGES/user_guide.po | 280 +- 7 files changed, 6592 insertions(+), 156 deletions(-) create mode 100644 locales/pt_BR/LC_MESSAGES/sphinx.po create mode 100644 locales/pt_BR/LC_MESSAGES/user_guide.po create mode 100644 locales/pt_PT/LC_MESSAGES/sphinx.po create mode 100644 locales/pt_PT/LC_MESSAGES/user_guide.po diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po index 97ae0c66..322bade8 100644 --- a/locales/pt/LC_MESSAGES/user_guide.po +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -9,8 +9,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-27 16:02+0100\n" -"PO-Revision-Date: 2023-03-01 05:35+0000\n" -"Last-Translator: \"Bruno P. Kinoshita\" \n" +"PO-Revision-Date: 2023-04-03 19:41+0000\n" +"Last-Translator: ssantos \n" "Language-Team: Portuguese \n" "Language: pt\n" @@ -18,7 +18,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=2; plural=n > 1;\n" -"X-Generator: Weblate 4.16-rc\n" +"X-Generator: Weblate 4.17-dev\n" "Generated-By: Babel 2.10.3\n" #: ../../LICENSE.md:2 3eb955b4f3dd4c3188924b97ea6ab592 @@ -45,7 +45,7 @@ msgstr "" #: ../../LICENSE.md:12 a8e98ad541c642e58e201afa625ec791 msgid "You are free:" -msgstr "Você tem o direito de:" +msgstr "Tem o direito de:" #: ../../LICENSE.md:14 b4cb4bc4261347fcb0d2c8a93995ab76 msgid "" @@ -93,9 +93,9 @@ msgid "" "technological measures that legally restrict others from doing anything the " "license permits. With the understanding that:" msgstr "" -"**Sem restrições adicionais**---Você não pode aplicar termos jurídicos ou " -"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " -"algo que a licença permita. Com o entendimento de que:" +"**Sem restrições adicionais**---Não pode aplicar termos jurídicos ou medidas " +"de caráter tecnológico que restrinjam legalmente outros de fazerem algo que " +"a licença permita. Com o entendimento de que:" #: ../../LICENSE.md:36 3cfedee64d4e46098a159cb2acdba4ef msgid "" @@ -171,8 +171,8 @@ msgid "" "contents) to browse the User Guide." msgstr "" "O conteúdo desta página está desatualizado e foi mantido para preservar os " -"links do antigo Guia do Usuário. Por favor, use o novo [Índice](index.md" -"#table-of-contents) para navegar o Guia do Usuário." +"links do antigo Guia do Utilizador. Por favor, use o novo [Índice](index.md" +"#table-of-contents) para navegar o Guia do Utilizador." #: ../../src/faq.md:1 f2c4882e0e164c2b869e3eb969241061 msgid "FAQ" @@ -247,7 +247,8 @@ msgid "" "scripts)." msgstr "" "E finalmente, modifique o seu `PATH` para adicionar o diretório que contém o " -"seu script. (É boa prática usar `$HOME/bin` para scripts do usuário local)." +"seu script. (É boa prática usar `$HOME/bin` para scripts do utilizador " +"local)." #: ../../src/faq.md:104 dd6fc2a04e3b476892f05bc5b746d0fa msgid "" @@ -438,7 +439,7 @@ msgid "" "checks` to `cwltool`." msgstr "" "Se você não tem opção e precisa utilizar estes caracteres apesar do risco, " -"você deve então passar `--relax-path-checks` ao chamar o `cwltool`." +"você deve então passar `--relax-path-verificks` ao chamar o `cwltool`." #: ../../src/faq.md:373 857024702f624885be706c405b7a088e msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" @@ -1216,7 +1217,7 @@ msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -"Você pode utilizar este arquivo de Objetos de Inputs agora para executar o " +"Pode utilizar este arquivo de Objetos de Inputs agora para executar o " "workflow “Hello World”:" #: ../../src/introduction/quick-start.md:82 98b6d400cb274d08ad6489adbef08c4b @@ -1233,7 +1234,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:96 48beaccb16a24427bd015c63f9e06d37 msgid "Continue reading the next sections of this User Guide!" -msgstr "Continue lendo as seções seguintes deste Guia do Usuário!" +msgstr "Continue lendo as secções seguintes deste Guia do Utilizador!" #: ../../src/introduction/quick-start.md:97 68035ead1c6844128011ca32c04fd20f msgid "" @@ -1288,8 +1289,8 @@ msgid "" "md) section of the new user guide." msgstr "" "O conteúdo desta página está desatualizado mas foi mantido aqui para " -"preservar os links do antigo Guia do Usuário. A informação desta página foi " -"migrada para a seção [FAQ](/faq.md) do novo guia do usuário." +"preservar os links do antigo Guia do Utilizador. A informação desta página " +"foi migrada para a secção [FAQ](/faq.md) do novo guia do utilizador." #: ../../src/topics/additional-arguments-and-parameters.md:1 #: 3821c2d16b254672a494522e47386cb0 diff --git a/locales/pt_BR/LC_MESSAGES/sphinx.po b/locales/pt_BR/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..2d131c35 --- /dev/null +++ b/locales/pt_BR/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt_BR\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "" diff --git a/locales/pt_BR/LC_MESSAGES/user_guide.po b/locales/pt_BR/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..e1d33500 --- /dev/null +++ b/locales/pt_BR/LC_MESSAGES/user_guide.po @@ -0,0 +1,3125 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: 2023-03-12 10:39+0000\n" +"Last-Translator: \"Bruno P. Kinoshita\" \n" +"Language-Team: Portuguese (Brazil) \n" +"Language: pt_BR\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.16.2-dev\n" + +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "Licenças" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "Material Instrucional" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 4dee8504a8e5496081dadc386ab45540 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 674c238b25e240eda05e22e399f2f78f +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: b651f80f47b4442fbf29454a233697fc +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: ecf2b9c0b1664afe9c4e180610610021 +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: e24cb13d98014e558b6a6946758359e0 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: 928e3df7ca3e479ca6474a8e72cf36eb +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: d355f035676446c88b028f327aeb4829 +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 339b852df24242189d6efcd2898a3396 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: 3ef57e6862f240bebcf193a52397af0a +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: fae385da16aa443da996fa23ac03d6ae +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: 92430be71ecc40e18bbbb80d5576c613 +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 387d83db81024f65aa9a890c2d07874a +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: d8e2280a75a74916a1630afaa2fe2ae3 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: f1c1340f9745458980e0fbd641738687 +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 5424e5472c3d466fa2a3d2022c6cb475 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: 12f57b2ba76b492abe1816e06bfb1417 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: e1f657a46ce94a0d83671540e2cc2dab +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a5eacdbc9aa142c890b177869da4143d +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: e3bdaceae8784ab0807b2cf356a98580 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: ed521ac365db4a6ba5a1051fbaa2932e +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 67573252cc064b27ab13eebc468ac58a +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 73e68b3af9cf41338d843c0c40e50cdc +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: a999b1acda2641598086648c64aa3831 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: f8c12a58cb0b46a488823c6ae95f25ea +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: f25a63e0926d4932bbe64b2e4bdabf9e +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: d718630a296545f3a989c8c71e9ddc77 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 9a97acd430064710bcdf76edbd9f711c +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: 48deb71f361a43e48a56ed483075bca8 +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 716b56506ca7470299899c5d820a9ea2 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: e3ecac0a8e604f2b98a2a12b0579990a +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 007a345b4bad49cf996c4301b8386473 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: efb5fd14988c4e2a8f834ee5369d4102 +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: 276f688ba7cc471a842f085ca852b1d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 8b70a1ad70514039b97164fa630c12e4 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 2f28ab412d2843ffa5f14acdc01fc732 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: cbec9277b5004e50af2728cbda0df740 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: e259f55f8000479bbd8009e25cf0ca6c +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 8210b36347a749889450529ecdf4ff0e +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 23088850ad02459696f6bbd385109aac +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: f02257a822ad46ac93c5981531cc85d5 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: d289541e460147aa933f7878996f8649 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: f495da32f05a4a5ba9539be0a54c1a59 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: bdb4c68a175047ddbe141ca24960127f +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 97b61352363f47cb890e8937c5613fa3 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: 0bc424ef2ca346099f29b937379908a0 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 29b73e1dd72744f68377f0a38c10f062 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 38a2afaf4a6c4d04909af22c93f2808d +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: cd74f34b21af4de9be96fd897efc469b +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: f12e371f3f1a4b0cb2cff9800352d48c +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 8f0e8f050e334ac08334e9215e1dcf61 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 7a6be0005a6441feb67f036d005d7885 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 06635145b441418aaae84dc804f3d6ac +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 04eaf1f7c630450db318dcd8b7626e15 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: fd4579a3c9844492b314b5c3c1775fc7 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: e024bcb70e04412e90e1838426d1b69a +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: a3db21c0b3114802a8a5b610e252ef13 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 0f5bc8520d6a4dafa37c65343da9702a +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 5cb830da47464a8b9c3950983fa4d56f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: a2ce43b391864e8bbde16328cc19b32b +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 56ee4dcfff6141d5bef80eb96559876d +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 96671c56523c4ea9992fb5dfcfa6490e +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: bcc6246742cb46bfb185e415c4a3431a +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 86dce36de687449c88fb5eb9d64eb045 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 7dc630ea86464b1dba3a4e5079260b3b +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: 651e032007ea4a119d20c820bb61f86b +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 0b056dde9e87428996e47870b12119da +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 628124a1670b4b058bb0fb6e495a099c +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: ec2adb3912bc46e28891229e9e0d9a1c +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: a519be60726a44af9941fdce04735353 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: cb8fc8c4c79e467eac5fab4ca685201e +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: a26cc105716f47cb807174c9003153b0 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: cc159dd5fe5748caac838862f5b8c4d1 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 6812698e9ad84d3385de5e88e9dde0b3 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: d1f02be278754267893dfce5a940997d +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: 75d59e395c66416cae9b352db5081516 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 874c6f19abbf45d7ab7d30a378c4048d +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: dea0d4b681f94e73b13965dcfe75cf7d +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: 750474486a84482292eeba45f118287f +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 1eb0e39bb6d04b8cab300f44a79f3add +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 4b2ab812f62c4f949dd25c8527f2411c +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 2c3b884cb1c54521900cc90782e8a58d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: a1073b6306044dffb414319ae01f68bb +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: 9a1d92334685449386dfa3b3a899ed48 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: fb623af4c480411b8fde28d01c981411 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: e98e165f6bba40809c90473d72f9d592 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 5565c1b2d8a349169a305a9b26b4574d +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: 88160cef4cfa4add9020aa89511a5749 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 730ba1434a1445ae847ec6153b6a3b72 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: a25d0b1e13324b40a6b8fcd227948c4f +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: d661df070e3040869da412d07a71f716 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: a11585474d3849cca5467512ed964743 +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 2682f9ca8e604a0c9986f7746fdec960 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 22447a560f6f4317bf67bd7c4336126c +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 52703d6b7f914097934bfad13663abeb +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 5e1c79df657d4a6e84e055dd6b300a5d +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 329d2809dfae4f90bc638f5f03a47ee3 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 9647019d8c37466886e7aab6f176634d +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: cc067051f22f433bbece08f60933e002 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: dbfe2c1123144316aa026374b0f353d3 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: 074cf5d912854d8c864607cc24b15302 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: b54240bb94f746bba7511633aa969db0 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 8b70a072aa87414c88e89a3e19af0a51 +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: eea20f89c45f424a888178df53713b28 +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7647e0229a924f988cf02b7812a55c06 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 9d663249666045618a0d3acddb85a9a9 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: dbf6153cd02542a6a01c172803122b7f +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: b6250cf6fa8a4a0c94b33302e0decca5 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: fa6ca3bbc6784380a03a950a6f49a180 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: b92b516e537a4773ad67b4af586e7a25 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: 467a701228504d06b971b79a59c69064 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: 2634f989eb304009a8568d70ed42786c +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: fbe0c65b444441f785d0054176d036a6 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 9a710602e00c4934ae3a3b471aa68458 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: 21b5be7270a14f0987240c81d1ec879b +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: cfe9d8241fe84bd5b74042a5625d933f +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 764d933cc4da446abd8dd8f913f05dac +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: c93efc6d4e004859981ee7f5fa28ed03 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: 546601da44cb49bd9611b1c85807fd90 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: e07f33d01b804663a25ffb08aad74821 +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: 7a644506619a4f08958ec7d4540cd557 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: b5195b7d8eaa419fb2b90cb33a57783a +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: 2713594c937d4c528fc8d04d9e9819ed +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: cf94c1424fc2413c85647fd1ee73d951 +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: dc0452107c604e29bdf32bb289fe5db8 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 483181f498fc4d968b5fe6ef427709f7 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 7487485d6aa4458089a4b4bdf107ea64 +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 93188ed43ee949cc98b3ea679ce14feb +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 24aca0bea4d94e3593b844cf0586cffe +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 9c56528acd5f49deb139e034dfbfac7c +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: a2dd833fdca4443181648e41051a5232 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: 7e40cc9f9e1341c195e843c009575b94 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: def35d6021394def80a53ae49a2cdbde +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: c84d4450bc6a475dbf34e0b22cea9130 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: cca9665f6daa44b49233baf34ab9fcc7 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: 547edbf5fa424b8286cc21674ff159b0 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 7ca248888b9d484cb544cd76ba538662 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: ae6b240718104380b08db5552d7355ea +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: e5a8b7f84be64020b191099f3fad30ed +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 12a06d8358534102b202965d4258c18e +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: b7f93705e5b8416696be01850072e8c0 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: e87045829b344089ab59dc27063ddd7a +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: 42ef2f145b824d69b63abc1da175c216 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: c61cedf543664d388183e04b3939cc39 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: 9e39e3f1501c4fcaab3e8962e090f6be +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: 03e2f767c4da461982fc3c0f3ba94762 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 3bea5822b8694e2aa32c446e1c54a045 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: 0d498cd4caf54c15891ca1afe58e2727 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: b2d75045e02741b4850f5ff1243f7858 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: 5fa79c62049a447c8328ebf9db54ebf4 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: d947c54933d64aad90df392a1cedd63f +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 651d35997332404186aa6d5711da4a3d +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: b662c1a5a4424c8d8350a806356acc61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 04d6babfd87343d7a5f13867ea02b65f +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 2eaacf1a90204a2b9bd621344560f2a1 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: e3a7182f00f440b8b5461da91194a64b +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: b5338f39e8c74ff28e139da68089a742 +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: f6d92156d67c4a339bcfd194cff897df +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: d80ab383eec9402faba997b548fe42eb +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: 49217c02f58c43ff9ec00f10da8d4e84 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 8dbd56473f8c40c0bb12a48be06117e3 +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 78d7f3ede2c746d482042adef050b2c4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: cbbf93c70fe04ba7932ba25758ddc611 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: cfa1c1fde4454df283f87cc54a9c59ec +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 1a8be2950cbb475bbb2617e005f0fac9 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: 5d83c56102e141cc978500f678dd0c1c +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: cda73485875d4c8e9464679a20558616 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 98cae24919b74c088a5d89706aec581b +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: b4b0940b4b5743c09637b36b964202d0 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 9ca3554d771d45998e88aaede525b227 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 3fca839cede94cfd8e4f605c73ba699d +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: 3ded0f125249485c921994b6e6b93ac9 +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 53ece35d309a4c8d99f1efb2122a7092 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 87bafb845c714b109874f6137b84462d +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: fcd05b1ef31a4046946a2399c7fc5575 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: 859368c1f25c4a4aad57abfd046c63f5 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" diff --git a/locales/pt_PT/LC_MESSAGES/sphinx.po b/locales/pt_PT/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..cbb0bd34 --- /dev/null +++ b/locales/pt_PT/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: pt_PT\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "" diff --git a/locales/pt_PT/LC_MESSAGES/user_guide.po b/locales/pt_PT/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..53e29057 --- /dev/null +++ b/locales/pt_PT/LC_MESSAGES/user_guide.po @@ -0,0 +1,3250 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: 2023-04-03 19:41+0000\n" +"Last-Translator: ssantos \n" +"Language-Team: Portuguese (Portugal) \n" +"Language: pt_PT\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.17-dev\n" + +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "Licenças" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "Material Instrucional" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" +"Todo o material instrucional do projeto Common Workflow Language e " +"alterações na estrutura também são disponibilizados sob a [licença Creative " +"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " +"humanos de (e não um substituto para) o [texto legal completo da licença CC " +"BY 4.0][cc-by-legal]." + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "Tem o direito de:" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" +"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " +"formato" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "para qualquer fim, mesmo que comercial." + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" +"O licenciante não pode revogar estes direitos desde que você respeite os " +"termos da licença:" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" +"**Sem restrições adicionais**---Não pode aplicar termos jurídicos ou medidas " +"de caráter tecnológico que restrinjam legalmente outros de fazerem algo que " +"a licença permita. Com o entendimento de que:" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" +"Não tem de cumprir com os termos da licença relativamente a elementos do " +"material que estejam no domínio público ou cuja utilização seja permitida " +"por uma exceção ou limitação que seja aplicável." + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" +"Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " +"autorizações necessárias para o uso pretendido. Por exemplo, outros " +"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " +"podem limitar o uso do material." + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "Software" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" +"Salvo indicação em contrário, os programas de exemplo e outro software " +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a [" +"licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" +"A menos que exigido pela lei aplicável ou acordado por escrito, o software " +"distribuído sob a Licença é distribuído \"COMO ESTÁ\", SEM GARANTIAS OU " +"CONDIÇÕES DE QUALQUER TIPO, expressas ou implícitas. Consulte a Licença para " +"obter o texto específico sobre as permissões e limitações sob a Licença." + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" +"CWL é uma maneira de descrever ferramentas de linha de comando e de conectá-" +"las formando workflows. Como a CWL é uma especificação e não um software, " +"ferramentas e workflows descritos com a CWL são portáveis entre uma " +"variedade de plataformas que suportam o padrão CWL." + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "Esta página foi movida" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" +"O conteúdo desta página está desatualizado e foi mantido para preservar os " +"links do antigo Guia do Utilizador. Por favor, use o novo [Índice](index.md" +"#table-of-contents) para navegar o Guia do Utilizador." + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "Perguntas Frequentes (FAQ)" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "Usando `evalFrom` para Tipos Diferentes de \"`File`\"" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "Renomear um Arquivo de Entrada" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" +"Este exemplo demonstra como mudar o nome de um arquivo de entrada como parte " +"da descrição da ferramenta. Isso pode ser útil quando você tem arquivos " +"produzidos em outro passo de um workflow, mas prefere não utilizar os nomes " +"dados por padrão quando estes arquivos foram criados." + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "Renomear um Arquivo de Saída" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" +"Este exemplo demonstra como escolher o nome para um arquivo de saída " +"diferente do nome padrão criado por uma ferramenta:" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "Como Fazer Referência a um Script Local" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "Há duas maneiras de fazer uma referência a um script local:" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" +"A primeira maneira é adicionando o arquivo que contém os seus scripts para a " +"variável de ambiente `PATH`. Desta maneira você pode executar o shell script " +"diretamente sem utilizar comandos via `sh` ou `bash`." + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "Comece adicionando a _shebang_ no topo do seu arquivo:" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" +"Em seguida faça o seu script executável com o comando `chmod +x scriptname." +"sh`" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" +"E finalmente, modifique o seu `PATH` para adicionar o diretório que contém o " +"seu script. (É boa prática usar `$HOME/bin` para scripts do utilizador " +"local)." + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" +"Agora você pode utilizar `baseCommand: scriptname.sh` para rodar o script " +"diretamente." + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" +"Depois quando você quiser compartilhar o seu trabalho, é possível utilizar " +"um container de software com ferramentas como Docker." + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "O segundo método utiliza um input `type: File` diretamente no script:" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "Em CWL tudo deve ser declarado diretamente." + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "Definindo Bindings de Inputs utilizando `self` para Inputs Opcionais" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" +"No momento `cwltool` não funciona quando inputs opcionais não estão " +"presentes se o binding de input deles utilizar `self`. O exemplo abaixo " +"contém uma solução alternativa para este problema, até que haja uma solução " +"mais elegante para este problema." + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "Modelar um Parâmetro do tipo \"um-ou-o-outro\"" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" +"O exemplo abaixo demonstra como especificar diferentes strings que serão " +"adicionadas à linha de comando, dependendo do valor de um parâmetro Boolean." + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "Conectar um Único valor a um Input que Espera uma Lista daquele Tipo" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" +"Que significa \"criar uma lista com exatamente estes sources como elementos\"" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" +"Ou em outras palavras: se o parâmetro destino for do tipo `File[]` (uma " +"lista de `File`s) e a fonte é um único `File`, adicione então " +"`MultipleInputFeatureRequirement` ao `requirements` no nível do Workflow e " +"adicione `linkMerge: merge_nested` sob a entrada apropriada `in` ao step que " +"receberá o parâmetro (target)." + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "Inputs Opcionais 💯" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" +"Para fazer um parâmetro de entrada opcional, adicione um ponto de " +"interrogação à declaração do tipo." + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "Inputs Enum ⚜️" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" +"O tipo enum por ser utilizado em CWL para flags de linha de comando que " +"requerem um tipo de input específico como argumento. **Especificar null aqui " +"é tido como forma estendida. O resultado é o mesmo que o uso do ponto de " +"interrogação nos outros inputs.**" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "Inputs do tipo Record" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "Definindo Parâmetros Mutualmente Exclusivos" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "Utilizando Booleans" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "Estes são definidos através do campo padrão" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "Concatenando Strings em Inputs" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "O campo valueFrom deve ser utilizado ao invés do valor padrão." + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "Erros do `cwltool` devido a Nomes de Arquivos com Espaços" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" +"O `cwltool` não permite alguns caracteres em nomes de arquivos por padrão." + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" +"Por exemplo, o nome de arquivo `um espaco vai aqui.txt` inclui 3 espaços.." + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" +"Se você não tem opção e precisa utilizar estes caracteres apesar do risco, " +"você deve então passar `--relax-path-verificks` ao chamar o `cwltool`." + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" +"Erro de Referência em Parâmetro CWL devido a Hífen no Identificador de " +"Entrada" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "Se `cwltool --validate` valida com sucesso" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "Mas ao executar o workflow um erro como o seguinte aparece:" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "Este é o arquivo" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "O problema é causado pelo `-` (hífen)." + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "Para corrigir este erro, substitua o `-` (hífen) por `_` (sublinhado)" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" +"Se não for possível mudar o identificador do input, você pode reescrever " +"utilizando uma sintaxe alternativa para Referências de Parâmetros CWL:" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "Utilizar CWL e cwltool com Singularity" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "Depurar Expressões JavaScript" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "A Especificação CWL" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "Implementações" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "Saiba Mais" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "Versionamento Semântico - " + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" +"A página web da Especificação CWL: " + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" +"A especificação CWL atual no GitHub: {{ ''.format(cwl_version_text) }}" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" +"A lista de Implementações na página web da CWL: " + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "PROV-O: A Ontologia PROV - " + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "Introdução" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "Pré-requisitos" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "Implementações da CWL" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "Linux" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "macOS" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "Windows" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "Instalando `cwltool` com `pip` e `venv`." + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" +"Visite a [documentação](https://github.com/common-workflow-language/" +"cwltool#install) do `cwltool` para outras opções para instalar `cwltool` com " +"`apt` e `conda`." + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" +"Vamos usar uma simples descrição de ferramenta CWL `true.cwl` com `cwltool`." + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "`true.cwl`" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "Módulo Python cwl-runner" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "Executando `true.cwl` com `cwl-runner`." + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "Editor de Texto" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "Instalando `cwltool` com `pip`." + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "Executando \"Hello World\"" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "Executando `hello_world.cwl` com `cwltool`." + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" +"Pode utilizar este arquivo de Objetos de Inputs agora para executar o " +"workflow “Hello World”:" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "Passando um arquivo de Objeto de Inputs para o `cwltool`." + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "Continue lendo as secções seguintes deste Guia do Utilizador!" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" +"[Lista das Implementações da CWL](https://www.commonwl.org/implementations)." + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" +"A [organização`common-workflow-language`](https://github.com/common-workflow-" +"language) no GitHub." + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" +"[Common Workflow Language na Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" +"[YAML.org](http://yaml.org/) e [YAML at Wikipedia](https://en.wikipedia.org/" +"wiki/YAML)." + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" +"A {{'[Especificação CWL VERSION](https://www.commonwl.org/VERSION)'.replace(" +"'VERSION', cwl_version_text) }}." + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" +"[Workflow management system na Wikipedia](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" +"O conteúdo desta página está desatualizado mas foi mantido aqui para " +"preservar os links do antigo Guia do Utilizador. A informação desta página " +"foi migrada para a secção [FAQ](/faq.md) do novo guia do utilizador." + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "Argumentos e Parâmetros Adicionais" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "`arguments.cwl`" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "`arguments-job.yml`" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" +"Em seguida, crie um arquivo Java de exemplo para usar com a ferramenta de " +"linha de comando." + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" +"E agora execute `cwltool` utilizando a descrição de ferramenta e o objeto de " +"input na linha de comando:" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "Melhores Práticas" + +#: ../../src/topics/best-practices.md:3 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 4dee8504a8e5496081dadc386ab45540 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 674c238b25e240eda05e22e399f2f78f +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: b651f80f47b4442fbf29454a233697fc +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: ecf2b9c0b1664afe9c4e180610610021 +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: e24cb13d98014e558b6a6946758359e0 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: 928e3df7ca3e479ca6474a8e72cf36eb +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: d355f035676446c88b028f327aeb4829 +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 339b852df24242189d6efcd2898a3396 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: 3ef57e6862f240bebcf193a52397af0a +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: fae385da16aa443da996fa23ac03d6ae +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: 92430be71ecc40e18bbbb80d5576c613 +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 387d83db81024f65aa9a890c2d07874a +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: d8e2280a75a74916a1630afaa2fe2ae3 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: f1c1340f9745458980e0fbd641738687 +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 5424e5472c3d466fa2a3d2022c6cb475 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: 12f57b2ba76b492abe1816e06bfb1417 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: e1f657a46ce94a0d83671540e2cc2dab +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a5eacdbc9aa142c890b177869da4143d +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: e3bdaceae8784ab0807b2cf356a98580 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: ed521ac365db4a6ba5a1051fbaa2932e +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 67573252cc064b27ab13eebc468ac58a +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 73e68b3af9cf41338d843c0c40e50cdc +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: a999b1acda2641598086648c64aa3831 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: f8c12a58cb0b46a488823c6ae95f25ea +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: f25a63e0926d4932bbe64b2e4bdabf9e +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: d718630a296545f3a989c8c71e9ddc77 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 9a97acd430064710bcdf76edbd9f711c +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: 48deb71f361a43e48a56ed483075bca8 +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 716b56506ca7470299899c5d820a9ea2 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: e3ecac0a8e604f2b98a2a12b0579990a +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 007a345b4bad49cf996c4301b8386473 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: efb5fd14988c4e2a8f834ee5369d4102 +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: 276f688ba7cc471a842f085ca852b1d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 8b70a1ad70514039b97164fa630c12e4 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 2f28ab412d2843ffa5f14acdc01fc732 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: cbec9277b5004e50af2728cbda0df740 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: e259f55f8000479bbd8009e25cf0ca6c +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 8210b36347a749889450529ecdf4ff0e +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 23088850ad02459696f6bbd385109aac +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: f02257a822ad46ac93c5981531cc85d5 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: d289541e460147aa933f7878996f8649 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: f495da32f05a4a5ba9539be0a54c1a59 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: bdb4c68a175047ddbe141ca24960127f +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 97b61352363f47cb890e8937c5613fa3 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: 0bc424ef2ca346099f29b937379908a0 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 29b73e1dd72744f68377f0a38c10f062 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 38a2afaf4a6c4d04909af22c93f2808d +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: cd74f34b21af4de9be96fd897efc469b +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: f12e371f3f1a4b0cb2cff9800352d48c +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 8f0e8f050e334ac08334e9215e1dcf61 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 7a6be0005a6441feb67f036d005d7885 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 06635145b441418aaae84dc804f3d6ac +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 04eaf1f7c630450db318dcd8b7626e15 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: fd4579a3c9844492b314b5c3c1775fc7 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: e024bcb70e04412e90e1838426d1b69a +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: a3db21c0b3114802a8a5b610e252ef13 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 0f5bc8520d6a4dafa37c65343da9702a +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 5cb830da47464a8b9c3950983fa4d56f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: a2ce43b391864e8bbde16328cc19b32b +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "`sample.yml`" + +#: ../../src/topics/file-formats.md:45 +#: 56ee4dcfff6141d5bef80eb96559876d +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 96671c56523c4ea9992fb5dfcfa6490e +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: bcc6246742cb46bfb185e415c4a3431a +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 86dce36de687449c88fb5eb9d64eb045 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 7dc630ea86464b1dba3a4e5079260b3b +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: 651e032007ea4a119d20c820bb61f86b +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" +"Em sequência, cria um arquivo chamado whale.txt utilizando [touch] digitando " +"`touch whale.txt` na linha de comando." + +#: ../../src/topics/inputs.md:53 +#: 0b056dde9e87428996e47870b12119da +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 628124a1670b4b058bb0fb6e495a099c +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: ec2adb3912bc46e28891229e9e0d9a1c +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: a519be60726a44af9941fdce04735353 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: cb8fc8c4c79e467eac5fab4ca685201e +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: a26cc105716f47cb807174c9003153b0 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: cc159dd5fe5748caac838862f5b8c4d1 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 6812698e9ad84d3385de5e88e9dde0b3 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: d1f02be278754267893dfce5a940997d +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" +"Agora chame o `cwltool` passando a descrição da ferramenta e o objeto de " +"entrada na linha de comando:" + +#: ../../src/topics/inputs.md:178 +#: 75d59e395c66416cae9b352db5081516 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 874c6f19abbf45d7ab7d30a378c4048d +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: dea0d4b681f94e73b13965dcfe75cf7d +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: 750474486a84482292eeba45f118287f +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 1eb0e39bb6d04b8cab300f44a79f3add +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 4b2ab812f62c4f949dd25c8527f2411c +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 2c3b884cb1c54521900cc90782e8a58d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: a1073b6306044dffb414319ae01f68bb +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "`exclusive-parameter-expressions.cwl`" + +#: ../../src/topics/inputs.md:271 +#: 9a1d92334685449386dfa3b3a899ed48 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: fb623af4c480411b8fde28d01c981411 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: e98e165f6bba40809c90473d72f9d592 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 5565c1b2d8a349169a305a9b26b4574d +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "`operations.cwl`" + +#: ../../src/topics/operations.md:16 +#: 88160cef4cfa4add9020aa89511a5749 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 730ba1434a1445ae847ec6153b6a3b72 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: a25d0b1e13324b40a6b8fcd227948c4f +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: d661df070e3040869da412d07a71f716 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: a11585474d3849cca5467512ed964743 +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 2682f9ca8e604a0c9986f7746fdec960 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 22447a560f6f4317bf67bd7c4336126c +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "Agora, crie um arquivo tar para o exemplo." + +#: ../../src/topics/outputs.md:45 +#: 52703d6b7f914097934bfad13663abeb +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 5e1c79df657d4a6e84e055dd6b300a5d +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 329d2809dfae4f90bc638f5f03a47ee3 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 9647019d8c37466886e7aab6f176634d +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: cc067051f22f433bbece08f60933e002 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: dbfe2c1123144316aa026374b0f353d3 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "`tar-param-job.yml`" + +#: ../../src/topics/parameter-references.md:25 +#: 074cf5d912854d8c864607cc24b15302 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: b54240bb94f746bba7511633aa969db0 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 8b70a072aa87414c88e89a3e19af0a51 +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: eea20f89c45f424a888178df53713b28 +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7647e0229a924f988cf02b7812a55c06 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 9d663249666045618a0d3acddb85a9a9 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: dbf6153cd02542a6a01c172803122b7f +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: b6250cf6fa8a4a0c94b33302e0decca5 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: fa6ca3bbc6784380a03a950a6f49a180 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: b92b516e537a4773ad67b4af586e7a25 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: 467a701228504d06b971b79a59c69064 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" +"De [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) e [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" + +#: ../../src/topics/parameter-references.md:92 +#: 2634f989eb304009a8568d70ed42786c +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "`linkfile.cwl`" + +#: ../../src/topics/troubleshooting.md:1 +#: 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "Solucionando Problemas" + +#: ../../src/topics/troubleshooting.md:3 +#: fbe0c65b444441f785d0054176d036a6 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 9a710602e00c4934ae3a3b471aa68458 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: 21b5be7270a14f0987240c81d1ec879b +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: cfe9d8241fe84bd5b74042a5625d933f +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 764d933cc4da446abd8dd8f913f05dac +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: c93efc6d4e004859981ee7f5fa28ed03 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: 546601da44cb49bd9611b1c85807fd90 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "Utilizando Containers" + +#: ../../src/topics/using-containers.md:3 +#: 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: e07f33d01b804663a25ffb08aad74821 +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: 7a644506619a4f08958ec7d4540cd557 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: b5195b7d8eaa419fb2b90cb33a57783a +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: 2713594c937d4c528fc8d04d9e9819ed +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: cf94c1424fc2413c85647fd1ee73d951 +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: dc0452107c604e29bdf32bb289fe5db8 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 483181f498fc4d968b5fe6ef427709f7 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 7487485d6aa4458089a4b4bdf107ea64 +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 93188ed43ee949cc98b3ea679ce14feb +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 24aca0bea4d94e3593b844cf0586cffe +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 9c56528acd5f49deb139e034dfbfac7c +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: a2dd833fdca4443181648e41051a5232 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: 7e40cc9f9e1341c195e843c009575b94 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "`1st-workflow-job.yml`" + +#: ../../src/topics/workflows.md:191 +#: 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: def35d6021394def80a53ae49a2cdbde +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: c84d4450bc6a475dbf34e0b22cea9130 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: cca9665f6daa44b49233baf34ab9fcc7 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: 547edbf5fa424b8286cc21674ff159b0 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 7ca248888b9d484cb544cd76ba538662 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: ae6b240718104380b08db5552d7355ea +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: e5a8b7f84be64020b191099f3fad30ed +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 12a06d8358534102b202965d4258c18e +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "`nestedworkflows.cwl`" + +#: ../../src/topics/workflows.md:309 +#: b7f93705e5b8416696be01850072e8c0 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: e87045829b344089ab59dc27063ddd7a +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: 42ef2f145b824d69b63abc1da175c216 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: c61cedf543664d388183e04b3939cc39 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: 9e39e3f1501c4fcaab3e8962e090f6be +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: 03e2f767c4da461982fc3c0f3ba94762 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 3bea5822b8694e2aa32c446e1c54a045 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: 0d498cd4caf54c15891ca1afe58e2727 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: b2d75045e02741b4850f5ff1243f7858 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: 5fa79c62049a447c8328ebf9db54ebf4 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "`scatter-workflow.cwl`" + +#: ../../src/topics/workflows.md:421 +#: 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: d947c54933d64aad90df392a1cedd63f +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 651d35997332404186aa6d5711da4a3d +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "Usando o seguinte arquivo de entrada:" + +#: ../../src/topics/workflows.md:452 +#: 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: b662c1a5a4424c8d8350a806356acc61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 04d6babfd87343d7a5f13867ea02b65f +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 2eaacf1a90204a2b9bd621344560f2a1 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "`wc-tool.cwl`" + +#: ../../src/topics/workflows.md:489 +#: e3a7182f00f440b8b5461da91194a64b +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: b5338f39e8c74ff28e139da68089a742 +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: f6d92156d67c4a339bcfd194cff897df +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "`scatter-nested-workflow.cwl`" + +#: ../../src/topics/workflows.md:519 +#: d80ab383eec9402faba997b548fe42eb +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "Workflows Condicionais" + +#: ../../src/topics/workflows.md:524 +#: 49217c02f58c43ff9ec00f10da8d4e84 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 8dbd56473f8c40c0bb12a48be06117e3 +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 78d7f3ede2c746d482042adef050b2c4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: cbbf93c70fe04ba7932ba25758ddc611 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: cfa1c1fde4454df283f87cc54a9c59ec +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 1a8be2950cbb475bbb2617e005f0fac9 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "Guia de YAML" + +#: ../../src/topics/yaml-guide.md:6 +#: 5d83c56102e141cc978500f678dd0c1c +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "Conteúdo" + +#: ../../src/topics/yaml-guide.md:18 +#: 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "[Estilo JSON](#json-style)" + +#: ../../src/topics/yaml-guide.md:24 +#: 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "Pares de Chave-Valor" + +#: ../../src/topics/yaml-guide.md:26 +#: cda73485875d4c8e9464679a20558616 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" +"Em princípio, um arquivo escrito em YAML consiste de uma série de _pares de " +"chave-valor`. Cada par é escrito como `chave: valor`, onde o espaço em " +"branco entre o `:` é um requisito. Os nomes das chaves em arquivos CWL não " +"devem conter espaços em branco - [_camelCase_][camelCase] é usado para " +"valores de chaves que contém múltiplas palavras e possuem um valor especial " +"na especificação CWL, caso contrário os valores dos nomes de chaves aparecem " +"sublinhados. For exemplo:" + +#: ../../src/topics/yaml-guide.md:42 +#: 98cae24919b74c088a5d89706aec581b +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" +"O YAML acima define quatro chaves - `first_name`, `last_name`, `age_years`, " +"e `home` - com quatro valores respectivos. Os valores podem ser strings de " +"caracteres, númericos (integer, floating point, ou representação científica)" +", Boolean (`true` ou `false`), ou valores mais complexos com tipos aninhados " +"(veja abaixo)." + +#: ../../src/topics/yaml-guide.md:51 +#: b4b0940b4b5743c09637b36b964202d0 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 9ca3554d771d45998e88aaede525b227 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 3fca839cede94cfd8e4f605c73ba699d +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "Dicionários" + +#: ../../src/topics/yaml-guide.md:81 +#: 3ded0f125249485c921994b6e6b93ac9 +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 53ece35d309a4c8d99f1efb2122a7092 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "Estilo JSON" + +#: ../../src/topics/yaml-guide.md:169 +#: 87bafb845c714b109874f6137b84462d +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "e:" + +#: ../../src/topics/yaml-guide.md:184 +#: fcd05b1ef31a4046946a2399c7fc5575 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "Referencia" + +#: ../../src/topics/yaml-guide.md:196 +#: 859368c1f25c4a4aad57abfd046c63f5 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "Tutoriais" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "Tutoriais para Iniciantes" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" diff --git a/locales/zh_Hans/LC_MESSAGES/sphinx.po b/locales/zh_Hans/LC_MESSAGES/sphinx.po index e402725a..3db68528 100644 --- a/locales/zh_Hans/LC_MESSAGES/sphinx.po +++ b/locales/zh_Hans/LC_MESSAGES/sphinx.po @@ -8,8 +8,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-02-19 06:59+0000\n" -"Last-Translator: Rhea-Xiao \n" +"PO-Revision-Date: 2023-04-26 11:48+0000\n" +"Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified) \n" "Language: zh_Hans\n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 4.16-dev\n" +"X-Generator: Weblate 4.18-dev\n" #: ../../src/_templates/sidebar-nav-bs.html:1 #: d65b012160e9455eb4d2628279fffc42 @@ -27,4 +27,4 @@ msgstr "主导航" #: ../../src/_templates/sidebar-nav-bs.html:3 #: 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" -msgstr "部分导航" +msgstr "章节导航" diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 2955f3b6..c59732eb 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -8,8 +8,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-03-01 05:35+0000\n" -"Last-Translator: Rhea-Xiao \n" +"PO-Revision-Date: 2023-04-26 11:48+0000\n" +"Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified) \n" "Language: zh_Hans\n" @@ -17,78 +17,79 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 4.16-rc\n" +"X-Generator: Weblate 4.18-dev\n" #: ../../LICENSE.md:2 #: 4e203044f0464fd5a3256430391dde12 msgid "Licenses" -msgstr "许可证" +msgstr "许可协议" #: ../../LICENSE.md:4 #: 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" -msgstr "指导材料" +msgstr "指南资料" #: ../../LICENSE.md:6 #: 747f9dd48bc54f44adcd8b18c57f4d9d msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." msgstr "" -"所有通用工作流语言项目的指导材料及结构变更信息均可在[知识共享署名许可][cc-by-" -"human]下查阅。以下是[CC BY 4.0许可的完整法律文本][cc-by-" -"legal]的可读摘要（不能替代原文本）。" +"通用工作流语言项目的所有指南资料，以及对其结构的修改，均可在遵照[" +"知识共享署名公共许可协议 (Creative Commons Attribution license)][cc-by-" +"human]的前提下获得授权使用。以下是[CC BY 4.0许可完整法律条文][cc-by-" +"legal]的可读摘要（不能替代原条文）。" #: ../../LICENSE.md:12 #: 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" -msgstr "您可随时/自由执行以下操作：" +msgstr "您可以自由地：" #: ../../LICENSE.md:14 #: 466be810dd8d4a838e0edb5869f2c4eb msgid "to **Share**---copy and redistribute the material in any medium or format" -msgstr "**共享**——通过任何媒介或以任何格式复制和重新分发材料" +msgstr "**共享**——通过任何媒介、以任意格式复制和重新分发本作品" #: ../../LICENSE.md:15 #: 18a3a0aec35743848c97bc178f9c94ff msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "**改编**——调整、大幅修改及在原有材料基础上编写新材料" +msgstr "**演绎**——修改、转换或以本作品为基础进行创作" #: ../../LICENSE.md:17 #: b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." -msgstr "出于任何目的，甚至是商业目的。" +msgstr "在任何用途下，甚至商业目的。" #: ../../LICENSE.md:19 #: 6021e65292a149d5b15e14491f3eb05e msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" -msgstr "只要遵守以下许可条款，许可方便无法阻止您的自由操作：" +msgstr "只要你遵守许可协议条款，许可人就无法收回你的这些权利：" #: ../../LICENSE.md:24 #: 8fb7a2946c384364814c6ec3910997d3 msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" -"**归属**——您必须进行适当说明（提及您的作品源自版权属于 Common Workflow " -"Language 项目的作品，更明确地说，源自官网 https://www.commonwl.org/" -"），并提供[许可链接][cc-by-human]。如有改动，也请指明。您可通过任何合理的方式" -"进行操作，但不能以任何方式暗示许可方支持您/您的使用。" +"**署名**——您必须给出适当的署名，即声明您作品之原始版本的版权为 Common " +"Workflow Language Project 所有 (\"Copyright © the Common Workflow Language " +"project\")。如条件允许，您应提供 https://www.commonwl.org/ 和[许可协议][cc-" +"by-human]的链接，同时标明是否对原始作品作了修改。您可以用任何合理的方式来署名" +"，但是不得以任何方式暗示许可人为您或您的使用背书。" #: ../../LICENSE.md:32 #: 8161753b7526445db319210044566200 msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" -msgstr "**无额外限制**——您可能未运用法律条款，或未采用可合法限制他人执行许可操作的技" -"术手段。这点可以理解为：" +msgstr "**没有附加限制**——您不得适用法律术语或者技术措施从而限制其他人做许可协议允许" +"的事情。并且您理解：" #: ../../LICENSE.md:36 #: 15314ba527864eaa834cf1185cfcc4e3 msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." -msgstr "若材料内容衍自公有领域，或所采用部分为适用例外或限制所许可，您无需遵循许可条" -"款。" +msgstr "您不必因为公共领域的作品要素而遵守许可协议，或者您的使用被可适用的例外或限制" +"所允许。" #: ../../LICENSE.md:39 #: b351ddf9847d48b1a2a87fc78eaba4d2 msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." -msgstr "" -"未提供任何担保。许可证可能未赋予所有必要的许可，无法满足您出于特定用途使用材" -"料的需求。比如，出版权、隐私权或道德权等其他权利可能限制您使用材料的方式。" +msgstr "不提供担保。许可协议可能不会给与您意图使用的所必须的所有许可。例如，其他权利" +"比如形象权、隐私权或人格权可能限制您如何使用作品。" #: ../../LICENSE.md:44 #: a091addc2dea4830a06bb72ead56c5ea @@ -99,17 +100,17 @@ msgstr "软件" #: 84b2c685bbab48449fdc72d2a1e42bf4 msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" -"除非其他地方已注明，所有Common Workflow " -"Language项目提供的示例程序及其他软件均可从 [OSI][osi]-已批准 [Apache 2.0 " -"license][apache-2.0-license]下方获取。" +"除非另有注明，Common Workflow Language project " +"提供的示例程序及其他软件均可在遵照[OSI][osi]所批准的[Apache 2.0 " +"许可协议][apache-2.0-license]之前提下获取并使用。" #: ../../LICENSE.md:51 #: 0f68eafafaef4b54accba7e13bfaa702 msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" -"除非受适用法律要求或者书面同意，软件均根据在\"AS IS\" 基础上分发的许可证进行" -"发布，不提供任何形式的担保或条件，明示或默示。请查阅许可证，了解有关许可项下" -"管理许可和限制的特定语言。" +"除非受适用法律要求或者经书面许可，据本许可协议发行的软件均为“依照其原样”发行" +"，不存在任何类型的、无论是明文还是隐含的担保或合约条款。请查阅许可协议有关本" +"许可协议下授权行为和责任免除的具体条文。" #: ../../src/_includes/what-is-cwl.md:1 #: ../../src/_includes/what-is-cwl.md:2 @@ -118,28 +119,28 @@ msgstr "" #: d6ccd4b546254f56a597d67dd4fdc5d6 msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." msgstr "" -"CWL是一种描述命令行工具的方式，并连接这些工具以创建工作流。由于CWL是一种规范" -"，而不是一个具体的软件，使用CWL描述的工具和工作流可在支持CWL标准的各种平台上" -"移植。" +"CWL 的作用在于描述各种命令行工具，并且将它们连接起来，以创建工作流 " +"(workflow)。CWL 是一种规范，而非某种特定的软件。因此，由 CWL " +"描述的工具和工作流能够移植到支持 CWL 标准的多种平台。" #: ../../src/episodes.md:5 #: ../../src/setup.md:5 #: 0d3267f84f4e4aedb1e9fce00b4ea4bc #: 436cfca6f857469bbff7c652df32160f msgid "This page has moved" -msgstr "本页已被移除" +msgstr "此页面已转移" #: ../../src/episodes.md:9 #: cc11f5d29206492d9f2f0922882b6159 msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." msgstr "" -"此页面已过时，保留在此以保留旧用户指南链接，请使用新链接 [内容目录](index.md" -"#table-of-contents)浏览《用户指南》。" +"此页面已过时，保留在此仅用于留存旧版《用户指南》的链接。请使用[新版目录](inde" +"x.md#table-of-contents)浏览《用户指南》。" #: ../../src/faq.md:1 #: e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" -msgstr "最常见问题" +msgstr "常见问题" #: ../../src/faq.md:11 #: 61edb787dab04ca2ad3ed07616d878a0 @@ -149,25 +150,25 @@ msgstr "使用 `evalFrom` 的非“`File`”类型" #: ../../src/faq.md:41 #: d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" -msgstr "重命名“输入文件”" +msgstr "重命名输入文件" #: ../../src/faq.md:43 #: fc62427c0a004810b055dee90ec5e2d9 msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." msgstr "" -"本示例演示了如何更改“输入文件”名称，属于工具描述的内容。在打开创建于工作流其" -"他步骤的文件后，若您不想保留默认文件名（文件创建时的命名），此时该工具可为您" -"提供帮助。" +"本示例演示如何在工具描述 (tool description) 中更改输入文件名称。如果要使用工" +"作流中其它步骤产生的文件，但又不想使用这些文件创建时的默认名称，这时候更名操" +"作可以派上用场。" #: ../../src/faq.md:59 #: 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" -msgstr "重命名“输出文件”" +msgstr "重命名输出文件" #: ../../src/faq.md:61 #: bc7ad10c929848a3a9a240a3c501d299 msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" -msgstr "本示例演示了如何通过以下工具更改“输出文件”名称：" +msgstr "本示例演示更改输出文件名，不再使用某个工具赋予它的默认名称：" #: ../../src/faq.md:82 #: 7225a993d281421b95c8e3df2846a0e3 @@ -177,38 +178,40 @@ msgstr "引用本地脚本" #: ../../src/faq.md:84 #: 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" -msgstr "可通过两种方法引用本地脚本:" +msgstr "引用本地脚本有两种方法：" #: ../../src/faq.md:86 #: 450edf800a18423195bea4fe8793a2cb msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." -msgstr "第一种方法是将包含相关脚本的文件夹添加至`PATH`环境变量中，便可直接运行shell " -"脚本，无需使用`sh` 或 `bash`命令。" +msgstr "" +"第一种方法是将包含相关脚本的文件夹添加至`PATH`（路径）环境变量。" +"这样可以直接运行 shell 脚本，无需使用 `sh` 或 `bash` 命令。" #: ../../src/faq.md:89 #: 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "首先，在文件顶部添加一个 _shebang_ ：" +msgstr "首先，将 _\"shebang\"_ 添加为文件首行：" #: ../../src/faq.md:95 #: a7d84f740a714ec588503ee084fbbc34 msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" -msgstr "然后，使用 `chmod +x scriptname.sh`命令执行脚本" +msgstr "然后，用 `chmod +x scriptname.sh` 命令将脚本设为可执行。" #: ../../src/faq.md:97 #: 569d553abe85450c9d1c37456bf412f4 msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." -msgstr "最后，修改`PATH`以添加脚本所在目录。（最好使用 `$HOME/bin`存储脚本）。" +msgstr "最后，修改 `PATH`, 添加该脚本所在的目录。（把你自己的脚本保存在 `$HOME/bin` " +"目录下是较好的做法）。" #: ../../src/faq.md:104 #: 95f5dbbd21084a318413b9528fb867be msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "现在，您可使用 `baseCommand: scriptname.sh` 直接运行脚本。" +msgstr "这样，您就能用 `baseCommand: scriptname.sh` 直接运行脚本了。" #: ../../src/faq.md:113 #: 1b3cae80fa9a40ffb2259b8c1cd2b468 msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." -msgstr "若想稍后共享您的工作，您可将脚本放在一个Docker格式的软件容器中。" +msgstr "接下来若想共享您的工作，可将脚本存放在 Docker 格式的容器 (container) 中。" #: ../../src/faq.md:115 #: 8d86baa239364f799d4f9d5ea2b0e314 @@ -223,42 +226,42 @@ msgstr "在CWL中，一切都必须直接说明。" #: ../../src/faq.md:138 #: c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "为可选输入设置`self`的输入绑定" +msgstr "为可选输入项设置用到 `self` 变量的输入绑定" #: ../../src/faq.md:140 #: 2c38cc58cbb340bc935a5f00e96ba95c msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." -msgstr "现在，如果`cwltool`的输入绑定采用`self`，则无法处理缺少的可选输入。下方是一个" -"示例解决方法，等待更复杂的修复。" +msgstr "目前，如果缺失的可选输入项用到了 `self`, `cwltool` " +"将无法处理。在更高明的解决办法出现前，下面的例子可作为临时变通一用。" #: ../../src/faq.md:165 #: ce6db54bd0f54839a5beb948530a21f0 -#, fuzzy msgid "Model a \"one-or-the-other\" Parameter" -msgstr "对一个“非此即彼”参数进行建模" +msgstr "构建“非此即彼”参数的模型" #: ../../src/faq.md:167 #: d06cbf89028b4638ad54c2529bcbfa25 msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." -msgstr "下方示例演示了如何根据给定的布尔参数值，来指定要添加至命令行的不同字符串。" +msgstr "以下示例演示的，是根据某个布尔参数的取值，来指定添加到命令行的字符串。" #: ../../src/faq.md:188 #: d53fb28dcad04e7788cba9e280a2343c msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "将一个单独的值连接到一个期望有该类型数组的输入上" +msgstr "将某个元素值与期待该值类型的数组关联起来" #: ../../src/faq.md:190 #: d9e30e11533b4d53a144f5df7041268d msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -"使用 [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" -"Workflow.html#MultipleInputFeatureRequirement)及 [`linkMerge: " +"将 [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow" +".html#MultipleInputFeatureRequirement) 与 [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +" 联合使用" #: ../../src/faq.md:194 #: 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" -msgstr "" +msgstr "merge_nested" #: ../../src/faq.md:196 #: 937cb94a370640c788fbc3fe0b19f2e5 @@ -269,15 +272,16 @@ msgstr "输入必须是一个数组，每个输入链接只包含一个条目。 #: ../../src/faq.md:199 #: a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "这意味着“创建一个将这些源作为元素的列表”" +msgstr "这段话意思是，“创建一个列表，其中的元素正是这些源”" #: ../../src/faq.md:201 #: c8c235a9bf6240628f0b5493ffebf7e0 msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." msgstr "" -"换言之：如果目标类型为 `文件[]`（`File ` 的数组），并且源类型为单个 `文件 `，" -"则将 `MultipleInputFeatureRequirements` 添加到工作流级别 `requirements`，" -"并在目标步骤的相应 `` 条目下添加 `linkMerge： merge_nested`。" +"换言之：如果目标的类型是 `File[]`（元素类型为 `File ` 的数组），" +"而源是单独一个 `File`，那么将 `MultipleInputFeatureRequirements` " +"添加到工作流级别的 `requirements`，并在目标步骤相应的 `in` 条目下添加 " +"`linkMerge： merge_nested`。" #: ../../src/faq.md:229 #: 3da4dcb043eb4423a53a14182949d9cd @@ -287,12 +291,12 @@ msgstr "可选输入💯" #: ../../src/faq.md:231 #: 89b90d3bf1ea4ebd88482d435241fac5 msgid "To make an input parameter optional, add a question mark to the type declaration." -msgstr "若要使输入参数可选，请在类型声明中添加问号。" +msgstr "若要令某个输入参数为可选，请在其类型声明中添加问号。" #: ../../src/faq.md:247 #: a854006054ce4ffe94bbfa73bdbecbf2 msgid "" -msgstr "" +msgstr "" #: ../../src/faq.md:248 #: f80eb714e9df417fbba555b5dd5f4d8c @@ -303,8 +307,9 @@ msgstr "枚举输入 ⚜️" #: 10af80fa13af4158aec7060550485350 msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" msgstr "" -"对于需要特定输入作为参数的命令行标志，可以在 CWL 中声明枚举类型。**" -"在此处指定 null 称为长格式样式。它与其他输入上的问号执行相同的操作。**" +"某些命令行标志需要特定的参数值；对此，可以在 CWL 中声明枚举类型。**此处指定 " +"null, 这样的编程风格称为“长格式” (long " +"form)。它的作用与其他输入上的问号相同。**" #: ../../src/faq.md:267 #: ad1c26711ccd4efd8fdb25f9293d33fd @@ -319,109 +324,111 @@ msgstr "记录输入 📀" #: ../../src/faq.md:270 #: 52b8538177c64090af51f5f6a696c28c msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." -msgstr "对于 ** 互斥 ** 或 ** 依赖 ** 的命令行标志，可以定义特殊的记录类型。" -"您还可以在此处指定 null 以创建可选输入。" +msgstr "" +"如果部分命令行标志之间存在 ** 互斥 ** 或 ** 依赖 ** 的关系，" +"可以为其定义专门的记录类型 (record type)。此处也可以指定 null 创建可选输入。" #: ../../src/faq.md:322 #: f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" -msgstr "设置互斥参数" +msgstr "设定互斥参数" #: ../../src/faq.md:324 #: 7dc0540508084a3495ff3b2ac90fd323 msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." msgstr "" -"要在记录输入类型中正确设置字段，您需要将字典传递给输入，以正确设置参数。" -"此操作通过使用内联 JavaScript 并返回包含欲设置字段键的字典来完成。源字段应设" -"置为指示工作流中要充当值的输入。" +"为了正确地设置记录输入类型的字段，您需要将字典传递给输入，以正确设置参数。" +"具体方法是使用内联 JavaScript 返回以待设置字段为主键的字典。此处设定了 " +"source （源）字段，以指示工作流中要充当其键值的输入。" #: ../../src/faq.md:342 #: b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" -msgstr "设置布尔运算" +msgstr "设置布尔参数" #: ../../src/faq.md:344 #: cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" -msgstr "可使用默认字段进行设置" +msgstr "可使用 default（默认）字段设置" #: ../../src/faq.md:349 #: 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" -msgstr "在输入中连接字符串" +msgstr "在输入中串联字符串" #: ../../src/faq.md:351 #: 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." -msgstr "必须使用 valueFrom 字段，而不是默认值。" +msgstr "为此必须使用 valueFrom 而非 default 字段。" #: ../../src/faq.md:359 #: 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "由于文件名包含空格字符，显示`cwltool`错误" +msgstr "因文件名含有空格字符，`cwltool`报错" #: ../../src/faq.md:361 #: 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "在默认情况下，`cwltool`不允许在文件名中使用某些字符。" +msgstr "默认情况下，`cwltool`不允许某些字符出现在文件名中。" #: ../../src/faq.md:363 #: fdaec25650ab4b0fb1c527610e24ae5a msgid "For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "例如，文件名 `a space is here.txt`中包含了3个空格字符。" +msgstr "例如，文件名 `a space is here.txt`包含三个空格字符。" #: ../../src/faq.md:371 #: 182959fc9f4746d082994e07d05c8cde msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." -msgstr "如果无法避开这些危险的字符，您可以将 `--relax-path-checks`传送至 `cwltool`。" +msgstr "如果不能避开这些危险的字符，您可以为 `cwltool` 传递 `--relax-path-checks` " +"选项。" #: ../../src/faq.md:373 #: cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -msgstr "由于输入标识符中包含连字符，显示CWL参数引用错误" +msgstr "输入标识符中包含连字符导致 CWL 参数引用错误" #: ../../src/faq.md:375 #: 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" -msgstr "如`cwltool --validate`返回有效" +msgstr "如 `cwltool --validate` 返回 valid（验证通过）" #: ../../src/faq.md:384 #: 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" -msgstr "但执行时显示如下错误：" +msgstr "但执行时导致如下错误：" #: ../../src/faq.md:396 #: ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" -msgstr "文件在此处" +msgstr "该文件如下" #: ../../src/faq.md:410 #: e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." -msgstr "由`-`（连字符）引发的问题。" +msgstr "问题由 `-`（连字符）引发。" #: ../../src/faq.md:423 #: f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "要修复该错误，需将`-`（连字符）更改为`_` （下划线）" +msgstr "修复方法是将 `-`（连字符）更改为 `_`（下划线）" #: ../../src/faq.md:436 #: 190099a242a645c9b9f8bc3ce89d920d msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" -msgstr "如无法更改输入标识符，您可使用另一种CWL参数引用语法：" +msgstr "如果不能改动输入标识符，您可使用另一种 CWL 参数引用句法：" #: ../../src/faq.md:442 #: 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" -msgstr "将CWL和cwltool与Singularity一起使用" +msgstr "在 Singularity 下使用 CWL 和 cwltool" #: ../../src/faq.md:445 #: 1901c34201054a9cae199b0dbb8b945e msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." msgstr "" -"CWL标准是围绕（可选）Docker格式容器建立的，且引用运行程序和其他几种CWL执行均" -"支持通过Singularity引擎运行Docker格式容器，但直接指定一个Singularity " -"格式容器不属于CWL标准的内容。" +"CWL 标准是依照 Docker 容器格式建立的，其参考运行程序和另外几种 CWL " +"实现均支持适应 Singularity 引擎运行 Docker 格式容器。不过，直接指定 " +"Singularity 格式容器不在 CWL 标准之内。" #: ../../src/faq.md:450 #: 2d498470524d47f18f9936ace6acebb0 @@ -432,38 +439,37 @@ msgstr "调试 JavaScript 表达式" #: d7b044f5224a48eda09bc949cf645193 msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -"您可使用 --js-console option of cwltool，" -"或尝试为代码创建一个JavaScript 或 " -"TypeScript项目，并使用expressionLib进行加载， 比如： https://github.com/" +"您可使用 cwltool 的 --js-console 选项，" +"也可以考虑为您的代码创建 JavaScript 或 TypeScript 项目后使用 " +"expressionLib 加载， 比如： " +"template-tool.cwl#L6-L8\"> https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" #: ../../src/index.md:1 #: 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" -msgstr "《通用工作流语言用户指南》" +msgstr "通用工作流语言用户指南" #: ../../src/index.md:3 #: f8d6e4cd54cb42c88182a43171d97bab msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." msgstr "" -"本指南将指导您使用[Common Workflow Language](https://www.commonwl.org/) (CWL)" -" 开放标准编写工作流，并介绍了最新规范 {{ cwl_version }}。" +"这本指南将向您介绍使用 [Common Workflow Language](https://www.commonwl.org/) " +"(CWL) 开放标准编写工作流。本指南所描述的是 {{ cwl_version }} 版本最新规范。" #: ../../src/index.md:7 #: 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" -msgstr "欢迎投稿和反馈！" +msgstr "欢迎您的来稿和意见！" #: ../../src/index.md:9 #: 0f47157605a34ea58770ea898deebae4 msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" -"如您发现本指南存在内容缺失，或想提供其他反馈，请在[project repository for " -"this guide][repo]上提交问题。您也可单击页面右侧边栏的 “Edit this " -"page（编辑本页）”按钮，直接在Pull Request（拉取请求）中提交修改建议。" +"如您发现本指南的疏漏之处，或想提供其他反馈，请在[本指南项目源码库][repo]" +"上提交报告 (Issue). 您也可在任意页面点击右边栏的 “Edit this " +"page”（编辑本页）按钮，创建 Pull Request（拉取请求）直接提交修改建议。" #: ../../src/index.md:16 #: 6d269e8d70184034bcb56385a6ca198f @@ -474,15 +480,15 @@ msgstr "浏览《用户指南》" #: ed74c9a4b623464480e2c184668fcec0 msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." msgstr "" -"如您是初级用户，请查阅 [Introduction（介绍）](/introduction/index.md) " -"章节。而对于高级用户而言， [Topics主题](/topics/index." -"md)子章节则详细介绍了关于CWL的最常见主题。" +"如您是新用户，请从 [《入门》](/introduction/index.md) " +"章节出发。而对于进阶用户而言， [《主题》](/topics/index.md)" +"部分各小节涵盖了关于 CWL 最常见话题的详细信息。" #: ../../src/index.md:23 #: cfa67cf5521b414da6f7d34cbed283f7 msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." -msgstr "目录显示在菜单顶部和左侧边栏，也出现在本页的下方（但也附带子章节的链接）。每" -"页所在章节的链接显示在右侧边栏，而搜索窗口则显示在左侧边栏。" +msgstr "目录显示在顶部菜单和左侧边栏，本页更下方也有带小节链接的目录。右侧边栏有当前" +"单页分节链接，搜索功能在左侧边栏。" #: ../../src/index.md:28 #: ee6b82bd86264e4bb1e8e4065b1e6b9c @@ -498,36 +504,36 @@ msgstr "基本概念" #: ac62d326a68145b695e46b714d4e8156 msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." msgstr "" -"本章节介绍了一些基本概念，以帮助用户更顺利地开始使用通用工作流语言（CWL）工作" -"。我们相信读者已经非常熟悉工作流管理工具YAML，且能熟练地按照命令行说明进行操" -"作。用户指南另一章节也介绍了相同的概念，但内容更为详细。如果您已经十分熟悉CWL" -"或正在寻找更高级的内容，可能需要跳过本章节。" +"本章节介绍用户开始运用通用工作流语言（CWL）所需的基本概念。" +"读者应了解工作流管理工具和 YAML, 且能较为自如地按照文中指示操作命令行。这些概" +"念在《用户指南》其他部分有更详尽的说明。如果您已了解 CWL, " +"或想查阅进阶内容，可以考虑跳过本章节。" #: ../../src/introduction/basic-concepts.md:10 #: 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" -msgstr "CWL规范" +msgstr "CWL 规约" #: ../../src/introduction/basic-concepts.md:21 #: cbe1d761da5b403d9605fa1fb8e62fdf msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." -msgstr "CWL规范文档由CWL社区撰写并维护，此规范有不同版本，本用户指南所用版本为 {{ " -"cwl_version }}。" +msgstr "CWL 规约由 CWL 社群撰写并维护，此规约现有多个版本，本《用户指南》" +"所涵盖的是版本 {{ cwl_version }}." #: ../../src/introduction/basic-concepts.md:25 #: 3a71b269bd3c49eb913cf69b60373c24 msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." msgstr "" -"规范的版本最多包含三个数字，以 `.`（圆点）分隔。第一个数字说明主要版本，用于" -"标注删除弃用功能等向后不可兼容的更改。第二个数字说明次要版本，用于标注增添新" -"功能或小幅调整等向后兼容的更改。最后一个数字说明错误修复，用于标注拼写错误更" -"正或对规范的其他修正。" +"规约的版本号码由至多三个数字构成，以 `.`（圆点）分隔。第一个数字为主发布版本" +"，用于向后不可兼容的更改，例如删除过时的功能。第二个数字是次级发布版本，用于" +"新增功能或向后兼容的小幅调整。最后一个数字用于错误修复，例如打字错误或其他更" +"正。" #: ../../src/introduction/basic-concepts.md:33 #: b171b72c48d44050a3416a7a42c4021d msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." -msgstr "用于规范版本的模型称为“语义版本控制”，请参阅本章节末尾以[了解更多](#learn-" -"more)有关信息。" +msgstr "规约所使用的版本标号模型称为“语义化版本”，请参阅本章结尾以[了解更多](#learn-" +"more)相关信息。" #: ../../src/introduction/basic-concepts.md:37 #: b3df1607e9d242d78b22dc44335fbe2d @@ -538,20 +544,20 @@ msgstr "实现" #: 078b58ffc1cc4d25a7c4eea3bb76e025 msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." msgstr "" -"CWL规范的实现意味着所有软件的编写均需遵循规范文档中所定义版本的要求。但是，在" -"实现过程中可能无法满足规范的所有方面。目前，CWL规范已同时获取开源和商业许可的" -"授权。" +"所谓 CWL 规约的某种“实现” (implementation), 指的是任何一种依照某版本的规约内" +"容而编写的软件。然而，诸实现未必能将规约的每个方面都转化为软件实体。目前，" +"CWL 各种实现的许可协议包括开源和商业许可。" #: ../../src/introduction/basic-concepts.md:44 #: c3869b4ec5ff47d99e8da79770722e04 msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." -msgstr "CWL非常适用于描述集群、云和高性能计算环境中的大规模工作流情况，因为其中可以跨" -"节点并行调度任务。" +msgstr "CWL非常适用于描述集群、云计算和高性能计算 (HPC) " +"等多节点、任务并行调度环境中的大规模工作流。" #: ../../src/introduction/basic-concepts.md:51 #: 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." -msgstr "CWL规范、实现及其他工具。" +msgstr "CWL 规约、实现及其他工具。" #: ../../src/introduction/basic-concepts.md:105 #: a5ebc727fb3443f78e81d6b7ed5ac750 @@ -1063,7 +1069,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:16 #: 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" -msgstr "" +msgstr "`hello_world.cwl`" #: ../../src/introduction/quick-start.md:22 #: 7e475e3f3c4a4404bb0236124c0f7ce7 @@ -1144,7 +1150,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:74 #: 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" -msgstr "" +msgstr "`hello_world-job.json`" #: ../../src/introduction/quick-start.md:80 #: e76bfcc0c9f84bcdb3f6d5277869a88c @@ -1236,14 +1242,14 @@ msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 #: a74935dc31664e979ca8f90a6a4ba53c msgid "`arguments.cwl`" -msgstr "" +msgstr "`arguments.cwl`" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 #: 0a8065edd8af4eaea08989a1060ce48f #: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" -msgstr "" +msgstr "`arguments-job.yml`" #: ../../src/topics/additional-arguments-and-parameters.md:24 #: 6359191b4f684d5aa3602e4aaf394883 @@ -1459,7 +1465,7 @@ msgstr "CWL命令行工具。" #: ../../src/topics/command-line-tool.md:50 #: 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" -msgstr "" +msgstr "`echo.cwl`" #: ../../src/topics/command-line-tool.md:57 #: a5eacdbc9aa142c890b177869da4143d @@ -1503,7 +1509,7 @@ msgstr "要生成此类文件，我们可使用 `InitialWorkDirRequirements`。" #: ../../src/topics/creating-files-at-runtime.md:9 #: d3f74c3b094a427fbec831afab657d50 msgid "`createfile.cwl`" -msgstr "" +msgstr "`createfile.cwl`" #: ../../src/topics/creating-files-at-runtime.md:15 #: cfffc518ba6e4ed1a80762ed6f7d25df From 842324906ef6153bdf158853105a40a5477e3673 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Wed, 26 Apr 2023 14:21:06 +0200 Subject: [PATCH 063/179] switch to sphinx-favicon from deprecated "favicons" config (#388) --- setup.cfg | 1 + src/conf.py | 225 ++++++++++++++++++++++++++-------------------------- 2 files changed, 112 insertions(+), 114 deletions(-) diff --git a/setup.cfg b/setup.cfg index 7ccac7d0..2afc5085 100644 --- a/setup.cfg +++ b/setup.cfg @@ -40,6 +40,7 @@ install_requires = sphinx==5.* sphinx-reredirects==0.1.* sphinxcontrib-runcmd==0.2.* + sphinx-favicon python-Levenshtein sphinx-intl diff --git a/src/conf.py b/src/conf.py index dd428640..38617d94 100644 --- a/src/conf.py +++ b/src/conf.py @@ -20,12 +20,12 @@ # -- Project information ----------------------------------------------------- -project = 'Common Workflow Language User Guide' -copyright = '2013, CWL Project Team' -author = 'CWL Project Team' +project = "Common Workflow Language User Guide" +copyright = "2013, CWL Project Team" +author = "CWL Project Team" # The full version, including alpha/beta/rc tags -release = '0.1' +release = "0.1" # Define the version we use for matching in the version switcher. version_match = os.environ.get("READTHEDOCS_VERSION") @@ -37,35 +37,36 @@ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ - 'myst_parser', - 'sphinx.ext.graphviz', - 'sphinx_reredirects', - 'cwl.sphinx.runcmd' + "myst_parser", + "sphinx.ext.graphviz", + "sphinx_reredirects", + "sphinx_favicon", + "cwl.sphinx.runcmd", ] # myst-parser settings myst_heading_anchors = 4 myst_enable_extensions = [ - 'colon_fence', - 'deflist', - 'substitution', - 'replacements', + "colon_fence", + "deflist", + "substitution", + "replacements", ] -CWL_VERSION = 'v1.2' +CWL_VERSION = "v1.2" myst_substitutions = { - 'repo_url': 'https://github.com/common-workflow-language/user_guide/', - 'source_branch': 'main', - 'cwl_version': f'`{CWL_VERSION}`', - 'cwl_version_text': f'{CWL_VERSION}' + "repo_url": "https://github.com/common-workflow-language/user_guide/", + "source_branch": "main", + "cwl_version": f"`{CWL_VERSION}`", + "cwl_version_text": f"{CWL_VERSION}", } -master_doc = 'index' +master_doc = "index" # Set the default role so we can use `foo` instead of ``foo`` -default_role = 'literal' +default_role = "literal" # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. @@ -73,106 +74,126 @@ # CONTRIBUTING.md is referenced in the footer, but not linked via Sphinx # aio.md is also referenced in one page, but not directly via Sphinx, hence the exclusions here. exclude_patterns = [ - '**/Thumbs.db', - '**/.DS_Store', - '**/.git', - '.idea', - '.github', - '**/_build', - '**/_includes', - 'cwl', - 'venv', - 'README.md', - 'CODE_OF_CONDUCT.md', - 'CONTRIBUTING.md' + "**/Thumbs.db", + "**/.DS_Store", + "**/.git", + ".idea", + ".github", + "**/_build", + "**/_includes", + "cwl", + "venv", + "README.md", + "CODE_OF_CONDUCT.md", + "CONTRIBUTING.md", ] -source_suffix = ['.rst', '.md'] +source_suffix = [".rst", ".md"] # -- Options for URL redirects ----------------------------------------------- redirects = { - '01-introduction/index.md': '../introduction/quick-start.html', - '02-1st-example/index.md': '../introduction/quick-start.html', - '03-input/index.md': '../topics/inputs.html', - '04-output/index.md': '../topics/outputs.html', - '05-stdout/index.md': '../topics/outputs.html', - '06-params/index.md': '../topics/parameter-references.html', - '07-containers/index.md': '../topics/using-containers.html', - '08-arguments/index.md': '../topics/additional-arguments-and-parameters.html', - '09-array-inputs/index.md': '../topics/inputs.html', - '10-array-outputs/index.md': '../topics/outputs.html', - '11-records/index.md': '../topics/inputs.html', - '12-env/index.md': '../topics/environment-variables.html', - '13-expressions/index.md': '../topics/expressions.html', - '14-runtime/index.md': '../topics/creating-files-at-runtime.html', - '15-staging/index.md': '../topics/staging-input-files.html', - '16-file-formats/index.md': '../topics/file-formats.html', - '17-metadata/index.md': '../topics/metadata-and-authorship.html', - '19-custom-types/index.md': '../topics/custom-types.html', - '20-software-requirements/index.md': '../topics/specifying-software-requirements.html', - '21-1st-workflow/index.md': '../topics/workflows.html', - '22-nested-workflows/index.md': '../topics/workflows.html#nested-workflows', - '23-scatter-workflow/index.md': '../topics/workflows.html#scattering-workflows', - '24_conditional-workflow/index.md': '../topics/workflows.html#conditional-workflows', - 'rec-practices/index.md': '../topics/best-practices.html', - 'misc/index.md': '../faq.html', - 'episodes.md': 'index.html#table-of-contents', - 'setup.md': 'introduction/prerequisites.html', - 'extras.md': '/index.html', - 'yaml/index.md': '../topics/yaml-guide.html', - 'CODE_OF_CONDUCT.html': 'https://github.com/common-workflow-language/user_guide/blob/main/CODE_OF_CONDUCT.md' + "01-introduction/index.md": "../introduction/quick-start.html", + "02-1st-example/index.md": "../introduction/quick-start.html", + "03-input/index.md": "../topics/inputs.html", + "04-output/index.md": "../topics/outputs.html", + "05-stdout/index.md": "../topics/outputs.html", + "06-params/index.md": "../topics/parameter-references.html", + "07-containers/index.md": "../topics/using-containers.html", + "08-arguments/index.md": "../topics/additional-arguments-and-parameters.html", + "09-array-inputs/index.md": "../topics/inputs.html", + "10-array-outputs/index.md": "../topics/outputs.html", + "11-records/index.md": "../topics/inputs.html", + "12-env/index.md": "../topics/environment-variables.html", + "13-expressions/index.md": "../topics/expressions.html", + "14-runtime/index.md": "../topics/creating-files-at-runtime.html", + "15-staging/index.md": "../topics/staging-input-files.html", + "16-file-formats/index.md": "../topics/file-formats.html", + "17-metadata/index.md": "../topics/metadata-and-authorship.html", + "19-custom-types/index.md": "../topics/custom-types.html", + "20-software-requirements/index.md": "../topics/specifying-software-requirements.html", + "21-1st-workflow/index.md": "../topics/workflows.html", + "22-nested-workflows/index.md": "../topics/workflows.html#nested-workflows", + "23-scatter-workflow/index.md": "../topics/workflows.html#scattering-workflows", + "24_conditional-workflow/index.md": "../topics/workflows.html#conditional-workflows", + "rec-practices/index.md": "../topics/best-practices.html", + "misc/index.md": "../faq.html", + "episodes.md": "index.html#table-of-contents", + "setup.md": "introduction/prerequisites.html", + "extras.md": "/index.html", + "yaml/index.md": "../topics/yaml-guide.html", + "CODE_OF_CONDUCT.html": "https://github.com/common-workflow-language/user_guide/blob/main/CODE_OF_CONDUCT.md", } # -- Options for Pygments ---------------------------------------------------- -pygments_style = 'default' +pygments_style = "default" # TODO: maybe write our own lexer to customize tokens, keywords, etc? -lexers['cwl'] = YamlLexer() +lexers["cwl"] = YamlLexer() -highlight_options = { - 'default': { - 'stripall': True - } -} +highlight_options = {"default": {"stripall": True}} # -- GraphViz configuration -------------------------------------------------- from cwl.doc.graphs import create_processing_units_graph -graphviz_output_format = 'svg' +graphviz_output_format = "svg" -myst_substitutions['CWL_PROCESSING_UNITS_GRAPH'] = create_processing_units_graph() +myst_substitutions["CWL_PROCESSING_UNITS_GRAPH"] = create_processing_units_graph() # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = 'pydata_sphinx_theme' +html_theme = "pydata_sphinx_theme" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] +html_static_path = ["_static"] +favicons = [ + { + "rel": "icon", + "sizes": "16x16", + "href": "images/favicons/cwl/favicon-16x16.png", + }, + { + "rel": "icon", + "sizes": "32x32", + "href": "images/favicons/cwl/favicon-32x32.png", + }, + { + "rel": "icon", + "sizes": "96x96", + "href": "images/favicons/cwl/favicon-96x96.png", + }, + { + "rel": "icon", + "sizes": "128x128", + "href": "images/favicons/cwl/favicon-128.png", + }, + { + "rel": "icon", + "sizes": "196x196", + "href": "images/favicons/cwl/favicon-196x196.png", + }, +] + html_css_files = [ - 'css/custom.css', + "css/custom.css", ] -html_logo = '_static/images/logos/cwl/CWL-Logo-HD-cropped2.png' -html_favicon = '_static/images/favicons/cwl/favicon.ico' +html_logo = "_static/images/logos/cwl/CWL-Logo-HD-cropped2.png" +html_favicon = "_static/images/favicons/cwl/favicon.ico" -html_extra_path = [ - 'browserconfig.xml', - 'favicon.ico', - 'manifest.json' -] +html_extra_path = ["browserconfig.xml", "favicon.ico", "manifest.json"] html_theme_options = { "external_links": [ - {"name": "Community", "url": "https://www.commonwl.org/community/"}, + {"name": "Community", "url": "https://www.commonwl.org/community/"}, ], "header_links_before_dropdown": 6, "icon_links": [ @@ -191,39 +212,12 @@ "navbar_end": [ # "version-switcher", "theme-switcher", - "navbar-icon-links" + "navbar-icon-links", ], "show_nav_level": 2, "navigation_depth": 2, "collapse_navigation": True, "show_prev_next": True, - "favicons": [ - { - "rel": "icon", - "sizes": "16x16", - "href": "images/favicons/cwl/favicon-16x16.png" - }, - { - "rel": "icon", - "sizes": "32x32", - "href": "images/favicons/cwl/favicon-32x32.png" - }, - { - "rel": "icon", - "sizes": "96x96", - "href": "images/favicons/cwl/favicon-96x96.png" - }, - { - "rel": "icon", - "sizes": "128x128", - "href": "images/favicons/cwl/favicon-128.png" - }, - { - "rel": "icon", - "sizes": "196x196", - "href": "images/favicons/cwl/favicon-196x196.png" - } - ], "footer_items": ["copyright"], } @@ -232,12 +226,12 @@ "github_repo": "user_guide", "github_version": "main", "doc_path": "src", - "default_mode": "light" + "default_mode": "light", } gettext_uuid = True gettext_compact = "user_guide" -locale_dirs = ['../locales/'] +locale_dirs = ["../locales/"] # Patched MyST parser @@ -260,6 +254,7 @@ SPHINX_LOGGER = logging.getLogger(__name__) + class MystParser(SphinxParser): """Sphinx parser for Markedly Structured Text (MyST).""" @@ -309,7 +304,9 @@ def parse(self, inputstring: str, document: nodes.document) -> None: # gives you the translation without resolving the links. Here we just re-use the # ``md_env`` dictionary that contains the ``.references`` populated in the first # pass, fixing i18n with MyST Parser. - env = {} if not hasattr(document.settings, 'md_env') else document.settings.md_env + env = ( + {} if not hasattr(document.settings, "md_env") else document.settings.md_env + ) parser.options["document"] = document parser.render(inputstring, env) document.settings.md_env = parser.renderer.md_env From b6a365729f558349442d7dc990039c43b0359feb Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Wed, 26 Apr 2023 14:32:27 +0200 Subject: [PATCH 064/179] Added translation using Weblate (Portuguese (Portugal)) (#387) Added translation using Weblate (Portuguese (Brazil)) Co-authored-by: Michael Crusoe --- locales/pt_BR/LC_MESSAGES/user_guide.po | 3551 ++++++++++++---------- locales/pt_PT/LC_MESSAGES/user_guide.po | 3573 +++++++++++++---------- 2 files changed, 4175 insertions(+), 2949 deletions(-) diff --git a/locales/pt_BR/LC_MESSAGES/user_guide.po b/locales/pt_BR/LC_MESSAGES/user_guide.po index e1d33500..f0199e7a 100644 --- a/locales/pt_BR/LC_MESSAGES/user_guide.po +++ b/locales/pt_BR/LC_MESSAGES/user_guide.po @@ -19,463 +19,512 @@ msgstr "" "Plural-Forms: nplurals=2; plural=n > 1;\n" "X-Generator: Weblate 4.16.2-dev\n" -#: ../../LICENSE.md:2 -#: 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.md:4 -#: 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" msgstr "Material Instrucional" -#: ../../LICENSE.md:6 -#: 747f9dd48bc54f44adcd8b18c57f4d9d -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "" +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable summary " +"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" +"[cc-by-legal]." msgstr "" -#: ../../LICENSE.md:12 -#: 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" msgstr "" -#: ../../LICENSE.md:14 -#: 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +msgid "" +"to **Share**---copy and redistribute the material in any medium or format" msgstr "" -#: ../../LICENSE.md:15 -#: 18a3a0aec35743848c97bc178f9c94ff +#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "" -#: ../../LICENSE.md:17 -#: b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." msgstr "" -#: ../../LICENSE.md:19 -#: 6021e65292a149d5b15e14491f3eb05e -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the license " +"terms:" msgstr "" -#: ../../LICENSE.md:24 -#: 8fb7a2946c384364814c6ec3910997d3 -msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a [link to the license][cc-by-human], and indicate if changes were " +"made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." msgstr "" -#: ../../LICENSE.md:32 -#: 8161753b7526445db319210044566200 -msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" msgstr "" -#: ../../LICENSE.md:36 -#: 15314ba527864eaa834cf1185cfcc4e3 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +msgid "" +"You do not have to comply with the license for elements of the material in " +"the public domain or where your use is permitted by an applicable exception " +"or limitation." msgstr "" -#: ../../LICENSE.md:39 -#: b351ddf9847d48b1a2a87fc78eaba4d2 -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "" +"No warranties are given. The license may not give you all of the permissions " +"necessary for your intended use. For example, other rights such as " +"publicity, privacy, or moral rights may limit how you use the material." msgstr "" -#: ../../LICENSE.md:44 -#: a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea msgid "Software" msgstr "" -#: ../../LICENSE.md:46 -#: 84b2c685bbab48449fdc72d2a1e42bf4 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the " +"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" -#: ../../LICENSE.md:51 -#: 0f68eafafaef4b54accba7e13bfaa702 -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." msgstr "" -#: ../../src/_includes/what-is-cwl.md:1 -#: ../../src/_includes/what-is-cwl.md:2 -#: eab02dc13915490bb3c9ba744d78b6a7 -#: d4f35995b0f6494d9771a4be0a82538f +#: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 d4f35995b0f6494d9771a4be0a82538f #: d6ccd4b546254f56a597d67dd4fdc5d6 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece of " +"software, tools and workflows described using CWL are portable across a " +"variety of platforms that support the CWL standard." msgstr "" -#: ../../src/episodes.md:5 -#: ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc -#: 436cfca6f857469bbff7c652df32160f +#: ../../src/episodes.md:5 ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 -#: cc11f5d29206492d9f2f0922882b6159 -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 -#: e2ed894d325a4f50a5e2dc69da5531a1 +#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 -#: 61edb787dab04ca2ad3ed07616d878a0 +#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 -#: d5321589e7ed4f0db3c630cc39800791 +#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 -#: fc62427c0a004810b055dee90ec5e2d9 -msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +msgid "" +"This example demonstrates how to change the name of an input file as part of " +"a tool description. This could be useful when you are taking files produced " +"from another step in a workflow, and don't want to work with the default " +"names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 -#: 1c6b8a4194a14611b4061b1540c3807f +#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 -#: bc7ad10c929848a3a9a240a3c501d299 -msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +msgid "" +"This example demonstrates how to change the name of an output file from the " +"default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 -#: 7225a993d281421b95c8e3df2846a0e3 +#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 -#: 7ef1dbb81993473f948d9c6f3c64b381 +#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 -#: 450edf800a18423195bea4fe8793a2cb -msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +msgid "" +"The first method involves adding the folder containing your scripts to the " +"`PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 -#: 1a8cc75ea6174b9297871b2e58971077 +#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 -#: a7d84f740a714ec588503ee084fbbc34 -msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +msgid "" +"After that, make the script executable with the command `chmod +x scriptname." +"sh`" msgstr "" -#: ../../src/faq.md:97 -#: 569d553abe85450c9d1c37456bf412f4 -msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." msgstr "" -#: ../../src/faq.md:104 -#: 95f5dbbd21084a318413b9528fb867be -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be +msgid "" +"Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 -#: 1b3cae80fa9a40ffb2259b8c1cd2b468 -msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 -#: 8d86baa239364f799d4f9d5ea2b0e314 -msgid "The second method involves including an input of `type: File` in the script itself:" +#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +msgid "" +"The second method involves including an input of `type: File` in the script " +"itself:" msgstr "" -#: ../../src/faq.md:135 -#: f2c109998c76434893ff16b17fdb2bd0 +#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 -#: c2c752b86bf94d6fb3751f4dd81bc7a7 +#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 -#: 2c38cc58cbb340bc935a5f00e96ba95c -msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their input " +"binding makes use of `self`. Below is an example workaround for this, " +"pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 -#: ce6db54bd0f54839a5beb948530a21f0 +#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 -#: d06cbf89028b4638ad54c2529bcbfa25 -msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +msgid "" +"Below is an example showing how to specify different strings to be added to " +"a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 -#: d53fb28dcad04e7788cba9e280a2343c +#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 -#: d9e30e11533b4d53a144f5df7041268d -msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +msgid "" +"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 -#: 941077158ec54ae19bfa2e2ad6662da1 +#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 -#: 937cb94a370640c788fbc3fe0b19f2e5 -msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +msgid "" +"The input must be an array consisting of exactly one entry for each input " +"link. If \"merge_nested\" is specified with a single link, the value from " +"the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 -#: a1d57e15656548128a76a8b975c564c9 +#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 -#: c8c235a9bf6240628f0b5493ffebf7e0 -msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " +"add `linkMerge: merge_nested` under the appropriate `in` entry of the " +"destination step." msgstr "" -#: ../../src/faq.md:229 -#: 3da4dcb043eb4423a53a14182949d9cd +#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 -#: 89b90d3bf1ea4ebd88482d435241fac5 -msgid "To make an input parameter optional, add a question mark to the type declaration." +#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." msgstr "" -#: ../../src/faq.md:247 -#: a854006054ce4ffe94bbfa73bdbecbf2 +#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 msgid "" msgstr "" -#: ../../src/faq.md:248 -#: f80eb714e9df417fbba555b5dd5f4d8c +#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 -#: 10af80fa13af4158aec7060550485350 -msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +msgid "" +"For command line flags that require a specific input as the argument an enum " +"type can be declared in CWL. **Specifying null here is known as long form " +"style. It does the same thing as the question mark on the other inputs.**" msgstr "" -#: ../../src/faq.md:267 -#: ad1c26711ccd4efd8fdb25f9293d33fd +#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd msgid "" msgstr "" -#: ../../src/faq.md:268 -#: 49e2095b51f84f609f5d4bc088ad9745 +#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 -#: 52b8538177c64090af51f5f6a696c28c -msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 -#: f96c9257e3734b8aa0cc5e065f74f944 +#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 -#: 7dc0540508084a3495ff3b2ac90fd323 -msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +msgid "" +"To properly set fields in a record input type, you need to pass a dictionary " +"to the input to properly set the parameters. This is done by using inline " +"JavaScript and returning the dictionary with the key of the field you want " +"to set. The source field is set to indicate the input from the workflow to " +"be used as the value." msgstr "" -#: ../../src/faq.md:342 -#: b53dc77466b24a67b52b8aadf4fab724 +#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 -#: cf4e7f3977ae4f9b877072c2b1c4b533 +#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 -#: 99b37739ef18443ca7c0e715a131e0c7 +#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 -#: 9b00b5a55ee941e1adbfe89e133791e3 +#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 -#: 07922147f7ab487ba2a1e7c43c9f410c +#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 -#: 7a11806f0c7045b48fe58a271f814797 +#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 -#: fdaec25650ab4b0fb1c527610e24ae5a -msgid "For example, the filename `a space is here.txt` includes 3 space characters." +#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +msgid "" +"For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" -#: ../../src/faq.md:371 -#: 182959fc9f4746d082994e07d05c8cde -msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 -#: cc7752e9989e4a6d957682f479d6fc60 +#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 -#: 6db1ebd2d6c74ceca889662cd7df5cd5 +#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 -#: 3de2513c7d7b4569ba63f7e6d29137b7 +#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 -#: ae3a9188706649e28f97bc4ec34c0821 +#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 -#: e1ac97ab6ad3449b8c54933d25257f73 +#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 -#: f6c402f7f6974edbbb5582c8e22f3869 +#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 -#: 190099a242a645c9b9f8bc3ce89d920d -msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +msgid "" +"If it is not possible to change the input identifier, then you can use an " +"alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 -#: 06a4f6ffc2da4d43b453d4784b42efd3 +#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 -#: 1901c34201054a9cae199b0dbb8b945e -msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +msgid "" +"The CWL standards are built around (optional) Docker format containers. The " +"reference runner and several other CWL implementations support running those " +"Docker format containers using the Singularity engine. Directly specifying a " +"Singularity format container is not part of the CWL standards." msgstr "" -#: ../../src/faq.md:450 -#: 2d498470524d47f18f9936ace6acebb0 +#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 -#: d7b044f5224a48eda09bc949cf645193 -msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +msgid "" +"You can use the --js-console option of cwltool, or " +"you can try creating a JavaScript or TypeScript project for your code, and " +"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 -#: 2754519265eb426b940bbbd2b8d64e1e +#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 -#: f8d6e4cd54cb42c88182a43171d97bab -msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +msgid "" +"This guide will introduce you to writing workflows using the [Common " +"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " +"guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 -#: 132d40fee3b84469afa80d5ff613bf77 +#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 -#: 0f47157605a34ea58770ea898deebae4 -msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +msgid "" +"If you find that something is missing from this guide, or if you would like " +"to provide other feedback, file an Issue on the [project repository for this " +"guide][repo]. You can also suggest changes directly in a Pull Request by " +"clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" -#: ../../src/index.md:16 -#: 6d269e8d70184034bcb56385a6ca198f +#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 -#: ed74c9a4b623464480e2c184668fcec0 -msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +msgid "" +"If you are a beginner user get started with the [Introduction](/introduction/" +"index.md) section. For advanced users the subsections of the [Topics](/" +"topics/index.md) have detailed information about the most common topics for " +"CWL." msgstr "" -#: ../../src/index.md:23 -#: cfa67cf5521b414da6f7d34cbed283f7 -msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +msgid "" +"The Table of Contents is displayed at the top menu and also on the left " +"sidebar. It also appears further down this page but with links to " +"subsections. The right sidebar contains links to the sections of each page, " +"and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 -#: ee6b82bd86264e4bb1e8e4065b1e6b9c +#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 -#: e208c8a7506e41dcac9a403c5d2850c1 +#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 -#: ac62d326a68145b695e46b714d4e8156 -msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are expected " +"to be familiar with workflow managers, YAML, and comfortable with following " +"instructions for the command-line. The other sections of the user guide " +"cover the same concepts, but in more detail. If you are already familiar " +"with CWL or you are looking for more advanced content, you may want to skip " +"this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 -#: 984e6676b9d04c7092bc492f195dfb91 +#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 -#: cbe1d761da5b403d9605fa1fb8e62fdf -msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered in " +"this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 -#: 3a71b269bd3c49eb913cf69b60373c24 -msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes that " +"are backward-compatible. The last number is used for bug fixes, like typos " +"and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 -#: b171b72c48d44050a3416a7a42c4021d -msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +msgid "" +"The model used for the specification version is called Semantic Versioning. " +"See the end of this section to [learn more](#learn-more) about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 -#: b3df1607e9d242d78b22dc44335fbe2d +#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 -#: 078b58ffc1cc4d25a7c4eea3bb76e025 -msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "" +"An implementation of the CWL specification is any software written following " +"what is defined in a version of the specification document. However, " +"implementations may not implement every aspect of the specification. CWL " +"implementations are licensed under both Open Source and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 -#: c3869b4ec5ff47d99e8da79770722e04 -msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud " +"and high performance computing environments where tasks are scheduled in " +"parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 -#: 2482c84831fc4dfab629e7bfcfb41cbf +#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." msgstr "" @@ -486,7 +535,11 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:107 #: 86e6a06992dc4228bfda7add48e28ca3 -msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The " +"behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification " +"{{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 @@ -516,27 +569,44 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:119 #: cf2922f645904ac7955428ecddc37b8a -msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 #: 5f47aae608c041aeb4134d59dad314d2 -msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be used " +"to simplify workflows and command-line tools, moving common parts of a " +"workflow execution into reusable JavaScript code that takes inputs and " +"produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 #: f6f589481d0c4891beaccb63160619ef -msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgid "" +"Operation is an abstract process that also takes inputs, produces outputs, " +"and can be used in a workflow. But it is a special operation not so commonly " +"used. It is discussed in the [Operations section](../topics/operations.md) " +"of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 #: 73b0c1ccb18c4b74a2c0fdf9706eca85 -msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgid "" +"The workflow is a process that contains steps. Steps can be other workflows " +"(nested workflows), command-line tools, or expression tools. The inputs of a " +"workflow can be passed to any of its steps, while the outputs produced by " +"its steps can be used in the final output of the workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 #: 4ace6b92f4e04a07aa202840ebe36417 -msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through *requirements*. " +"There are many requirements defined in the CWL specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 @@ -551,17 +621,26 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:143 #: 907674a4ecff4826a2b880e28fc38f33 -msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgid "" +"`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 #: 037cd0e5ceda482eaeaca03d51745aee -msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgid "" +"Some CWL runners may provide requirements that are not in the specification. " +"For example, GPU requirements are supported in `cwltool` through the " +"`cwltool:CUDARequirement` requirement, but it is not part of the " +"{{ cwl_version }} specification and may not be supported by other CWL " +"runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 #: e4643938445b48cc80eb8973ceeb126e -msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgid "" +"Hints are similar to requirements, but while requirements list features that " +"are required, hints list optional features. Requirements are explained in " +"detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 @@ -571,17 +650,33 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:157 #: 3eb6a013a2a4478ca2ad134661f65c58 -msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created. It " +"is thus important that workflows support the creation of FAIR data and " +"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" +"workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 #: 074af9633627470485e5225326d5f20a -msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\", " +"CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 #: 847951c055b94a83b1e081594cef22ee -msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, and " +"scalability; tools and workflows described with CWL can transparently " +"leverage technologies such as Docker and be used with CWL implementations " +"from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 @@ -591,10 +686,8 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 -#: 65c24244713741e196da08cb9ba237b2 -#: f059896039524095b4deb65d693f8ddf -#: 3439764fab0e49d2bcb7c9fbae556e65 +#: ../../src/introduction/quick-start.md:94 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf 3439764fab0e49d2bcb7c9fbae556e65 msgid "Learn More" msgstr "" @@ -605,17 +698,23 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:181 #: 36eb4b3b966640af90faa55db3789cb6 -msgid "The CWL Specification page in the CWL website: " +msgid "" +"The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 #: 2ccb956baa6b4376a04ad9fcc4654631 -msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 #: 72889b830c514afe9a7cb1e64b5666a0 -msgid "The list of Implementations in the CWL website: " +msgid "" +"The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 @@ -625,397 +724,461 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:185 #: c377a7f5dbe645cebbb6c7eccf831a0b -msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 -#: 1769a0cbf4de4d77879c1f202cd11af9 +#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 -#: 950370f0a36048b38e1bde9b78f80816 -msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that " +"are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 -#: f01faaf1b253407cbbc2f353c24774f3 +#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 -#: 353b14f06ee845d0a06a829643e31534 -msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +msgid "" +"The software and configurations listed in this section are prerequisites for " +"following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements focuses " +"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " +"runner or workflow system, but the results and interface may look different " +"(though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 -#: b5a0607096814c0aa577f977c3b57c54 +#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 -#: ff2bb4c6504b456bac7ca9c514414dbf -msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +msgid "" +"There are many implementations of the CWL standards. Some are complete CWL " +"runners, while others could be plug-ins or extensions to workflow engines. " +"We have a better explanation in the [Implementations](basic-concepts." +"md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 -#: cbbcce4c2a96471b8b0ae3593ad59de4 +#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 -#: 5089fdba8aed4113983fa86e698df98b -msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +msgid "" +"We recommend using an up-to-date operating system. You can choose any of the " +"following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 -#: dbaa4bae22fe4d05b18d7351967ddbc3 +#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 -#: c05187af85be41b782678b79627f8fbf +#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 -#: beb6cf4d7c154eb9b6d7fe024a318ed7 +#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 -#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 -msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "" +"If you are using Windows, you will have to install the [Windows Subsystem " +"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " +"installing WSL2. Your operating system also needs internet access and a " +"recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 -#: 56d78c95daa54135b6aa9b2bfdc34d01 +#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 -#: 0f2704bf1f7148be95e999e312899f11 -msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL community. " +"It is also the CWL reference runner, which means it must support everything " +"in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 -#: 86264c9e56104ecea9146407c379aae2 -msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +msgid "" +"`cwltool` can be installed with `pip`. We recommend using a virtual " +"environment like `venv` or `conda`. The following commands will create and " +"activate a Python virtual environment using the `venv` module, and install " +"`cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 -#: 0a0f0e5151ab4c498b4f8a12c016f28d +#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 -#: f7aaafeee230400da056464c853582c2 -msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +msgid "" +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool#install) for other ways to install `cwltool` with `apt` and " +"`conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 -#: 5eced7e4cd084e8a806b1d3b12d0c000 +#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 -#: 040c019b6e844eda8c8c2b210852516b +#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 -#: 6391e08e0bde49f4b21286d8fdb97433 -msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the CWL " +"standards. However, these actions will be performed without running the " +"document. To validate CWL workflows (or even a standalone command line tool " +"description like the above) pass the `--validate` option to the `cwltool` " +"command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 -#: cdef47fca304479c9a9df75afc0afb35 +#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 -#: d41c4bc740aa474ea09a7cbd267c8840 -msgid "You can run the CWL tool description by omitting the `--validate` option:" +#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 +msgid "" +"You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 -#: 24d7be55d3994f0b82c38da47918e0c9 +#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 -#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 -#: 096d0a50f69e48bd9915238d1b4264c1 -msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be invoked " +"independently, and is not reliant on a particular CWL runner program name. " +"Users can invoke `cwl-runner` instead of invoking a CWL runner like " +"`cwltool` directly. The `cwl-runner` is installed by a system administrator " +"or user to point to the preferred CWL implementation. This is convenient for " +"environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 -#: f9df974a8e2645a6918e67466bd1fdc2 -msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +msgid "" +"The CWL community publishes a Python package with the name `cwlref-runner` " +"that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 -#: 71ebe91d4bda473abe87578929433212 +#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 -#: 746c6fc9c29d466494458a08d4c96672 -msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` executable, " +"which will invoke `cwltool`. You should have the same results and output as " +"in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 -#: b9cc5a843a0f49daad56e9303657bdd5 +#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 -#: 34ab40437ab646488ba3ee86cd7fe071 +#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 -#: 705807fae182425dbf4244dbf2be1226 -msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For " +"that, the first thing you need to do is copy `true.cwl` workflow into a new " +"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 -#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 -#: 164c438baab54ec19bbb4584a10dd411 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 +msgid "" +"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 -#: bf8be77af6154326b28442c5d2e2b852 +#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 -#: 695184d1b45a42f393e2da99c3721773 -msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +msgid "" +"And finally, you can execute it directly in the command-line. On execution, " +"the program specified in the shebang (`cwl-runner`) will be used to execute " +"the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 -#: 7c4f45b3e7b549e186126693aa4a3d4f +#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 -#: 3ba23b4ea01c46848e4e43bbeff5f5a1 -msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute the " +"script using the executable specified after the shebang. It is considered a " +"good practice to use `/usr/bin/env ` rather than using a hard-" +"coded location, since `/usr/bin/env ` looks for the " +"`` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 -#: eec6c07455384630809ff1c532bfe7d4 +#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 -#: f6b39b12bd5c495cb53e2795bf9200ed -msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 -#: 2fdb62a13f9447bc89183426260ce781 -msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting " +"and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 -#: 1f07135156254f74a6b043bf33d00cc3 -msgid "Visual Studio Code with the Benten (CWL) plugin - " +#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " msgstr "" -#: ../../src/introduction/prerequisites.md:172 -#: de344f356b1c466d9131cdbd4d7353a3 -msgid "cwl-plugin for IntelliJ - " +#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +msgid "" +"cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 -#: 3f9324ede11441f58d93875867034cf0 -msgid "The CWL community also maintains a list of editors and viewers: " +#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +msgid "" +"The CWL community also maintains a list of editors and viewers: " msgstr "" -#: ../../src/introduction/prerequisites.md:177 -#: 6ce8b81560e341c580d316d69202b268 +#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 -#: 40cfd559d6a848d1aae354d3bdaa8e9c -msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: ." msgstr "" -#: ../../src/introduction/prerequisites.md:185 -#: 8a9a50b0ebe847ce90593881ffe0d69c -msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models with " +"and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 -#: 923cf9dd6d6c417aabe42f9fa62ffa35 -msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for pulling " +"images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 -#: 9390b03889de44638141d705e0ef8322 -msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the next " +"section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 -#: 12042e411482458f8c35a2491f9433e0 +#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 -#: cdd4196f9aa34beba115901ec97913b6 +#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 -#: c43d9675ed134b78b02acb5a102a764a -msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +msgid "" +"This section will show you a brief overview of what CWL is, and where you " +"can learn more about it. No previous knowledge of CWL is required, but you " +"must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 -#: 280936bb2a22469799b2c9e9ba22adee +#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 -#: cb203354977d42a58112d09357f62565 -msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " +"example below shows a simple CWL “Hello World” workflow annotated with " +"comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 -#: 9e51962a7e5c47248f3e20703ae101eb +#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 -#: 7e475e3f3c4a4404bb0236124c0f7ce7 -msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the " +"same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 -#: 82613ca4e32b4ccab1b7735f5ba2d5a1 -msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "" +"In CWL, there is a distinction between a command-line tool and a workflow. " +"But for the sake of simplicity, we are using the term “workflow” here. You " +"will learn more about this in the [basic concepts](basic-concepts.md) " +"section." msgstr "" -#: ../../src/introduction/quick-start.md:32 -#: 498a43362a4749f3b8b433709d34a1d5 +#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 -#: f3e56aedd56b4b93bdc3894273e8c144 -msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the CWL " +"*Reference Runner* for the specification, and it is compliant with the " +"latest version of the specification: {{ cwl_version }}. You can install " +"`cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 -#: 81481f5b82e4488398f87f0a169bd359 +#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 -#: a81342e756d24c40acc15835d0a768f2 -msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the " +"[prerequisites](prerequisites.md) section contains other ways to install " +"`cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 -#: c12cf89f8b9a421ebd05330326e219b3 +#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 -#: 9b68bcb1a41849dc9601ab47c5bbb0fe -msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " +"workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 -#: ce04027dfcfe4b7b91ea3c2136b18b23 +#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 -#: 0d8a788402914ebd8f09a5ca80650011 -msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 -#: 6d0b679efab24813a7a3b709ade940d1 +#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 -#: 2ea056ab04b6419a9faf350de22a17f2 -msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +msgid "" +"Another way of passing values to your workflow input parameters is via an " +"*Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 -#: 1a44a545434b448aa956005deeed90a8 +#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 -#: e76bfcc0c9f84bcdb3f6d5277869a88c -msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 -#: d4cdbe870a6f4a68b542ca719d989062 +#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 -#: b6d59e4b9c854abab1b3f7a0fa26f504 -msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but it " +"is not a requirement. You can choose any name for your workflows and Inputs " +"Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 -#: 5535b98e8b1342f09f003ec6db2b44b1 +#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 -#: 77e43c7117fd4c52b140f0dd52cc3963 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 +msgid "" +"[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 -#: 7282abfa7155497ca47c30f9abfb6474 -msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 -#: 176d8d47830f4031bb95dc231ebf1303 -msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +msgid "" +"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 -#: 82a7ca3703bc4f0daa18942a1ac8943b -msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." +"org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 -#: d039a9d6461c44628d4660c00d9ce6ff -msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +msgid "" +"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." +"replace('VERSION', cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 -#: fbc3383d9e1c4eaca7931c3cc4f1752b -msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "" +"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 -#: 1330bd38c4b5495f890b98c669f81a9d -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +msgid "" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. The information on this page has been migrated to the [FAQ](/faq." +"md) section of the new user guide." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 @@ -1025,12 +1188,19 @@ msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 #: ad00d94d4fb64bbdac356e64dd3803b9 -msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 #: d8110ed19da94ad8a9f56e7006c4a2cf -msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files in " +"the same directory as the source file. However, CWL input files (and the " +"directories in which they appear) may be read-only, so we need to instruct " +"\"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 @@ -1039,8 +1209,7 @@ msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 -#: 0a8065edd8af4eaea08989a1060ce48f +#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f #: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "" @@ -1052,182 +1221,248 @@ msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 #: 9643449da1da46d7861866dce490cbcb -msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgid "" +"And now invoke `cwltool` providing the tool description and the input object " +"on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 #: 713666580a0a4466b4ba6e3eb2b54f0a -msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 #: d50574c8b9694f83aa376d39b9a6fcd6 -msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" +"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." +"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " +"specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 -#: 612c4a66c36a43d4ac5d74c1757d6845 +#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 -#: 939cd9e9eaff4e3ab74fe707a5d4eb21 -msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." -msgstr "" - -#: ../../src/topics/best-practices.md:8 -#: 4bcb84707acb40a0bfe2ea0853cb10b7 -msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "" +"The following are a set of recommended good practices to keep in mind when " +"writing a Common Workflow Language description for a tool or workflow. These " +"guidelines are presented for consideration on a scale of usefulness: " +"although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:11 -#: 4dee8504a8e5496081dadc386ab45540 -msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "" +"No `type: string` parameters for names of input or reference files/" +"directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:20 -#: 674c238b25e240eda05e22e399f2f78f -msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that " +"the usual rules of software licensing apply to this document. For example, " +"if the workflow is shared publicly, licensing terms must be clear so that a " +"future user understands under what conditions they can run the workflow, " +"modify it and/or combine it with other workflows. For this reason, please " +"consider including a license field in the document. The authors of this " +"guide urge you to choose a pre-existing license rather than trying to write " +"your own (see the link below to learn more about choosing a license), and " +"our recommended practice is to choose a license that allows for re-use by " +"anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +msgid "" +"If possible, the license should be specified with its corresponding [SPDX " +"identifier][spdx]. Construct the metadata field for the license by providing " +"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " +"taken from the list of identifiers linked above. See the example snippet " +"below for guidance. For non-standard licenses without an SPDX identifier, " +"provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 -#: b651f80f47b4442fbf29454a233697fc -msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 -#: 263a127a77cf4c41af76854f22f1f260 +#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 -#: 3a87a0fb2a364e3da5aaa4017e430b19 -msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "" +"For more examples of providing metadata within CWL descriptions, see [the " +"Metadata and Authorship section of this User Guide](../topics/metadata-and-" +"authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 -#: ecf2b9c0b1664afe9c4e180610610021 -msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +msgid "" +"Include [attribution information][license-example] for the author(s) of the " +"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" +"[orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 -#: e24cb13d98014e558b6a6946758359e0 -msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 -#: f2b14a92374e449d9fb1e8c86ae0dd61 -msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" +"identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 -#: 928e3df7ca3e479ca6474a8e72cf36eb -msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 -#: d355f035676446c88b028f327aeb4829 -msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 -#: 339b852df24242189d6efcd2898a3396 -msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" +"$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " +"[Full IANA media type list][iana-types] (also known as MIME types). For non-" +"bioinformatics tools, use or build an appropriate ontology/controlled " +"vocabulary in the same way. Please edit this page to let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 -#: 3ef57e6862f240bebcf193a52397af0a -msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." msgstr "" -#: ../../src/topics/best-practices.md:69 -#: f1a7c4f896a04a80b0c5f6a1db61ff8c -msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "" +"Each `CommandLineTool` description should focus on a single operation only, " +"even if the (sub)command is capable of more. Don't overcomplicate your tool " +"descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 -#: 1ac4c3d8c3e44bd1af3fc5df70051926 -msgid "Custom types should be defined with one external YAML per type definition for re-use." +#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "" +"Custom types should be defined with one external YAML per type definition " +"for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 -#: c858f64e66f048a5b0032ef3e4d83694 +#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 -#: fae385da16aa443da996fa23ac03d6ae -msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +msgid "" +"If useful, include a top-level `doc` as well. This should provide a longer, " +"more detailed description than was provided in the top-level `label` (see " +"above)." msgstr "" -#: ../../src/topics/best-practices.md:82 -#: 92430be71ecc40e18bbbb80d5576c613 -msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list of " +"valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 -#: 387d83db81024f65aa9a890c2d07874a -msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. One " +"common example: manipulating `File` names and paths? Consider whether one of " +"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 -#: d8e2280a75a74916a1630afaa2fe2ae3 -msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 -#: f1c1340f9745458980e0fbd641738687 -msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +msgid "" +"Complex workflows with individual components which can be abstracted should " +"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " +"workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 -#: 5424e5472c3d466fa2a3d2022c6cb475 -msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics " +"software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 -#: 3f4e98f6bfa141feba8c4b120e3d03e8 +#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 -#: 12f57b2ba76b492abe1816e06bfb1417 -msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +msgid "" +"A command-line tool is a type of Process object that can be run by itself or " +"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " +"etc. The command-line tool is defined in the `baseCommand` attribute of the " +"command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 -#: e1f657a46ce94a0d83671540e2cc2dab -msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The following " +"example contains a minimal example of a CWL command-line tool for the `echo` " +"Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 -#: abb83f0097654a43bd78639d3dbb2bc8 +#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 -#: 3b1a9ae3412f4d6e96a39b9a16934232 +#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 -#: a5eacdbc9aa142c890b177869da4143d -msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +msgid "" +"The example above uses a simplified form to define inputs and outputs. You " +"will learn more about in the [Inputs](../topics/inputs.md) and in the " +"[Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 -#: 1849b8f3ae1c4a84ae59a78ffd6b371e +#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 -#: e3bdaceae8784ab0807b2cf356a98580 -msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network access. " +"If a command-line tool is written manually in CWL v1.1+, there is a need to " +"specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 -#: ed521ac365db4a6ba5a1051fbaa2932e -msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " +"Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 @@ -1237,7 +1472,10 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 #: 0cf51b6da6884065ae42032abc20eb0d -msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgid "" +"Sometimes you need to create a file on the fly from input parameters, such " +"as tools that expect to read their input configuration from a file rather " +"than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 @@ -1252,879 +1490,982 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 #: cfffc518ba6e4ed1a80762ed6f7d25df -msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the value " +"at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 #: 9454a330b9324744b89448f2694b1b03 -msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later " +"during command line tool invocation. That means that any genuine need for " +"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " +"above is expanded to `${PREFIX}` in the generated file to be evaluated by " +"the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 #: 7f8d99a30b644457a62ac1523d0c72aa -msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 -#: ../../src/topics/outputs.md:77 -#: 2d2ef4769b2347e79db827655f1bcdeb -#: 2699fbc4376148af91b7a5a6cdac467c +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb 2699fbc4376148af91b7a5a6cdac467c #: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 #: 10d1373bb14a4a3cacd3b92a2f83382d -msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgid "" +"Before we run this, let us look at each step in a little more detail. The " +"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 #: 70e257091bdb456e8957f90a8fa90e8c -msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " +"array, we need a `-` on the first line of each element of the array, in this " +"case we have just one element. `entryname:` can have any value, but it must " +"match what was specified in the `baseCommand`. The final part is `entry:`, " +"this is followed by `|-` which is YAML quoting syntax, and means that you " +"are using a multiline string (without it, we would need to write the whole " +"script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 #: 1741804e33aa43ce88b4320c11ae5973 -msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:54 #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 -#: ../../src/topics/staging-input-files.md:20 -#: ../../src/topics/workflows.md:198 -#: b372f33c65bb4707b2a462a960bb1373 -#: 293fb1d428b849aebccad598a932992d -#: f924d65fed0c4cb5b0a019b084a8b535 -#: d6255506eebe44be94c5ce703c44a513 +#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 d6255506eebe44be94c5ce703c44a513 #: 7bbd2d738fc54649aeb10f8d2bc38b6f -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgid "" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 -#: cb34fd4c8cb04053ada491a227651048 +#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 -#: 67573252cc064b27ab13eebc468ac58a -msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +msgid "" +"Sometimes you may want to write your own custom types for use and reuse in " +"CWL descriptions. Use of such custom types can reduce redundancy between " +"multiple descriptions that all use the same type, and also allow for " +"additional customisation/configuration of a tool/analysis without the need " +"to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 -#: 73e68b3af9cf41338d843c0c40e50cdc -msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +msgid "" +"The example below is a CWL description of the [biom convert format][biom] " +"tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 -#: ef5f35acb97f4ddfad7b688712f53484 +#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 -#: 7015dfa99a6f4cfb87ebf0ed61e8043c +#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 -#: a999b1acda2641598086648c64aa3831 -msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +msgid "" +"___Note:___ To follow the example below, you need to [download the example " +"input file](https://github.com/common-workflow-language/user_guide/blob/main/" +"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " +"*rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 -#: f8c12a58cb0b46a488823c6ae95f25ea -msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to be " +"used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 -#: f25a63e0926d4932bbe64b2e4bdabf9e -msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +msgid "" +"The reference to a custom type is a combination of the name of the file in " +"which the object is defined (`biom-convert-table.yaml`) and the name of the " +"object within that file (`table_type`) that defines the custom type. In this " +"case the `symbols` array from the imported `biom-convert-table.yaml` file " +"define the allowable table options. For example, in `custom-types.yml`, we " +"pass `OTU table` as an `input` that tells the tool to create an OTU table in " +"hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 -#: b0a4df0fd3ca42338cff4689235dcf4e -msgid "The contents of the YAML file describing the custom type are given below:" +#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e +msgid "" +"The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 -#: fecfbb44456640d8ba05e519bf2ff564 +#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 -#: d718630a296545f3a989c8c71e9ddc77 -msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +msgid "" +"In order for the custom type to be used in the CWL description, it must be " +"imported. Imports are described in `requirements:SchemaDefRequirement`, as " +"below in the example `custom-types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 -#: 9a97acd430064710bcdf76edbd9f711c -msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +msgid "" +"Note also that the author of this CWL description has also included " +"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " +"cores required for the tool to run successfully, as well as details of the " +"version of the software that the description was written for and other " +"useful metadata. These features are discussed further in other chapters of " +"this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 -#: 59014808cbef4c02aaef03129d8a29b0 +#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 -#: 3c821c9c46d841ec89b8a5b1018f3af8 -msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "" +"Tools run in a restricted environment and do not inherit most environment " +"variables from the parent process. You can set environment variables for " +"the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 -#: bfdebb32440a4034beb42135e38884e8 +#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 -#: 777d4a52f7554eff84db2df6d4d0f729 +#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 -#: 48deb71f361a43e48a56ed483075bca8 -msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +msgid "" +"An expression tool is a type of Process that can be run by itself or as a " +"Workflow step. It executes a pure JavaScript expression. It is meant to be " +"used as a way to isolate complex JavaScript expressions that need to operate " +"on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 -#: 716b56506ca7470299899c5d820a9ea2 -msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 -#: b63e6f5a2e89431c8fc7d04f47fd69fe +#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 -#: 39727e9058f24b62b8746a46d3f812c2 +#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 -#: e3ecac0a8e604f2b98a2a12b0579990a -msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +msgid "" +"We had to use an `InlineJavascriptRequirement` as our expression contains a " +"JavaScript call in `.toUpperCase()`. This means to tools using the " +"expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 -#: c8d648b765ec499a8e9c464590838492 +#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 -#: 007a345b4bad49cf996c4301b8386473 -msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +msgid "" +"If you need to manipulate input parameters, include the requirement " +"`InlineJavascriptRequirement` and then anywhere a parameter reference is " +"legal you can provide a fragment of Javascript that will be evaluated by the " +"CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 -#: 2edbd398eadb458b8eacd5fa5496f0a2 -msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "" +"JavaScript expressions should only be used when absolutely necessary. When " +"manipulating file names, extensions, paths etc, consider whether one of the " +"[built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc, could be used instead. See the [list of best practices](best-" +"practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 -#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 -#: efb5fd14988c4e2a8f834ee5369d4102 -msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost) " +"empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 -#: e833649b951841c49397796f996d29f3 +#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 -#: 276f688ba7cc471a842f085ca852b1d9 -msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object is " +"represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 -#: ebf399ea4d5f47b9be03e24f04c69f2d +#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 -#: 65e0cdd505b944caa40f65e612cdddfc +#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 -#: 8b70a1ad70514039b97164fa630c12e4 -msgid "Note that requirements can be provided with the map syntax, as in the example above:" +#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" msgstr "" -#: ../../src/topics/expressions.md:54 -#: 2f28ab412d2843ffa5f14acdc01fc732 -msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " +"describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 -#: d957f55a6377422c9834f85d45e35009 +#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 -#: cbec9277b5004e50af2728cbda0df740 -msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 -#: e259f55f8000479bbd8009e25cf0ca6c -msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +msgid "" +"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 -#: 1acb064f7a4a482aa0174bdc847c6382 +#: ../../src/topics/parameter-references.md:64 1acb064f7a4a482aa0174bdc847c6382 #: 0222780b98ac48e89b1b4f57c9df8590 msgid "`arguments`" msgstr "" -#: ../../src/topics/expressions.md:68 -#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 -#: ef2b8433778a40408f179c3e6f0cf99e -#: 224732683a9c41f3ba1b778851e745a8 -#: 17b10d1e91b24dc582df98fcd2ac850e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 -#: e4e68011dc5f42e4918c747afa7d764b +#: ../../src/topics/parameter-references.md:86 ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 e4e68011dc5f42e4918c747afa7d764b #: d44e3cfa661840eb851782e24caf1b68 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 -#: 0bddedfe40e841f7878e09792531e6bf +#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf #: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 -#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 #: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 -#: 2437656e20354d63bede1b98d5348e2c +#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c #: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 -#: 8210b36347a749889450529ecdf4ff0e -msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +msgid "" +"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" -#: ../../src/topics/expressions.md:73 -#: ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 -#: ../../src/topics/expressions.md:93 +#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 -#: d0a92a3792b549e9b5ddce4667d168d2 -#: 801729c7c71b4109824b035437e69bf9 -#: 1bc510d525f0414e88692e356e67fbbc -#: d2e246ae56a24e4abdd6b7d9812a86e2 -#: b1446bab2732412e91f721a08067b0bd -#: e89dbeb22f41430ca39c923d9fdf68cb -#: bd61499b71e64164878dea08d6d7141e +#: ../../src/topics/parameter-references.md:90 d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb bd61499b71e64164878dea08d6d7141e #: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" -#: ../../src/topics/expressions.md:74 -#: ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 -#: ../../src/topics/expressions.md:94 +#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 -#: 8a1748579de14f0888d5ee9023e37c2d -#: f760465a49d64d4c8468ad9c4fea62b1 -#: 28b6b5ffa7524374aaa9525ebfafb762 -#: d11f6a19ddf34cf19ec856bacf998e29 -#: bcb7cd10cb5947bb9d85c040f57f954f -#: da5188d3bedc4997a35bdf417f2f643c -#: cd7a0190511d4613b09600a3b1e9d55f +#: ../../src/topics/parameter-references.md:91 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c cd7a0190511d4613b09600a3b1e9d55f #: 47def3b078e2402182039be0227090ae msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 -#: 23088850ad02459696f6bbd385109aac -msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +msgid "" +"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 -#: f02257a822ad46ac93c5981531cc85d5 -msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +msgid "" +"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 -#: 989a1c4aaa1143be9f53b90cd8b6d500 -msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "" +"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 -#: 582b03ac742745a89f4dfc86b7404db2 +#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 #: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 -#: d555a3d991e344a5a8e1289168d7c6d1 +#: ../../src/topics/parameter-references.md:79 d555a3d991e344a5a8e1289168d7c6d1 #: 44b3f123c9b04a308c1161b742a7b34b msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 -#: e9fa9430535c424fa3e8be5d460d2ba4 +#: ../../src/topics/parameter-references.md:80 e9fa9430535c424fa3e8be5d460d2ba4 #: 0e306cc923974d1db83fdfb45105a11c msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 -#: d289541e460147aa933f7878996f8649 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +msgid "" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 -#: b0290d1a477b48119e17cf1fed9d6dff +#: ../../src/topics/parameter-references.md:84 b0290d1a477b48119e17cf1fed9d6dff #: 446f1190af7a40a0913ff04ce7aa938c msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 -#: 81b4d1f23a3642bfa9bb395b94260cd1 -msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "" +"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 -#: e1cde4aa32c041238ed2596173c6d824 +#: ../../src/topics/parameter-references.md:87 e1cde4aa32c041238ed2596173c6d824 #: 557694f82e314baa9ccafba14d6ff2c9 -msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgid "" +"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." +"html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 -#: c2a92d3eca7f4ee39cec649170eeea53 +#: ../../src/topics/parameter-references.md:88 c2a92d3eca7f4ee39cec649170eeea53 #: 3c939769ede94602a67fc50c435741cf msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 -#: f495da32f05a4a5ba9539be0a54c1a59 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +msgid "" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](https://www." +"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 -#: bdb4c68a175047ddbe141ca24960127f -msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +msgid "" +"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 -#: 4b73495cf18a4d908525292b6f23c419 +#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 #: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 -#: 718ceee9973240ec9c100977bbcc8921 +#: ../../src/topics/parameter-references.md:94 718ceee9973240ec9c100977bbcc8921 #: 2b25152f6df5494a8632f3ce631c20d8 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 -#: c07ab08eb75d4528949c56a3d7c12b28 +#: ../../src/topics/parameter-references.md:95 c07ab08eb75d4528949c56a3d7c12b28 #: 846cd427ae25410eae7c920b237edcb0 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 -#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 #: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 -#: 700c57ccd5e347be86702c83a8af24b3 +#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 #: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 -#: 509a5e2ec52d413eb57754d359f133e4 +#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 #: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 -#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 #: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b -#: e3b76f42c924489f9a0bcf5a7b636d23 +#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 -#: 97b61352363f47cb890e8937c5613fa3 -msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +msgid "" +"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e -#: a258554d462f4f5f83ece28d5b2fc584 +#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 -#: 8d0b142bb7ed4e61b8fb03de197240ce +#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: effc0208cf4f4551958db6e526c0528b -#: 9d4889c8cec24351a7a9e3c547e331b6 +#: effc0208cf4f4551958db6e526c0528b 9d4889c8cec24351a7a9e3c547e331b6 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: be6c1e85c7b6495d8086c262daad20e7 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +#: be6c1e85c7b6495d8086c262daad20e7 af4f7f232a9d42388c0ba1cfc7c2cdf7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 -#: 6abeba392b0444b19f92a19f178a4682 +#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 -#: 0bc424ef2ca346099f29b937379908a0 -msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +msgid "" +"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd -#: 949c376120d8441796ec9c89364f8851 +#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 -#: 10d36a1adfd04144b401c993b12b4094 -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +msgid "" +"Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 -#: 29b73e1dd72744f68377f0a38c10f062 -msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +msgid "" +"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " +"attribute that allows users to load external JavaScript files, or to provide " +"inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 -#: 38a2afaf4a6c4d04909af22c93f2808d -msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts of " +"the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 -#: cd74f34b21af4de9be96fd897efc469b -msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +msgid "" +"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." +"org/v1.0/CommandLineTool.html#Expressions) that the only version of " +"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" +"international.org/5.1/). This means that any code that you include or write " +"in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 -#: f12e371f3f1a4b0cb2cff9800352d48c -msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " +"function inline in `expressionLib`. That function can then be used in other " +"parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 -#: 49d0fda2fc144e0b8b7c92afc1d8945e +#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 -#: 8f0e8f050e334ac08334e9215e1dcf61 -msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result in " +"the `echo` command printing the input message with capital initial letters:" msgstr "" -#: ../../src/topics/expressions.md:149 -#: 26c74b11bb1849cea0763bb74ec43e42 +#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 -#: 7a6be0005a6441feb67f036d005d7885 -msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 -#: ed590f9e6f4f425da886b110295c45db +#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 -#: 093235307d6f47d4858e559b780ef5e5 +#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 -#: 06635145b441418aaae84dc804f3d6ac -msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +msgid "" +"The `custom-functions.js` file is included in the CWL document with the `" +"$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 -#: 973a9b257b1a4f0dbd4444d4f11dadd7 +#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 -#: 04eaf1f7c630450db318dcd8b7626e15 -msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +msgid "" +"Finally, note that you can have both inline and external JavaScript code in " +"your CWL document. In this final example we have added another entry to the " +"`expressionLib` attribute with the new function `createHelloWorldMessage`, " +"that calls the `capitalizeWords` function from the external file `custom-" +"functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 -#: c4098489fbb049789f022cd3e5c3d49b +#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 -#: 5979e4ae5c424276bdbc47f69b379d0f +#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 -#: fd4579a3c9844492b314b5c3c1775fc7 -msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +msgid "" +"The `$include` statement can be used to include a file from the local disk " +"or from a remote location. It works with both relative and absolute paths. " +"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." +"html#Include) from the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 -#: 3f038e7371f84ed9b4547358dfb55a11 +#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 -#: e024bcb70e04412e90e1838426d1b69a -msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +msgid "" +"Tools and workflows can take `File` types as input and produce them as " +"output. We also recommend indicating the format for `File` types. This helps " +"document for others how to use your tool while allowing you to do some " +"simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 -#: a3db21c0b3114802a8a5b610e252ef13 -msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM in " +"our example), reference a local ontology for your institution, or do not add " +"a file format initially for quick development before sharing your tool with " +"others. You can browse existing [IANA file format listings][IANA] and [EDAM " +"file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 -#: 0f5bc8520d6a4dafa37c65343da9702a -msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` section " +"of the document in greater detail, so don't worry about these for now." msgstr "" -#: ../../src/topics/file-formats.md:17 -#: 5cb830da47464a8b9c3950983fa4d56f -msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 -#: 0535d5de416b4ea3b2f5996583deecc1 +#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 -#: fb47f73c38cf4ec59bd3021866a631f8 +#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 -#: 74b28c1b09c6429b82e462e4ec61808e +#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 -#: a2ce43b391864e8bbde16328cc19b32b -msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +msgid "" +"Below is an example of a parameter file for the example above. We encourage " +"checking in working examples of parameter files for your tool. This allows " +"others to quickly work with your tool, starting from a \"known good\" " +"parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 -#: aebee48b742c4145a600fd2daf8c75dc +#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 -#: 56ee4dcfff6141d5bef80eb96559876d -msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +msgid "" +"___Note:___ To follow the example below, you need to download the example " +"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 -#: 8d3a6d83e2e54c56995893c41590b7ff +#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 -#: 5abcdebfa1cb401bb8892553be285fd3 +#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 -#: d3a55f71dc244026a97902de9ed819ea +#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 -#: 96671c56523c4ea9992fb5dfcfa6490e -msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to run " +"the tool. Each parameter has an `id` for the name of parameter, and `type` " +"describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 -#: bcc6246742cb46bfb185e415c4a3431a -msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +msgid "" +"Available primitive types are *string*, *int*, *long*, *float*, *double*, " +"and *null*; complex types are *array* and *record*; in addition there are " +"special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 -#: 86dce36de687449c88fb5eb9d64eb045 -msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 -#: cd9cea15f57b492ba4098237cd7c5bed +#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 -#: 8bdb875b63104f699efe28ea0abb1e3d +#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 -#: c6a0151a68494c0cb0176781e65e252e +#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 -#: dc5e6b5e01d64226bd5dbbf3175fe010 +#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 -#: 36ab1d9edafc4831bb1bca5f123b04b0 -msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "" +"You can use `cwltool` to create a template input object. That saves you from " +"having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 -#: 7dc630ea86464b1dba3a4e5079260b3b -msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " +"> inp-job.yml`, and then modify the default values with your desired input " +"values." msgstr "" -#: ../../src/topics/inputs.md:44 -#: ae37901a8dbe48a59e27ab4e2e6e2d30 -msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 -#: 651e032007ea4a119d20c820bb61f86b -msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " +"command line." msgstr "" -#: ../../src/topics/inputs.md:53 -#: 0b056dde9e87428996e47870b12119da -msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +msgid "" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " +"boxed text describes these two commands and the expected output from the " +"command line:" msgstr "" -#: ../../src/topics/inputs.md:64 -#: 628124a1670b4b058bb0fb6e495a099c -msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not explicitly " +"specified" msgstr "" -#: ../../src/topics/inputs.md:70 -#: 10ca6321ce3e4b08ab6a5bb380b19c11 -msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "" +"The field `inputBinding` is optional and indicates whether and how the input " +"parameter should appear on the tool's command line. If `inputBinding` is " +"missing, the parameter does not appear on the command line. Let's look at " +"each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 -#: ec2adb3912bc46e28891229e9e0d9a1c -msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +msgid "" +"Boolean types are treated as a flag. If the input parameter \"example_flag" +"\" is \"true\", then `prefix` will be added to the command line. If false, " +"no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 -#: a519be60726a44af9941fdce04735353 -msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +msgid "" +"String types appear on the command line as literal values. The `prefix` is " +"optional, if provided, it appears as a separate argument on the command line " +"before the parameter . In the example above, this is rendered as `--example-" +"string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 -#: cb8fc8c4c79e467eac5fab4ca685201e -msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +msgid "" +"Integer (and floating point) types appear on the command line with decimal " +"text representation. When the option `separate` is false (the default value " +"is true), the prefix and value are combined into a single argument. In the " +"example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 -#: a26cc105716f47cb807174c9003153b0 -msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the parameter " +"is optional. In the example above, this is rendered as `--file=/tmp/random/" +"path/whale.txt`. However, if the \"example_file\" parameter were not " +"provided in the input, nothing would appear on the command line." msgstr "" -#: ../../src/topics/inputs.md:131 -#: cc159dd5fe5748caac838862f5b8c4d1 -msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +msgid "" +"Input files are read-only. If you wish to update an input file, you must " +"[first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 -#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 -msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "" +"The value of `position` is used to determine where parameter should appear " +"on the command line. Positions are relative to one another, not absolute. " +"As a result, positions do not have to be sequential, three parameters with " +"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " +"than one parameter can have the same position (ties are broken using the " +"parameter name), and the position field itself is optional. The default " +"position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 -#: 6812698e9ad84d3385de5e88e9dde0b3 -msgid "The `baseCommand` field will always appear in the final command line before the parameters." +#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +msgid "" +"The `baseCommand` field will always appear in the final command line before " +"the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 -#: 9654e65b1c0642dbb5d4f34edb211989 +#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 -#: d1f02be278754267893dfce5a940997d -msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to provide " +"`type` field with `type: array` and `items` defining the valid data types " +"that may appear in the array. Alternatively, brackets `[]` may be added " +"after the type name to indicate that input parameter is array of that type." msgstr "" -#: ../../src/topics/inputs.md:154 -#: 01f30e38dfdd452dba3a996073936e16 +#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 -#: 787d4bfb093c4ad287b902084706b751 +#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:166 -#: ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 -#: 588f0f7f967f4d69af27c9729d6d3119 -#: 02adef8ee8204842b5b4a0408f3bac33 -#: 9db68837918a4a349f32f15f12697a1d -msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 9db68837918a4a349f32f15f12697a1d +msgid "" +"Now invoke `cwltool` providing the tool description and the input object on " +"the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 -#: 75d59e395c66416cae9b352db5081516 -msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +msgid "" +"The `inputBinding` can appear either on the outer array parameter definition " +"or the inner array element definition, and these produce different behavior " +"when constructing the command line, as shown above. In addition, the " +"`itemSeparator` field, if provided, specifies that array values should be " +"concatenated into a single argument separated by the item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 -#: 874c6f19abbf45d7ab7d30a378c4048d -msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` in " +"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " +"where array values that are not defined with an associated key are marked by " +"a leading `-`. This will be demonstrated in the next lesson and is discussed " +"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " +"arrays of arrays, arrays of records, and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 -#: 5d7d7a28cc5d4862803032aec78174d9 +#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 -#: dea0d4b681f94e73b13965dcfe75cf7d -msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be provided " +"together (they are exclusive). You can use records and type unions to group " +"parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 -#: ddf598abf4f34aca9fffa045860fbf96 +#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 -#: d52a8089920e45bd89d582533b50e3a1 +#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 -#: 750474486a84482292eeba45f118287f -msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 -#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 -#: 1eb0e39bb6d04b8cab300f44a79f3add -msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the first " +"matching item (`itemC`) is added to the command line and remaining item " +"(`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 -#: bc21ee10bff843689cc98ac6630edcea +#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 -#: 4b2ab812f62c4f949dd25c8527f2411c -msgid "In the third example, only `itemD` is provided, so it appears on the command line." +#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +msgid "" +"In the third example, only `itemD` is provided, so it appears on the command " +"line." msgstr "" -#: ../../src/topics/inputs.md:255 -#: b771302d1bec4050a9417b080eef76c9 +#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 -#: 2c3b884cb1c54521900cc90782e8a58d -msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +msgid "" +"If you use exclusive input parameters combined with expressions, you need to " +"be aware that the `inputs` JavaScript object will contain one of the " +"exclusive input values. This means that you might need to use an **or** " +"boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 -#: a1073b6306044dffb414319ae01f68bb -msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from an " +"enum." msgstr "" -#: ../../src/topics/inputs.md:265 -#: 4a31c733092142b1af834eab1747c224 +#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 -#: 9a1d92334685449386dfa3b3a899ed48 -msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you provide a " +"valid value, such as “fasta” (one of the values of the enum), your command " +"should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 -#: fb623af4c480411b8fde28d01c981411 -msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +msgid "" +"However, if you do not provide any input value, then `file_format` will be " +"evaluated to a `null` value, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your workflow." msgstr "" -#: ../../src/topics/inputs.md:289 -#: e98e165f6bba40809c90473d72f9d592 -msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +msgid "" +"To correct it, you must remember to use an or operator in your JavaScript " +"expression when using exclusive parameters, or any parameter that allows " +"`null`. For example, the expression could be changed to `$(inputs." +"file_format || 'auto')`, to have a default value if none was provided in the " +"command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 @@ -2134,12 +2475,25 @@ msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 #: cd64d2d828834cbbb24ea5358caf5405 -msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgid "" +"Implementation extensions not required for correct execution (for example, " +"fields related to GUI presentation) and metadata about the tool or workflow " +"itself (for example, authorship for use in citations) may be provided as " +"additional fields on any object. Such extensions fields (e.g. `format: edam:" +"format_2572`) can use a namespace prefix listed in the `$namespaces` section " +"of the document (e.g. edam: http://edamontology.org/) as described in the " +"[Schema Salad specification][schema-salad]. Once you add the namespace " +"prefix, you can access it anywhere in the document as shown below. " +"Otherwise, one must use full URLs: `format: http://edamontology.org/" +"format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 #: 80af387fe3ff4e2da999903385bd602b -msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to cite " +"your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 @@ -2154,7 +2508,12 @@ msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 #: cb9980db4e5f4c74b01c2dec6d5e92d0 -msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgid "" +"For those that are highly motivated, it is also possible to annotate your " +"tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints at " +"hardware requirements in order to use the tool, and a few more metadata " +"fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 @@ -2162,259 +2521,301 @@ msgstr "" msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 -#: 8acf361cf77c4d45ba3f2e344146259f +#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 -#: 83d3b9a0ed3148fda9ce72cd108cb9e1 -msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-line " +"tool, or an expression tool. It is a step of a workflow that specifies " +"inputs and outputs, but it does not provide enough information to be " +"executed." msgstr "" -#: ../../src/topics/operations.md:7 -#: 5565c1b2d8a349169a305a9b26b4574d -msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +msgid "" +"You can create operations to visualize a workflow during development, before " +"you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 -#: 49cf614893d8438299b3bca384eb40cf +#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 -#: 88160cef4cfa4add9020aa89511a5749 -msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +msgid "" +"The `uppercase` step of the workflow is an operation. It can be used like a " +"command line tool or an expression. You can also plot it with the CWL Viewer " +"or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 -#: 2f73a786b5d94dc0b23ed0cdd185afc8 -msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "" +"The output of the command above can be rendered with a Graphviz renderer. " +"The following image is rendered with the Sphinx Graphviz directive (this " +"user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 -#: 730ba1434a1445ae847ec6153b6a3b72 -msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +msgid "" +"If you try running it with `cwltool`, the command will fail since `cwltool` " +"does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 -#: 98d9b8d867594543890af99e77e24edb +#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 -#: a25d0b1e13324b40a6b8fcd227948c4f -msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A " +"CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 -#: da077da5eb8a4ffebfde041fc16300de +#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 -#: 1b3016f0462f42deb42ddaa33f28bf3d +#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 -#: d661df070e3040869da412d07a71f716 -msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name of " +"parameter, and `type` describing what types of values are valid for that " +"parameter." msgstr "" -#: ../../src/topics/outputs.md:10 -#: a11585474d3849cca5467512ed964743 -msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +msgid "" +"When a tool runs under CWL, the starting working directory is the designated " +"output directory. The underlying tool or script must record its results in " +"the form of files created in the output directory. The output parameters " +"returned by the CWL tool are either the output files themselves, or come " +"from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 -#: 2682f9ca8e604a0c9986f7746fdec960 -msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 -#: 7e3fa7baf0f549ec89457e7004ac9545 +#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 -#: 22447a560f6f4317bf67bd7c4336126c -msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string we can use an " +"_array of strings_. The first element is the command to run, and any " +"subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 -#: f1ee2e00b0cc4112b51c9df3a919b73f +#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 -#: ad8e1acb251246d2a47c39b20d4e483a +#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 -#: dc200c6960ae4476a772645d021f14b8 +#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 -#: 52703d6b7f914097934bfad13663abeb -msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +msgid "" +"And now invoke `cwltool` with the tool description and the input object on " +"the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 -#: 5e1c79df657d4a6e84e055dd6b300a5d -msgid "The field `outputBinding` describes how to set the value of each output parameter." +#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +msgid "" +"The field `outputBinding` describes how to set the value of each output " +"parameter." msgstr "" -#: ../../src/topics/outputs.md:62 -#: 329d2809dfae4f90bc638f5f03a47ee3 -msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +msgid "" +"The `glob` field consists of the name of a file in the output directory. If " +"you don't know name of the file in advance, you can use a wildcard pattern " +"like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 -#: 96df2d45e42441d49ce193ccbfab78a3 +#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 -#: c6bcf7c6a8774dd6be41cc775848c3b8 -msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "" +"To capture a tool's standard output stream, add the `stdout` field with the " +"name of the file where the output stream should go. Then add `type: stdout` " +"on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 -#: 9d86c03ab44841c785b924cc44727e31 +#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 -#: 2fb58c2feaa84970bb5274c49f4b5b64 +#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 -#: 9647019d8c37466886e7aab6f176634d -msgid "You can also capture multiple output files into an array of files using `glob`." +#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 -#: b9eaf21f5e014eefaae301c47dafd144 +#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 -#: cffff6c43b4945daa3b2a49763bc50ae +#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 -#: cc067051f22f433bbece08f60933e002 -msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions to " +"mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 -#: a190a6440ec34898990cdac05d809f22 +#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 -#: dbfe2c1123144316aa026374b0f353d3 -msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../src/topics/parameter-references.md:13 -#: 280f1a07d0ae41d7a4674504f832fcf0 +#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file we " +"were interested in was called \"hello.txt\", and this was written into the `." +"cwl` file. This is not the best way to do this, as the \"hello.txt\" " +"filename may vary or be dependent on the input file(s) used. To avoid this " +"we can specify the name of the file we want in the job parameters file (`." +"yml`). In this example, you will see how to reference the value of input " +"parameters dynamically from other fields, which will allow us to then " +"specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 -#: 5c64d938862747cb9fb52515a656ce27 +#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 -#: 074cf5d912854d8c864607cc24b15302 -msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +msgid "" +"Create your input files and invoke `cwltool` with the tool description and " +"the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 -#: 0290af3e3cbb4b32b0450c8771f3bf95 -msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "" +"Certain fields permit parameter references which are enclosed in `$(...)`. " +"These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 -#: b54240bb94f746bba7511633aa969db0 -msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" +"$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 -#: 8b70a072aa87414c88e89a3e19af0a51 -msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +msgid "" +"The value of the \"inputs\" variable is the input object provided when the " +"CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 -#: eea20f89c45f424a888178df53713b28 -msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +msgid "" +"Note that because `File` parameters are objects, to get the path to an input " +"file you must reference the path field on a file object; to reference the " +"path to the tar file in the above example you would write `$(inputs.tarfile." +"path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 -#: cb4ea13f5db84c0da43df3f7f2478d78 +#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 -#: 6d3fb423e6c4434697cd113fb27e28ad +#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 -#: 7647e0229a924f988cf02b7812a55c06 -msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +msgid "" +"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 -#: 9d663249666045618a0d3acddb85a9a9 -msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +msgid "" +"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 -#: 5fed4984f6784347b4cbe0630b1dd2c2 -msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "" +"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 -#: dbf6153cd02542a6a01c172803122b7f -msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +msgid "" +"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 -#: b6250cf6fa8a4a0c94b33302e0decca5 -msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +msgid "" +"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 -#: fa6ca3bbc6784380a03a950a6f49a180 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +msgid "" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 -#: b92b516e537a4773ad67b4af586e7a25 -msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +msgid "" +"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 -#: 467a701228504d06b971b79a59c69064 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +msgid "" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 -#: 2634f989eb304009a8568d70ed42786c -msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +msgid "" +"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 #: 5d8bed66282c408695292ea92a03b2c4 -msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgid "" +"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 @@ -2424,7 +2825,9 @@ msgstr "" #: ../../src/topics/parameter-references.md:107 #: 9a6b311ded8d4e43ae635b1b927dbdf2 -msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgid "" +"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 @@ -2439,687 +2842,897 @@ msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 #: 574d93d1d592458a985f259519c036cb -msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a `SoftwareRequirement` field in the `hints` section. This may also " +"help to avoid confusion about which version of a tool the description was " +"written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 #: 82e48b3e3c3f451480cc0b6a529271f6 -msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgid "" +"In this example, the software requirement being described is InterProScan " +"version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 #: 02e40154eac74ecc98d0447d03475b44 -msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the [dependency " +"resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 #: 8cb1c5d9b1a54c40924099494eb766c6 -msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 -#: b85eb83e05e845d7a179f1b1d74db444 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the tool " +"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " +"up in the [SciCrunch][scicrunch] registry, which provides a portal for " +"finding, tracking, and referring to scientific resources consistently. If " +"you want to specify a tool as a `SoftwareRequirement`, search for the tool " +"on SciCrunch and use the RRID that it has been assigned in the registry. " +"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " +"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." +"org][identifiers]) in the `specs` field of your requirement description. " +"Other good choices, in order of preference, are to include the DOI for the " +"main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 -#: 35f97d37492b4c7ca3ad6cfc1e6fa366 -msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "" +"Normally, input files are located in a read-only directory separate from the " +"output directory. This causes problems if the underlying tool expects to " +"write its output files alongside the input file in the same directory. You " +"use `InitialWorkDirRequirement` to stage input files into the output " +"directory. In this example, we use a JavaScript expression to extract the " +"base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 -#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 -#: 0f7508ce59754a7eb230dea6042244c6 +#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 -#: fbe0c65b444441f785d0054176d036a6 -msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +msgid "" +"In this section you will find ways to troubleshoot when you have problems " +"executing CWL. We focus on `cwltool` here but some of these techniques may " +"apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 -#: 1b6b7a75cc754775bf9dd80c0941e8da +#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 -#: 9a710602e00c4934ae3a3b471aa68458 -msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor output " +"files, but created while your workflow is running). By default, these files " +"are created in a temporary directory but writing them to a separate " +"directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 -#: 21b5be7270a14f0987240c81d1ec879b -msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " +"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " +"olleH\". However, the second step, `step_b`, **has a typo**, where instead " +"of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 -#: 0490b1fab86749e49b473949c52bbe8b +#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 -#: cfe9d8241fe84bd5b74042a5625d933f -msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " +"(`cwltool` will create the directory for you if it does not exist already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 -#: 764d933cc4da446abd8dd8f913f05dac -msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. You " +"can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 -#: c93efc6d4e004859981ee7f5fa28ed03 -msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +msgid "" +"Each workflow step has received a unique ID (the long value that looks like " +"a hash). The `${HASH}.status` files display the status of each step executed " +"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " +"output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 -#: 546601da44cb49bd9611b1c85807fd90 -msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " +"the `step_b`). After fixing the typo, when you execute `cwltool` with the " +"same arguments as the previous time, note that now `cwltool` output contains " +"information about pre-cached outputs for `step_a`, and about a new cache " +"entry for the output of `step_b`. Also note that the status of `step_b` is " +"now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 -#: 7e0bf00f8ce542b9b009cdcf1945a9e5 -msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had " +"been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for " +"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " +"re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 -#: eff5f28ca83c458a9b07faf7a81f7e91 +#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 -#: 2e634f3737d04d279ae78ceee4b0a664 +#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 -#: e07f33d01b804663a25ffb08aad74821 -msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 -#: 7a644506619a4f08958ec7d4540cd557 -msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +msgid "" +"[Docker][docker] containers simplify software installation by providing a " +"complete known-good runtime for software and its dependencies. However, " +"containers are also purposefully isolated from the host system, so in order " +"to run a tool inside a Docker container there is additional work to ensure " +"that input files are available inside the container and output files can be " +"recovered from the container. A CWL runner can perform this work " +"automatically, allowing you to use Docker to simplify your software " +"management while avoiding the complexity of invoking and managing Docker " +"containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the container." msgstr "" -#: ../../src/topics/using-containers.md:18 -#: b5195b7d8eaa419fb2b90cb33a57783a -msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +msgid "" +"This example runs a simple Node.js script inside a Docker container which " +"will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 -#: 7921a837ee744c5aa9a5bda04b0c8db1 +#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 -#: 387e9bc9381a4450af54aff77e4df6a2 +#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 -#: 2713594c937d4c528fc8d04d9e9819ed -msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 -#: cf94c1424fc2413c85647fd1ee73d951 -msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that is " +"really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:52 -#: dc0452107c604e29bdf32bb289fe5db8 -msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using the " +"Node Js runtime that is meant for Javascript files. We then need to specify " +"some `hints` for how to find the container we want. In this case we list " +"just our requirements for the docker container in `DockerRequirements`. The " +"`dockerPull:` parameter takes the same value that you would pass to a " +"`docker pull` command. That is, the name of the container image (you can " +"even specify the tag, which is good idea for best practices when using " +"containers for reproducible research). In this case we have used a container " +"called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " +"the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 -#: 1a5596243cec4c948d9b6bf0bb12fad0 +#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 -#: 483181f498fc4d968b5fe6ef427709f7 -msgid "Notice the CWL runner has constructed a Docker command line to run the script." +#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." msgstr "" -#: ../../src/topics/using-containers.md:72 -#: 7487485d6aa4458089a4b4bdf107ea64 -msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +msgid "" +"In this example, the path to the script `hello.js` is `/home/me/cwl/" +"user_guide/hello.js` outside the container but `/var/lib/cwl/" +"job369354770_examples/hello.js` inside the container, as reflected in the " +"invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 -#: 7394e7690f934043af617436b40845f0 +#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 -#: b9ae9e9a896048caad7e6c38a5bc1bd1 -msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 -#: f228fb7953ea48ed99d89880205f4620 +#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 -#: 5870ac44e4c24b8daf5f06c49f95ce04 -msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier examples." msgstr "" -#: ../../src/topics/workflows.md:51 -#: a913c76d06164fa18718a8a6a7dcf0d6 +#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 -#: 93188ed43ee949cc98b3ea679ce14feb -msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +msgid "" +"A command-line tool or expression tool can also be written directly in the " +"same CWL document as the workflow. For example, we can rewrite the `echo-" +"uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 -#: 36618126a4df4326b236ebe2ea42cffa +#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 -#: 1cc17ad26e9c474b895ba5cd20c8b66a -msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "" +"Having separate files helps with modularity and code organization. But it " +"can be helpful writing everything in a single file for development. There " +"are other ways to combine multiple files into a single file (e.g. `cwltool --" +"pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 -#: 24aca0bea4d94e3593b844cf0586cffe -msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this " +"user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 -#: 46cc4859856e4367a9e5e68eecd48b73 +#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 -#: 9c56528acd5f49deb139e034dfbfac7c -msgid "This workflow extracts a java source file from a tar file and then compiles it." +#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +msgid "" +"This workflow extracts a java source file from a tar file and then compiles " +"it." msgstr "" -#: ../../src/topics/workflows.md:170 -#: 55ab007d472f43388e4c77aae8f165e7 +#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:179 -#: ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa -#: 307b6618a92948fca4203ccb497c77e6 +#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 -#: a2dd833fdca4443181648e41051a5232 -msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +msgid "" +"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" +"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 -#: 7e40cc9f9e1341c195e843c009575b94 -msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a " +"run:" msgstr "" -#: ../../src/topics/workflows.md:185 -#: 26c51dcb76364ed780376aecb7cbacda +#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 -#: 6fcf8ad3d1bd49afa4a105622437bd59 -msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 -#: 71cb81fa4511495b80422244849979e4 +#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 -#: def35d6021394def80a53ae49a2cdbde -msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a workflow." msgstr "" -#: ../../src/topics/workflows.md:221 -#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 -msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a list " +"of input parameters where each parameter consists of an identifier and a " +"data type. These parameters can be used as sources for input to specific " +"workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 -#: c84d4450bc6a475dbf34e0b22cea9130 -msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a list " +"of output parameters where each parameter consists of an identifier and a " +"data type. The `outputSource` connects the output parameter `classfile` of " +"the `compile` step to the workflow output parameter `compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 -#: cca9665f6daa44b49233baf34ab9fcc7 -msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second step " +"compiles the file from the first step using the java compiler. Workflow " +"steps are not necessarily run in the order they are listed, instead the " +"order is determined by the dependencies between steps (using `source`). In " +"addition, workflow steps which do not depend on one another may run in " +"parallel." msgstr "" -#: ../../src/topics/workflows.md:256 -#: 547edbf5fa424b8286cc21674ff159b0 -msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input " +"parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 -#: 7ca248888b9d484cb544cd76ba538662 -msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +msgid "" +"The ``in`` section of the workflow step connects these two input parameters " +"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " +"`source`. This means that when the workflow step is executed, the values " +"assigned to `tarball` and `name_of_file_to_extract` will be used for the " +"parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 -#: ae6b240718104380b08db5552d7355ea -msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +msgid "" +"The `out` section of the workflow step lists the output parameters that are " +"expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 -#: e5a8b7f84be64020b191099f3fad30ed -msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " +"in [Additional Arguments and Parameters](additional-arguments-and-parameters." +"md)). The output of this step `classfile` is connected to the `outputs` " +"section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 -#: f0b04849253c4693904512ddd7f9ce84 +#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 -#: 12a06d8358534102b202965d4258c18e -msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +msgid "" +"Workflows are ways to combine multiple tools to perform a larger operations. " +"We can also think of a workflow as being a tool itself; a CWL workflow can " +"be used as a step in another CWL workflow, if the workflow engine supports " +"the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 -#: 1658cac0de1b47e9b60f6d4a4ad9bb19 -msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 -#: 49ed137fe996452a8534c68d100db941 +#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 -#: b7f93705e5b8416696be01850072e8c0 -msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 -#: e87045829b344089ab59dc27063ddd7a -msgid "\"Visualization \"Visualization" +#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +msgid "" +"This two-step workflow starts with the `create-tar` step which is connected " +"to the `compile` step in orange; `compile` is another workflow, diagrammed " +"on the right. In purple we see the fixed string `\"Hello.java\"` being " +"supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:322 -#: 42ef2f145b824d69b63abc1da175c216 -msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +msgid "" +" \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " +"CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " +"to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 -#: c61cedf543664d388183e04b3939cc39 -msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and `*.java` " +"filename. This is generally best-practice, as it means it can be reused in " +"multiple parent workflows, or even in multiple steps within the same " +"workflow." msgstr "" -#: ../../src/topics/workflows.md:341 -#: 9e39e3f1501c4fcaab3e8962e090f6be -msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar " +"file at `tarball`, which we will prepare in the `create-tar` step. At this " +"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " +"specific input/output names, as those also appear in its usage as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 -#: 03e2f767c4da461982fc3c0f3ba94762 -msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 -#: 3bea5822b8694e2aa32c446e1c54a045 -msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +msgid "" +"In this case our step can assume `Hello.java` rather than be parameterized, " +"so we can use hardcoded values `hello.tar` and `Hello.java` in a " +"`baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 -#: 426023bd6e3a471cbb30dbda3d6f9e57 -msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This is " +"generally not best practice, as the tool then can't be reused. The reason " +"for doing it in this case is because the command line is hard-coded with " +"filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 -#: 0d498cd4caf54c15891ca1afe58e2727 -msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +msgid "" +"In this example we had to prepare a tar file outside, but only because our " +"inner workflow was designed to take that as an input. A better refactoring " +"of the inner workflow would be to take a list of Java files to compile, " +"which would simplify its usage as a tool step in other workflows." msgstr "" -#: ../../src/topics/workflows.md:394 -#: b2d75045e02741b4850f5ff1243f7858 -msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL " +"Tool description, care must be taken to improve its usability in multiple " +"workflows." msgstr "" -#: ../../src/topics/workflows.md:398 -#: cfa765264a27411ab914de569aa3dac4 +#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 -#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 -msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " +"run a tool or workflow multiple times over a list of inputs. The workflow " +"then takes the input(s) as an array and will run the specified step(s) on " +"each element of the array as if it were a single input. This allows you to " +"run the same workflow on multiple inputs without having to generate many " +"different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 -#: 5fa79c62049a447c8328ebf9db54ebf4 -msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +msgid "" +"The most common reason a new user might want to use scatter is to perform " +"the same analysis on different samples. Let's start with a simple workflow " +"that calls our first example (`hello_world.cwl`) and takes an array of " +"strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 -#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 -#: 3a67d77a2e7b4c0bb61cc3585ceae942 -msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "" +"Aside from the `requirements` section including `ScatterFeatureRequirement`, " +"what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 -#: f1cb55fc59824cc18a95fd6dcb32cf4c -msgid "First of all, notice that the main workflow level input here requires an array of strings." +#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 -#: d947c54933d64aad90df392a1cedd63f -msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This field " +"tells the runner that we'd like to scatter over this input for this " +"particular step. Note that the input name listed after scatter is the one of " +"the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 -#: 651d35997332404186aa6d5711da4a3d -msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if you " +"expect that the final output of your workflow will now have multiple outputs " +"to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 -#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 -#: 842b926ae34542cb9023021f137b08be +#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 -#: b662c1a5a4424c8d8350a806356acc61 -msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " +"calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 -#: 04d6babfd87343d7a5f13867ea02b65f -msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +msgid "" +"You can see that the workflow calls echo multiple times on each element of " +"our `message_array`. Ok, so how about if we want to scatter over two steps " +"in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 -#: 2eaacf1a90204a2b9bd621344560f2a1 -msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding the " +"following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 -#: 242993d42b164ee5abe7ca10d45856de +#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 -#: 4a94e5f7e1bc4d628702140e4e51d6d3 -msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "" +"And add a second step that uses `wc` to count the characters in each file. " +"See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 -#: e61d93b848184c8e8e573928427b4d0a +#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 -#: e3a7182f00f440b8b5461da91194a64b -msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under each " +"step:" msgstr "" -#: ../../src/topics/workflows.md:491 -#: 99fa96caacaa45cb97aded9a24fcac6d +#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 -#: b5338f39e8c74ff28e139da68089a742 -msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 -#: f6d92156d67c4a339bcfd194cff897df -msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +msgid "" +"Here we have placed the scatter field under each step. This is fine for this " +"example since it runs quickly, but if you're running many samples for a more " +"complex workflow, you may wish to consider an alternative. Here we are " +"running scatter on each step independently, but since the second step is not " +"dependent on the first step completing all languages, we aren't using the " +"scatter functionality efficiently. The second step expects an array as input " +"from the first step, so it will wait until everything in step one is " +"finished before doing anything. Pretend that `echo Hello World!` takes 1 " +"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " +"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " +"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " +"actually finish in 8 minutes because the first step must wait on `echo Hallo " +"welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can " +"make an entire workflow a single step in another workflow! Convert our two-" +"step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 -#: 1c9e386922324ec8a59306572c19fb8b +#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 -#: d80ab383eec9402faba997b548fe42eb -msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +msgid "" +"Now the scatter acts on a single step, but that step consists of two steps " +"so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 -#: f7d2827d97db4bf4ab84b5d6621c3b48 +#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 -#: 49217c02f58c43ff9ec00f10da8d4e84 -msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 -#: 20b9f181420c401d8615c17a10027517 +#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 -#: 8dbd56473f8c40c0bb12a48be06117e3 -msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +msgid "" +"The first thing you'll notice is that this workflow is only compatible for " +"version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 -#: 78d7f3ede2c746d482042adef050b2c4 -msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when` is " +"where the condition validation takes place. In this case only when `in1` " +"from the workflow contains a value `< 1` this step will be executed." msgstr "" -#: ../../src/topics/workflows.md:587 -#: cbbf93c70fe04ba7932ba25758ddc611 -msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " +"will pass the first conditional step and will therefore be executed and is " +"shown in the log by `INFO [step step1] start` whereas the second step is " +"skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 -#: cfa1c1fde4454df283f87cc54a9c59ec -msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +msgid "" +"When a value of 3 is given the first conditional step will not be executed " +"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 -#: 1a8be2950cbb475bbb2617e005f0fac9 -msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +msgid "" +"If no conditions are met for example when using `--val 2` the workflow will " +"raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 -#: 5f09d4d897cf457d80b9a11b8c01747e +#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 -#: 5d83c56102e141cc978500f678dd0c1c -msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers and " +"humans. This guide introduces the features of YAML that are relevant when " +"writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 -#: c38438fbf9a04e729ec2e3c962435289 +#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 -#: fdb9cc750cec43ee962517e637dc5fea +#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 -#: 08da9cd8056b4ddd8f5150cc85ba72ee +#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 -#: b027fc234ed943bbb00d4c6bc03c040a +#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 -#: b8befec0d8684638aaa616a659e0100c +#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 -#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 -#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 -#: 98056c5cfd5640ad9de0679360797cc7 +#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 -#: cda73485875d4c8e9464679a20558616 -msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " +"is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have special " +"meaning in the CWL specification and underscored key names otherwise. For " +"example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 -#: 98cae24919b74c088a5d89706aec581b -msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " +"and `home` - with their four respective values. Values can be character " +"strings, numeric (integer, floating point, or scientific representation), " +"Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 -#: b4b0940b4b5743c09637b36b964202d0 -msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may change " +"the way that they are interpreted i.e. `\"1234\"` will be treated as a " +"character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a " +"command: in CWL all parts of `baseCommand` must be strings so, if you want " +"to specify a fixed numeric value to a command, make sure that you wrap that " +"numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 -#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 -#: 9ca3554d771d45998e88aaede525b227 -msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program interpreting " +"the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 -#: 3fca839cede94cfd8e4f605c73ba699d -msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +msgid "" +"If there is anything on the line before the comment, be sure to add at least " +"one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 -#: da34c635707345b2a5e85a2fcd30bbaf +#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 -#: 3ded0f125249485c921994b6e6b93ac9 -msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, these " +"hierarchical structures are described in YAML by providing additional key-" +"value pairs as the value of any key. These pairs (sometimes referred to as " +"\"children\") are written on new lines under the key to which they belong " +"(the \"parent\"), and should be indented with two spaces (⇥tab characters " +"are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 -#: 53ece35d309a4c8d99f1efb2122a7092 -msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " +"while one of these children, `inputBinding`, contains a further two key-" +"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " +"below for more information about providing multiple values/key-value pairs " +"for a single key. For comparison with the example YAML above, here is a " +"graphical representation of the `inputs` object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 -#: d74321b111d84ae7a515f2f17dd39e23 +#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 -#: 7fc0bdf2489a44f2a29e71b86f7c0055 -msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) section " +"above, more than one key-value pair can be mapped to a single key. However, " +"it is also possible to define multiple values for a key without having to " +"provide a unique key for each value. We can achieve this with an _array_, " +"where each value is defined on its own line and preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 -#: fd64dd818ec64bb6aa9a11586a5747f6 +#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 -#: 8c06e542dd4144fa83388d8142552c8d +#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 -#: 87bafb845c714b109874f6137b84462d -msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " +"can also be defined in YAML using the native JSON syntax. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 -#: 5ab9ddf613a540a2b8228e37600cc5dc +#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 -#: fcd05b1ef31a4046946a2399c7fc5575 -msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +msgid "" +"Native JSON can be useful in indicating where a field is intentionally left " +"empty (such as `[]` for an empty array), as well as where it makes more " +"sense for the values to be located on the same line (For example, when " +"providing option flags and their values in a shell command). However, as the " +"second example above shows, it can severely affect the readability of a YAML " +"file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 -#: f4b8fc8236044fada420def13a02813d +#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 -#: 859368c1f25c4a4aad57abfd046c63f5 -msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " +"while we wrote this guide, though it also covers features that are not valid " +"in CWL." msgstr "" -#: ../../src/tutorials.md:1 -#: 2203c93f02ac4514a43508ecb98dfcc5 +#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 -#: 5d92464923c245818c070fbef102be89 -msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to the " +"list." msgstr "" -#: ../../src/tutorials.md:7 -#: 8a5cd557dab5456bb41cdc24af73b50c +#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 -#: 13d7e2e92e96432787c712cf6a595424 -msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +msgid "" +"[Introduction to Workflows with Common Workflow Language: For Contributors.]" +"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 -#: 0abdd85c9b964a4e89ba3d80a6c78d6f +#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 -#: 3cbf1f69a5514fd3bee90e68b201190f +#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 -#: 68c97a7065634d02956f3f5c1d4eeb9f +#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 -#: a67c7e0eaf4e4d27b3e5db303333a088 +#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" diff --git a/locales/pt_PT/LC_MESSAGES/user_guide.po b/locales/pt_PT/LC_MESSAGES/user_guide.po index 53e29057..3f68a232 100644 --- a/locales/pt_PT/LC_MESSAGES/user_guide.po +++ b/locales/pt_PT/LC_MESSAGES/user_guide.po @@ -19,19 +19,21 @@ msgstr "" "Plural-Forms: nplurals=2; plural=n > 1;\n" "X-Generator: Weblate 4.17-dev\n" -#: ../../LICENSE.md:2 -#: 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.md:4 -#: 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" msgstr "Material Instrucional" -#: ../../LICENSE.md:6 -#: 747f9dd48bc54f44adcd8b18c57f4d9d -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "" +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable summary " +"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" +"[cc-by-legal]." msgstr "" "Todo o material instrucional do projeto Common Workflow Language e " "alterações na estrutura também são disponibilizados sob a [licença Creative " @@ -39,267 +41,292 @@ msgstr "" "humanos de (e não um substituto para) o [texto legal completo da licença CC " "BY 4.0][cc-by-legal]." -#: ../../LICENSE.md:12 -#: 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" msgstr "Tem o direito de:" -#: ../../LICENSE.md:14 -#: 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +msgid "" +"to **Share**---copy and redistribute the material in any medium or format" msgstr "" "**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " "formato" -#: ../../LICENSE.md:15 -#: 18a3a0aec35743848c97bc178f9c94ff +#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" -#: ../../LICENSE.md:17 -#: b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." msgstr "para qualquer fim, mesmo que comercial." -#: ../../LICENSE.md:19 -#: 6021e65292a149d5b15e14491f3eb05e -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the license " +"terms:" msgstr "" "O licenciante não pode revogar estes direitos desde que você respeite os " "termos da licença:" -#: ../../LICENSE.md:24 -#: 8fb7a2946c384364814c6ec3910997d3 -msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a [link to the license][cc-by-human], and indicate if changes were " +"made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." msgstr "" -#: ../../LICENSE.md:32 -#: 8161753b7526445db319210044566200 -msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" msgstr "" "**Sem restrições adicionais**---Não pode aplicar termos jurídicos ou medidas " "de caráter tecnológico que restrinjam legalmente outros de fazerem algo que " "a licença permita. Com o entendimento de que:" -#: ../../LICENSE.md:36 -#: 15314ba527864eaa834cf1185cfcc4e3 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +msgid "" +"You do not have to comply with the license for elements of the material in " +"the public domain or where your use is permitted by an applicable exception " +"or limitation." msgstr "" "Não tem de cumprir com os termos da licença relativamente a elementos do " "material que estejam no domínio público ou cuja utilização seja permitida " "por uma exceção ou limitação que seja aplicável." -#: ../../LICENSE.md:39 -#: b351ddf9847d48b1a2a87fc78eaba4d2 -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "" +"No warranties are given. The license may not give you all of the permissions " +"necessary for your intended use. For example, other rights such as " +"publicity, privacy, or moral rights may limit how you use the material." msgstr "" "Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " "autorizações necessárias para o uso pretendido. Por exemplo, outros " "direitos, tais como direitos de imagem, de privacidade ou direitos morais, " "podem limitar o uso do material." -#: ../../LICENSE.md:44 -#: a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea msgid "Software" msgstr "Software" -#: ../../LICENSE.md:46 -#: 84b2c685bbab48449fdc72d2a1e42bf4 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the " +"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Salvo indicação em contrário, os programas de exemplo e outro software " -"fornecido pelo projecto Common Workflow Language são disponibilizados sob a [" -"licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a " +"[licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." -#: ../../LICENSE.md:51 -#: 0f68eafafaef4b54accba7e13bfaa702 -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." msgstr "" "A menos que exigido pela lei aplicável ou acordado por escrito, o software " "distribuído sob a Licença é distribuído \"COMO ESTÁ\", SEM GARANTIAS OU " "CONDIÇÕES DE QUALQUER TIPO, expressas ou implícitas. Consulte a Licença para " "obter o texto específico sobre as permissões e limitações sob a Licença." -#: ../../src/_includes/what-is-cwl.md:1 -#: ../../src/_includes/what-is-cwl.md:2 -#: eab02dc13915490bb3c9ba744d78b6a7 -#: d4f35995b0f6494d9771a4be0a82538f +#: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 d4f35995b0f6494d9771a4be0a82538f #: d6ccd4b546254f56a597d67dd4fdc5d6 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece of " +"software, tools and workflows described using CWL are portable across a " +"variety of platforms that support the CWL standard." msgstr "" "CWL é uma maneira de descrever ferramentas de linha de comando e de conectá-" "las formando workflows. Como a CWL é uma especificação e não um software, " "ferramentas e workflows descritos com a CWL são portáveis entre uma " "variedade de plataformas que suportam o padrão CWL." -#: ../../src/episodes.md:5 -#: ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc -#: 436cfca6f857469bbff7c652df32160f +#: ../../src/episodes.md:5 ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f msgid "This page has moved" msgstr "Esta página foi movida" -#: ../../src/episodes.md:9 -#: cc11f5d29206492d9f2f0922882b6159 -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." msgstr "" "O conteúdo desta página está desatualizado e foi mantido para preservar os " -"links do antigo Guia do Utilizador. Por favor, use o novo [Índice](index.md" -"#table-of-contents) para navegar o Guia do Utilizador." +"links do antigo Guia do Utilizador. Por favor, use o novo [Índice](index." +"md#table-of-contents) para navegar o Guia do Utilizador." -#: ../../src/faq.md:1 -#: e2ed894d325a4f50a5e2dc69da5531a1 +#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" msgstr "Perguntas Frequentes (FAQ)" -#: ../../src/faq.md:11 -#: 61edb787dab04ca2ad3ed07616d878a0 +#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "Usando `evalFrom` para Tipos Diferentes de \"`File`\"" -#: ../../src/faq.md:41 -#: d5321589e7ed4f0db3c630cc39800791 +#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" msgstr "Renomear um Arquivo de Entrada" -#: ../../src/faq.md:43 -#: fc62427c0a004810b055dee90ec5e2d9 -msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +msgid "" +"This example demonstrates how to change the name of an input file as part of " +"a tool description. This could be useful when you are taking files produced " +"from another step in a workflow, and don't want to work with the default " +"names that these files were given when they were created." msgstr "" "Este exemplo demonstra como mudar o nome de um arquivo de entrada como parte " "da descrição da ferramenta. Isso pode ser útil quando você tem arquivos " "produzidos em outro passo de um workflow, mas prefere não utilizar os nomes " "dados por padrão quando estes arquivos foram criados." -#: ../../src/faq.md:59 -#: 1c6b8a4194a14611b4061b1540c3807f +#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" msgstr "Renomear um Arquivo de Saída" -#: ../../src/faq.md:61 -#: bc7ad10c929848a3a9a240a3c501d299 -msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +msgid "" +"This example demonstrates how to change the name of an output file from the " +"default name given to it by a tool:" msgstr "" "Este exemplo demonstra como escolher o nome para um arquivo de saída " "diferente do nome padrão criado por uma ferramenta:" -#: ../../src/faq.md:82 -#: 7225a993d281421b95c8e3df2846a0e3 +#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 msgid "Referencing a Local Script" msgstr "Como Fazer Referência a um Script Local" -#: ../../src/faq.md:84 -#: 7ef1dbb81993473f948d9c6f3c64b381 +#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" msgstr "Há duas maneiras de fazer uma referência a um script local:" -#: ../../src/faq.md:86 -#: 450edf800a18423195bea4fe8793a2cb -msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +msgid "" +"The first method involves adding the folder containing your scripts to the " +"`PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." msgstr "" "A primeira maneira é adicionando o arquivo que contém os seus scripts para a " "variável de ambiente `PATH`. Desta maneira você pode executar o shell script " "diretamente sem utilizar comandos via `sh` ou `bash`." -#: ../../src/faq.md:89 -#: 1a8cc75ea6174b9297871b2e58971077 +#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "Comece adicionando a _shebang_ no topo do seu arquivo:" -#: ../../src/faq.md:95 -#: a7d84f740a714ec588503ee084fbbc34 -msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +msgid "" +"After that, make the script executable with the command `chmod +x scriptname." +"sh`" msgstr "" "Em seguida faça o seu script executável com o comando `chmod +x scriptname." "sh`" -#: ../../src/faq.md:97 -#: 569d553abe85450c9d1c37456bf412f4 -msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." msgstr "" "E finalmente, modifique o seu `PATH` para adicionar o diretório que contém o " "seu script. (É boa prática usar `$HOME/bin` para scripts do utilizador " "local)." -#: ../../src/faq.md:104 -#: 95f5dbbd21084a318413b9528fb867be -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be +msgid "" +"Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" "Agora você pode utilizar `baseCommand: scriptname.sh` para rodar o script " "diretamente." -#: ../../src/faq.md:113 -#: 1b3cae80fa9a40ffb2259b8c1cd2b468 -msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." msgstr "" "Depois quando você quiser compartilhar o seu trabalho, é possível utilizar " "um container de software com ferramentas como Docker." -#: ../../src/faq.md:115 -#: 8d86baa239364f799d4f9d5ea2b0e314 -msgid "The second method involves including an input of `type: File` in the script itself:" +#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +msgid "" +"The second method involves including an input of `type: File` in the script " +"itself:" msgstr "O segundo método utiliza um input `type: File` diretamente no script:" -#: ../../src/faq.md:135 -#: f2c109998c76434893ff16b17fdb2bd0 +#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." msgstr "Em CWL tudo deve ser declarado diretamente." -#: ../../src/faq.md:138 -#: c2c752b86bf94d6fb3751f4dd81bc7a7 +#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "Definindo Bindings de Inputs utilizando `self` para Inputs Opcionais" -#: ../../src/faq.md:140 -#: 2c38cc58cbb340bc935a5f00e96ba95c -msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their input " +"binding makes use of `self`. Below is an example workaround for this, " +"pending a more sophisticated fix." msgstr "" "No momento `cwltool` não funciona quando inputs opcionais não estão " "presentes se o binding de input deles utilizar `self`. O exemplo abaixo " "contém uma solução alternativa para este problema, até que haja uma solução " "mais elegante para este problema." -#: ../../src/faq.md:165 -#: ce6db54bd0f54839a5beb948530a21f0 +#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" msgstr "Modelar um Parâmetro do tipo \"um-ou-o-outro\"" -#: ../../src/faq.md:167 -#: d06cbf89028b4638ad54c2529bcbfa25 -msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +msgid "" +"Below is an example showing how to specify different strings to be added to " +"a command line, based on the value given to a Boolean parameter." msgstr "" "O exemplo abaixo demonstra como especificar diferentes strings que serão " "adicionadas à linha de comando, dependendo do valor de um parâmetro Boolean." -#: ../../src/faq.md:188 -#: d53fb28dcad04e7788cba9e280a2343c +#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "Conectar um Único valor a um Input que Espera uma Lista daquele Tipo" -#: ../../src/faq.md:190 -#: d9e30e11533b4d53a144f5df7041268d -msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +msgid "" +"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 -#: 941077158ec54ae19bfa2e2ad6662da1 +#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 -#: 937cb94a370640c788fbc3fe0b19f2e5 -msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +msgid "" +"The input must be an array consisting of exactly one entry for each input " +"link. If \"merge_nested\" is specified with a single link, the value from " +"the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 -#: a1d57e15656548128a76a8b975c564c9 +#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" "Que significa \"criar uma lista com exatamente estes sources como elementos\"" -#: ../../src/faq.md:201 -#: c8c235a9bf6240628f0b5493ffebf7e0 -msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " +"add `linkMerge: merge_nested` under the appropriate `in` entry of the " +"destination step." msgstr "" "Ou em outras palavras: se o parâmetro destino for do tipo `File[]` (uma " "lista de `File`s) e a fonte é um único `File`, adicione então " @@ -307,252 +334,274 @@ msgstr "" "adicione `linkMerge: merge_nested` sob a entrada apropriada `in` ao step que " "receberá o parâmetro (target)." -#: ../../src/faq.md:229 -#: 3da4dcb043eb4423a53a14182949d9cd +#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" msgstr "Inputs Opcionais 💯" -#: ../../src/faq.md:231 -#: 89b90d3bf1ea4ebd88482d435241fac5 -msgid "To make an input parameter optional, add a question mark to the type declaration." +#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." msgstr "" "Para fazer um parâmetro de entrada opcional, adicione um ponto de " "interrogação à declaração do tipo." -#: ../../src/faq.md:247 -#: a854006054ce4ffe94bbfa73bdbecbf2 +#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 msgid "" msgstr "" -#: ../../src/faq.md:248 -#: f80eb714e9df417fbba555b5dd5f4d8c +#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c msgid "Enum Inputs ⚜️" msgstr "Inputs Enum ⚜️" -#: ../../src/faq.md:250 -#: 10af80fa13af4158aec7060550485350 -msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +msgid "" +"For command line flags that require a specific input as the argument an enum " +"type can be declared in CWL. **Specifying null here is known as long form " +"style. It does the same thing as the question mark on the other inputs.**" msgstr "" "O tipo enum por ser utilizado em CWL para flags de linha de comando que " "requerem um tipo de input específico como argumento. **Especificar null aqui " "é tido como forma estendida. O resultado é o mesmo que o uso do ponto de " "interrogação nos outros inputs.**" -#: ../../src/faq.md:267 -#: ad1c26711ccd4efd8fdb25f9293d33fd +#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd msgid "" msgstr "" -#: ../../src/faq.md:268 -#: 49e2095b51f84f609f5d4bc088ad9745 +#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 msgid "Record Inputs 📀" msgstr "Inputs do tipo Record" -#: ../../src/faq.md:270 -#: 52b8538177c64090af51f5f6a696c28c -msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 -#: f96c9257e3734b8aa0cc5e065f74f944 +#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" msgstr "Definindo Parâmetros Mutualmente Exclusivos" -#: ../../src/faq.md:324 -#: 7dc0540508084a3495ff3b2ac90fd323 -msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +msgid "" +"To properly set fields in a record input type, you need to pass a dictionary " +"to the input to properly set the parameters. This is done by using inline " +"JavaScript and returning the dictionary with the key of the field you want " +"to set. The source field is set to indicate the input from the workflow to " +"be used as the value." msgstr "" -#: ../../src/faq.md:342 -#: b53dc77466b24a67b52b8aadf4fab724 +#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" msgstr "Utilizando Booleans" -#: ../../src/faq.md:344 -#: cf4e7f3977ae4f9b877072c2b1c4b533 +#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" msgstr "Estes são definidos através do campo padrão" -#: ../../src/faq.md:349 -#: 99b37739ef18443ca7c0e715a131e0c7 +#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" msgstr "Concatenando Strings em Inputs" -#: ../../src/faq.md:351 -#: 9b00b5a55ee941e1adbfe89e133791e3 +#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." msgstr "O campo valueFrom deve ser utilizado ao invés do valor padrão." -#: ../../src/faq.md:359 -#: 07922147f7ab487ba2a1e7c43c9f410c +#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "Erros do `cwltool` devido a Nomes de Arquivos com Espaços" -#: ../../src/faq.md:361 -#: 7a11806f0c7045b48fe58a271f814797 +#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" "O `cwltool` não permite alguns caracteres em nomes de arquivos por padrão." -#: ../../src/faq.md:363 -#: fdaec25650ab4b0fb1c527610e24ae5a -msgid "For example, the filename `a space is here.txt` includes 3 space characters." +#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +msgid "" +"For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" "Por exemplo, o nome de arquivo `um espaco vai aqui.txt` inclui 3 espaços.." -#: ../../src/faq.md:371 -#: 182959fc9f4746d082994e07d05c8cde -msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." msgstr "" "Se você não tem opção e precisa utilizar estes caracteres apesar do risco, " "você deve então passar `--relax-path-verificks` ao chamar o `cwltool`." -#: ../../src/faq.md:373 -#: cc7752e9989e4a6d957682f479d6fc60 +#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" "Erro de Referência em Parâmetro CWL devido a Hífen no Identificador de " "Entrada" -#: ../../src/faq.md:375 -#: 6db1ebd2d6c74ceca889662cd7df5cd5 +#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" msgstr "Se `cwltool --validate` valida com sucesso" -#: ../../src/faq.md:384 -#: 3de2513c7d7b4569ba63f7e6d29137b7 +#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" msgstr "Mas ao executar o workflow um erro como o seguinte aparece:" -#: ../../src/faq.md:396 -#: ae3a9188706649e28f97bc4ec34c0821 +#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" msgstr "Este é o arquivo" -#: ../../src/faq.md:410 -#: e1ac97ab6ad3449b8c54933d25257f73 +#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." msgstr "O problema é causado pelo `-` (hífen)." -#: ../../src/faq.md:423 -#: f6c402f7f6974edbbb5582c8e22f3869 +#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "Para corrigir este erro, substitua o `-` (hífen) por `_` (sublinhado)" -#: ../../src/faq.md:436 -#: 190099a242a645c9b9f8bc3ce89d920d -msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +msgid "" +"If it is not possible to change the input identifier, then you can use an " +"alternative CWL Parameter Reference syntax:" msgstr "" "Se não for possível mudar o identificador do input, você pode reescrever " "utilizando uma sintaxe alternativa para Referências de Parâmetros CWL:" -#: ../../src/faq.md:442 -#: 06a4f6ffc2da4d43b453d4784b42efd3 +#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" msgstr "Utilizar CWL e cwltool com Singularity" -#: ../../src/faq.md:445 -#: 1901c34201054a9cae199b0dbb8b945e -msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +msgid "" +"The CWL standards are built around (optional) Docker format containers. The " +"reference runner and several other CWL implementations support running those " +"Docker format containers using the Singularity engine. Directly specifying a " +"Singularity format container is not part of the CWL standards." msgstr "" -#: ../../src/faq.md:450 -#: 2d498470524d47f18f9936ace6acebb0 +#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" msgstr "Depurar Expressões JavaScript" -#: ../../src/faq.md:452 -#: d7b044f5224a48eda09bc949cf645193 -msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +msgid "" +"You can use the --js-console option of cwltool, or " +"you can try creating a JavaScript or TypeScript project for your code, and " +"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 -#: 2754519265eb426b940bbbd2b8d64e1e +#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 -#: f8d6e4cd54cb42c88182a43171d97bab -msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +msgid "" +"This guide will introduce you to writing workflows using the [Common " +"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " +"guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 -#: 132d40fee3b84469afa80d5ff613bf77 +#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 -#: 0f47157605a34ea58770ea898deebae4 -msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +msgid "" +"If you find that something is missing from this guide, or if you would like " +"to provide other feedback, file an Issue on the [project repository for this " +"guide][repo]. You can also suggest changes directly in a Pull Request by " +"clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" -#: ../../src/index.md:16 -#: 6d269e8d70184034bcb56385a6ca198f +#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 -#: ed74c9a4b623464480e2c184668fcec0 -msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +msgid "" +"If you are a beginner user get started with the [Introduction](/introduction/" +"index.md) section. For advanced users the subsections of the [Topics](/" +"topics/index.md) have detailed information about the most common topics for " +"CWL." msgstr "" -#: ../../src/index.md:23 -#: cfa67cf5521b414da6f7d34cbed283f7 -msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +msgid "" +"The Table of Contents is displayed at the top menu and also on the left " +"sidebar. It also appears further down this page but with links to " +"subsections. The right sidebar contains links to the sections of each page, " +"and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 -#: ee6b82bd86264e4bb1e8e4065b1e6b9c +#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 -#: e208c8a7506e41dcac9a403c5d2850c1 +#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 -#: ac62d326a68145b695e46b714d4e8156 -msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are expected " +"to be familiar with workflow managers, YAML, and comfortable with following " +"instructions for the command-line. The other sections of the user guide " +"cover the same concepts, but in more detail. If you are already familiar " +"with CWL or you are looking for more advanced content, you may want to skip " +"this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 -#: 984e6676b9d04c7092bc492f195dfb91 +#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" msgstr "A Especificação CWL" -#: ../../src/introduction/basic-concepts.md:21 -#: cbe1d761da5b403d9605fa1fb8e62fdf -msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered in " +"this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 -#: 3a71b269bd3c49eb913cf69b60373c24 -msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes that " +"are backward-compatible. The last number is used for bug fixes, like typos " +"and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 -#: b171b72c48d44050a3416a7a42c4021d -msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +msgid "" +"The model used for the specification version is called Semantic Versioning. " +"See the end of this section to [learn more](#learn-more) about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 -#: b3df1607e9d242d78b22dc44335fbe2d +#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" msgstr "Implementações" -#: ../../src/introduction/basic-concepts.md:39 -#: 078b58ffc1cc4d25a7c4eea3bb76e025 -msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "" +"An implementation of the CWL specification is any software written following " +"what is defined in a version of the specification document. However, " +"implementations may not implement every aspect of the specification. CWL " +"implementations are licensed under both Open Source and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 -#: c3869b4ec5ff47d99e8da79770722e04 -msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud " +"and high performance computing environments where tasks are scheduled in " +"parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 -#: 2482c84831fc4dfab629e7bfcfb41cbf +#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." msgstr "" @@ -563,7 +612,11 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:107 #: 86e6a06992dc4228bfda7add48e28ca3 -msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The " +"behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification " +"{{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 @@ -593,27 +646,44 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:119 #: cf2922f645904ac7955428ecddc37b8a -msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 #: 5f47aae608c041aeb4134d59dad314d2 -msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be used " +"to simplify workflows and command-line tools, moving common parts of a " +"workflow execution into reusable JavaScript code that takes inputs and " +"produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 #: f6f589481d0c4891beaccb63160619ef -msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgid "" +"Operation is an abstract process that also takes inputs, produces outputs, " +"and can be used in a workflow. But it is a special operation not so commonly " +"used. It is discussed in the [Operations section](../topics/operations.md) " +"of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 #: 73b0c1ccb18c4b74a2c0fdf9706eca85 -msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgid "" +"The workflow is a process that contains steps. Steps can be other workflows " +"(nested workflows), command-line tools, or expression tools. The inputs of a " +"workflow can be passed to any of its steps, while the outputs produced by " +"its steps can be used in the final output of the workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 #: 4ace6b92f4e04a07aa202840ebe36417 -msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through *requirements*. " +"There are many requirements defined in the CWL specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 @@ -628,17 +698,26 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:143 #: 907674a4ecff4826a2b880e28fc38f33 -msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgid "" +"`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 #: 037cd0e5ceda482eaeaca03d51745aee -msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgid "" +"Some CWL runners may provide requirements that are not in the specification. " +"For example, GPU requirements are supported in `cwltool` through the " +"`cwltool:CUDARequirement` requirement, but it is not part of the " +"{{ cwl_version }} specification and may not be supported by other CWL " +"runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 #: e4643938445b48cc80eb8973ceeb126e -msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgid "" +"Hints are similar to requirements, but while requirements list features that " +"are required, hints list optional features. Requirements are explained in " +"detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 @@ -648,17 +727,33 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:157 #: 3eb6a013a2a4478ca2ad134661f65c58 -msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created. It " +"is thus important that workflows support the creation of FAIR data and " +"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" +"workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 #: 074af9633627470485e5225326d5f20a -msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\", " +"CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 #: 847951c055b94a83b1e081594cef22ee -msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, and " +"scalability; tools and workflows described with CWL can transparently " +"leverage technologies such as Docker and be used with CWL implementations " +"from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 @@ -668,10 +763,8 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 -#: 65c24244713741e196da08cb9ba237b2 -#: f059896039524095b4deb65d693f8ddf -#: 3439764fab0e49d2bcb7c9fbae556e65 +#: ../../src/introduction/quick-start.md:94 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf 3439764fab0e49d2bcb7c9fbae556e65 msgid "Learn More" msgstr "Saiba Mais" @@ -682,20 +775,26 @@ msgstr "Versionamento Semântico - " #: ../../src/introduction/basic-concepts.md:181 #: 36eb4b3b966640af90faa55db3789cb6 -msgid "The CWL Specification page in the CWL website: " +msgid "" +"The CWL Specification page in the CWL website: " msgstr "" "A página web da Especificação CWL: " #: ../../src/introduction/basic-concepts.md:182 #: 2ccb956baa6b4376a04ad9fcc4654631 -msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" -"A especificação CWL atual no GitHub: {{ ''.format(cwl_version_text) }}" +"A especificação CWL atual no GitHub: {{ ''.format(cwl_version_text) }}" #: ../../src/introduction/basic-concepts.md:183 #: 72889b830c514afe9a7cb1e64b5666a0 -msgid "The list of Implementations in the CWL website: " +msgid "" +"The list of Implementations in the CWL website: " msgstr "" "A lista de Implementações na página web da CWL: " @@ -707,414 +806,478 @@ msgstr "PROV-O: A Ontologia PROV - " #: ../../src/introduction/basic-concepts.md:185 #: c377a7f5dbe645cebbb6c7eccf831a0b -msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 -#: 1769a0cbf4de4d77879c1f202cd11af9 +#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" msgstr "Introdução" -#: ../../src/introduction/index.md:3 -#: 950370f0a36048b38e1bde9b78f80816 -msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that " +"are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 -#: f01faaf1b253407cbbc2f353c24774f3 +#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" msgstr "Pré-requisitos" -#: ../../src/introduction/prerequisites.md:6 -#: 353b14f06ee845d0a06a829643e31534 -msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +msgid "" +"The software and configurations listed in this section are prerequisites for " +"following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements focuses " +"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " +"runner or workflow system, but the results and interface may look different " +"(though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 -#: b5a0607096814c0aa577f977c3b57c54 +#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" msgstr "Implementações da CWL" -#: ../../src/introduction/prerequisites.md:14 -#: ff2bb4c6504b456bac7ca9c514414dbf -msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +msgid "" +"There are many implementations of the CWL standards. Some are complete CWL " +"runners, while others could be plug-ins or extensions to workflow engines. " +"We have a better explanation in the [Implementations](basic-concepts." +"md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 -#: cbbcce4c2a96471b8b0ae3593ad59de4 +#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 -#: 5089fdba8aed4113983fa86e698df98b -msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +msgid "" +"We recommend using an up-to-date operating system. You can choose any of the " +"following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 -#: dbaa4bae22fe4d05b18d7351967ddbc3 +#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" msgstr "Linux" -#: ../../src/introduction/prerequisites.md:25 -#: c05187af85be41b782678b79627f8fbf +#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf msgid "macOS" msgstr "macOS" -#: ../../src/introduction/prerequisites.md:26 -#: beb6cf4d7c154eb9b6d7fe024a318ed7 +#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" msgstr "Windows" -#: ../../src/introduction/prerequisites.md:29 -#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 -msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "" +"If you are using Windows, you will have to install the [Windows Subsystem " +"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " +"installing WSL2. Your operating system also needs internet access and a " +"recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 -#: 56d78c95daa54135b6aa9b2bfdc34d01 +#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 -#: 0f2704bf1f7148be95e999e312899f11 -msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL community. " +"It is also the CWL reference runner, which means it must support everything " +"in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 -#: 86264c9e56104ecea9146407c379aae2 -msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +msgid "" +"`cwltool` can be installed with `pip`. We recommend using a virtual " +"environment like `venv` or `conda`. The following commands will create and " +"activate a Python virtual environment using the `venv` module, and install " +"`cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 -#: 0a0f0e5151ab4c498b4f8a12c016f28d +#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." msgstr "Instalando `cwltool` com `pip` e `venv`." -#: ../../src/introduction/prerequisites.md:62 -#: f7aaafeee230400da056464c853582c2 -msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +msgid "" +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool#install) for other ways to install `cwltool` with `apt` and " +"`conda`." msgstr "" "Visite a [documentação](https://github.com/common-workflow-language/" "cwltool#install) do `cwltool` para outras opções para instalar `cwltool` com " "`apt` e `conda`." -#: ../../src/introduction/prerequisites.md:65 -#: 5eced7e4cd084e8a806b1d3b12d0c000 +#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" "Vamos usar uma simples descrição de ferramenta CWL `true.cwl` com `cwltool`." -#: ../../src/introduction/prerequisites.md:67 -#: 040c019b6e844eda8c8c2b210852516b +#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" msgstr "`true.cwl`" -#: ../../src/introduction/prerequisites.md:73 -#: 6391e08e0bde49f4b21286d8fdb97433 -msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the CWL " +"standards. However, these actions will be performed without running the " +"document. To validate CWL workflows (or even a standalone command line tool " +"description like the above) pass the `--validate` option to the `cwltool` " +"command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 -#: cdef47fca304479c9a9df75afc0afb35 +#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 -#: d41c4bc740aa474ea09a7cbd267c8840 -msgid "You can run the CWL tool description by omitting the `--validate` option:" +#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 +msgid "" +"You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 -#: 24d7be55d3994f0b82c38da47918e0c9 +#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 -#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" msgstr "Módulo Python cwl-runner" -#: ../../src/introduction/prerequisites.md:93 -#: 096d0a50f69e48bd9915238d1b4264c1 -msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be invoked " +"independently, and is not reliant on a particular CWL runner program name. " +"Users can invoke `cwl-runner` instead of invoking a CWL runner like " +"`cwltool` directly. The `cwl-runner` is installed by a system administrator " +"or user to point to the preferred CWL implementation. This is convenient for " +"environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 -#: f9df974a8e2645a6918e67466bd1fdc2 -msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +msgid "" +"The CWL community publishes a Python package with the name `cwlref-runner` " +"that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 -#: 71ebe91d4bda473abe87578929433212 +#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 -#: 746c6fc9c29d466494458a08d4c96672 -msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` executable, " +"which will invoke `cwltool`. You should have the same results and output as " +"in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 -#: b9cc5a843a0f49daad56e9303657bdd5 +#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 -#: 34ab40437ab646488ba3ee86cd7fe071 +#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." msgstr "Executando `true.cwl` com `cwl-runner`." -#: ../../src/introduction/prerequisites.md:125 -#: 705807fae182425dbf4244dbf2be1226 -msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For " +"that, the first thing you need to do is copy `true.cwl` workflow into a new " +"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 -#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 -#: 164c438baab54ec19bbb4584a10dd411 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 +msgid "" +"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 -#: bf8be77af6154326b28442c5d2e2b852 +#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 -#: 695184d1b45a42f393e2da99c3721773 -msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +msgid "" +"And finally, you can execute it directly in the command-line. On execution, " +"the program specified in the shebang (`cwl-runner`) will be used to execute " +"the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 -#: 7c4f45b3e7b549e186126693aa4a3d4f +#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 -#: 3ba23b4ea01c46848e4e43bbeff5f5a1 -msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute the " +"script using the executable specified after the shebang. It is considered a " +"good practice to use `/usr/bin/env ` rather than using a hard-" +"coded location, since `/usr/bin/env ` looks for the " +"`` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 -#: eec6c07455384630809ff1c532bfe7d4 +#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" msgstr "Editor de Texto" -#: ../../src/introduction/prerequisites.md:163 -#: f6b39b12bd5c495cb53e2795bf9200ed -msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 -#: 2fdb62a13f9447bc89183426260ce781 -msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting " +"and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 -#: 1f07135156254f74a6b043bf33d00cc3 -msgid "Visual Studio Code with the Benten (CWL) plugin - " +#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " msgstr "" -#: ../../src/introduction/prerequisites.md:172 -#: de344f356b1c466d9131cdbd4d7353a3 -msgid "cwl-plugin for IntelliJ - " +#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +msgid "" +"cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 -#: 3f9324ede11441f58d93875867034cf0 -msgid "The CWL community also maintains a list of editors and viewers: " +#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +msgid "" +"The CWL community also maintains a list of editors and viewers: " msgstr "" -#: ../../src/introduction/prerequisites.md:177 -#: 6ce8b81560e341c580d316d69202b268 +#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 -#: 40cfd559d6a848d1aae354d3bdaa8e9c -msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: ." msgstr "" -#: ../../src/introduction/prerequisites.md:185 -#: 8a9a50b0ebe847ce90593881ffe0d69c -msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models with " +"and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 -#: 923cf9dd6d6c417aabe42f9fa62ffa35 -msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for pulling " +"images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 -#: 9390b03889de44638141d705e0ef8322 -msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the next " +"section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 -#: 12042e411482458f8c35a2491f9433e0 +#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 -#: cdd4196f9aa34beba115901ec97913b6 +#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 -#: c43d9675ed134b78b02acb5a102a764a -msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +msgid "" +"This section will show you a brief overview of what CWL is, and where you " +"can learn more about it. No previous knowledge of CWL is required, but you " +"must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 -#: 280936bb2a22469799b2c9e9ba22adee +#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 -#: cb203354977d42a58112d09357f62565 -msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " +"example below shows a simple CWL “Hello World” workflow annotated with " +"comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 -#: 9e51962a7e5c47248f3e20703ae101eb +#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 -#: 7e475e3f3c4a4404bb0236124c0f7ce7 -msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the " +"same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 -#: 82613ca4e32b4ccab1b7735f5ba2d5a1 -msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "" +"In CWL, there is a distinction between a command-line tool and a workflow. " +"But for the sake of simplicity, we are using the term “workflow” here. You " +"will learn more about this in the [basic concepts](basic-concepts.md) " +"section." msgstr "" -#: ../../src/introduction/quick-start.md:32 -#: 498a43362a4749f3b8b433709d34a1d5 +#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 -#: f3e56aedd56b4b93bdc3894273e8c144 -msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the CWL " +"*Reference Runner* for the specification, and it is compliant with the " +"latest version of the specification: {{ cwl_version }}. You can install " +"`cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 -#: 81481f5b82e4488398f87f0a169bd359 +#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." msgstr "Instalando `cwltool` com `pip`." -#: ../../src/introduction/quick-start.md:47 -#: a81342e756d24c40acc15835d0a768f2 -msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the " +"[prerequisites](prerequisites.md) section contains other ways to install " +"`cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 -#: c12cf89f8b9a421ebd05330326e219b3 +#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" msgstr "Executando \"Hello World\"" -#: ../../src/introduction/quick-start.md:53 -#: 9b68bcb1a41849dc9601ab47c5bbb0fe -msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " +"workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 -#: ce04027dfcfe4b7b91ea3c2136b18b23 +#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "Executando `hello_world.cwl` com `cwltool`." -#: ../../src/introduction/quick-start.md:62 -#: 0d8a788402914ebd8f09a5ca80650011 -msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 -#: 6d0b679efab24813a7a3b709ade940d1 +#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 -#: 2ea056ab04b6419a9faf350de22a17f2 -msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +msgid "" +"Another way of passing values to your workflow input parameters is via an " +"*Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 -#: 1a44a545434b448aa956005deeed90a8 +#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 -#: e76bfcc0c9f84bcdb3f6d5277869a88c -msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" msgstr "" "Pode utilizar este arquivo de Objetos de Inputs agora para executar o " "workflow “Hello World”:" -#: ../../src/introduction/quick-start.md:82 -#: d4cdbe870a6f4a68b542ca719d989062 +#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." msgstr "Passando um arquivo de Objeto de Inputs para o `cwltool`." -#: ../../src/introduction/quick-start.md:88 -#: b6d59e4b9c854abab1b3f7a0fa26f504 -msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but it " +"is not a requirement. You can choose any name for your workflows and Inputs " +"Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 -#: 5535b98e8b1342f09f003ec6db2b44b1 +#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" msgstr "Continue lendo as secções seguintes deste Guia do Utilizador!" -#: ../../src/introduction/quick-start.md:97 -#: 77e43c7117fd4c52b140f0dd52cc3963 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 +msgid "" +"[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" "[Lista das Implementações da CWL](https://www.commonwl.org/implementations)." -#: ../../src/introduction/quick-start.md:98 -#: 7282abfa7155497ca47c30f9abfb6474 -msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." msgstr "" "A [organização`common-workflow-language`](https://github.com/common-workflow-" "language) no GitHub." -#: ../../src/introduction/quick-start.md:99 -#: 176d8d47830f4031bb95dc231ebf1303 -msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +msgid "" +"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." msgstr "" "[Common Workflow Language na Wikipedia](https://en.wikipedia.org/wiki/" "Common_Workflow_Language)." -#: ../../src/introduction/quick-start.md:100 -#: 82a7ca3703bc4f0daa18942a1ac8943b -msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." +"org/wiki/YAML)." msgstr "" "[YAML.org](http://yaml.org/) e [YAML at Wikipedia](https://en.wikipedia.org/" "wiki/YAML)." -#: ../../src/introduction/quick-start.md:101 -#: d039a9d6461c44628d4660c00d9ce6ff -msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +msgid "" +"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." +"replace('VERSION', cwl_version_text) }}." msgstr "" -"A {{'[Especificação CWL VERSION](https://www.commonwl.org/VERSION)'.replace(" -"'VERSION', cwl_version_text) }}." +"A {{'[Especificação CWL VERSION](https://www.commonwl.org/VERSION)'." +"replace('VERSION', cwl_version_text) }}." -#: ../../src/introduction/quick-start.md:102 -#: fbc3383d9e1c4eaca7931c3cc4f1752b -msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "" +"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." msgstr "" "[Workflow management system na Wikipedia](https://en.wikipedia.org/wiki/" "Workflow_management_system)." -#: ../../src/setup.md:9 -#: 1330bd38c4b5495f890b98c669f81a9d -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +msgid "" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. The information on this page has been migrated to the [FAQ](/faq." +"md) section of the new user guide." msgstr "" "O conteúdo desta página está desatualizado mas foi mantido aqui para " "preservar os links do antigo Guia do Utilizador. A informação desta página " @@ -1127,12 +1290,19 @@ msgstr "Argumentos e Parâmetros Adicionais" #: ../../src/topics/additional-arguments-and-parameters.md:3 #: ad00d94d4fb64bbdac356e64dd3803b9 -msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 #: d8110ed19da94ad8a9f56e7006c4a2cf -msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files in " +"the same directory as the source file. However, CWL input files (and the " +"directories in which they appear) may be read-only, so we need to instruct " +"\"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 @@ -1141,8 +1311,7 @@ msgid "`arguments.cwl`" msgstr "`arguments.cwl`" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 -#: 0a8065edd8af4eaea08989a1060ce48f +#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f #: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "`arguments-job.yml`" @@ -1156,184 +1325,250 @@ msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 #: 9643449da1da46d7861866dce490cbcb -msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgid "" +"And now invoke `cwltool` providing the tool description and the input object " +"on the command line:" msgstr "" "E agora execute `cwltool` utilizando a descrição de ferramenta e o objeto de " "input na linha de comando:" #: ../../src/topics/additional-arguments-and-parameters.md:36 #: 713666580a0a4466b4ba6e3eb2b54f0a -msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 #: d50574c8b9694f83aa376d39b9a6fcd6 -msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" +"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." +"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " +"specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 -#: 612c4a66c36a43d4ac5d74c1757d6845 +#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "Melhores Práticas" -#: ../../src/topics/best-practices.md:3 -#: 939cd9e9eaff4e3ab74fe707a5d4eb21 -msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." -msgstr "" - -#: ../../src/topics/best-practices.md:8 -#: 4bcb84707acb40a0bfe2ea0853cb10b7 -msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "" +"The following are a set of recommended good practices to keep in mind when " +"writing a Common Workflow Language description for a tool or workflow. These " +"guidelines are presented for consideration on a scale of usefulness: " +"although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:11 -#: 4dee8504a8e5496081dadc386ab45540 -msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "" +"No `type: string` parameters for names of input or reference files/" +"directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:20 -#: 674c238b25e240eda05e22e399f2f78f -msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that " +"the usual rules of software licensing apply to this document. For example, " +"if the workflow is shared publicly, licensing terms must be clear so that a " +"future user understands under what conditions they can run the workflow, " +"modify it and/or combine it with other workflows. For this reason, please " +"consider including a license field in the document. The authors of this " +"guide urge you to choose a pre-existing license rather than trying to write " +"your own (see the link below to learn more about choosing a license), and " +"our recommended practice is to choose a license that allows for re-use by " +"anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +msgid "" +"If possible, the license should be specified with its corresponding [SPDX " +"identifier][spdx]. Construct the metadata field for the license by providing " +"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " +"taken from the list of identifiers linked above. See the example snippet " +"below for guidance. For non-standard licenses without an SPDX identifier, " +"provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 -#: b651f80f47b4442fbf29454a233697fc -msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 -#: 263a127a77cf4c41af76854f22f1f260 +#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 -#: 3a87a0fb2a364e3da5aaa4017e430b19 -msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "" +"For more examples of providing metadata within CWL descriptions, see [the " +"Metadata and Authorship section of this User Guide](../topics/metadata-and-" +"authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 -#: ecf2b9c0b1664afe9c4e180610610021 -msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +msgid "" +"Include [attribution information][license-example] for the author(s) of the " +"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" +"[orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 -#: e24cb13d98014e558b6a6946758359e0 -msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 -#: f2b14a92374e449d9fb1e8c86ae0dd61 -msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" +"identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 -#: 928e3df7ca3e479ca6474a8e72cf36eb -msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 -#: d355f035676446c88b028f327aeb4829 -msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 -#: 339b852df24242189d6efcd2898a3396 -msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" +"$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " +"[Full IANA media type list][iana-types] (also known as MIME types). For non-" +"bioinformatics tools, use or build an appropriate ontology/controlled " +"vocabulary in the same way. Please edit this page to let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 -#: 3ef57e6862f240bebcf193a52397af0a -msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." msgstr "" -#: ../../src/topics/best-practices.md:69 -#: f1a7c4f896a04a80b0c5f6a1db61ff8c -msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "" +"Each `CommandLineTool` description should focus on a single operation only, " +"even if the (sub)command is capable of more. Don't overcomplicate your tool " +"descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 -#: 1ac4c3d8c3e44bd1af3fc5df70051926 -msgid "Custom types should be defined with one external YAML per type definition for re-use." +#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "" +"Custom types should be defined with one external YAML per type definition " +"for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 -#: c858f64e66f048a5b0032ef3e4d83694 +#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 -#: fae385da16aa443da996fa23ac03d6ae -msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +msgid "" +"If useful, include a top-level `doc` as well. This should provide a longer, " +"more detailed description than was provided in the top-level `label` (see " +"above)." msgstr "" -#: ../../src/topics/best-practices.md:82 -#: 92430be71ecc40e18bbbb80d5576c613 -msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list of " +"valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 -#: 387d83db81024f65aa9a890c2d07874a -msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. One " +"common example: manipulating `File` names and paths? Consider whether one of " +"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 -#: d8e2280a75a74916a1630afaa2fe2ae3 -msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 -#: f1c1340f9745458980e0fbd641738687 -msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +msgid "" +"Complex workflows with individual components which can be abstracted should " +"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " +"workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 -#: 5424e5472c3d466fa2a3d2022c6cb475 -msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics " +"software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 -#: 3f4e98f6bfa141feba8c4b120e3d03e8 +#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 -#: 12f57b2ba76b492abe1816e06bfb1417 -msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +msgid "" +"A command-line tool is a type of Process object that can be run by itself or " +"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " +"etc. The command-line tool is defined in the `baseCommand` attribute of the " +"command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 -#: e1f657a46ce94a0d83671540e2cc2dab -msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The following " +"example contains a minimal example of a CWL command-line tool for the `echo` " +"Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 -#: abb83f0097654a43bd78639d3dbb2bc8 +#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 -#: 3b1a9ae3412f4d6e96a39b9a16934232 +#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 -#: a5eacdbc9aa142c890b177869da4143d -msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +msgid "" +"The example above uses a simplified form to define inputs and outputs. You " +"will learn more about in the [Inputs](../topics/inputs.md) and in the " +"[Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 -#: 1849b8f3ae1c4a84ae59a78ffd6b371e +#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 -#: e3bdaceae8784ab0807b2cf356a98580 -msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network access. " +"If a command-line tool is written manually in CWL v1.1+, there is a need to " +"specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 -#: ed521ac365db4a6ba5a1051fbaa2932e -msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " +"Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 @@ -1343,7 +1578,10 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 #: 0cf51b6da6884065ae42032abc20eb0d -msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgid "" +"Sometimes you need to create a file on the fly from input parameters, such " +"as tools that expect to read their input configuration from a file rather " +"than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 @@ -1358,883 +1596,986 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 #: cfffc518ba6e4ed1a80762ed6f7d25df -msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the value " +"at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 #: 9454a330b9324744b89448f2694b1b03 -msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later " +"during command line tool invocation. That means that any genuine need for " +"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " +"above is expanded to `${PREFIX}` in the generated file to be evaluated by " +"the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 #: 7f8d99a30b644457a62ac1523d0c72aa -msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 -#: ../../src/topics/outputs.md:77 -#: 2d2ef4769b2347e79db827655f1bcdeb -#: 2699fbc4376148af91b7a5a6cdac467c +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb 2699fbc4376148af91b7a5a6cdac467c #: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 #: 10d1373bb14a4a3cacd3b92a2f83382d -msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgid "" +"Before we run this, let us look at each step in a little more detail. The " +"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 #: 70e257091bdb456e8957f90a8fa90e8c -msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " +"array, we need a `-` on the first line of each element of the array, in this " +"case we have just one element. `entryname:` can have any value, but it must " +"match what was specified in the `baseCommand`. The final part is `entry:`, " +"this is followed by `|-` which is YAML quoting syntax, and means that you " +"are using a multiline string (without it, we would need to write the whole " +"script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 #: 1741804e33aa43ce88b4320c11ae5973 -msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:54 #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 -#: ../../src/topics/staging-input-files.md:20 -#: ../../src/topics/workflows.md:198 -#: b372f33c65bb4707b2a462a960bb1373 -#: 293fb1d428b849aebccad598a932992d -#: f924d65fed0c4cb5b0a019b084a8b535 -#: d6255506eebe44be94c5ce703c44a513 +#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 d6255506eebe44be94c5ce703c44a513 #: 7bbd2d738fc54649aeb10f8d2bc38b6f -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgid "" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 -#: cb34fd4c8cb04053ada491a227651048 +#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 -#: 67573252cc064b27ab13eebc468ac58a -msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +msgid "" +"Sometimes you may want to write your own custom types for use and reuse in " +"CWL descriptions. Use of such custom types can reduce redundancy between " +"multiple descriptions that all use the same type, and also allow for " +"additional customisation/configuration of a tool/analysis without the need " +"to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 -#: 73e68b3af9cf41338d843c0c40e50cdc -msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +msgid "" +"The example below is a CWL description of the [biom convert format][biom] " +"tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 -#: ef5f35acb97f4ddfad7b688712f53484 +#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 -#: 7015dfa99a6f4cfb87ebf0ed61e8043c +#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 -#: a999b1acda2641598086648c64aa3831 -msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +msgid "" +"___Note:___ To follow the example below, you need to [download the example " +"input file](https://github.com/common-workflow-language/user_guide/blob/main/" +"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " +"*rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 -#: f8c12a58cb0b46a488823c6ae95f25ea -msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to be " +"used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 -#: f25a63e0926d4932bbe64b2e4bdabf9e -msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +msgid "" +"The reference to a custom type is a combination of the name of the file in " +"which the object is defined (`biom-convert-table.yaml`) and the name of the " +"object within that file (`table_type`) that defines the custom type. In this " +"case the `symbols` array from the imported `biom-convert-table.yaml` file " +"define the allowable table options. For example, in `custom-types.yml`, we " +"pass `OTU table` as an `input` that tells the tool to create an OTU table in " +"hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 -#: b0a4df0fd3ca42338cff4689235dcf4e -msgid "The contents of the YAML file describing the custom type are given below:" +#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e +msgid "" +"The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 -#: fecfbb44456640d8ba05e519bf2ff564 +#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 -#: d718630a296545f3a989c8c71e9ddc77 -msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +msgid "" +"In order for the custom type to be used in the CWL description, it must be " +"imported. Imports are described in `requirements:SchemaDefRequirement`, as " +"below in the example `custom-types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 -#: 9a97acd430064710bcdf76edbd9f711c -msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +msgid "" +"Note also that the author of this CWL description has also included " +"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " +"cores required for the tool to run successfully, as well as details of the " +"version of the software that the description was written for and other " +"useful metadata. These features are discussed further in other chapters of " +"this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 -#: 59014808cbef4c02aaef03129d8a29b0 +#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 -#: 3c821c9c46d841ec89b8a5b1018f3af8 -msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "" +"Tools run in a restricted environment and do not inherit most environment " +"variables from the parent process. You can set environment variables for " +"the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 -#: bfdebb32440a4034beb42135e38884e8 +#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 -#: 777d4a52f7554eff84db2df6d4d0f729 +#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 -#: 48deb71f361a43e48a56ed483075bca8 -msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +msgid "" +"An expression tool is a type of Process that can be run by itself or as a " +"Workflow step. It executes a pure JavaScript expression. It is meant to be " +"used as a way to isolate complex JavaScript expressions that need to operate " +"on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 -#: 716b56506ca7470299899c5d820a9ea2 -msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 -#: b63e6f5a2e89431c8fc7d04f47fd69fe +#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 -#: 39727e9058f24b62b8746a46d3f812c2 +#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 -#: e3ecac0a8e604f2b98a2a12b0579990a -msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +msgid "" +"We had to use an `InlineJavascriptRequirement` as our expression contains a " +"JavaScript call in `.toUpperCase()`. This means to tools using the " +"expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 -#: c8d648b765ec499a8e9c464590838492 +#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 -#: 007a345b4bad49cf996c4301b8386473 -msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +msgid "" +"If you need to manipulate input parameters, include the requirement " +"`InlineJavascriptRequirement` and then anywhere a parameter reference is " +"legal you can provide a fragment of Javascript that will be evaluated by the " +"CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 -#: 2edbd398eadb458b8eacd5fa5496f0a2 -msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "" +"JavaScript expressions should only be used when absolutely necessary. When " +"manipulating file names, extensions, paths etc, consider whether one of the " +"[built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc, could be used instead. See the [list of best practices](best-" +"practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 -#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 -#: efb5fd14988c4e2a8f834ee5369d4102 -msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost) " +"empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 -#: e833649b951841c49397796f996d29f3 +#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 -#: 276f688ba7cc471a842f085ca852b1d9 -msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object is " +"represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 -#: ebf399ea4d5f47b9be03e24f04c69f2d +#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 -#: 65e0cdd505b944caa40f65e612cdddfc +#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 -#: 8b70a1ad70514039b97164fa630c12e4 -msgid "Note that requirements can be provided with the map syntax, as in the example above:" +#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" msgstr "" -#: ../../src/topics/expressions.md:54 -#: 2f28ab412d2843ffa5f14acdc01fc732 -msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " +"describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 -#: d957f55a6377422c9834f85d45e35009 +#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 -#: cbec9277b5004e50af2728cbda0df740 -msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 -#: e259f55f8000479bbd8009e25cf0ca6c -msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +msgid "" +"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 -#: 1acb064f7a4a482aa0174bdc847c6382 +#: ../../src/topics/parameter-references.md:64 1acb064f7a4a482aa0174bdc847c6382 #: 0222780b98ac48e89b1b4f57c9df8590 msgid "`arguments`" msgstr "" -#: ../../src/topics/expressions.md:68 -#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 -#: ef2b8433778a40408f179c3e6f0cf99e -#: 224732683a9c41f3ba1b778851e745a8 -#: 17b10d1e91b24dc582df98fcd2ac850e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 -#: e4e68011dc5f42e4918c747afa7d764b +#: ../../src/topics/parameter-references.md:86 ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 e4e68011dc5f42e4918c747afa7d764b #: d44e3cfa661840eb851782e24caf1b68 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 -#: 0bddedfe40e841f7878e09792531e6bf +#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf #: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 -#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 #: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 -#: 2437656e20354d63bede1b98d5348e2c +#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c #: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 -#: 8210b36347a749889450529ecdf4ff0e -msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +msgid "" +"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" -#: ../../src/topics/expressions.md:73 -#: ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 -#: ../../src/topics/expressions.md:93 +#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 -#: d0a92a3792b549e9b5ddce4667d168d2 -#: 801729c7c71b4109824b035437e69bf9 -#: 1bc510d525f0414e88692e356e67fbbc -#: d2e246ae56a24e4abdd6b7d9812a86e2 -#: b1446bab2732412e91f721a08067b0bd -#: e89dbeb22f41430ca39c923d9fdf68cb -#: bd61499b71e64164878dea08d6d7141e +#: ../../src/topics/parameter-references.md:90 d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb bd61499b71e64164878dea08d6d7141e #: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" -#: ../../src/topics/expressions.md:74 -#: ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 -#: ../../src/topics/expressions.md:94 +#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 -#: 8a1748579de14f0888d5ee9023e37c2d -#: f760465a49d64d4c8468ad9c4fea62b1 -#: 28b6b5ffa7524374aaa9525ebfafb762 -#: d11f6a19ddf34cf19ec856bacf998e29 -#: bcb7cd10cb5947bb9d85c040f57f954f -#: da5188d3bedc4997a35bdf417f2f643c -#: cd7a0190511d4613b09600a3b1e9d55f +#: ../../src/topics/parameter-references.md:91 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c cd7a0190511d4613b09600a3b1e9d55f #: 47def3b078e2402182039be0227090ae msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 -#: 23088850ad02459696f6bbd385109aac -msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +msgid "" +"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 -#: f02257a822ad46ac93c5981531cc85d5 -msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +msgid "" +"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 -#: 989a1c4aaa1143be9f53b90cd8b6d500 -msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "" +"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 -#: 582b03ac742745a89f4dfc86b7404db2 +#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 #: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 -#: d555a3d991e344a5a8e1289168d7c6d1 +#: ../../src/topics/parameter-references.md:79 d555a3d991e344a5a8e1289168d7c6d1 #: 44b3f123c9b04a308c1161b742a7b34b msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 -#: e9fa9430535c424fa3e8be5d460d2ba4 +#: ../../src/topics/parameter-references.md:80 e9fa9430535c424fa3e8be5d460d2ba4 #: 0e306cc923974d1db83fdfb45105a11c msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 -#: d289541e460147aa933f7878996f8649 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +msgid "" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 -#: b0290d1a477b48119e17cf1fed9d6dff +#: ../../src/topics/parameter-references.md:84 b0290d1a477b48119e17cf1fed9d6dff #: 446f1190af7a40a0913ff04ce7aa938c msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 -#: 81b4d1f23a3642bfa9bb395b94260cd1 -msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "" +"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 -#: e1cde4aa32c041238ed2596173c6d824 +#: ../../src/topics/parameter-references.md:87 e1cde4aa32c041238ed2596173c6d824 #: 557694f82e314baa9ccafba14d6ff2c9 -msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgid "" +"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." +"html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 -#: c2a92d3eca7f4ee39cec649170eeea53 +#: ../../src/topics/parameter-references.md:88 c2a92d3eca7f4ee39cec649170eeea53 #: 3c939769ede94602a67fc50c435741cf msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 -#: f495da32f05a4a5ba9539be0a54c1a59 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +msgid "" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](https://www." +"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 -#: bdb4c68a175047ddbe141ca24960127f -msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +msgid "" +"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 -#: 4b73495cf18a4d908525292b6f23c419 +#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 #: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 -#: 718ceee9973240ec9c100977bbcc8921 +#: ../../src/topics/parameter-references.md:94 718ceee9973240ec9c100977bbcc8921 #: 2b25152f6df5494a8632f3ce631c20d8 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 -#: c07ab08eb75d4528949c56a3d7c12b28 +#: ../../src/topics/parameter-references.md:95 c07ab08eb75d4528949c56a3d7c12b28 #: 846cd427ae25410eae7c920b237edcb0 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 -#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 #: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 -#: 700c57ccd5e347be86702c83a8af24b3 +#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 #: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 -#: 509a5e2ec52d413eb57754d359f133e4 +#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 #: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 -#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 #: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b -#: e3b76f42c924489f9a0bcf5a7b636d23 +#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 -#: 97b61352363f47cb890e8937c5613fa3 -msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +msgid "" +"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e -#: a258554d462f4f5f83ece28d5b2fc584 +#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 -#: 8d0b142bb7ed4e61b8fb03de197240ce +#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: effc0208cf4f4551958db6e526c0528b -#: 9d4889c8cec24351a7a9e3c547e331b6 +#: effc0208cf4f4551958db6e526c0528b 9d4889c8cec24351a7a9e3c547e331b6 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: be6c1e85c7b6495d8086c262daad20e7 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +#: be6c1e85c7b6495d8086c262daad20e7 af4f7f232a9d42388c0ba1cfc7c2cdf7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 -#: 6abeba392b0444b19f92a19f178a4682 +#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 -#: 0bc424ef2ca346099f29b937379908a0 -msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +msgid "" +"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd -#: 949c376120d8441796ec9c89364f8851 +#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 -#: 10d36a1adfd04144b401c993b12b4094 -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +msgid "" +"Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 -#: 29b73e1dd72744f68377f0a38c10f062 -msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +msgid "" +"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " +"attribute that allows users to load external JavaScript files, or to provide " +"inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 -#: 38a2afaf4a6c4d04909af22c93f2808d -msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts of " +"the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 -#: cd74f34b21af4de9be96fd897efc469b -msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +msgid "" +"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." +"org/v1.0/CommandLineTool.html#Expressions) that the only version of " +"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" +"international.org/5.1/). This means that any code that you include or write " +"in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 -#: f12e371f3f1a4b0cb2cff9800352d48c -msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " +"function inline in `expressionLib`. That function can then be used in other " +"parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 -#: 49d0fda2fc144e0b8b7c92afc1d8945e +#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 -#: 8f0e8f050e334ac08334e9215e1dcf61 -msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result in " +"the `echo` command printing the input message with capital initial letters:" msgstr "" -#: ../../src/topics/expressions.md:149 -#: 26c74b11bb1849cea0763bb74ec43e42 +#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 -#: 7a6be0005a6441feb67f036d005d7885 -msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 -#: ed590f9e6f4f425da886b110295c45db +#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 -#: 093235307d6f47d4858e559b780ef5e5 +#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 -#: 06635145b441418aaae84dc804f3d6ac -msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +msgid "" +"The `custom-functions.js` file is included in the CWL document with the `" +"$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 -#: 973a9b257b1a4f0dbd4444d4f11dadd7 +#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 -#: 04eaf1f7c630450db318dcd8b7626e15 -msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +msgid "" +"Finally, note that you can have both inline and external JavaScript code in " +"your CWL document. In this final example we have added another entry to the " +"`expressionLib` attribute with the new function `createHelloWorldMessage`, " +"that calls the `capitalizeWords` function from the external file `custom-" +"functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 -#: c4098489fbb049789f022cd3e5c3d49b +#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 -#: 5979e4ae5c424276bdbc47f69b379d0f +#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 -#: fd4579a3c9844492b314b5c3c1775fc7 -msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +msgid "" +"The `$include` statement can be used to include a file from the local disk " +"or from a remote location. It works with both relative and absolute paths. " +"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." +"html#Include) from the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 -#: 3f038e7371f84ed9b4547358dfb55a11 +#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 -#: e024bcb70e04412e90e1838426d1b69a -msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +msgid "" +"Tools and workflows can take `File` types as input and produce them as " +"output. We also recommend indicating the format for `File` types. This helps " +"document for others how to use your tool while allowing you to do some " +"simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 -#: a3db21c0b3114802a8a5b610e252ef13 -msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM in " +"our example), reference a local ontology for your institution, or do not add " +"a file format initially for quick development before sharing your tool with " +"others. You can browse existing [IANA file format listings][IANA] and [EDAM " +"file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 -#: 0f5bc8520d6a4dafa37c65343da9702a -msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` section " +"of the document in greater detail, so don't worry about these for now." msgstr "" -#: ../../src/topics/file-formats.md:17 -#: 5cb830da47464a8b9c3950983fa4d56f -msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 -#: 0535d5de416b4ea3b2f5996583deecc1 +#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 -#: fb47f73c38cf4ec59bd3021866a631f8 +#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 -#: 74b28c1b09c6429b82e462e4ec61808e +#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 -#: a2ce43b391864e8bbde16328cc19b32b -msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +msgid "" +"Below is an example of a parameter file for the example above. We encourage " +"checking in working examples of parameter files for your tool. This allows " +"others to quickly work with your tool, starting from a \"known good\" " +"parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 -#: aebee48b742c4145a600fd2daf8c75dc +#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "`sample.yml`" -#: ../../src/topics/file-formats.md:45 -#: 56ee4dcfff6141d5bef80eb96559876d -msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +msgid "" +"___Note:___ To follow the example below, you need to download the example " +"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 -#: 8d3a6d83e2e54c56995893c41590b7ff +#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 -#: 5abcdebfa1cb401bb8892553be285fd3 +#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 -#: d3a55f71dc244026a97902de9ed819ea +#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 -#: 96671c56523c4ea9992fb5dfcfa6490e -msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to run " +"the tool. Each parameter has an `id` for the name of parameter, and `type` " +"describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 -#: bcc6246742cb46bfb185e415c4a3431a -msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +msgid "" +"Available primitive types are *string*, *int*, *long*, *float*, *double*, " +"and *null*; complex types are *array* and *record*; in addition there are " +"special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 -#: 86dce36de687449c88fb5eb9d64eb045 -msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 -#: cd9cea15f57b492ba4098237cd7c5bed +#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 -#: 8bdb875b63104f699efe28ea0abb1e3d +#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 -#: c6a0151a68494c0cb0176781e65e252e +#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 -#: dc5e6b5e01d64226bd5dbbf3175fe010 +#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 -#: 36ab1d9edafc4831bb1bca5f123b04b0 -msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "" +"You can use `cwltool` to create a template input object. That saves you from " +"having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 -#: 7dc630ea86464b1dba3a4e5079260b3b -msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " +"> inp-job.yml`, and then modify the default values with your desired input " +"values." msgstr "" -#: ../../src/topics/inputs.md:44 -#: ae37901a8dbe48a59e27ab4e2e6e2d30 -msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 -#: 651e032007ea4a119d20c820bb61f86b -msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " +"command line." msgstr "" "Em sequência, cria um arquivo chamado whale.txt utilizando [touch] digitando " "`touch whale.txt` na linha de comando." -#: ../../src/topics/inputs.md:53 -#: 0b056dde9e87428996e47870b12119da -msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +msgid "" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " +"boxed text describes these two commands and the expected output from the " +"command line:" msgstr "" -#: ../../src/topics/inputs.md:64 -#: 628124a1670b4b058bb0fb6e495a099c -msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not explicitly " +"specified" msgstr "" -#: ../../src/topics/inputs.md:70 -#: 10ca6321ce3e4b08ab6a5bb380b19c11 -msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "" +"The field `inputBinding` is optional and indicates whether and how the input " +"parameter should appear on the tool's command line. If `inputBinding` is " +"missing, the parameter does not appear on the command line. Let's look at " +"each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 -#: ec2adb3912bc46e28891229e9e0d9a1c -msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +msgid "" +"Boolean types are treated as a flag. If the input parameter \"example_flag" +"\" is \"true\", then `prefix` will be added to the command line. If false, " +"no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 -#: a519be60726a44af9941fdce04735353 -msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +msgid "" +"String types appear on the command line as literal values. The `prefix` is " +"optional, if provided, it appears as a separate argument on the command line " +"before the parameter . In the example above, this is rendered as `--example-" +"string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 -#: cb8fc8c4c79e467eac5fab4ca685201e -msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +msgid "" +"Integer (and floating point) types appear on the command line with decimal " +"text representation. When the option `separate` is false (the default value " +"is true), the prefix and value are combined into a single argument. In the " +"example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 -#: a26cc105716f47cb807174c9003153b0 -msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the parameter " +"is optional. In the example above, this is rendered as `--file=/tmp/random/" +"path/whale.txt`. However, if the \"example_file\" parameter were not " +"provided in the input, nothing would appear on the command line." msgstr "" -#: ../../src/topics/inputs.md:131 -#: cc159dd5fe5748caac838862f5b8c4d1 -msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +msgid "" +"Input files are read-only. If you wish to update an input file, you must " +"[first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 -#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 -msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "" +"The value of `position` is used to determine where parameter should appear " +"on the command line. Positions are relative to one another, not absolute. " +"As a result, positions do not have to be sequential, three parameters with " +"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " +"than one parameter can have the same position (ties are broken using the " +"parameter name), and the position field itself is optional. The default " +"position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 -#: 6812698e9ad84d3385de5e88e9dde0b3 -msgid "The `baseCommand` field will always appear in the final command line before the parameters." +#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +msgid "" +"The `baseCommand` field will always appear in the final command line before " +"the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 -#: 9654e65b1c0642dbb5d4f34edb211989 +#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 -#: d1f02be278754267893dfce5a940997d -msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to provide " +"`type` field with `type: array` and `items` defining the valid data types " +"that may appear in the array. Alternatively, brackets `[]` may be added " +"after the type name to indicate that input parameter is array of that type." msgstr "" -#: ../../src/topics/inputs.md:154 -#: 01f30e38dfdd452dba3a996073936e16 +#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 -#: 787d4bfb093c4ad287b902084706b751 +#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:166 -#: ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 -#: 588f0f7f967f4d69af27c9729d6d3119 -#: 02adef8ee8204842b5b4a0408f3bac33 -#: 9db68837918a4a349f32f15f12697a1d -msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 9db68837918a4a349f32f15f12697a1d +msgid "" +"Now invoke `cwltool` providing the tool description and the input object on " +"the command line:" msgstr "" "Agora chame o `cwltool` passando a descrição da ferramenta e o objeto de " "entrada na linha de comando:" -#: ../../src/topics/inputs.md:178 -#: 75d59e395c66416cae9b352db5081516 -msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +msgid "" +"The `inputBinding` can appear either on the outer array parameter definition " +"or the inner array element definition, and these produce different behavior " +"when constructing the command line, as shown above. In addition, the " +"`itemSeparator` field, if provided, specifies that array values should be " +"concatenated into a single argument separated by the item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 -#: 874c6f19abbf45d7ab7d30a378c4048d -msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` in " +"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " +"where array values that are not defined with an associated key are marked by " +"a leading `-`. This will be demonstrated in the next lesson and is discussed " +"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " +"arrays of arrays, arrays of records, and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 -#: 5d7d7a28cc5d4862803032aec78174d9 +#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 -#: dea0d4b681f94e73b13965dcfe75cf7d -msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be provided " +"together (they are exclusive). You can use records and type unions to group " +"parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 -#: ddf598abf4f34aca9fffa045860fbf96 +#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 -#: d52a8089920e45bd89d582533b50e3a1 +#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 -#: 750474486a84482292eeba45f118287f -msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 -#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 -#: 1eb0e39bb6d04b8cab300f44a79f3add -msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the first " +"matching item (`itemC`) is added to the command line and remaining item " +"(`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 -#: bc21ee10bff843689cc98ac6630edcea +#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 -#: 4b2ab812f62c4f949dd25c8527f2411c -msgid "In the third example, only `itemD` is provided, so it appears on the command line." +#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +msgid "" +"In the third example, only `itemD` is provided, so it appears on the command " +"line." msgstr "" -#: ../../src/topics/inputs.md:255 -#: b771302d1bec4050a9417b080eef76c9 +#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 -#: 2c3b884cb1c54521900cc90782e8a58d -msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +msgid "" +"If you use exclusive input parameters combined with expressions, you need to " +"be aware that the `inputs` JavaScript object will contain one of the " +"exclusive input values. This means that you might need to use an **or** " +"boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 -#: a1073b6306044dffb414319ae01f68bb -msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from an " +"enum." msgstr "" -#: ../../src/topics/inputs.md:265 -#: 4a31c733092142b1af834eab1747c224 +#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "`exclusive-parameter-expressions.cwl`" -#: ../../src/topics/inputs.md:271 -#: 9a1d92334685449386dfa3b3a899ed48 -msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you provide a " +"valid value, such as “fasta” (one of the values of the enum), your command " +"should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 -#: fb623af4c480411b8fde28d01c981411 -msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +msgid "" +"However, if you do not provide any input value, then `file_format` will be " +"evaluated to a `null` value, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your workflow." msgstr "" -#: ../../src/topics/inputs.md:289 -#: e98e165f6bba40809c90473d72f9d592 -msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +msgid "" +"To correct it, you must remember to use an or operator in your JavaScript " +"expression when using exclusive parameters, or any parameter that allows " +"`null`. For example, the expression could be changed to `$(inputs." +"file_format || 'auto')`, to have a default value if none was provided in the " +"command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 @@ -2244,12 +2585,25 @@ msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 #: cd64d2d828834cbbb24ea5358caf5405 -msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgid "" +"Implementation extensions not required for correct execution (for example, " +"fields related to GUI presentation) and metadata about the tool or workflow " +"itself (for example, authorship for use in citations) may be provided as " +"additional fields on any object. Such extensions fields (e.g. `format: edam:" +"format_2572`) can use a namespace prefix listed in the `$namespaces` section " +"of the document (e.g. edam: http://edamontology.org/) as described in the " +"[Schema Salad specification][schema-salad]. Once you add the namespace " +"prefix, you can access it anywhere in the document as shown below. " +"Otherwise, one must use full URLs: `format: http://edamontology.org/" +"format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 #: 80af387fe3ff4e2da999903385bd602b -msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to cite " +"your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 @@ -2264,7 +2618,12 @@ msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 #: cb9980db4e5f4c74b01c2dec6d5e92d0 -msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgid "" +"For those that are highly motivated, it is also possible to annotate your " +"tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints at " +"hardware requirements in order to use the tool, and a few more metadata " +"fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 @@ -2272,262 +2631,304 @@ msgstr "" msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 -#: 8acf361cf77c4d45ba3f2e344146259f +#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 -#: 83d3b9a0ed3148fda9ce72cd108cb9e1 -msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-line " +"tool, or an expression tool. It is a step of a workflow that specifies " +"inputs and outputs, but it does not provide enough information to be " +"executed." msgstr "" -#: ../../src/topics/operations.md:7 -#: 5565c1b2d8a349169a305a9b26b4574d -msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +msgid "" +"You can create operations to visualize a workflow during development, before " +"you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 -#: 49cf614893d8438299b3bca384eb40cf +#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "`operations.cwl`" -#: ../../src/topics/operations.md:16 -#: 88160cef4cfa4add9020aa89511a5749 -msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +msgid "" +"The `uppercase` step of the workflow is an operation. It can be used like a " +"command line tool or an expression. You can also plot it with the CWL Viewer " +"or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 -#: 2f73a786b5d94dc0b23ed0cdd185afc8 -msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "" +"The output of the command above can be rendered with a Graphviz renderer. " +"The following image is rendered with the Sphinx Graphviz directive (this " +"user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 -#: 730ba1434a1445ae847ec6153b6a3b72 -msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +msgid "" +"If you try running it with `cwltool`, the command will fail since `cwltool` " +"does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 -#: 98d9b8d867594543890af99e77e24edb +#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 -#: a25d0b1e13324b40a6b8fcd227948c4f -msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A " +"CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 -#: da077da5eb8a4ffebfde041fc16300de +#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 -#: 1b3016f0462f42deb42ddaa33f28bf3d +#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 -#: d661df070e3040869da412d07a71f716 -msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name of " +"parameter, and `type` describing what types of values are valid for that " +"parameter." msgstr "" -#: ../../src/topics/outputs.md:10 -#: a11585474d3849cca5467512ed964743 -msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +msgid "" +"When a tool runs under CWL, the starting working directory is the designated " +"output directory. The underlying tool or script must record its results in " +"the form of files created in the output directory. The output parameters " +"returned by the CWL tool are either the output files themselves, or come " +"from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 -#: 2682f9ca8e604a0c9986f7746fdec960 -msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 -#: 7e3fa7baf0f549ec89457e7004ac9545 +#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 -#: 22447a560f6f4317bf67bd7c4336126c -msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string we can use an " +"_array of strings_. The first element is the command to run, and any " +"subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 -#: f1ee2e00b0cc4112b51c9df3a919b73f +#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 -#: ad8e1acb251246d2a47c39b20d4e483a +#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 -#: dc200c6960ae4476a772645d021f14b8 +#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "Agora, crie um arquivo tar para o exemplo." -#: ../../src/topics/outputs.md:45 -#: 52703d6b7f914097934bfad13663abeb -msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +msgid "" +"And now invoke `cwltool` with the tool description and the input object on " +"the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 -#: 5e1c79df657d4a6e84e055dd6b300a5d -msgid "The field `outputBinding` describes how to set the value of each output parameter." +#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +msgid "" +"The field `outputBinding` describes how to set the value of each output " +"parameter." msgstr "" -#: ../../src/topics/outputs.md:62 -#: 329d2809dfae4f90bc638f5f03a47ee3 -msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +msgid "" +"The `glob` field consists of the name of a file in the output directory. If " +"you don't know name of the file in advance, you can use a wildcard pattern " +"like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 -#: 96df2d45e42441d49ce193ccbfab78a3 +#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 -#: c6bcf7c6a8774dd6be41cc775848c3b8 -msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "" +"To capture a tool's standard output stream, add the `stdout` field with the " +"name of the file where the output stream should go. Then add `type: stdout` " +"on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 -#: 9d86c03ab44841c785b924cc44727e31 +#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 -#: 2fb58c2feaa84970bb5274c49f4b5b64 +#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 -#: 9647019d8c37466886e7aab6f176634d -msgid "You can also capture multiple output files into an array of files using `glob`." +#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 -#: b9eaf21f5e014eefaae301c47dafd144 +#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 -#: cffff6c43b4945daa3b2a49763bc50ae +#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 -#: cc067051f22f433bbece08f60933e002 -msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions to " +"mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 -#: a190a6440ec34898990cdac05d809f22 +#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 -#: dbfe2c1123144316aa026374b0f353d3 -msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../src/topics/parameter-references.md:13 -#: 280f1a07d0ae41d7a4674504f832fcf0 +#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file we " +"were interested in was called \"hello.txt\", and this was written into the `." +"cwl` file. This is not the best way to do this, as the \"hello.txt\" " +"filename may vary or be dependent on the input file(s) used. To avoid this " +"we can specify the name of the file we want in the job parameters file (`." +"yml`). In this example, you will see how to reference the value of input " +"parameters dynamically from other fields, which will allow us to then " +"specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 -#: 5c64d938862747cb9fb52515a656ce27 +#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "`tar-param-job.yml`" -#: ../../src/topics/parameter-references.md:25 -#: 074cf5d912854d8c864607cc24b15302 -msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +msgid "" +"Create your input files and invoke `cwltool` with the tool description and " +"the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 -#: 0290af3e3cbb4b32b0450c8771f3bf95 -msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "" +"Certain fields permit parameter references which are enclosed in `$(...)`. " +"These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 -#: b54240bb94f746bba7511633aa969db0 -msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" +"$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 -#: 8b70a072aa87414c88e89a3e19af0a51 -msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +msgid "" +"The value of the \"inputs\" variable is the input object provided when the " +"CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 -#: eea20f89c45f424a888178df53713b28 -msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +msgid "" +"Note that because `File` parameters are objects, to get the path to an input " +"file you must reference the path field on a file object; to reference the " +"path to the tar file in the above example you would write `$(inputs.tarfile." +"path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 -#: cb4ea13f5db84c0da43df3f7f2478d78 +#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 -#: 6d3fb423e6c4434697cd113fb27e28ad +#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 -#: 7647e0229a924f988cf02b7812a55c06 -msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +msgid "" +"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 -#: 9d663249666045618a0d3acddb85a9a9 -msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +msgid "" +"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 -#: 5fed4984f6784347b4cbe0630b1dd2c2 -msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "" +"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 -#: dbf6153cd02542a6a01c172803122b7f -msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +msgid "" +"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 -#: b6250cf6fa8a4a0c94b33302e0decca5 -msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +msgid "" +"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 -#: fa6ca3bbc6784380a03a950a6f49a180 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +msgid "" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 -#: b92b516e537a4773ad67b4af586e7a25 -msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +msgid "" +"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 -#: 467a701228504d06b971b79a59c69064 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +msgid "" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" "De [InputParameter](http://www.commonwl.org/v1.0/Workflow." "html#InputParameter) e [ExpressionToolOutputParameter](http://www.commonwl." "org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -#: ../../src/topics/parameter-references.md:92 -#: 2634f989eb304009a8568d70ed42786c -msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +msgid "" +"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 #: 5d8bed66282c408695292ea92a03b2c4 -msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgid "" +"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 @@ -2537,7 +2938,9 @@ msgstr "" #: ../../src/topics/parameter-references.md:107 #: 9a6b311ded8d4e43ae635b1b927dbdf2 -msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgid "" +"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 @@ -2552,564 +2955,746 @@ msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 #: 574d93d1d592458a985f259519c036cb -msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a `SoftwareRequirement` field in the `hints` section. This may also " +"help to avoid confusion about which version of a tool the description was " +"written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 #: 82e48b3e3c3f451480cc0b6a529271f6 -msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgid "" +"In this example, the software requirement being described is InterProScan " +"version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 #: 02e40154eac74ecc98d0447d03475b44 -msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the [dependency " +"resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 #: 8cb1c5d9b1a54c40924099494eb766c6 -msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 -#: b85eb83e05e845d7a179f1b1d74db444 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the tool " +"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " +"up in the [SciCrunch][scicrunch] registry, which provides a portal for " +"finding, tracking, and referring to scientific resources consistently. If " +"you want to specify a tool as a `SoftwareRequirement`, search for the tool " +"on SciCrunch and use the RRID that it has been assigned in the registry. " +"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " +"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." +"org][identifiers]) in the `specs` field of your requirement description. " +"Other good choices, in order of preference, are to include the DOI for the " +"main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 -#: 35f97d37492b4c7ca3ad6cfc1e6fa366 -msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "" +"Normally, input files are located in a read-only directory separate from the " +"output directory. This causes problems if the underlying tool expects to " +"write its output files alongside the input file in the same directory. You " +"use `InitialWorkDirRequirement` to stage input files into the output " +"directory. In this example, we use a JavaScript expression to extract the " +"base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 -#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "`linkfile.cwl`" -#: ../../src/topics/troubleshooting.md:1 -#: 0f7508ce59754a7eb230dea6042244c6 +#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "Solucionando Problemas" -#: ../../src/topics/troubleshooting.md:3 -#: fbe0c65b444441f785d0054176d036a6 -msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +msgid "" +"In this section you will find ways to troubleshoot when you have problems " +"executing CWL. We focus on `cwltool` here but some of these techniques may " +"apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 -#: 1b6b7a75cc754775bf9dd80c0941e8da +#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 -#: 9a710602e00c4934ae3a3b471aa68458 -msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor output " +"files, but created while your workflow is running). By default, these files " +"are created in a temporary directory but writing them to a separate " +"directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 -#: 21b5be7270a14f0987240c81d1ec879b -msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " +"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " +"olleH\". However, the second step, `step_b`, **has a typo**, where instead " +"of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 -#: 0490b1fab86749e49b473949c52bbe8b +#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 -#: cfe9d8241fe84bd5b74042a5625d933f -msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " +"(`cwltool` will create the directory for you if it does not exist already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 -#: 764d933cc4da446abd8dd8f913f05dac -msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. You " +"can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 -#: c93efc6d4e004859981ee7f5fa28ed03 -msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +msgid "" +"Each workflow step has received a unique ID (the long value that looks like " +"a hash). The `${HASH}.status` files display the status of each step executed " +"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " +"output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 -#: 546601da44cb49bd9611b1c85807fd90 -msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " +"the `step_b`). After fixing the typo, when you execute `cwltool` with the " +"same arguments as the previous time, note that now `cwltool` output contains " +"information about pre-cached outputs for `step_a`, and about a new cache " +"entry for the output of `step_b`. Also note that the status of `step_b` is " +"now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 -#: 7e0bf00f8ce542b9b009cdcf1945a9e5 -msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had " +"been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for " +"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " +"re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 -#: eff5f28ca83c458a9b07faf7a81f7e91 +#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "Utilizando Containers" -#: ../../src/topics/using-containers.md:3 -#: 2e634f3737d04d279ae78ceee4b0a664 +#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 -#: e07f33d01b804663a25ffb08aad74821 -msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 -#: 7a644506619a4f08958ec7d4540cd557 -msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +msgid "" +"[Docker][docker] containers simplify software installation by providing a " +"complete known-good runtime for software and its dependencies. However, " +"containers are also purposefully isolated from the host system, so in order " +"to run a tool inside a Docker container there is additional work to ensure " +"that input files are available inside the container and output files can be " +"recovered from the container. A CWL runner can perform this work " +"automatically, allowing you to use Docker to simplify your software " +"management while avoiding the complexity of invoking and managing Docker " +"containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the container." msgstr "" -#: ../../src/topics/using-containers.md:18 -#: b5195b7d8eaa419fb2b90cb33a57783a -msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +msgid "" +"This example runs a simple Node.js script inside a Docker container which " +"will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 -#: 7921a837ee744c5aa9a5bda04b0c8db1 +#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 -#: 387e9bc9381a4450af54aff77e4df6a2 +#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 -#: 2713594c937d4c528fc8d04d9e9819ed -msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 -#: cf94c1424fc2413c85647fd1ee73d951 -msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that is " +"really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:52 -#: dc0452107c604e29bdf32bb289fe5db8 -msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using the " +"Node Js runtime that is meant for Javascript files. We then need to specify " +"some `hints` for how to find the container we want. In this case we list " +"just our requirements for the docker container in `DockerRequirements`. The " +"`dockerPull:` parameter takes the same value that you would pass to a " +"`docker pull` command. That is, the name of the container image (you can " +"even specify the tag, which is good idea for best practices when using " +"containers for reproducible research). In this case we have used a container " +"called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " +"the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 -#: 1a5596243cec4c948d9b6bf0bb12fad0 +#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 -#: 483181f498fc4d968b5fe6ef427709f7 -msgid "Notice the CWL runner has constructed a Docker command line to run the script." +#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." msgstr "" -#: ../../src/topics/using-containers.md:72 -#: 7487485d6aa4458089a4b4bdf107ea64 -msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +msgid "" +"In this example, the path to the script `hello.js` is `/home/me/cwl/" +"user_guide/hello.js` outside the container but `/var/lib/cwl/" +"job369354770_examples/hello.js` inside the container, as reflected in the " +"invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 -#: 7394e7690f934043af617436b40845f0 +#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 -#: b9ae9e9a896048caad7e6c38a5bc1bd1 -msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 -#: f228fb7953ea48ed99d89880205f4620 +#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 -#: 5870ac44e4c24b8daf5f06c49f95ce04 -msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier examples." msgstr "" -#: ../../src/topics/workflows.md:51 -#: a913c76d06164fa18718a8a6a7dcf0d6 +#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 -#: 93188ed43ee949cc98b3ea679ce14feb -msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +msgid "" +"A command-line tool or expression tool can also be written directly in the " +"same CWL document as the workflow. For example, we can rewrite the `echo-" +"uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 -#: 36618126a4df4326b236ebe2ea42cffa +#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 -#: 1cc17ad26e9c474b895ba5cd20c8b66a -msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "" +"Having separate files helps with modularity and code organization. But it " +"can be helpful writing everything in a single file for development. There " +"are other ways to combine multiple files into a single file (e.g. `cwltool --" +"pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 -#: 24aca0bea4d94e3593b844cf0586cffe -msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this " +"user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 -#: 46cc4859856e4367a9e5e68eecd48b73 +#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 -#: 9c56528acd5f49deb139e034dfbfac7c -msgid "This workflow extracts a java source file from a tar file and then compiles it." +#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +msgid "" +"This workflow extracts a java source file from a tar file and then compiles " +"it." msgstr "" -#: ../../src/topics/workflows.md:170 -#: 55ab007d472f43388e4c77aae8f165e7 +#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:179 -#: ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa -#: 307b6618a92948fca4203ccb497c77e6 +#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 -#: a2dd833fdca4443181648e41051a5232 -msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +msgid "" +"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" +"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 -#: 7e40cc9f9e1341c195e843c009575b94 -msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a " +"run:" msgstr "" -#: ../../src/topics/workflows.md:185 -#: 26c51dcb76364ed780376aecb7cbacda +#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "`1st-workflow-job.yml`" -#: ../../src/topics/workflows.md:191 -#: 6fcf8ad3d1bd49afa4a105622437bd59 -msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 -#: 71cb81fa4511495b80422244849979e4 +#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 -#: def35d6021394def80a53ae49a2cdbde -msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a workflow." msgstr "" -#: ../../src/topics/workflows.md:221 -#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 -msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a list " +"of input parameters where each parameter consists of an identifier and a " +"data type. These parameters can be used as sources for input to specific " +"workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 -#: c84d4450bc6a475dbf34e0b22cea9130 -msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a list " +"of output parameters where each parameter consists of an identifier and a " +"data type. The `outputSource` connects the output parameter `classfile` of " +"the `compile` step to the workflow output parameter `compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 -#: cca9665f6daa44b49233baf34ab9fcc7 -msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second step " +"compiles the file from the first step using the java compiler. Workflow " +"steps are not necessarily run in the order they are listed, instead the " +"order is determined by the dependencies between steps (using `source`). In " +"addition, workflow steps which do not depend on one another may run in " +"parallel." msgstr "" -#: ../../src/topics/workflows.md:256 -#: 547edbf5fa424b8286cc21674ff159b0 -msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input " +"parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 -#: 7ca248888b9d484cb544cd76ba538662 -msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +msgid "" +"The ``in`` section of the workflow step connects these two input parameters " +"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " +"`source`. This means that when the workflow step is executed, the values " +"assigned to `tarball` and `name_of_file_to_extract` will be used for the " +"parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 -#: ae6b240718104380b08db5552d7355ea -msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +msgid "" +"The `out` section of the workflow step lists the output parameters that are " +"expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 -#: e5a8b7f84be64020b191099f3fad30ed -msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " +"in [Additional Arguments and Parameters](additional-arguments-and-parameters." +"md)). The output of this step `classfile` is connected to the `outputs` " +"section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 -#: f0b04849253c4693904512ddd7f9ce84 +#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 -#: 12a06d8358534102b202965d4258c18e -msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +msgid "" +"Workflows are ways to combine multiple tools to perform a larger operations. " +"We can also think of a workflow as being a tool itself; a CWL workflow can " +"be used as a step in another CWL workflow, if the workflow engine supports " +"the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 -#: 1658cac0de1b47e9b60f6d4a4ad9bb19 -msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 -#: 49ed137fe996452a8534c68d100db941 +#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "`nestedworkflows.cwl`" -#: ../../src/topics/workflows.md:309 -#: b7f93705e5b8416696be01850072e8c0 -msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 -#: e87045829b344089ab59dc27063ddd7a -msgid "\"Visualization \"Visualization" +#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +msgid "" +"This two-step workflow starts with the `create-tar` step which is connected " +"to the `compile` step in orange; `compile` is another workflow, diagrammed " +"on the right. In purple we see the fixed string `\"Hello.java\"` being " +"supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:322 -#: 42ef2f145b824d69b63abc1da175c216 -msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +msgid "" +" \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " +"CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " +"to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 -#: c61cedf543664d388183e04b3939cc39 -msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and `*.java` " +"filename. This is generally best-practice, as it means it can be reused in " +"multiple parent workflows, or even in multiple steps within the same " +"workflow." msgstr "" -#: ../../src/topics/workflows.md:341 -#: 9e39e3f1501c4fcaab3e8962e090f6be -msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar " +"file at `tarball`, which we will prepare in the `create-tar` step. At this " +"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " +"specific input/output names, as those also appear in its usage as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 -#: 03e2f767c4da461982fc3c0f3ba94762 -msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 -#: 3bea5822b8694e2aa32c446e1c54a045 -msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +msgid "" +"In this case our step can assume `Hello.java` rather than be parameterized, " +"so we can use hardcoded values `hello.tar` and `Hello.java` in a " +"`baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 -#: 426023bd6e3a471cbb30dbda3d6f9e57 -msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This is " +"generally not best practice, as the tool then can't be reused. The reason " +"for doing it in this case is because the command line is hard-coded with " +"filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 -#: 0d498cd4caf54c15891ca1afe58e2727 -msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +msgid "" +"In this example we had to prepare a tar file outside, but only because our " +"inner workflow was designed to take that as an input. A better refactoring " +"of the inner workflow would be to take a list of Java files to compile, " +"which would simplify its usage as a tool step in other workflows." msgstr "" -#: ../../src/topics/workflows.md:394 -#: b2d75045e02741b4850f5ff1243f7858 -msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL " +"Tool description, care must be taken to improve its usability in multiple " +"workflows." msgstr "" -#: ../../src/topics/workflows.md:398 -#: cfa765264a27411ab914de569aa3dac4 +#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 -#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 -msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " +"run a tool or workflow multiple times over a list of inputs. The workflow " +"then takes the input(s) as an array and will run the specified step(s) on " +"each element of the array as if it were a single input. This allows you to " +"run the same workflow on multiple inputs without having to generate many " +"different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 -#: 5fa79c62049a447c8328ebf9db54ebf4 -msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +msgid "" +"The most common reason a new user might want to use scatter is to perform " +"the same analysis on different samples. Let's start with a simple workflow " +"that calls our first example (`hello_world.cwl`) and takes an array of " +"strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 -#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "`scatter-workflow.cwl`" -#: ../../src/topics/workflows.md:421 -#: 3a67d77a2e7b4c0bb61cc3585ceae942 -msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "" +"Aside from the `requirements` section including `ScatterFeatureRequirement`, " +"what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 -#: f1cb55fc59824cc18a95fd6dcb32cf4c -msgid "First of all, notice that the main workflow level input here requires an array of strings." +#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 -#: d947c54933d64aad90df392a1cedd63f -msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This field " +"tells the runner that we'd like to scatter over this input for this " +"particular step. Note that the input name listed after scatter is the one of " +"the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 -#: 651d35997332404186aa6d5711da4a3d -msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if you " +"expect that the final output of your workflow will now have multiple outputs " +"to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 -#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "Usando o seguinte arquivo de entrada:" -#: ../../src/topics/workflows.md:452 -#: 842b926ae34542cb9023021f137b08be +#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 -#: b662c1a5a4424c8d8350a806356acc61 -msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " +"calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 -#: 04d6babfd87343d7a5f13867ea02b65f -msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +msgid "" +"You can see that the workflow calls echo multiple times on each element of " +"our `message_array`. Ok, so how about if we want to scatter over two steps " +"in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 -#: 2eaacf1a90204a2b9bd621344560f2a1 -msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding the " +"following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 -#: 242993d42b164ee5abe7ca10d45856de +#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 -#: 4a94e5f7e1bc4d628702140e4e51d6d3 -msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "" +"And add a second step that uses `wc` to count the characters in each file. " +"See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 -#: e61d93b848184c8e8e573928427b4d0a +#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "`wc-tool.cwl`" -#: ../../src/topics/workflows.md:489 -#: e3a7182f00f440b8b5461da91194a64b -msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under each " +"step:" msgstr "" -#: ../../src/topics/workflows.md:491 -#: 99fa96caacaa45cb97aded9a24fcac6d +#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 -#: b5338f39e8c74ff28e139da68089a742 -msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 -#: f6d92156d67c4a339bcfd194cff897df -msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +msgid "" +"Here we have placed the scatter field under each step. This is fine for this " +"example since it runs quickly, but if you're running many samples for a more " +"complex workflow, you may wish to consider an alternative. Here we are " +"running scatter on each step independently, but since the second step is not " +"dependent on the first step completing all languages, we aren't using the " +"scatter functionality efficiently. The second step expects an array as input " +"from the first step, so it will wait until everything in step one is " +"finished before doing anything. Pretend that `echo Hello World!` takes 1 " +"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " +"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " +"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " +"actually finish in 8 minutes because the first step must wait on `echo Hallo " +"welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can " +"make an entire workflow a single step in another workflow! Convert our two-" +"step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 -#: 1c9e386922324ec8a59306572c19fb8b +#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "`scatter-nested-workflow.cwl`" -#: ../../src/topics/workflows.md:519 -#: d80ab383eec9402faba997b548fe42eb -msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +msgid "" +"Now the scatter acts on a single step, but that step consists of two steps " +"so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 -#: f7d2827d97db4bf4ab84b5d6621c3b48 +#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "Workflows Condicionais" -#: ../../src/topics/workflows.md:524 -#: 49217c02f58c43ff9ec00f10da8d4e84 -msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 -#: 20b9f181420c401d8615c17a10027517 +#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 -#: 8dbd56473f8c40c0bb12a48be06117e3 -msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +msgid "" +"The first thing you'll notice is that this workflow is only compatible for " +"version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 -#: 78d7f3ede2c746d482042adef050b2c4 -msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when` is " +"where the condition validation takes place. In this case only when `in1` " +"from the workflow contains a value `< 1` this step will be executed." msgstr "" -#: ../../src/topics/workflows.md:587 -#: cbbf93c70fe04ba7932ba25758ddc611 -msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " +"will pass the first conditional step and will therefore be executed and is " +"shown in the log by `INFO [step step1] start` whereas the second step is " +"skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 -#: cfa1c1fde4454df283f87cc54a9c59ec -msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +msgid "" +"When a value of 3 is given the first conditional step will not be executed " +"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 -#: 1a8be2950cbb475bbb2617e005f0fac9 -msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +msgid "" +"If no conditions are met for example when using `--val 2` the workflow will " +"raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 -#: 5f09d4d897cf457d80b9a11b8c01747e +#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "Guia de YAML" -#: ../../src/topics/yaml-guide.md:6 -#: 5d83c56102e141cc978500f678dd0c1c -msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers and " +"humans. This guide introduces the features of YAML that are relevant when " +"writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 -#: c38438fbf9a04e729ec2e3c962435289 +#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 -#: fdb9cc750cec43ee962517e637dc5fea +#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "Conteúdo" -#: ../../src/topics/yaml-guide.md:18 -#: 08da9cd8056b4ddd8f5150cc85ba72ee +#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 -#: b027fc234ed943bbb00d4c6bc03c040a +#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 -#: b8befec0d8684638aaa616a659e0100c +#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 -#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 -#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "[Estilo JSON](#json-style)" -#: ../../src/topics/yaml-guide.md:24 -#: 98056c5cfd5640ad9de0679360797cc7 +#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "Pares de Chave-Valor" -#: ../../src/topics/yaml-guide.md:26 -#: cda73485875d4c8e9464679a20558616 -msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " +"is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have special " +"meaning in the CWL specification and underscored key names otherwise. For " +"example:" msgstr "" "Em princípio, um arquivo escrito em YAML consiste de uma série de _pares de " "chave-valor`. Cada par é escrito como `chave: valor`, onde o espaço em " @@ -3119,132 +3704,160 @@ msgstr "" "na especificação CWL, caso contrário os valores dos nomes de chaves aparecem " "sublinhados. For exemplo:" -#: ../../src/topics/yaml-guide.md:42 -#: 98cae24919b74c088a5d89706aec581b -msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " +"and `home` - with their four respective values. Values can be character " +"strings, numeric (integer, floating point, or scientific representation), " +"Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" "O YAML acima define quatro chaves - `first_name`, `last_name`, `age_years`, " "e `home` - com quatro valores respectivos. Os valores podem ser strings de " -"caracteres, númericos (integer, floating point, ou representação científica)" -", Boolean (`true` ou `false`), ou valores mais complexos com tipos aninhados " -"(veja abaixo)." +"caracteres, númericos (integer, floating point, ou representação " +"científica), Boolean (`true` ou `false`), ou valores mais complexos com " +"tipos aninhados (veja abaixo)." -#: ../../src/topics/yaml-guide.md:51 -#: b4b0940b4b5743c09637b36b964202d0 -msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may change " +"the way that they are interpreted i.e. `\"1234\"` will be treated as a " +"character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a " +"command: in CWL all parts of `baseCommand` must be strings so, if you want " +"to specify a fixed numeric value to a command, make sure that you wrap that " +"numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 -#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 -#: 9ca3554d771d45998e88aaede525b227 -msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program interpreting " +"the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 -#: 3fca839cede94cfd8e4f605c73ba699d -msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +msgid "" +"If there is anything on the line before the comment, be sure to add at least " +"one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 -#: da34c635707345b2a5e85a2fcd30bbaf +#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "Dicionários" -#: ../../src/topics/yaml-guide.md:81 -#: 3ded0f125249485c921994b6e6b93ac9 -msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, these " +"hierarchical structures are described in YAML by providing additional key-" +"value pairs as the value of any key. These pairs (sometimes referred to as " +"\"children\") are written on new lines under the key to which they belong " +"(the \"parent\"), and should be indented with two spaces (⇥tab characters " +"are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 -#: 53ece35d309a4c8d99f1efb2122a7092 -msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " +"while one of these children, `inputBinding`, contains a further two key-" +"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " +"below for more information about providing multiple values/key-value pairs " +"for a single key. For comparison with the example YAML above, here is a " +"graphical representation of the `inputs` object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 -#: d74321b111d84ae7a515f2f17dd39e23 +#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 -#: 7fc0bdf2489a44f2a29e71b86f7c0055 -msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) section " +"above, more than one key-value pair can be mapped to a single key. However, " +"it is also possible to define multiple values for a key without having to " +"provide a unique key for each value. We can achieve this with an _array_, " +"where each value is defined on its own line and preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 -#: fd64dd818ec64bb6aa9a11586a5747f6 +#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 -#: 8c06e542dd4144fa83388d8142552c8d +#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "Estilo JSON" -#: ../../src/topics/yaml-guide.md:169 -#: 87bafb845c714b109874f6137b84462d -msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " +"can also be defined in YAML using the native JSON syntax. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 -#: 5ab9ddf613a540a2b8228e37600cc5dc +#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "e:" -#: ../../src/topics/yaml-guide.md:184 -#: fcd05b1ef31a4046946a2399c7fc5575 -msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +msgid "" +"Native JSON can be useful in indicating where a field is intentionally left " +"empty (such as `[]` for an empty array), as well as where it makes more " +"sense for the values to be located on the same line (For example, when " +"providing option flags and their values in a shell command). However, as the " +"second example above shows, it can severely affect the readability of a YAML " +"file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 -#: f4b8fc8236044fada420def13a02813d +#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "Referencia" -#: ../../src/topics/yaml-guide.md:196 -#: 859368c1f25c4a4aad57abfd046c63f5 -msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " +"while we wrote this guide, though it also covers features that are not valid " +"in CWL." msgstr "" -#: ../../src/tutorials.md:1 -#: 2203c93f02ac4514a43508ecb98dfcc5 +#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" msgstr "Tutoriais" -#: ../../src/tutorials.md:5 -#: 5d92464923c245818c070fbef102be89 -msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to the " +"list." msgstr "" -#: ../../src/tutorials.md:7 -#: 8a5cd557dab5456bb41cdc24af73b50c +#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" msgstr "Tutoriais para Iniciantes" -#: ../../src/tutorials.md:9 -#: 13d7e2e92e96432787c712cf6a595424 -msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +msgid "" +"[Introduction to Workflows with Common Workflow Language: For Contributors.]" +"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 -#: 0abdd85c9b964a4e89ba3d80a6c78d6f +#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 -#: 3cbf1f69a5514fd3bee90e68b201190f +#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 -#: 68c97a7065634d02956f3f5c1d4eeb9f +#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 -#: a67c7e0eaf4e4d27b3e5db303333a088 +#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" From 823afd497ea480ff67f2a6033b82647347b2db15 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Wed, 26 Apr 2023 14:39:21 +0200 Subject: [PATCH 065/179] move pt to pt_BR (#389) --- locales/pt/LC_MESSAGES/sphinx.po | 30 - locales/pt/LC_MESSAGES/user_guide.po | 3875 ----------------------- locales/pt_BR/LC_MESSAGES/sphinx.po | 24 +- locales/pt_BR/LC_MESSAGES/user_guide.po | 1639 +++++----- 4 files changed, 901 insertions(+), 4667 deletions(-) delete mode 100644 locales/pt/LC_MESSAGES/sphinx.po delete mode 100644 locales/pt/LC_MESSAGES/user_guide.po diff --git a/locales/pt/LC_MESSAGES/sphinx.po b/locales/pt/LC_MESSAGES/sphinx.po deleted file mode 100644 index fc56cb08..00000000 --- a/locales/pt/LC_MESSAGES/sphinx.po +++ /dev/null @@ -1,30 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-01-26 13:55+0000\n" -"Last-Translator: Michael Crusoe \n" -"Language-Team: Portuguese \n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=2; plural=n > 1;\n" -"X-Generator: Weblate 4.16-dev\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../src/_templates/sidebar-nav-bs.html:1 d65b012160e9455eb4d2628279fffc42 -msgid "Main navigation" -msgstr "Navegação principal" - -#: ../../src/_templates/sidebar-nav-bs.html:3 4b3441eb77f448daa60718b7bfa862db -msgid "Section Navigation" -msgstr "Seção Navegação" diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po deleted file mode 100644 index 322bade8..00000000 --- a/locales/pt/LC_MESSAGES/user_guide.po +++ /dev/null @@ -1,3875 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-27 16:02+0100\n" -"PO-Revision-Date: 2023-04-03 19:41+0000\n" -"Last-Translator: ssantos \n" -"Language-Team: Portuguese \n" -"Language: pt\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=2; plural=n > 1;\n" -"X-Generator: Weblate 4.17-dev\n" -"Generated-By: Babel 2.10.3\n" - -#: ../../LICENSE.md:2 3eb955b4f3dd4c3188924b97ea6ab592 -msgid "Licenses" -msgstr "Licenças" - -#: ../../LICENSE.md:4 bf4480e7fff4460a87e8f43c11599f07 -msgid "Instructional Material" -msgstr "Material Instrucional" - -#: ../../LICENSE.md:6 9e9eab12205d4e82b4fedca520370f4c -msgid "" -"All Common Workflow Language project instructional material and changes to " -"the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable summary " -"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" -"[cc-by-legal]." -msgstr "" -"Todo o material instrucional do projeto Common Workflow Language e " -"alterações na estrutura também são disponibilizados sob a [licença Creative " -"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " -"humanos de (e não um substituto para) o [texto legal completo da licença CC " -"BY 4.0][cc-by-legal]." - -#: ../../LICENSE.md:12 a8e98ad541c642e58e201afa625ec791 -msgid "You are free:" -msgstr "Tem o direito de:" - -#: ../../LICENSE.md:14 b4cb4bc4261347fcb0d2c8a93995ab76 -msgid "" -"to **Share**---copy and redistribute the material in any medium or format" -msgstr "" -"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " -"formato" - -#: ../../LICENSE.md:15 d66dcbf95ccc41aaa53be523487ec913 -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" - -#: ../../LICENSE.md:17 ca1c299a1b834b868bcdd4ca9f244696 -msgid "for any purpose, even commercially." -msgstr "para qualquer fim, mesmo que comercial." - -#: ../../LICENSE.md:19 6133f79f93be4991a6f5290f72d1a63d -msgid "" -"The licensor cannot revoke these freedoms as long as you follow the license " -"terms:" -msgstr "" -"O licenciante não pode revogar estes direitos desde que você respeite os " -"termos da licença:" - -#: ../../LICENSE.md:24 2d6ce81add1043629b676187f890288c -msgid "" -"**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow Language " -"project, and, where practical, linking to https://www.commonwl.org/ ), " -"provide a [link to the license][cc-by-human], and indicate if changes were " -"made. You may do so in any reasonable manner, but not in any way that " -"suggests the licensor endorses you or your use." -msgstr "" -"Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " -"trabalho deriva de um trabalho que é «Copyright © The Common Workflow " -"Language project», e, quando prático, criar uma ligação para https://www." -"commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " -"se foram feitas alterações. Você pode fazê-lo de qualquer forma razoável, " -"mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " -"uso." - -#: ../../LICENSE.md:32 f3f22597b6f845208a0cce3b3b2c8f5d -msgid "" -"**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything the " -"license permits. With the understanding that:" -msgstr "" -"**Sem restrições adicionais**---Não pode aplicar termos jurídicos ou medidas " -"de caráter tecnológico que restrinjam legalmente outros de fazerem algo que " -"a licença permita. Com o entendimento de que:" - -#: ../../LICENSE.md:36 3cfedee64d4e46098a159cb2acdba4ef -msgid "" -"You do not have to comply with the license for elements of the material in " -"the public domain or where your use is permitted by an applicable exception " -"or limitation." -msgstr "" -"Não tem de cumprir com os termos da licença relativamente a elementos do " -"material que estejam no domínio público ou cuja utilização seja permitida " -"por uma exceção ou limitação que seja aplicável." - -#: ../../LICENSE.md:39 c836a570faaf449d9716da5f75556627 -msgid "" -"No warranties are given. The license may not give you all of the permissions " -"necessary for your intended use. For example, other rights such as " -"publicity, privacy, or moral rights may limit how you use the material." -msgstr "" -"Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " -"autorizações necessárias para o uso pretendido. Por exemplo, outros " -"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " -"podem limitar o uso do material." - -#: ../../LICENSE.md:44 896f9966e5014e8a88b060be3063fe09 -msgid "Software" -msgstr "Software" - -#: ../../LICENSE.md:46 007f8613dc234c3fa8d5d92b18af0eb1 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the " -"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." -msgstr "" -"Salvo indicação em contrário, os programas de exemplo e outro software " -"fornecido pelo projecto Common Workflow Language são disponibilizados sob a " -"[licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." - -#: ../../LICENSE.md:51 227bc635a06f49dbb771fd9b62157d00 -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." -msgstr "" -"A menos que exigido pela lei aplicável ou acordado por escrito, o software " -"distribuído sob a Licença é distribuído \"COMO ESTÁ\", SEM GARANTIAS OU " -"CONDIÇÕES DE QUALQUER TIPO, expressas ou implícitas. Consulte a Licença para " -"obter o texto específico sobre as permissões e limitações sob a Licença." - -#: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 1861131d3df648ae9e74ce1c87f0be7b a2ffa927deb2451d95ec63528e8078dd -#: d6055d3f15604ce6940770c7b561d4c5 -msgid "" -"CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece of " -"software, tools and workflows described using CWL are portable across a " -"variety of platforms that support the CWL standard." -msgstr "" -"CWL é uma maneira de descrever ferramentas de linha de comando e de conectá-" -"las formando workflows. Como a CWL é uma especificação e não um software, " -"ferramentas e workflows descritos com a CWL são portáveis entre uma " -"variedade de plataformas que suportam o padrão CWL." - -#: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 38b062f219b34e08a46bd8f6525353ec 89e7e1dd05474344a1d929cb492e9caf -msgid "This page has moved" -msgstr "Esta página foi movida" - -#: ../../src/episodes.md:9 d3357ff3c8874e368aea0d6062ef6190 -msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. Please use the new [Table of Contents](index.md#table-of-" -"contents) to browse the User Guide." -msgstr "" -"O conteúdo desta página está desatualizado e foi mantido para preservar os " -"links do antigo Guia do Utilizador. Por favor, use o novo [Índice](index.md" -"#table-of-contents) para navegar o Guia do Utilizador." - -#: ../../src/faq.md:1 f2c4882e0e164c2b869e3eb969241061 -msgid "FAQ" -msgstr "Perguntas Frequentes (FAQ)" - -#: ../../src/faq.md:11 41099ab64e0544d894bd9e3af2718bda -msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "Usando `evalFrom` para Tipos Diferentes de \"`File`\"" - -#: ../../src/faq.md:41 bb6aff70534148fa8a4b01140f7be150 -msgid "Rename an Input File" -msgstr "Renomear um Arquivo de Entrada" - -#: ../../src/faq.md:43 70ebc653b0d54d60a866edc0dbf56b57 -msgid "" -"This example demonstrates how to change the name of an input file as part of " -"a tool description. This could be useful when you are taking files produced " -"from another step in a workflow, and don't want to work with the default " -"names that these files were given when they were created." -msgstr "" -"Este exemplo demonstra como mudar o nome de um arquivo de entrada como parte " -"da descrição da ferramenta. Isso pode ser útil quando você tem arquivos " -"produzidos em outro passo de um workflow, mas prefere não utilizar os nomes " -"dados por padrão quando estes arquivos foram criados." - -#: ../../src/faq.md:59 38b687f707d2438b85df08a445ab816f -msgid "Rename an Output File" -msgstr "Renomear um Arquivo de Saída" - -#: ../../src/faq.md:61 d48422c020004ef084ca11e6229b5450 -msgid "" -"This example demonstrates how to change the name of an output file from the " -"default name given to it by a tool:" -msgstr "" -"Este exemplo demonstra como escolher o nome para um arquivo de saída " -"diferente do nome padrão criado por uma ferramenta:" - -#: ../../src/faq.md:82 48765409ab9d48ccbcecceb46ddf2e91 -msgid "Referencing a Local Script" -msgstr "Como Fazer Referência a um Script Local" - -#: ../../src/faq.md:84 a59b8acd72124e2c95d1905ae494d928 -msgid "There are two ways to reference a local script:" -msgstr "Há duas maneiras de fazer uma referência a um script local:" - -#: ../../src/faq.md:86 f36088ba90d24f9f9c7c1bd59deb6f49 -msgid "" -"The first method involves adding the folder containing your scripts to the " -"`PATH` environment variable. This allows you to run the shell script " -"directly without using `sh` or `bash` commands." -msgstr "" -"A primeira maneira é adicionando o arquivo que contém os seus scripts para a " -"variável de ambiente `PATH`. Desta maneira você pode executar o shell script " -"diretamente sem utilizar comandos via `sh` ou `bash`." - -#: ../../src/faq.md:89 45ee965ee4a7494a8354b82208e2ab45 -msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "Comece adicionando a _shebang_ no topo do seu arquivo:" - -#: ../../src/faq.md:95 734cc1abe1c841ffac8d0895463d91fc -msgid "" -"After that, make the script executable with the command `chmod +x scriptname." -"sh`" -msgstr "" -"Em seguida faça o seu script executável com o comando `chmod +x scriptname." -"sh`" - -#: ../../src/faq.md:97 f01bc8c4d6134f0ea27dc7f5b39def24 -msgid "" -"Finally, modify your `PATH` to add the directory where your script is " -"located. (It is good practice to use `$HOME/bin` for storing your own " -"scripts)." -msgstr "" -"E finalmente, modifique o seu `PATH` para adicionar o diretório que contém o " -"seu script. (É boa prática usar `$HOME/bin` para scripts do utilizador " -"local)." - -#: ../../src/faq.md:104 dd6fc2a04e3b476892f05bc5b746d0fa -msgid "" -"Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "" -"Agora você pode utilizar `baseCommand: scriptname.sh` para rodar o script " -"diretamente." - -#: ../../src/faq.md:113 e309eaad55144052866ce131eb80fd14 -msgid "" -"When you wish to share your work later, you can place your script in a " -"software container in the Docker format." -msgstr "" -"Depois quando você quiser compartilhar o seu trabalho, é possível utilizar " -"um container de software com ferramentas como Docker." - -#: ../../src/faq.md:115 f0d649a60a13404ebecd540789202b87 -msgid "" -"The second method involves including an input of `type: File` in the script " -"itself:" -msgstr "O segundo método utiliza um input `type: File` diretamente no script:" - -#: ../../src/faq.md:135 e2b782f88d494de398af0c9002a3ccdc -msgid "In CWL, everything must be directly stated." -msgstr "Em CWL tudo deve ser declarado diretamente." - -#: ../../src/faq.md:138 b4a033731fcd4322bd2bb71c609a4cb7 -msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "Definindo Bindings de Inputs utilizando `self` para Inputs Opcionais" - -#: ../../src/faq.md:140 43a64810b12b4c7d82a5803c3b910fe5 -msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their input " -"binding makes use of `self`. Below is an example workaround for this, " -"pending a more sophisticated fix." -msgstr "" -"No momento `cwltool` não funciona quando inputs opcionais não estão " -"presentes se o binding de input deles utilizar `self`. O exemplo abaixo " -"contém uma solução alternativa para este problema, até que haja uma solução " -"mais elegante para este problema." - -#: ../../src/faq.md:165 60f009e3714c405695da069204b196ea -msgid "Model a \"one-or-the-other\" Parameter" -msgstr "Modelar um Parâmetro do tipo \"um-ou-o-outro\"" - -#: ../../src/faq.md:167 98916ed9355842e49bef073430e10675 -msgid "" -"Below is an example showing how to specify different strings to be added to " -"a command line, based on the value given to a Boolean parameter." -msgstr "" -"O exemplo abaixo demonstra como especificar diferentes strings que serão " -"adicionadas à linha de comando, dependendo do valor de um parâmetro Boolean." - -#: ../../src/faq.md:188 9b8f2d0b33db4bbc82aaf5836b6f7ed8 -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "Conectar um Único valor a um Input que Espera uma Lista daquele Tipo" - -#: ../../src/faq.md:190 a251693354d24bf0bda4938c8890090a -msgid "" -"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" -"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/faq.md:194 f46740ac0acb473583facb9f7528d03c -msgid "merge_nested" -msgstr "merge_nested" - -#: ../../src/faq.md:196 7de1f9e3175b4c2ab156192f28fd3535 -msgid "" -"The input must be an array consisting of exactly one entry for each input " -"link. If \"merge_nested\" is specified with a single link, the value from " -"the link must be wrapped in a single-item list." -msgstr "" - -#: ../../src/faq.md:199 225c6f08068e41f58eb62f99dc06210f -msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "" -"Que significa \"criar uma lista com exatamente estes sources como elementos\"" - -#: ../../src/faq.md:201 4e741f4e3bc74e10bd9568826e81c478 -msgid "" -"Or in other words: if the destination is of type `File[]` (an array of " -"`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " -"add `linkMerge: merge_nested` under the appropriate `in` entry of the " -"destination step." -msgstr "" -"Ou em outras palavras: se o parâmetro destino for do tipo `File[]` (uma " -"lista de `File`s) e a fonte é um único `File`, adicione então " -"`MultipleInputFeatureRequirement` ao `requirements` no nível do Workflow e " -"adicione `linkMerge: merge_nested` sob a entrada apropriada `in` ao step que " -"receberá o parâmetro (target)." - -#: ../../src/faq.md:229 bfdb011cb81c4ef9b9e56b24f1e9ccd5 -msgid "Optional Inputs 💯" -msgstr "Inputs Opcionais 💯" - -#: ../../src/faq.md:231 09f385e325f942afaa3dd195c16a18d2 -msgid "" -"To make an input parameter optional, add a question mark to the type " -"declaration." -msgstr "" -"Para fazer um parâmetro de entrada opcional, adicione um ponto de " -"interrogação à declaração do tipo." - -#: ../../src/faq.md:247 c5d087082bb2468483e7ccda3ca45a07 -msgid "" -msgstr "" - -#: ../../src/faq.md:248 41e30b0224a0492f9047b4f320f39a23 -msgid "Enum Inputs ⚜️" -msgstr "Inputs Enum ⚜️" - -#: ../../src/faq.md:250 f06d073014a44f33a60d947a8c5b0e59 -msgid "" -"For command line flags that require a specific input as the argument an enum " -"type can be declared in CWL. **Specifying null here is known as long form " -"style. It does the same thing as the question mark on the other inputs.**" -msgstr "" -"O tipo enum por ser utilizado em CWL para flags de linha de comando que " -"requerem um tipo de input específico como argumento. **Especificar null aqui " -"é tido como forma estendida. O resultado é o mesmo que o uso do ponto de " -"interrogação nos outros inputs.**" - -#: ../../src/faq.md:267 2fb74cd1b41e4fdb81a8f9b3b6c84373 -msgid "" -msgstr "" - -#: ../../src/faq.md:268 09e19f34d0fd4e388d4939cbc2be3436 -msgid "Record Inputs 📀" -msgstr "Inputs do tipo Record" - -#: ../../src/faq.md:270 1ecae448dfcf45a4ae0dd39bd011e449 -msgid "" -"For commandline flags that are either **mutually exclusive** or " -"**dependent** a special record type can be defined. You can also specify " -"null here to create optional inputs." -msgstr "" - -#: ../../src/faq.md:322 6df3d4e918cc4bccb823859ce07b197a -msgid "Setting Mutually Exclusive Parameters" -msgstr "Definindo Parâmetros Mutualmente Exclusivos" - -#: ../../src/faq.md:324 086db1a093e64caa88d958150accc19c -msgid "" -"To properly set fields in a record input type, you need to pass a dictionary " -"to the input to properly set the parameters. This is done by using inline " -"JavaScript and returning the dictionary with the key of the field you want " -"to set. The source field is set to indicate the input from the workflow to " -"be used as the value." -msgstr "" - -#: ../../src/faq.md:342 da77c818d8694ab99fb2eccf73083047 -msgid "Setting Booleans" -msgstr "Utilizando Booleans" - -#: ../../src/faq.md:344 254259509ed6462d8ebc296b5f811f44 -msgid "These can be set by using the default field" -msgstr "Estes são definidos através do campo padrão" - -#: ../../src/faq.md:349 f7a44f76579d4709a61d2d61bc352b76 -msgid "Concatenating Strings in Inputs" -msgstr "Concatenando Strings em Inputs" - -#: ../../src/faq.md:351 d67278e99c684f488f1e3418e1c8c207 -msgid "The valueFrom field must be used instead of default." -msgstr "O campo valueFrom deve ser utilizado ao invés do valor padrão." - -#: ../../src/faq.md:359 f5e35ee06cd24edf831589ebaa6193d2 -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "Erros do `cwltool` devido a Nomes de Arquivos com Espaços" - -#: ../../src/faq.md:361 2ffb67e547c446499625a8db9a102da6 -msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "" -"O `cwltool` não permite alguns caracteres em nomes de arquivos por padrão." - -#: ../../src/faq.md:363 ee653ff9fefe4771b35e2e76199b536a -msgid "" -"For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "" -"Por exemplo, o nome de arquivo `um espaco vai aqui.txt` inclui 3 espaços.." - -#: ../../src/faq.md:371 02b1eb159e934fd692929f7c30319ddd -msgid "" -"If you can not avoid these dangerous characters, then pass `--relax-path-" -"checks` to `cwltool`." -msgstr "" -"Se você não tem opção e precisa utilizar estes caracteres apesar do risco, " -"você deve então passar `--relax-path-verificks` ao chamar o `cwltool`." - -#: ../../src/faq.md:373 857024702f624885be706c405b7a088e -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -msgstr "" -"Erro de Referência em Parâmetro CWL devido a Hífen no Identificador de " -"Entrada" - -#: ../../src/faq.md:375 d664e30899bd463bb48d38adec318dd4 -msgid "If `cwltool --validate` returns valid" -msgstr "Se `cwltool --validate` valida com sucesso" - -#: ../../src/faq.md:384 9f3957bbe205454e8bffc4b5caac5970 -msgid "But executing it causes an error like:" -msgstr "Mas ao executar o workflow um erro como o seguinte aparece:" - -#: ../../src/faq.md:396 6ec3bbc6a1ca4e23b47f025f0732e609 -msgid "The file is here" -msgstr "Este é o arquivo" - -#: ../../src/faq.md:410 3e727d79e65e4c6cb157550e80261c53 -msgid "Problem caused by `-` (hyphen character)." -msgstr "O problema é causado pelo `-` (hífen)." - -#: ../../src/faq.md:423 6e0705f4ab4b4e9093794cb4fccb6be9 -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "Para corrigir este erro, substitua o `-` (hífen) por `_` (sublinhado)" - -#: ../../src/faq.md:436 0047d039317349679fb6a66d18ec8487 -msgid "" -"If it is not possible to change the input identifier, then you can use an " -"alternative CWL Parameter Reference syntax:" -msgstr "" -"Se não for possível mudar o identificador do input, você pode reescrever " -"utilizando uma sintaxe alternativa para Referências de Parâmetros CWL:" - -#: ../../src/faq.md:442 8c39608ad0494bee9a4a422cbeb34387 -msgid "Use CWL and cwltool with Singularity" -msgstr "Utilizar CWL e cwltool com Singularity" - -#: ../../src/faq.md:445 7dac53bca8c14a3f9af75cb162cba4f9 -msgid "" -"The CWL standards are built around (optional) Docker format containers. The " -"reference runner and several other CWL implementations support running those " -"Docker format containers using the Singularity engine. Directly specifying a " -"Singularity format container is not part of the CWL standards." -msgstr "" - -#: ../../src/faq.md:450 ffcc38ff98324d71bfeb8d66d4901da7 -msgid "Debug JavaScript Expressions" -msgstr "Depurar Expressões JavaScript" - -#: ../../src/faq.md:452 0d7bf2cefe4a4e22b186bdf4d0ed793d -msgid "" -"You can use the --js-console option of cwltool, or " -"you can try creating a JavaScript or TypeScript project for your code, and " -"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" -"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" -msgstr "" - -#: ../../src/index.md:1 1506b4e7ee014a01bfdb067489501a9e -msgid "Common Workflow Language User Guide" -msgstr "" - -#: ../../src/index.md:3 0ce058b5210d46a0b78eb78dbca07a9f -msgid "" -"This guide will introduce you to writing workflows using the [Common " -"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " -"guide describes the latest specification {{ cwl_version }}." -msgstr "" - -#: ../../src/index.md:7 3404c064950d453d8af446e8b6554cb6 -msgid "Contributions and Feedback are Welcome!" -msgstr "" - -#: ../../src/index.md:9 1e239cad669648e48694eaf91284766a -msgid "" -"If you find that something is missing from this guide, or if you would like " -"to provide other feedback, file an Issue on the [project repository for this " -"guide][repo]. You can also suggest changes directly in a Pull Request by " -"clicking the \"Edit this page\" button at the right sidebar of each page." -msgstr "" - -#: ../../src/index.md:16 9dba2e06f1be4a50b1fabaaf216d02b4 -msgid "Navigating the User Guide" -msgstr "" - -#: ../../src/index.md:18 ba4074bbb69e4096a808001afaf2e0dc -msgid "" -"If you are a beginner user get started with the [Introduction](/introduction/" -"index.md) section. For advanced users the subsections of the [Topics](/" -"topics/index.md) have detailed information about the most common topics for " -"CWL." -msgstr "" - -#: ../../src/index.md:23 ad34a37bf4ec488bb825a34456f4fe8d -msgid "" -"The Table of Contents is displayed at the top menu and also on the left " -"sidebar. It also appears further down this page but with links to " -"subsections. The right sidebar contains links to the sections of each page, " -"and the Search form is on the left sidebar." -msgstr "" - -#: ../../src/index.md:28 2bd8eb5957ed40f4a72a6b7408044c78 -msgid "Table of Contents" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:1 8bb0df5531474301a185f1ba375320df -msgid "Basic Concepts" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:3 653373e1f11e4f81ad561378854a71fc -msgid "" -"This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are expected " -"to be familiar with workflow managers, YAML, and comfortable with following " -"instructions for the command-line. The other sections of the user guide " -"cover the same concepts, but in more detail. If you are already familiar " -"with CWL or you are looking for more advanced content, you may want to skip " -"this section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:10 7766227bf91b48b2b9752b625e5a9084 -msgid "The CWL Specification" -msgstr "A Especificação CWL" - -#: ../../src/introduction/basic-concepts.md:21 032d414ac29740aa9041d89d0ebf70e6 -msgid "" -"The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered in " -"this user guide is the {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:25 74e92eb0a4e64098b5aaf08d043e0641 -msgid "" -"The specification version can have up to three numbers separated by `.`s " -"(dots). The first number is the major release, used for backward-" -"incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes that " -"are backward-compatible. The last number is used for bug fixes, like typos " -"and other corrections to the specification." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:33 baa40b445f3c409b9a3e10a85fa38bfd -msgid "" -"The model used for the specification version is called Semantic Versioning. " -"See the end of this section to [learn more](#learn-more) about it." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:37 648e94a9d368450dbdac706445254c9f -msgid "Implementations" -msgstr "Implementações" - -#: ../../src/introduction/basic-concepts.md:39 e9ae15124dcd408395fc67e16b50696a -msgid "" -"An implementation of the CWL specification is any software written following " -"what is defined in a version of the specification document. However, " -"implementations may not implement every aspect of the specification. CWL " -"implementations are licensed under both Open Source and commercial licenses." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:44 b1c864d6775048cab01eb3de641f6475 -msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud " -"and high performance computing environments where tasks are scheduled in " -"parallel across many nodes." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:51 a05d24121e534d65947eb26e4dada5b7 -msgid "CWL specification, implementations, and other tools." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:105 -#: ace0388fd04845e79d31ec99a48a8a3f -msgid "Processes and Requirements" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:107 -#: 70ecd37237e14ae19539f2bf692882ed -msgid "" -"A process is a computing unit that takes inputs and produces outputs. The " -"behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification " -"{{ cwl_version }}:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:112 -#: 38121b4b00324bebb6499184b3dcb5c1 -msgid "A command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:113 -#: e0c278f52e824673ac708885d985b7d2 -msgid "An expression tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:114 -#: 6b4d0f0651cc46f5abf195b281967913 -msgid "An operation." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:115 -#: 88bdc9e046e4487cb0eee3f1d4819e57 -msgid "A workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:118 -#: 12eed3ef7d444585b150bbdab0665bc8 -msgid "The processing units available in the CWL objects model." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:119 -#: dfc85226313d46f9868dc4de53546a69 -msgid "" -"A command-line tool is a wrapper for a command-line utility like `echo`, " -"`ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:122 -#: f636b10c47734e589291de95443d8115 -msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be used " -"to simplify workflows and command-line tools, moving common parts of a " -"workflow execution into reusable JavaScript code that takes inputs and " -"produces outputs like a command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:127 -#: bb51025d04444dd5b16000d5d6a3f41a -msgid "" -"Operation is an abstract process that also takes inputs, produces outputs, " -"and can be used in a workflow. But it is a special operation not so commonly " -"used. It is discussed in the [Operations section](../topics/operations.md) " -"of this user guide." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:131 -#: 93dbaa0aa2c6493ab22a937c6861fac4 -msgid "" -"The workflow is a process that contains steps. Steps can be other workflows " -"(nested workflows), command-line tools, or expression tools. The inputs of a " -"workflow can be passed to any of its steps, while the outputs produced by " -"its steps can be used in the final output of the workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:137 -#: fcde5ef65ebf45a3b4b67eec993a1729 -msgid "" -"The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through *requirements*. " -"There are many requirements defined in the CWL specification, for instance:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:141 -#: c8ff34ff5d3b4a508e8c291196d08067 -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:142 -#: fe25f15fc11c49ab827b884d081c3df0 -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:143 -#: 2b93b6219142431ca748a404a56ced5d -msgid "" -"`InitialWorkDirRequirement` - controls staging files in the input directory." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:145 -#: 0094b13b26014ba3be61769b422802f5 -msgid "" -"Some CWL runners may provide requirements that are not in the specification. " -"For example, GPU requirements are supported in `cwltool` through the " -"`cwltool:CUDARequirement` requirement, but it is not part of the " -"{{ cwl_version }} specification and may not be supported by other CWL " -"runners." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:151 -#: 576a0778d3dd44f68cb241346f441660 -msgid "" -"Hints are similar to requirements, but while requirements list features that " -"are required, hints list optional features. Requirements are explained in " -"detail in the [Requirements](../topics/requirements-and-hints.md) section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:155 -#: 7d98949fe97744158fad81f41d780de9 -msgid "FAIR Workflows" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:157 -#: fc142b791aa1434aa75b0782248de988 -msgid "" -"The FAIR principles have laid a foundation for sharing and publishing " -"digital assets, and in particular, data. The FAIR principles emphasize " -"machine accessibility and that all digital assets should be Findable, " -"Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created. It " -"is thus important that workflows support the creation of FAIR data and " -"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" -"workflows.community/groups/fair/), Workflows Community Initiative." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:167 -#: c3fc91ae3bae4e3db60e8271e95135a2 -msgid "" -"CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\", " -"CWL tasks are isolated, and you must be explicit about your inputs and " -"outputs." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:171 -#: 8f097ae5ff6a4be0b7428345362dc55e -msgid "" -"The benefit of explicitness and isolation are flexibility, portability, and " -"scalability; tools and workflows described with CWL can transparently " -"leverage technologies such as Docker and be used with CWL implementations " -"from different vendors." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:176 -#: 60c56fa6a67346d6966f0d841213e11b -msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 7377b155e8694798994bbc911a3f3152 -#: 7699685836064bd89db530a9c1918865 7d187a209ebd4e3ba6c6aeb05743041a -msgid "Learn More" -msgstr "Saiba Mais" - -#: ../../src/introduction/basic-concepts.md:180 -#: 3fcbf810c86f4cf7b8499de88147aa95 -msgid "Semantic Versioning - " -msgstr "Versionamento Semântico - " - -#: ../../src/introduction/basic-concepts.md:181 -#: e242228b6b3d440cbca8418050220267 -msgid "" -"The CWL Specification page in the CWL website: " -msgstr "" -"A página web da Especificação CWL: " - -#: ../../src/introduction/basic-concepts.md:182 -#: 6e01963a01cb49e39692455256679bfc -msgid "" -"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" -msgstr "" -"A especificação CWL atual no GitHub: {{ ''.format(cwl_version_text) }}" - -#: ../../src/introduction/basic-concepts.md:183 -#: ed81ea2234b041c79449dcd20f886cb6 -msgid "" -"The list of Implementations in the CWL website: " -msgstr "" -"A lista de Implementações na página web da CWL: " - -#: ../../src/introduction/basic-concepts.md:184 -#: e8e3996f6a894b4f9cc266b46cb8d756 -msgid "PROV-O: The PROV Ontology - " -msgstr "PROV-O: A Ontologia PROV - " - -#: ../../src/introduction/basic-concepts.md:185 -#: 085e4d1a7a9744d2884f3003c64ca174 -msgid "" -"CWL Operations are covered in the [Operations](../topics/operations.md) " -"section of this user guide." -msgstr "" - -#: ../../src/introduction/index.md:1 dcd96950854f47a6ad4169320c1dab34 -msgid "Introduction" -msgstr "Introdução" - -#: ../../src/introduction/index.md:3 c4d17eec31874bf1ae9b49d73537d86c -msgid "" -"This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that " -"are useful to know before reading the rest of the user guide." -msgstr "" - -#: ../../src/introduction/prerequisites.md:1 98a8bdfc7c91436d9cb46abbb7c19c57 -msgid "Prerequisites" -msgstr "Pré-requisitos" - -#: ../../src/introduction/prerequisites.md:6 244a716e267540c782e627adaea3a413 -msgid "" -"The software and configurations listed in this section are prerequisites for " -"following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements focuses " -"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " -"runner or workflow system, but the results and interface may look different " -"(though the exact workflow outputs should be identical)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:12 2cdf453d2c8b4e2ea50555ef0b7364e5 -msgid "CWL Implementations" -msgstr "Implementações da CWL" - -#: ../../src/introduction/prerequisites.md:14 53643a4f190c412d9552d1908f408318 -msgid "" -"There are many implementations of the CWL standards. Some are complete CWL " -"runners, while others could be plug-ins or extensions to workflow engines. " -"We have a better explanation in the [Implementations](basic-concepts." -"md#implementations) section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:19 1df6c63de3914af68f758054fe6955f4 -msgid "Operating System" -msgstr "" - -#: ../../src/introduction/prerequisites.md:21 ceaa3a6bebab45a0907ee0cad01429a2 -msgid "" -"We recommend using an up-to-date operating system. You can choose any of the " -"following options for your operating system:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:24 1506ac904c6345c5806704a0ccf235aa -msgid "Linux" -msgstr "Linux" - -#: ../../src/introduction/prerequisites.md:25 a616213ed24e427bb91ee33cb21ec131 -msgid "macOS" -msgstr "macOS" - -#: ../../src/introduction/prerequisites.md:26 a4e9ae38103843739f13c62befd21f3e -msgid "Windows" -msgstr "Windows" - -#: ../../src/introduction/prerequisites.md:29 2cd231aac42c4a69a925cea369999a8b -msgid "" -"If you are using Windows, you will have to install the [Windows Subsystem " -"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " -"installing WSL2. Your operating system also needs internet access and a " -"recent version of Python (3.6+)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:35 051d7cd7d3a94baa865d180afdd71688 -msgid "CWL Runner" -msgstr "" - -#: ../../src/introduction/prerequisites.md:41 1a93aaf5bd5e4862b15e0636b4478640 -msgid "" -"The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL community. " -"It is also the CWL reference runner, which means it must support everything " -"in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/prerequisites.md:46 edd0613118a2493c876652bdcb9e0fbf -msgid "" -"`cwltool` can be installed with `pip`. We recommend using a virtual " -"environment like `venv` or `conda`. The following commands will create and " -"activate a Python virtual environment using the `venv` module, and install " -"`cwltool` in that environment:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:51 3448d215c2434866b8a4b340872ba81e -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "Instalando `cwltool` com `pip` e `venv`." - -#: ../../src/introduction/prerequisites.md:62 4c24d05f65794735b816024c78b63f1c -msgid "" -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool#install) for other ways to install `cwltool` with `apt` and " -"`conda`." -msgstr "" -"Visite a [documentação](https://github.com/common-workflow-language/" -"cwltool#install) do `cwltool` para outras opções para instalar `cwltool` com " -"`apt` e `conda`." - -#: ../../src/introduction/prerequisites.md:65 3167f4a2a8394feda1f848334be62022 -msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" -"Vamos usar uma simples descrição de ferramenta CWL `true.cwl` com `cwltool`." - -#: ../../src/introduction/prerequisites.md:67 3c4b67d62c9c4d658ccaafcd1977ec08 -msgid "`true.cwl`" -msgstr "`true.cwl`" - -#: ../../src/introduction/prerequisites.md:73 30792f78348942e0acdde411342e8830 -msgid "" -"The `cwltool` command has an option to validate CWL tool and workflow " -"descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the CWL " -"standards. However, these actions will be performed without running the " -"document. To validate CWL workflows (or even a standalone command line tool " -"description like the above) pass the `--validate` option to the `cwltool` " -"command:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:79 4473e41281fb4e738e4eb26c2d178934 -msgid "Validating `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:84 548393974d4d4acc91738f9bc13a3a48 -msgid "" -"You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:86 2ab3963cf9504ec097eda2b14f3448c4 -msgid "Running `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:91 690882dcc29c48acbeb215a8be52eb9e -msgid "Cwl-runner Python Module" -msgstr "Módulo Python cwl-runner" - -#: ../../src/introduction/prerequisites.md:93 6c3ba51b1e9a4add9203d62cec6ebae9 -msgid "" -"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be invoked " -"independently, and is not reliant on a particular CWL runner program name. " -"Users can invoke `cwl-runner` instead of invoking a CWL runner like " -"`cwltool` directly. The `cwl-runner` is installed by a system administrator " -"or user to point to the preferred CWL implementation. This is convenient for " -"environments with multiple CWL runners." -msgstr "" - -#: ../../src/introduction/prerequisites.md:101 b2360ef646854422ad6c0f90fa49306f -msgid "" -"The CWL community publishes a Python package with the name `cwlref-runner` " -"that installs an alias for `cwltool` under the name `cwl-runner`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:104 c9fadfa85a2641378e99a462e8e8d940 -msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:111 abb8993ede4d4e479d88d2e848546f68 -msgid "" -"Now you can validate and run your workflow with the `cwl-runner` executable, " -"which will invoke `cwltool`. You should have the same results and output as " -"in the previous section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:115 ba0f7606e6174e53a8bf23c1ccd99250 -msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:120 dd2e10f43e8f498cb01de5faa4fccb70 -msgid "Running `true.cwl` with `cwl-runner`." -msgstr "Executando `true.cwl` com `cwl-runner`." - -#: ../../src/introduction/prerequisites.md:125 e500e9c71c7042169c25b31f21a09142 -msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For " -"that, the first thing you need to do is copy `true.cwl` workflow into a new " -"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:129 d989516c873f4446bba005f42796b8b9 -msgid "`true_shebang.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:135 e9d8610478094a98b5b5a0f568a315de -msgid "" -"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:137 d6d8131f91b740189e56ab9d90bee55a -msgid "Making `true.cwl` executable." -msgstr "" - -#: ../../src/introduction/prerequisites.md:144 def7400a00e84070a4bd80c2367d3bde -msgid "" -"And finally, you can execute it directly in the command-line. On execution, " -"the program specified in the shebang (`cwl-runner`) will be used to execute " -"the rest of the file." -msgstr "" - -#: ../../src/introduction/prerequisites.md:148 564e7be94d254e52a6c44b234d6ddc63 -msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" - -#: ../../src/introduction/prerequisites.md:154 bb5fe42ddd814ad4ac1071c0b18f24c2 -msgid "" -"The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute the " -"script using the executable specified after the shebang. It is considered a " -"good practice to use `/usr/bin/env ` rather than using a hard-" -"coded location, since `/usr/bin/env ` looks for the " -"`` program in the system `PATH`," -msgstr "" - -#: ../../src/introduction/prerequisites.md:161 53bb712a68cd49fca4db11e9e507c9a4 -msgid "Text Editor" -msgstr "Editor de Texto" - -#: ../../src/introduction/prerequisites.md:163 bdcf61cce5294e45a9f964628a8a66bd -msgid "" -"You can use any text editor with CWL, but for syntax highlighting we " -"recommend an editor with YAML support. Popular editors are Visual Studio " -"Code, Sublime, WebStorm, vim/neovim, and Emacs." -msgstr "" - -#: ../../src/introduction/prerequisites.md:167 28d33daee6e246c8a6d1382208e19c39 -msgid "" -"There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting " -"and better auto-complete:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:171 b071d7c87b7a4817b871085a652cd580 -msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:172 97658a1b16874ba8b0bb748242d0da64 -msgid "" -"cwl-plugin for IntelliJ - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:174 6198aa6769b74ef0a2a1ba539789f3ee -msgid "" -"The CWL community also maintains a list of editors and viewers: " -msgstr "" - -#: ../../src/introduction/prerequisites.md:177 0c17235a374e40099be37b9b8ac8f1f0 -msgid "Docker" -msgstr "Docker" - -#: ../../src/introduction/prerequisites.md:181 e3690e656b5a4348845c654689935a88 -msgid "" -"`cwltool` uses Docker to run tools, workflows, and workflow steps that " -"specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: ." -msgstr "" - -#: ../../src/introduction/prerequisites.md:185 2db34e925a81422986ccb868463a7a42 -msgid "" -"You do not need to know how to write and build Docker containers. In the " -"rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models with " -"and without containers." -msgstr "" - -#: ../../src/introduction/prerequisites.md:191 d677fb155b0343ba8771398cca967fed -msgid "" -"`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for pulling " -"images." -msgstr "" - -#: ../../src/introduction/prerequisites.md:198 22ed0b55de38408393af4a8309a995ea -msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the next " -"section, Basic Concepts." -msgstr "" - -#: ../../src/introduction/prerequisites.md:199 5ded73cae5db40ad840c3022e7cd447f -msgid "The Python `venv` module: " -msgstr "" - -#: ../../src/introduction/quick-start.md:1 23e5613df7c94e5f938c85b14f5441e4 -msgid "Quick Start" -msgstr "" - -#: ../../src/introduction/quick-start.md:3 3b425afc63d841d4be57c92b25b4ed2d -msgid "" -"This section will show you a brief overview of what CWL is, and where you " -"can learn more about it. No previous knowledge of CWL is required, but you " -"must be comfortable following instructions for the command-line." -msgstr "" - -#: ../../src/introduction/quick-start.md:7 75a26c48d3e04e24abb96d81cb31c94e -msgid "“Hello World”" -msgstr "" - -#: ../../src/introduction/quick-start.md:12 88b4ecd45ea44dd4befe3ce89b30f6c2 -msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " -"example below shows a simple CWL “Hello World” workflow annotated with " -"comments. Note that comments start with `#`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:16 e1789ef78bd64332a18d8601094a0f72 -msgid "`hello_world.cwl`" -msgstr "" - -#: ../../src/introduction/quick-start.md:22 196ceef96c27434eb4b0b7222c2fe73c -msgid "" -"The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the " -"same result as the command-line `echo \"Hello World\"`." -msgstr "" - -#: ../../src/introduction/quick-start.md:27 e6a44130c6b44d5bb6451a147f28dd8c -msgid "" -"In CWL, there is a distinction between a command-line tool and a workflow. " -"But for the sake of simplicity, we are using the term “workflow” here. You " -"will learn more about this in the [basic concepts](basic-concepts.md) " -"section." -msgstr "" - -#: ../../src/introduction/quick-start.md:32 340b46acc7a34b7b978f5a734f529553 -msgid "Installing a CWL Runner" -msgstr "" - -#: ../../src/introduction/quick-start.md:34 139e48dcf0474fea932ca07a0001d208 -msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the CWL " -"*Reference Runner* for the specification, and it is compliant with the " -"latest version of the specification: {{ cwl_version }}. You can install " -"`cwltool` using `pip`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:39 d6f6e061c0f4434eb6d70f9d84759042 -msgid "Installing `cwltool` with `pip`." -msgstr "Instalando `cwltool` com `pip`." - -#: ../../src/introduction/quick-start.md:47 cb2b548489df45ee9d49b36116440eea -msgid "" -"If installing the cwltool using the pip command doesn't work for you, the " -"[prerequisites](prerequisites.md) section contains other ways to install " -"`cwltool` and a more detailed list of software and libraries used for " -"following the rest of this user guide." -msgstr "" - -#: ../../src/introduction/quick-start.md:51 aa751bda67ec44ba988642b061e2a094 -msgid "Running \"Hello World\"" -msgstr "Executando \"Hello World\"" - -#: ../../src/introduction/quick-start.md:53 a7e0209af0544b0ab31012864a43886c -msgid "" -"The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " -"workflow without specifying any option:" -msgstr "" - -#: ../../src/introduction/quick-start.md:57 d0f424f0041c4635a0559fa32a76c86f -msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "Executando `hello_world.cwl` com `cwltool`." - -#: ../../src/introduction/quick-start.md:62 eeee96c4e59447aea6b239c63e4bb3e5 -msgid "" -"Or you can override the default value of the input parameter `message`, " -"similar to how you would change the argument of the `echo` base command:" -msgstr "" - -#: ../../src/introduction/quick-start.md:65 961a385b340141e980aa4f8791fa2f12 -msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" - -#: ../../src/introduction/quick-start.md:70 c48cd1be543d4ccbab964b28c2e08584 -msgid "" -"Another way of passing values to your workflow input parameters is via an " -"*Inputs Object*. This is a file containing the input fields with their " -"corresponding values. The Inputs Objects file can be written in JSON or " -"YAML. For example:" -msgstr "" - -#: ../../src/introduction/quick-start.md:74 e5619164bdf242f0b09cac668adc0ef7 -msgid "`hello_world-job.json`" -msgstr "`hello_world-job.json`" - -#: ../../src/introduction/quick-start.md:80 9f80772a53154bbeb27895d35435de10 -msgid "" -"You can use this Inputs Object file now to execute the “Hello World” " -"workflow:" -msgstr "" -"Pode utilizar este arquivo de Objetos de Inputs agora para executar o " -"workflow “Hello World”:" - -#: ../../src/introduction/quick-start.md:82 98b6d400cb274d08ad6489adbef08c4b -msgid "Passing an Inputs Object file to `cwltool`." -msgstr "Passando um arquivo de Objeto de Inputs para o `cwltool`." - -#: ../../src/introduction/quick-start.md:88 4faabaab56f1444da290cf64cc389f37 -msgid "" -"We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but it " -"is not a requirement. You can choose any name for your workflows and Inputs " -"Object files." -msgstr "" - -#: ../../src/introduction/quick-start.md:96 48beaccb16a24427bd015c63f9e06d37 -msgid "Continue reading the next sections of this User Guide!" -msgstr "Continue lendo as secções seguintes deste Guia do Utilizador!" - -#: ../../src/introduction/quick-start.md:97 68035ead1c6844128011ca32c04fd20f -msgid "" -"[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" -"[Lista das Implementações da CWL](https://www.commonwl.org/implementations)." - -#: ../../src/introduction/quick-start.md:98 8fc1ebf21a6f4894a4acfba74a80602b -msgid "" -"The [`common-workflow-language` organization](https://github.com/common-" -"workflow-language) at GitHub." -msgstr "" -"A [organização`common-workflow-language`](https://github.com/common-workflow-" -"language) no GitHub." - -#: ../../src/introduction/quick-start.md:99 27fbad579d8b4ebeacc6fd3ef7e85a39 -msgid "" -"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" -"Common_Workflow_Language)." -msgstr "" -"[Common Workflow Language na Wikipedia](https://en.wikipedia.org/wiki/" -"Common_Workflow_Language)." - -#: ../../src/introduction/quick-start.md:100 a8791b670848474da292a467f01f8c45 -msgid "" -"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." -"org/wiki/YAML)." -msgstr "" -"[YAML.org](http://yaml.org/) e [YAML at Wikipedia](https://en.wikipedia.org/" -"wiki/YAML)." - -#: ../../src/introduction/quick-start.md:101 fc20fa4c04104417b541a67ada2ab9a9 -msgid "" -"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." -"replace('VERSION', cwl_version_text) }}." -msgstr "" -"A {{'[Especificação CWL VERSION](https://www.commonwl.org/VERSION)'.replace(" -"'VERSION', cwl_version_text) }}." - -#: ../../src/introduction/quick-start.md:102 a93a7797a12b48dfa5bc3a7c50ab88e7 -msgid "" -"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" -"Workflow_management_system)." -msgstr "" -"[Workflow management system na Wikipedia](https://en.wikipedia.org/wiki/" -"Workflow_management_system)." - -#: ../../src/setup.md:9 6f02fa47aca14c59a35b3ab750f5f236 -msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. The information on this page has been migrated to the [FAQ](/faq." -"md) section of the new user guide." -msgstr "" -"O conteúdo desta página está desatualizado mas foi mantido aqui para " -"preservar os links do antigo Guia do Utilizador. A informação desta página " -"foi migrada para a secção [FAQ](/faq.md) do novo guia do utilizador." - -#: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 3821c2d16b254672a494522e47386cb0 -msgid "Additional Arguments and Parameters" -msgstr "Argumentos e Parâmetros Adicionais" - -#: ../../src/topics/additional-arguments-and-parameters.md:3 -#: 412a05f3492349a7bd26ea0c30e9bd80 -msgid "" -"Sometimes tools require additional command line options that don't " -"correspond exactly to input parameters." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 1232f6c81da141cb8482294eee5955dc -msgid "" -"In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files in " -"the same directory as the source file. However, CWL input files (and the " -"directories in which they appear) may be read-only, so we need to instruct " -"\"javac\" to write the class file to the designated output directory instead." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 485bb71673144e3f90f05b420b7079ac -msgid "`arguments.cwl`" -msgstr "`arguments.cwl`" - -#: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0beb10c3133643f6b62c7d4aeec33709 -#: 5d48d9a2e977431f9a3625abaa466f5f -msgid "`arguments-job.yml`" -msgstr "`arguments-job.yml`" - -#: ../../src/topics/additional-arguments-and-parameters.md:24 -#: fcc1151a2e8b4a84b8595c7f913781a1 -msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "" -"Em seguida, crie um arquivo Java de exemplo para usar com a ferramenta de " -"linha de comando." - -#: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 4a291c7ac7c84257b7402567d8364a36 -msgid "" -"And now invoke `cwltool` providing the tool description and the input object " -"on the command line:" -msgstr "" -"E agora execute `cwltool` utilizando a descrição de ferramenta e o objeto de " -"input na linha de comando:" - -#: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 3b1ae26038fd498ca0ae23aa70a35d3f -msgid "" -"Here we use the `arguments` field to add an additional argument to the " -"command line that isn't tied to a specific input parameter." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:43 -#: 40388ebefb6947089c4a0f6d5d6e92e8 -msgid "" -"This example references a runtime parameter. Runtime parameters provide " -"information about the hardware or software environment when the tool is " -"actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include `$(runtime.tmpdir)`, " -"`$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and " -"`$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of " -"the CWL specification for details." -msgstr "" - -#: ../../src/topics/best-practices.md:1 a417fdd330db47a3aac07f7006c83ca9 -msgid "Best Practices" -msgstr "Melhores Práticas" - -#: ../../src/topics/best-practices.md:3 99bad0fd9bee428a8d936d5a8e84d97d -msgid "" -"The following are a set of recommended good practices to keep in mind when " -"writing a Common Workflow Language description for a tool or workflow. These " -"guidelines are presented for consideration on a scale of usefulness: " -"although more is better, not all are required." -msgstr "" - -#: ../../src/topics/best-practices.md:8 935500b0e6e249eba585644cddbd0253 -msgid "" -"No `type: string` parameters for names of input or reference files/" -"directories; use `type: File` or `type: Directory` as appropriate." -msgstr "" - -#: ../../src/topics/best-practices.md:11 96f924d6e02f4005b35d463e49be2982 -msgid "" -"A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that " -"the usual rules of software licensing apply to this document. For example, " -"if the workflow is shared publicly, licensing terms must be clear so that a " -"future user understands under what conditions they can run the workflow, " -"modify it and/or combine it with other workflows. For this reason, please " -"consider including a license field in the document. The authors of this " -"guide urge you to choose a pre-existing license rather than trying to write " -"your own (see the link below to learn more about choosing a license), and " -"our recommended practice is to choose a license that allows for re-use by " -"anyone, e.g. [Apache 2.0][apache-license]." -msgstr "" - -#: ../../src/topics/best-practices.md:20 25e0a5c93ccc49bc8b6206c7c2e3de5c -msgid "" -"If possible, the license should be specified with its corresponding [SPDX " -"identifier][spdx]. Construct the metadata field for the license by providing " -"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " -"taken from the list of identifiers linked above. See the example snippet " -"below for guidance. For non-standard licenses without an SPDX identifier, " -"provide a URL to the license." -msgstr "" - -#: ../../src/topics/best-practices.md:26 34ad53bc5a40446daa0dac4571600d1e -msgid "" -"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" -"Programmer][sci-license]\"" -msgstr "" - -#: ../../src/topics/best-practices.md:28 4c397ffd2e9148e39bdd614683a98a78 -msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" - -#: ../../src/topics/best-practices.md:37 1ed7f7e73afb4bd2ad2e29b65d020ff1 -msgid "" -"For more examples of providing metadata within CWL descriptions, see [the " -"Metadata and Authorship section of this User Guide](../topics/metadata-and-" -"authorship.md)." -msgstr "" - -#: ../../src/topics/best-practices.md:40 13b058dfa3cd4bbea54ae7d5a56c4c50 -msgid "" -"Include [attribution information][license-example] for the author(s) of the " -"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" -"[orcid]." -msgstr "" - -#: ../../src/topics/best-practices.md:44 69369b917c1a45199343266650b1b220 -msgid "" -"In tool descriptions, list dependencies using short name(s) under " -"`SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:47 0245a61fd2ef4fb69cbb8d732086fb8f -msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" -"identifiers.org/rrid/RRID:SCR_NNNNNN` format." -msgstr "" - -#: ../../src/topics/best-practices.md:50 e9a56e3634a042279cae1745b7820658 -msgid "" -"All `input` and `output` identifiers should reflect their conceptual " -"identity. Use informative names like `unaligned_sequences`, " -"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " -"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." -msgstr "" - -#: ../../src/topics/best-practices.md:55 8a180861a66c4aaa9e8fdefd929ed829 -msgid "" -"In tool descriptions, include a list of version(s) of the tool that are " -"known to work with this description under `SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:58 00f333a383b64578b32c687b42924a77 -msgid "" -"`format` should be specified for all input and output `File`s. " -"Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with " -"`$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " -"[Full IANA media type list][iana-types] (also known as MIME types). For non-" -"bioinformatics tools, use or build an appropriate ontology/controlled " -"vocabulary in the same way. Please edit this page to let us know about it." -msgstr "" - -#: ../../src/topics/best-practices.md:66 6b960d362bb540299f0560c14c5f2d8c -msgid "" -"Mark all input and output `File`s that are read from or written to in a " -"streaming compatible way (only once, no random-access), as `streamable: " -"true`." -msgstr "" - -#: ../../src/topics/best-practices.md:69 9cf9342bf0864e87b495913d8e06d021 -msgid "" -"Each `CommandLineTool` description should focus on a single operation only, " -"even if the (sub)command is capable of more. Don't overcomplicate your tool " -"descriptions with options that you don't need or use." -msgstr "" - -#: ../../src/topics/best-practices.md:73 587b048324e447cb85844d8c64ae9a1e -msgid "" -"Custom types should be defined with one external YAML per type definition " -"for re-use." -msgstr "" - -#: ../../src/topics/best-practices.md:76 d8df6bbd5d324f7c9f48edb33e113b75 -msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "" - -#: ../../src/topics/best-practices.md:78 2235174088ad48a89d4fc21223e627b7 -msgid "" -"If useful, include a top-level `doc` as well. This should provide a longer, " -"more detailed description than was provided in the top-level `label` (see " -"above)." -msgstr "" - -#: ../../src/topics/best-practices.md:82 a0f0953a1a9f40cebd4dbe028784ff96 -msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list of " -"valid values." -msgstr "" - -#: ../../src/topics/best-practices.md:85 0ec380c683534892b6b8b8fcea84f765 -msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. One " -"common example: manipulating `File` names and paths? Consider whether one of " -"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " -"`nameext`, etc., could be used instead." -msgstr "" - -#: ../../src/topics/best-practices.md:90 65f23741db4e4a6abda8e5f7e036753a -msgid "" -"Give the tool description to a colleague (preferably at a different " -"institution) to test and provide feedback." -msgstr "" - -#: ../../src/topics/best-practices.md:93 34c2caee8eb84e01a37033b67eb4aaba -msgid "" -"Complex workflows with individual components which can be abstracted should " -"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " -"workflow modular and allow sections of them to be easily reused." -msgstr "" - -#: ../../src/topics/best-practices.md:97 d7c7484b2f1048aea9802400410f0858 -msgid "" -"Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics " -"software\"][containers] (also useful to other disciplines)." -msgstr "" - -#: ../../src/topics/command-line-tool.md:1 a905abc2eead4dbaa035235936025499 -msgid "Command Line Tool" -msgstr "" - -#: ../../src/topics/command-line-tool.md:3 eb91b6dab34d4d5f9854ac580a6cbde2 -msgid "" -"A command-line tool is a type of Process object that can be run by itself or " -"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " -"etc. The command-line tool is defined in the `baseCommand` attribute of the " -"command-line tool CWL document." -msgstr "" - -#: ../../src/topics/command-line-tool.md:8 7caeb91564634091a932f1270c4f5ef9 -msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The following " -"example contains a minimal example of a CWL command-line tool for the `echo` " -"Linux command, using inputs and outputs." -msgstr "" - -#: ../../src/topics/command-line-tool.md:19 c6ac4a60d102407991f40b892fb60560 -msgid "CWL command-line tool." -msgstr "" - -#: ../../src/topics/command-line-tool.md:50 51d3ce421db345f5ab19e02fbbc51df2 -msgid "`echo.cwl`" -msgstr "" - -#: ../../src/topics/command-line-tool.md:57 8311d1430e624435b7b04bf2574a90c5 -msgid "" -"The example above uses a simplified form to define inputs and outputs. You " -"will learn more about in the [Inputs](../topics/inputs.md) and in the " -"[Outputs](../topics/outputs.md) sections." -msgstr "" - -#: ../../src/topics/command-line-tool.md:68 d1c03e5f19d64ea89276d126de6e4bda -msgid "Network Access" -msgstr "" - -#: ../../src/topics/command-line-tool.md:69 8494b43e98dd424db7d57aa1d731f7b4 -msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network access. " -"If a command-line tool is written manually in CWL v1.1+, there is a need to " -"specify when network access is required." -msgstr "" - -#: ../../src/topics/command-line-tool.md:83 8c4573fb120149269a0fe3a1ba6c9ef8 -msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " -"Access automatically." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:1 -#: e1c709ac0fb249928d14aeced6551ae0 -msgid "Creating Files at Runtime" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:3 -#: c26c9c640e0747c8b2c2977c860c9d82 -msgid "" -"Sometimes you need to create a file on the fly from input parameters, such " -"as tools that expect to read their input configuration from a file rather " -"than the command line parameters, or need a small wrapper shell script." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:7 -#: edbe918d7df14cafb440e171e46c6de3 -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:9 -#: 6d457d9b4ae746d384e65d9a37ca3591 -msgid "`createfile.cwl`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:15 -#: 868394c1b8374ee6bbd43463e73d7edc -msgid "" -"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the value " -"at the input `message`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:20 -#: 08a9e08cba674db09c9bfbef37e9579f -msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later " -"during command line tool invocation. That means that any genuine need for " -"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " -"above is expanded to `${PREFIX}` in the generated file to be evaluated by " -"the shell script instead of the CWL engine." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:27 -#: 6f6f437753dd4eddae0b2ea62046fe39 -msgid "" -"To test the above CWL tool, use this job to provide the input value " -"`message`:" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 096b17907bc3452d9927ef2fb6f5c11f 78ed5d8fb9bd4e068023d2c717e20f62 -#: c3a2e9e6b4414597a17db6d55d98e9d1 -msgid "`echo-job.yml`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:35 -#: ac783e6415a44cb59d4b425bac5087b7 -msgid "" -"Before we run this, let us look at each step in a little more detail. The " -"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " -"command `sh example.sh`. This will run the file we create in the shell." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:40 -#: b9e6e15b541149c6a2d3922c11405267 -msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " -"array, we need a `-` on the first line of each element of the array, in this " -"case we have just one element. `entryname:` can have any value, but it must " -"match what was specified in the `baseCommand`. The final part is `entry:`, " -"this is followed by `|-` which is YAML quoting syntax, and means that you " -"are using a multiline string (without it, we would need to write the whole " -"script on one line)." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:51 -#: 87088899567a4402aeb34605d3c6b06b -msgid "" -"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " -"formatting." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:54 -#: ../../src/topics/environment-variables.md:18 -#: ../../src/topics/file-formats.md:52 -#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 304c1bfe5ecd4d26b5dfaf9ad2e2c7f8 3ef7f0e3099147d78fd2d30bfa73cc6b -#: 4fef79a30282456eb9b5dd34a5eec0b1 afe775762ed348e5982b99bcf1451606 -#: f0689cd0e5b34414b6693331186ee4a3 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on the " -"command line:" -msgstr "" - -#: ../../src/topics/custom-types.md:1 9f1967411aa7497fa43a4851f0645d6e -msgid "Custom Types" -msgstr "" - -#: ../../src/topics/custom-types.md:3 90bd62e4ef8b41e398a5c9b31f132774 -msgid "" -"Sometimes you may want to write your own custom types for use and reuse in " -"CWL descriptions. Use of such custom types can reduce redundancy between " -"multiple descriptions that all use the same type, and also allow for " -"additional customisation/configuration of a tool/analysis without the need " -"to fiddle with the CWL description directly." -msgstr "" - -#: ../../src/topics/custom-types.md:9 3465527b8ff4407587f7c46fa9fa2a98 -msgid "" -"The example below is a CWL description of the [biom convert format][biom] " -"tool for converting a standard biom table file to hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:12 c0cc869690804ada96a5c1813d17b895 -msgid "`custom-types.cwl`" -msgstr "" - -#: ../../src/topics/custom-types.md:18 01f369931c8142c08fe821a0ca31bf92 -msgid "`custom-types.yml`" -msgstr "" - -#: ../../src/topics/custom-types.md:24 0b3ff704cdea44e28aee3c704ca98e27 -msgid "" -"___Note:___ To follow the example below, you need to [download the example " -"input file](https://github.com/common-workflow-language/user_guide/blob/main/" -"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " -"*rich_sparse_otu_table.biom* e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/custom-types.md:30 cb456bcae0dd41ffbc514eeea283e130 -msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to be " -"used in the table conversion are imported as a custom object:" -msgstr "" - -#: ../../src/topics/custom-types.md:46 c610173365d04c57900b22f4024b47b4 -msgid "" -"The reference to a custom type is a combination of the name of the file in " -"which the object is defined (`biom-convert-table.yaml`) and the name of the " -"object within that file (`table_type`) that defines the custom type. In this " -"case the `symbols` array from the imported `biom-convert-table.yaml` file " -"define the allowable table options. For example, in `custom-types.yml`, we " -"pass `OTU table` as an `input` that tells the tool to create an OTU table in " -"hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:53 c2b2e18d55c94721812431583cfc4725 -msgid "" -"The contents of the YAML file describing the custom type are given below:" -msgstr "" - -#: ../../src/topics/custom-types.md:55 3e61c3920a7a45db8917c348bd44384d -msgid "`biom-convert-table.yaml`" -msgstr "" - -#: ../../src/topics/custom-types.md:61 cd87d210b03c4da2a7608b40a6bbcca0 -msgid "" -"In order for the custom type to be used in the CWL description, it must be " -"imported. Imports are described in `requirements:SchemaDefRequirement`, as " -"below in the example `custom-types.cwl` description:" -msgstr "" - -#: ../../src/topics/custom-types.md:76 7af9ba3219e44ed49b8da781db5d6fb5 -msgid "" -"Note also that the author of this CWL description has also included " -"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " -"cores required for the tool to run successfully, as well as details of the " -"version of the software that the description was written for and other " -"useful metadata. These features are discussed further in other chapters of " -"this user guide." -msgstr "" - -#: ../../src/topics/environment-variables.md:1 eae1994f3a4d481b863b5125c7f4a383 -msgid "Environment Variables" -msgstr "" - -#: ../../src/topics/environment-variables.md:3 8bd8c06d416740b69d126eb9f5f24ad3 -msgid "" -"Tools run in a restricted environment and do not inherit most environment " -"variables from the parent process. You can set environment variables for " -"the tool using `EnvVarRequirement`." -msgstr "" - -#: ../../src/topics/environment-variables.md:7 11c6bffc620b4c789b29ab4034a8bfbd -msgid "`env.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:1 89888b1b994546ce8a93f9630b4bb07e -msgid "Expression Tool" -msgstr "" - -#: ../../src/topics/expression-tool.md:3 191d3010b9244b39bc3bc50246ac7ad7 -msgid "" -"An expression tool is a type of Process that can be run by itself or as a " -"Workflow step. It executes a pure JavaScript expression. It is meant to be " -"used as a way to isolate complex JavaScript expressions that need to operate " -"on input data and produce some result as output." -msgstr "" - -#: ../../src/topics/expression-tool.md:8 3437ed6e184748e4af1ef62f32c8cef1 -msgid "" -"Similar to the command-line tool it requires `inputs` and `outputs`. But " -"instead of `baseCommand`, it requires an `expression` attribute." -msgstr "" - -#: ../../src/topics/expression-tool.md:17 c3ae1ef318bb4e0fada76c353dd5f6f1 -msgid "CWL expression tool." -msgstr "" - -#: ../../src/topics/expression-tool.md:48 a7f5e04d242c48a7b3deffb5ff6528be -msgid "`uppercase.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:67 32b6841faed044409bc618cba54a22f0 -msgid "" -"We had to use an `InlineJavascriptRequirement` as our expression contains a " -"JavaScript call in `.toUpperCase()`. This means to tools using the " -"expression tool that JavaScript is a requirement." -msgstr "" - -#: ../../src/topics/expressions.md:1 6821ba7a84a44d309d245c429948ad09 -msgid "Expressions" -msgstr "" - -#: ../../src/topics/expressions.md:3 8167269bc3a64c72bd6c909362350a15 -msgid "" -"If you need to manipulate input parameters, include the requirement " -"`InlineJavascriptRequirement` and then anywhere a parameter reference is " -"legal you can provide a fragment of Javascript that will be evaluated by the " -"CWL runner." -msgstr "" - -#: ../../src/topics/expressions.md:9 c0f75603a6024063a6911f17c70908cc -msgid "" -"JavaScript expressions should only be used when absolutely necessary. When " -"manipulating file names, extensions, paths etc, consider whether one of the " -"[built in `File` properties][file-prop] like `basename`, `nameroot`, " -"`nameext`, etc, could be used instead. See the [list of best practices](best-" -"practices.md)." -msgstr "" - -#: ../../src/topics/expressions.md:16 7faec63b389a4c07b6929b7a78f0cc70 -msgid "`expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:22 d7dca89942f949d58cb18cb94bb7de72 -msgid "" -"As this tool does not require any `inputs` we can run it with an (almost) " -"empty job file:" -msgstr "" - -#: ../../src/topics/expressions.md:25 1abc1a21c0764415b138099e0e21432b -msgid "`empty.yml`" -msgstr "" - -#: ../../src/topics/expressions.md:31 b8b5a50a82e44e49a37c6396f1ff9464 -msgid "" -"`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object is " -"represented simply by a set of empty brackets." -msgstr "" - -#: ../../src/topics/expressions.md:35 b38d66c12ab74dfc9395e69d9c04bbf5 -msgid "We can then run `expression.cwl`:" -msgstr "" - -#: ../../src/topics/expressions.md:37 8417aa7a9d034361a41def6b71e93413 -msgid "Running `expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:47 c1f672b377da4605b9c5098ebb6e1147 -msgid "" -"Note that requirements can be provided with the map syntax, as in the " -"example above:" -msgstr "" - -#: ../../src/topics/expressions.md:54 af52f5197e8545d2be22cc0f7f03648c -msgid "" -"Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " -"describe the additional command line arguments." -msgstr "" - -#: ../../src/topics/expressions.md:62 5e12ce15018942bf9010ce6519c17b00 -msgid "Where are JavaScript expressions allowed?" -msgstr "" - -#: ../../src/topics/expressions.md:64 e2e9c5f7b681427a9589476649e5a9d8 -msgid "" -"Just like [parameter references](parameter-references.md), you can use " -"JavaScript Expressions only in certain fields. These are:" -msgstr "" - -#: ../../src/topics/expressions.md:66 8a74763ead0147bbaf3892e552fad546 -msgid "" -"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 0aab7de8d69f49438d4eeed17316df68 -#: 75f90cb870d14d0dbb4c4ee80d32a65e -msgid "`arguments`" -msgstr "" - -#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 -#: ../../src/topics/expressions.md:89 -#: ../../src/topics/parameter-references.md:65 -#: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 0b9d8268c177489b86b8eaa638dfa063 -#: 204cd6d8375a4462a8247863a96df906 2b7e56ceb4ad49a8b29a58b10bad7c0a -#: 81f15c64379941d8ac2a681b3879761c f11ae7d801db45989b598864dc6291c9 -#: fc4534b475334f7281d1740c9a78f640 -msgid "`valueFrom`" -msgstr "" - -#: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 70e9085b21f640d6893309a3375c0511 -#: f529003dd7a64bc7be0ccef8dbfa84b3 -msgid "`stdin`" -msgstr "" - -#: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 3fceb522ba6245129b826c342eaf31b4 -#: a5f71add5b8345a4bfa02853ef8a6d35 -msgid "`stdout`" -msgstr "" - -#: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 018300196ea24550988a0156894b5e85 -#: 2c799286e8204ed9a83c3fc006988139 -msgid "`stderr`" -msgstr "" - -#: ../../src/topics/expressions.md:72 25d91d6624bd42e7948e29c684e8e441 -msgid "" -"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 -#: ../../src/topics/parameter-references.md:70 -#: ../../src/topics/parameter-references.md:75 -#: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 0944d6525c3c460aa4b5a0e72552ca4d -#: 1187b0d330cb470fbea82a8b8c95aa28 265602307ccd42458ba47ac1b689242c -#: 2febce1b1ad74b18af3a9b3fa137c780 3215ee41f96541cbbda60a1167386c2f -#: 80efeab6ec0e447bbe158cbaa57f83d8 8d2bbd91b4ab4faa923fc1a14ec49dd5 -#: b4a6e640275b4fc7a18e3083e86b72a1 -msgid "`format`" -msgstr "" - -#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 -#: ../../src/topics/parameter-references.md:71 -#: ../../src/topics/parameter-references.md:76 -#: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 480b2e4207574b27b8d33dfe5e9ab64e -#: 4b4149a3b97a4de5b2d7fd84bd547ffe 7af1a82df41e40d0a430babafe1bc5e2 -#: be01787b66e34074af32bb45dcce8657 be099ab533504a7596fd56ec1ce7ca5d -#: c8b96271665444608f601a460dd28fb3 cb6dfa7bc68b41929a5247d929c2f94a -#: f7f452e92f6d4a14ba3912c62699019a -msgid "`secondaryFiles`" -msgstr "" - -#: ../../src/topics/expressions.md:75 4811c1b9867b44caa70dec4b91970484 -msgid "" -"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:77 0b1f2a8986e0419a90e484d3a945a037 -msgid "" -"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:80 dbc02876870d49d2b9e39db4133a0f62 -msgid "" -"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 97339a3fa43849f7b292f4643b5fe35c -#: da8b81b1e1884406a188fb04825ef90e -msgid "`glob`" -msgstr "" - -#: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 077e7b0d2dde443699050af8c63ab912 -#: c8cbe3dfd0984221ae72012ea26edc6f -msgid "`outputEval`" -msgstr "" - -#: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 3f07f4a8594640c2b2da4da521872b59 -#: 573f7e4b72ec4c47ab2e54e2c4877d9c -msgid "From `Workflow`" -msgstr "" - -#: ../../src/topics/expressions.md:84 f03011b3479b47c690604c508d95c263 -msgid "" -"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" -"v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 1ec3f913909b4e04bb602767d23bd85d -#: 2f7130500b8c450fa4af226b18e38407 -msgid "From `steps`" -msgstr "" - -#: ../../src/topics/expressions.md:88 a5849a856a374cda807ecf48034af915 -msgid "" -"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 bd8bbd60aaff4e7aacec91bcbad500f4 -#: f0c99004211e4adf8c0b524d5bbcc12b -msgid "" -"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." -"html#ExpressionTool)" -msgstr "" - -#: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 96c544cf213245cfb3d1f5196223c6cc -#: c6a04d4f3ef24104b0a86f9093935c13 -msgid "`expression`" -msgstr "" - -#: ../../src/topics/expressions.md:92 946e0437a48b4d5da2a29d489250cbaa -msgid "" -"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [ExpressionToolOutputParameter](https://www." -"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:95 1f287ebf87ae4e93bd1ac65cc1d01bf4 -msgid "" -"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 0d0f4f0e12174d588c131afef70efc5f -#: a74e0e3499d644b4a9d999d3555f03de -msgid "`coresMin`" -msgstr "" - -#: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 b2e31c38f7cb4ecabd6b9b89ef051c0e -#: ddc9d9ae72a64a76a2a8e2bba22584ee -msgid "`coresMax`" -msgstr "" - -#: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 12f86817dfc14f2bb39509886d56017f -#: 8a94f2c3b1674162a268f67935a3025b -msgid "`ramMin`" -msgstr "" - -#: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 a800acfefb3f433fae2cdda9ac4a795a -#: bcb58fc2447a4472b86913871b8c12ee -msgid "`ramMax`" -msgstr "" - -#: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 5be337d412ba4d48877e991d535e810c -#: e6cf2f8498db4f549193be20d87e16f9 -msgid "`tmpdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 3bc61c8197664f12a98d1ac38b421b38 -#: 9973a87f747445ad89ce959420cac5fd -msgid "`tmpdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 0f5dc4f5a4c64f818e2e22f20472ae84 -#: 2ec9d1f191f44686b1cb8622336d6b92 -msgid "`outdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:103 -#: ../../src/topics/parameter-references.md:100 -#: 5382ff97ad2f419dbe1bed266997aa84 74406f77013443f28d4d6306c54b0df1 -msgid "`outdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:104 f594a20dc038457e815dc17bae6e031d -msgid "" -"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" -"CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:105 -#: ../../src/topics/parameter-references.md:102 -#: 5814f96ee4ec4822aecad33c8eda0473 c46c44268b2a4b96b1df13e53e82e54c -msgid "`listing`" -msgstr "" - -#: ../../src/topics/expressions.md:106 b9824103ef8745bab30b65887c82f62f -msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/expressions.md:107 -#: ../../src/topics/parameter-references.md:104 -#: 28b23f84c64549e7a0fe444ccc3e1b05 fdd5d742a6764e5db2281ed844bf3475 -msgid "`entry`" -msgstr "" - -#: ../../src/topics/expressions.md:108 -#: ../../src/topics/parameter-references.md:105 -#: b6123c911c804f3c8cb596d2aa495b2b d81a7d8b7db444409b286e5f1d863968 -msgid "`entryname`" -msgstr "" - -#: ../../src/topics/expressions.md:109 -#: ../../src/topics/parameter-references.md:106 -#: eb6255a0f8d748588d87e7ad38e507bd fffc5a80bd68495396d32b7a1821eb4e -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../src/topics/expressions.md:110 b00a8a2a572742e0929470550433e929 -msgid "" -"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/expressions.md:111 -#: ../../src/topics/parameter-references.md:108 -#: 9b34c95e483e47f3828e79bf929a23b4 c968eebaf0114b23b789e9ce68e7588d -msgid "`envValue`" -msgstr "" - -#: ../../src/topics/expressions.md:116 7c8fb996d1af4cfdb0d49d8ed2696745 -msgid "" -"Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" - -#: ../../src/topics/expressions.md:118 75a29e9ff2cf4b5bb6afa87a741a111b -msgid "" -"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " -"attribute that allows users to load external JavaScript files, or to provide " -"inline JavaScript code." -msgstr "" - -#: ../../src/topics/expressions.md:122 5233d8baa8b74391bf8fee5ae2324234 -msgid "" -"Entries added to the `expressionLib` attribute are parsed with the " -"JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts of " -"the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:128 343e8b78a1f94b8cbafac05212e5a333 -msgid "" -"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." -"org/v1.0/CommandLineTool.html#Expressions) that the only version of " -"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" -"international.org/5.1/). This means that any code that you include or write " -"in your CWL Document must be compliant with ECMAScript 5.1." -msgstr "" - -#: ../../src/topics/expressions.md:135 0657ee8f03d8462ca6ca6fc538386b0d -msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " -"function inline in `expressionLib`. That function can then be used in other " -"parts of the CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:139 e3c593cf50da426f8d9df215c7db0bc9 -msgid "`hello-world-expressionlib-inline.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:146 b971e53c3ed847f1b7c7a6d50e344baf -msgid "" -"Running this CWL workflow will invoke the JavaScript function and result in " -"the `echo` command printing the input message with capital initial letters:" -msgstr "" - -#: ../../src/topics/expressions.md:149 d2315d46369f4e9d9c871d7f88f7006e -msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:155 04fdaa45a7ed47d5830181611bda924e -msgid "" -"Let's move the `capitalizeWords` function to an external file, `custom-" -"functions.js`, and import it in our CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:158 8d7686f62f314d98aae8c262befd5283 -msgid "`custom-functions.js`" -msgstr "" - -#: ../../src/topics/expressions.md:164 e68ee17607be4a06a66f9fc67624aff5 -msgid "`hello-world-expressionlib-external.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:171 76b85d3729274fc08adfadcbf1172650 -msgid "" -"The `custom-functions.js` file is included in the CWL document with the " -"`$include: custom-functions.js` statement. That makes the functions and " -"variables available to be used in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:175 29f334957fa940c289f385160cca6d63 -msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:181 6d255ae6b92a48fa9b7b98443cc2f5bb -msgid "" -"Finally, note that you can have both inline and external JavaScript code in " -"your CWL document. In this final example we have added another entry to the " -"`expressionLib` attribute with the new function `createHelloWorldMessage`, " -"that calls the `capitalizeWords` function from the external file `custom-" -"functions.js`." -msgstr "" - -#: ../../src/topics/expressions.md:186 89734e7855654b2e8bfddeea96241539 -msgid "`hello-world-expressionlib.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:193 1915f8e68f624027827d28f8e17d2dec -msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:200 750f94edb4f84e45a276f6ab28fad95e -msgid "" -"The `$include` statement can be used to include a file from the local disk " -"or from a remote location. It works with both relative and absolute paths. " -"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." -"html#Include) from the CWL specification to learn more about it." -msgstr "" - -#: ../../src/topics/file-formats.md:1 2e9e8cfaf48a43a88c31a855dac4f748 -msgid "File Formats" -msgstr "" - -#: ../../src/topics/file-formats.md:3 c574b54d998243f28d2caa91434968a7 -msgid "" -"Tools and workflows can take `File` types as input and produce them as " -"output. We also recommend indicating the format for `File` types. This helps " -"document for others how to use your tool while allowing you to do some " -"simple type-checking when creating parameter files." -msgstr "" - -#: ../../src/topics/file-formats.md:8 b0ec34507eea473c91d6ada09a1c5c09 -msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM in " -"our example), reference a local ontology for your institution, or do not add " -"a file format initially for quick development before sharing your tool with " -"others. You can browse existing [IANA file format listings][IANA] and [EDAM " -"file format listings][EDAM] on their websites." -msgstr "" - -#: ../../src/topics/file-formats.md:14 a688e39859734a518c0fcc19f532a432 -msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` section " -"of the document in greater detail, so don't worry about these for now." -msgstr "" - -#: ../../src/topics/file-formats.md:17 e068422ad9b84ca1b27008127928cc0f -msgid "" -"Note that for added value `cwltool` can do some basic reasoning based on " -"file formats and warn you if there seem to be some obvious mismatches." -msgstr "" - -#: ../../src/topics/file-formats.md:20 8c3ef5e145b14299bf3671add0da56ac -msgid "`metadata_example.cwl`" -msgstr "" - -#: ../../src/topics/file-formats.md:26 -#: ../../src/topics/metadata-and-authorship.md:22 -#: 0d92f1c0f1ce448fb698e9b390b45c15 fc4773204ebc4e3789bb076dff0d0393 -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../src/topics/file-formats.md:32 900abc5aa6a940f48f9c93e79cd1c47f -msgid "Sample Parameter Files" -msgstr "" - -#: ../../src/topics/file-formats.md:34 0390555b96c84aadbd9325c152972087 -msgid "" -"Below is an example of a parameter file for the example above. We encourage " -"checking in working examples of parameter files for your tool. This allows " -"others to quickly work with your tool, starting from a \"known good\" " -"parameterization." -msgstr "" - -#: ../../src/topics/file-formats.md:39 d5752ee5437b496ca10f4f12b76fc5dc -msgid "`sample.yml`" -msgstr "`sample.yml`" - -#: ../../src/topics/file-formats.md:45 91dc76bb4565473ab948eecf628a405c -msgid "" -"___Note:___ To follow the example below, you need to download the example " -"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/index.md:1 0b8b9b7f533543a49f876421ce6057d9 -msgid "Topics" -msgstr "" - -#: ../../src/topics/inputs.md:1 1b6cfac3a92347d4b98bb54de1e26870 -msgid "Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:3 53dd5f476f064cbf9b9826d1e80eb830 -msgid "Essential Input Parameters" -msgstr "" - -#: ../../src/topics/inputs.md:5 420b33d143fc44d1b237bc678f0af663 -msgid "" -"The `inputs` of a tool is a list of input parameters that control how to run " -"the tool. Each parameter has an `id` for the name of parameter, and `type` " -"describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/inputs.md:9 55136332e3bb48f892cf6a74c67a4ac6 -msgid "" -"Available primitive types are *string*, *int*, *long*, *float*, *double*, " -"and *null*; complex types are *array* and *record*; in addition there are " -"special types *File*, *Directory* and *Any*." -msgstr "" - -#: ../../src/topics/inputs.md:13 cb2527899cc04b6d8060c4d57883beb5 -msgid "" -"The following example demonstrates some input parameters with different " -"types and appearing on the command line in different ways." -msgstr "" - -#: ../../src/topics/inputs.md:16 c79668b856b14243b4fad0f46dc5d6d7 -msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "" - -#: ../../src/topics/inputs.md:18 ed6f3e5c7b3f403a9a94359983107645 -msgid "`inp.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:24 034075eb09db4897a96d3332408427db -msgid "Create a file called `inp-job.yml`:" -msgstr "" - -#: ../../src/topics/inputs.md:26 08181d391cc543a5a81d3257654df213 -msgid "`inp-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:33 15215522e38242c4b17ec3aa089269d4 -msgid "" -"You can use `cwltool` to create a template input object. That saves you from " -"having to type all the input parameters in a input object file:" -msgstr "" - -#: ../../src/topics/inputs.md:40 64bd3382ec234ec8a50217b794b96916 -msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " -"> inp-job.yml`, and then modify the default values with your desired input " -"values." -msgstr "" - -#: ../../src/topics/inputs.md:44 3611c1ca498a4197a4a6612c60f5f565 -msgid "" -"Notice that \"example_file\", as a `File` type, must be provided as an " -"object with the fields `class: File` and `path`." -msgstr "" - -#: ../../src/topics/inputs.md:47 da924e8142d34e86bcb5de1cd1da71ca -msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " -"command line." -msgstr "" -"Em sequência, cria um arquivo chamado whale.txt utilizando [touch] digitando " -"`touch whale.txt` na linha de comando." - -#: ../../src/topics/inputs.md:53 13c97256a5ee49c99f4010edf9dbc9bf -msgid "" -"Now invoke `cwltool` with the tool description and the input object on the " -"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " -"boxed text describes these two commands and the expected output from the " -"command line:" -msgstr "" - -#: ../../src/topics/inputs.md:64 dcc3f2a47a6449efb857af63ed4b65d0 -msgid "" -"The CWL reference runner (cwltool) and other runners create temporary " -"directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not explicitly " -"specified" -msgstr "" - -#: ../../src/topics/inputs.md:70 cf54a30ae24f4013bb19f379a7ca67be -msgid "" -"The field `inputBinding` is optional and indicates whether and how the input " -"parameter should appear on the tool's command line. If `inputBinding` is " -"missing, the parameter does not appear on the command line. Let's look at " -"each example in detail." -msgstr "" - -#: ../../src/topics/inputs.md:83 ff75644bae9c46af8379d78360d4c696 -msgid "" -"Boolean types are treated as a flag. If the input parameter " -"\"example_flag\" is \"true\", then `prefix` will be added to the command " -"line. If false, no flag is added." -msgstr "" - -#: ../../src/topics/inputs.md:95 e90abe59a84e48d4b8d6caa737e087aa -msgid "" -"String types appear on the command line as literal values. The `prefix` is " -"optional, if provided, it appears as a separate argument on the command line " -"before the parameter . In the example above, this is rendered as `--example-" -"string hello`." -msgstr "" - -#: ../../src/topics/inputs.md:109 9275236d87b646cab1058dd750e11a50 -msgid "" -"Integer (and floating point) types appear on the command line with decimal " -"text representation. When the option `separate` is false (the default value " -"is true), the prefix and value are combined into a single argument. In the " -"example above, this is rendered as `-i42`." -msgstr "" - -#: ../../src/topics/inputs.md:124 6a39929af73f4ba9b6455ed9fd287e08 -msgid "" -"File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the parameter " -"is optional. In the example above, this is rendered as `--file=/tmp/random/" -"path/whale.txt`. However, if the \"example_file\" parameter were not " -"provided in the input, nothing would appear on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:131 44ce716561cc4dff8fef1ca59f816c7c -msgid "" -"Input files are read-only. If you wish to update an input file, you must " -"[first copy it to the output directory](staging-input-files.md)." -msgstr "" - -#: ../../src/topics/inputs.md:134 9f1da592350f40ee88920465e2004148 -msgid "" -"The value of `position` is used to determine where parameter should appear " -"on the command line. Positions are relative to one another, not absolute. " -"As a result, positions do not have to be sequential, three parameters with " -"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " -"than one parameter can have the same position (ties are broken using the " -"parameter name), and the position field itself is optional. The default " -"position is 0." -msgstr "" - -#: ../../src/topics/inputs.md:142 5116d91f247f44518eb21840415f6eaa -msgid "" -"The `baseCommand` field will always appear in the final command line before " -"the parameters." -msgstr "" - -#: ../../src/topics/inputs.md:146 08b26d1688e3470288e73d587f052d88 -msgid "Array Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:148 f91994a4279a41bda3de41fe79008c62 -msgid "" -"It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to provide " -"`type` field with `type: array` and `items` defining the valid data types " -"that may appear in the array. Alternatively, brackets `[]` may be added " -"after the type name to indicate that input parameter is array of that type." -msgstr "" - -#: ../../src/topics/inputs.md:154 4b93a4f980634e88a8f34a38703fc906 -msgid "`array-inputs.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:160 de3e760ebb0e4ae099deddb978046a2c -msgid "`array-inputs-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 06ec811e8f0e43b8b929198533ac8082 -#: 797c06f0605d4e4ba306c2803a7834f9 d76d42c490a24b6daed944f45fe7a351 -msgid "" -"Now invoke `cwltool` providing the tool description and the input object on " -"the command line:" -msgstr "" -"Agora chame o `cwltool` passando a descrição da ferramenta e o objeto de " -"entrada na linha de comando:" - -#: ../../src/topics/inputs.md:178 49406f30f62346968bb1250efc940f70 -msgid "" -"The `inputBinding` can appear either on the outer array parameter definition " -"or the inner array element definition, and these produce different behavior " -"when constructing the command line, as shown above. In addition, the " -"`itemSeparator` field, if provided, specifies that array values should be " -"concatenated into a single argument separated by the item separator string." -msgstr "" - -#: ../../src/topics/inputs.md:185 3d8711f0135e4ab1b59fce94c83b97c0 -msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` in " -"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " -"where array values that are not defined with an associated key are marked by " -"a leading `-`. This will be demonstrated in the next lesson and is discussed " -"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " -"arrays of arrays, arrays of records, and other complex types." -msgstr "" - -#: ../../src/topics/inputs.md:191 6f146779d6a84888948751b8b1fd0515 -msgid "Inclusive and Exclusive Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:193 e5970a83876e4b5e9a02f2ab0030eb83 -msgid "" -"Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be provided " -"together (they are exclusive). You can use records and type unions to group " -"parameters together to describe these two conditions." -msgstr "" - -#: ../../src/topics/inputs.md:198 0db71b22173846d7b8d4aeb66d2ed8ed -msgid "`record.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:204 f90fd48656a7424aac304987adf1b068 -msgid "`record-job1.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:215 3c8bd9134a1c4bda9461362df3257d6b -msgid "" -"In the first example, you can't provide `itemA` without also providing " -"`itemB`." -msgstr "" - -#: ../../src/topics/inputs.md:217 63bd06780bb949e5b1a1d10389c8c23f -msgid "`record-job2.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:233 0d448baa57f14e7783d3167611e8c659 -msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the first " -"matching item (`itemC`) is added to the command line and remaining item " -"(`itemD`) is ignored." -msgstr "" - -#: ../../src/topics/inputs.md:236 202239a6e90044e39b676d641aa6d58a -msgid "`record-job3.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:252 512ecb3349b0450cb741de4ed2d2e850 -msgid "" -"In the third example, only `itemD` is provided, so it appears on the command " -"line." -msgstr "" - -#: ../../src/topics/inputs.md:255 185ff0bb49e841c592b29112eb171bdc -msgid "Exclusive Input Parameters with Expressions" -msgstr "" - -#: ../../src/topics/inputs.md:257 6cd5df09e4594d78a526f199ac577881 -msgid "" -"If you use exclusive input parameters combined with expressions, you need to " -"be aware that the `inputs` JavaScript object will contain one of the " -"exclusive input values. This means that you might need to use an **or** " -"boolean operator to check which values are present." -msgstr "" - -#: ../../src/topics/inputs.md:262 9db9f784a5cd4ca5b90691d1e2e827ea -msgid "" -"Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from an " -"enum." -msgstr "" - -#: ../../src/topics/inputs.md:265 09b1db3cc6c845058cf0ad4c24d71733 -msgid "`exclusive-parameter-expressions.cwl`" -msgstr "`exclusive-parameter-expressions.cwl`" - -#: ../../src/topics/inputs.md:271 84aa6e0c479f4528836691005129056e -msgid "" -"Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you provide a " -"valid value, such as “fasta” (one of the values of the enum), your command " -"should execute successfully:" -msgstr "" - -#: ../../src/topics/inputs.md:280 76611ebb19764bdc8a1f6eacfb76138f -msgid "" -"However, if you do not provide any input value, then `file_format` will be " -"evaluated to a `null` value, which does not match the expected type for the " -"output field (a `string`), resulting in failure when running your workflow." -msgstr "" - -#: ../../src/topics/inputs.md:289 bf9750d215be4294b1cf1e0490a0796a -msgid "" -"To correct it, you must remember to use an or operator in your JavaScript " -"expression when using exclusive parameters, or any parameter that allows " -"`null`. For example, the expression could be changed to `$(inputs." -"file_format || 'auto')`, to have a default value if none was provided in the " -"command line or job input file." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:1 -#: 612f9efa0ed04559a174c37958def6f7 -msgid "Metadata and Authorship" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:3 -#: 57eb990c11f044dfb60c012a92a30eb1 -msgid "" -"Implementation extensions not required for correct execution (for example, " -"fields related to GUI presentation) and metadata about the tool or workflow " -"itself (for example, authorship for use in citations) may be provided as " -"additional fields on any object. Such extensions fields (e.g. `format: edam:" -"format_2572`) can use a namespace prefix listed in the `$namespaces` section " -"of the document (e.g. edam: http://edamontology.org/) as described in the " -"[Schema Salad specification][schema-salad]. Once you add the namespace " -"prefix, you can access it anywhere in the document as shown below. " -"Otherwise, one must use full URLs: `format: http://edamontology.org/" -"format_2572`." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:13 -#: a6e6155cb8ff40fb9d8b1fff3e94fb02 -msgid "" -"For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to cite " -"your tool." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:16 -#: 063c28fc9e654dfd91c66da164ac1d3d -msgid "`metadata_example2.cwl`" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:28 -#: 8fcd2ae1ce8d4c7f951281ced81ab32d -msgid "Extended Example" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:30 -#: 639533652456427480fa311da7beb4f0 -msgid "" -"For those that are highly motivated, it is also possible to annotate your " -"tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints at " -"hardware requirements in order to use the tool, and a few more metadata " -"fields." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:35 -#: 266808daf2004bbd9830045fbc67a541 -msgid "`metadata_example3.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:1 fd9b715bfa3243b19a919ad19843232d -msgid "Operations" -msgstr "" - -#: ../../src/topics/operations.md:3 fb568063fa7a4cbe83c271772d3d62bc -msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-line " -"tool, or an expression tool. It is a step of a workflow that specifies " -"inputs and outputs, but it does not provide enough information to be " -"executed." -msgstr "" - -#: ../../src/topics/operations.md:7 981486166754435cbcd8152e93679405 -msgid "" -"You can create operations to visualize a workflow during development, before " -"you are ready to submit the workflow to a CWL runner:" -msgstr "" - -#: ../../src/topics/operations.md:10 7b165718ffeb42e793c97fad807f216f -msgid "`operations.cwl`" -msgstr "`operations.cwl`" - -#: ../../src/topics/operations.md:16 5e31cddd14414d31b7bd0a6c2745d272 -msgid "" -"The `uppercase` step of the workflow is an operation. It can be used like a " -"command line tool or an expression. You can also plot it with the CWL Viewer " -"or `cwltool`:" -msgstr "" - -#: ../../src/topics/operations.md:24 02c372245dc9453ea0841026335e405b -msgid "" -"The output of the command above can be rendered with a Graphviz renderer. " -"The following image is rendered with the Sphinx Graphviz directive (this " -"user guide is built with Sphinx):" -msgstr "" - -#: ../../src/topics/operations.md:55 d331327285d1434e8c17187737345919 -msgid "" -"If you try running it with `cwltool`, the command will fail since `cwltool` " -"does not have enough information to know how to execute it:" -msgstr "" - -#: ../../src/topics/operations.md:58 72705f8940bb4194bc5554fcc29eed49 -msgid "`cwltool` does not know how to run operations" -msgstr "" - -#: ../../src/topics/operations.md:66 76b7c63107e94323859904415d07d31c -msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A " -"CWL runner could, for instance, use abstract operations with ID's that " -"correspond to steps executed by a different workflow engine." -msgstr "" - -#: ../../src/topics/outputs.md:1 ebf56d267612461799bf801136e61b69 -msgid "Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:3 f9cff6b272a24ef6ada90e263c1b1784 -msgid "Returning Output Files" -msgstr "" - -#: ../../src/topics/outputs.md:5 e482821911004cdd8c3ff1539c69368a -msgid "" -"The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name of " -"parameter, and `type` describing what types of values are valid for that " -"parameter." -msgstr "" - -#: ../../src/topics/outputs.md:10 e11fcfe1e84b476ea879810b76ff2cb8 -msgid "" -"When a tool runs under CWL, the starting working directory is the designated " -"output directory. The underlying tool or script must record its results in " -"the form of files created in the output directory. The output parameters " -"returned by the CWL tool are either the output files themselves, or come " -"from examining the content of those files." -msgstr "" - -#: ../../src/topics/outputs.md:16 65c73a37f06a4782bf43f4acf4f1c77e -msgid "" -"The following example demonstrates how to return a file that has been " -"extracted from a tar file." -msgstr "" - -#: ../../src/topics/outputs.md:19 e172dde545164fefac826d910ddd399e -msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "" - -#: ../../src/topics/outputs.md:21 225f4d04c28149898f06bd771f741358 -msgid "" -"In previous examples, the `baseCommand` was just a string, with any " -"arguments passed as CWL inputs. Instead of a single string we can use an " -"_array of strings_. The first element is the command to run, and any " -"subsequent elements are mandatory command line arguments" -msgstr "" - -#: ../../src/topics/outputs.md:26 14e9e446768a454ea786b3256b49632e -msgid "`tar.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:32 4bd659cee1904868a7c33345f94f1300 -msgid "`tar-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:38 8803a28ccff846eea7d06f4bd908c763 -msgid "Next, create a tar file for the example." -msgstr "Agora, crie um arquivo tar para o exemplo." - -#: ../../src/topics/outputs.md:45 661b62e554d64e449c69e475e5188f99 -msgid "" -"And now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - -#: ../../src/topics/outputs.md:51 44cdca5b777441baa246c87940df7264 -msgid "" -"The field `outputBinding` describes how to set the value of each output " -"parameter." -msgstr "" - -#: ../../src/topics/outputs.md:62 edb34af3b22d418d9a6178c0ecbb8b80 -msgid "" -"The `glob` field consists of the name of a file in the output directory. If " -"you don't know name of the file in advance, you can use a wildcard pattern " -"like `glob: '*.txt'`." -msgstr "" - -#: ../../src/topics/outputs.md:65 10e68fad866f4187981f0b365b957b03 -msgid "Capturing Standard Output" -msgstr "" - -#: ../../src/topics/outputs.md:67 77e1261484964ba9ac67d9fc9139a1d6 -msgid "" -"To capture a tool's standard output stream, add the `stdout` field with the " -"name of the file where the output stream should go. Then add `type: stdout` " -"on the corresponding output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:71 c66bd08354d54ccb9e3e1da89634a816 -msgid "`stdout.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:89 7d4056355da1451dbed6733fba8c3c38 -msgid "Array Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:91 8fed80f9633a4e87a67c651dc3160ce6 -msgid "" -"You can also capture multiple output files into an array of files using " -"`glob`." -msgstr "" - -#: ../../src/topics/outputs.md:93 6cba36e037d54f93add05fb16d2359bd -msgid "`array-outputs.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:99 08862892ecf849a1ba2f25ecc9e98227 -msgid "`array-outputs-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:112 c5dcc68bb28041b3b96ac1af716b0db8 -msgid "" -"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " -"expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions to " -"mark entries in arrays, as demonstrated in several of the upcoming sections." -msgstr "" - -#: ../../src/topics/parameter-references.md:1 53b95fd10d61462daf153d45e5517dad -msgid "Parameter References" -msgstr "" - -#: ../../src/topics/parameter-references.md:3 0702e71de81e493dac08a91d667569e3 -msgid "" -"In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file we " -"were interested in was called \"hello.txt\", and this was written into the `." -"cwl` file. This is not the best way to do this, as the \"hello.txt\" " -"filename may vary or be dependent on the input file(s) used. To avoid this " -"we can specify the name of the file we want in the job parameters file (`." -"yml`). In this example, you will see how to reference the value of input " -"parameters dynamically from other fields, which will allow us to then " -"specify the name of the file to extract." -msgstr "" - -#: ../../src/topics/parameter-references.md:13 a1703da32ad64fd2b8bdd423605b50bd -msgid "`tar-param.cwl`" -msgstr "" - -#: ../../src/topics/parameter-references.md:19 2f32531e47b4465594d41ddd218fb2fd -msgid "`tar-param-job.yml`" -msgstr "`tar-param-job.yml`" - -#: ../../src/topics/parameter-references.md:25 501dd6f9dbb1438f9a59f6a025639f35 -msgid "" -"Create your input files and invoke `cwltool` with the tool description and " -"the input object on the command line:" -msgstr "" - -#: ../../src/topics/parameter-references.md:36 1bcdd99111bd4bc5b75a8297bb61d9bb -msgid "" -"Certain fields permit parameter references which are enclosed in `$(...)`. " -"These are evaluated and replaced with value being referenced." -msgstr "" - -#: ../../src/topics/parameter-references.md:47 32eae36c593e43a9a6b4e103a0c2028a -msgid "" -"References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " -"`$(inputs['extractfile'])` are equivalent." -msgstr "" - -#: ../../src/topics/parameter-references.md:51 1d785e8a450140a982142aa0fa906257 -msgid "" -"The value of the \"inputs\" variable is the input object provided when the " -"CWL tool was invoked." -msgstr "" - -#: ../../src/topics/parameter-references.md:54 e862bb8bc3e84e24a2aa5ec34298cfd5 -msgid "" -"Note that because `File` parameters are objects, to get the path to an input " -"file you must reference the path field on a file object; to reference the " -"path to the tar file in the above example you would write `$(inputs.tarfile." -"path)`." -msgstr "" - -#: ../../src/topics/parameter-references.md:59 46ffaab11be040cea96a294d9a814738 -msgid "Where are parameter references allowed?" -msgstr "" - -#: ../../src/topics/parameter-references.md:61 890d619c415741179c83ffcd56833fbe -msgid "You can only use parameter references in certain fields. These are:" -msgstr "" - -#: ../../src/topics/parameter-references.md:63 373e1847d9f745d7a749928642c8e0e3 -msgid "" -"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/parameter-references.md:69 90d3624e062c41c7a6d1a9824515d0df -msgid "" -"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:72 76d09490bd464b708c28991dbff0104e -msgid "" -"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:74 f33c76e590dd4feaac1e3cf568069d33 -msgid "" -"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:77 74ed4a06c1984c58826ddceb1a45a4ea -msgid "" -"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:81 eba3362d34354daa89dc516722c6fbd0 -msgid "" -"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" -"v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:85 e924874af32d4be19c5e8446768226dd -#, fuzzy -msgid "" -"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" -msgstr "" -"De [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" - -#: ../../src/topics/parameter-references.md:89 b162113f364445af9ff1bfc8a6610e13 -msgid "" -"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." -"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" -"De [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) e [ExpressionToolOutputParameter](http://www.commonwl." -"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" - -#: ../../src/topics/parameter-references.md:92 aa721077e16948c3a5bb8ef5bd7aff04 -msgid "" -"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:101 -#: 2fad0c2bc2834350826b22c454d33cf0 -msgid "" -"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" -"CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:103 -#: 9e303aa89a9b4447b0dbdc5ac0a0eb9e -msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/parameter-references.md:107 -#: 7a4eb47c25a54d11a00eb73e9333ad1c -msgid "" -"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/requirements-and-hints.md:5 -#: 8a957bc8e577476bb59647661b3c0990 -msgid "Requirements and Hints" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:1 -#: 2b31f1dec3f5498e9e363a4f1f50dc8d -msgid "Specifying Software Requirements" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:3 -#: 5a5f84ecc2f449bf9f037dc9da0ac670 -msgid "" -"Often, tool descriptions will be written for a specific version of a " -"software. To make it easier for others to use your descriptions, you can " -"include a `SoftwareRequirement` field in the `hints` section. This may also " -"help to avoid confusion about which version of a tool the description was " -"written for." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:13 -#: ee89f1526c1f4452b4e36ba67bb59747 -msgid "" -"In this example, the software requirement being described is InterProScan " -"version 5.21-60." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:25 -#: c76cec44f5424f6087df28aa33c521a2 -msgid "" -"Depending on your CWL runner, these hints may be used to check that the " -"required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the [dependency " -"resolvers configuration][dependencies]." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:29 -#: 072d7b3ce3284ed994ff0736b43bbb86 -msgid "" -"As well as a version number, a unique resource identifier (URI) for the tool " -"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " -"up in the [SciCrunch][scicrunch] registry, which provides a portal for " -"finding, tracking, and referring to scientific resources consistently. If " -"you want to specify a tool as a `SoftwareRequirement`, search for the tool " -"on SciCrunch and use the RRID that it has been assigned in the registry. " -"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " -"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." -"org][identifiers]) in the `specs` field of your requirement description. " -"Other good choices, in order of preference, are to include the DOI for the " -"main tool citation and the URL to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 395d611104604a28b78e11b112a95027 -msgid "Staging Input Files" -msgstr "" - -#: ../../src/topics/staging-input-files.md:3 811b4db0b1794fa89dc870f6cb59a3cd -msgid "" -"Normally, input files are located in a read-only directory separate from the " -"output directory. This causes problems if the underlying tool expects to " -"write its output files alongside the input file in the same directory. You " -"use `InitialWorkDirRequirement` to stage input files into the output " -"directory. In this example, we use a JavaScript expression to extract the " -"base name of the input file from its leading directory path." -msgstr "" - -#: ../../src/topics/staging-input-files.md:9 7159b5c5023c47128057c4116cce69f4 -msgid "`linkfile.cwl`" -msgstr "`linkfile.cwl`" - -#: ../../src/topics/troubleshooting.md:1 3bfa6791d78f43629de90345f4441ebb -msgid "Troubleshooting" -msgstr "Solucionando Problemas" - -#: ../../src/topics/troubleshooting.md:3 9a6bd5b684a740ed9e8993d9f8607774 -msgid "" -"In this section you will find ways to troubleshoot when you have problems " -"executing CWL. We focus on `cwltool` here but some of these techniques may " -"apply to other CWL Runners." -msgstr "" - -#: ../../src/topics/troubleshooting.md:6 6db8a02139644598894220d538c590b9 -msgid "Run `cwltool` with `cachedir`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:8 f0da0f6283d44bcc95224eb9fe2d1764 -msgid "" -"You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor output " -"files, but created while your workflow is running). By default, these files " -"are created in a temporary directory but writing them to a separate " -"directory makes accessing them easier." -msgstr "" - -#: ../../src/topics/troubleshooting.md:14 e2fc28b44ffe4254892a7c7973dc80c4 -msgid "" -"In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " -"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " -"olleH\". However, the second step, `step_b`, **has a typo**, where instead " -"of executing the `rev` command it tries to execute `revv`, which fails." -msgstr "" - -#: ../../src/topics/troubleshooting.md:20 505c7cf9ee9c4af1aeed29002eed1b33 -msgid "`troubleshooting-wf1.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:27 4c31fd11a28943538690d04baa2b5dd0 -msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " -"(`cwltool` will create the directory for you if it does not exist already):" -msgstr "" - -#: ../../src/topics/troubleshooting.md:35 a8532ac700014db4bd8ef690a27fb844 -msgid "" -"The workflow is in the `permanentFail` status due to `step_b` failing to " -"execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. You " -"can inspect the intermediate files created:" -msgstr "" - -#: ../../src/topics/troubleshooting.md:44 94a6148512b24b90b87fd1312a926d75 -msgid "" -"Each workflow step has received a unique ID (the long value that looks like " -"a hash). The `${HASH}.status` files display the status of each step executed " -"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " -"output of the command above." -msgstr "" - -#: ../../src/topics/troubleshooting.md:48 ec4165b7c25c449db6a8804161805e80 -msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " -"the `step_b`). After fixing the typo, when you execute `cwltool` with the " -"same arguments as the previous time, note that now `cwltool` output contains " -"information about pre-cached outputs for `step_a`, and about a new cache " -"entry for the output of `step_b`. Also note that the status of `step_b` is " -"now of success." -msgstr "" - -#: ../../src/topics/troubleshooting.md:59 5c0b71a6376848d4aa491854ea2d185d -msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had " -"been cached, and there was no change in its execution or output. " -"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for " -"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " -"re-evaluate steps unnecessarily." -msgstr "" - -#: ../../src/topics/using-containers.md:1 95b832552e8443ea9c652f8c95afc01e -msgid "Using Containers" -msgstr "Utilizando Containers" - -#: ../../src/topics/using-containers.md:3 561fc9c561bc492ea82c17784dfd439c -msgid "Running Tools Inside Docker" -msgstr "" - -#: ../../src/topics/using-containers.md:5 2420b16855cf4b25af5bcb87413f6dd9 -msgid "" -"[Docker][docker] containers simplify software installation by providing a " -"complete known-good runtime for software and its dependencies. However, " -"containers are also purposefully isolated from the host system, so in order " -"to run a tool inside a Docker container there is additional work to ensure " -"that input files are available inside the container and output files can be " -"recovered from the container. A CWL runner can perform this work " -"automatically, allowing you to use Docker to simplify your software " -"management while avoiding the complexity of invoking and managing Docker " -"containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 f5266ee2c2b34170bc89cb501b869893 -msgid "" -"One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the container." -msgstr "" - -#: ../../src/topics/using-containers.md:18 728166bf41504e1d89b755400742a1b4 -msgid "" -"This example runs a simple Node.js script inside a Docker container which " -"will then print \"Hello World\" to the standard output." -msgstr "" - -#: ../../src/topics/using-containers.md:21 104351ac29d247cb8e017228e2c9b3d8 -msgid "`docker.cwl`" -msgstr "" - -#: ../../src/topics/using-containers.md:27 e11a38bfb30b404c99d223647960cb16 -msgid "`docker-job.yml`" -msgstr "" - -#: ../../src/topics/using-containers.md:33 7ed0bd21e998417cb02fdcb8e44734b6 -msgid "" -"Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that is " -"really new is the `dockerRequirement` section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 9dcddf6812ba4bc2a7d6c5fcdb978a68 -msgid "" -"`baseCommand: node` tells CWL that we will be running this command using the " -"Node Js runtime that is meant for Javascript files. We then need to specify " -"some `hints` for how to find the container we want. In this case we list " -"just our requirements for the docker container in `DockerRequirements`. The " -"`dockerPull:` parameter takes the same value that you would pass to a " -"`docker pull` command. That is, the name of the container image (you can " -"even specify the tag, which is good idea for best practices when using " -"containers for reproducible research). In this case we have used a container " -"called `node:slim`." -msgstr "" - -#: ../../src/topics/using-containers.md:52 bc1a09475f154562a4db445bf81ac92f -msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " -"the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/using-containers.md:55 2e117019ace84604a8ed5a31214c2587 -msgid "`hello.js`" -msgstr "" - -#: ../../src/topics/using-containers.md:69 d0d5b2a1a008411e92859a72101088c1 -msgid "" -"Notice the CWL runner has constructed a Docker command line to run the " -"script." -msgstr "" - -#: ../../src/topics/using-containers.md:72 591d1cd0282b4095a267b44da7d59804 -msgid "" -"In this example, the path to the script `hello.js` is `/home/me/cwl/" -"user_guide/hello.js` outside the container but `/var/lib/cwl/" -"job369354770_examples/hello.js` inside the container, as reflected in the " -"invocation of the `node` command." -msgstr "" - -#: ../../src/topics/workflows.md:1 9f989fff165448ecbcaad6adc0f58d6b -msgid "Workflows" -msgstr "Workflows" - -#: ../../src/topics/workflows.md:3 212c82dca23645e89d8b5bb7599f2d25 -msgid "" -"A workflow is a CWL processing unit that executes command-line tools, " -"expression tools, or workflows (sub-workflows) as steps. It must have " -"`inputs`, `outputs`, and `steps` defined in the CWL document." -msgstr "" - -#: ../../src/topics/workflows.md:13 7530029ec04746f2a888dcbc10aa5ce4 -msgid "CWL workflow." -msgstr "" - -#: ../../src/topics/workflows.md:41 c1f1d644b37b4f018b87e15249d8758d -msgid "" -"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier examples." -msgstr "" - -#: ../../src/topics/workflows.md:51 2d07232b7d9c415b8ad971e8cbcd9577 -msgid "`echo-uppercase.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:81 fa1f770ffeba4b74bcb200cd3949e070 -msgid "" -"A command-line tool or expression tool can also be written directly in the " -"same CWL document as the workflow. For example, we can rewrite the `echo-" -"uppercase.cwl` workflow as a single file:" -msgstr "" - -#: ../../src/topics/workflows.md:91 570020792e824c2ba732bcc2c0134aa1 -msgid "`echo-uppercase-single-file.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:150 8a50c511004941d0917a8f0d471467f0 -msgid "" -"Having separate files helps with modularity and code organization. But it " -"can be helpful writing everything in a single file for development. There " -"are other ways to combine multiple files into a single file (e.g. `cwltool --" -"pack`) discussed further in other sections of this user guide." -msgstr "" - -#: ../../src/topics/workflows.md:160 4d2bf0341836405d9729c47d8020faea -msgid "" -"For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this " -"user guide in more detail." -msgstr "" - -#: ../../src/topics/workflows.md:165 dd6fc85f74984517b284853a0d46c122 -msgid "Writing Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:167 f857d80cd5d84622a560c895ab260a92 -msgid "" -"This workflow extracts a java source file from a tar file and then compiles " -"it." -msgstr "" - -#: ../../src/topics/workflows.md:170 02e7e81cdf7e4226973f910cd57b8ccf -msgid "`1st-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 3a88d92f41aa4daaad4f4cc6829184b3 646367f222ea41e5987561941d17c4f9 -msgid "Visualization of 1st-workflow.cwl" -msgstr "" - -#: ../../src/topics/workflows.md:180 aaba75eb272245db82d072fed97b311c -msgid "" -"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" -"github.com/common-workflow-language/user_guide/blob/" -"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" -"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" -"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" -msgstr "" - -#: ../../src/topics/workflows.md:183 f8a6e1af5f0349a5a384be0629c37ac8 -msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a " -"run:" -msgstr "" - -#: ../../src/topics/workflows.md:185 c4f854c7a279404da3688bdf424c7c5e -msgid "`1st-workflow-job.yml`" -msgstr "`1st-workflow-job.yml`" - -#: ../../src/topics/workflows.md:191 d383ce45139944cb85768627965d9467 -msgid "" -"Next, create a sample Java file and add it to a tar file to use with the " -"command-line tool." -msgstr "" - -#: ../../src/topics/workflows.md:205 84293afa7a6c40f2af0b980c89581fc7 -msgid "What's going on here? Let's break it down:" -msgstr "" - -#: ../../src/topics/workflows.md:212 e66daf8af53849109936c36ca7d2b2c9 -msgid "" -"The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a workflow." -msgstr "" - -#: ../../src/topics/workflows.md:221 8fbfbb587b264dcf98a3cea16dd36ef3 -msgid "" -"The `inputs` section describes the inputs of the workflow. This is a list " -"of input parameters where each parameter consists of an identifier and a " -"data type. These parameters can be used as sources for input to specific " -"workflows steps." -msgstr "" - -#: ../../src/topics/workflows.md:233 5cdbc4771ea841b4960362b930de2af6 -msgid "" -"The `outputs` section describes the outputs of the workflow. This is a list " -"of output parameters where each parameter consists of an identifier and a " -"data type. The `outputSource` connects the output parameter `classfile` of " -"the `compile` step to the workflow output parameter `compiled_class`." -msgstr "" - -#: ../../src/topics/workflows.md:248 2e8a41fe43984dc6b4cf430e1ff66b28 -msgid "" -"The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second step " -"compiles the file from the first step using the java compiler. Workflow " -"steps are not necessarily run in the order they are listed, instead the " -"order is determined by the dependencies between steps (using `source`). In " -"addition, workflow steps which do not depend on one another may run in " -"parallel." -msgstr "" - -#: ../../src/topics/workflows.md:256 78c20aa5a5724da6a4c908849c571334 -msgid "" -"The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input " -"parameters, `tarfile` and `extractfile` and one output parameter " -"`extracted_file`." -msgstr "" - -#: ../../src/topics/workflows.md:261 1606a2f059eb4b0c9e90f2f0cbbe779b -msgid "" -"The ``in`` section of the workflow step connects these two input parameters " -"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " -"`source`. This means that when the workflow step is executed, the values " -"assigned to `tarball` and `name_of_file_to_extract` will be used for the " -"parameters `tarfile` and `extractfile` in order to run the tool." -msgstr "" - -#: ../../src/topics/workflows.md:267 b456b11e2760479bbf81a773a3e1f8ee -msgid "" -"The `out` section of the workflow step lists the output parameters that are " -"expected from the tool." -msgstr "" - -#: ../../src/topics/workflows.md:278 0fa01fcec32049c989ad1d68841c74de -msgid "" -"The second step `compile` depends on the results from the first step by " -"connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " -"in [Additional Arguments and Parameters](additional-arguments-and-parameters." -"md)). The output of this step `classfile` is connected to the `outputs` " -"section for the Workflow, described above." -msgstr "" - -#: ../../src/topics/workflows.md:285 2bc9829f95584a269eb577c610b2a80c -msgid "Nested Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:287 0e5e6445bfcb42a4bd03612316dd7225 -msgid "" -"Workflows are ways to combine multiple tools to perform a larger operations. " -"We can also think of a workflow as being a tool itself; a CWL workflow can " -"be used as a step in another CWL workflow, if the workflow engine supports " -"the `SubworkflowFeatureRequirement`:" -msgstr "" - -#: ../../src/topics/workflows.md:297 0b83c1028b0e43ba972609e4302bc8a2 -msgid "" -"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " -"workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:300 cbe1ef068b0c417b953655e132333447 -msgid "`nestedworkflows.cwl`" -msgstr "`nestedworkflows.cwl`" - -#: ../../src/topics/workflows.md:309 a691c36a15044b11a6d037d16f818a6d -msgid "" -"This two-step workflow starts with the `create-tar` step which is connected " -"to the `compile` step in orange; `compile` is another workflow, diagrammed " -"on the right. In purple we see the fixed string `\"Hello.java\"` being " -"supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 2e9797fcd4f04f56b5d2b2f1a3e306d5 -msgid "" -"\"Visualization \"Visualization" -msgstr "" - -#: ../../src/topics/workflows.md:322 28f4139911b44eeeb7afd31e9f7cae7b -msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " -"CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " -"to become the step's input/outputs." -msgstr "" - -#: ../../src/topics/workflows.md:336 4a6cb397a20241beab24d956920a8379 -msgid "" -"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and `*.java` " -"filename. This is generally best-practice, as it means it can be reused in " -"multiple parent workflows, or even in multiple steps within the same " -"workflow." -msgstr "" - -#: ../../src/topics/workflows.md:341 dccb5472a5dc42b7946dd9245a71ecf0 -msgid "" -"Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar " -"file at `tarball`, which we will prepare in the `create-tar` step. At this " -"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " -"specific input/output names, as those also appear in its usage as a tool." -msgstr "" - -#: ../../src/topics/workflows.md:347 de1e18b69f654cabb75e52b47058030a -msgid "" -"It is also possible to do a less generic approach and avoid external " -"dependencies in the job file. So in this workflow we can generate a hard-" -"coded `Hello.java` file using the previously mentioned " -"`InitialWorkDirRequirement` requirement, before adding it to a tar file." -msgstr "" - -#: ../../src/topics/workflows.md:366 b947e62f4b3b4c10b95737f1839bcc5a -msgid "" -"In this case our step can assume `Hello.java` rather than be parameterized, " -"so we can use hardcoded values `hello.tar` and `Hello.java` in a " -"`baseCommand` and the resulting `outputs`:" -msgstr "" - -#: ../../src/topics/workflows.md:383 2ed0258a3a104ed5ba3b6b95ad998839 -msgid "" -"Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This is " -"generally not best practice, as the tool then can't be reused. The reason " -"for doing it in this case is because the command line is hard-coded with " -"filenames that only make sense within this workflow." -msgstr "" - -#: ../../src/topics/workflows.md:389 6584c0995288450b8a01c35fa231afb6 -msgid "" -"In this example we had to prepare a tar file outside, but only because our " -"inner workflow was designed to take that as an input. A better refactoring " -"of the inner workflow would be to take a list of Java files to compile, " -"which would simplify its usage as a tool step in other workflows." -msgstr "" - -#: ../../src/topics/workflows.md:394 19237513fd134c33801a7af08f74e70c -msgid "" -"Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL " -"Tool description, care must be taken to improve its usability in multiple " -"workflows." -msgstr "" - -#: ../../src/topics/workflows.md:398 b66e0d0a36994b3182a3784bda8ffc19 -msgid "Scattering Steps" -msgstr "" - -#: ../../src/topics/workflows.md:400 3bfb9851302248568bb4535ddc87a27f -msgid "" -"Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " -"run a tool or workflow multiple times over a list of inputs. The workflow " -"then takes the input(s) as an array and will run the specified step(s) on " -"each element of the array as if it were a single input. This allows you to " -"run the same workflow on multiple inputs without having to generate many " -"different commands or input yaml files." -msgstr "" - -#: ../../src/topics/workflows.md:411 78a5a600f8cc49ce8055c77a596ad833 -msgid "" -"The most common reason a new user might want to use scatter is to perform " -"the same analysis on different samples. Let's start with a simple workflow " -"that calls our first example (`hello_world.cwl`) and takes an array of " -"strings as input to the workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:415 f9618882e0a14a0b84ff9751346dc291 -msgid "`scatter-workflow.cwl`" -msgstr "`scatter-workflow.cwl`" - -#: ../../src/topics/workflows.md:421 4fe03daddd304a9b828fdd1c29f0d072 -msgid "" -"Aside from the `requirements` section including `ScatterFeatureRequirement`, " -"what is going on here?" -msgstr "" - -#: ../../src/topics/workflows.md:429 7ab022708a9642ab8aa2e79ea7810381 -msgid "" -"First of all, notice that the main workflow level input here requires an " -"array of strings." -msgstr "" - -#: ../../src/topics/workflows.md:441 fe144641fc8040b283f15b2b99ecb5a2 -msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This field " -"tells the runner that we'd like to scatter over this input for this " -"particular step. Note that the input name listed after scatter is the one of " -"the step's input, not a workflow level input." -msgstr "" - -#: ../../src/topics/workflows.md:445 f13d1b071a7f4a75a4cdee40ecef14fa -msgid "" -"For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if you " -"expect that the final output of your workflow will now have multiple outputs " -"to collect, be sure to update that to an array type as well!" -msgstr "" - -#: ../../src/topics/workflows.md:450 b0b2e63d2b8a4fd0983e976c16440da4 -msgid "Using the following input file:" -msgstr "Usando o seguinte arquivo de entrada:" - -#: ../../src/topics/workflows.md:452 47ac993a90fe46ca92e97d6b67b3276b -msgid "`scatter-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:458 f5b8681b3c3b4890a86d7b9fb812d958 -msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " -"calls the command `echo` on a message. If we invoke `cwltool scatter-" -"workflow.cwl scatter-job.yml` on the command line:" -msgstr "" - -#: ../../src/topics/workflows.md:466 74e70fec6d2447bbbd2a5bc8af1fa58c -msgid "" -"You can see that the workflow calls echo multiple times on each element of " -"our `message_array`. Ok, so how about if we want to scatter over two steps " -"in a workflow?" -msgstr "" - -#: ../../src/topics/workflows.md:469 76fed9e7ad1d4792b7bb364bb684eeb2 -msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding the " -"following lines instead of `outputs: []`" -msgstr "" - -#: ../../src/topics/workflows.md:472 bef387d9be1f4ca19a97023cfdd1c910 -msgid "`hello_world_to_stdout.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:480 eea1be83da574f39914566d835701b4a -msgid "" -"And add a second step that uses `wc` to count the characters in each file. " -"See the tool below:" -msgstr "" - -#: ../../src/topics/workflows.md:483 2043f12eb2ce4424b133e0dc0b62aafc -msgid "`wc-tool.cwl`" -msgstr "`wc-tool.cwl`" - -#: ../../src/topics/workflows.md:489 87ba95507fc44dbca4cb6c5283ce50f9 -msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under each " -"step:" -msgstr "" - -#: ../../src/topics/workflows.md:491 e6e1a79638d74547b00c64e3c8b05710 -msgid "`scatter-two-steps.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:497 03fb16e74bf14c49b43e35ef6cb45030 -msgid "" -"Here we have placed the scatter field under each step. This is fine for this " -"example since it runs quickly, but if you're running many samples for a more " -"complex workflow, you may wish to consider an alternative. Here we are " -"running scatter on each step independently, but since the second step is not " -"dependent on the first step completing all languages, we aren't using the " -"scatter functionality efficiently. The second step expects an array as input " -"from the first step, so it will wait until everything in step one is " -"finished before doing anything. Pretend that `echo Hello World!` takes 1 " -"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " -"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " -"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " -"actually finish in 8 minutes because the first step must wait on `echo Hallo " -"welt!`. You can see how this might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 eca3380c60094df2b91b44b5f7718fae -msgid "" -"Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can " -"make an entire workflow a single step in another workflow! Convert our two-" -"step workflow to a single step subworkflow:" -msgstr "" - -#: ../../src/topics/workflows.md:513 6c61733fe4284f51a6b46e89cafe78c4 -msgid "`scatter-nested-workflow.cwl`" -msgstr "`scatter-nested-workflow.cwl`" - -#: ../../src/topics/workflows.md:519 0585f83162c349969391c9456a884f28 -msgid "" -"Now the scatter acts on a single step, but that step consists of two steps " -"so each step is performed in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:522 f209343966db4d46b4611d3620c3b496 -msgid "Conditional Workflows" -msgstr "Workflows Condicionais" - -#: ../../src/topics/workflows.md:524 5a2661ce35dc4d79a15da1e17c0a95ec -msgid "" -"This workflow contains a conditional step and is executed based on the " -"input. This allows workflows to skip additional steps based on input " -"parameters given at the start of the program or by previous steps." -msgstr "" - -#: ../../src/topics/workflows.md:527 8f7ee09c9d6b491195e2d80315dae398 -msgid "`conditional-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:566 966acff0d3d24104ae9673df8a790fb1 -msgid "" -"The first thing you'll notice is that this workflow is only compatible for " -"version 1.2 or greater of the CWL standards." -msgstr "" - -#: ../../src/topics/workflows.md:573 d60e1df759654f1b873276cf0296f234 -msgid "" -"The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when` is " -"where the condition validation takes place. In this case only when `in1` " -"from the workflow contains a value `< 1` this step will be executed." -msgstr "" - -#: ../../src/topics/workflows.md:587 69aa8d3c9d9a4fe4a62875827648d95f -msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " -"will pass the first conditional step and will therefore be executed and is " -"shown in the log by `INFO [step step1] start` whereas the second step is " -"skipped as indicated by `INFO [step step2] will be skipped`." -msgstr "" - -#: ../../src/topics/workflows.md:607 fee34c880e964e08b040adf2d3831803 -msgid "" -"When a value of 3 is given the first conditional step will not be executed " -"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." -msgstr "" - -#: ../../src/topics/workflows.md:627 cb9e82cf4b484ca7be19612b14fbdf33 -msgid "" -"If no conditions are met for example when using `--val 2` the workflow will " -"raise a permanentFail." -msgstr "" - -#: ../../src/topics/yaml-guide.md:1 8e7c3365f0f94038930f71666f05170f -msgid "YAML Guide" -msgstr "Guia de YAML" - -#: ../../src/topics/yaml-guide.md:6 cbe6f35c21044054a010767f2f0cae46 -msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers and " -"humans. This guide introduces the features of YAML that are relevant when " -"writing CWL descriptions and input parameter files." -msgstr "" - -#: ../../src/topics/yaml-guide.md:13 2cc21093311548cd837aa7b3f0939093 -msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" - -#: ../../src/topics/yaml-guide.md:16 6e7ea76e8aeb477cbb8197efed33e53d -msgid "Contents" -msgstr "Conteúdo" - -#: ../../src/topics/yaml-guide.md:18 482e121a6e74428dbe6ad1f772f14684 -msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:19 179290eee12343dd9aa4d49207cf7c68 -msgid "[Comments](#comments)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:20 7880db40e98e4aaabdc96def3d9f515d -msgid "[Maps](#maps)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:21 75f3b499494b445f9f9a532d178cbc10 -msgid "[Arrays](#arrays)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:22 2b900b2779c84de5bbd3c933c56e5922 -msgid "[JSON Style](#json-style)" -msgstr "[Estilo JSON](#json-style)" - -#: ../../src/topics/yaml-guide.md:24 189db6d0e54a400eb5615e259354827e -msgid "Key-Value Pairs" -msgstr "Pares de Chave-Valor" - -#: ../../src/topics/yaml-guide.md:26 e689c0e1dcd645348ceed51e91eb9ad0 -msgid "" -"Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " -"is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have special " -"meaning in the CWL specification and underscored key names otherwise. For " -"example:" -msgstr "" -"Em princípio, um arquivo escrito em YAML consiste de uma série de _pares de " -"chave-valor`. Cada par é escrito como `chave: valor`, onde o espaço em " -"branco entre o `:` é um requisito. Os nomes das chaves em arquivos CWL não " -"devem conter espaços em branco - [_camelCase_][camelCase] é usado para " -"valores de chaves que contém múltiplas palavras e possuem um valor especial " -"na especificação CWL, caso contrário os valores dos nomes de chaves aparecem " -"sublinhados. For exemplo:" - -#: ../../src/topics/yaml-guide.md:42 9532ac8e1dda479e890bf970323a0a32 -msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " -"and `home` - with their four respective values. Values can be character " -"strings, numeric (integer, floating point, or scientific representation), " -"Boolean (`true` or `false`), or more complex nested types (see below)." -msgstr "" -"O YAML acima define quatro chaves - `first_name`, `last_name`, `age_years`, " -"e `home` - com quatro valores respectivos. Os valores podem ser strings de " -"caracteres, númericos (integer, floating point, ou representação científica)" -", Boolean (`true` ou `false`), ou valores mais complexos com tipos aninhados " -"(veja abaixo)." - -#: ../../src/topics/yaml-guide.md:51 91a057a7d10f438fad10338dd44c013c -msgid "" -"Values may be wrapped in quotation marks, but be aware that this may change " -"the way that they are interpreted i.e. `\"1234\"` will be treated as a " -"character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a " -"command: in CWL all parts of `baseCommand` must be strings so, if you want " -"to specify a fixed numeric value to a command, make sure that you wrap that " -"numeric value in quotes: `baseCommand: [echo, \"42\"]`." -msgstr "" - -#: ../../src/topics/yaml-guide.md:61 d18c1f5ef55d4bb6b8334438fcbc96b8 -msgid "Comments" -msgstr "" - -#: ../../src/topics/yaml-guide.md:63 dc6869049fc143b4af91d172a419a125 -msgid "" -"You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program interpreting " -"the YAML. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:76 c3c7f5ecfedb4884ad5e91bb79ba2a7c -msgid "" -"If there is anything on the line before the comment, be sure to add at least " -"one space before the `#`!" -msgstr "" - -#: ../../src/topics/yaml-guide.md:79 84f16419237a4789ac0f3c682b3a11ee -msgid "Maps" -msgstr "Dicionários" - -#: ../../src/topics/yaml-guide.md:81 269ca8e05ce14e899fc8b2a00b1e458e -msgid "" -"When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, these " -"hierarchical structures are described in YAML by providing additional key-" -"value pairs as the value of any key. These pairs (sometimes referred to as " -"\"children\") are written on new lines under the key to which they belong " -"(the \"parent\"), and should be indented with two spaces (⇥tab characters " -"are not allowed). For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:104 ce790af50da540eb9108ad89eae037cf -msgid "" -"The YAML above illustrates how to build up complex nested object " -"descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " -"while one of these children, `inputBinding`, contains a further two key-" -"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " -"below for more information about providing multiple values/key-value pairs " -"for a single key. For comparison with the example YAML above, here is a " -"graphical representation of the `inputs` object it describes." -msgstr "" - -#: ../../src/topics/yaml-guide.md:127 c3c9ef616b5d472a894ad6330267bcd2 -msgid "Arrays" -msgstr "" - -#: ../../src/topics/yaml-guide.md:129 b8a7360f6e0640aa9a2c4907c1ba3fe8 -msgid "" -"In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) section " -"above, more than one key-value pair can be mapped to a single key. However, " -"it is also possible to define multiple values for a key without having to " -"provide a unique key for each value. We can achieve this with an _array_, " -"where each value is defined on its own line and preceded by `-`. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:146 363da878600a4d229efe0ba79835d73c -msgid "and a more complex example combining maps and arrays:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:167 209dfb0d0a1148ed962dbb33890a3160 -msgid "JSON Style" -msgstr "Estilo JSON" - -#: ../../src/topics/yaml-guide.md:169 cd3a174dae334d0d977a3234e258bd25 -msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " -"can also be defined in YAML using the native JSON syntax. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:177 b0f0b10de8f54e1e951e480f696976f1 -msgid "and:" -msgstr "e:" - -#: ../../src/topics/yaml-guide.md:184 b5597e8984ad4e0bad33433c1dab89bd -msgid "" -"Native JSON can be useful in indicating where a field is intentionally left " -"empty (such as `[]` for an empty array), as well as where it makes more " -"sense for the values to be located on the same line (For example, when " -"providing option flags and their values in a shell command). However, as the " -"second example above shows, it can severely affect the readability of a YAML " -"file, and should be used sparingly." -msgstr "" - -#: ../../src/topics/yaml-guide.md:194 5ad7d551d3d347a097508a8488f9d15c -msgid "Reference" -msgstr "Referencia" - -#: ../../src/topics/yaml-guide.md:196 58f80e6944f9402a810b9b02ba3ad917 -msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " -"while we wrote this guide, though it also covers features that are not valid " -"in CWL." -msgstr "" - -#: ../../src/tutorials.md:1 8fdcc745f4684fa7816c62782507438e -msgid "Tutorials" -msgstr "Tutoriais" - -#: ../../src/tutorials.md:5 3c933ac074ee4d94b7aeacb7abeaf388 -msgid "" -"This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to the " -"list." -msgstr "" - -#: ../../src/tutorials.md:7 1d6cdf13aa834cb4a682553227d9f725 -msgid "Beginner Tutorials" -msgstr "Tutoriais para Iniciantes" - -#: ../../src/tutorials.md:9 606cc939c5014e2abdab163e4d726f1b -msgid "" -"[Introduction to Workflows with Common Workflow Language: For Contributors.]" -"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" -msgstr "" - -#: ../../src/tutorials.md:11 3505468d39c34a20bc55f431a3c697f7 -msgid "Advanced Tutorials" -msgstr "" - -#: ../../src/tutorials.md:13 e5731a11b89e492d8d751100a46c5226 -msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" - -#: ../../src/tutorials.md:15 cdfeabb88f6245d9a687197d242ed3f9 -msgid "Bioinformatics Tutorials" -msgstr "" - -#: ../../src/tutorials.md:17 997679b781a84add9b6d8b1900deec35 -msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" diff --git a/locales/pt_BR/LC_MESSAGES/sphinx.po b/locales/pt_BR/LC_MESSAGES/sphinx.po index 2d131c35..0f718690 100644 --- a/locales/pt_BR/LC_MESSAGES/sphinx.po +++ b/locales/pt_BR/LC_MESSAGES/sphinx.po @@ -1,27 +1,29 @@ # SOME DESCRIPTIVE TITLE. # Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. # msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" +"PO-Revision-Date: 2023-01-26 13:55+0000\n" +"Last-Translator: Michael Crusoe \n" "Language-Team: none\n" "Language: pt_BR\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" +"Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.16-dev\n" +"Generated-By: Babel 2.10.3\n" -#: ../../src/_templates/sidebar-nav-bs.html:1 -#: d65b012160e9455eb4d2628279fffc42 +#: ../../src/_templates/sidebar-nav-bs.html:1 d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" -msgstr "" +msgstr "Navegação principal" -#: ../../src/_templates/sidebar-nav-bs.html:3 -#: 4b3441eb77f448daa60718b7bfa862db +#: ../../src/_templates/sidebar-nav-bs.html:3 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" -msgstr "" +msgstr "Seção Navegação" diff --git a/locales/pt_BR/LC_MESSAGES/user_guide.po b/locales/pt_BR/LC_MESSAGES/user_guide.po index f0199e7a..bd7a19e6 100644 --- a/locales/pt_BR/LC_MESSAGES/user_guide.po +++ b/locales/pt_BR/LC_MESSAGES/user_guide.po @@ -1,33 +1,35 @@ # SOME DESCRIPTIVE TITLE. # Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. # msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-03-12 10:39+0000\n" -"Last-Translator: \"Bruno P. Kinoshita\" \n" +"POT-Creation-Date: 2023-01-27 16:02+0100\n" +"PO-Revision-Date: 2023-04-03 19:41+0000\n" +"Last-Translator: ssantos \n" "Language-Team: Portuguese (Brazil) \n" "Language: pt_BR\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" +"Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=2; plural=n > 1;\n" -"X-Generator: Weblate 4.16.2-dev\n" +"X-Generator: Weblate 4.17-dev\n" +"Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.md:2 3eb955b4f3dd4c3188924b97ea6ab592 msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.md:4 bf4480e7fff4460a87e8f43c11599f07 msgid "Instructional Material" msgstr "Material Instrucional" -#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +#: ../../LICENSE.md:6 9e9eab12205d4e82b4fedca520370f4c msgid "" "All Common Workflow Language project instructional material and changes to " "the structure are also made available under the [Creative Commons " @@ -35,31 +37,40 @@ msgid "" "of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" "[cc-by-legal]." msgstr "" +"Todo o material instrucional do projeto Common Workflow Language e " +"alterações na estrutura também são disponibilizados sob a [licença Creative " +"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " +"humanos de (e não um substituto para) o [texto legal completo da licença CC " +"BY 4.0][cc-by-legal]." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.md:12 a8e98ad541c642e58e201afa625ec791 msgid "You are free:" -msgstr "" +msgstr "Tem o direito de:" -#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +#: ../../LICENSE.md:14 b4cb4bc4261347fcb0d2c8a93995ab76 msgid "" "to **Share**---copy and redistribute the material in any medium or format" msgstr "" +"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " +"formato" -#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +#: ../../LICENSE.md:15 d66dcbf95ccc41aaa53be523487ec913 msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" +msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.md:17 ca1c299a1b834b868bcdd4ca9f244696 msgid "for any purpose, even commercially." -msgstr "" +msgstr "para qualquer fim, mesmo que comercial." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +#: ../../LICENSE.md:19 6133f79f93be4991a6f5290f72d1a63d msgid "" "The licensor cannot revoke these freedoms as long as you follow the license " "terms:" msgstr "" +"O licenciante não pode revogar estes direitos desde que você respeite os " +"termos da licença:" -#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +#: ../../LICENSE.md:24 2d6ce81add1043629b676187f890288c msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " "work is derived from work that is Copyright © the Common Workflow Language " @@ -68,40 +79,60 @@ msgid "" "made. You may do so in any reasonable manner, but not in any way that " "suggests the licensor endorses you or your use." msgstr "" +"Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " +"trabalho deriva de um trabalho que é «Copyright © The Common Workflow " +"Language project», e, quando prático, criar uma ligação para https://www." +"commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " +"se foram feitas alterações. Você pode fazê-lo de qualquer forma razoável, " +"mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " +"uso." -#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +#: ../../LICENSE.md:32 f3f22597b6f845208a0cce3b3b2c8f5d msgid "" "**No additional restrictions**---You may not apply legal terms or " "technological measures that legally restrict others from doing anything the " "license permits. With the understanding that:" msgstr "" +"**Sem restrições adicionais**---Não pode aplicar termos jurídicos ou medidas " +"de caráter tecnológico que restrinjam legalmente outros de fazerem algo que " +"a licença permita. Com o entendimento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +#: ../../LICENSE.md:36 3cfedee64d4e46098a159cb2acdba4ef msgid "" "You do not have to comply with the license for elements of the material in " "the public domain or where your use is permitted by an applicable exception " "or limitation." msgstr "" +"Não tem de cumprir com os termos da licença relativamente a elementos do " +"material que estejam no domínio público ou cuja utilização seja permitida " +"por uma exceção ou limitação que seja aplicável." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +#: ../../LICENSE.md:39 c836a570faaf449d9716da5f75556627 msgid "" "No warranties are given. The license may not give you all of the permissions " "necessary for your intended use. For example, other rights such as " "publicity, privacy, or moral rights may limit how you use the material." msgstr "" +"Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " +"autorizações necessárias para o uso pretendido. Por exemplo, outros " +"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " +"podem limitar o uso do material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.md:44 896f9966e5014e8a88b060be3063fe09 msgid "Software" -msgstr "" +msgstr "Software" -#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +#: ../../LICENSE.md:46 007f8613dc234c3fa8d5d92b18af0eb1 msgid "" "Except where otherwise noted, the example programs and other software " "provided by Common Workflow Language project are made available under the " "[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" +"Salvo indicação em contrário, os programas de exemplo e outro software " +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a " +"[licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." -#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +#: ../../LICENSE.md:51 227bc635a06f49dbb771fd9b62157d00 msgid "" "Unless required by applicable law or agreed to in writing, software " "distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " @@ -109,160 +140,196 @@ msgid "" "License for the specific language governing permissions and limitations " "under the License." msgstr "" +"A menos que exigido pela lei aplicável ou acordado por escrito, o software " +"distribuído sob a Licença é distribuído \"COMO ESTÁ\", SEM GARANTIAS OU " +"CONDIÇÕES DE QUALQUER TIPO, expressas ou implícitas. Consulte a Licença para " +"obter o texto específico sobre as permissões e limitações sob a Licença." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: eab02dc13915490bb3c9ba744d78b6a7 d4f35995b0f6494d9771a4be0a82538f -#: d6ccd4b546254f56a597d67dd4fdc5d6 +#: 1861131d3df648ae9e74ce1c87f0be7b a2ffa927deb2451d95ec63528e8078dd +#: d6055d3f15604ce6940770c7b561d4c5 msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece of " "software, tools and workflows described using CWL are portable across a " "variety of platforms that support the CWL standard." msgstr "" +"CWL é uma maneira de descrever ferramentas de linha de comando e de conectá-" +"las formando workflows. Como a CWL é uma especificação e não um software, " +"ferramentas e workflows descritos com a CWL são portáveis entre uma " +"variedade de plataformas que suportam o padrão CWL." #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +#: 38b062f219b34e08a46bd8f6525353ec 89e7e1dd05474344a1d929cb492e9caf msgid "This page has moved" -msgstr "" +msgstr "Esta página foi movida" -#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +#: ../../src/episodes.md:9 d3357ff3c8874e368aea0d6062ef6190 msgid "" "This page is out-of-date and was kept here to preserve the links of the old " "User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" +"O conteúdo desta página está desatualizado e foi mantido para preservar os " +"links do antigo Guia do Utilizador. Por favor, use o novo [Índice](index.md" +"#table-of-contents) para navegar o Guia do Utilizador." -#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +#: ../../src/faq.md:1 f2c4882e0e164c2b869e3eb969241061 msgid "FAQ" -msgstr "" +msgstr "Perguntas Frequentes (FAQ)" -#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +#: ../../src/faq.md:11 41099ab64e0544d894bd9e3af2718bda msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "" +msgstr "Usando `evalFrom` para Tipos Diferentes de \"`File`\"" -#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 +#: ../../src/faq.md:41 bb6aff70534148fa8a4b01140f7be150 msgid "Rename an Input File" -msgstr "" +msgstr "Renomear um Arquivo de Entrada" -#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +#: ../../src/faq.md:43 70ebc653b0d54d60a866edc0dbf56b57 msgid "" "This example demonstrates how to change the name of an input file as part of " "a tool description. This could be useful when you are taking files produced " "from another step in a workflow, and don't want to work with the default " "names that these files were given when they were created." msgstr "" +"Este exemplo demonstra como mudar o nome de um arquivo de entrada como parte " +"da descrição da ferramenta. Isso pode ser útil quando você tem arquivos " +"produzidos em outro passo de um workflow, mas prefere não utilizar os nomes " +"dados por padrão quando estes arquivos foram criados." -#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f +#: ../../src/faq.md:59 38b687f707d2438b85df08a445ab816f msgid "Rename an Output File" -msgstr "" +msgstr "Renomear um Arquivo de Saída" -#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +#: ../../src/faq.md:61 d48422c020004ef084ca11e6229b5450 msgid "" "This example demonstrates how to change the name of an output file from the " "default name given to it by a tool:" msgstr "" +"Este exemplo demonstra como escolher o nome para um arquivo de saída " +"diferente do nome padrão criado por uma ferramenta:" -#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 +#: ../../src/faq.md:82 48765409ab9d48ccbcecceb46ddf2e91 msgid "Referencing a Local Script" -msgstr "" +msgstr "Como Fazer Referência a um Script Local" -#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +#: ../../src/faq.md:84 a59b8acd72124e2c95d1905ae494d928 msgid "There are two ways to reference a local script:" -msgstr "" +msgstr "Há duas maneiras de fazer uma referência a um script local:" -#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +#: ../../src/faq.md:86 f36088ba90d24f9f9c7c1bd59deb6f49 msgid "" "The first method involves adding the folder containing your scripts to the " "`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" +"A primeira maneira é adicionando o arquivo que contém os seus scripts para a " +"variável de ambiente `PATH`. Desta maneira você pode executar o shell script " +"diretamente sem utilizar comandos via `sh` ou `bash`." -#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +#: ../../src/faq.md:89 45ee965ee4a7494a8354b82208e2ab45 msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" +msgstr "Comece adicionando a _shebang_ no topo do seu arquivo:" -#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +#: ../../src/faq.md:95 734cc1abe1c841ffac8d0895463d91fc msgid "" "After that, make the script executable with the command `chmod +x scriptname." "sh`" msgstr "" +"Em seguida faça o seu script executável com o comando `chmod +x scriptname." +"sh`" -#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +#: ../../src/faq.md:97 f01bc8c4d6134f0ea27dc7f5b39def24 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" +"E finalmente, modifique o seu `PATH` para adicionar o diretório que contém o " +"seu script. (É boa prática usar `$HOME/bin` para scripts do utilizador " +"local)." -#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be +#: ../../src/faq.md:104 dd6fc2a04e3b476892f05bc5b746d0fa msgid "" "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" +"Agora você pode utilizar `baseCommand: scriptname.sh` para rodar o script " +"diretamente." -#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +#: ../../src/faq.md:113 e309eaad55144052866ce131eb80fd14 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" +"Depois quando você quiser compartilhar o seu trabalho, é possível utilizar " +"um container de software com ferramentas como Docker." -#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +#: ../../src/faq.md:115 f0d649a60a13404ebecd540789202b87 msgid "" "The second method involves including an input of `type: File` in the script " "itself:" -msgstr "" +msgstr "O segundo método utiliza um input `type: File` diretamente no script:" -#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 +#: ../../src/faq.md:135 e2b782f88d494de398af0c9002a3ccdc msgid "In CWL, everything must be directly stated." -msgstr "" +msgstr "Em CWL tudo deve ser declarado diretamente." -#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +#: ../../src/faq.md:138 b4a033731fcd4322bd2bb71c609a4cb7 msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "" +msgstr "Definindo Bindings de Inputs utilizando `self` para Inputs Opcionais" -#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +#: ../../src/faq.md:140 43a64810b12b4c7d82a5803c3b910fe5 msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their input " "binding makes use of `self`. Below is an example workaround for this, " "pending a more sophisticated fix." msgstr "" +"No momento `cwltool` não funciona quando inputs opcionais não estão " +"presentes se o binding de input deles utilizar `self`. O exemplo abaixo " +"contém uma solução alternativa para este problema, até que haja uma solução " +"mais elegante para este problema." -#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 +#: ../../src/faq.md:165 60f009e3714c405695da069204b196ea msgid "Model a \"one-or-the-other\" Parameter" -msgstr "" +msgstr "Modelar um Parâmetro do tipo \"um-ou-o-outro\"" -#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +#: ../../src/faq.md:167 98916ed9355842e49bef073430e10675 msgid "" "Below is an example showing how to specify different strings to be added to " "a command line, based on the value given to a Boolean parameter." msgstr "" +"O exemplo abaixo demonstra como especificar diferentes strings que serão " +"adicionadas à linha de comando, dependendo do valor de um parâmetro Boolean." -#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +#: ../../src/faq.md:188 9b8f2d0b33db4bbc82aaf5836b6f7ed8 msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "" +msgstr "Conectar um Único valor a um Input que Espera uma Lista daquele Tipo" -#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +#: ../../src/faq.md:190 a251693354d24bf0bda4938c8890090a msgid "" "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" "Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +#: ../../src/faq.md:194 f46740ac0acb473583facb9f7528d03c msgid "merge_nested" -msgstr "" +msgstr "merge_nested" -#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +#: ../../src/faq.md:196 7de1f9e3175b4c2ab156192f28fd3535 msgid "" "The input must be an array consisting of exactly one entry for each input " "link. If \"merge_nested\" is specified with a single link, the value from " "the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +#: ../../src/faq.md:199 225c6f08068e41f58eb62f99dc06210f msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" +"Que significa \"criar uma lista com exatamente estes sources como elementos\"" -#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +#: ../../src/faq.md:201 4e741f4e3bc74e10bd9568826e81c478 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -270,52 +337,63 @@ msgid "" "add `linkMerge: merge_nested` under the appropriate `in` entry of the " "destination step." msgstr "" +"Ou em outras palavras: se o parâmetro destino for do tipo `File[]` (uma " +"lista de `File`s) e a fonte é um único `File`, adicione então " +"`MultipleInputFeatureRequirement` ao `requirements` no nível do Workflow e " +"adicione `linkMerge: merge_nested` sob a entrada apropriada `in` ao step que " +"receberá o parâmetro (target)." -#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd +#: ../../src/faq.md:229 bfdb011cb81c4ef9b9e56b24f1e9ccd5 msgid "Optional Inputs 💯" -msgstr "" +msgstr "Inputs Opcionais 💯" -#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +#: ../../src/faq.md:231 09f385e325f942afaa3dd195c16a18d2 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" +"Para fazer um parâmetro de entrada opcional, adicione um ponto de " +"interrogação à declaração do tipo." -#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +#: ../../src/faq.md:247 c5d087082bb2468483e7ccda3ca45a07 msgid "" -msgstr "" +msgstr "" -#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c +#: ../../src/faq.md:248 41e30b0224a0492f9047b4f320f39a23 msgid "Enum Inputs ⚜️" -msgstr "" +msgstr "Inputs Enum ⚜️" -#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +#: ../../src/faq.md:250 f06d073014a44f33a60d947a8c5b0e59 msgid "" "For command line flags that require a specific input as the argument an enum " "type can be declared in CWL. **Specifying null here is known as long form " "style. It does the same thing as the question mark on the other inputs.**" msgstr "" +"O tipo enum por ser utilizado em CWL para flags de linha de comando que " +"requerem um tipo de input específico como argumento. **Especificar null aqui " +"é tido como forma estendida. O resultado é o mesmo que o uso do ponto de " +"interrogação nos outros inputs.**" -#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +#: ../../src/faq.md:267 2fb74cd1b41e4fdb81a8f9b3b6c84373 msgid "" -msgstr "" +msgstr "" -#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 +#: ../../src/faq.md:268 09e19f34d0fd4e388d4939cbc2be3436 msgid "Record Inputs 📀" -msgstr "" +msgstr "Inputs do tipo Record" -#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +#: ../../src/faq.md:270 1ecae448dfcf45a4ae0dd39bd011e449 msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 +#: ../../src/faq.md:322 6df3d4e918cc4bccb823859ce07b197a msgid "Setting Mutually Exclusive Parameters" -msgstr "" +msgstr "Definindo Parâmetros Mutualmente Exclusivos" -#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +#: ../../src/faq.md:324 086db1a093e64caa88d958150accc19c msgid "" "To properly set fields in a record input type, you need to pass a dictionary " "to the input to properly set the parameters. This is done by using inline " @@ -324,76 +402,84 @@ msgid "" "be used as the value." msgstr "" -#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 +#: ../../src/faq.md:342 da77c818d8694ab99fb2eccf73083047 msgid "Setting Booleans" -msgstr "" +msgstr "Utilizando Booleans" -#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +#: ../../src/faq.md:344 254259509ed6462d8ebc296b5f811f44 msgid "These can be set by using the default field" -msgstr "" +msgstr "Estes são definidos através do campo padrão" -#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 +#: ../../src/faq.md:349 f7a44f76579d4709a61d2d61bc352b76 msgid "Concatenating Strings in Inputs" -msgstr "" +msgstr "Concatenando Strings em Inputs" -#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +#: ../../src/faq.md:351 d67278e99c684f488f1e3418e1c8c207 msgid "The valueFrom field must be used instead of default." -msgstr "" +msgstr "O campo valueFrom deve ser utilizado ao invés do valor padrão." -#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c +#: ../../src/faq.md:359 f5e35ee06cd24edf831589ebaa6193d2 msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "" +msgstr "Erros do `cwltool` devido a Nomes de Arquivos com Espaços" -#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +#: ../../src/faq.md:361 2ffb67e547c446499625a8db9a102da6 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" +"O `cwltool` não permite alguns caracteres em nomes de arquivos por padrão." -#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +#: ../../src/faq.md:363 ee653ff9fefe4771b35e2e76199b536a msgid "" "For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" +"Por exemplo, o nome de arquivo `um espaco vai aqui.txt` inclui 3 espaços.." -#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +#: ../../src/faq.md:371 02b1eb159e934fd692929f7c30319ddd msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" +"Se você não tem opção e precisa utilizar estes caracteres apesar do risco, " +"você deve então passar `--relax-path-verificks` ao chamar o `cwltool`." -#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +#: ../../src/faq.md:373 857024702f624885be706c405b7a088e msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" +"Erro de Referência em Parâmetro CWL devido a Hífen no Identificador de " +"Entrada" -#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +#: ../../src/faq.md:375 d664e30899bd463bb48d38adec318dd4 msgid "If `cwltool --validate` returns valid" -msgstr "" +msgstr "Se `cwltool --validate` valida com sucesso" -#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +#: ../../src/faq.md:384 9f3957bbe205454e8bffc4b5caac5970 msgid "But executing it causes an error like:" -msgstr "" +msgstr "Mas ao executar o workflow um erro como o seguinte aparece:" -#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +#: ../../src/faq.md:396 6ec3bbc6a1ca4e23b47f025f0732e609 msgid "The file is here" -msgstr "" +msgstr "Este é o arquivo" -#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +#: ../../src/faq.md:410 3e727d79e65e4c6cb157550e80261c53 msgid "Problem caused by `-` (hyphen character)." -msgstr "" +msgstr "O problema é causado pelo `-` (hífen)." -#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 +#: ../../src/faq.md:423 6e0705f4ab4b4e9093794cb4fccb6be9 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" +msgstr "Para corrigir este erro, substitua o `-` (hífen) por `_` (sublinhado)" -#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +#: ../../src/faq.md:436 0047d039317349679fb6a66d18ec8487 msgid "" "If it is not possible to change the input identifier, then you can use an " "alternative CWL Parameter Reference syntax:" msgstr "" +"Se não for possível mudar o identificador do input, você pode reescrever " +"utilizando uma sintaxe alternativa para Referências de Parâmetros CWL:" -#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 +#: ../../src/faq.md:442 8c39608ad0494bee9a4a422cbeb34387 msgid "Use CWL and cwltool with Singularity" -msgstr "" +msgstr "Utilizar CWL e cwltool com Singularity" -#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +#: ../../src/faq.md:445 7dac53bca8c14a3f9af75cb162cba4f9 msgid "" "The CWL standards are built around (optional) Docker format containers. The " "reference runner and several other CWL implementations support running those " @@ -401,11 +487,11 @@ msgid "" "Singularity format container is not part of the CWL standards." msgstr "" -#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 +#: ../../src/faq.md:450 ffcc38ff98324d71bfeb8d66d4901da7 msgid "Debug JavaScript Expressions" -msgstr "" +msgstr "Depurar Expressões JavaScript" -#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +#: ../../src/faq.md:452 0d7bf2cefe4a4e22b186bdf4d0ed793d msgid "" "You can use the --js-console option of cwltool, or " "you can try creating a JavaScript or TypeScript project for your code, and " @@ -416,22 +502,22 @@ msgid "" "dd>" msgstr "" -#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +#: ../../src/index.md:1 1506b4e7ee014a01bfdb067489501a9e msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +#: ../../src/index.md:3 0ce058b5210d46a0b78eb78dbca07a9f msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +#: ../../src/index.md:7 3404c064950d453d8af446e8b6554cb6 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +#: ../../src/index.md:9 1e239cad669648e48694eaf91284766a msgid "" "If you find that something is missing from this guide, or if you would like " "to provide other feedback, file an Issue on the [project repository for this " @@ -439,11 +525,11 @@ msgid "" "clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" -#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +#: ../../src/index.md:16 9dba2e06f1be4a50b1fabaaf216d02b4 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +#: ../../src/index.md:18 ba4074bbb69e4096a808001afaf2e0dc msgid "" "If you are a beginner user get started with the [Introduction](/introduction/" "index.md) section. For advanced users the subsections of the [Topics](/" @@ -451,7 +537,7 @@ msgid "" "CWL." msgstr "" -#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +#: ../../src/index.md:23 ad34a37bf4ec488bb825a34456f4fe8d msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -459,15 +545,15 @@ msgid "" "and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +#: ../../src/index.md:28 2bd8eb5957ed40f4a72a6b7408044c78 msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +#: ../../src/introduction/basic-concepts.md:1 8bb0df5531474301a185f1ba375320df msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +#: ../../src/introduction/basic-concepts.md:3 653373e1f11e4f81ad561378854a71fc msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are expected " @@ -478,18 +564,18 @@ msgid "" "this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +#: ../../src/introduction/basic-concepts.md:10 7766227bf91b48b2b9752b625e5a9084 msgid "The CWL Specification" -msgstr "" +msgstr "A Especificação CWL" -#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +#: ../../src/introduction/basic-concepts.md:21 032d414ac29740aa9041d89d0ebf70e6 msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered in " "this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +#: ../../src/introduction/basic-concepts.md:25 74e92eb0a4e64098b5aaf08d043e0641 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -499,17 +585,17 @@ msgid "" "and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +#: ../../src/introduction/basic-concepts.md:33 baa40b445f3c409b9a3e10a85fa38bfd msgid "" "The model used for the specification version is called Semantic Versioning. " "See the end of this section to [learn more](#learn-more) about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +#: ../../src/introduction/basic-concepts.md:37 648e94a9d368450dbdac706445254c9f msgid "Implementations" -msgstr "" +msgstr "Implementações" -#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +#: ../../src/introduction/basic-concepts.md:39 e9ae15124dcd408395fc67e16b50696a msgid "" "An implementation of the CWL specification is any software written following " "what is defined in a version of the specification document. However, " @@ -517,24 +603,24 @@ msgid "" "implementations are licensed under both Open Source and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +#: ../../src/introduction/basic-concepts.md:44 b1c864d6775048cab01eb3de641f6475 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud " "and high performance computing environments where tasks are scheduled in " "parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +#: ../../src/introduction/basic-concepts.md:51 a05d24121e534d65947eb26e4dada5b7 msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: ace0388fd04845e79d31ec99a48a8a3f msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 +#: 70ecd37237e14ae19539f2bf692882ed msgid "" "A process is a computing unit that takes inputs and produces outputs. The " "behavior of a process can be affected by the inputs, requirements, and " @@ -543,39 +629,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 38121b4b00324bebb6499184b3dcb5c1 msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: e0c278f52e824673ac708885d985b7d2 msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: 6b4d0f0651cc46f5abf195b281967913 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: 88bdc9e046e4487cb0eee3f1d4819e57 msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 12eed3ef7d444585b150bbdab0665bc8 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a +#: dfc85226313d46f9868dc4de53546a69 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 +#: f636b10c47734e589291de95443d8115 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be used " "to simplify workflows and command-line tools, moving common parts of a " @@ -584,7 +670,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef +#: bb51025d04444dd5b16000d5d6a3f41a msgid "" "Operation is an abstract process that also takes inputs, produces outputs, " "and can be used in a workflow. But it is a special operation not so commonly " @@ -593,7 +679,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#: 93dbaa0aa2c6493ab22a937c6861fac4 msgid "" "The workflow is a process that contains steps. Steps can be other workflows " "(nested workflows), command-line tools, or expression tools. The inputs of a " @@ -602,7 +688,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 +#: fcde5ef65ebf45a3b4b67eec993a1729 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through *requirements*. " @@ -610,23 +696,23 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 +#: c8ff34ff5d3b4a508e8c291196d08067 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 +#: fe25f15fc11c49ab827b884d081c3df0 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 +#: 2b93b6219142431ca748a404a56ced5d msgid "" "`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee +#: 0094b13b26014ba3be61769b422802f5 msgid "" "Some CWL runners may provide requirements that are not in the specification. " "For example, GPU requirements are supported in `cwltool` through the " @@ -636,7 +722,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e +#: 576a0778d3dd44f68cb241346f441660 msgid "" "Hints are similar to requirements, but while requirements list features that " "are required, hints list optional features. Requirements are explained in " @@ -644,12 +730,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: 7d98949fe97744158fad81f41d780de9 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 +#: fc142b791aa1434aa75b0782248de988 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -662,7 +748,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a +#: c3fc91ae3bae4e3db60e8271e95135a2 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\", " @@ -671,7 +757,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee +#: 8f097ae5ff6a4be0b7428345362dc55e msgid "" "The benefit of explicitness and isolation are flexibility, portability, and " "scalability; tools and workflows described with CWL can transparently " @@ -680,71 +766,76 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: 60c56fa6a67346d6966f0d841213e11b msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 65c24244713741e196da08cb9ba237b2 -#: f059896039524095b4deb65d693f8ddf 3439764fab0e49d2bcb7c9fbae556e65 +#: ../../src/introduction/quick-start.md:94 7377b155e8694798994bbc911a3f3152 +#: 7699685836064bd89db530a9c1918865 7d187a209ebd4e3ba6c6aeb05743041a msgid "Learn More" -msgstr "" +msgstr "Saiba Mais" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 3fcbf810c86f4cf7b8499de88147aa95 msgid "Semantic Versioning - " -msgstr "" +msgstr "Versionamento Semântico - " #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 +#: e242228b6b3d440cbca8418050220267 msgid "" "The CWL Specification page in the CWL website: " msgstr "" +"A página web da Especificação CWL: " #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 +#: 6e01963a01cb49e39692455256679bfc msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" +"A especificação CWL atual no GitHub: {{ ''.format(cwl_version_text) }}" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 +#: ed81ea2234b041c79449dcd20f886cb6 msgid "" "The list of Implementations in the CWL website: " msgstr "" +"A lista de Implementações na página web da CWL: " #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: e8e3996f6a894b4f9cc266b46cb8d756 msgid "PROV-O: The PROV Ontology - " -msgstr "" +msgstr "PROV-O: A Ontologia PROV - " #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b +#: 085e4d1a7a9744d2884f3003c64ca174 msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +#: ../../src/introduction/index.md:1 dcd96950854f47a6ad4169320c1dab34 msgid "Introduction" -msgstr "" +msgstr "Introdução" -#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +#: ../../src/introduction/index.md:3 c4d17eec31874bf1ae9b49d73537d86c msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that " "are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +#: ../../src/introduction/prerequisites.md:1 98a8bdfc7c91436d9cb46abbb7c19c57 msgid "Prerequisites" -msgstr "" +msgstr "Pré-requisitos" -#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +#: ../../src/introduction/prerequisites.md:6 244a716e267540c782e627adaea3a413 msgid "" "The software and configurations listed in this section are prerequisites for " "following this user guide. The CWL standards are implemented by many " @@ -754,11 +845,11 @@ msgid "" "(though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +#: ../../src/introduction/prerequisites.md:12 2cdf453d2c8b4e2ea50555ef0b7364e5 msgid "CWL Implementations" -msgstr "" +msgstr "Implementações da CWL" -#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +#: ../../src/introduction/prerequisites.md:14 53643a4f190c412d9552d1908f408318 msgid "" "There are many implementations of the CWL standards. Some are complete CWL " "runners, while others could be plug-ins or extensions to workflow engines. " @@ -766,29 +857,29 @@ msgid "" "md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +#: ../../src/introduction/prerequisites.md:19 1df6c63de3914af68f758054fe6955f4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +#: ../../src/introduction/prerequisites.md:21 ceaa3a6bebab45a0907ee0cad01429a2 msgid "" "We recommend using an up-to-date operating system. You can choose any of the " "following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +#: ../../src/introduction/prerequisites.md:24 1506ac904c6345c5806704a0ccf235aa msgid "Linux" -msgstr "" +msgstr "Linux" -#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +#: ../../src/introduction/prerequisites.md:25 a616213ed24e427bb91ee33cb21ec131 msgid "macOS" -msgstr "" +msgstr "macOS" -#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +#: ../../src/introduction/prerequisites.md:26 a4e9ae38103843739f13c62befd21f3e msgid "Windows" -msgstr "" +msgstr "Windows" -#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +#: ../../src/introduction/prerequisites.md:29 2cd231aac42c4a69a925cea369999a8b msgid "" "If you are using Windows, you will have to install the [Windows Subsystem " "for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " @@ -798,11 +889,11 @@ msgid "" "recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +#: ../../src/introduction/prerequisites.md:35 051d7cd7d3a94baa865d180afdd71688 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +#: ../../src/introduction/prerequisites.md:41 1a93aaf5bd5e4862b15e0636b4478640 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL community. " @@ -810,7 +901,7 @@ msgid "" "in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +#: ../../src/introduction/prerequisites.md:46 edd0613118a2493c876652bdcb9e0fbf msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create and " @@ -818,26 +909,30 @@ msgid "" "`cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +#: ../../src/introduction/prerequisites.md:51 3448d215c2434866b8a4b340872ba81e msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" +msgstr "Instalando `cwltool` com `pip` e `venv`." -#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +#: ../../src/introduction/prerequisites.md:62 4c24d05f65794735b816024c78b63f1c msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` and " "`conda`." msgstr "" +"Visite a [documentação](https://github.com/common-workflow-language/" +"cwltool#install) do `cwltool` para outras opções para instalar `cwltool` com " +"`apt` e `conda`." -#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +#: ../../src/introduction/prerequisites.md:65 3167f4a2a8394feda1f848334be62022 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" +"Vamos usar uma simples descrição de ferramenta CWL `true.cwl` com `cwltool`." -#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +#: ../../src/introduction/prerequisites.md:67 3c4b67d62c9c4d658ccaafcd1977ec08 msgid "`true.cwl`" -msgstr "" +msgstr "`true.cwl`" -#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +#: ../../src/introduction/prerequisites.md:73 30792f78348942e0acdde411342e8830 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -848,24 +943,24 @@ msgid "" "command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +#: ../../src/introduction/prerequisites.md:79 4473e41281fb4e738e4eb26c2d178934 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 +#: ../../src/introduction/prerequisites.md:84 548393974d4d4acc91738f9bc13a3a48 msgid "" "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +#: ../../src/introduction/prerequisites.md:86 2ab3963cf9504ec097eda2b14f3448c4 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: ../../src/introduction/prerequisites.md:91 690882dcc29c48acbeb215a8be52eb9e msgid "Cwl-runner Python Module" -msgstr "" +msgstr "Módulo Python cwl-runner" -#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +#: ../../src/introduction/prerequisites.md:93 6c3ba51b1e9a4add9203d62cec6ebae9 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be invoked " @@ -876,63 +971,63 @@ msgid "" "environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +#: ../../src/introduction/prerequisites.md:101 b2360ef646854422ad6c0f90fa49306f msgid "" "The CWL community publishes a Python package with the name `cwlref-runner` " "that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +#: ../../src/introduction/prerequisites.md:104 c9fadfa85a2641378e99a462e8e8d940 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +#: ../../src/introduction/prerequisites.md:111 abb8993ede4d4e479d88d2e848546f68 msgid "" "Now you can validate and run your workflow with the `cwl-runner` executable, " "which will invoke `cwltool`. You should have the same results and output as " "in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +#: ../../src/introduction/prerequisites.md:115 ba0f7606e6174e53a8bf23c1ccd99250 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +#: ../../src/introduction/prerequisites.md:120 dd2e10f43e8f498cb01de5faa4fccb70 msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" +msgstr "Executando `true.cwl` com `cwl-runner`." -#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +#: ../../src/introduction/prerequisites.md:125 e500e9c71c7042169c25b31f21a09142 msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For " "that, the first thing you need to do is copy `true.cwl` workflow into a new " "file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: ../../src/introduction/prerequisites.md:129 d989516c873f4446bba005f42796b8b9 msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 +#: ../../src/introduction/prerequisites.md:135 e9d8610478094a98b5b5a0f568a315de msgid "" "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +#: ../../src/introduction/prerequisites.md:137 d6d8131f91b740189e56ab9d90bee55a msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +#: ../../src/introduction/prerequisites.md:144 def7400a00e84070a4bd80c2367d3bde msgid "" "And finally, you can execute it directly in the command-line. On execution, " "the program specified in the shebang (`cwl-runner`) will be used to execute " "the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +#: ../../src/introduction/prerequisites.md:148 564e7be94d254e52a6c44b234d6ddc63 msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +#: ../../src/introduction/prerequisites.md:154 bb5fe42ddd814ad4ac1071c0b18f24c2 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute the " @@ -942,47 +1037,47 @@ msgid "" "`` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +#: ../../src/introduction/prerequisites.md:161 53bb712a68cd49fca4db11e9e507c9a4 msgid "Text Editor" -msgstr "" +msgstr "Editor de Texto" -#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +#: ../../src/introduction/prerequisites.md:163 bdcf61cce5294e45a9f964628a8a66bd msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +#: ../../src/introduction/prerequisites.md:167 28d33daee6e246c8a6d1382208e19c39 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting " "and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +#: ../../src/introduction/prerequisites.md:171 b071d7c87b7a4817b871085a652cd580 msgid "" "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" -#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +#: ../../src/introduction/prerequisites.md:172 97658a1b16874ba8b0bb748242d0da64 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +#: ../../src/introduction/prerequisites.md:174 6198aa6769b74ef0a2a1ba539789f3ee msgid "" "The CWL community also maintains a list of editors and viewers: " msgstr "" -#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +#: ../../src/introduction/prerequisites.md:177 0c17235a374e40099be37b9b8ac8f1f0 msgid "Docker" -msgstr "" +msgstr "Docker" -#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +#: ../../src/introduction/prerequisites.md:181 e3690e656b5a4348845c654689935a88 msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -990,7 +1085,7 @@ msgid "" "com/>." msgstr "" -#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +#: ../../src/introduction/prerequisites.md:185 2db34e925a81422986ccb868463a7a42 msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -998,57 +1093,57 @@ msgid "" "and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +#: ../../src/introduction/prerequisites.md:191 d677fb155b0343ba8771398cca967fed msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for pulling " "images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +#: ../../src/introduction/prerequisites.md:198 22ed0b55de38408393af4a8309a995ea msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the next " "section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +#: ../../src/introduction/prerequisites.md:199 5ded73cae5db40ad840c3022e7cd447f msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +#: ../../src/introduction/quick-start.md:1 23e5613df7c94e5f938c85b14f5441e4 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +#: ../../src/introduction/quick-start.md:3 3b425afc63d841d4be57c92b25b4ed2d msgid "" "This section will show you a brief overview of what CWL is, and where you " "can learn more about it. No previous knowledge of CWL is required, but you " "must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +#: ../../src/introduction/quick-start.md:7 75a26c48d3e04e24abb96d81cb31c94e msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +#: ../../src/introduction/quick-start.md:12 88b4ecd45ea44dd4befe3ce89b30f6c2 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " "example below shows a simple CWL “Hello World” workflow annotated with " "comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +#: ../../src/introduction/quick-start.md:16 e1789ef78bd64332a18d8601094a0f72 msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +#: ../../src/introduction/quick-start.md:22 196ceef96c27434eb4b0b7222c2fe73c msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the " "same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +#: ../../src/introduction/quick-start.md:27 e6a44130c6b44d5bb6451a147f28dd8c msgid "" "In CWL, there is a distinction between a command-line tool and a workflow. " "But for the sake of simplicity, we are using the term “workflow” here. You " @@ -1056,11 +1151,11 @@ msgid "" "section." msgstr "" -#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +#: ../../src/introduction/quick-start.md:32 340b46acc7a34b7b978f5a734f529553 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +#: ../../src/introduction/quick-start.md:34 139e48dcf0474fea932ca07a0001d208 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the CWL " "*Reference Runner* for the specification, and it is compliant with the " @@ -1068,11 +1163,11 @@ msgid "" "`cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +#: ../../src/introduction/quick-start.md:39 d6f6e061c0f4434eb6d70f9d84759042 msgid "Installing `cwltool` with `pip`." -msgstr "" +msgstr "Instalando `cwltool` com `pip`." -#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +#: ../../src/introduction/quick-start.md:47 cb2b548489df45ee9d49b36116440eea msgid "" "If installing the cwltool using the pip command doesn't work for you, the " "[prerequisites](prerequisites.md) section contains other ways to install " @@ -1080,32 +1175,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +#: ../../src/introduction/quick-start.md:51 aa751bda67ec44ba988642b061e2a094 msgid "Running \"Hello World\"" -msgstr "" +msgstr "Executando \"Hello World\"" -#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +#: ../../src/introduction/quick-start.md:53 a7e0209af0544b0ab31012864a43886c msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " "workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +#: ../../src/introduction/quick-start.md:57 d0f424f0041c4635a0559fa32a76c86f msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" +msgstr "Executando `hello_world.cwl` com `cwltool`." -#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +#: ../../src/introduction/quick-start.md:62 eeee96c4e59447aea6b239c63e4bb3e5 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +#: ../../src/introduction/quick-start.md:65 961a385b340141e980aa4f8791fa2f12 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +#: ../../src/introduction/quick-start.md:70 c48cd1be543d4ccbab964b28c2e08584 msgid "" "Another way of passing values to your workflow input parameters is via an " "*Inputs Object*. This is a file containing the input fields with their " @@ -1113,21 +1208,23 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +#: ../../src/introduction/quick-start.md:74 e5619164bdf242f0b09cac668adc0ef7 msgid "`hello_world-job.json`" -msgstr "" +msgstr "`hello_world-job.json`" -#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +#: ../../src/introduction/quick-start.md:80 9f80772a53154bbeb27895d35435de10 msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" +"Pode utilizar este arquivo de Objetos de Inputs agora para executar o " +"workflow “Hello World”:" -#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +#: ../../src/introduction/quick-start.md:82 98b6d400cb274d08ad6489adbef08c4b msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" +msgstr "Passando um arquivo de Objeto de Inputs para o `cwltool`." -#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +#: ../../src/introduction/quick-start.md:88 4faabaab56f1444da290cf64cc389f37 msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but it " @@ -1135,66 +1232,80 @@ msgid "" "Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +#: ../../src/introduction/quick-start.md:96 48beaccb16a24427bd015c63f9e06d37 msgid "Continue reading the next sections of this User Guide!" -msgstr "" +msgstr "Continue lendo as secções seguintes deste Guia do Utilizador!" -#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 +#: ../../src/introduction/quick-start.md:97 68035ead1c6844128011ca32c04fd20f msgid "" "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" +"[Lista das Implementações da CWL](https://www.commonwl.org/implementations)." -#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +#: ../../src/introduction/quick-start.md:98 8fc1ebf21a6f4894a4acfba74a80602b msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" +"A [organização`common-workflow-language`](https://github.com/common-workflow-" +"language) no GitHub." -#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +#: ../../src/introduction/quick-start.md:99 27fbad579d8b4ebeacc6fd3ef7e85a39 msgid "" "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" "Common_Workflow_Language)." msgstr "" +"[Common Workflow Language na Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." -#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +#: ../../src/introduction/quick-start.md:100 a8791b670848474da292a467f01f8c45 msgid "" "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." "org/wiki/YAML)." msgstr "" +"[YAML.org](http://yaml.org/) e [YAML at Wikipedia](https://en.wikipedia.org/" +"wiki/YAML)." -#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +#: ../../src/introduction/quick-start.md:101 fc20fa4c04104417b541a67ada2ab9a9 msgid "" "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." "replace('VERSION', cwl_version_text) }}." msgstr "" +"A {{'[Especificação CWL VERSION](https://www.commonwl.org/VERSION)'.replace(" +"'VERSION', cwl_version_text) }}." -#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +#: ../../src/introduction/quick-start.md:102 a93a7797a12b48dfa5bc3a7c50ab88e7 msgid "" "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" "Workflow_management_system)." msgstr "" +"[Workflow management system na Wikipedia](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." -#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +#: ../../src/setup.md:9 6f02fa47aca14c59a35b3ab750f5f236 msgid "" "This page is out-of-date and was kept here to preserve the links of the old " "User Guide. The information on this page has been migrated to the [FAQ](/faq." "md) section of the new user guide." msgstr "" +"O conteúdo desta página está desatualizado mas foi mantido aqui para " +"preservar os links do antigo Guia do Utilizador. A informação desta página " +"foi migrada para a secção [FAQ](/faq.md) do novo guia do utilizador." #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 3821c2d16b254672a494522e47386cb0 msgid "Additional Arguments and Parameters" -msgstr "" +msgstr "Argumentos e Parâmetros Adicionais" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 +#: 412a05f3492349a7bd26ea0c30e9bd80 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf +#: 1232f6c81da141cb8482294eee5955dc msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files in " @@ -1204,52 +1315,56 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: 485bb71673144e3f90f05b420b7079ac msgid "`arguments.cwl`" -msgstr "" +msgstr "`arguments.cwl`" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: ../../src/topics/staging-input-files.md:15 0beb10c3133643f6b62c7d4aeec33709 +#: 5d48d9a2e977431f9a3625abaa466f5f msgid "`arguments-job.yml`" -msgstr "" +msgstr "`arguments-job.yml`" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: fcc1151a2e8b4a84b8595c7f913781a1 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" +"Em seguida, crie um arquivo Java de exemplo para usar com a ferramenta de " +"linha de comando." #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb +#: 4a291c7ac7c84257b7402567d8364a36 msgid "" "And now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" +"E agora execute `cwltool` utilizando a descrição de ferramenta e o objeto de " +"input na linha de comando:" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a +#: 3b1ae26038fd498ca0ae23aa70a35d3f msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 +#: 40388ebefb6947089c4a0f6d5d6e92e8 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" -"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." -"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " -"specification for details." +"designated output directory. Other parameters include `$(runtime.tmpdir)`, " +"`$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and " +"`$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of " +"the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +#: ../../src/topics/best-practices.md:1 a417fdd330db47a3aac07f7006c83ca9 msgid "Best Practices" -msgstr "" +msgstr "Melhores Práticas" -#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +#: ../../src/topics/best-practices.md:3 99bad0fd9bee428a8d936d5a8e84d97d msgid "" "The following are a set of recommended good practices to keep in mind when " "writing a Common Workflow Language description for a tool or workflow. These " @@ -1257,13 +1372,13 @@ msgid "" "although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +#: ../../src/topics/best-practices.md:8 935500b0e6e249eba585644cddbd0253 msgid "" "No `type: string` parameters for names of input or reference files/" "directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +#: ../../src/topics/best-practices.md:11 96f924d6e02f4005b35d463e49be2982 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that " @@ -1278,7 +1393,7 @@ msgid "" "anyone, e.g. [Apache 2.0][apache-license]." msgstr "" -#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +#: ../../src/topics/best-practices.md:20 25e0a5c93ccc49bc8b6206c7c2e3de5c msgid "" "If possible, the license should be specified with its corresponding [SPDX " "identifier][spdx]. Construct the metadata field for the license by providing " @@ -1288,43 +1403,43 @@ msgid "" "provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +#: ../../src/topics/best-practices.md:26 34ad53bc5a40446daa0dac4571600d1e msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +#: ../../src/topics/best-practices.md:28 4c397ffd2e9148e39bdd614683a98a78 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +#: ../../src/topics/best-practices.md:37 1ed7f7e73afb4bd2ad2e29b65d020ff1 msgid "" "For more examples of providing metadata within CWL descriptions, see [the " "Metadata and Authorship section of this User Guide](../topics/metadata-and-" "authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +#: ../../src/topics/best-practices.md:40 13b058dfa3cd4bbea54ae7d5a56c4c50 msgid "" "Include [attribution information][license-example] for the author(s) of the " "CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" "[orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +#: ../../src/topics/best-practices.md:44 69369b917c1a45199343266650b1b220 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +#: ../../src/topics/best-practices.md:47 0245a61fd2ef4fb69cbb8d732086fb8f msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" "identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +#: ../../src/topics/best-practices.md:50 e9a56e3634a042279cae1745b7820658 msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1332,61 +1447,61 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +#: ../../src/topics/best-practices.md:55 8a180861a66c4aaa9e8fdefd929ed829 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +#: ../../src/topics/best-practices.md:58 00f333a383b64578b32c687b42924a77 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" -"$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with " +"`$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " "[Full IANA media type list][iana-types] (also known as MIME types). For non-" "bioinformatics tools, use or build an appropriate ontology/controlled " "vocabulary in the same way. Please edit this page to let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +#: ../../src/topics/best-practices.md:66 6b960d362bb540299f0560c14c5f2d8c msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +#: ../../src/topics/best-practices.md:69 9cf9342bf0864e87b495913d8e06d021 msgid "" "Each `CommandLineTool` description should focus on a single operation only, " "even if the (sub)command is capable of more. Don't overcomplicate your tool " "descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +#: ../../src/topics/best-practices.md:73 587b048324e447cb85844d8c64ae9a1e msgid "" "Custom types should be defined with one external YAML per type definition " "for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +#: ../../src/topics/best-practices.md:76 d8df6bbd5d324f7c9f48edb33e113b75 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +#: ../../src/topics/best-practices.md:78 2235174088ad48a89d4fc21223e627b7 msgid "" "If useful, include a top-level `doc` as well. This should provide a longer, " "more detailed description than was provided in the top-level `label` (see " "above)." msgstr "" -#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +#: ../../src/topics/best-practices.md:82 a0f0953a1a9f40cebd4dbe028784ff96 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list of " "valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +#: ../../src/topics/best-practices.md:85 0ec380c683534892b6b8b8fcea84f765 msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. One " "common example: manipulating `File` names and paths? Consider whether one of " @@ -1394,31 +1509,31 @@ msgid "" "`nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +#: ../../src/topics/best-practices.md:90 65f23741db4e4a6abda8e5f7e036753a msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +#: ../../src/topics/best-practices.md:93 34c2caee8eb84e01a37033b67eb4aaba msgid "" "Complex workflows with individual components which can be abstracted should " "utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " "workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +#: ../../src/topics/best-practices.md:97 d7c7484b2f1048aea9802400410f0858 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics " "software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +#: ../../src/topics/command-line-tool.md:1 a905abc2eead4dbaa035235936025499 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +#: ../../src/topics/command-line-tool.md:3 eb91b6dab34d4d5f9854ac580a6cbde2 msgid "" "A command-line tool is a type of Process object that can be run by itself or " "as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " @@ -1426,52 +1541,52 @@ msgid "" "command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +#: ../../src/topics/command-line-tool.md:8 7caeb91564634091a932f1270c4f5ef9 msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The following " "example contains a minimal example of a CWL command-line tool for the `echo` " "Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +#: ../../src/topics/command-line-tool.md:19 c6ac4a60d102407991f40b892fb60560 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +#: ../../src/topics/command-line-tool.md:50 51d3ce421db345f5ab19e02fbbc51df2 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +#: ../../src/topics/command-line-tool.md:57 8311d1430e624435b7b04bf2574a90c5 msgid "" "The example above uses a simplified form to define inputs and outputs. You " "will learn more about in the [Inputs](../topics/inputs.md) and in the " "[Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +#: ../../src/topics/command-line-tool.md:68 d1c03e5f19d64ea89276d126de6e4bda msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +#: ../../src/topics/command-line-tool.md:69 8494b43e98dd424db7d57aa1d731f7b4 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network access. " "If a command-line tool is written manually in CWL v1.1+, there is a need to " "specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +#: ../../src/topics/command-line-tool.md:83 8c4573fb120149269a0fe3a1ba6c9ef8 msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " "Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: e1c709ac0fb249928d14aeced6551ae0 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d +#: c26c9c640e0747c8b2c2977c860c9d82 msgid "" "Sometimes you need to create a file on the fly from input parameters, such " "as tools that expect to read their input configuration from a file rather " @@ -1479,17 +1594,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff +#: edbe918d7df14cafb440e171e46c6de3 msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: 6d457d9b4ae746d384e65d9a37ca3591 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df +#: 868394c1b8374ee6bbd43463e73d7edc msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the value " @@ -1497,7 +1612,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 +#: 08a9e08cba674db09c9bfbef37e9579f msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later " "during command line tool invocation. That means that any genuine need for " @@ -1507,7 +1622,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa +#: 6f6f437753dd4eddae0b2ea62046fe39 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1515,13 +1630,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 2d2ef4769b2347e79db827655f1bcdeb 2699fbc4376148af91b7a5a6cdac467c -#: ca03defa3ad14cf698171cb09e3055c1 +#: 096b17907bc3452d9927ef2fb6f5c11f 78ed5d8fb9bd4e068023d2c717e20f62 +#: c3a2e9e6b4414597a17db6d55d98e9d1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d +#: ac783e6415a44cb59d4b425bac5087b7 msgid "" "Before we run this, let us look at each step in a little more detail. The " "base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1529,7 +1644,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c +#: b9e6e15b541149c6a2d3922c11405267 msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " "array, we need a `-` on the first line of each element of the array, in this " @@ -1541,7 +1656,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 +#: 87088899567a4402aeb34605d3c6b06b msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1551,19 +1666,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: b372f33c65bb4707b2a462a960bb1373 293fb1d428b849aebccad598a932992d -#: f924d65fed0c4cb5b0a019b084a8b535 d6255506eebe44be94c5ce703c44a513 -#: 7bbd2d738fc54649aeb10f8d2bc38b6f +#: 304c1bfe5ecd4d26b5dfaf9ad2e2c7f8 3ef7f0e3099147d78fd2d30bfa73cc6b +#: 4fef79a30282456eb9b5dd34a5eec0b1 afe775762ed348e5982b99bcf1451606 +#: f0689cd0e5b34414b6693331186ee4a3 msgid "" "Now invoke `cwltool` with the tool description and the input object on the " "command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +#: ../../src/topics/custom-types.md:1 9f1967411aa7497fa43a4851f0645d6e msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +#: ../../src/topics/custom-types.md:3 90bd62e4ef8b41e398a5c9b31f132774 msgid "" "Sometimes you may want to write your own custom types for use and reuse in " "CWL descriptions. Use of such custom types can reduce redundancy between " @@ -1572,21 +1687,21 @@ msgid "" "to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +#: ../../src/topics/custom-types.md:9 3465527b8ff4407587f7c46fa9fa2a98 msgid "" "The example below is a CWL description of the [biom convert format][biom] " "tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +#: ../../src/topics/custom-types.md:12 c0cc869690804ada96a5c1813d17b895 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +#: ../../src/topics/custom-types.md:18 01f369931c8142c08fe821a0ca31bf92 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +#: ../../src/topics/custom-types.md:24 0b3ff704cdea44e28aee3c704ca98e27 msgid "" "___Note:___ To follow the example below, you need to [download the example " "input file](https://github.com/common-workflow-language/user_guide/blob/main/" @@ -1594,13 +1709,13 @@ msgid "" "*rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +#: ../../src/topics/custom-types.md:30 cb456bcae0dd41ffbc514eeea283e130 msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to be " "used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +#: ../../src/topics/custom-types.md:46 c610173365d04c57900b22f4024b47b4 msgid "" "The reference to a custom type is a combination of the name of the file in " "which the object is defined (`biom-convert-table.yaml`) and the name of the " @@ -1611,23 +1726,23 @@ msgid "" "hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e +#: ../../src/topics/custom-types.md:53 c2b2e18d55c94721812431583cfc4725 msgid "" "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +#: ../../src/topics/custom-types.md:55 3e61c3920a7a45db8917c348bd44384d msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +#: ../../src/topics/custom-types.md:61 cd87d210b03c4da2a7608b40a6bbcca0 msgid "" "In order for the custom type to be used in the CWL description, it must be " "imported. Imports are described in `requirements:SchemaDefRequirement`, as " "below in the example `custom-types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +#: ../../src/topics/custom-types.md:76 7af9ba3219e44ed49b8da781db5d6fb5 msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number of " @@ -1637,26 +1752,26 @@ msgid "" "this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +#: ../../src/topics/environment-variables.md:1 eae1994f3a4d481b863b5125c7f4a383 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +#: ../../src/topics/environment-variables.md:3 8bd8c06d416740b69d126eb9f5f24ad3 msgid "" "Tools run in a restricted environment and do not inherit most environment " "variables from the parent process. You can set environment variables for " "the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +#: ../../src/topics/environment-variables.md:7 11c6bffc620b4c789b29ab4034a8bfbd msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +#: ../../src/topics/expression-tool.md:1 89888b1b994546ce8a93f9630b4bb07e msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +#: ../../src/topics/expression-tool.md:3 191d3010b9244b39bc3bc50246ac7ad7 msgid "" "An expression tool is a type of Process that can be run by itself or as a " "Workflow step. It executes a pure JavaScript expression. It is meant to be " @@ -1664,32 +1779,32 @@ msgid "" "on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +#: ../../src/topics/expression-tool.md:8 3437ed6e184748e4af1ef62f32c8cef1 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +#: ../../src/topics/expression-tool.md:17 c3ae1ef318bb4e0fada76c353dd5f6f1 msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +#: ../../src/topics/expression-tool.md:48 a7f5e04d242c48a7b3deffb5ff6528be msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +#: ../../src/topics/expression-tool.md:67 32b6841faed044409bc618cba54a22f0 msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains a " "JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +#: ../../src/topics/expressions.md:1 6821ba7a84a44d309d245c429948ad09 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +#: ../../src/topics/expressions.md:3 8167269bc3a64c72bd6c909362350a15 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1697,7 +1812,7 @@ msgid "" "CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +#: ../../src/topics/expressions.md:9 c0f75603a6024063a6911f17c70908cc msgid "" "JavaScript expressions should only be used when absolutely necessary. When " "manipulating file names, extensions, paths etc, consider whether one of the " @@ -1706,67 +1821,67 @@ msgid "" "practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: ../../src/topics/expressions.md:16 7faec63b389a4c07b6929b7a78f0cc70 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +#: ../../src/topics/expressions.md:22 d7dca89942f949d58cb18cb94bb7de72 msgid "" "As this tool does not require any `inputs` we can run it with an (almost) " "empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +#: ../../src/topics/expressions.md:25 1abc1a21c0764415b138099e0e21432b msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +#: ../../src/topics/expressions.md:31 b8b5a50a82e44e49a37c6396f1ff9464 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object is " "represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +#: ../../src/topics/expressions.md:35 b38d66c12ab74dfc9395e69d9c04bbf5 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +#: ../../src/topics/expressions.md:37 8417aa7a9d034361a41def6b71e93413 msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +#: ../../src/topics/expressions.md:47 c1f672b377da4605b9c5098ebb6e1147 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +#: ../../src/topics/expressions.md:54 af52f5197e8545d2be22cc0f7f03648c msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " "describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +#: ../../src/topics/expressions.md:62 5e12ce15018942bf9010ce6519c17b00 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +#: ../../src/topics/expressions.md:64 e2e9c5f7b681427a9589476649e5a9d8 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +#: ../../src/topics/expressions.md:66 8a74763ead0147bbaf3892e552fad546 msgid "" "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 1acb064f7a4a482aa0174bdc847c6382 -#: 0222780b98ac48e89b1b4f57c9df8590 +#: ../../src/topics/parameter-references.md:64 0aab7de8d69f49438d4eeed17316df68 +#: 75f90cb870d14d0dbb4c4ee80d32a65e msgid "`arguments`" msgstr "" @@ -1774,32 +1889,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 ef2b8433778a40408f179c3e6f0cf99e -#: 224732683a9c41f3ba1b778851e745a8 17b10d1e91b24dc582df98fcd2ac850e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 e4e68011dc5f42e4918c747afa7d764b -#: d44e3cfa661840eb851782e24caf1b68 +#: ../../src/topics/parameter-references.md:86 0b9d8268c177489b86b8eaa638dfa063 +#: 204cd6d8375a4462a8247863a96df906 2b7e56ceb4ad49a8b29a58b10bad7c0a +#: 81f15c64379941d8ac2a681b3879761c f11ae7d801db45989b598864dc6291c9 +#: fc4534b475334f7281d1740c9a78f640 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: ../../src/topics/parameter-references.md:66 70e9085b21f640d6893309a3375c0511 +#: f529003dd7a64bc7be0ccef8dbfa84b3 msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: ../../src/topics/parameter-references.md:67 3fceb522ba6245129b826c342eaf31b4 +#: a5f71add5b8345a4bfa02853ef8a6d35 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: ../../src/topics/parameter-references.md:68 018300196ea24550988a0156894b5e85 +#: 2c799286e8204ed9a83c3fc006988139 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +#: ../../src/topics/expressions.md:72 25d91d6624bd42e7948e29c684e8e441 msgid "" "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandInputParameter)" @@ -1810,11 +1925,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 d0a92a3792b549e9b5ddce4667d168d2 -#: 801729c7c71b4109824b035437e69bf9 1bc510d525f0414e88692e356e67fbbc -#: d2e246ae56a24e4abdd6b7d9812a86e2 b1446bab2732412e91f721a08067b0bd -#: e89dbeb22f41430ca39c923d9fdf68cb bd61499b71e64164878dea08d6d7141e -#: ed875a006df64f9e8a55fa5e9fa87404 +#: ../../src/topics/parameter-references.md:90 0944d6525c3c460aa4b5a0e72552ca4d +#: 1187b0d330cb470fbea82a8b8c95aa28 265602307ccd42458ba47ac1b689242c +#: 2febce1b1ad74b18af3a9b3fa137c780 3215ee41f96541cbbda60a1167386c2f +#: 80efeab6ec0e447bbe158cbaa57f83d8 8d2bbd91b4ab4faa923fc1a14ec49dd5 +#: b4a6e640275b4fc7a18e3083e86b72a1 msgid "`format`" msgstr "" @@ -1823,51 +1938,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 8a1748579de14f0888d5ee9023e37c2d -#: f760465a49d64d4c8468ad9c4fea62b1 28b6b5ffa7524374aaa9525ebfafb762 -#: d11f6a19ddf34cf19ec856bacf998e29 bcb7cd10cb5947bb9d85c040f57f954f -#: da5188d3bedc4997a35bdf417f2f643c cd7a0190511d4613b09600a3b1e9d55f -#: 47def3b078e2402182039be0227090ae +#: ../../src/topics/parameter-references.md:91 480b2e4207574b27b8d33dfe5e9ab64e +#: 4b4149a3b97a4de5b2d7fd84bd547ffe 7af1a82df41e40d0a430babafe1bc5e2 +#: be01787b66e34074af32bb45dcce8657 be099ab533504a7596fd56ec1ce7ca5d +#: c8b96271665444608f601a460dd28fb3 cb6dfa7bc68b41929a5247d929c2f94a +#: f7f452e92f6d4a14ba3912c62699019a msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +#: ../../src/topics/expressions.md:75 4811c1b9867b44caa70dec4b91970484 msgid "" "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +#: ../../src/topics/expressions.md:77 0b1f2a8986e0419a90e484d3a945a037 msgid "" "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +#: ../../src/topics/expressions.md:80 dbc02876870d49d2b9e39db4133a0f62 msgid "" "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: ../../src/topics/parameter-references.md:78 97339a3fa43849f7b292f4643b5fe35c +#: da8b81b1e1884406a188fb04825ef90e msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 d555a3d991e344a5a8e1289168d7c6d1 -#: 44b3f123c9b04a308c1161b742a7b34b +#: ../../src/topics/parameter-references.md:79 077e7b0d2dde443699050af8c63ab912 +#: c8cbe3dfd0984221ae72012ea26edc6f msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 e9fa9430535c424fa3e8be5d460d2ba4 -#: 0e306cc923974d1db83fdfb45105a11c +#: ../../src/topics/parameter-references.md:80 3f07f4a8594640c2b2da4da521872b59 +#: 573f7e4b72ec4c47ab2e54e2c4877d9c msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +#: ../../src/topics/expressions.md:84 f03011b3479b47c690604c508d95c263 msgid "" "From [InputParameter](https://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" @@ -1875,93 +1990,93 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 b0290d1a477b48119e17cf1fed9d6dff -#: 446f1190af7a40a0913ff04ce7aa938c +#: ../../src/topics/parameter-references.md:84 1ec3f913909b4e04bb602767d23bd85d +#: 2f7130500b8c450fa4af226b18e38407 msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +#: ../../src/topics/expressions.md:88 a5849a856a374cda807ecf48034af915 msgid "" "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." "html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 e1cde4aa32c041238ed2596173c6d824 -#: 557694f82e314baa9ccafba14d6ff2c9 +#: ../../src/topics/parameter-references.md:87 bd8bbd60aaff4e7aacec91bcbad500f4 +#: f0c99004211e4adf8c0b524d5bbcc12b msgid "" "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." "html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 c2a92d3eca7f4ee39cec649170eeea53 -#: 3c939769ede94602a67fc50c435741cf +#: ../../src/topics/parameter-references.md:88 96c544cf213245cfb3d1f5196223c6cc +#: c6a04d4f3ef24104b0a86f9093935c13 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +#: ../../src/topics/expressions.md:92 946e0437a48b4d5da2a29d489250cbaa msgid "" "From [InputParameter](https://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [ExpressionToolOutputParameter](https://www." "commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +#: ../../src/topics/expressions.md:95 1f287ebf87ae4e93bd1ac65cc1d01bf4 msgid "" "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." "html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: ../../src/topics/parameter-references.md:93 0d0f4f0e12174d588c131afef70efc5f +#: a74e0e3499d644b4a9d999d3555f03de msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 718ceee9973240ec9c100977bbcc8921 -#: 2b25152f6df5494a8632f3ce631c20d8 +#: ../../src/topics/parameter-references.md:94 b2e31c38f7cb4ecabd6b9b89ef051c0e +#: ddc9d9ae72a64a76a2a8e2bba22584ee msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 c07ab08eb75d4528949c56a3d7c12b28 -#: 846cd427ae25410eae7c920b237edcb0 +#: ../../src/topics/parameter-references.md:95 12f86817dfc14f2bb39509886d56017f +#: 8a94f2c3b1674162a268f67935a3025b msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: ../../src/topics/parameter-references.md:96 a800acfefb3f433fae2cdda9ac4a795a +#: bcb58fc2447a4472b86913871b8c12ee msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: ../../src/topics/parameter-references.md:97 5be337d412ba4d48877e991d535e810c +#: e6cf2f8498db4f549193be20d87e16f9 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: ../../src/topics/parameter-references.md:98 3bc61c8197664f12a98d1ac38b421b38 +#: 9973a87f747445ad89ce959420cac5fd msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: ../../src/topics/parameter-references.md:99 0f5dc4f5a4c64f818e2e22f20472ae84 +#: 2ec9d1f191f44686b1cb8622336d6b92 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +#: 5382ff97ad2f419dbe1bed266997aa84 74406f77013443f28d4d6306c54b0df1 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +#: ../../src/topics/expressions.md:104 f594a20dc038457e815dc17bae6e031d msgid "" "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" "CommandLineTool.html#InitialWorkDirRequirement)" @@ -1969,33 +2084,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +#: 5814f96ee4ec4822aecad33c8eda0473 c46c44268b2a4b96b1df13e53e82e54c msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +#: ../../src/topics/expressions.md:106 b9824103ef8745bab30b65887c82f62f msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: effc0208cf4f4551958db6e526c0528b 9d4889c8cec24351a7a9e3c547e331b6 +#: 28b23f84c64549e7a0fe444ccc3e1b05 fdd5d742a6764e5db2281ed844bf3475 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: be6c1e85c7b6495d8086c262daad20e7 af4f7f232a9d42388c0ba1cfc7c2cdf7 +#: b6123c911c804f3c8cb596d2aa495b2b d81a7d8b7db444409b286e5f1d863968 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +#: eb6255a0f8d748588d87e7ad38e507bd fffc5a80bd68495396d32b7a1821eb4e msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +#: ../../src/topics/expressions.md:110 b00a8a2a572742e0929470550433e929 msgid "" "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." "html#EnvironmentDef)" @@ -2003,23 +2118,23 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +#: 9b34c95e483e47f3828e79bf929a23b4 c968eebaf0114b23b789e9ce68e7588d msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +#: ../../src/topics/expressions.md:116 7c8fb996d1af4cfdb0d49d8ed2696745 msgid "" "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +#: ../../src/topics/expressions.md:118 75a29e9ff2cf4b5bb6afa87a741a111b msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib` " "attribute that allows users to load external JavaScript files, or to provide " "inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +#: ../../src/topics/expressions.md:122 5233d8baa8b74391bf8fee5ae2324234 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2027,7 +2142,7 @@ msgid "" "the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +#: ../../src/topics/expressions.md:128 343e8b78a1f94b8cbafac05212e5a333 msgid "" "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." "org/v1.0/CommandLineTool.html#Expressions) that the only version of " @@ -2036,53 +2151,53 @@ msgid "" "in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +#: ../../src/topics/expressions.md:135 0657ee8f03d8462ca6ca6fc538386b0d msgid "" "For example, we can use `InlineJavascriptRequirement` and write a JavaScript " "function inline in `expressionLib`. That function can then be used in other " "parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +#: ../../src/topics/expressions.md:139 e3c593cf50da426f8d9df215c7db0bc9 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +#: ../../src/topics/expressions.md:146 b971e53c3ed847f1b7c7a6d50e344baf msgid "" "Running this CWL workflow will invoke the JavaScript function and result in " "the `echo` command printing the input message with capital initial letters:" msgstr "" -#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +#: ../../src/topics/expressions.md:149 d2315d46369f4e9d9c871d7f88f7006e msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +#: ../../src/topics/expressions.md:155 04fdaa45a7ed47d5830181611bda924e msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +#: ../../src/topics/expressions.md:158 8d7686f62f314d98aae8c262befd5283 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +#: ../../src/topics/expressions.md:164 e68ee17607be4a06a66f9fc67624aff5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +#: ../../src/topics/expressions.md:171 76b85d3729274fc08adfadcbf1172650 msgid "" -"The `custom-functions.js` file is included in the CWL document with the `" -"$include: custom-functions.js` statement. That makes the functions and " +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +#: ../../src/topics/expressions.md:175 29f334957fa940c289f385160cca6d63 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +#: ../../src/topics/expressions.md:181 6d255ae6b92a48fa9b7b98443cc2f5bb msgid "" "Finally, note that you can have both inline and external JavaScript code in " "your CWL document. In this final example we have added another entry to the " @@ -2091,15 +2206,15 @@ msgid "" "functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +#: ../../src/topics/expressions.md:186 89734e7855654b2e8bfddeea96241539 msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +#: ../../src/topics/expressions.md:193 1915f8e68f624027827d28f8e17d2dec msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +#: ../../src/topics/expressions.md:200 750f94edb4f84e45a276f6ab28fad95e msgid "" "The `$include` statement can be used to include a file from the local disk " "or from a remote location. It works with both relative and absolute paths. " @@ -2107,11 +2222,11 @@ msgid "" "html#Include) from the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +#: ../../src/topics/file-formats.md:1 2e9e8cfaf48a43a88c31a855dac4f748 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +#: ../../src/topics/file-formats.md:3 c574b54d998243f28d2caa91434968a7 msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This helps " @@ -2119,7 +2234,7 @@ msgid "" "simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +#: ../../src/topics/file-formats.md:8 b0ec34507eea473c91d6ada09a1c5c09 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM in " "our example), reference a local ontology for your institution, or do not add " @@ -2128,33 +2243,33 @@ msgid "" "file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +#: ../../src/topics/file-formats.md:14 a688e39859734a518c0fcc19f532a432 msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` section " "of the document in greater detail, so don't worry about these for now." msgstr "" -#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +#: ../../src/topics/file-formats.md:17 e068422ad9b84ca1b27008127928cc0f msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +#: ../../src/topics/file-formats.md:20 8c3ef5e145b14299bf3671add0da56ac msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +#: 0d92f1c0f1ce448fb698e9b390b45c15 fc4773204ebc4e3789bb076dff0d0393 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +#: ../../src/topics/file-formats.md:32 900abc5aa6a940f48f9c93e79cd1c47f msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +#: ../../src/topics/file-formats.md:34 0390555b96c84aadbd9325c152972087 msgid "" "Below is an example of a parameter file for the example above. We encourage " "checking in working examples of parameter files for your tool. This allows " @@ -2162,11 +2277,11 @@ msgid "" "parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +#: ../../src/topics/file-formats.md:39 d5752ee5437b496ca10f4f12b76fc5dc msgid "`sample.yml`" -msgstr "" +msgstr "`sample.yml`" -#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +#: ../../src/topics/file-formats.md:45 91dc76bb4565473ab948eecf628a405c msgid "" "___Note:___ To follow the example below, you need to download the example " "input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +#: ../../src/topics/index.md:1 0b8b9b7f533543a49f876421ce6057d9 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +#: ../../src/topics/inputs.md:1 1b6cfac3a92347d4b98bb54de1e26870 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +#: ../../src/topics/inputs.md:3 53dd5f476f064cbf9b9826d1e80eb830 msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +#: ../../src/topics/inputs.md:5 420b33d143fc44d1b237bc678f0af663 msgid "" "The `inputs` of a tool is a list of input parameters that control how to run " "the tool. Each parameter has an `id` for the name of parameter, and `type` " "describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +#: ../../src/topics/inputs.md:9 55136332e3bb48f892cf6a74c67a4ac6 msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*, " "and *null*; complex types are *array* and *record*; in addition there are " "special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +#: ../../src/topics/inputs.md:13 cb2527899cc04b6d8060c4d57883beb5 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +#: ../../src/topics/inputs.md:16 c79668b856b14243b4fad0f46dc5d6d7 msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +#: ../../src/topics/inputs.md:18 ed6f3e5c7b3f403a9a94359983107645 msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +#: ../../src/topics/inputs.md:24 034075eb09db4897a96d3332408427db msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +#: ../../src/topics/inputs.md:26 08181d391cc543a5a81d3257654df213 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +#: ../../src/topics/inputs.md:33 15215522e38242c4b17ec3aa089269d4 msgid "" "You can use `cwltool` to create a template input object. That saves you from " "having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +#: ../../src/topics/inputs.md:40 64bd3382ec234ec8a50217b794b96916 msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " "> inp-job.yml`, and then modify the default values with your desired input " "values." msgstr "" -#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +#: ../../src/topics/inputs.md:44 3611c1ca498a4197a4a6612c60f5f565 msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +#: ../../src/topics/inputs.md:47 da924e8142d34e86bcb5de1cd1da71ca msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " "command line." msgstr "" +"Em sequência, cria um arquivo chamado whale.txt utilizando [touch] digitando " +"`touch whale.txt` na linha de comando." -#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +#: ../../src/topics/inputs.md:53 13c97256a5ee49c99f4010edf9dbc9bf msgid "" "Now invoke `cwltool` with the tool description and the input object on the " "command line, using the command `cwltool inp.cwl inp-job.yml`. The following " @@ -2255,7 +2372,7 @@ msgid "" "command line:" msgstr "" -#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +#: ../../src/topics/inputs.md:64 dcc3f2a47a6449efb857af63ed4b65d0 msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2263,7 +2380,7 @@ msgid "" "specified" msgstr "" -#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +#: ../../src/topics/inputs.md:70 cf54a30ae24f4013bb19f379a7ca67be msgid "" "The field `inputBinding` is optional and indicates whether and how the input " "parameter should appear on the tool's command line. If `inputBinding` is " @@ -2271,14 +2388,14 @@ msgid "" "each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +#: ../../src/topics/inputs.md:83 ff75644bae9c46af8379d78360d4c696 msgid "" -"Boolean types are treated as a flag. If the input parameter \"example_flag" -"\" is \"true\", then `prefix` will be added to the command line. If false, " -"no flag is added." +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +#: ../../src/topics/inputs.md:95 e90abe59a84e48d4b8d6caa737e087aa msgid "" "String types appear on the command line as literal values. The `prefix` is " "optional, if provided, it appears as a separate argument on the command line " @@ -2286,7 +2403,7 @@ msgid "" "string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +#: ../../src/topics/inputs.md:109 9275236d87b646cab1058dd750e11a50 msgid "" "Integer (and floating point) types appear on the command line with decimal " "text representation. When the option `separate` is false (the default value " @@ -2294,7 +2411,7 @@ msgid "" "example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +#: ../../src/topics/inputs.md:124 6a39929af73f4ba9b6455ed9fd287e08 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the parameter " @@ -2303,13 +2420,13 @@ msgid "" "provided in the input, nothing would appear on the command line." msgstr "" -#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +#: ../../src/topics/inputs.md:131 44ce716561cc4dff8fef1ca59f816c7c msgid "" "Input files are read-only. If you wish to update an input file, you must " "[first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +#: ../../src/topics/inputs.md:134 9f1da592350f40ee88920465e2004148 msgid "" "The value of `position` is used to determine where parameter should appear " "on the command line. Positions are relative to one another, not absolute. " @@ -2320,17 +2437,17 @@ msgid "" "position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +#: ../../src/topics/inputs.md:142 5116d91f247f44518eb21840415f6eaa msgid "" "The `baseCommand` field will always appear in the final command line before " "the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +#: ../../src/topics/inputs.md:146 08b26d1688e3470288e73d587f052d88 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +#: ../../src/topics/inputs.md:148 f91994a4279a41bda3de41fe79008c62 msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to provide " @@ -2339,23 +2456,25 @@ msgid "" "after the type name to indicate that input parameter is array of that type." msgstr "" -#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +#: ../../src/topics/inputs.md:154 4b93a4f980634e88a8f34a38703fc906 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +#: ../../src/topics/inputs.md:160 de3e760ebb0e4ae099deddb978046a2c msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 588f0f7f967f4d69af27c9729d6d3119 -#: 02adef8ee8204842b5b4a0408f3bac33 9db68837918a4a349f32f15f12697a1d +#: ../../src/topics/outputs.md:105 06ec811e8f0e43b8b929198533ac8082 +#: 797c06f0605d4e4ba306c2803a7834f9 d76d42c490a24b6daed944f45fe7a351 msgid "" "Now invoke `cwltool` providing the tool description and the input object on " "the command line:" msgstr "" +"Agora chame o `cwltool` passando a descrição da ferramenta e o objeto de " +"entrada na linha de comando:" -#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +#: ../../src/topics/inputs.md:178 49406f30f62346968bb1250efc940f70 msgid "" "The `inputBinding` can appear either on the outer array parameter definition " "or the inner array element definition, and these produce different behavior " @@ -2364,7 +2483,7 @@ msgid "" "concatenated into a single argument separated by the item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +#: ../../src/topics/inputs.md:185 3d8711f0135e4ab1b59fce94c83b97c0 msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` in " "`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " @@ -2374,11 +2493,11 @@ msgid "" "arrays of arrays, arrays of records, and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +#: ../../src/topics/inputs.md:191 6f146779d6a84888948751b8b1fd0515 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +#: ../../src/topics/inputs.md:193 e5970a83876e4b5e9a02f2ab0030eb83 msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be provided " @@ -2386,46 +2505,46 @@ msgid "" "parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +#: ../../src/topics/inputs.md:198 0db71b22173846d7b8d4aeb66d2ed8ed msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +#: ../../src/topics/inputs.md:204 f90fd48656a7424aac304987adf1b068 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +#: ../../src/topics/inputs.md:215 3c8bd9134a1c4bda9461362df3257d6b msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: ../../src/topics/inputs.md:217 63bd06780bb949e5b1a1d10389c8c23f msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +#: ../../src/topics/inputs.md:233 0d448baa57f14e7783d3167611e8c659 msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the first " "matching item (`itemC`) is added to the command line and remaining item " "(`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +#: ../../src/topics/inputs.md:236 202239a6e90044e39b676d641aa6d58a msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +#: ../../src/topics/inputs.md:252 512ecb3349b0450cb741de4ed2d2e850 msgid "" "In the third example, only `itemD` is provided, so it appears on the command " "line." msgstr "" -#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +#: ../../src/topics/inputs.md:255 185ff0bb49e841c592b29112eb171bdc msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +#: ../../src/topics/inputs.md:257 6cd5df09e4594d78a526f199ac577881 msgid "" "If you use exclusive input parameters combined with expressions, you need to " "be aware that the `inputs` JavaScript object will contain one of the " @@ -2433,18 +2552,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +#: ../../src/topics/inputs.md:262 9db9f784a5cd4ca5b90691d1e2e827ea msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from an " "enum." msgstr "" -#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +#: ../../src/topics/inputs.md:265 09b1db3cc6c845058cf0ad4c24d71733 msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" +msgstr "`exclusive-parameter-expressions.cwl`" -#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +#: ../../src/topics/inputs.md:271 84aa6e0c479f4528836691005129056e msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you provide a " @@ -2452,14 +2571,14 @@ msgid "" "should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +#: ../../src/topics/inputs.md:280 76611ebb19764bdc8a1f6eacfb76138f msgid "" "However, if you do not provide any input value, then `file_format` will be " "evaluated to a `null` value, which does not match the expected type for the " "output field (a `string`), resulting in failure when running your workflow." msgstr "" -#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +#: ../../src/topics/inputs.md:289 bf9750d215be4294b1cf1e0490a0796a msgid "" "To correct it, you must remember to use an or operator in your JavaScript " "expression when using exclusive parameters, or any parameter that allows " @@ -2469,12 +2588,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: 612f9efa0ed04559a174c37958def6f7 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 +#: 57eb990c11f044dfb60c012a92a30eb1 msgid "" "Implementation extensions not required for correct execution (for example, " "fields related to GUI presentation) and metadata about the tool or workflow " @@ -2489,7 +2608,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b +#: a6e6155cb8ff40fb9d8b1fff3e94fb02 msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to cite " @@ -2497,17 +2616,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: 063c28fc9e654dfd91c66da164ac1d3d msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: 8fcd2ae1ce8d4c7f951281ced81ab32d msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 +#: 639533652456427480fa311da7beb4f0 msgid "" "For those that are highly motivated, it is also possible to annotate your " "tool with a much larger amount of metadata. This example includes EDAM " @@ -2517,15 +2636,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: 266808daf2004bbd9830045fbc67a541 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +#: ../../src/topics/operations.md:1 fd9b715bfa3243b19a919ad19843232d msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +#: ../../src/topics/operations.md:3 fb568063fa7a4cbe83c271772d3d62bc msgid "" "An Operation is a type of CWL process, just like a workflow, a command-line " "tool, or an expression tool. It is a step of a workflow that specifies " @@ -2533,56 +2652,56 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +#: ../../src/topics/operations.md:7 981486166754435cbcd8152e93679405 msgid "" "You can create operations to visualize a workflow during development, before " "you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +#: ../../src/topics/operations.md:10 7b165718ffeb42e793c97fad807f216f msgid "`operations.cwl`" -msgstr "" +msgstr "`operations.cwl`" -#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +#: ../../src/topics/operations.md:16 5e31cddd14414d31b7bd0a6c2745d272 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like a " "command line tool or an expression. You can also plot it with the CWL Viewer " "or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +#: ../../src/topics/operations.md:24 02c372245dc9453ea0841026335e405b msgid "" "The output of the command above can be rendered with a Graphviz renderer. " "The following image is rendered with the Sphinx Graphviz directive (this " "user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +#: ../../src/topics/operations.md:55 d331327285d1434e8c17187737345919 msgid "" "If you try running it with `cwltool`, the command will fail since `cwltool` " "does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +#: ../../src/topics/operations.md:58 72705f8940bb4194bc5554fcc29eed49 msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +#: ../../src/topics/operations.md:66 76b7c63107e94323859904415d07d31c msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A " "CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +#: ../../src/topics/outputs.md:1 ebf56d267612461799bf801136e61b69 msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +#: ../../src/topics/outputs.md:3 f9cff6b272a24ef6ada90e263c1b1784 msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +#: ../../src/topics/outputs.md:5 e482821911004cdd8c3ff1539c69368a msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name of " @@ -2590,7 +2709,7 @@ msgid "" "parameter." msgstr "" -#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +#: ../../src/topics/outputs.md:10 e11fcfe1e84b476ea879810b76ff2cb8 msgid "" "When a tool runs under CWL, the starting working directory is the designated " "output directory. The underlying tool or script must record its results in " @@ -2599,17 +2718,17 @@ msgid "" "from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +#: ../../src/topics/outputs.md:16 65c73a37f06a4782bf43f4acf4f1c77e msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +#: ../../src/topics/outputs.md:19 e172dde545164fefac826d910ddd399e msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +#: ../../src/topics/outputs.md:21 225f4d04c28149898f06bd771f741358 msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2617,71 +2736,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +#: ../../src/topics/outputs.md:26 14e9e446768a454ea786b3256b49632e msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +#: ../../src/topics/outputs.md:32 4bd659cee1904868a7c33345f94f1300 msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +#: ../../src/topics/outputs.md:38 8803a28ccff846eea7d06f4bd908c763 msgid "Next, create a tar file for the example." -msgstr "" +msgstr "Agora, crie um arquivo tar para o exemplo." -#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +#: ../../src/topics/outputs.md:45 661b62e554d64e449c69e475e5188f99 msgid "" "And now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +#: ../../src/topics/outputs.md:51 44cdca5b777441baa246c87940df7264 msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +#: ../../src/topics/outputs.md:62 edb34af3b22d418d9a6178c0ecbb8b80 msgid "" "The `glob` field consists of the name of a file in the output directory. If " "you don't know name of the file in advance, you can use a wildcard pattern " "like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +#: ../../src/topics/outputs.md:65 10e68fad866f4187981f0b365b957b03 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +#: ../../src/topics/outputs.md:67 77e1261484964ba9ac67d9fc9139a1d6 msgid "" "To capture a tool's standard output stream, add the `stdout` field with the " "name of the file where the output stream should go. Then add `type: stdout` " "on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +#: ../../src/topics/outputs.md:71 c66bd08354d54ccb9e3e1da89634a816 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +#: ../../src/topics/outputs.md:89 7d4056355da1451dbed6733fba8c3c38 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +#: ../../src/topics/outputs.md:91 8fed80f9633a4e87a67c651dc3160ce6 msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +#: ../../src/topics/outputs.md:93 6cba36e037d54f93add05fb16d2359bd msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +#: ../../src/topics/outputs.md:99 08862892ecf849a1ba2f25ecc9e98227 msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +#: ../../src/topics/outputs.md:112 c5dcc68bb28041b3b96ac1af716b0db8 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2689,11 +2808,11 @@ msgid "" "mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +#: ../../src/topics/parameter-references.md:1 53b95fd10d61462daf153d45e5517dad msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +#: ../../src/topics/parameter-references.md:3 0702e71de81e493dac08a91d667569e3 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file we " @@ -2706,40 +2825,40 @@ msgid "" "specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +#: ../../src/topics/parameter-references.md:13 a1703da32ad64fd2b8bdd423605b50bd msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +#: ../../src/topics/parameter-references.md:19 2f32531e47b4465594d41ddd218fb2fd msgid "`tar-param-job.yml`" -msgstr "" +msgstr "`tar-param-job.yml`" -#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +#: ../../src/topics/parameter-references.md:25 501dd6f9dbb1438f9a59f6a025639f35 msgid "" "Create your input files and invoke `cwltool` with the tool description and " "the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +#: ../../src/topics/parameter-references.md:36 1bcdd99111bd4bc5b75a8297bb61d9bb msgid "" "Certain fields permit parameter references which are enclosed in `$(...)`. " "These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +#: ../../src/topics/parameter-references.md:47 32eae36c593e43a9a6b4e103a0c2028a msgid "" "References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" -"$(inputs['extractfile'])` are equivalent." +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +#: ../../src/topics/parameter-references.md:51 1d785e8a450140a982142aa0fa906257 msgid "" "The value of the \"inputs\" variable is the input object provided when the " "CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +#: ../../src/topics/parameter-references.md:54 e862bb8bc3e84e24a2aa5ec34298cfd5 msgid "" "Note that because `File` parameters are objects, to get the path to an input " "file you must reference the path field on a file object; to reference the " @@ -2747,101 +2866,107 @@ msgid "" "path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +#: ../../src/topics/parameter-references.md:59 46ffaab11be040cea96a294d9a814738 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +#: ../../src/topics/parameter-references.md:61 890d619c415741179c83ffcd56833fbe msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +#: ../../src/topics/parameter-references.md:63 373e1847d9f745d7a749928642c8e0e3 msgid "" "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +#: ../../src/topics/parameter-references.md:69 90d3624e062c41c7a6d1a9824515d0df msgid "" "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +#: ../../src/topics/parameter-references.md:72 76d09490bd464b708c28991dbff0104e msgid "" "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +#: ../../src/topics/parameter-references.md:74 f33c76e590dd4feaac1e3cf568069d33 msgid "" "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +#: ../../src/topics/parameter-references.md:77 74ed4a06c1984c58826ddceb1a45a4ea msgid "" "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +#: ../../src/topics/parameter-references.md:81 eba3362d34354daa89dc516722c6fbd0 msgid "" "From [InputParameter](http://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" "v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +#: ../../src/topics/parameter-references.md:85 e924874af32d4be19c5e8446768226dd +#, fuzzy msgid "" "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." "html#WorkflowStepInput)" msgstr "" +"De [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" -#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +#: ../../src/topics/parameter-references.md:89 b162113f364445af9ff1bfc8a6610e13 msgid "" "From [InputParameter](http://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." "org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" +"De [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) e [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +#: ../../src/topics/parameter-references.md:92 aa721077e16948c3a5bb8ef5bd7aff04 msgid "" "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." "html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 +#: 2fad0c2bc2834350826b22c454d33cf0 msgid "" "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" "CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: 9e303aa89a9b4447b0dbdc5ac0a0eb9e msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 +#: 7a4eb47c25a54d11a00eb73e9333ad1c msgid "" "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." "html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: 8a957bc8e577476bb59647661b3c0990 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: 2b31f1dec3f5498e9e363a4f1f50dc8d msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb +#: 5a5f84ecc2f449bf9f037dc9da0ac670 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2851,14 +2976,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 +#: ee89f1526c1f4452b4e36ba67bb59747 msgid "" "In this example, the software requirement being described is InterProScan " "version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 +#: c76cec44f5424f6087df28aa33c521a2 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2867,7 +2992,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 +#: 072d7b3ce3284ed994ff0736b43bbb86 msgid "" "As well as a version number, a unique resource identifier (URI) for the tool " "is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " @@ -2882,11 +3007,11 @@ msgid "" "main tool citation and the URL to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +#: ../../src/topics/staging-input-files.md:1 395d611104604a28b78e11b112a95027 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +#: ../../src/topics/staging-input-files.md:3 811b4db0b1794fa89dc870f6cb59a3cd msgid "" "Normally, input files are located in a read-only directory separate from the " "output directory. This causes problems if the underlying tool expects to " @@ -2896,26 +3021,26 @@ msgid "" "base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: ../../src/topics/staging-input-files.md:9 7159b5c5023c47128057c4116cce69f4 msgid "`linkfile.cwl`" -msgstr "" +msgstr "`linkfile.cwl`" -#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +#: ../../src/topics/troubleshooting.md:1 3bfa6791d78f43629de90345f4441ebb msgid "Troubleshooting" -msgstr "" +msgstr "Solucionando Problemas" -#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +#: ../../src/topics/troubleshooting.md:3 9a6bd5b684a740ed9e8993d9f8607774 msgid "" "In this section you will find ways to troubleshoot when you have problems " "executing CWL. We focus on `cwltool` here but some of these techniques may " "apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +#: ../../src/topics/troubleshooting.md:6 6db8a02139644598894220d538c590b9 msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +#: ../../src/topics/troubleshooting.md:8 f0da0f6283d44bcc95224eb9fe2d1764 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor output " @@ -2924,7 +3049,7 @@ msgid "" "directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +#: ../../src/topics/troubleshooting.md:14 e2fc28b44ffe4254892a7c7973dc80c4 msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " @@ -2933,17 +3058,17 @@ msgid "" "of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +#: ../../src/topics/troubleshooting.md:20 505c7cf9ee9c4af1aeed29002eed1b33 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +#: ../../src/topics/troubleshooting.md:27 4c31fd11a28943538690d04baa2b5dd0 msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " "(`cwltool` will create the directory for you if it does not exist already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +#: ../../src/topics/troubleshooting.md:35 a8532ac700014db4bd8ef690a27fb844 msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -2951,7 +3076,7 @@ msgid "" "can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +#: ../../src/topics/troubleshooting.md:44 94a6148512b24b90b87fd1312a926d75 msgid "" "Each workflow step has received a unique ID (the long value that looks like " "a hash). The `${HASH}.status` files display the status of each step executed " @@ -2959,7 +3084,7 @@ msgid "" "output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +#: ../../src/topics/troubleshooting.md:48 ec4165b7c25c449db6a8804161805e80 msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " "the `step_b`). After fixing the typo, when you execute `cwltool` with the " @@ -2969,7 +3094,7 @@ msgid "" "now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +#: ../../src/topics/troubleshooting.md:59 5c0b71a6376848d4aa491854ea2d185d msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had " "been cached, and there was no change in its execution or output. " @@ -2979,15 +3104,15 @@ msgid "" "re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +#: ../../src/topics/using-containers.md:1 95b832552e8443ea9c652f8c95afc01e msgid "Using Containers" -msgstr "" +msgstr "Utilizando Containers" -#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +#: ../../src/topics/using-containers.md:3 561fc9c561bc492ea82c17784dfd439c msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +#: ../../src/topics/using-containers.md:5 2420b16855cf4b25af5bcb87413f6dd9 msgid "" "[Docker][docker] containers simplify software installation by providing a " "complete known-good runtime for software and its dependencies. However, " @@ -3000,34 +3125,34 @@ msgid "" "containers." msgstr "" -#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +#: ../../src/topics/using-containers.md:15 f5266ee2c2b34170bc89cb501b869893 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the container." msgstr "" -#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +#: ../../src/topics/using-containers.md:18 728166bf41504e1d89b755400742a1b4 msgid "" "This example runs a simple Node.js script inside a Docker container which " "will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +#: ../../src/topics/using-containers.md:21 104351ac29d247cb8e017228e2c9b3d8 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +#: ../../src/topics/using-containers.md:27 e11a38bfb30b404c99d223647960cb16 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +#: ../../src/topics/using-containers.md:33 7ed0bd21e998417cb02fdcb8e44734b6 msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that is " "really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +#: ../../src/topics/using-containers.md:44 9dcddf6812ba4bc2a7d6c5fcdb978a68 msgid "" "`baseCommand: node` tells CWL that we will be running this command using the " "Node Js runtime that is meant for Javascript files. We then need to specify " @@ -3040,23 +3165,23 @@ msgid "" "called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +#: ../../src/topics/using-containers.md:52 bc1a09475f154562a4db445bf81ac92f msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " "the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +#: ../../src/topics/using-containers.md:55 2e117019ace84604a8ed5a31214c2587 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +#: ../../src/topics/using-containers.md:69 d0d5b2a1a008411e92859a72101088c1 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +#: ../../src/topics/using-containers.md:72 591d1cd0282b4095a267b44da7d59804 msgid "" "In this example, the path to the script `hello.js` is `/home/me/cwl/" "user_guide/hello.js` outside the container but `/var/lib/cwl/" @@ -3064,43 +3189,43 @@ msgid "" "invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +#: ../../src/topics/workflows.md:1 9f989fff165448ecbcaad6adc0f58d6b msgid "Workflows" -msgstr "" +msgstr "Workflows" -#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +#: ../../src/topics/workflows.md:3 212c82dca23645e89d8b5bb7599f2d25 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +#: ../../src/topics/workflows.md:13 7530029ec04746f2a888dcbc10aa5ce4 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +#: ../../src/topics/workflows.md:41 c1f1d644b37b4f018b87e15249d8758d msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier examples." msgstr "" -#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +#: ../../src/topics/workflows.md:51 2d07232b7d9c415b8ad971e8cbcd9577 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +#: ../../src/topics/workflows.md:81 fa1f770ffeba4b74bcb200cd3949e070 msgid "" "A command-line tool or expression tool can also be written directly in the " "same CWL document as the workflow. For example, we can rewrite the `echo-" "uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +#: ../../src/topics/workflows.md:91 570020792e824c2ba732bcc2c0134aa1 msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +#: ../../src/topics/workflows.md:150 8a50c511004941d0917a8f0d471467f0 msgid "" "Having separate files helps with modularity and code organization. But it " "can be helpful writing everything in a single file for development. There " @@ -3108,33 +3233,33 @@ msgid "" "pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +#: ../../src/topics/workflows.md:160 4d2bf0341836405d9729c47d8020faea msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this " "user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +#: ../../src/topics/workflows.md:165 dd6fc85f74984517b284853a0d46c122 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +#: ../../src/topics/workflows.md:167 f857d80cd5d84622a560c895ab260a92 msgid "" "This workflow extracts a java source file from a tar file and then compiles " "it." msgstr "" -#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +#: ../../src/topics/workflows.md:170 02e7e81cdf7e4226973f910cd57b8ccf msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +#: 3a88d92f41aa4daaad4f4cc6829184b3 646367f222ea41e5987561941d17c4f9 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +#: ../../src/topics/workflows.md:180 aaba75eb272245db82d072fed97b311c msgid "" "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" "github.com/common-workflow-language/user_guide/blob/" @@ -3144,33 +3269,33 @@ msgid "" "_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +#: ../../src/topics/workflows.md:183 f8a6e1af5f0349a5a384be0629c37ac8 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a " "run:" msgstr "" -#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +#: ../../src/topics/workflows.md:185 c4f854c7a279404da3688bdf424c7c5e msgid "`1st-workflow-job.yml`" -msgstr "" +msgstr "`1st-workflow-job.yml`" -#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +#: ../../src/topics/workflows.md:191 d383ce45139944cb85768627965d9467 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +#: ../../src/topics/workflows.md:205 84293afa7a6c40f2af0b980c89581fc7 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +#: ../../src/topics/workflows.md:212 e66daf8af53849109936c36ca7d2b2c9 msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a workflow." msgstr "" -#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#: ../../src/topics/workflows.md:221 8fbfbb587b264dcf98a3cea16dd36ef3 msgid "" "The `inputs` section describes the inputs of the workflow. This is a list " "of input parameters where each parameter consists of an identifier and a " @@ -3178,7 +3303,7 @@ msgid "" "workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +#: ../../src/topics/workflows.md:233 5cdbc4771ea841b4960362b930de2af6 msgid "" "The `outputs` section describes the outputs of the workflow. This is a list " "of output parameters where each parameter consists of an identifier and a " @@ -3186,7 +3311,7 @@ msgid "" "the `compile` step to the workflow output parameter `compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +#: ../../src/topics/workflows.md:248 2e8a41fe43984dc6b4cf430e1ff66b28 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second step " @@ -3197,7 +3322,7 @@ msgid "" "parallel." msgstr "" -#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +#: ../../src/topics/workflows.md:256 78c20aa5a5724da6a4c908849c571334 msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input " @@ -3205,7 +3330,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +#: ../../src/topics/workflows.md:261 1606a2f059eb4b0c9e90f2f0cbbe779b msgid "" "The ``in`` section of the workflow step connects these two input parameters " "to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " @@ -3214,13 +3339,13 @@ msgid "" "parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +#: ../../src/topics/workflows.md:267 b456b11e2760479bbf81a773a3e1f8ee msgid "" "The `out` section of the workflow step lists the output parameters that are " "expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +#: ../../src/topics/workflows.md:278 0fa01fcec32049c989ad1d68841c74de msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3230,11 +3355,11 @@ msgid "" "section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +#: ../../src/topics/workflows.md:285 2bc9829f95584a269eb577c610b2a80c msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +#: ../../src/topics/workflows.md:287 0e5e6445bfcb42a4bd03612316dd7225 msgid "" "Workflows are ways to combine multiple tools to perform a larger operations. " "We can also think of a workflow as being a tool itself; a CWL workflow can " @@ -3242,17 +3367,17 @@ msgid "" "the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +#: ../../src/topics/workflows.md:297 0b83c1028b0e43ba972609e4302bc8a2 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +#: ../../src/topics/workflows.md:300 cbe1ef068b0c417b953655e132333447 msgid "`nestedworkflows.cwl`" -msgstr "" +msgstr "`nestedworkflows.cwl`" -#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +#: ../../src/topics/workflows.md:309 a691c36a15044b11a6d037d16f818a6d msgid "" "This two-step workflow starts with the `create-tar` step which is connected " "to the `compile` step in orange; `compile` is another workflow, diagrammed " @@ -3260,21 +3385,21 @@ msgid "" "supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +#: ../../src/topics/workflows.md:314 2e9797fcd4f04f56b5d2b2f1a3e306d5 msgid "" " \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/nestedworkflows." +"cwl\">\"Visualization \"Visualization" msgstr "" -#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +#: ../../src/topics/workflows.md:322 28f4139911b44eeeb7afd31e9f7cae7b msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " "CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3282,7 +3407,7 @@ msgid "" "to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +#: ../../src/topics/workflows.md:336 4a6cb397a20241beab24d956920a8379 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and `*.java` " @@ -3291,7 +3416,7 @@ msgid "" "workflow." msgstr "" -#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +#: ../../src/topics/workflows.md:341 dccb5472a5dc42b7946dd9245a71ecf0 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar " @@ -3300,7 +3425,7 @@ msgid "" "specific input/output names, as those also appear in its usage as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +#: ../../src/topics/workflows.md:347 de1e18b69f654cabb75e52b47058030a msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3308,14 +3433,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +#: ../../src/topics/workflows.md:366 b947e62f4b3b4c10b95737f1839bcc5a msgid "" "In this case our step can assume `Hello.java` rather than be parameterized, " "so we can use hardcoded values `hello.tar` and `Hello.java` in a " "`baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +#: ../../src/topics/workflows.md:383 2ed0258a3a104ed5ba3b6b95ad998839 msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This is " @@ -3324,7 +3449,7 @@ msgid "" "filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +#: ../../src/topics/workflows.md:389 6584c0995288450b8a01c35fa231afb6 msgid "" "In this example we had to prepare a tar file outside, but only because our " "inner workflow was designed to take that as an input. A better refactoring " @@ -3332,7 +3457,7 @@ msgid "" "which would simplify its usage as a tool step in other workflows." msgstr "" -#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +#: ../../src/topics/workflows.md:394 19237513fd134c33801a7af08f74e70c msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL " @@ -3340,11 +3465,11 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +#: ../../src/topics/workflows.md:398 b66e0d0a36994b3182a3784bda8ffc19 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +#: ../../src/topics/workflows.md:400 3bfb9851302248568bb4535ddc87a27f msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish to " @@ -3355,7 +3480,7 @@ msgid "" "different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +#: ../../src/topics/workflows.md:411 78a5a600f8cc49ce8055c77a596ad833 msgid "" "The most common reason a new user might want to use scatter is to perform " "the same analysis on different samples. Let's start with a simple workflow " @@ -3363,23 +3488,23 @@ msgid "" "strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: ../../src/topics/workflows.md:415 f9618882e0a14a0b84ff9751346dc291 msgid "`scatter-workflow.cwl`" -msgstr "" +msgstr "`scatter-workflow.cwl`" -#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +#: ../../src/topics/workflows.md:421 4fe03daddd304a9b828fdd1c29f0d072 msgid "" "Aside from the `requirements` section including `ScatterFeatureRequirement`, " "what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +#: ../../src/topics/workflows.md:429 7ab022708a9642ab8aa2e79ea7810381 msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +#: ../../src/topics/workflows.md:441 fe144641fc8040b283f15b2b99ecb5a2 msgid "" "Here we've added a new field to the step `echo` called `scatter`. This field " "tells the runner that we'd like to scatter over this input for this " @@ -3387,7 +3512,7 @@ msgid "" "the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +#: ../../src/topics/workflows.md:445 f13d1b071a7f4a75a4cdee40ecef14fa msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if you " @@ -3395,59 +3520,59 @@ msgid "" "to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: ../../src/topics/workflows.md:450 b0b2e63d2b8a4fd0983e976c16440da4 msgid "Using the following input file:" -msgstr "" +msgstr "Usando o seguinte arquivo de entrada:" -#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +#: ../../src/topics/workflows.md:452 47ac993a90fe46ca92e97d6b67b3276b msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +#: ../../src/topics/workflows.md:458 f5b8681b3c3b4890a86d7b9fb812d958 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " "calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +#: ../../src/topics/workflows.md:466 74e70fec6d2447bbbd2a5bc8af1fa58c msgid "" "You can see that the workflow calls echo multiple times on each element of " "our `message_array`. Ok, so how about if we want to scatter over two steps " "in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +#: ../../src/topics/workflows.md:469 76fed9e7ad1d4792b7bb364bb684eeb2 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding the " "following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +#: ../../src/topics/workflows.md:472 bef387d9be1f4ca19a97023cfdd1c910 msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +#: ../../src/topics/workflows.md:480 eea1be83da574f39914566d835701b4a msgid "" "And add a second step that uses `wc` to count the characters in each file. " "See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +#: ../../src/topics/workflows.md:483 2043f12eb2ce4424b133e0dc0b62aafc msgid "`wc-tool.cwl`" -msgstr "" +msgstr "`wc-tool.cwl`" -#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +#: ../../src/topics/workflows.md:489 87ba95507fc44dbca4cb6c5283ce50f9 msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under each " "step:" msgstr "" -#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +#: ../../src/topics/workflows.md:491 e6e1a79638d74547b00c64e3c8b05710 msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +#: ../../src/topics/workflows.md:497 03fb16e74bf14c49b43e35ef6cb45030 msgid "" "Here we have placed the scatter field under each step. This is fine for this " "example since it runs quickly, but if you're running many samples for a more " @@ -3464,7 +3589,7 @@ msgid "" "welt!`. You can see how this might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +#: ../../src/topics/workflows.md:509 eca3380c60094df2b91b44b5f7718fae msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can " @@ -3472,38 +3597,38 @@ msgid "" "step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +#: ../../src/topics/workflows.md:513 6c61733fe4284f51a6b46e89cafe78c4 msgid "`scatter-nested-workflow.cwl`" -msgstr "" +msgstr "`scatter-nested-workflow.cwl`" -#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +#: ../../src/topics/workflows.md:519 0585f83162c349969391c9456a884f28 msgid "" "Now the scatter acts on a single step, but that step consists of two steps " "so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +#: ../../src/topics/workflows.md:522 f209343966db4d46b4611d3620c3b496 msgid "Conditional Workflows" -msgstr "" +msgstr "Workflows Condicionais" -#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +#: ../../src/topics/workflows.md:524 5a2661ce35dc4d79a15da1e17c0a95ec msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +#: ../../src/topics/workflows.md:527 8f7ee09c9d6b491195e2d80315dae398 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +#: ../../src/topics/workflows.md:566 966acff0d3d24104ae9673df8a790fb1 msgid "" "The first thing you'll notice is that this workflow is only compatible for " "version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +#: ../../src/topics/workflows.md:573 d60e1df759654f1b873276cf0296f234 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when` is " @@ -3511,7 +3636,7 @@ msgid "" "from the workflow contains a value `< 1` this step will be executed." msgstr "" -#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +#: ../../src/topics/workflows.md:587 69aa8d3c9d9a4fe4a62875827648d95f msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " "will pass the first conditional step and will therefore be executed and is " @@ -3519,62 +3644,62 @@ msgid "" "skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +#: ../../src/topics/workflows.md:607 fee34c880e964e08b040adf2d3831803 msgid "" "When a value of 3 is given the first conditional step will not be executed " "but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +#: ../../src/topics/workflows.md:627 cb9e82cf4b484ca7be19612b14fbdf33 msgid "" "If no conditions are met for example when using `--val 2` the workflow will " "raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +#: ../../src/topics/yaml-guide.md:1 8e7c3365f0f94038930f71666f05170f msgid "YAML Guide" -msgstr "" +msgstr "Guia de YAML" -#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +#: ../../src/topics/yaml-guide.md:6 cbe6f35c21044054a010767f2f0cae46 msgid "" "[YAML][yaml] is a file format designed to be readable by both computers and " "humans. This guide introduces the features of YAML that are relevant when " "writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +#: ../../src/topics/yaml-guide.md:13 2cc21093311548cd837aa7b3f0939093 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +#: ../../src/topics/yaml-guide.md:16 6e7ea76e8aeb477cbb8197efed33e53d msgid "Contents" -msgstr "" +msgstr "Conteúdo" -#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +#: ../../src/topics/yaml-guide.md:18 482e121a6e74428dbe6ad1f772f14684 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +#: ../../src/topics/yaml-guide.md:19 179290eee12343dd9aa4d49207cf7c68 msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +#: ../../src/topics/yaml-guide.md:20 7880db40e98e4aaabdc96def3d9f515d msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: ../../src/topics/yaml-guide.md:21 75f3b499494b445f9f9a532d178cbc10 msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: ../../src/topics/yaml-guide.md:22 2b900b2779c84de5bbd3c933c56e5922 msgid "[JSON Style](#json-style)" -msgstr "" +msgstr "[Estilo JSON](#json-style)" -#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +#: ../../src/topics/yaml-guide.md:24 189db6d0e54a400eb5615e259354827e msgid "Key-Value Pairs" -msgstr "" +msgstr "Pares de Chave-Valor" -#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +#: ../../src/topics/yaml-guide.md:26 e689c0e1dcd645348ceed51e91eb9ad0 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the `:` " @@ -3583,16 +3708,28 @@ msgid "" "meaning in the CWL specification and underscored key names otherwise. For " "example:" msgstr "" +"Em princípio, um arquivo escrito em YAML consiste de uma série de _pares de " +"chave-valor`. Cada par é escrito como `chave: valor`, onde o espaço em " +"branco entre o `:` é um requisito. Os nomes das chaves em arquivos CWL não " +"devem conter espaços em branco - [_camelCase_][camelCase] é usado para " +"valores de chaves que contém múltiplas palavras e possuem um valor especial " +"na especificação CWL, caso contrário os valores dos nomes de chaves aparecem " +"sublinhados. For exemplo:" -#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +#: ../../src/topics/yaml-guide.md:42 9532ac8e1dda479e890bf970323a0a32 msgid "" "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " "and `home` - with their four respective values. Values can be character " "strings, numeric (integer, floating point, or scientific representation), " "Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" +"O YAML acima define quatro chaves - `first_name`, `last_name`, `age_years`, " +"e `home` - com quatro valores respectivos. Os valores podem ser strings de " +"caracteres, númericos (integer, floating point, ou representação científica)" +", Boolean (`true` ou `false`), ou valores mais complexos com tipos aninhados " +"(veja abaixo)." -#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +#: ../../src/topics/yaml-guide.md:51 91a057a7d10f438fad10338dd44c013c msgid "" "Values may be wrapped in quotation marks, but be aware that this may change " "the way that they are interpreted i.e. `\"1234\"` will be treated as a " @@ -3603,28 +3740,28 @@ msgid "" "numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: ../../src/topics/yaml-guide.md:61 d18c1f5ef55d4bb6b8334438fcbc96b8 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +#: ../../src/topics/yaml-guide.md:63 dc6869049fc143b4af91d172a419a125 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program interpreting " "the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +#: ../../src/topics/yaml-guide.md:76 c3c7f5ecfedb4884ad5e91bb79ba2a7c msgid "" "If there is anything on the line before the comment, be sure to add at least " "one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +#: ../../src/topics/yaml-guide.md:79 84f16419237a4789ac0f3c682b3a11ee msgid "Maps" -msgstr "" +msgstr "Dicionários" -#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +#: ../../src/topics/yaml-guide.md:81 269ca8e05ce14e899fc8b2a00b1e458e msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, these " @@ -3635,7 +3772,7 @@ msgid "" "are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +#: ../../src/topics/yaml-guide.md:104 ce790af50da540eb9108ad89eae037cf msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3647,11 +3784,11 @@ msgid "" "graphical representation of the `inputs` object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +#: ../../src/topics/yaml-guide.md:127 c3c9ef616b5d472a894ad6330267bcd2 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +#: ../../src/topics/yaml-guide.md:129 b8a7360f6e0640aa9a2c4907c1ba3fe8 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) section " @@ -3661,25 +3798,25 @@ msgid "" "where each value is defined on its own line and preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +#: ../../src/topics/yaml-guide.md:146 363da878600a4d229efe0ba79835d73c msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +#: ../../src/topics/yaml-guide.md:167 209dfb0d0a1148ed962dbb33890a3160 msgid "JSON Style" -msgstr "" +msgstr "Estilo JSON" -#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +#: ../../src/topics/yaml-guide.md:169 cd3a174dae334d0d977a3234e258bd25 msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " "can also be defined in YAML using the native JSON syntax. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +#: ../../src/topics/yaml-guide.md:177 b0f0b10de8f54e1e951e480f696976f1 msgid "and:" -msgstr "" +msgstr "e:" -#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +#: ../../src/topics/yaml-guide.md:184 b5597e8984ad4e0bad33433c1dab89bd msgid "" "Native JSON can be useful in indicating where a field is intentionally left " "empty (such as `[]` for an empty array), as well as where it makes more " @@ -3689,50 +3826,50 @@ msgid "" "file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +#: ../../src/topics/yaml-guide.md:194 5ad7d551d3d347a097508a8488f9d15c msgid "Reference" -msgstr "" +msgstr "Referencia" -#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +#: ../../src/topics/yaml-guide.md:196 58f80e6944f9402a810b9b02ba3ad917 msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " "while we wrote this guide, though it also covers features that are not valid " "in CWL." msgstr "" -#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +#: ../../src/tutorials.md:1 8fdcc745f4684fa7816c62782507438e msgid "Tutorials" -msgstr "" +msgstr "Tutoriais" -#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +#: ../../src/tutorials.md:5 3c933ac074ee4d94b7aeacb7abeaf388 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to the " "list." msgstr "" -#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +#: ../../src/tutorials.md:7 1d6cdf13aa834cb4a682553227d9f725 msgid "Beginner Tutorials" -msgstr "" +msgstr "Tutoriais para Iniciantes" -#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +#: ../../src/tutorials.md:9 606cc939c5014e2abdab163e4d726f1b msgid "" "[Introduction to Workflows with Common Workflow Language: For Contributors.]" "(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +#: ../../src/tutorials.md:11 3505468d39c34a20bc55f431a3c697f7 msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +#: ../../src/tutorials.md:13 e5731a11b89e492d8d751100a46c5226 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +#: ../../src/tutorials.md:15 cdfeabb88f6245d9a687197d242ed3f9 msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +#: ../../src/tutorials.md:17 997679b781a84add9b6d8b1900deec35 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" From 1dea5697b67b4750629b1cc60f39a09f262a7c5d Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Tue, 2 May 2023 14:58:01 +0200 Subject: [PATCH 066/179] Translations update from Hosted Weblate (#390) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Translated using Weblate (Chinese (Simplified)) Currently translated at 68.2% (408 of 598 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 68.2% (408 of 598 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 68.2% (408 of 598 strings) Co-authored-by: Zoë Ma Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Portuguese (Brazil)) Currently translated at 23.4% (140 of 598 strings) Co-authored-by: Michael Crusoe Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/pt_BR/ Translation: Common Workflow Language/CWL User Guide --------- Co-authored-by: Zoë Ma Co-authored-by: Michael Crusoe --- locales/pt_BR/LC_MESSAGES/user_guide.po | 8 +- locales/zh_Hans/LC_MESSAGES/user_guide.po | 316 +++++++++++----------- 2 files changed, 163 insertions(+), 161 deletions(-) diff --git a/locales/pt_BR/LC_MESSAGES/user_guide.po b/locales/pt_BR/LC_MESSAGES/user_guide.po index bd7a19e6..c81087b9 100644 --- a/locales/pt_BR/LC_MESSAGES/user_guide.po +++ b/locales/pt_BR/LC_MESSAGES/user_guide.po @@ -9,8 +9,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-27 16:02+0100\n" -"PO-Revision-Date: 2023-04-03 19:41+0000\n" -"Last-Translator: ssantos \n" +"PO-Revision-Date: 2023-04-29 16:47+0000\n" +"Last-Translator: Michael Crusoe \n" "Language-Team: Portuguese (Brazil) \n" "Language: pt_BR\n" @@ -18,7 +18,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=2; plural=n > 1;\n" -"X-Generator: Weblate 4.17-dev\n" +"X-Generator: Weblate 4.18-dev\n" "Generated-By: Babel 2.10.3\n" #: ../../LICENSE.md:2 3eb955b4f3dd4c3188924b97ea6ab592 @@ -79,7 +79,7 @@ msgid "" "made. You may do so in any reasonable manner, but not in any way that " "suggests the licensor endorses you or your use." msgstr "" -"Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " +"**Atribuição**---Você deve atribuir o devido crédito (mencionando que o seu " "trabalho deriva de um trabalho que é «Copyright © The Common Workflow " "Language project», e, quando prático, criar uma ligação para https://www." "commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index c59732eb..a5d90759 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-04-26 11:48+0000\n" +"PO-Revision-Date: 2023-05-02 11:00+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified) \n" @@ -109,8 +109,8 @@ msgstr "" msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" "除非受适用法律要求或者经书面许可，据本许可协议发行的软件均为“依照其原样”发行" -"，不存在任何类型的、无论是明文还是隐含的担保或合约条款。请查阅许可协议有关本" -"许可协议下授权行为和责任免除的具体条文。" +"，不存在任何种类的、无论是明文还是隐含的担保或合约要件。请查阅许可协议中关于" +"本协议下授权许可行为和责任免除的具体条文。" #: ../../src/_includes/what-is-cwl.md:1 #: ../../src/_includes/what-is-cwl.md:2 @@ -532,7 +532,7 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:33 #: b171b72c48d44050a3416a7a42c4021d msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." -msgstr "规约所使用的版本标号模型称为“语义化版本”，请参阅本章结尾以[了解更多](#learn-" +msgstr "规约所使用的版本标号模型称为“语义型版本”，请参阅本章结尾以[了解更多](#learn-" "more)相关信息。" #: ../../src/introduction/basic-concepts.md:37 @@ -568,8 +568,9 @@ msgstr "流程和要求" #: 86e6a06992dc4228bfda7add48e28ca3 msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" msgstr "" -"流程是指接收输入并产生输出的计算单元，流程的行为可能受到输入、要求及提示的影" -"响。CWL规范{{ cwl_version }}定义的流程包括如下四种：" +"流程 (process) 是指接收输入并生成输出的计算单元，影响其行为的包括输入 " +"(input)、要求 (requirement) 及提示 (hint)。CWL 规约 {{ cwl_version }} " +"版定义了如下四种流程：" #: ../../src/introduction/basic-concepts.md:112 #: 8c9772f96caf4169924d22eb929a4f0f @@ -594,73 +595,73 @@ msgstr "工作流。" #: ../../src/introduction/basic-concepts.md:118 #: 6e352ac1f8e144c392ac5adf18c28298 msgid "The processing units available in the CWL objects model." -msgstr "CWL对象模型中可用的处理单元。" +msgstr "可用在 CWL 对象模型中的处理单元。" #: ../../src/introduction/basic-concepts.md:119 #: cf2922f645904ac7955428ecddc37b8a msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "命令行工具是 `echo`、`ls` 及 `tar` " -"等命令行实用程序的包装器。可从工作流中调用命令行工具。" +msgstr "“命令行工具”指的是 `echo`、`ls` 及 `tar` 等命令行程序的包装器 " +"(wrapper)。从工作流中可以调用命令行工具。" #: ../../src/introduction/basic-concepts.md:122 #: 5f47aae608c041aeb4134d59dad314d2 msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." msgstr "" -"表达式工具是 JavaScript 表达式的包装器，可用于简化工作流和命令行工具，" -"将工作流执行的常见部分移动到可重用的 JavaScript " -"代码中，这些代码像命令行工具一样接受输入并生成输出。" +"“表达式工具”是 JavaScript 表达式的包装器。" +"通过将工作流执行过程中的相同部分整理为可重用的 JavaScript " +"代码，像命令行工具一样接受输入并生成输出，工作流和命令行工具可以得到简化。" #: ../../src/introduction/basic-concepts.md:127 #: f6f589481d0c4891beaccb63160619ef msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." msgstr "" -"操作是一个抽象的流程，同样可接受输入并生成输出，且可用于工作流中。但是，这是" -"一种特殊的操作，并不十分常用。在本用户指南的 [操作章节](../topics/operations." -"md)中，我们对它进行了相关讨论。" +"“操作”是一种抽象的过程，它同样可接受输入、生成输出，并用于工作流中。但是，这" +"一类特殊操作并不十分常用。用户指南的 [《操作》](../topics/operations." +"md)一节将进行讨论。" #: ../../src/introduction/basic-concepts.md:131 #: 73b0c1ccb18c4b74a2c0fdf9706eca85 msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." msgstr "" -"工作流是包含步骤的流程。步骤可以是其他工作流（嵌套工作流）、命令行工具或表达" -"式工具。工作流的输入可以传送到其他任何步骤，而步骤生成的输出可用作工作流的最" -"终输出。" +"“工作流”指的是可分为步骤的流程。“步骤”可以是其他工作流（嵌套工作流），也可以" +"是命令行工具或表达式工具。工作流的输入可以传递给它的任一步骤，而其步骤生成的" +"输出可用作工作流的最终输出。" #: ../../src/introduction/basic-concepts.md:137 #: 4ace6b92f4e04a07aa202840ebe36417 msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" -msgstr "CWL规范允许实现提供额外的功能或通过 " -"*requirements*指定工作流的先决条件。CWL规范中定义了很多要求，比如：" +msgstr "CWL 规约允许其实现提供额外功能，或通过 *requirements* " +"（要求）指定工作流的先决条件。CWL 规约定义了诸种要求，如：" #: ../../src/introduction/basic-concepts.md:141 #: cc6cd8cb81564cadb8e6a4c49423b7f7 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "`InlineJavascriptWorkflow`——在表达式中启用JavaScript。" +msgstr "`InlineJavascriptWorkflow` —— 在表达式中启用 JavaScript。" #: ../../src/introduction/basic-concepts.md:142 #: 2d9f53b6ed5041dbb6c0b54835897856 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "`SubworkflowFeatureRequirement` ——启用嵌套工作流。" +msgstr "`SubworkflowFeatureRequirement` —— 启用嵌套工作流。" #: ../../src/introduction/basic-concepts.md:143 #: 907674a4ecff4826a2b880e28fc38f33 msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." -msgstr "`InitialWorkDirRequirement`——控制输入目录中的暂存文件。" +msgstr "`InitialWorkDirRequirement` —— 控制输入目录中的暂存文件。" #: ../../src/introduction/basic-concepts.md:145 #: 037cd0e5ceda482eaeaca03d51745aee msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." msgstr "" -"某些CWL运行程序可能提供规范之外的需求，比如`cwltool` 通过 " -"`cwltool:CUDARequirement` 需求来支持GPU需求，但这不属于 {{ cwl_version " -"}}版本规范的内容，可能不受其他CWL运行程序支持。" +"某些 CWL 运行程序可能提供规约之外的需求。例如 `cwltool` 提供 " +"`cwltool:CUDARequirement` 以支持GPU需求，但这不在 {{ cwl_version }} " +"版本规约之内，可能不受其他 CWL 运行程序支持。" #: ../../src/introduction/basic-concepts.md:151 #: e4643938445b48cc80eb8973ceeb126e msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" -"提示类似于需求。但是，需求列出必需功能，而提示仅列出可选功能。[需求](../" -"topics/requirements-and-hints.md)章节对需求进行了详细介绍。" +"“提示”与需求类似。其区别是，列为“需求”的功能是不可缺少的，而提示仅列出可选功" +"能。更详细介绍请见 [《需求》](../topics/requirements-and-hints.md)一章。" #: ../../src/introduction/basic-concepts.md:155 #: c4c3315c96714e81b364f8cc003b87e6 @@ -671,30 +672,32 @@ msgstr "FAIR 工作流" #: 3eb6a013a2a4478ca2ad134661f65c58 msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" -"FAIR 原则为共享和公开数字资产（尤其是数据）提供了基础。FAIR 原则强调访问计算" -"机的重要性，且所有数字资产都应是可发现、可访问、可互操及可重用的。工作流解码" -"了执行科学流程的方法，并利用该方法来创建数据。因此，工作流必须支持FAIR数据的" -"创建且始终坚持FAIR原则。—— [FAIRFAIR计算工作流](https://workflows.community/" -"groups/fair/)，工作流社区协议。" +"FAIR 为数字资源（尤其是数据）的共享和发布提供了一组基本原则。FAIR " +"四项原则强调了“机器可读”的重要性，进而提出应使所有数字资源可发现、可访问、" +"可互操作以及可重用 (Findable, Accessible, Interoperable, and Reusable)。工作" +"流通过代码所描述的，正是科学工作得以开展、数据得以创建的过程。因此，" +"应强调工作流须支持创建 FAIR 数据，遵从 FAIR 原则。—— 工作流社群行动之[FAIR " +"计算工作流](https://workflows.community/groups/fair/)。" #: ../../src/introduction/basic-concepts.md:167 #: 074af9633627470485e5225326d5f20a msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." msgstr "" -"CWL源于\"make\"，且拥有很多类似的工具，可基于任务间的依赖关系决定执行顺序。" -"但不同于\"make\"的是，CWL任务是独立的，您必须明确输入和输出。" +"CWL 滥觞于“make”一类推定任务间依赖关系，并据此决定其执行次序的工具。但与“" +"make\"的不同在于，CWL 任务是存在于独立环境中的，其输入和输出需要明确指定。" #: ../../src/introduction/basic-concepts.md:171 #: 847951c055b94a83b1e081594cef22ee msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." msgstr "" -"任务明确且独立的好处在于灵活、可移植及可拓展。使用CWL描述的工具和工作流可公开" -"透明地使用Docker等技术，并与来自不同供应商的CWL实现一起使用。" +"明确而独立，其益处在于灵活、可移植及可扩缩。CWL 所描述的工具和工作流，" +"既能无缝对接 Docker 等技术以发挥其优势，又能通用于不同供应方的 CWL " +"实现环境中。" #: ../../src/introduction/basic-concepts.md:176 #: 44bde1fae06b4678bcac4f3224601296 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "`cwltool` 也使用PROV-O标准本体来追溯数据来源。" +msgstr "同时，`cwltool` 将 PROV-O 标准本体 (standard ontology) 运用于数据来源的保证。" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 @@ -708,72 +711,73 @@ msgstr "了解更多信息" #: ../../src/introduction/basic-concepts.md:180 #: 9d5100c7d0a040aea1020bf633ad17de msgid "Semantic Versioning - " -msgstr "语义版本控制 —— " +msgstr "语义型版本 —— " #: ../../src/introduction/basic-concepts.md:181 #: 36eb4b3b966640af90faa55db3789cb6 msgid "The CWL Specification page in the CWL website: " -msgstr "在CWL网站上查阅CWL规范页面，请前往： " +msgstr "CWL网站上的规约页面： " #: ../../src/introduction/basic-concepts.md:182 #: 2ccb956baa6b4376a04ad9fcc4654631 msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" -"在Github上查阅当前版本CWL规范，请前往： {{ ''.format(cwl_version_text) }}" #: ../../src/introduction/basic-concepts.md:183 #: 72889b830c514afe9a7cb1e64b5666a0 msgid "The list of Implementations in the CWL website: " -msgstr "在CWL网站上查阅实现列表，请前往：" +msgstr "CWL 网站所列的诸种实现：" #: ../../src/introduction/basic-concepts.md:184 #: e29bd7f973544600be589c3b3f84cf63 msgid "PROV-O: The PROV Ontology - " -msgstr "PROV-O：PROV 本体——" +msgstr "PROV-O：PROV 本体 —— " #: ../../src/introduction/basic-concepts.md:185 #: c377a7f5dbe645cebbb6c7eccf831a0b msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." -msgstr "本用户指南的[操作](../topics/operations.md)章节详细介绍了CWL操作。" +msgstr "CWL 操作 (operations) 见于本《用户指南》中[《操作》](../topics/operations." +"md)一章。" #: ../../src/introduction/index.md:1 #: 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" -msgstr "介绍" +msgstr "概述" #: ../../src/introduction/index.md:3 #: 950370f0a36048b38e1bde9b78f80816 msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." -msgstr "本章节将简要介绍CWL、遵循本用户指南的先决条件及一些基本概念，这些概念有助于阅" -"读（理解）用户指南的其他内容。" +msgstr "本章节将引导您了解 CWL简介、学习本《用户指南》所需的准备，以及有利于您阅读理" +"解本《指南》的若干基本概念。" #: ../../src/introduction/prerequisites.md:1 #: f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" -msgstr "先决条件" +msgstr "学习前的准备" #: ../../src/introduction/prerequisites.md:6 #: 353b14f06ee845d0a06a829643e31534 msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." msgstr "" -"本章节所列的软件和配置是遵循本用户指南的先决条件。CWL标准通过不同的工作流运行" -"程序和平台实现。需求列表的重点在于CWL引用运行程序`cwltool`。您也可使用其他的" -"兼容CWL的运行程序或工作流系统，但结果和界面可能看上去不同（尽管精确的工作流输" -"出应该相同）。" +"学习本《用户指南》前，首先需要准备好本节所述的软件及其配置。CWL " +"标准现有多种工作流运行器和平台实现。本节列出的要求主要着眼于 CWL " +"的参考运行程序即 `cwltool`。您也可以使用与之兼容的其他 CWL 运行程序或工作流系" +"统，但运行结果和界面可能有所出入（尽管严格意义上属于工作流的输出应该相同）。" #: ../../src/introduction/prerequisites.md:12 #: b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" -msgstr "CWL实现" +msgstr "CWL 实现" #: ../../src/introduction/prerequisites.md:14 #: ff2bb4c6504b456bac7ca9c514414dbf msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." msgstr "" -"CWL标准有很多种实现形式，可能是完整的CWL运行程序，或者是工作流引擎的插件或拓" -"展程序。 [实现](basic-concepts.md#implementations)章节对此提供了更好的解释。" +"CWL 标准有多种实现，既包括完整的 CWL " +"运行程序，也有工作流引擎的插件或扩展程序。 详见[《实现》](basic-concepts." +"md#implementations)一章。" #: ../../src/introduction/prerequisites.md:19 #: cbbcce4c2a96471b8b0ae3593ad59de4 @@ -783,71 +787,71 @@ msgstr "操作系统" #: ../../src/introduction/prerequisites.md:21 #: 5089fdba8aed4113983fa86e698df98b msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" -msgstr "建议使用最新的操作系统，您可从下选项选择合适的操作系统：" +msgstr "建议使用以下任一可选系统的最新版本：" #: ../../src/introduction/prerequisites.md:24 #: dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" -msgstr "Linux操作系统" +msgstr "Linux" #: ../../src/introduction/prerequisites.md:25 #: c05187af85be41b782678b79627f8fbf msgid "macOS" -msgstr "macOS操作系统" +msgstr "macOS" #: ../../src/introduction/prerequisites.md:26 #: beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" -msgstr "Windows操作系统" +msgstr "Windows" #: ../../src/introduction/prerequisites.md:29 #: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." msgstr "" -"如您使用的是Windows操作系统，必须安装 [适用于 Linux " -"2的Windows子系统](https://learn.microsoft.com/en-us/windows/wsl/install) " -"(WSL2)。请参阅 `cwltool` [documentation](https://github.com/" -"common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) ，了" -"解更多关于安装WSL2的信息。同时，您的操作系统需要网络访问及最新版本的Python(3." -"56+)。" +"如使用 Windows 操作系统，须首先安装[适用于 Linux 的 Windows 子系统 " +"2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2)。请参阅 " +"`cwltool` [说明文件](https://github.com/common-workflow-language/cwltool/" +"blob/main/README.rst#ms-windows-users) ，了解关于安装 WSL2 " +"的细节。同时，您的操作系统还需能接入互联网，以及运行较新版本（3.6 以上）的 " +"Python." #: ../../src/introduction/prerequisites.md:35 #: 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" -msgstr "CWL运行程序" +msgstr "CWL 运行程序" #: ../../src/introduction/prerequisites.md:41 #: 0f2704bf1f7148be95e999e312899f11 msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -"要运行CWL工作流，首先需要一个CWL运行程序。`cwltool`是由CWL社区维护的Python开" -"源项目，也是CWL引用运行程序，这意味着其必须支持当前版本CWL规范{{ cwl_version " -"}}的所有规定。" +"要运行CWL工作流，首先要用到的就是 CWL 运行程序 (runner). `cwltool`作为 CWL " +"社群共同维护开发的 Python 开源项目，正是 CWL 运行程序的参考实现，也就是说，" +"它必须完整支持当前 {{ cwl_version }} 版本 CWL 规约。" #: ../../src/introduction/prerequisites.md:46 #: 86264c9e56104ecea9146407c379aae2 msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" msgstr "" -"可通过`pip`安装`cwltool` ，建议您使用`venv` 或 " -"`conda`等虚拟环境进行安装。以下命令将使用`venv`模块创建和激活Python虚拟环境，" -"并在该环境中安装 `cwltool`：" +"`cwltool` 可以用 `pip` 命令安装，而且我们推荐使用 `venv` 或 `conda` " +"等虚拟环境。以下命令将使用 `venv` 模块创建并激活一个 Python 虚拟环境，" +"并在该环境中安装 `cwltool`:" #: ../../src/introduction/prerequisites.md:51 #: 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "使用 `pip` 和 `venv`安装`cwltool`。" +msgstr "使用 `pip` 和 `venv` 安装 `cwltool`." #: ../../src/introduction/prerequisites.md:62 #: f7aaafeee230400da056464c853582c2 msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." msgstr "" -"请参阅`cwltool` [documentation](https://github.com/common-workflow-language/" -"cwltool#install)，了解使用 `apt` 和 `conda`安装`cwltool`的其他方法。" +"请参阅 `cwltool` [说明文件](https://github.com/common-workflow-language/" +"cwltool#install)查看其他安装方法，包括用 `apt` 或 `conda`." #: ../../src/introduction/prerequisites.md:65 #: 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "让我们使用`cwltool` 来执行一个简单的CWL工具描述`true.cwl`。" +msgstr "我们来用`cwltool` 处理名为 `true.cwl` 的一个简单 CWL 工具描述。" #: ../../src/introduction/prerequisites.md:67 #: 040c019b6e844eda8c8c2b210852516b @@ -858,77 +862,77 @@ msgstr "`true.cwl`" #: 6391e08e0bde49f4b21286d8fdb97433 msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" msgstr "" -"`cwltool` 命令具有验证 CWL 工具和工作流描述的选项，此选项将解析 CWL " -"文档，查找语法错误，并验证工作流描述是否符合 CWL " -"标准。但是，这些操作将在不运行文档的情况下执行。要验证 CWL " -"工作流（甚至是像上面这样的独立命令行工具描述），请将 `--validate` 选项传递给 " -"`cwltool` 命令：" +"`cwltool` 命令有一个选项可用于“确认” (validate) 也就是检验 CWL " +"工具和工作流描述。使用该选项可以进行 CWL 文件语法分析，查找语法错误，并以 " +"CWL 标准验证工作流描述的规范性。然而，进行这一系列操作并不会运行 CWL 文件。" +"要确认 CWL 工作流（包括类似前例的独立命令行工具描述），请将 `--validate` " +"选项传递给 `cwltool` 命令：" #: ../../src/introduction/prerequisites.md:79 #: cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." -msgstr "使用 `cwltool`验证 `true.cwl` 。" +msgstr "用 `cwltool` 确认（即检验）`true.cwl`." #: ../../src/introduction/prerequisites.md:84 #: d41c4bc740aa474ea09a7cbd267c8840 msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "您也可以通过省略`--validate`选项来运行CWL工具描述：" +msgstr "去掉 `--validate` 选项，才能运行 CWL 工具描述：" #: ../../src/introduction/prerequisites.md:86 #: 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." -msgstr "使用 `cwltool` 运行 `true.cwl`。" +msgstr "用 `cwltool` 运行 `true.cwl`." #: ../../src/introduction/prerequisites.md:91 #: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" -msgstr "Cwl-runner Python 模块" +msgstr "Python 模块 cwl-runner" #: ../../src/introduction/prerequisites.md:93 #: 096d0a50f69e48bd9915238d1b4264c1 msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." msgstr "" -"`cwl-runner` 是任何符合标准的CWL运行程序的别名，其与实现无关。这仅仅意味着" -"`cwl-runner` 别名命令可独立调用，且不依赖于特定CWL运行程序名。用户可调用`cwl-" -"runner` ，而无需直接调用诸如 `cwltool`的CWL运行程序。 `cwl-" -"runner`由系统管理员安装，或用户通过指定偏好CWL实现来安装， " -"这对于拥有多个CWL运行程序的环境而言十分方便。" +"`cwl-runner` 是任何符合标准的 CWL 运行程序“不分实现”的别名 (alias). 简言之" +"，`cwl-runner` 这个别名命令可独立地启用，不依赖于 CWL 运行程序的具体名称。" +"用户只需调用 `cwl-runner`, 而无需直接调用诸如 `cwltool` 这样的某个 CWL " +"运行程序。经系统管理员或用户安装后，`cwl-runner` 命令用来代指其首选的 CWL " +"实现。这样的安排更便利于多个 CWL 运行程序共存的环境。" #: ../../src/introduction/prerequisites.md:101 #: f9df974a8e2645a6918e67466bd1fdc2 msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -"CWL 社区发布了一个名为 `cwlref-runner` 的 Python 包，该软件包以 `cwl-" -"runner`作为`cwltool` 的别名" +"CWL 社群发布有名为 `cwlref-runner` 的 Python 包，以安装 `cwl-runner` 作为 " +"`cwltool` 的别名" #: ../../src/introduction/prerequisites.md:104 #: 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "使用 `pip`为cwltool安装`cwl-runner`别名。" +msgstr "用 `pip` 为 cwltool 安装别名 `cwl-runner`." #: ../../src/introduction/prerequisites.md:111 #: 746c6fc9c29d466494458a08d4c96672 msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." -msgstr "" -"现在，执行 `cwl-runner` 以调用 `cwltool`，便可验证和运行您的工作流。执行此操" -"作后，您应该得到与上一章节相同的结果和输出。" +msgstr "现在要检验或运行工作流就可以用 `cwl-runner` 这个命令了，它将为你调用 " +"`cwltool`. 其运行结果和输出应当与上一节中相同。" #: ../../src/introduction/prerequisites.md:115 #: b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "使用 `cwl-runner`验证 `true.cwl`。" +msgstr "用 `cwl-runner` 检验 `true.cwl`." #: ../../src/introduction/prerequisites.md:120 #: 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." -msgstr "使用 `cwl-runner` 运行 `true.cwl`。" +msgstr "用 `cwl-runner` 运行 `true.cwl`." #: ../../src/introduction/prerequisites.md:125 #: 705807fae182425dbf4244dbf2be1226 msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" -"执行 `cwl-runner` 的另一种方法是直接调用文件。为此，首先您需要将`true.cwl` " -"工作流复制到一个新文件中：`true_shebang.cwl`，并添加特殊的首行，即*shebang*：" +"执行 `cwl-runner` 还有一种方法，即直接调用 CWL 文件。为此，首先将 `true.cwl` " +"工作流复制为新文件 `true_shebang.cwl`, 然后加入特定的 *shebang* (即 \"hash-" +"bang\") 作为首行：" #: ../../src/introduction/prerequisites.md:129 #: f74dd9bd4ff84bf48f3f8e8c8d6fb51a @@ -938,32 +942,34 @@ msgstr "`true_shebang.cwl`" #: ../../src/introduction/prerequisites.md:135 #: 164c438baab54ec19bbb4584a10dd411 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "现在，您可使用 `chmod u+x` 执行 `true_shebang.cwl` 文件。" +msgstr "现在，用 `chmod u+x` 命令将 `true_shebang.cwl` 设为可执行。" #: ../../src/introduction/prerequisites.md:137 #: bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." -msgstr "执行 `true.cwl`文件。" +msgstr "令 `true.cwl` 可执行。" #: ../../src/introduction/prerequisites.md:144 #: 695184d1b45a42f393e2da99c3721773 msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." -msgstr "最后，您可直接在命令行执行此文件。在执行时，shebang （`cwl-runner`） " -"中指定的程序将用于执行文件的其余部分。" +msgstr "" +"到此，此 CWL 文件即可在命令行直接执行了。一旦下令执行这个文件，“shebang”" +"所指定的程序 (即 `cwl-runner`) 将实际执行其余部分。" #: ../../src/introduction/prerequisites.md:148 #: 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." -msgstr "使用 shebang 运行 `true_shebang.cwl`。" +msgstr "使用 shebang 运行 `true_shebang.cwl`." #: ../../src/introduction/prerequisites.md:154 #: 3ba23b4ea01c46848e4e43bbeff5f5a1 msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," msgstr "" -"*shebang*是以`#！`两个字符序列开头的脚本。执行脚本时，" -"操作系统将使用在shebang 之后指定的可执行文件来执行脚本。最好使用 `/usr/bin/" -"env `， 而不是硬编码位置，因为/usr/bin/env 可在系统 " -"`PATH`中寻找``程序，" +"所谓 *shebang* 是指脚本起始处的 `#!` 两个连续字符。如果脚本可执行，" +"操作系统将用紧跟在 shebang 之后写明的可执行程序来执行此脚本。一个好习惯是用 " +"`/usr/bin/env <可执行程序名>`， 而不是硬性编码其所在路径，理由是 `/usr/" +"bin/env <可执行程序名>` 进行的，是在系统 `PATH`（命令路径环境变量）" +"中查找 `<可执行程序名>` 的实际路径" #: ../../src/introduction/prerequisites.md:161 #: eec6c07455384630809ff1c532bfe7d4 @@ -974,36 +980,34 @@ msgstr "文本编辑器" #: f6b39b12bd5c495cb53e2795bf9200ed msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -"您可使用任何带有CWL " -"的文本编辑器，但对于语法高亮而言，建议使用YAML支持的编辑器。" -"流行的编辑器包括Visual Studio Code、Sublime、WebStorm、vim / " -"neovim以及Emacs。" +"任何文本编辑器都可以用于 CWL 编程。不过，我们建议使用支持显示 YAML " +"语法的编辑器。常用的编辑器包括 Visual Studio Code、Sublime、WebStorm、vim/" +"neovim 以及 Emacs 等。" #: ../../src/introduction/prerequisites.md:167 #: 2fdb62a13f9447bc89183426260ce781 msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" -msgstr "以下Visual Studio Code和WebStorm的拓展程序支持与CWL集成，且具备自定义语法高亮" -"及更好的自动补全等功能：" +msgstr "以下 Visual Studio Code 和 WebStorm 的扩展程序支持 CWL " +"集成，提供自定义语法显示、改进的自动补全等功能：" #: ../../src/introduction/prerequisites.md:171 #: 1f07135156254f74a6b043bf33d00cc3 msgid "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" -"带有 Benten (CWL) 插件的 Visual Studio Code —— " +"带 Benten (CWL) 插件的 Visual Studio Code —— " #: ../../src/introduction/prerequisites.md:172 #: de344f356b1c466d9131cdbd4d7353a3 msgid "cwl-plugin for IntelliJ - " msgstr "" -"IntelliJ支持的cwl插件 —— " +"IntelliJ 的 cwl-plugin 插件 —— " #: ../../src/introduction/prerequisites.md:174 #: 3f9324ede11441f58d93875867034cf0 msgid "The CWL community also maintains a list of editors and viewers: " -msgstr "CWL社区也在维护一个编辑器和阅读器清单：" +msgstr "CWL 社群维护的编辑器和阅览器列表：" #: ../../src/introduction/prerequisites.md:177 #: 6ce8b81560e341c580d316d69202b268 @@ -1014,33 +1018,32 @@ msgstr "Docker" #: 40cfd559d6a848d1aae354d3bdaa8e9c msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." msgstr "" -"`cwltool` 使用 Docker 运行指定软件容器的工具、工作流及工作流步骤。" -"请按照Docker 文档中的说明，为您的操作系统安装Docker：。" +"`cwltool` 使用 Docker 运行指定了软件容器的工具、工作流及工作流步骤。请按照 " +"Docker 文档在您的操作系统中安装 Docker: 。" #: ../../src/introduction/prerequisites.md:185 #: 8a9a50b0ebe847ce90593881ffe0d69c msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." msgstr "" -"您无需了解如何编写和构建 Docker 容器。在用户指南的其余部分，我们将使用现有的 " -"Docker 镜像来运行示例，并解释带容器和不带容器的执行模型之间的差异。" +"您无需掌握如何编写和构建 Docker 容器。在接下来的部分里，我们将用现成的 " +"Docker 映像来运行范例，并阐明有无容器的执行模型之间有何不同。" #: ../../src/introduction/prerequisites.md:191 #: 923cf9dd6d6c417aabe42f9fa62ffa35 msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." msgstr "" "`cwltool` 支持使用 Docker、Podman、udocker 和 Singularity " -"运行容器，您也可使用其他容器注册表来拉取镜像。" +"运行容器，并支持从非官方容器仓库拉取映像。" #: ../../src/introduction/prerequisites.md:198 #: 9390b03889de44638141d705e0ef8322 msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." -msgstr "下一章节（基本概念）中的 [实现](basic-concepts.md#implementations)主题。" +msgstr "下一节《基本概念》之[“实现”](basic-concepts.md#implementations)主题。" #: ../../src/introduction/prerequisites.md:199 #: 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " -msgstr "Python`venv`模块：" +msgstr "Python `venv` 模块：" #: ../../src/introduction/quick-start.md:1 #: cdd4196f9aa34beba115901ec97913b6 @@ -1050,21 +1053,21 @@ msgstr "快速入门" #: ../../src/introduction/quick-start.md:3 #: c43d9675ed134b78b02acb5a102a764a msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." -msgstr "本章节将向您简要介绍 CWL的定义以及您可以在哪里了解更多信息。不需要先前的 CWL " -"知识，但您必须能够熟练地按照命令行说明进行操作。" +msgstr "本节将为您概述 CWL 是什么，以及在何处可以进一步学习。您不需要有 CWL " +"知识储备，但要能较为自如地按照文中指示操作命令行。" #: ../../src/introduction/quick-start.md:7 #: 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" -msgstr "“Hello World”" +msgstr "“Hello World”（“世界您好”程序）" #: ../../src/introduction/quick-start.md:12 #: cb203354977d42a58112d09357f62565 msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" msgstr "" -"CWL 文档是[YAML](../topics/index.md) (and/or JSON)中编写的。" -"下方例子演示了一个简单的 CWL“Hello World”工作流程，并带有注释。请注意，" -"注释以 `#` 开头：" +"CWL 文件按照 [YAML](../topics/index.md) 或者 JSON 格式编写的。" +"下例演示了一个简单的 CWL 工作流“Hello World”，并且标有注释，即 `#` " +"符号后面的文字：" #: ../../src/introduction/quick-start.md:16 #: 9e51962a7e5c47248f3e20703ae101eb @@ -1075,15 +1078,16 @@ msgstr "`hello_world.cwl`" #: 7e475e3f3c4a4404bb0236124c0f7ce7 msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." msgstr "" -"上面的示例只是 `echo` 命令行工具的包装器。" -"使用默认输入值运行上述工作流将生成与命令行 `echo “Hello World”` 相同的结果。" +"上面的示例不过是 `echo` 命令行工具的包装器 (wrapper). " +"使用默认输入值运行上述工作流，产生的结果会和命令 `echo \"Hello World\"` " +"别无二致。" #: ../../src/introduction/quick-start.md:27 #: 82613ca4e32b4ccab1b7735f5ba2d5a1 msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." msgstr "" -"在 CWL 中，命令行工具和工作流之间是有区别的。但为了简单起见，我们在这里使用术" -"语“工作流”。您将在[基本概念ba](basic-concepts.md)章节了解更多有关信息。" +"CWL 中“命令行工具”和“工作流”是有所区别的。但为了简单起见，这里我们仍然用了“工" +"作流”一次。更多有关信息可在[《基本概念》](basic-concepts.md)一节中学到。" #: ../../src/introduction/quick-start.md:32 #: 498a43362a4749f3b8b433709d34a1d5 @@ -1094,58 +1098,56 @@ msgstr "安装 CWL 运行程序" #: f3e56aedd56b4b93bdc3894273e8c144 msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" msgstr "" -"`cwltool` 是 CWL 规范的实现，也是符合规范的 CWL " -"*引用程序*，且符合最新版本的规范：{{ cwl_version }}。您可使用 `pip` 安装 " -"`cwltool`：" +"`cwltool` 是 CWL 规约的一种实现，也为该规约编写的 CWL *参考运行程序*。" +"它符合规约的最新版本 {{ cwl_version }} 版。您可用 `pip` 安装 `cwltool`:" #: ../../src/introduction/quick-start.md:39 #: 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." -msgstr "使用 `pip` 安装 `cwltool`。" +msgstr "使用 `pip` 安装 `cwltool`." #: ../../src/introduction/quick-start.md:47 #: a81342e756d24c40acc15835d0a768f2 msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." msgstr "" -"如您无法使用 pip 命令安装 cwltool，请参阅[先决条件p](prerequisites.md) 章节，" -"了解安装 `cwltool` " -"的其他方法，以及了解助于遵循用户指南其余内容的软件和库详细清单。" +"如果您无法用 pip 命令安装 cwltool，请参阅[《学习前的准备》](prerequisites.md)" +" 一节，了解安装 `cwltool` " +"的其他方法，以及继续学习《用户指南》所需软件和库的详细列表。" #: ../../src/introduction/quick-start.md:51 #: c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" -msgstr "运行 “Hello World”" +msgstr "运行“Hello World”" #: ../../src/introduction/quick-start.md:53 #: 9b68bcb1a41849dc9601ab47c5bbb0fe msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" msgstr "" -"执行 `cwltool`命令行的流程大致是 `cwltool [OPTIONS] " -"[INPUTS_OBJECT]`，因此您可直接运行 `hello_world." -"cwl`工作流，无需指定以下任何选项：" +"`cwltool` 命令行程序的基本用法是 `cwltool [选项] <CWL 文件名> " +"[输入对象]`. 您可以不指定任何选项，直接运行 `hello_world.cwl` 工作流：" #: ../../src/introduction/quick-start.md:57 #: ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "使用 `cwltool` 运行 `hello_world.cwl`。" +msgstr "使用 `cwltool` 运行 `hello_world.cwl`." #: ../../src/introduction/quick-start.md:62 #: 0d8a788402914ebd8f09a5ca80650011 msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" -msgstr "或者，您可替换输入参数 `message` 的默认值，方法类似于更改 `echo` " -"基本命令的参数：" +msgstr "您还可以撤销输入参数 `message` 的默认值，有如更改 `echo` 基本命令的参数：" #: ../../src/introduction/quick-start.md:65 #: 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "使用传递输入参数的 `cwltool` 运行 `hello_world.cwl`。" +msgstr "向 `cwltool` 传递输入参数值运行 `hello_world.cwl`." #: ../../src/introduction/quick-start.md:70 #: 2ea056ab04b6419a9faf350de22a17f2 msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" msgstr "" -"将值传递给工作流输入参数的另一种方法是通过*Inputs Object* " -"实现，这是一个包含对应值输入字段的文件，可使用 JSON 或 YAML 编写。例如：" +"将值传递给工作流输入参数的另一种方法是利用*输入对象* (Inputs " +"Object)。它是由输入字段及其相应值构成的文件，可使用 JSON 或 YAML " +"格式编写。例如：" #: ../../src/introduction/quick-start.md:74 #: 1a44a545434b448aa956005deeed90a8 From ec38935808a82aead9636c9143098894d7310a19 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Sat, 6 May 2023 11:23:36 +0200 Subject: [PATCH 067/179] Translated using Weblate (Chinese (Simplified)) (#394) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Currently translated at 68.2% (408 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Zoë Ma --- locales/zh_Hans/LC_MESSAGES/user_guide.po | 104 +++++++++++----------- 1 file changed, 53 insertions(+), 51 deletions(-) diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index a5d90759..fb0fa715 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-05-02 11:00+0000\n" +"PO-Revision-Date: 2023-05-06 08:50+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified) \n" @@ -1157,88 +1157,89 @@ msgstr "`hello_world-job.json`" #: ../../src/introduction/quick-start.md:80 #: e76bfcc0c9f84bcdb3f6d5277869a88c msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" -msgstr "您现在可以使用此输入对象文件来执行“Hello World”工作流：" +msgstr "这样就可以在执行“Hello World”工作流时使用此输入对象文件：" #: ../../src/introduction/quick-start.md:82 #: d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." -msgstr "将输入对象文件传递给 `cwltool`。" +msgstr "将输入对象文件传递给 `cwltool`." #: ../../src/introduction/quick-start.md:88 #: b6d59e4b9c854abab1b3f7a0fa26f504 msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." msgstr "" -"我们为工作流和输入对象文件使用了类似的文件名。*-job.json* 后缀在输入对象文件" -"中很常见，但非必需要求，您可为工作流和输入对象文件选择任何名称。" +"我们为工作流和输入对象文件起了类似的文件名。输入对象文件名中的 *-job.json* " +"后缀是很常见的，但并非规定。工作流和输入对象文件的命名方式可由您任意选择。" #: ../../src/introduction/quick-start.md:96 #: 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" -msgstr "继续阅读本用户指南的下一章节！" +msgstr "请继续阅读《用户指南》后续部分！" #: ../../src/introduction/quick-start.md:97 #: 77e43c7117fd4c52b140f0dd52cc3963 msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "[ CWL 实现清单](https://www.commonwl.org/implementations)。" +msgstr "[ 各种 CWL 实现汇总](https://www.commonwl.org/implementations)。" #: ../../src/introduction/quick-start.md:98 #: 7282abfa7155497ca47c30f9abfb6474 msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." msgstr "" -"在Github上访问 [`common-workflow-language` 组织](https://github.com/common-" +"GitHub上的 [`common-workflow-language` 组织](https://github.com/common-" "workflow-language)。" #: ../../src/introduction/quick-start.md:99 #: 176d8d47830f4031bb95dc231ebf1303 msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -"[在Wikipedia上查阅Common Workflow Language ](https://en.wikipedia.org/wiki/" -"Common_Workflow_Language)。" +"[英文维基百科中的 Common Workflow Language 条目](https://en.wikipedia.org/" +"wiki/Common_Workflow_Language)。" #: ../../src/introduction/quick-start.md:100 #: 82a7ca3703bc4f0daa18942a1ac8943b msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -"访问[YAML.org](http://yaml.org/) 网站和[ 在Wikipedia上查阅YAML](https://en." -"wikipedia.org/wiki/YAML)." +"[YAML.org](http://yaml.org/) 网站，以及[维基百科中的 YAML 条目](https://en." +"wikipedia.org/wiki/YAML)。" #: ../../src/introduction/quick-start.md:101 #: d039a9d6461c44628d4660c00d9ce6ff msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." msgstr "" -"{{'[CWL 规范版本](https://www.commonwl.org/VERSION)'.替代('VERSION', " -"cwl_version_text) }}。" +"{{'[CWL 规约 VERSION 版](https://www.commonwl.org/VERSION)'.replace(" +"'VERSION', cwl_version_text) }}." #: ../../src/introduction/quick-start.md:102 #: fbc3383d9e1c4eaca7931c3cc4f1752b msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -"[在 Wikipedia上查阅工作流管理系统 ](https://en.wikipedia.org/wiki/" -"Workflow_management_system)。" +"[Wikipedia 条目 Workflow Management System ](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." #: ../../src/setup.md:9 #: 1330bd38c4b5495f890b98c669f81a9d msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." -msgstr "此页面已过时，保留在此以保留旧用户指南链接。此页面上的信息已迁移到新用户指南" -"的[最常见问题](/faq.md)章节。" +msgstr "此页面已过时，存留在此仅用于保留旧《用户指南》链接。此页面上的内容已迁移到新" +"《用户指南》的[《常见问题》](/faq.md)一节。" #: ../../src/topics/additional-arguments-and-parameters.md:1 #: 9c87c76c690948ac8e18088a0fffe679 msgid "Additional Arguments and Parameters" -msgstr "额外参数和指定参数" +msgstr "附加参数" #: ../../src/topics/additional-arguments-and-parameters.md:3 #: ad00d94d4fb64bbdac356e64dd3803b9 msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." -msgstr "有时工具需要额外的命令行选项，这些选项并不完全对应于输入参数。" +msgstr "有时，一些工具需要额外的命令行选项，但我们无法让它们与 (CWL) " +"输入参数一一对应。" #: ../../src/topics/additional-arguments-and-parameters.md:6 #: d8110ed19da94ad8a9f56e7006c4a2cf msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." msgstr "" -"在此示例中，我们将包装 Java 编译器，以将 java 源文件编译为类文件。 " -"默认情况下，“javac”将在与源文件相同的目录中创建类文件。 但是，CWL " -"输入文件（以及它们所在的目录）可能是只读的，因此我们需要指示 “javac” " +"本例中，我们将包装 Java 编译器，将 java 源文件编译为类 (class) 文件。 " +"默认情况下，“javac” 将在源文件所在目录中创建类文件。 然而，CWL " +"输入文件（及其所在目录）可能是只读的，因此我们需要令 “javac” " "将类文件写入指定的输出目录。" #: ../../src/topics/additional-arguments-and-parameters.md:13 @@ -1256,78 +1257,79 @@ msgstr "`arguments-job.yml`" #: ../../src/topics/additional-arguments-and-parameters.md:24 #: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "接下来，创建一个用于命令行工具的示例 Java 文件。" +msgstr "接下来，创建一个示例 Java 文件，用来让命令行工具处理它。" #: ../../src/topics/additional-arguments-and-parameters.md:30 #: 9643449da1da46d7861866dce490cbcb msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "现在，调用在命令行上提供工具描述和输入对象的 `cwltool`：" +msgstr "现在，将刚才创建的工具描述和输入对象通过命令行传递给 `cwltool` ：" #: ../../src/topics/additional-arguments-and-parameters.md:36 #: 713666580a0a4466b4ba6e3eb2b54f0a msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." -msgstr "此处我们使用`arguments`字段将一个额外的参数添加至命令行，此参数与指定输出参数" -"无关。" +msgstr "此处我们使用 `arguments` " +"字段，给命令行添加一个与任何具体输入参数都无关的附加参数。" #: ../../src/topics/additional-arguments-and-parameters.md:43 #: d50574c8b9694f83aa376d39b9a6fcd6 msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." msgstr "" -"此示例引用了运行时参数。运行时参数提供有关工具实际执行时硬件或软件环境的信息" -"。 `$(runtime.outdir)`参数是指定输出目录的路径。其他参数包括 `$(runtime." -"tmpdir)`、 `$(runtime.ram)`、`$(runtime.cores)`、 `$(runtime." -"outdirSize)`,以及`$(runtime.tmpdirSize)`。有关详细信息，请参阅 CWL 规范的 " -"[运行时环境][运行时] 章节。" +"此示例用到了运行时 (runtime) " +"参数，它们提供的是工具实际执行时的硬件或软件环境信息。 `$(runtime.outdir)` " +"参数是指定输出目录的路径。其他运行时参数还有 `$(runtime.tmpdir)`、`$(runtime." +"ram)`、`$(runtime.cores)`、`$(runtime.outdirSize)`, 以及 `$(runtime." +"tmpdirSize)` 等，详见 CWL 规约的 [Runtime " +"Environment][runtime]（运行环境）部分。" #: ../../src/topics/best-practices.md:1 #: 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" -msgstr "最佳实践" +msgstr "优良习惯" #: ../../src/topics/best-practices.md:3 #: 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." -msgstr "" -"以下提供了一些关于为工具或工作流编写通用语言描述的建议，请牢记在心。此处仅基" -"于有用性量表提供部分指导原则：虽然越多越好，但并非所有原则都是必需的。" +msgstr "本节列举一组值得留心的好习惯，推荐您在用 CWL " +"编写工具或工作流描述时参考。您只需结合实际尽量做到，无需求全。" #: ../../src/topics/best-practices.md:8 #: 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -"无用于输入名称或引用文件/目录的`type: string`参数，请根据需要使用 `type: " -"File`或`type: Directory`。" +"不要将 `type: string` 参数用于输入或引用文件、目录的名称；请根据实际情况选用 " +"`type: File` 或 `type: Directory`." #: ../../src/topics/best-practices.md:11 #: 4dee8504a8e5496081dadc386ab45540 msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." msgstr "" -"CWL 文档（结合 `Dockerfile`等外部组件）是软件代码。工作流开发人员应注意，软件" -"许可的常规规则适用于本文档。例如，如果工作流是公开共享的，则许可条款必须明确" -"，以便将来的用户了解在什么条件下可以运行工作流、修改工作流和/或将其与其他工作" -"流组合。因此，请考虑在文档中包含许可证字段。本指南的作者敦促您选择预先存在的" -"许可证，而不是尝试编写自己的许可证（请访问下方链接，了解有关选择许可证的更多" -"信息），我们建议您选择允许任何人重复使用的许可证，例如 [Apache 2.0][apache-" -"license]。" +"CWL 文件（连同 `Dockerfile` " +"等外部组件）是一种软件代码。工作流开发人员应明白的是，" +"关于软件许可的通用规则也同样适用于您编写的 CWL 文件。例如，如果您的工作流是公" +"开共享的，则许可条款一定要明确，以便将来的用户了解在什么条件下可以将它运行、" +"修改、或并入其他工作流。因此，请考虑在 CWL 文件中加入 license（许可协议）字段" +"。笔者敦促您选用现成的许可协议，不要独辟蹊径（关于挑选许可协议请参见下文链接" +"）。同时，建议您选取允许任何人重复使用的许可证，如 [Apache 2.0][apache-" +"license]." #: ../../src/topics/best-practices.md:20 #: 674c238b25e240eda05e22e399f2f78f msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." msgstr "" -"如可能，请使用相应的 [SPDX 标识符][spdx] 指定许可证。通过提供 `https://spdx." -"org/licenses/[SPDX-ID]` 形式的URL构建许可证的元数据字段，其中 `SPDX-ID` " -"取自上方链接的标识符列表。有关指导，请参阅下方的示例代码段。对于没有 SPDX " -"标识符的非标准许可证，请提供许可证的 URL。" +"请尽可能使用 [SPDX 标识符][spdx] 指定许可协议。许可协议的元数据字段由形如 " +"`https://spdx.org/licenses/[SPDX-ID]` 的 URL 构成，其中 `SPDX-ID` " +"取自前面链接提到的标识符列表，参见下例这段代码。对于没有 SPDX " +"标识符的非标准许可协议，请提供许可协议的 URL。" #: ../../src/topics/best-practices.md:26 #: b651f80f47b4442fbf29454a233697fc msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" -msgstr "有用的阅读材料：“[A Quick科学家－程序员的软件许可快速入门指南 ][sci-license]”" +msgstr "相关阅读：《[给科学界程序员的软件许可简明指南][sci-license]》" #: ../../src/topics/best-practices.md:28 #: 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "_带有SPDX识别符的许可证元数据字段示例：_" +msgstr "_用 SPDX 标识符指定许可协议的元数据字段示例：_" #: ../../src/topics/best-practices.md:37 #: 3a87a0fb2a364e3da5aaa4017e430b19 From 2f88e802c82ba462d10be83edb909da536db1766 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Tue, 9 May 2023 12:50:09 +0200 Subject: [PATCH 068/179] Translations update from Hosted Weblate (#395) * Translated using Weblate (Japanese) Currently translated at 0.6% (4 of 598 strings) Translated using Weblate (Japanese) Currently translated at 0.3% (2 of 598 strings) Added translation using Weblate (Japanese) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Added translation using Weblate (Japanese) Co-authored-by: Weblate --------- Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/sphinx.po | 27 + locales/ja/LC_MESSAGES/user_guide.po | 3125 ++++++++++++++++++++++++++ 2 files changed, 3152 insertions(+) create mode 100644 locales/ja/LC_MESSAGES/sphinx.po create mode 100644 locales/ja/LC_MESSAGES/user_guide.po diff --git a/locales/ja/LC_MESSAGES/sphinx.po b/locales/ja/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..e0513de9 --- /dev/null +++ b/locales/ja/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: ja\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "" diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..57026500 --- /dev/null +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -0,0 +1,3125 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: 2023-05-09 10:35+0000\n" +"Last-Translator: Manabu ISHII \n" +"Language-Team: Japanese \n" +"Language: ja\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=1; plural=0;\n" +"X-Generator: Weblate 4.18-dev\n" + +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "ライセンス" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "ソフトウェア" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "このページは移動しました" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "入力ファイル名を変更します" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 4dee8504a8e5496081dadc386ab45540 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 674c238b25e240eda05e22e399f2f78f +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: b651f80f47b4442fbf29454a233697fc +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: ecf2b9c0b1664afe9c4e180610610021 +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: e24cb13d98014e558b6a6946758359e0 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: 928e3df7ca3e479ca6474a8e72cf36eb +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: d355f035676446c88b028f327aeb4829 +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 339b852df24242189d6efcd2898a3396 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: 3ef57e6862f240bebcf193a52397af0a +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: fae385da16aa443da996fa23ac03d6ae +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: 92430be71ecc40e18bbbb80d5576c613 +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 387d83db81024f65aa9a890c2d07874a +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: d8e2280a75a74916a1630afaa2fe2ae3 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: f1c1340f9745458980e0fbd641738687 +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 5424e5472c3d466fa2a3d2022c6cb475 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: 12f57b2ba76b492abe1816e06bfb1417 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: e1f657a46ce94a0d83671540e2cc2dab +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a5eacdbc9aa142c890b177869da4143d +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: e3bdaceae8784ab0807b2cf356a98580 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: ed521ac365db4a6ba5a1051fbaa2932e +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 67573252cc064b27ab13eebc468ac58a +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 73e68b3af9cf41338d843c0c40e50cdc +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: a999b1acda2641598086648c64aa3831 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: f8c12a58cb0b46a488823c6ae95f25ea +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: f25a63e0926d4932bbe64b2e4bdabf9e +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: d718630a296545f3a989c8c71e9ddc77 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 9a97acd430064710bcdf76edbd9f711c +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: 48deb71f361a43e48a56ed483075bca8 +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 716b56506ca7470299899c5d820a9ea2 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: e3ecac0a8e604f2b98a2a12b0579990a +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 007a345b4bad49cf996c4301b8386473 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: efb5fd14988c4e2a8f834ee5369d4102 +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: 276f688ba7cc471a842f085ca852b1d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 8b70a1ad70514039b97164fa630c12e4 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 2f28ab412d2843ffa5f14acdc01fc732 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: cbec9277b5004e50af2728cbda0df740 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: e259f55f8000479bbd8009e25cf0ca6c +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 8210b36347a749889450529ecdf4ff0e +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 23088850ad02459696f6bbd385109aac +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: f02257a822ad46ac93c5981531cc85d5 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: d289541e460147aa933f7878996f8649 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: f495da32f05a4a5ba9539be0a54c1a59 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: bdb4c68a175047ddbe141ca24960127f +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 97b61352363f47cb890e8937c5613fa3 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: 0bc424ef2ca346099f29b937379908a0 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 29b73e1dd72744f68377f0a38c10f062 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 38a2afaf4a6c4d04909af22c93f2808d +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: cd74f34b21af4de9be96fd897efc469b +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: f12e371f3f1a4b0cb2cff9800352d48c +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 8f0e8f050e334ac08334e9215e1dcf61 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 7a6be0005a6441feb67f036d005d7885 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 06635145b441418aaae84dc804f3d6ac +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 04eaf1f7c630450db318dcd8b7626e15 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: fd4579a3c9844492b314b5c3c1775fc7 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: e024bcb70e04412e90e1838426d1b69a +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: a3db21c0b3114802a8a5b610e252ef13 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 0f5bc8520d6a4dafa37c65343da9702a +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 5cb830da47464a8b9c3950983fa4d56f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: a2ce43b391864e8bbde16328cc19b32b +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 56ee4dcfff6141d5bef80eb96559876d +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 96671c56523c4ea9992fb5dfcfa6490e +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: bcc6246742cb46bfb185e415c4a3431a +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 86dce36de687449c88fb5eb9d64eb045 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 7dc630ea86464b1dba3a4e5079260b3b +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: 651e032007ea4a119d20c820bb61f86b +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 0b056dde9e87428996e47870b12119da +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 628124a1670b4b058bb0fb6e495a099c +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: ec2adb3912bc46e28891229e9e0d9a1c +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: a519be60726a44af9941fdce04735353 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: cb8fc8c4c79e467eac5fab4ca685201e +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: a26cc105716f47cb807174c9003153b0 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: cc159dd5fe5748caac838862f5b8c4d1 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 6812698e9ad84d3385de5e88e9dde0b3 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: d1f02be278754267893dfce5a940997d +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: 75d59e395c66416cae9b352db5081516 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 874c6f19abbf45d7ab7d30a378c4048d +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: dea0d4b681f94e73b13965dcfe75cf7d +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: 750474486a84482292eeba45f118287f +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 1eb0e39bb6d04b8cab300f44a79f3add +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 4b2ab812f62c4f949dd25c8527f2411c +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 2c3b884cb1c54521900cc90782e8a58d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: a1073b6306044dffb414319ae01f68bb +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: 9a1d92334685449386dfa3b3a899ed48 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: fb623af4c480411b8fde28d01c981411 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: e98e165f6bba40809c90473d72f9d592 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 5565c1b2d8a349169a305a9b26b4574d +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: 88160cef4cfa4add9020aa89511a5749 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 730ba1434a1445ae847ec6153b6a3b72 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: a25d0b1e13324b40a6b8fcd227948c4f +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: d661df070e3040869da412d07a71f716 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: a11585474d3849cca5467512ed964743 +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 2682f9ca8e604a0c9986f7746fdec960 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 22447a560f6f4317bf67bd7c4336126c +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 52703d6b7f914097934bfad13663abeb +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 5e1c79df657d4a6e84e055dd6b300a5d +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 329d2809dfae4f90bc638f5f03a47ee3 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 9647019d8c37466886e7aab6f176634d +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: cc067051f22f433bbece08f60933e002 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: dbfe2c1123144316aa026374b0f353d3 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: 074cf5d912854d8c864607cc24b15302 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: b54240bb94f746bba7511633aa969db0 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 8b70a072aa87414c88e89a3e19af0a51 +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: eea20f89c45f424a888178df53713b28 +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7647e0229a924f988cf02b7812a55c06 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 9d663249666045618a0d3acddb85a9a9 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: dbf6153cd02542a6a01c172803122b7f +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: b6250cf6fa8a4a0c94b33302e0decca5 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: fa6ca3bbc6784380a03a950a6f49a180 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: b92b516e537a4773ad67b4af586e7a25 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: 467a701228504d06b971b79a59c69064 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: 2634f989eb304009a8568d70ed42786c +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: fbe0c65b444441f785d0054176d036a6 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 9a710602e00c4934ae3a3b471aa68458 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: 21b5be7270a14f0987240c81d1ec879b +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: cfe9d8241fe84bd5b74042a5625d933f +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 764d933cc4da446abd8dd8f913f05dac +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: c93efc6d4e004859981ee7f5fa28ed03 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: 546601da44cb49bd9611b1c85807fd90 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: e07f33d01b804663a25ffb08aad74821 +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: 7a644506619a4f08958ec7d4540cd557 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: b5195b7d8eaa419fb2b90cb33a57783a +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: 2713594c937d4c528fc8d04d9e9819ed +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: cf94c1424fc2413c85647fd1ee73d951 +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: dc0452107c604e29bdf32bb289fe5db8 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 483181f498fc4d968b5fe6ef427709f7 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 7487485d6aa4458089a4b4bdf107ea64 +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 93188ed43ee949cc98b3ea679ce14feb +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 24aca0bea4d94e3593b844cf0586cffe +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 9c56528acd5f49deb139e034dfbfac7c +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: a2dd833fdca4443181648e41051a5232 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: 7e40cc9f9e1341c195e843c009575b94 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: def35d6021394def80a53ae49a2cdbde +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: c84d4450bc6a475dbf34e0b22cea9130 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: cca9665f6daa44b49233baf34ab9fcc7 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: 547edbf5fa424b8286cc21674ff159b0 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 7ca248888b9d484cb544cd76ba538662 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: ae6b240718104380b08db5552d7355ea +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: e5a8b7f84be64020b191099f3fad30ed +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 12a06d8358534102b202965d4258c18e +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: b7f93705e5b8416696be01850072e8c0 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: e87045829b344089ab59dc27063ddd7a +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: 42ef2f145b824d69b63abc1da175c216 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: c61cedf543664d388183e04b3939cc39 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: 9e39e3f1501c4fcaab3e8962e090f6be +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: 03e2f767c4da461982fc3c0f3ba94762 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 3bea5822b8694e2aa32c446e1c54a045 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: 0d498cd4caf54c15891ca1afe58e2727 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: b2d75045e02741b4850f5ff1243f7858 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: 5fa79c62049a447c8328ebf9db54ebf4 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: d947c54933d64aad90df392a1cedd63f +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 651d35997332404186aa6d5711da4a3d +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: b662c1a5a4424c8d8350a806356acc61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 04d6babfd87343d7a5f13867ea02b65f +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 2eaacf1a90204a2b9bd621344560f2a1 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: e3a7182f00f440b8b5461da91194a64b +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: b5338f39e8c74ff28e139da68089a742 +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: f6d92156d67c4a339bcfd194cff897df +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: d80ab383eec9402faba997b548fe42eb +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: 49217c02f58c43ff9ec00f10da8d4e84 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 8dbd56473f8c40c0bb12a48be06117e3 +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 78d7f3ede2c746d482042adef050b2c4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: cbbf93c70fe04ba7932ba25758ddc611 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: cfa1c1fde4454df283f87cc54a9c59ec +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 1a8be2950cbb475bbb2617e005f0fac9 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: 5d83c56102e141cc978500f678dd0c1c +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: cda73485875d4c8e9464679a20558616 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 98cae24919b74c088a5d89706aec581b +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: b4b0940b4b5743c09637b36b964202d0 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 9ca3554d771d45998e88aaede525b227 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 3fca839cede94cfd8e4f605c73ba699d +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: 3ded0f125249485c921994b6e6b93ac9 +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 53ece35d309a4c8d99f1efb2122a7092 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 87bafb845c714b109874f6137b84462d +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: fcd05b1ef31a4046946a2399c7fc5575 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: 859368c1f25c4a4aad57abfd046c63f5 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" From 499d120c2d16bd41e358ec03a8ed95832a18bff1 Mon Sep 17 00:00:00 2001 From: "Bruno P. Kinoshita" Date: Tue, 30 May 2023 16:46:13 +0200 Subject: [PATCH 069/179] Replace "a" by "an" (#398) --- src/topics/inputs.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/topics/inputs.md b/src/topics/inputs.md index 646098f5..88b8ea72 100644 --- a/src/topics/inputs.md +++ b/src/topics/inputs.md @@ -31,7 +31,7 @@ Create a file called `inp-job.yml`: ````{note} You can use `cwltool` to create a template input object. That saves you from having -to type all the input parameters in a input object file: +to type all the input parameters in an input object file: ```{runcmd} cwltool --make-template inp.cwl :working-directory: src/_includes/cwl/inputs From 7e53fe40e34747a4ce843e6424d657f0c33d8c82 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Tue, 27 Jun 2023 07:54:16 +0200 Subject: [PATCH 070/179] Translated using Weblate (Chinese (Simplified)) (#399) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Currently translated at 75.5% (452 of 598 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 75.4% (451 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Zoë Ma --- locales/zh_Hans/LC_MESSAGES/user_guide.po | 555 +++++++++++----------- 1 file changed, 286 insertions(+), 269 deletions(-) diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index fb0fa715..0dca075e 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-05-06 08:50+0000\n" +"PO-Revision-Date: 2023-06-27 04:50+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified) \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 4.18-dev\n" +"X-Generator: Weblate 4.18.1\n" #: ../../LICENSE.md:2 #: 4e203044f0464fd5a3256430391dde12 @@ -325,7 +325,7 @@ msgstr "记录输入 📀" #: 52b8538177c64090af51f5f6a696c28c msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." msgstr "" -"如果部分命令行标志之间存在 ** 互斥 ** 或 ** 依赖 ** 的关系，" +"如果部分命令行标志之间存在 **互斥** 或 **依赖** 的关系，" "可以为其定义专门的记录类型 (record type)。此处也可以指定 null 创建可选输入。" #: ../../src/faq.md:322 @@ -683,8 +683,8 @@ msgstr "" #: 074af9633627470485e5225326d5f20a msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." msgstr "" -"CWL 滥觞于“make”一类推定任务间依赖关系，并据此决定其执行次序的工具。但与“" -"make\"的不同在于，CWL 任务是存在于独立环境中的，其输入和输出需要明确指定。" +"CWL 滥觞于“make”一类推定任务间依赖关系，并据此决定其执行次序的工具。但与“make" +"”的不同在于，CWL 任务是存在于独立环境中的，其输入和输出需要明确指定。" #: ../../src/introduction/basic-concepts.md:171 #: 847951c055b94a83b1e081594cef22ee @@ -1335,110 +1335,118 @@ msgstr "_用 SPDX 标识符指定许可协议的元数据字段示例：_" #: 3a87a0fb2a364e3da5aaa4017e430b19 msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." msgstr "" -"有关在CWL描述中提供更多元数据的示例，请查阅[本用户指南中的元数据和作者授权章" -"节](../topics/metadata-and-authorship.md)。" +"关于在 CWL " +"描述中提供元数据的更多示例，请参见[《用户指南》的“元数据和著作权”一节](../" +"topics/metadata-and-authorship.md)。" #: ../../src/topics/best-practices.md:40 #: ecf2b9c0b1664afe9c4e180610610021 msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." -msgstr "包括CWL工具或工作流描述作者的 " -"[归属信息][许可证示例]。请使用明确的标识符，比如[ORCID][orcid]。" +msgstr "" +"为 CWL 工具或工作流描述的作者添加[署名信息][license-" +"example]。请使用明确、独一无二的标识符，如[ORCID][orcid]." #: ../../src/topics/best-practices.md:44 #: e24cb13d98014e558b6a6946758359e0 msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." -msgstr "在工具需求中，使用 `SoftwareRequirement`下方的短命名列出依赖关系。" +msgstr "在工具描述中，将所依赖的软件在 `SoftwareRequirement` 下以简短的名称列出。" #: ../../src/topics/best-practices.md:47 #: f2b14a92374e449d9fb1e8c86ae0dd61 msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -"包括表示依赖关系的[SciCrunch][scicrunch]识别符，其格式为`https://identifiers." -"org/rrid/RRID:SCR_NNNNNN`。" +"为依赖关系添加 [SciCrunch][scicrunch] 标识符。其格式形如 `https://identifiers" +".org/rrid/RRID:SCR_NNNNNN`." #: ../../src/topics/best-practices.md:50 #: 928e3df7ca3e479ca6474a8e72cf36eb msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -"所有`输入` 和`输出` " -"的标识符均应反映其概念特性，请使用`unaligned_sequences`、`reference_genome`、" -" `phylogeny`、或 `aligned_sequences` 等信息性名称，而不是`foo_input`、`foo_fi" -"le`、`result`、`input`及`output`等非信息性名称。" +"一切 `input`（输入）和 `output`（输出）标识符均应体现其概念上的特质。" +"请使用类似 `unaligned_sequences`、`reference_genome`、 `phylogeny`、或 " +"`aligned_sequences` 这样望文知义的变量名，而非 " +"`foo_input`、`foo_file`、`result`、`input`、`output` 等缺乏明确内涵的名称。" #: ../../src/topics/best-practices.md:55 #: d355f035676446c88b028f327aeb4829 msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." -msgstr "在工具描述中， `SoftwareRequirement` 下方包含已知可使用此描述的工具版本列表。" +msgstr "在工具描述中 `SoftwareRequirement` 下，请列出已知能与该描述兼容的工具版本。" #: ../../src/topics/best-practices.md:58 #: 339b852df24242189d6efcd2898a3396 msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." msgstr "" -"应为所有输入和输出 `文件` 指定`格式` 。生物信息学工具应使用来自 [EDAM][edam-" -"example] 的格式标识符。另请参阅 `iana:text/plain`、`iana:text/tab-separated-" -"values` 和 `$namespaces: { iana: \"https://www.iana.org/assignments/" -"media-types/\" }。[完整的 IANA 媒体列表][iana类型] (（也称为 MIME 类型）。对" -"于非生物信息学工具，请以相同的方式使用或创建适当的本体/受控词汇表。请编辑此页" -"面，让告知我们。" +"所有输入和输出 `File`（文件）都需要指明 `format`（格式）。" +"生物信息学工具应使用来自 [EDAM][edam-example] 的格式标识符。另请参考 `iana:" +"text/plain`、`iana:text/tab-separated-values` 等在 `$namespaces: { iana: " +"\"https://www.iana.org/assignments/media-types//" } 下使用的格式名，以及[" +"IANA 媒体类型][iana-types]（又称 MIME " +"类型）的完整列表。对于非生物信息学工具，请同样运用或创建合适的本体或受控词表 " +"(controlled vocabulary). 如果您对此有经验，请编辑此页面，以告知我们。" #: ../../src/topics/best-practices.md:66 #: 3ef57e6862f240bebcf193a52397af0a msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." -msgstr "将所有以流式兼容方式读取或编写的输入和输出 `文件`（仅一次，无随机访问）" -"标记为 `流式传输：true`。" +msgstr "将所有能作为流读写（即单次、非随机访问）的输入和输出 `File`（文件）标记为 " +"`streamable: true`." #: ../../src/topics/best-practices.md:69 #: f1a7c4f896a04a80b0c5f6a1db61ff8c msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." msgstr "" -"每个 `CommandLineTool` 描述应仅关注单个操作，即使 （子） " -"命令能够执行更多操作。请勿选择非必需或不使用的选项，以免工作描述过于复杂。" +"即使某个命令或其子命令能够执行更多操作，每个 `CommandLineTool`（命令行工具）" +"描述也应侧重于单个操作。请勿添加非必需或用不到的选项，以免工作描述过于复杂。" #: ../../src/topics/best-practices.md:73 #: 1ac4c3d8c3e44bd1af3fc5df70051926 msgid "Custom types should be defined with one external YAML per type definition for re-use." -msgstr "为了方便重复使用，每个类型定义都应使用一个外部 YAML 来定义自定义的类型。" +msgstr "关于自定义类型，每个外部 YAML 文件应与单个类型定义一一对应，以便重复使用。" #: ../../src/topics/best-practices.md:76 #: c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "包括总结工具/工作流的顶级短 ` 标签 `。" +msgstr "请使用位于顶级的简短 `label`（标签）对工具或工作流加以概括。" #: ../../src/topics/best-practices.md:78 #: fae385da16aa443da996fa23ac03d6ae msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." -msgstr "如有需要，也可增加一个顶级`doc`。相比顶级 " -"`label`（见上方），此标签应长度更长且内容更详细。" +msgstr "在用得到的时候，还应添加顶级 `doc`. 相比上述顶级 `label`, " +"此处应提供更长、更详细的描述。" #: ../../src/topics/best-practices.md:82 #: 92430be71ecc40e18bbbb80d5576c613 msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." -msgstr "对于带有固定有效值列表的元素，请使用 `type： enum` ，而不是 `type： string`。" +msgstr "对于有效取值为若干固定值的元素，应使用 `type: enum` 而非 `type: string`." #: ../../src/topics/best-practices.md:85 #: 387d83db81024f65aa9a890c2d07874a msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." msgstr "" -"评估所有 JavaScript 的使用，以了解可能的消除或替代情况。一个常见示例：操作 `" -"文件 ` 名称和路径？考虑是否可使用 [内置 `文件` 属性][file-" -"prop]中的其中一种（如`basename`、`nameroot`和`nameext`等）来替代。" +"所有用到 JavaScript " +"之处都应进行评估，考虑是否能将它去除或替代。经常遇到的一例，是处理 `File` " +"（文件）名称和路径。这时应考虑是否能用 [`File` 的内置属性][file-" +"prop]（如`basename`、`nameroot` 和 `nameext` 等）取代 JavaScript." #: ../../src/topics/best-practices.md:90 #: d8e2280a75a74916a1630afaa2fe2ae3 msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." -msgstr "邀请同事（最好来自其他公司）对工作描述进行测试并提供反馈。" +msgstr "写好工具描述后， 把它交给同行（最好来自其他机构）进行测试并获取反馈。" #: ../../src/topics/best-practices.md:93 #: f1c1340f9745458980e0fbd641738687 msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." msgstr "" -"具有可抽象的单个组件的复杂工作流应利用 [`SubworkflowFeatureRequirement`][子工" -"作流]使其工作流模块化，并允许轻松重用工作流的各个部分。" +"若复杂的工作流中包含可以抽象出来的单独组件，应利用 " +"[`SubworkflowFeatureRequirement`][subworkflow] " +"将工作流模块化，以便重复使用其组成部分。" #: ../../src/topics/best-practices.md:97 #: 5424e5472c3d466fa2a3d2022c6cb475 msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." -msgstr "软件容器应符合[“生物信息学软件封装和容器化建议”][容器] （其他学科也适用）。" +msgstr "" +"应使软件容器 (container) 符合 [Recommendations for the packaging and " +"containerizing of bioinformatics software][containers]（《生物信息学软件封装" +"与容器化建议》）一文提出的标准。该文对其他学科也有参考价值。" #: ../../src/topics/command-line-tool.md:1 #: 3f4e98f6bfa141feba8c4b120e3d03e8 @@ -1449,22 +1457,21 @@ msgstr "命令行工具" #: 12f57b2ba76b492abe1816e06bfb1417 msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." msgstr "" -"命令行工具是一种流程对象，可以单独运行或作为工作流步骤运行，它是 " -"`ls`、`echo`、`tar` 等命令的包装器。命令行工具 CWL " -"文档的`baseCommand`属性对命令行工具进行了定义。" +"命令行工具是可以单独运行或作为工作流步骤运行的一类流程 (process) 对象。" +"它是诸如 `ls`、`echo`、`tar` 等命令的包装器，由相应的 CWL 文件中 " +"`baseCommand` 这一属性定义。" #: ../../src/topics/command-line-tool.md:8 #: e1f657a46ce94a0d83671540e2cc2dab -#, fuzzy msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." msgstr "" -"CWL 命令行工具还必具有 ` 输入 ` 和 ` 输出 `。以下示例包含一个最小示例，演示了" -"支持`echo`Linux命令的CWL命令行工具如何使用输入和输出。" +"CWL 命令行工具还必具有 `inputs`（输入）和 `outputs`（输出）。以下是一个 CWL " +"命令行工具的极简示例，用 Linux 下的 `echo` 命令演示输入和输出。" #: ../../src/topics/command-line-tool.md:19 #: abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." -msgstr "CWL命令行工具。" +msgstr "CWL 命令行工具。" #: ../../src/topics/command-line-tool.md:50 #: 3b1a9ae3412f4d6e96a39b9a16934232 @@ -1475,24 +1482,25 @@ msgstr "`echo.cwl`" #: a5eacdbc9aa142c890b177869da4143d msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." msgstr "" -"上方示例仅使用简化形式来定义输入和输出。了解更多有关信息，请查阅[输入](../" -"topics/inputs.md) 和 [输出](../topics/outputs.md) 章节。" +"上例以简化的形式定义了输入和输出。在[《输入》](../topics/inputs." +"md)和[《输出》](../topics/outputs.md) 章节中，您将进一步学习。" #: ../../src/topics/command-line-tool.md:68 #: 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" -msgstr "网络访问" +msgstr "网络访问 (Network Access)" #: ../../src/topics/command-line-tool.md:69 #: e3bdaceae8784ab0807b2cf356a98580 msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." -msgstr "这指示进程是否需要传出 IPv4/IPv6 网络访问。如果在 CWL v1.1+ " -"中手动编写命令行工具，则需指定何时需要网络访问。" +msgstr "" +"这指的是流程是否需要发起 IPv4/IPv6 网络访问。如果命令行工具是基于 CWL v1.1+ " +"版本新编写的，则有必要明文指定何时需要访问网络。" #: ../../src/topics/command-line-tool.md:83 #: ed521ac365db4a6ba5a1051fbaa2932e msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." -msgstr "升级到至版本1.1或 1.2的 CWL v1.0 命令行工具将自动获取网络访问权限。" +msgstr "从 CWL v1.0 版本升级到 1.1 或 1.2 版的命令行工具将自动获取网络访问权限。" #: ../../src/topics/creating-files-at-runtime.md:1 #: a2a0f0eb0f404eb3aaf19cfd3cdb559b @@ -1502,13 +1510,14 @@ msgstr "在运行时创建文件" #: ../../src/topics/creating-files-at-runtime.md:3 #: 0cf51b6da6884065ae42032abc20eb0d msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." -msgstr "有时，您需要从输入参数动态创建文件，例如需要可从文件（而不是命令行参数）中读" -"取输入配置的工具，或者需要一个小型包装器的 shell 脚本。" +msgstr "" +"有些情况下，您需要根据输入参数动态创建文件。例如有的工具需要通过文件（而非命" +"令行参数）读取输入配置，还有的需要小型 shell 脚本作为包装器 (wrapper)." #: ../../src/topics/creating-files-at-runtime.md:7 #: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "要生成此类文件，我们可使用 `InitialWorkDirRequirements`。" +msgstr "要生成此类文件，我们可以使用 `InitialWorkDirRequirements`." #: ../../src/topics/creating-files-at-runtime.md:9 #: d3f74c3b094a427fbec831afab657d50 @@ -1519,23 +1528,22 @@ msgstr "`createfile.cwl`" #: cfffc518ba6e4ed1a80762ed6f7d25df msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." msgstr "" -"在创建文件之前，CWL引擎将拓展所有诸如 `$(inputs.message)`的 [表达式](../" -"topics/expressions.md)。此处，应在输入`消息`中插入值。" +"在创建文件之前，CWL引擎将扩展所有形如 `$(inputs.message)` 的[表达式](../" +"topics/expressions.md)。此处将插入输入项`message` 实际的值。" #: ../../src/topics/creating-files-at-runtime.md:20 #: 9454a330b9324744b89448f2694b1b03 -#, fuzzy msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." msgstr "" -"_CWL 表达式 _ 独立于稍后在命令行工具调用期间使用的所有 _shell 变量 _，" -"这意味着字符 `$` 的所有真实需要必须** 删除 ** `\\` 。例如，上面的 `\\" -"${PREFIX}` 在生成的文件中扩展为 `${PREFIX}`，以供 shell 脚本（而不是 CWL " -"引擎）评估。" +"_CWL 表达式 _ 与后期在命令行工具调用时用到的任何 _shell 变量 _ " +"是相互独立的。这意味着，所有（后期）实际用到字符 `$` 的地方必须由 `\\` " +"（斜线）字符加以** 转义 **。例如，上例中的 `\\${PREFIX}` " +"在生成的文件中扩展为 `${PREFIX}`，以供 shell 脚本（而非 CWL 引擎）计算其值。" #: ../../src/topics/creating-files-at-runtime.md:27 #: 7f8d99a30b644457a62ac1523d0c72aa msgid "To test the above CWL tool, use this job to provide the input value `message`:" -msgstr "若要测试上述 CWL 工具，请使用此作业提供输入值 `消息`：" +msgstr "测试上述 CWL 工具时，请使用此作业提供输入项 `message` 的值：" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 @@ -1544,31 +1552,30 @@ msgstr "若要测试上述 CWL 工具，请使用此作业提供输入值 `消 #: 2699fbc4376148af91b7a5a6cdac467c #: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" -msgstr "" +msgstr "`echo-job.yml`" #: ../../src/topics/creating-files-at-runtime.md:35 #: 10d1373bb14a4a3cacd3b92a2f83382d msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." msgstr "" -"在运行此步骤之前，让我们详细地看一下每个步骤。基本命令 `baseCommand： [“sh”，" -" “example.sh”]` 将执行命令 `sh example.sh`，此步骤将运行我们在 shell " -"中创建的文件。" +"运行前，我们来细看一下每个步骤。基础命令 `baseCommand: [\"sh\", \"example." +"sh\"]` 将执行的命令是 `sh example.sh`. 这将在 shell 中运行我们创建的文件。" #: ../../src/topics/creating-files-at-runtime.md:40 #: 70e257091bdb456e8957f90a8fa90e8c msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." msgstr "" -"`InitialWorkDirRequirements` 需要 `列表 `。由于 `列表` 是一个 YAML 数组，" -"我们需要在数组每个元素的首行添加一个 " -"`-`，而在本示例中我们只有一个元素。`entryname:` 可以具有任何值，但它必须与 " -"`baseCommand` 中指定的值相匹配。最后一个步骤是 `entry：`，后面跟着 `|-`，" -"这是 YAML 引用语法，意味着正在使用多行字符串（没有它，我们则需要在一行上编写" -"整个脚本）。" +"`InitialWorkDirRequirements` 需要一个 `listing`。由于 `listing` 是个 YAML " +"数组，我们需要在数组每个元素的首行添加一个 `-` " +"字符，不过本示例中只有一个元素。`entryname:` 可以取任何值，但它必须与 " +"`baseCommand` 中指定的值相匹配。最后的部分是 `entry:`，后面跟着 `|-`，这是 " +"YAML 中表示引用的语法，意味着此处使用的是多行字符串（要是没有它，我们就得将整" +"个脚本写在同一行之内）。" #: ../../src/topics/creating-files-at-runtime.md:51 #: 1741804e33aa43ce88b4320c11ae5973 msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." -msgstr "参阅 [YAML指南 ](../topics/yaml-guide.md#maps) ，了解更多有关格式的信息。" +msgstr "请参阅[《YAML 指南》 ](../topics/yaml-guide.md#maps) ，进一步了解代码格式。" #: ../../src/topics/creating-files-at-runtime.md:54 #: ../../src/topics/environment-variables.md:18 @@ -1581,7 +1588,7 @@ msgstr "参阅 [YAML指南 ](../topics/yaml-guide.md#maps) ，了解更多有关 #: d6255506eebe44be94c5ce703c44a513 #: 7bbd2d738fc54649aeb10f8d2bc38b6f msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "现在，通过命令行上的工具描述和输入对象调用 `cwltool`：" +msgstr "现在，在命令行上以工具描述和输入对象为参数调用 `cwltool`:" #: ../../src/topics/custom-types.md:1 #: cb34fd4c8cb04053ada491a227651048 @@ -1592,75 +1599,74 @@ msgstr "自定义类型" #: 67573252cc064b27ab13eebc468ac58a msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." msgstr "" -"有时您可能希望编写自己的自定义类型，以便在 CWL 描述中使用和重用。使用此类自定" -"义类型可以减少全部使用相同类型的多个描述之间的冗余工作，并且还允许对工具/分析" -"进行额外的自定义/配置，而无需直接修改 CWL 描述。" +"有时您可能希望自己编写自定义的类型，以便用于 CWL 描述中并重复利用。在多个描述" +"用到相同类型的情况下，使用这样的自定义类型可以删繁就简，还可以让我们对工具或" +"分析进行额外的自定义和配置，而无需直接在 CWL 描述上做手脚。" #: ../../src/topics/custom-types.md:9 #: 73e68b3af9cf41338d843c0c40e50cdc msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." -msgstr "下方示例为 [biom 转换格式][biom] 工具的 CWL 描述，该工具可将标准 biom " -"表格文件转换为 hdf5 格式。" +msgstr "下例用 CWL 描述了一个 [biom 转换格式][biom]工具，用于将标准 biom " +"表文件转换为 hdf5 格式。" #: ../../src/topics/custom-types.md:12 #: ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" -msgstr "" +msgstr "`custom-types.cwl`" #: ../../src/topics/custom-types.md:18 #: 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" -msgstr "" +msgstr "`custom-types.yml`" #: ../../src/topics/custom-types.md:24 #: a999b1acda2641598086648c64aa3831 msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" -"___注意：___要访问下方示例，您需要 [下载示例输入文件](https://github.com/" +"___注意：___ 按照下例演练前，您需要先[下载示例输入文件](https://github.com/" "common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/" -"rich_sparse_otu_table.biom)， *rich_sparse_otu_table.biom* 比如通过 `wget`：" +"rich_sparse_otu_table.biom) *rich_sparse_otu_table.biom*. 例如，使用 `wget`:" #: ../../src/topics/custom-types.md:30 #: f8c12a58cb0b46a488823c6ae95f25ea msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" -msgstr "在29行的`inputs:table_type`中，可用于表格转换的表选项列表以自定义对象形式导入" -"：" +msgstr "在文件第 29 行，`inputs:table_type` " +"项目中，允许用于数据表转换的选项列表以自定义对象的形式导入：" #: ../../src/topics/custom-types.md:46 #: f25a63e0926d4932bbe64b2e4bdabf9e msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." msgstr "" -"自定义类型的引用是采用定义对象的文件名（`biom-convert-table.yaml` " -"）和该文件中定义自定义类型的对象名（`table_type` ）的组合。在本示例中，导入的" -"`biom-convert-table.yaml` 文件中的`符号` 数组定义了允许的表选项。例如，在 " -"`custom-types.yml` ，我们把`OTU表` " -"作为一个`输入`进行传递，告诉工具创建一个hdf5格式的OTU表。" +"对自定义类型的引用由两部分构成：对象定义所在的文件名（`biom-convert-table." +"yaml` ），和该文件中定义该类型的对象名（`table_type` ）。这里，导入的 `biom-" +"convert-table.yaml` 文件中的 `symbols` 数组定义了允许的表选项。例如，在 " +"`custom-types.yml` 中，我们把 `OTU table` 作为一个 `input`（输入）传入，" +"令工具创建一个 hdf5 格式的 OTU 表。" #: ../../src/topics/custom-types.md:53 #: b0a4df0fd3ca42338cff4689235dcf4e msgid "The contents of the YAML file describing the custom type are given below:" -msgstr "描述自定义类型的 YAML 文件的内容如下所示：" +msgstr "描述自定义类型的 YAML 文件内容如下：" #: ../../src/topics/custom-types.md:55 #: fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" -msgstr "" +msgstr "`biom-convert-table.yaml`" #: ../../src/topics/custom-types.md:61 #: d718630a296545f3a989c8c71e9ddc77 msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" msgstr "" -"为了在 CWL 描述中使用自定义类型，必须导入该类型。 " -"`requirements：SchemaDefRequirements` 对导入进行了描述，如下方示例 `custom-" -"types.cwl` 的描述所示：" +"为了在 CWL 描述中使用自定义类型，必须首先导入。 关于导入的描述位于 " +"`requirements:SchemaDefRequirement` 项，如下例 `custom-types.cwl` 所示：" #: ../../src/topics/custom-types.md:76 #: 9a97acd430064710bcdf76edbd9f711c msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." msgstr "" -"另请注意，此 CWL 描述的作者还增添了 `ResourceRequirement`，其指定了工具成功运" -"行所需的最小内存量和内核数、编写描述的软件版本的详细信息以及其他有用的元数据" -"。这些功能将在本用户指南的其他章节中进一步讨论。" +"另请注意，作者还在此 CWL 描述中加入了 `ResourceRequirement`, 指定了工具正常运" +"行所需的最低内存容量和内核数、该描述针对的软件具体版本、以及其他有用的元数据" +"。这些功能将在《用户指南》其他章节中进一步讨论。" #: ../../src/topics/environment-variables.md:1 #: 59014808cbef4c02aaef03129d8a29b0 @@ -1670,13 +1676,13 @@ msgstr "环境变量" #: ../../src/topics/environment-variables.md:3 #: 3c821c9c46d841ec89b8a5b1018f3af8 msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." -msgstr "工具在受限环境中运行，不会从父进程继承大多数环境变量。 您可以使用 " +msgstr "CWL 工具运行于受限环境中，大多数环境变量都不会从父进程继承。 您可以使用 " "`EnvVarRequirements` 为该工具设置环境变量。" #: ../../src/topics/environment-variables.md:7 #: bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" -msgstr "" +msgstr "`env.cwl`" #: ../../src/topics/expression-tool.md:1 #: 777d4a52f7554eff84db2df6d4d0f729 @@ -1687,15 +1693,17 @@ msgstr "表达式工具" #: 48deb71f361a43e48a56ed483075bca8 msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." msgstr "" -"表达式工具是一种流程类型，可单独运行，或作为工作流的一个步骤运行。" -"其执行一个纯 JavaScript 表达式，旨在隔离复杂的 JavaScript " -"表达式，这些表达式需要对输入数据进行操作并产生一些结果作为输出。" +"表达式工具是一种类型的流程 (process), " +"可单独运行，或作为工作流的一个步骤运行。它执行纯 JavaScript 表达式，" +"意在隔离复杂的 JavaScript 表达式，以对输入数据进行运算，并生成结果作为输出。" #: ../../src/topics/expression-tool.md:8 #: 716b56506ca7470299899c5d820a9ea2 msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." -msgstr "与命令行工具类似，其需要 ` 输入 ` 和 ` 输出 `，但需要的是`表达式 ` 属性，" -"而不是 `baseCommand`。" +msgstr "" +"与命令行工具一样，它需要 `inputs`（输入）和 " +"`outputs`（输出），但与之不同的是，它需要的是 `expression` 属性，而非 " +"`baseCommand`." #: ../../src/topics/expression-tool.md:17 #: b63e6f5a2e89431c8fc7d04f47fd69fe @@ -1705,15 +1713,15 @@ msgstr "CWL 表达式工具。" #: ../../src/topics/expression-tool.md:48 #: 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" -msgstr "" +msgstr "`uppercase.cwl`" #: ../../src/topics/expression-tool.md:67 #: e3ecac0a8e604f2b98a2a12b0579990a msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." msgstr "" -"我们必须使用 `InlineJavascriptRequirements`，因为我们的表达式包含 `." -"toUpperCase（）` 中的 JavaScript " -"调用，这意味着使用表达式工具必须调用JavaScript。" +"因为我们的表达式在 `.toUpperCase()` 处含有一个 JavaScript 调用，所以必须使用 " +"`InlineJavascriptRequirements`. 这向使用表达式工具的其他工具表明 JavaScript " +"是必备条件。" #: ../../src/topics/expressions.md:1 #: c8d648b765ec499a8e9c464590838492 @@ -1724,43 +1732,45 @@ msgstr "表达式" #: 007a345b4bad49cf996c4301b8386473 msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." msgstr "" -"如果需要操作输入参数，请添加需求 `InlineJavascriptRequirement`，" -"然后在参数引用合法的任何地方提供将由 CWL 运行程序评估的 Javascript 片段。" +"如果需要对输入参数进行处理，请添加需求 `InlineJavascriptRequirement`. " +"然后，在可以合法引用参数的任何地方，您都可以提供一 JavaScript 片段，让 CWL " +"运行程序计算其值。" #: ../../src/topics/expressions.md:9 #: 2edbd398eadb458b8eacd5fa5496f0a2 msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." msgstr "" -"只能在绝对必要时使用JavaScript表达式。操作文件名、扩展名、路径等时，请优先考" -"虑能否使用`basename`、`nameroot`、`nameext`等 [内置 `文件` 属性][file-" -"prop]。相关详细信息，请参阅[最佳实践列表]（bestpractice.md）。" +"JavaScript 表达式应当仅在绝对必要时使用。要处理文件名、扩展名、路径等，" +"请优先考虑能否使用 `basename`、`nameroot`、`nameext` 等 [`File` 内置属性" +"][file-prop]。对此，请参阅[优良习惯一览](best-practice.md)。" #: ../../src/topics/expressions.md:16 #: 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" -msgstr "" +msgstr "`expression.cwl`" #: ../../src/topics/expressions.md:22 #: efb5fd14988c4e2a8f834ee5369d4102 msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" -msgstr "由于此工具不需要任何 ` 输入 " -"`，因此我们可以使用一个（几乎）空的作业文件运行它：" +msgstr "由于此工具不需要任何 " +"`inputs`（输入），因此运行的时候可以使用一个几乎为空的作业文件：" #: ../../src/topics/expressions.md:25 #: e833649b951841c49397796f996d29f3 msgid "`empty.yml`" -msgstr "" +msgstr "`empty.yml`" #: ../../src/topics/expressions.md:31 #: 276f688ba7cc471a842f085ca852b1d9 msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." -msgstr "`empty.yml` 包含一个空 JSON 对象的描述。JSON 对象描述包含在大括号 `{}` " -"内，因此空对象仅由一组空括号表示。" +msgstr "" +"`empty.yml` 的内容是一个空 JSON 对象的描述。JSON 对象描述是用大括号 `{}` " +"围起来的，因此，表示空对象仅需一对空括号就够了。" #: ../../src/topics/expressions.md:35 #: ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" -msgstr "然后我们可以运行 `expression.cwl`：" +msgstr "然后我们可以运行 `expression.cwl`:" #: ../../src/topics/expressions.md:37 #: 65e0cdd505b944caa40f65e612cdddfc @@ -1770,40 +1780,39 @@ msgstr "运行 `expression.cwl`" #: ../../src/topics/expressions.md:47 #: 8b70a1ad70514039b97164fa630c12e4 msgid "Note that requirements can be provided with the map syntax, as in the example above:" -msgstr "请注意，如上例所示，可通过映射语法来提供要求：" +msgstr "请注意，如上例所示，requirements（要求）可通过映射语法来提供：" #: ../../src/topics/expressions.md:54 #: 2f28ab412d2843ffa5f14acdc01fc732 msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." msgstr "" -"或者作为一个数组，每个条目（在本示例中，只有`class: " -"InlineJavascriptRequirement` ）均用 `-` " -"标记，便可使用相同的语法描述其他命令行参数。" +"也可以作为一个数组，每个元素均用 `-` 标记（本例中只有一个 `class: " +"InlineJavascriptRequirement` ），就和描述额外命令行参数的语法一样。" #: ../../src/topics/expressions.md:62 #: d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" -msgstr "哪里允许使用 JavaScript 表达式？" +msgstr "哪里可以使用 JavaScript 表达式？" #: ../../src/topics/expressions.md:64 #: cbec9277b5004e50af2728cbda0df740 msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" -msgstr "和 [参数引用](parameter-references.md)一样，只能在某些字段中使用 JavaScript " -"表达式。 这些字段是：" +msgstr "JavaScript 表达式如同[参数引用](parameter-references." +"md)一样，只能用于某些特定字段，即：" #: ../../src/topics/expressions.md:66 #: e259f55f8000479bbd8009e25cf0ca6c msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -"来自[`CommandLineTool`] （https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool）" +"来自 [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 #: 1acb064f7a4a482aa0174bdc847c6382 #: 0222780b98ac48e89b1b4f57c9df8590 msgid "`arguments`" -msgstr "" +msgstr "`arguments`" #: ../../src/topics/expressions.md:68 #: ../../src/topics/expressions.md:76 @@ -1818,28 +1827,28 @@ msgstr "" #: e4e68011dc5f42e4918c747afa7d764b #: d44e3cfa661840eb851782e24caf1b68 msgid "`valueFrom`" -msgstr "" +msgstr "`valueFrom`" #: ../../src/topics/expressions.md:69 #: ../../src/topics/parameter-references.md:66 #: 0bddedfe40e841f7878e09792531e6bf #: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" -msgstr "" +msgstr "`stdin`" #: ../../src/topics/expressions.md:70 #: ../../src/topics/parameter-references.md:67 #: 58a6510ef69a4c51a4ea348cd98ef0d2 #: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" -msgstr "" +msgstr "`stdout`" #: ../../src/topics/expressions.md:71 #: ../../src/topics/parameter-references.md:68 #: 2437656e20354d63bede1b98d5348e2c #: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" -msgstr "" +msgstr "`stderr`" #: ../../src/topics/expressions.md:72 #: 8210b36347a749889450529ecdf4ff0e @@ -1865,7 +1874,7 @@ msgstr "" #: bd61499b71e64164878dea08d6d7141e #: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" -msgstr "" +msgstr "`format`" #: ../../src/topics/expressions.md:74 #: ../../src/topics/expressions.md:79 @@ -1884,13 +1893,13 @@ msgstr "" #: cd7a0190511d4613b09600a3b1e9d55f #: 47def3b078e2402182039be0227090ae msgid "`secondaryFiles`" -msgstr "" +msgstr "`secondaryFiles`" #: ../../src/topics/expressions.md:75 #: 23088850ad02459696f6bbd385109aac msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -"来自[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." +"来自 [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineBinding)" #: ../../src/topics/expressions.md:77 @@ -1898,13 +1907,13 @@ msgstr "" msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" "来自 [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)的" +"html#CommandOutputParameter)" #: ../../src/topics/expressions.md:80 #: 989a1c4aaa1143be9f53b90cd8b6d500 msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -"来自[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." +"来自 [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputBinding)" #: ../../src/topics/expressions.md:81 @@ -1912,21 +1921,21 @@ msgstr "" #: 582b03ac742745a89f4dfc86b7404db2 #: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" -msgstr "" +msgstr "`glob`" #: ../../src/topics/expressions.md:82 #: ../../src/topics/parameter-references.md:79 #: d555a3d991e344a5a8e1289168d7c6d1 #: 44b3f123c9b04a308c1161b742a7b34b msgid "`outputEval`" -msgstr "" +msgstr "`outputEval`" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 #: e9fa9430535c424fa3e8be5d460d2ba4 #: 0e306cc923974d1db83fdfb45105a11c msgid "From `Workflow`" -msgstr "来自`Workflow`" +msgstr "来自 `Workflow`" #: ../../src/topics/expressions.md:84 #: d289541e460147aa933f7878996f8649 @@ -1941,7 +1950,7 @@ msgstr "" #: b0290d1a477b48119e17cf1fed9d6dff #: 446f1190af7a40a0913ff04ce7aa938c msgid "From `steps`" -msgstr "来自`steps`" +msgstr "来自 `steps`" #: ../../src/topics/expressions.md:88 #: 81b4d1f23a3642bfa9bb395b94260cd1 @@ -1964,7 +1973,7 @@ msgstr "" #: c2a92d3eca7f4ee39cec649170eeea53 #: 3c939769ede94602a67fc50c435741cf msgid "`expression`" -msgstr "" +msgstr "`expression`" #: ../../src/topics/expressions.md:92 #: f495da32f05a4a5ba9539be0a54c1a59 @@ -1978,7 +1987,7 @@ msgstr "" #: bdb4c68a175047ddbe141ca24960127f msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" -"来自[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"来自 [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." "html#ResourceRequirement)" #: ../../src/topics/expressions.md:96 @@ -1986,56 +1995,56 @@ msgstr "" #: 4b73495cf18a4d908525292b6f23c419 #: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" -msgstr "" +msgstr "`coresMin`" #: ../../src/topics/expressions.md:97 #: ../../src/topics/parameter-references.md:94 #: 718ceee9973240ec9c100977bbcc8921 #: 2b25152f6df5494a8632f3ce631c20d8 msgid "`coresMax`" -msgstr "" +msgstr "`coresMax`" #: ../../src/topics/expressions.md:98 #: ../../src/topics/parameter-references.md:95 #: c07ab08eb75d4528949c56a3d7c12b28 #: 846cd427ae25410eae7c920b237edcb0 msgid "`ramMin`" -msgstr "" +msgstr "`ramMin`" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 #: 594bc5b7e5be4be9b5e1f6b2502e3bd3 #: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" -msgstr "" +msgstr "`ramMax`" #: ../../src/topics/expressions.md:100 #: ../../src/topics/parameter-references.md:97 #: 700c57ccd5e347be86702c83a8af24b3 #: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" -msgstr "" +msgstr "`tmpdirMin`" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 #: 509a5e2ec52d413eb57754d359f133e4 #: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" -msgstr "" +msgstr "`tmpdirMax`" #: ../../src/topics/expressions.md:102 #: ../../src/topics/parameter-references.md:99 #: 5a60ab5ee19446f8a6f49ab8583101a9 #: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" -msgstr "" +msgstr "`outdirMin`" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 #: 1f39f016524a459895ed03c72d74932b #: e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" -msgstr "" +msgstr "`outdirMax`" #: ../../src/topics/expressions.md:104 #: 97b61352363f47cb890e8937c5613fa3 @@ -2049,26 +2058,26 @@ msgstr "" #: 9359ef94c41249ea8e76fe629926054e #: a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" -msgstr "" +msgstr "`listing`" #: ../../src/topics/expressions.md:106 #: 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "在 [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)中" +msgstr "来自 [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 #: effc0208cf4f4551958db6e526c0528b #: 9d4889c8cec24351a7a9e3c547e331b6 msgid "`entry`" -msgstr "" +msgstr "`entry`" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 #: be6c1e85c7b6495d8086c262daad20e7 #: af4f7f232a9d42388c0ba1cfc7c2cdf7 msgid "`entryname`" -msgstr "" +msgstr "`entryname`" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 @@ -2089,7 +2098,7 @@ msgstr "" #: 107b54b832df4d408d1315bdba05b4dd #: 949c376120d8441796ec9c89364f8851 msgid "`envValue`" -msgstr "" +msgstr "`envValue`" #: ../../src/topics/expressions.md:116 #: 10d36a1adfd04144b401c993b12b4094 @@ -2100,101 +2109,105 @@ msgstr "通过 `expressionLib` 使用外部库和内联 JavaScript 代码" #: 29b73e1dd72744f68377f0a38c10f062 msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." msgstr "" -"需求 `InlineJavascriptRequirements` 支持 `expressionLib` 属性，" -"该属性允许用户加载外部 JavaScript 文件或提供内联 JavaScript 代码。" +"`InlineJavascriptRequirements` 这一需求支持 `expressionLib` 属性，" +"可以让用户加载外部 JavaScript 文件或提供内联 JavaScript 代码。" #: ../../src/topics/expressions.md:122 #: 38a2afaf4a6c4d04909af22c93f2808d msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." msgstr "" -"添加到 `expressionLib`属性的条目通过CWL运行程序的JavaScript引擎进行解析，可用" -"于增添内部文件或创建可在CWL文档其他部分调用的JavaScript函数。" +"添加到 `expressionLib` 属性的条目将由 CWL 运行程序的 JavaScript " +"引擎进行语法分析。这可以用来纳入外部文件中的代码，或创建可在 CWL " +"文件其他部分调用的 JavaScript 函数。" #: ../../src/topics/expressions.md:128 #: cd74f34b21af4de9be96fd897efc469b msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" -"CWL 标准（版本 1.0 到 1.2）[声明](https://www.commonwl.org/v1.0/" -"CommandLineTool.html#Expressions)在 CWL 表达式中唯一有效的 JavaScript 版本是[" -"ECMAScript 5.1](https://262.ecma-international.org/5.1/) ，这意味着在 CWL " -"文档中添加或编写的所有代码都必须符合此版本。" +"版本 1.0 到 1.2 的 CWL 标准中[写道](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#Expressions)，在 CWL 表达式中唯一有效的 JavaScript " +"版本是 [ECMAScript 5.1](https://262.ecma-international.org/5.1/) . 也就是说，" +"在 CWL 文件中纳入或写入的所有 JS 代码都必须符合该版本。" #: ../../src/topics/expressions.md:135 #: f12e371f3f1a4b0cb2cff9800352d48c msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" msgstr "" -"例如，我们可以使用 `InlineJavascriptRequirements` 并在 `expressionLib` " -"中编写一个 内联JavaScript 函数，便可在 CWL 文档其他部分调用此函数：" +"例如，我们可以使用 `InlineJavascriptRequirements`, 在 `expressionLib` " +"下编写内联 JavaScript 函数，让它能在 CWL 文件其他部分调用：" #: ../../src/topics/expressions.md:139 #: 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" -msgstr "" +msgstr "`hello-world-expressionlib-inline.cwl`" #: ../../src/topics/expressions.md:146 #: 8f0e8f050e334ac08334e9215e1dcf61 msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" -msgstr "运行此CWL工作流，将调用JavaScript函数并生成`echo` " -"命令，以用大写首字母打印输入信息：" +msgstr "运行此 CWL 工作流将调用这个 JavaScript 函数，使得 `echo` " +"命令以大写首字母排印输入的“报文”：" #: ../../src/topics/expressions.md:149 #: 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "运行 `hello-world-expressionlib-inline.cwl`。" +msgstr "运行 `hello-world-expressionlib-inline.cwl`." #: ../../src/topics/expressions.md:155 #: 7a6be0005a6441feb67f036d005d7885 msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" -msgstr "让我们将 `capitalizeWords` 函数移动到外部文件 `custom-functions.js`，" -"并将其导入CWL 文档中：" +msgstr "" +"我们来将 `capitalizeWords` 函数移动到外部文件 `custom-functions.js`, " +"并将它导入我们的 CWL 文件：" #: ../../src/topics/expressions.md:158 #: ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" -msgstr "" +msgstr "`custom-functions.js`" #: ../../src/topics/expressions.md:164 #: 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" -msgstr "" +msgstr "`hello-world-expressionlib-external.cwl`" #: ../../src/topics/expressions.md:171 #: 06635145b441418aaae84dc804f3d6ac msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." msgstr "" -"已通过 `$include: custom-functions.js`语句将`custom-functions." -"js`文件添加至CWL文档，因此可在CWL文档其他部分调用相关函数和 变量。" +"文件 `custom-functions.js` 通过 `$include: custom-functions.js` " +"语句纳入到这个 CWL 文件里，使这个 JavaScript 文件中定义的函数和变量可在 CWL " +"文件其他部分使用。" #: ../../src/topics/expressions.md:175 #: 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "运行 `hello-world-expressionlib-external.cwl`。" +msgstr "运行 `hello-world-expressionlib-external.cwl`." #: ../../src/topics/expressions.md:181 #: 04eaf1f7c630450db318dcd8b7626e15 msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." msgstr "" -"最后，请注意可在CWL文档中同时拥有内联和外部JavaScript代码。在最后一个示例中，" -"通过新建函数`createHelloWorldMessage`调用外部文件`custom-functions." -"js`中的`capitalizeWords` 函数，我们将其他条目添加至expressionLib`属性。" +"最后请注意，CWL 文件中可以同时运用内联和外部 JavaScript " +"代码。下面是最后一个例子，这里我们向 `expressionLib` 属性中加入新函数 " +"`createHelloWorldMessage`, 调用外部文件 `custom-functions.js` 中的 " +"`capitalizeWords` 函数。" #: ../../src/topics/expressions.md:186 #: c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" -msgstr "" +msgstr "`hello-world-expressionlib.cwl`" #: ../../src/topics/expressions.md:193 #: 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." -msgstr "运行 `hello-world-expressionlib.cwl`。" +msgstr "运行 `hello-world-expressionlib.cwl`." #: ../../src/topics/expressions.md:200 #: fd4579a3c9844492b314b5c3c1775fc7 msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." msgstr "" -"可使用`$include` 语句添加本地磁盘或远程位置的文件。相对路径和绝对路径均可用。" -"了解更多相关信息，请查阅 CWL 规范中关于 `$include`](https://www.commonwl.org/" -"v1.0/SchemaSalad.html#Include) 的文本。" +"`$include` 语句可以用来添加位于本地或远程的文件，并且接受相对路径和绝对路径。" +"详情请参见 CWL 规约中[关于 `$include`](https://www.commonwl.org/v1.0/" +"SchemaSalad.html#Include) 的内容。" #: ../../src/topics/file-formats.md:1 #: 3f038e7371f84ed9b4547358dfb55a11 @@ -2205,69 +2218,66 @@ msgstr "文件格式" #: e024bcb70e04412e90e1838426d1b69a msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." msgstr "" -"工具和工作流可将 `File` 类型作为输入，并将其生成为输出。同时，我们建议指定 `" -"文件 ` 类型的格式，这有助于其他人记录如何使用您的工具，同时允许您在创建参数文" -"件时执行一些简单的类型检查。" +"`File` 类型既可作为工具和工作流的输入，也可以成为它们生成的输出。另外，" +"我们建议指明 `File` 类型的格式，以便向他人说明您的工具如何使用，同时还能让您" +"在创建参数文件时进行简单的类型检验。" #: ../../src/topics/file-formats.md:8 #: a3db21c0b3114802a8a5b610e252ef13 msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -"对于文件格式，我们建议引用现有本体（如示例中的 EDAM），引用您所在机构的本地本" -"体，或者在与他人共享工具之前不要添加文件格式以便快速开发。" -"您可以在其网站上浏览现有的 [IANA 文件格式列表][IANA] 和 [EDAM " -"文件格式列表][EDAM]。" +"对于文件格式，我们建议参考现有本体（如示例中的 EDAM）或您所在机构内部使用的本" +"体，不然，则在与他人共享工具之前不要先添加文件格式，以便快速开发。" +"您可以通过网站浏览现有的 [IANA][IANA] 和 [EDAM 文件格式列表][EDAM]。" #: ../../src/topics/file-formats.md:14 #: 0f5bc8520d6a4dafa37c65343da9702a msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." -msgstr "在下一个教程中，我们将更详细地解释文档的 `$namespaces` 和 `$schemas` " -"章节，因此暂时不必担心这些。" +msgstr "我们将在下一篇教程中更详细地解释文件中的 `$namespaces` 和 `$schemas` " +"部分，眼下无需为此分心。" #: ../../src/topics/file-formats.md:17 #: 5cb830da47464a8b9c3950983fa4d56f msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." -msgstr "请注意，对于附加值而言， `cwltool` " -"可以根据文件格式进行一些基本推理，并在出现一些明显的不匹配时发出警告。" +msgstr "请注意， `cwltool` 有一项附加功能，即依据文件格式做一些初步推断，一旦出现较明" +"显的不匹配则发出警告。" #: ../../src/topics/file-formats.md:20 #: 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" -msgstr "" +msgstr "`metadata_example.cwl`" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 #: f558bcf2a993482195cd418b37761809 #: fb47f73c38cf4ec59bd3021866a631f8 -#, fuzzy msgid "The equivalent of this CWL description in command line format is:" -msgstr "CWL描述的等效项在命令行的格式是：" +msgstr "这一 CWL 描述的等效命令行形式为：" #: ../../src/topics/file-formats.md:32 #: 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" -msgstr "样本参数文件" +msgstr "参数文件样本" #: ../../src/topics/file-formats.md:34 #: a2ce43b391864e8bbde16328cc19b32b msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." msgstr "" -"下方是一个样本参数文件的示例。我们鼓励您检查自己工具中的参数文件作业示例，这" -"将帮助其他人从一个“已知良好的”参数文件入手，更快地上手使用您的工具。" +"以上例子的样本参数文件见下。我们提倡为您的工具加入经您测试可用的参数文件样例" +"，这将帮助他人从做好的“合格品”参数文件入手，更快地上手操作您的工具。" #: ../../src/topics/file-formats.md:39 #: aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" -msgstr "" +msgstr "`sample.yml`" #: ../../src/topics/file-formats.md:45 #: 56ee4dcfff6141d5bef80eb96559876d msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" -"___注意：___ 要查阅以下示例，您需要下载示例输入文件*file-formats.bam*，" -"该文件可从 获取，且可通过 " -"`wget`等工具下载：" +"___注意：___ 按照下例演练前，您需要先下载示例输入文件 *file-formats.bam*. " +"该文件位于 , 可以用 `wget` 等工具下载：" #: ../../src/topics/index.md:1 #: 8d3a6d83e2e54c56995893c41590b7ff @@ -2277,7 +2287,7 @@ msgstr "主题" #: ../../src/topics/inputs.md:1 #: 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" -msgstr "输入" +msgstr "输入 (inputs)" #: ../../src/topics/inputs.md:3 #: d3a55f71dc244026a97902de9ed819ea @@ -2287,137 +2297,143 @@ msgstr "基本输入参数" #: ../../src/topics/inputs.md:5 #: 96671c56523c4ea9992fb5dfcfa6490e msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "工具`输入`是一张控制工具运行方式的输入参数列表。" -"每个参数都包含一个表示参数名称的 `id`和用于描述参数有效值类型的`type`。" +msgstr "" +"工具的 `inputs`（输入）用于列出控制工具运行方式的输入参数。每个参数都包含 " +"`id` 字段作为名称，以及 `type` 字段描述有效参数值的类型。" #: ../../src/topics/inputs.md:9 #: bcc6246742cb46bfb185e415c4a3431a msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." msgstr "" -"可用的基元类型包括*string*、 *int*、*long*、 *float*、*double*以及 " -"*null*；复杂类型包括*array* 和*record* ；此外还有*File*、*Directory* 以及 " -"*Any*等特殊类型。" +"可用的原始类型有 *string*（字符串）、 *int*（整型）、*long*（长整型）、 " +"*float*（浮点数）、*double*（双精度浮点数）以及 *null*（空）等；" +"复合类型指的是 *array*（数组）和 *record*（记录）；此外还有特殊类型 " +"*File*（文件）、*Directory*（目录）以及 *Any*（任意）等。" #: ../../src/topics/inputs.md:13 #: 86dce36de687449c88fb5eb9d64eb045 msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." -msgstr "下面的示例演示了一些不同类型的输入参数，并以不同的方式显示在命令行上。" +msgstr "下面的例子展示了一些类型各异、以不同方式出现在命令行上的输入参数。" #: ../../src/topics/inputs.md:16 #: cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "首先，新建一个名为 `inp.cwl` 的文件，包含以下内容：" +msgstr "首先，创建一个名为 `inp.cwl` 的文件，包含以下内容：" #: ../../src/topics/inputs.md:18 #: 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" -msgstr "" +msgstr "`inp.cwl`" #: ../../src/topics/inputs.md:24 #: c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" -msgstr "新建一个名为`inp-job.yml`的文件：" +msgstr "创建名为 `inp-job.yml` 的文件：" #: ../../src/topics/inputs.md:26 #: dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" -msgstr "" +msgstr "`inp-job.yml`" #: ../../src/topics/inputs.md:33 #: 36ab1d9edafc4831bb1bca5f123b04b0 msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" -msgstr "您可以使用 `cwltool` " -"创建模板输入对象，便无需在输入对象文件中键入所有输入参数：" +msgstr "您可以用 `cwltool` 创建模板输入对象，以省去在输入对象文件中一一键入输入参数：" #: ../../src/topics/inputs.md:40 #: 7dc630ea86464b1dba3a4e5079260b3b msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." msgstr "" -"您可将输出重定向到一个文件，即`cwltool --make-template inp.cwl > inp-job." -"yml`，然后将默认值更改为预期输入值。" +"您可将输出重定向到一个文件：`cwltool --make-template inp.cwl > inp-job." +"yml`，然后将生成的默认值改为您想要的输入值。" #: ../../src/topics/inputs.md:44 #: ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." -msgstr "注意: \"example_file\"是一种`文件` 类型，必须作为一个带有字段`class: File`和 " -"`path`的对象提供。" +msgstr "" +"注意，“example_file” 属于 `File`（文件）类型，因此必须作为含有 `class: File` " +"和 `path` 字段的对象出现。" #: ../../src/topics/inputs.md:47 #: 651e032007ea4a119d20c820bb61f86b msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." -msgstr "然后，在命令行键入 `touch whale.txt`，以使用[touch]新建一个whale.txt 。" +msgstr "然后，在命令行键入 `touch whale.txt`, 用 [touch] 命令创建文件 whale.txt." #: ../../src/topics/inputs.md:53 #: 0b056dde9e87428996e47870b12119da msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" msgstr "" -"现在，使用`cwltool inp.cwl inp-job.yml`命令，以通过命令行上的工具描述和输入对" -"象调用`cwltool`。下方方框内文本描述了这两个命令及命令行的预期输出：" +"现在，使用 `cwltool inp.cwl inp-job.yml` 命令，即指定工具描述和输入对象、" +"通过命令行调用 `cwltool`. 下方文本框描述了这两个命令及命令行的预期输出：" #: ../../src/topics/inputs.md:64 #: 628124a1670b4b058bb0fb6e495a099c msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" -msgstr "CWL 引用运行程序 （cwltool） 和其他运行程序通过输入文件符号（“软”）链接创建临" -"时目录，以确保工具不会意外访问未明确指定的文件" +msgstr "" +"CWL 参考运行程序 (cwltool) 和其他运行程序会建立临时目录，在其中创建指向您文件" +"的符号链接（又称“软”链接），以防工具意外访问未经明文指定的文件" #: ../../src/topics/inputs.md:70 #: 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." msgstr "" "字段 `inputBinding` " -"为可选项，指示输入参数是否应显示在工具的命令行上以及以何种方式显示。 " -"如果`inputBinding`缺失 ，则该参数不会出现在命令行上。 " -"让我们来详细看看每个示例。" +"为可选项，用来说明该输入参数是否应出现在工具的命令行上、以何种方式出现。 " +"如果没有 `inputBinding`, 则该参数不会出现在命令行上。 " +"我们来仔细看看每个示例。" #: ../../src/topics/inputs.md:83 #: ec2adb3912bc46e28891229e9e0d9a1c msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." -msgstr "布尔类型充当一种标志。如果输入参数“example_flag”为“真”，则命令行会添加`前缀`" -"。如果为假，则不添加任何标志。" +msgstr "" +"布尔类型的处理相当于一种“旗标”。如果输入参数“example_flag”为“true”（真），则 " +"`prefix` 会被添加到命令行，否则将不添加旗标。" #: ../../src/topics/inputs.md:95 #: a519be60726a44af9941fdce04735353 msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." msgstr "" -"字符串类型在命令行上显示为文本值。 `前缀`是可选的，如果提供，它将在命令行上作" -"为单独的参数出现，且位于指定参数之前。 在上面的示例中，其显示为 `--example-" -"string hello`。" +"字符串类型以字面值 (literal value) 的方式出现在命令行上。 `prefix` " +"是可选的；如果提供，它将作为单独的参数，在命令行上出现在参数值之前。上例中，" +"相应的结果是 `--example-string hello`." #: ../../src/topics/inputs.md:109 #: cb8fc8c4c79e467eac5fab4ca685201e msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." msgstr "" -"整数（和浮点）类型在命令行中以十进制文本显示。 若选项 `separate`为假（默认值" -"为真），前缀和值被合并为一个参数。在上方的示例中，其显示为`-i42` 。" +"整型和浮点型以其十进制表示，作为文本出现在命令行上。 若选项 `separate` 为 " +"false（伪，默认为 true 真），前缀将和它的值合并为一个参数。上例中，其产物为 " +"`-i42`." #: ../../src/topics/inputs.md:124 #: a26cc105716f47cb807174c9003153b0 msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." msgstr "" -"文件类型在命令行中显示为文件路径。若参数类型以问号 `?` " -"结尾，表示该参数为可选。在上方的示例中，其呈现为 `--file=/tmp/random/path/" -"whale." -"txt`。但是，如果输入中未提供“example_file”参数，则命令行上不会出现任何内容。" +"文件类型在命令行上以文件路径的方式出现。参数类型末尾如有问号 `?` " +"意指该参数为可选。上例中，这一部分的命令行产物是 `--file=/tmp/random/path/" +"whale.txt`. " +"不过，如果输入中未提供“example_file”参数，则不会在命令行上加入任何内容。" #: ../../src/topics/inputs.md:131 #: cc159dd5fe5748caac838862f5b8c4d1 msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." -msgstr "输入文件为只读。 如果要更新输入文件，必须 [首先将其复制到输出目录](staging-" +msgstr "输入文件是只读的。 如果要更新输入文件，必须将它[事先复制到输出目录](staging-" "input-files.md)。" #: ../../src/topics/inputs.md:134 #: 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." msgstr "" -"`位置` 的值用于确定参数在命令行中应出现的位置。 位置是相对的，不是绝对的。 因" -"此，位置不一定是连续的，位置1、3、5的三个参数会生成与位置1、2、3相同的命令行" -"。 多个参数可以有相同的位置（使用参数名称断开连接），而位置字段本身是可选的。" -" 默认的位置是0。" +"`position`（位置）的值用于指定参数在命令行上应出现的位置 — " +"并非绝对位置，而是彼此间的相对顺序。这意味着，位置值不一定要连续；`position` " +"值为 1、3、5 的三个参数生成的命令行将与其值分别为 1、2、3 时相同。 " +"多个参数可能有相同的 `position` 值（这种情况下由参数名进一步决定顺序），而且 " +"`position` 字段本身是可选的。 默认的位置是0." #: ../../src/topics/inputs.md:142 #: 6812698e9ad84d3385de5e88e9dde0b3 msgid "The `baseCommand` field will always appear in the final command line before the parameters." -msgstr "`baseCommand` 字段将始终出现在最后的命令行中，且位于指定参数之前。" +msgstr "`baseCommand` 字段一定会出现在最终生成的命令行中，而且位于所有参数之前。" #: ../../src/topics/inputs.md:146 #: 9654e65b1c0642dbb5d4f34edb211989 @@ -2428,20 +2444,20 @@ msgstr "数组输入" #: d1f02be278754267893dfce5a940997d msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." msgstr "" -"将显示的输入参数数组添加至命令行很简单。可通过两种方法指定数组参数。首先，" -"可提供带有 `type： array` 和 `items`的 `type` " -"字段，以定义数组中可能出现的有效数据类型。或者，可以在类型名称后添加方括号 " -"`[]`，以指示输入参数为此类型的数组。" +"将以数组形式出现的参数添加至命令行很简单。指定数组参数有两种办法。第一种是在 " +"`type` 字段下给出 `type: array`, 并且用 `items` " +"定义数组中允许出现的有效数据类型。另一种办法，是在类型的名称后添加方括号 " +"`[]`，以表明输入参数为此类型的数组。" #: ../../src/topics/inputs.md:154 #: 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" -msgstr "" +msgstr "`array-inputs.cwl`" #: ../../src/topics/inputs.md:160 #: 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" -msgstr "" +msgstr "`array-inputs-job.yml`" #: ../../src/topics/inputs.md:166 #: ../../src/topics/outputs.md:82 @@ -2450,30 +2466,31 @@ msgstr "" #: 02adef8ee8204842b5b4a0408f3bac33 #: 9db68837918a4a349f32f15f12697a1d msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "现在，调用在命令行上提供工具描述和输入对象的 `cwltool`：" +msgstr "现在，调用命令 `cwltool` 并为它提供工具描述和输入对象：" #: ../../src/topics/inputs.md:178 #: 75d59e395c66416cae9b352db5081516 msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." msgstr "" -"`inputBinding` 可以出现在外部数组参数定义或内部数组元素定义中，如上所示，它们" -"在构造命令行时会产生不同的行为。此外，`itemSeparator` " -"字段（如提供的话）指明数组值应合并成一个独立参数，并以项目分隔符字符串分隔。" +"`inputBinding` 既可以出现在外部，即数组参数本身的定义中，也可以出现在内部，即" +"数组元素的定义中。如上所示，这两种定义方式在构建命令行时所产生的行为是不一样" +"的。另外，`itemSeparator`（项目分隔符）字段如果出现，则指明数组各元素的值应并" +"入单独的一个参数，以指定的项目分隔符插入相邻的元素值之间。" #: ../../src/topics/inputs.md:185 #: 874c6f19abbf45d7ab7d30a378c4048d msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." msgstr "" -"请注意，输入数组在 `array-inputs-job.yml` 的方括号 `[]` " -"内指定。数组也可以用多行表示，其中未使用关联键定义的数组值由前导 `-` " -"标记。这将在下一课中演示，并在 [YAML 指南]（yaml-guide.md#arrays） " -"中详细讨论。你可以指定数组的数组、记录的数组及其他复杂类型的数组。" +"请注意，在 `array-inputs-job.yml` 中，数组输入由方括号 `[]` " +"指定。表达数组的另一种形式是多行句法，即用行首的 `-` " +"标明数组元素，示意它并非键值。下一课中将演示后一种用法，在[《YAML 指南" +"》](yaml-guide.md#arrays) 中也有详细讨论。可以指定的数组包括数组的数组、记录" +"的数组及其他复合类型的数组。" #: ../../src/topics/inputs.md:191 #: 5d7d7a28cc5d4862803032aec78174d9 -#, fuzzy msgid "Inclusive and Exclusive Inputs" -msgstr "包容性和互斥性输入" +msgstr "相容和互斥输入" #: ../../src/topics/inputs.md:193 #: dea0d4b681f94e73b13965dcfe75cf7d From de3fbd393ceabf4662b5ac7ace38afe02c6b4558 Mon Sep 17 00:00:00 2001 From: zoe-translates Date: Wed, 28 Jun 2023 22:15:14 +0800 Subject: [PATCH 071/179] Topics > Outputs: Clarifying the nature of `glob`; minor fixes. (#405) - Make it clear that `glob` is a pattern (that can happen to be a file name). - Minor fixes for grammar and clarity. --- src/topics/outputs.md | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/src/topics/outputs.md b/src/topics/outputs.md index 5de5639f..b2513f32 100644 --- a/src/topics/outputs.md +++ b/src/topics/outputs.md @@ -11,16 +11,18 @@ When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files -themselves, or come from examining the content of those files. +themselves, or the result of examining the content of those files. The following example demonstrates how to return a file that has been extracted from a tar file. ```{tip} Passing mandatory arguments to the `baseCommand` -In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. -Instead of a single string we can use an _array of strings_. The first element is the command to run, and -any subsequent elements are mandatory command line arguments +In previous examples, the `baseCommand` was just a string, with any arguments +passed as CWL inputs. Instead of a single string, we can use an _array of +strings_ as the value of `baseCommand`. The first element of the array is the +command to run, and any subsequent elements are mandatory command line +arguments ``` ```{literalinclude} /_includes/cwl/outputs/tar.cwl @@ -59,8 +61,10 @@ outputs: glob: hello.txt ``` -The [`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) field consists of the name of a file in the output directory. -If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`. +The [`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) +field consists of the pattern to match file names in the output directory. +This can simply be the file's exact name. But if you don't know the name of the +file in advance, you can use a wildcard pattern like `glob: '*.txt'`. ## Capturing Standard Output From dbeb91c9aa4e0343cc129f9986f9482986efe6a3 Mon Sep 17 00:00:00 2001 From: zoe-translates Date: Wed, 28 Jun 2023 22:20:03 +0800 Subject: [PATCH 072/179] Operations: Don't imply an operation is straightforwardly useable (#404) The doc says "[An operation] can be used like use a command line tool or an expression", which may be read as "you can use an (abstract) operation just like how you use a (concrete) command line tool or expression". This is of course false and directly contradicted by the next example. To avoid this implication, reword it as "it can appear...". Also, a minor clarification about "Sphinx Graphviz", which referred to a specific processing directive in the Sphinx doc. --- src/topics/operations.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/topics/operations.md b/src/topics/operations.md index b6afca2a..875a533d 100644 --- a/src/topics/operations.md +++ b/src/topics/operations.md @@ -13,16 +13,17 @@ you are ready to submit the workflow to a CWL runner: :caption: "`operations.cwl`" ``` -The `uppercase` step of the workflow is an operation. It can be used like -a command line tool or an expression. You can also plot it with the +The `uppercase` step of the workflow is an operation. It can appear where a +command line tool or an expression is expected. You can also plot it with the CWL Viewer or `cwltool`: ```{runcmd} cwltool --print-dot operations.cwl :working-directory: src/_includes/cwl/operations/ ``` -The output of the command above can be rendered with a Graphviz renderer. The following -image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx): +The output of the command above can be rendered with a Graphviz renderer. The +following image is rendered with the Sphinx `{graphviz}` directive (this user +guide is built with Sphinx): ```{graphviz} From 481ea7557f51cb95bf9c691e1616996da6dec265 Mon Sep 17 00:00:00 2001 From: Tomoya Tanjo Date: Thu, 29 Jun 2023 11:30:22 +0900 Subject: [PATCH 073/179] Add explanation of what happens when modifying `basename` (#401) * Add explanation of what happens when modifying `basename` make the example complete --------- Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com> --- src/faq.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/src/faq.md b/src/faq.md index 91c234f7..3e64ca74 100644 --- a/src/faq.md +++ b/src/faq.md @@ -62,14 +62,15 @@ This example demonstrates how to change the name of an output file from the default name given to it by a tool: ```yaml -cwlVersion: v1.0 # or v1.1 +cwlVersion: v1.0 class: CommandLineTool requirements: InlineJavascriptRequirement: {} -baseCommand: [] +baseCommand: [ touch, otu_table.txt ] -inputs: [] +inputs: + otu_table_name: string outputs: otu_table: @@ -79,6 +80,9 @@ outputs: outputEval: ${self[0].basename=inputs.otu_table_name; return self;} ``` +By modifying the `basename` field in the `outputEval` field, CWL workflow engines will rename +the file using the new name for subsequent steps or as a workflow-level output. + ## How do I reference a local script? There are two ways to reference a local script: From 08909eac829291254b6e4c25df566fc8ac51db43 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Thu, 29 Jun 2023 12:21:41 +0900 Subject: [PATCH 074/179] symlink old name for Simplified Chinese to new name --- locales/zh_CN | 1 + 1 file changed, 1 insertion(+) create mode 120000 locales/zh_CN diff --git a/locales/zh_CN b/locales/zh_CN new file mode 120000 index 00000000..6b8cf0dc --- /dev/null +++ b/locales/zh_CN @@ -0,0 +1 @@ +zh_Hans/ \ No newline at end of file From 03e07df110cd1f1b057169dca3d4a461e67acda8 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Thu, 29 Jun 2023 06:52:38 +0200 Subject: [PATCH 075/179] Translations update from Hosted Weblate (#408) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Translated using Weblate (Chinese (Simplified)) Currently translated at 77.9% (466 of 598 strings) Co-authored-by: Zoë Ma Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 3.8% (23 of 598 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide --------- Co-authored-by: Zoë Ma Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 50 ++++--- locales/zh_Hans/LC_MESSAGES/user_guide.po | 175 +++++++++++----------- 2 files changed, 120 insertions(+), 105 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 57026500..6dfd535f 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-05-09 10:35+0000\n" +"PO-Revision-Date: 2023-06-29 03:51+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 4.18-dev\n" +"X-Generator: Weblate 4.18.1\n" #: ../../LICENSE.md:2 #: 4e203044f0464fd5a3256430391dde12 @@ -117,7 +117,7 @@ msgstr "" #: ../../src/faq.md:1 #: e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" -msgstr "" +msgstr "よくある質問" #: ../../src/faq.md:11 #: 61edb787dab04ca2ad3ed07616d878a0 @@ -127,7 +127,7 @@ msgstr "" #: ../../src/faq.md:41 #: d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" -msgstr "入力ファイル名を変更します" +msgstr "入力ファイルの名前を変更する" #: ../../src/faq.md:43 #: fc62427c0a004810b055dee90ec5e2d9 @@ -137,22 +137,23 @@ msgstr "" #: ../../src/faq.md:59 #: 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" -msgstr "" +msgstr "出力ファイルの名前を変更する" #: ../../src/faq.md:61 #: bc7ad10c929848a3a9a240a3c501d299 msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" -msgstr "" +msgstr "この例では、出力ファイルの名前を、ツールから与えられたデフォルトの名前から変" +"更する方法を示します：" #: ../../src/faq.md:82 #: 7225a993d281421b95c8e3df2846a0e3 msgid "Referencing a Local Script" -msgstr "" +msgstr "ローカルスクリプトを参照する" #: ../../src/faq.md:84 #: 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" -msgstr "" +msgstr "ローカルスクリプトを参照するには、2つの方法があります：" #: ../../src/faq.md:86 #: 450edf800a18423195bea4fe8793a2cb @@ -167,12 +168,16 @@ msgstr "" #: ../../src/faq.md:95 #: a7d84f740a714ec588503ee084fbbc34 msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" -msgstr "" +msgstr "その後、`chmod +x scriptname.sh` " +"というコマンドでスクリプトを実行可能な状態にします。" #: ../../src/faq.md:97 #: 569d553abe85450c9d1c37456bf412f4 msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." msgstr "" +"最後に、`PATH` " +"を変更し、スクリプトが置かれているディレクトリを追加します。(`$HOME/bin` " +"を自分のスクリプトを保存するために使用するのは良い習慣です）。" #: ../../src/faq.md:104 #: 95f5dbbd21084a318413b9528fb867be @@ -392,12 +397,16 @@ msgstr "" #: ../../src/index.md:1 #: 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" -msgstr "" +msgstr "Common Workflow Language ユーザーガイド" #: ../../src/index.md:3 #: f8d6e4cd54cb42c88182a43171d97bab msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." msgstr "" +"本ガイドは、オープンスタンダードである [Common Workflow Language](https://www" +".commonwl.org/) (CWL) " +"を使用したワークフローの書き方を紹介するものです。本ガイドは、最新仕様{{ " +"cwl_version }}を解説しています。" #: ../../src/index.md:7 #: 132d40fee3b84469afa80d5ff613bf77 @@ -721,7 +730,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:67 #: 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" -msgstr "" +msgstr "`truc.cwl`" #: ../../src/introduction/prerequisites.md:73 #: 6391e08e0bde49f4b21286d8fdb97433 @@ -731,7 +740,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:79 #: cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." -msgstr "" +msgstr "`cwltool` を使って `true.cwl` を検証します。" #: ../../src/introduction/prerequisites.md:84 #: d41c4bc740aa474ea09a7cbd267c8840 @@ -741,7 +750,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:86 #: 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." -msgstr "" +msgstr "`cwltool` を使って `true.cwl` を実行します。" #: ../../src/introduction/prerequisites.md:91 #: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 @@ -771,7 +780,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:115 #: b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" +msgstr "検証`true.cwl` with`cwl-runner`." #: ../../src/introduction/prerequisites.md:120 #: 34ab40437ab646488ba3ee86cd7fe071 @@ -846,7 +855,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:177 #: 6ce8b81560e341c580d316d69202b268 msgid "Docker" -msgstr "" +msgstr "Docker" #: ../../src/introduction/prerequisites.md:181 #: 40cfd559d6a848d1aae354d3bdaa8e9c @@ -876,7 +885,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:1 #: cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" -msgstr "" +msgstr "クイックスタート" #: ../../src/introduction/quick-start.md:3 #: c43d9675ed134b78b02acb5a102a764a @@ -921,7 +930,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:39 #: 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." -msgstr "" +msgstr "`cwltool` を`pip` でインストールします。" #: ../../src/introduction/quick-start.md:47 #: a81342e756d24c40acc15835d0a768f2 @@ -3103,6 +3112,9 @@ msgstr "" #: 13d7e2e92e96432787c712cf6a595424 msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" +"[Common Workflow " +"Languageによるワークフロー入門：コントリビューターのために】(https" +"://carpentries-incubator.github.io/cwl-novice-tutorial/)" #: ../../src/tutorials.md:11 #: 0abdd85c9b964a4e89ba3d80a6c78d6f @@ -3112,7 +3124,7 @@ msgstr "" #: ../../src/tutorials.md:13 #: 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" +msgstr "[CWLでのTypeScript](https://github.com/umccr/cwl-ica/wiki/TypeScript)" #: ../../src/tutorials.md:15 #: 68c97a7065634d02956f3f5c1d4eeb9f @@ -3122,4 +3134,4 @@ msgstr "" #: ../../src/tutorials.md:17 #: a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" +msgstr "[CWLでrnaseq](https://arvados.github.io/rnaseq-cwl-training/)" diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 0dca075e..f70ab516 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-06-27 04:50+0000\n" +"PO-Revision-Date: 2023-06-29 03:51+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified) \n" @@ -2497,192 +2497,195 @@ msgstr "相容和互斥输入" msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." msgstr "" "有时，基础工具具有多个必须一起提供的参数（它们是相互依赖的）或多个不能一起提" -"供的参数（它们是互斥的）。 " -"您可以使用记录和类型联合将参数组合在一起，以描述这两种情况。" +"供的参数（它们是互斥的）。 您可以使用记录类型或共用体 (union) " +"类型将参数加以组合，以分别描述这两种情况。" #: ../../src/topics/inputs.md:198 #: ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" -msgstr "" +msgstr "`record.cwl`" #: ../../src/topics/inputs.md:204 #: d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" -msgstr "" +msgstr "`record-job1.yml`" #: ../../src/topics/inputs.md:215 #: 750474486a84482292eeba45f118287f msgid "In the first example, you can't provide `itemA` without also providing `itemB`." -msgstr "在第一个示例中，如果不同时提供 `itemB`，则无法提供 `itemA`。" +msgstr "在第一个示例中，一旦提供 `itemA` 就必须同时提供 `itemB`." #: ../../src/topics/inputs.md:217 #: 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" -msgstr "" +msgstr "`record-job2.yml`" #: ../../src/topics/inputs.md:233 #: 1eb0e39bb6d04b8cab300f44a79f3add msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." msgstr "" -"在第二个示例中，`itemC` 和 `itemD` 是互斥的，因此只有第一个匹配的项 " -"（`itemC`） 被添加到命令行，其余项 （`itemD`） 将被忽略。" +"在第二个示例中，`itemC` 和 `itemD` 是互斥的。因此，只有第一个匹配项 (`itemC`)" +" 会添加到命令行，而余下的 (`itemD`) 将被忽略。" #: ../../src/topics/inputs.md:236 #: bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" -msgstr "" +msgstr "`record-job3.yml`" #: ../../src/topics/inputs.md:252 #: 4b2ab812f62c4f949dd25c8527f2411c msgid "In the third example, only `itemD` is provided, so it appears on the command line." -msgstr "在第三个示例中，仅提供了 `itemD`，因此它显示在命令行上。" +msgstr "在第三个示例中，仅提供了 `itemD`, 因此它出现在命令行上。" #: ../../src/topics/inputs.md:255 #: b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" -msgstr "带有表达式的互斥输入参数" +msgstr "互斥输入参数与表达式" #: ../../src/topics/inputs.md:257 #: 2c3b884cb1c54521900cc90782e8a58d msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." msgstr "" -"若要将互斥的输入参数与表达式结合，需意识到`inputs`JavaScript对象将包含互斥输" -"入值中的一个，这意味着你可能需要使用一个**or**布尔运算符来检查存在哪些值。" +"将互斥的输入参数与表达式结合使用时，需要注意 `inputs` 这个 JavaScript 对象可" +"能包含互斥输入值中的任何一个。这意味着你可能需要用逻辑“**或**”运算符来检查哪" +"些值是存在的。" #: ../../src/topics/inputs.md:262 #: a1073b6306044dffb414319ae01f68bb msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." -msgstr "让我们来一个示例，其包含了一个互斥的 `file_format`输入参数，该参数接受 " -"`null`（即未提供任何值）或任何枚举的值。" +msgstr "" +"我们来看一个例子，其中 `file_format` 输入参数的取值是互斥的。该参数接受 " +"`null`（即未提供任何值），或一个特定的枚举类型所包括的值。" #: ../../src/topics/inputs.md:265 #: 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" +msgstr "`exclusive-parameter-expressions.cwl`" #: ../../src/topics/inputs.md:271 #: 9a1d92334685449386dfa3b3a899ed48 msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" msgstr "" -"请留意，在不考虑`null`值的情况下，JavaScript表达式如何使用互斥输入参数的值。" -"如果提供一个有效值，比如 “fasta” （其中一个枚举的值），命令将成功执行：" +"请注意，这里的 JavaScript 表达式用到了互斥输入参数的值，但没有考虑到空值 " +"`null` 的情况。如果提供的值有效，比如 “fasta” " +"（枚举中的一个值），命令将会成功执行：" #: ../../src/topics/inputs.md:280 #: fb623af4c480411b8fde28d01c981411 msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." msgstr "" -"但是，如果未提供任何输入值，则 `file_format` 将被评估为 `null` " -"值。由于该值与输出字段的预期类型（`字符串`）不匹配，工作流将运行失败。" +"但是，如果未提供任何输入值，则 `file_format` 的值为 `null`, " +"从而不符合输出字段的预期类型（字符串 `string`），导致工作流运行失败。" #: ../../src/topics/inputs.md:289 #: e98e165f6bba40809c90473d72f9d592 msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." msgstr "" -"要进行纠正，请务必记住在使用互斥参数或任何允许 `null` 的参数时，应在 " -"JavaScript 表达式中采用 or 运算符。例如，表达式可以更改为 `$（" -"inputs.file_format " -"||'auto'）`，如果命令行或作业输入文件中未提供默认值，则表达式具有默认值。" +"为了修正这个问题，需要记住的，是在 JavaScript " +"表达式中使用互斥参数或任何允许为空 (`null`) " +"的参数时，应使用逻辑“或”运算符。例如，表达式可以修改为 `$(inputs.file_format " +"|| 'auto')`, 从而在命令行或作业输入文件未提供值的情况下有默认值可用。" #: ../../src/topics/metadata-and-authorship.md:1 #: d33aa2353ad44fb885d3a1ee48263dc4 -#, fuzzy msgid "Metadata and Authorship" -msgstr "元数据和授权" +msgstr "元数据和著作人信息" #: ../../src/topics/metadata-and-authorship.md:3 #: cd64d2d828834cbbb24ea5358caf5405 msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." msgstr "" -"正确执行不需要的实现扩展（例如，与 GUI 表示相关的字段）和有关工具或工作流本身" -"的元数据（例如，用于引文的作者身份）可以作为任何对象的附加字段提供。正如 [" -"Schema Salad 规范][schema-salad]中所述，此类扩展字段（例如 `format: " -"edam:format_2572`）可以使用文档的 `$namespaces` 章节中所列的命名空间前缀（" -"例如 edam：http://edamontology.org/" -"）。如下所示，添加命名空间前缀后，便可在文档的任何位置访问该字段。否则，" -"必须使用完整的 URL：`格式：http://edamontology.org/format_2572`。" +"由某个实现所提供的非必需、不影响正确执行的扩展（如关于图形界面中展示的字段）" +"，以及关于工具或工作流本身的元数据（如用于引文的作者信息），都可以作为任意对" +"象的附加字段提供。这种扩展字段（形如 `format: edam:format_2572`）" +"可以使用文件 `$namespaces`（命名空间）部分依照 [Schema Salad 规约][schema-" +"salad]的要求列举的命名空间前缀（例如 `edam：http://edamontology.org/" +"`）。如下所示，一旦添加了命名空间前缀，便可在文档的任何位置使用它。否则，" +"必须使用完整的 URL: `format: http://edamontology.org/format_2572`." #: ../../src/topics/metadata-and-authorship.md:13 #: 80af387fe3ff4e2da999903385bd602b msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." -msgstr "对于所有的开发人员，我们建议为你的工具和工作流程提供以下最小元数据。本示例包" -"含允许他人引用您工具的元数据。" +msgstr "我们建议所有的开发者为自己编写的工具和工作流提供类似下面所示的精简版元数据。" +"此例中的元数据向他人说明如何在文献中引用你的工具。" #: ../../src/topics/metadata-and-authorship.md:16 #: 0d5200bbbfdc43e6a78b4e4c3096ebd7 msgid "`metadata_example2.cwl`" -msgstr "" +msgstr "`metadata_example2.cwl`" #: ../../src/topics/metadata-and-authorship.md:28 #: d402bf528c7f4eb69aaaa275be2bf1d4 msgid "Extended Example" -msgstr "扩展示例" +msgstr "进一步扩展的例子" #: ../../src/topics/metadata-and-authorship.md:30 #: cb9980db4e5f4c74b01c2dec6d5e92d0 msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." msgstr "" -"对于积极性高的人而言，也可使用更多的元数据来注释工具。此示例包括作为关键字的 " -"EDAM 本体标记（允许对相关工具进行分组）、使用该工具所需的硬件要求的提示以及更" -"多元数据字段。" +"如果您积极性更高，也可以加入更多的元数据来注释工具。此例中加入了 EDAM 本体标" +"签作为关键字（以便将彼此关联的工具分组）、关于硬件要求的软性提示，以及其他元" +"数据字段。" #: ../../src/topics/metadata-and-authorship.md:35 #: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" -msgstr "" +msgstr "`metadata_example3.cwl`" #: ../../src/topics/operations.md:1 #: 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" -msgstr "操作" +msgstr "抽象操作" #: ../../src/topics/operations.md:3 #: 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." -msgstr "操作是一种 CWL 流程，与工作流、命令行工具或表达式工具类似。操作是工作流的一个" -"步骤，用于指定输入和输出，但没有提供足够的信息来执行。" +msgstr "" +"抽象操作 (Operation) 与工作流、命令行工具或表达式工具类似，是一种 CWL 流程。" +"作为工作流中的一个步骤，它可以指定输入和输出，但不完全提供具体执行所需的信息" +"。" #: ../../src/topics/operations.md:7 #: 5565c1b2d8a349169a305a9b26b4574d msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" -msgstr "在准备将工作流提交至 CWL " -"运行程序之前，您可以在开发期间创建操作以可视化工作流：" +msgstr "在开发周期中，工作流准备就绪、可以提交给 CWL " +"运行程序之前，您可以创建抽象操作，将工作流可视化：" #: ../../src/topics/operations.md:10 #: 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" -msgstr "" +msgstr "`operations.cwl`" #: ../../src/topics/operations.md:16 #: 88160cef4cfa4add9020aa89511a5749 msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" -msgstr "工作流中的 `uppercase`步骤是一个操作，可以像命令行工具或表达式一样使用，" -"也可以使用 CWL 查看器或 `cwltool`进行绘制：" +msgstr "" +"工作流中的 `uppercase` 步骤是一个抽象操作，可以充当命令行工具或表达式使用。" +"您可以用 CWL Viewer 或 `cwltool` 将它绘制出来：" #: ../../src/topics/operations.md:24 #: 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" msgstr "" -"上述命令的输出可使用Graphviz渲染器进行渲染。下面的图片是使用Sphinx " -"Graphviz指令来渲染的（本用户指南是使用Sphinx构建的）：" +"以上命令的输出可用 Graphviz 渲染出来。下面的图片是使用 Sphinx Graphviz " +"指令来渲染的（本《用户指南》是以 Sphinx 编译）：" #: ../../src/topics/operations.md:55 #: 730ba1434a1445ae847ec6153b6a3b72 msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" -msgstr "如果您尝试通过`cwltool`来运行，命令将运行失败，因为`cwltool`缺少足够信息来了" -"解执行的方法：" +msgstr "如果您尝试用 `cwltool` 运行它，该命令会失败，因为 `cwltool` " +"缺少足够信息，无从知晓如何运行它：" #: ../../src/topics/operations.md:58 #: 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" -msgstr "`cwltool`不知道如何运行操作" +msgstr "`cwltool` 不知道如何运行抽象操作" #: ../../src/topics/operations.md:66 #: a25d0b1e13324b40a6b8fcd227948c4f msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." -msgstr "" -"CWL 运行程序可能会提出将操作绑定到具体步骤的方法。例如，CWL " -"运行程序可以使用带有 ID " -"的抽象操作，而这些操作对应于不同工作流引擎执行的步骤。" +msgstr "CWL 运行程序可能安排一些将抽象操作绑定到具体步骤的方法。例如，带有 ID " +"的抽象操作有可能对映到其他工作流引擎中执行的步骤。" #: ../../src/topics/outputs.md:1 #: da077da5eb8a4ffebfde041fc16300de @@ -2697,66 +2700,66 @@ msgstr "返回输出文件" #: ../../src/topics/outputs.md:5 #: d661df070e3040869da412d07a71f716 msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "工具的 ` 输出 ` 是运行工具后应返回的输出参数列表。 " -"每个参数都有一个代表其名称的 `id`以及描述其有效值类型的 `type`。" +msgstr "" +"某个工具的 ` outputs `（输出）项是运行该工具后应返回的输出参数列表。 " +"每个参数都有一个代表其名称的 `id`字段，以及描述其有效值类型的 `type` 字段。" #: ../../src/topics/outputs.md:10 #: a11585474d3849cca5467512ed964743 msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." msgstr "" -"工具在 CWL 下运行时，起始工作目录即为指定的输出目录。 " -"基础工具或脚本必须以在输出目录中创建的文件形式记录其结果。 CWL " -"工具返回的输出参数要么是输出文件本身，要么来自检查这些文件的内容。" +"工具在 CWL 下运行时，起始工作目录即指定输出目录。 " +"基础工具或脚本记录运行结果，必须以输出目录下文件的形式实现。 CWL " +"工具返回的输出参数要么是输出文件本身，要么是分析这些文件的内容而得出的信息。" #: ../../src/topics/outputs.md:16 #: 2682f9ca8e604a0c9986f7746fdec960 msgid "The following example demonstrates how to return a file that has been extracted from a tar file." -msgstr "下面的示例演示了如何返回已从 tar 文件中提取的文件。" +msgstr "下例演示怎样返回从 tar 文件中提取的文件。" #: ../../src/topics/outputs.md:19 #: 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "将强制参数传递至 `baseCommand`" +msgstr "将必要参数传递给 `baseCommand`" #: ../../src/topics/outputs.md:21 #: 22447a560f6f4317bf67bd7c4336126c msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" msgstr "" -"在前面的示例中，`baseCommand` 只是一个字符串，任何参数都作为 CWL 输入传递。" -"我们可以使用 _ 字符串数组 _ ，而不是单个字符串。 " -"第一个元素是要运行的命令，所有后续元素均为强制命令行参数" +"在此前的例子里，`baseCommand` 命令不过是一个字符串，命令的参数都由 CWL 输入传" +"递而来。不过，我们也可以用字符串数组构建命令。为此，只需要让待运行的命令成为" +"数组的第一个元素，这样所有后续元素均成为命令行的必要参数" #: ../../src/topics/outputs.md:26 #: f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" -msgstr "" +msgstr "`tar.cwl`" #: ../../src/topics/outputs.md:32 #: ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" -msgstr "" +msgstr "`tar-job.yml`" #: ../../src/topics/outputs.md:38 #: dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." -msgstr "接下来，为此示例新建一个 tar 文件。" +msgstr "接下来，新建一个 tar 文件供本示例使用。" #: ../../src/topics/outputs.md:45 #: 52703d6b7f914097934bfad13663abeb msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "现在，通过命令行上的工具描述和输入对象调用 `cwltool`：" +msgstr "现在，在命令行上结合工具描述和输入对象运行 `cwltool`:" #: ../../src/topics/outputs.md:51 #: 5e1c79df657d4a6e84e055dd6b300a5d msgid "The field `outputBinding` describes how to set the value of each output parameter." -msgstr "`outputBinding` 字段描述了如何设置每个输出参数的值。" +msgstr "`outputBinding` 字段描述如何设置每个输出参数的值。" #: ../../src/topics/outputs.md:62 #: 329d2809dfae4f90bc638f5f03a47ee3 msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." -msgstr "`glob` " -"字段由输出目录中的文件名称组成。如果事先不知道文件名，可以使用通配符模式，" -"例如 `glob：“*.txt”`。" +msgstr "`glob` 字段由输出目录中的文件名组成。如果事先不知道文件名，可以使用通配符，" +"例如 `glob: '*.txt'`." #: ../../src/topics/outputs.md:65 #: 96df2d45e42441d49ce193ccbfab78a3 @@ -2767,13 +2770,13 @@ msgstr "捕获标准输出" #: c6bcf7c6a8774dd6be41cc775848c3b8 msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." msgstr "" -"要捕获工具的标准输出流，请添加 `stdout` 字段及文件名（即输出流目标位置）。 " -"然后，在相应的输出参数上添加 `type： stdout`。" +"要捕获工具的标准输出流，请添加 `stdout` 字段，配上输出流应定向到的文件名。 " +"然后，给相应的输出参数添加 `type: stdout` 字段。" #: ../../src/topics/outputs.md:71 #: 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" -msgstr "" +msgstr "`stdout.cwl`" #: ../../src/topics/outputs.md:89 #: 2fb58c2feaa84970bb5274c49f4b5b64 @@ -2783,25 +2786,25 @@ msgstr "数组输出" #: ../../src/topics/outputs.md:91 #: 9647019d8c37466886e7aab6f176634d msgid "You can also capture multiple output files into an array of files using `glob`." -msgstr "您也可使用`glob`捕获多个输出文件，并将其保存为一个文件数组。" +msgstr "您也可以用 `glob` 将多个输出文件捕获至一个文件数组。" #: ../../src/topics/outputs.md:93 #: b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" -msgstr "" +msgstr "`array-outputs.cwl`" #: ../../src/topics/outputs.md:99 #: cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" -msgstr "" +msgstr "`array-outputs-job.yml`" #: ../../src/topics/outputs.md:112 #: cc067051f22f433bbece08f60933e002 msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" -"如 [YAML 指南](yaml-guide.md#arrays)中所述，预期输出数组在 `array-outputs-job" -".yml` 中指定，每个条目均以前导符 `-`标记。这种格式也可以在 CWL " -"描述中用于标记数组中的条目，这将在接下来几个章节中进行演示。" +"如[《YAML 指南》](yaml-guide.md#arrays)中所述，`array-outputs-job.yml` " +"文件中行首为 `-` 的成员代表数组元素，用以指明我们期待的各个输出。" +"这种格式还可以用在 CWL 描述中表示数组成员。接下来若干章节中会演示这一用法。" #: ../../src/topics/parameter-references.md:1 #: a190a6440ec34898990cdac05d809f22 From 1ecadfc50a38c9ae5ccf3e01ab0c21ef9f9e2b5d Mon Sep 17 00:00:00 2001 From: zoe-translates Date: Thu, 29 Jun 2023 13:38:59 +0800 Subject: [PATCH 076/179] Metadata and Authorship: Harmonize examples and highlight difference (#403) The examples in `metadata_example2.cwl` and `metadata_example3.cwl` are meant to be compared, and the latter is an extension of the former. However, the differences are not obvious in the wall of text. For this, line-highlighting is used in the latter to point out the different parts. In addition, minor/trivial differences in the pair are removed, so they differ *only* in the highlighted lines. This also fixes some minor, inconsistent indentations. --- .../cwl/metadata-and-authorship/metadata_example2.cwl | 4 ++-- .../cwl/metadata-and-authorship/metadata_example3.cwl | 8 ++++---- src/topics/metadata-and-authorship.md | 1 + 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl b/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl index ca2b59bd..31b92dd7 100755 --- a/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl +++ b/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl @@ -45,5 +45,5 @@ $namespaces: edam: http://edamontology.org/ $schemas: - - https://schema.org/version/latest/schemaorg-current-https.rdf - - http://edamontology.org/EDAM_1.18.owl + - https://schema.org/version/latest/schemaorg-current-https.rdf + - http://edamontology.org/EDAM_1.18.owl diff --git a/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl b/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl index e30a3c64..1c8a5858 100755 --- a/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl +++ b/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl @@ -48,9 +48,9 @@ s:keywords: edam:topic_0091 , edam:topic_0622 s:programmingLanguage: C $namespaces: - s: https://schema.org/ - edam: http://edamontology.org/ + s: https://schema.org/ + edam: http://edamontology.org/ $schemas: - - https://schema.org/version/latest/schemaorg-current-http.rdf - - http://edamontology.org/EDAM_1.18.owl + - https://schema.org/version/latest/schemaorg-current-https.rdf + - http://edamontology.org/EDAM_1.18.owl diff --git a/src/topics/metadata-and-authorship.md b/src/topics/metadata-and-authorship.md index b71acf54..57850533 100644 --- a/src/topics/metadata-and-authorship.md +++ b/src/topics/metadata-and-authorship.md @@ -36,6 +36,7 @@ requirements in order to use the tool, and a few more metadata fields. :language: cwl :caption: "`metadata_example3.cwl`" :name: metadata_example3.cwl +:emphasize-lines: 8-10, 47-48 ``` [schema-salad]: https://www.commonwl.org/v1.0/SchemaSalad.html#Explicit_context From b6c2f66a69f2eb63ba37b9a012eaa73743320701 Mon Sep 17 00:00:00 2001 From: zoe-translates Date: Fri, 30 Jun 2023 08:44:25 +0800 Subject: [PATCH 077/179] Topics > Inputs: Clarify the purpose of handling nullables in JS. (#402) * Topics > Inputs: Clarify the purpose of handling nullables in JS. - The narrative about "using an or operator" appeared to have missed the point about the purpose. In fact, there's nothing special about the "or" (double-pipe || ) logical operator in the JS expression when it comes to checking the actual underlying type of a union-typed value. The problem is twofold: 1. The underlying issue is not that the *value* may "contain one of the exclusive input values"; it's their *type* difference that causes incompatibilities. 2. For this, the solution is to *handle* the possible types, and it only happens that in this particular example, a standard "default" syntax with the shortcircuiting boolean operator would do. Therefore the content is revised to explicitly warn of the possibility of encountering the "wrong" type, and give a better rationale of using the || syntax in the expression. - Minor normalization of blocks. Use three backticks when these blocks are siblings without nesting. * Topics > Inputs: Further clarify how || works in the JS expression - No need to mention "any other" falsy value - Quantify the word "expression" to mean the expression as a whole, not any of its parts that may also stand as an expression. * Topics > Inputs: Remove the mentions of "truthy" and "falsy". These terms are too specific to JS, and likely a distraction from the main point. --- src/topics/inputs.md | 42 +++++++++++++++++++++++++----------------- 1 file changed, 25 insertions(+), 17 deletions(-) diff --git a/src/topics/inputs.md b/src/topics/inputs.md index 88b8ea72..7cc5c7d2 100644 --- a/src/topics/inputs.md +++ b/src/topics/inputs.md @@ -56,7 +56,7 @@ two commands and the expected output from the command line: ```{runcmd} cwltool inp.cwl inp-job.yml :working-directory: src/_includes/cwl/inputs -```` +``` ```{tip}

Where did those `/tmp` paths come from?

@@ -223,7 +223,7 @@ In the first example, you can't provide `itemA` without also providing `itemB`. ```{runcmd} cwltool record.cwl record-job2.yml :working-directory: src/_includes/cwl/inputs :emphasize-lines: 4, 10-11, 23 -```` +``` ```{code-block} console $ cat output.txt @@ -242,7 +242,7 @@ matching item (`itemC`) is added to the command line and remaining item (`itemD` ```{runcmd} cwltool record.cwl record-job3.yml :working-directory: src/_includes/cwl/inputs :emphasize-lines: 9-10, 22 -```` +``` ```{code-block} console $ cat output.txt @@ -254,10 +254,11 @@ command line. ### Exclusive Input Parameters with Expressions -If you use exclusive input parameters combined with expressions, you need to be -aware that the `inputs` JavaScript object will contain one of the exclusive -input values. This means that you might need to use an **or** boolean operator -to check which values are present. +If you use exclusive input parameters and reference them in expressions, you +need to be aware that the `inputs` JavaScript object will contain one of the +possible, mutually-exclusive input values. Because the types of these exclusive +values may differ, you may need to check which type is in use when you +reference the properties of the `input` object. Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum. @@ -268,17 +269,17 @@ that accepts `null` (i.e. no value provided), or any value from an enum. :name: exclusive-parameter-expressions.cwl ``` -Note how the JavaScript expression uses the value of the exclusive input parameter -without taking into consideration a `null` value. If you provide a valid value, -such as “fasta” (one of the values of the enum), your command should execute -successfully: +Note how the JavaScript expression uses the value of the exclusive input +parameter without taking into consideration a `null` value. If you provide a +valid value, such as `fasta` (one of the possible values of the enum), your +command should execute successfully: ```{runcmd} cwltool exclusive-parameter-expressions.cwl --file_format fasta :working-directory: src/_includes/cwl/inputs -```` +``` However, if you do not provide any input value, then `file_format` will be -evaluated to a `null` value, which does not match the expected type for the +evaluated to `null`, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow. ```{runcmd} cwltool exclusive-parameter-expressions.cwl @@ -286,10 +287,17 @@ output field (a `string`), resulting in failure when running your workflow. :emphasize-lines: 5-10 ``` -To correct it, you must remember to use an or operator in your JavaScript expression -when using exclusive parameters, or any parameter that allows `null`. For example, -the expression could be changed to `$(inputs.file_format || 'auto')`, to have -a default value if none was provided in the command line or job input file. +To correct it, you should explicitly handle the possibility of a `null` value. +For example, the expression could be changed to `$(inputs.file_format || +'auto')`, to have a default value `"auto"` if none was provided in the command +line or job input file. + +Here, the boolean “or” operator `||` in JavaScript is used for its +_short-circuiting_ property. If `inputs.file_format` is “true” in a boolean +context (e.g. a valid non-empty string from the enum), the evaluation of the +expression stops at the first operand of `||`; it “short-circuits”. If however +`inputs.file_format` is `null`, the whole expression’s value becomes that of +the second operand, which is why a reasonable default can be provided there. % TODO % From 3ef436e36b33323abdf6b86d47009afe00e16d96 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Sat, 1 Jul 2023 06:31:03 +0200 Subject: [PATCH 078/179] Translations update from Hosted Weblate (#410) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Translated using Weblate (Chinese (Simplified)) Currently translated at 78.2% (468 of 598 strings) Co-authored-by: Zoë Ma Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 4.0% (24 of 598 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 4.0% (24 of 598 strings) Co-authored-by: Michael Crusoe Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide --------- Co-authored-by: Zoë Ma Co-authored-by: Manabu ISHII Co-authored-by: Michael Crusoe --- locales/ja/LC_MESSAGES/user_guide.po | 14 +++--- locales/zh_Hans/LC_MESSAGES/user_guide.po | 57 +++++++++++------------ 2 files changed, 35 insertions(+), 36 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 6dfd535f..78d7b5eb 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,8 +8,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-06-29 03:51+0000\n" -"Last-Translator: Manabu ISHII \n" +"PO-Revision-Date: 2023-07-01 03:53+0000\n" +"Last-Translator: Michael Crusoe \n" "Language-Team: Japanese \n" "Language: ja\n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 4.18.1\n" +"X-Generator: Weblate 5.0-dev\n" #: ../../LICENSE.md:2 #: 4e203044f0464fd5a3256430391dde12 @@ -169,7 +169,7 @@ msgstr "" #: a7d84f740a714ec588503ee084fbbc34 msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" msgstr "その後、`chmod +x scriptname.sh` " -"というコマンドでスクリプトを実行可能な状態にします。" +"というコマンドでスクリプトを実行可能な状態にします" #: ../../src/faq.md:97 #: 569d553abe85450c9d1c37456bf412f4 @@ -730,7 +730,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:67 #: 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" -msgstr "`truc.cwl`" +msgstr "`true.cwl`" #: ../../src/introduction/prerequisites.md:73 #: 6391e08e0bde49f4b21286d8fdb97433 @@ -785,7 +785,7 @@ msgstr "検証`true.cwl` with`cwl-runner`." #: ../../src/introduction/prerequisites.md:120 #: 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" +msgstr "`true.cwl` を `cwl-runner` で実行します。" #: ../../src/introduction/prerequisites.md:125 #: 705807fae182425dbf4244dbf2be1226 @@ -3113,7 +3113,7 @@ msgstr "" msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" "[Common Workflow " -"Languageによるワークフロー入門：コントリビューターのために】(https" +"Languageによるワークフロー入門：コントリビューターのために](https" "://carpentries-incubator.github.io/cwl-novice-tutorial/)" #: ../../src/tutorials.md:11 diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index f70ab516..5f3d463a 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-06-29 03:51+0000\n" +"PO-Revision-Date: 2023-07-01 03:53+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified) \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 4.18.1\n" +"X-Generator: Weblate 5.0-dev\n" #: ../../LICENSE.md:2 #: 4e203044f0464fd5a3256430391dde12 @@ -2815,64 +2815,63 @@ msgstr "参数引用" #: dbfe2c1123144316aa026374b0f353d3 msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." msgstr "" -"在前面的示例中，我们使用“tar”程序提取了一个文件。但是，该示例非常有限，因为它" -"假定我们感兴趣的文件称为“hello.txt”，并将其写入 `.cwl` " -"文件中。这不是执行此操作的最佳方法，因为“hello." -"txt”文件名可能会有所不同或取决于所使用的输入文件。 为了避免这种情况，" -"我们可以在作业参数文件 （`.yml`） 中指定文件名称。本示例将演示如何从其他字段" -"动态引用输入参数值，这将允许我们指定要提取的文件名称。" +"在前面的例子中，我们使用 “tar” 程序提取了一个文件。但是，该示例局限性很强，" +"因为它假定了我们感兴趣的文件名就是 “hello.txt”, 而且这种假设直接写入了 `.cwl`" +" 代码文件里。这种做法有欠妥当，因为文件名 “hello.txt” " +"可能会改变，也可能依赖我们实际用到的输入文件。 为了避免这类情况，" +"我们可以在作业参数 (`.yml`) 文件中指定我们想要的文件名。本示例将演示如何从其" +"他字段动态引用输入参数值，以便指定待提取的文件名。" #: ../../src/topics/parameter-references.md:13 #: 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" -msgstr "" +msgstr "`tar-param.cwl`" #: ../../src/topics/parameter-references.md:19 #: 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" -msgstr "" +msgstr "`tar-param-job.yml`" #: ../../src/topics/parameter-references.md:25 #: 074cf5d912854d8c864607cc24b15302 msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "新建输入文件，并使用命令行上的工具描述和输入对象调用 `cwltool`：" +msgstr "创建输入文件，然后以工具描述和输入对象为命令行参数调用 `cwltool`:" #: ../../src/topics/parameter-references.md:36 #: 0290af3e3cbb4b32b0450c8771f3bf95 msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." -msgstr "某些字段允许 `$（...） " -"中所列的参数引用`，将对这些字段进行评估并替换为被引用的值。" +msgstr "某些字段允许出现用 `$(...)` 符号括起来的参数引用，由求值的结果代入。" #: ../../src/topics/parameter-references.md:47 #: b54240bb94f746bba7511633aa969db0 msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." msgstr "" -"需使用Javascript语法的子集编写引用。 在此示例中，`$（inputs." -"extractfile）`、`$（inputs[“extractfile”]）` 以及 " -"`$（inputs['extractfile']）` 为等效项。" +"引用的编写用的是 JavaScript 语法的一个子集。 本例中，`$(inputs." +"extractfile)`、`$(inputs[\"extractfile\"])` 和 `$(inputs['extractfile'])` " +"效果相同。" #: ../../src/topics/parameter-references.md:51 #: 8b70a072aa87414c88e89a3e19af0a51 msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." -msgstr "“输入”变量的值是调用 CWL 工具时提供的输入对象。" +msgstr "“inputs” 变量的取值为 CWL 工具被调用时获得的输入对象。" #: ../../src/topics/parameter-references.md:54 #: eea20f89c45f424a888178df53713b28 msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." msgstr "" -"请注意，由于 `File` " -"参数是对象，要获取输入文件的路径，必须引用文件对象上的路径字段；" -"若要引用上方示例中 tar 文件的路径，您需要编写 `$（inputs.tarfile.path）`。" +"请注意，由于 `File`（文件）参数是对象。因此，要获取输入文件的路径，须引用文件" +"对象上的“path”（路径）字段。例如，要引用上面例子中 tar 文件的路径，" +"则需要写为 `$(inputs.tarfile.path)`." #: ../../src/topics/parameter-references.md:59 #: cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" -msgstr "哪里允许参数引用？" +msgstr "参数引用可以出现在哪些地方？" #: ../../src/topics/parameter-references.md:61 #: 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" -msgstr "您只能在某些字段中使用参数引用。 这些字段是：" +msgstr "参数引用只能出现在有限的字段中，即：" #: ../../src/topics/parameter-references.md:63 #: 7647e0229a924f988cf02b7812a55c06 @@ -2949,7 +2948,7 @@ msgstr "" #: ../../src/topics/parameter-references.md:103 #: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "位于 [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "[Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent) 对象中" #: ../../src/topics/parameter-references.md:107 #: 9a6b311ded8d4e43ae635b1b927dbdf2 @@ -2972,21 +2971,21 @@ msgstr "指定软件需求" #: 574d93d1d592458a985f259519c036cb msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." msgstr "" -"通常，工具描述将针对特定版本的软件编写。为了方便其他人使用您的描述，您可以在 " -"`提示 ` 部分添加`SoftwareRequirement` " -"字段，这也可能有助于他人了解此描述所适用的工具版本。" +"工具描述往往是针对特定版本的软件而编写。为了方便他人使用您的工具描述，" +"您可以在 `hints` 部分添加`SoftwareRequirement` " +"字段，用来指明该描述适用于哪些版本的工具。" #: ../../src/topics/specifying-software-requirements.md:13 #: 82e48b3e3c3f451480cc0b6a529271f6 msgid "In this example, the software requirement being described is InterProScan version 5.21-60." -msgstr "在本示例中，所描述的软件要求是InterProScan版本5.21-60。" +msgstr "本例中描述的软件要求为 5.21-60 版本的 InterProScan." #: ../../src/topics/specifying-software-requirements.md:25 #: 02e40154eac74ecc98d0447d03475b44 msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." msgstr "" -"根据您的 CWL 运行程序，可在运行作业之前使用这些提示检查所需软件是否已安装且可" -"用。要使用参考实现启用这些检查，请使用 [依赖项解析程序配置][依赖项]。" +"您的 CWL 运行程序有可能支持在运行作业之前，根据提示检查所需软件是否已安装就绪" +"。如果要让参考实现启用这些检查，请使用[依赖项解析配置][dependencies]。" #: ../../src/topics/specifying-software-requirements.md:29 #: 8cb1c5d9b1a54c40924099494eb766c6 From 704f8a77d1905c1caf78bc62745075a9c730909f Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Wed, 5 Jul 2023 14:24:19 +0200 Subject: [PATCH 079/179] Translations update from Hosted Weblate (#411) * Translated using Weblate (Japanese) Currently translated at 4.0% (24 of 598 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Chinese (Simplified)) Currently translated at 80.7% (483 of 598 strings) Co-authored-by: Michael Crusoe Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide --------- Co-authored-by: Manabu ISHII Co-authored-by: Michael Crusoe --- locales/ja/LC_MESSAGES/user_guide.po | 3580 ++++++++++++--------- locales/zh_Hans/LC_MESSAGES/user_guide.po | 34 +- 2 files changed, 2113 insertions(+), 1501 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 78d7b5eb..70df9bb6 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -10,8 +10,8 @@ msgstr "" "POT-Creation-Date: 2023-01-25 14:33+0100\n" "PO-Revision-Date: 2023-07-01 03:53+0000\n" "Last-Translator: Michael Crusoe \n" -"Language-Team: Japanese \n" +"Language-Team: Japanese \n" "Language: ja\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" @@ -19,472 +19,521 @@ msgstr "" "Plural-Forms: nplurals=1; plural=0;\n" "X-Generator: Weblate 5.0-dev\n" -#: ../../LICENSE.md:2 -#: 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" msgstr "ライセンス" -#: ../../LICENSE.md:4 -#: 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" msgstr "" -#: ../../LICENSE.md:6 -#: 747f9dd48bc54f44adcd8b18c57f4d9d -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "" +"All Common Workflow Language project instructional material and changes to " +"the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable summary " +"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" +"[cc-by-legal]." msgstr "" -#: ../../LICENSE.md:12 -#: 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" msgstr "" -#: ../../LICENSE.md:14 -#: 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +msgid "" +"to **Share**---copy and redistribute the material in any medium or format" msgstr "" -#: ../../LICENSE.md:15 -#: 18a3a0aec35743848c97bc178f9c94ff +#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "" -#: ../../LICENSE.md:17 -#: b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." msgstr "" -#: ../../LICENSE.md:19 -#: 6021e65292a149d5b15e14491f3eb05e -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the license " +"terms:" msgstr "" -#: ../../LICENSE.md:24 -#: 8fb7a2946c384364814c6ec3910997d3 -msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow Language " +"project, and, where practical, linking to https://www.commonwl.org/ ), " +"provide a [link to the license][cc-by-human], and indicate if changes were " +"made. You may do so in any reasonable manner, but not in any way that " +"suggests the licensor endorses you or your use." msgstr "" -#: ../../LICENSE.md:32 -#: 8161753b7526445db319210044566200 -msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything the " +"license permits. With the understanding that:" msgstr "" -#: ../../LICENSE.md:36 -#: 15314ba527864eaa834cf1185cfcc4e3 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +msgid "" +"You do not have to comply with the license for elements of the material in " +"the public domain or where your use is permitted by an applicable exception " +"or limitation." msgstr "" -#: ../../LICENSE.md:39 -#: b351ddf9847d48b1a2a87fc78eaba4d2 -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "" +"No warranties are given. The license may not give you all of the permissions " +"necessary for your intended use. For example, other rights such as " +"publicity, privacy, or moral rights may limit how you use the material." msgstr "" -#: ../../LICENSE.md:44 -#: a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea msgid "Software" msgstr "ソフトウェア" -#: ../../LICENSE.md:46 -#: 84b2c685bbab48449fdc72d2a1e42bf4 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the " +"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" -#: ../../LICENSE.md:51 -#: 0f68eafafaef4b54accba7e13bfaa702 -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." msgstr "" -#: ../../src/_includes/what-is-cwl.md:1 -#: ../../src/_includes/what-is-cwl.md:2 -#: eab02dc13915490bb3c9ba744d78b6a7 -#: d4f35995b0f6494d9771a4be0a82538f +#: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 d4f35995b0f6494d9771a4be0a82538f #: d6ccd4b546254f56a597d67dd4fdc5d6 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece of " +"software, tools and workflows described using CWL are portable across a " +"variety of platforms that support the CWL standard." msgstr "" -#: ../../src/episodes.md:5 -#: ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc -#: 436cfca6f857469bbff7c652df32160f +#: ../../src/episodes.md:5 ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f msgid "This page has moved" msgstr "このページは移動しました" -#: ../../src/episodes.md:9 -#: cc11f5d29206492d9f2f0922882b6159 -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 -#: e2ed894d325a4f50a5e2dc69da5531a1 +#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" msgstr "よくある質問" -#: ../../src/faq.md:11 -#: 61edb787dab04ca2ad3ed07616d878a0 +#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 -#: d5321589e7ed4f0db3c630cc39800791 +#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" msgstr "入力ファイルの名前を変更する" -#: ../../src/faq.md:43 -#: fc62427c0a004810b055dee90ec5e2d9 -msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +msgid "" +"This example demonstrates how to change the name of an input file as part of " +"a tool description. This could be useful when you are taking files produced " +"from another step in a workflow, and don't want to work with the default " +"names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 -#: 1c6b8a4194a14611b4061b1540c3807f +#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" msgstr "出力ファイルの名前を変更する" -#: ../../src/faq.md:61 -#: bc7ad10c929848a3a9a240a3c501d299 -msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" -msgstr "この例では、出力ファイルの名前を、ツールから与えられたデフォルトの名前から変" +#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +msgid "" +"This example demonstrates how to change the name of an output file from the " +"default name given to it by a tool:" +msgstr "" +"この例では、出力ファイルの名前を、ツールから与えられたデフォルトの名前から変" "更する方法を示します：" -#: ../../src/faq.md:82 -#: 7225a993d281421b95c8e3df2846a0e3 +#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 msgid "Referencing a Local Script" msgstr "ローカルスクリプトを参照する" -#: ../../src/faq.md:84 -#: 7ef1dbb81993473f948d9c6f3c64b381 +#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" msgstr "ローカルスクリプトを参照するには、2つの方法があります：" -#: ../../src/faq.md:86 -#: 450edf800a18423195bea4fe8793a2cb -msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +msgid "" +"The first method involves adding the folder containing your scripts to the " +"`PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 -#: 1a8cc75ea6174b9297871b2e58971077 +#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 -#: a7d84f740a714ec588503ee084fbbc34 -msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" -msgstr "その後、`chmod +x scriptname.sh` " -"というコマンドでスクリプトを実行可能な状態にします" +#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +msgid "" +"After that, make the script executable with the command `chmod +x scriptname." +"sh`" +msgstr "" +"その後、`chmod +x scriptname.sh` というコマンドでスクリプトを実行可能な状態に" +"します" -#: ../../src/faq.md:97 -#: 569d553abe85450c9d1c37456bf412f4 -msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." msgstr "" -"最後に、`PATH` " -"を変更し、スクリプトが置かれているディレクトリを追加します。(`$HOME/bin` " -"を自分のスクリプトを保存するために使用するのは良い習慣です）。" +"最後に、`PATH` を変更し、スクリプトが置かれているディレクトリを追加します。(`" +"$HOME/bin` を自分のスクリプトを保存するために使用するのは良い習慣です）。" -#: ../../src/faq.md:104 -#: 95f5dbbd21084a318413b9528fb867be -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be +msgid "" +"Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 -#: 1b3cae80fa9a40ffb2259b8c1cd2b468 -msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 -#: 8d86baa239364f799d4f9d5ea2b0e314 -msgid "The second method involves including an input of `type: File` in the script itself:" +#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +msgid "" +"The second method involves including an input of `type: File` in the script " +"itself:" msgstr "" -#: ../../src/faq.md:135 -#: f2c109998c76434893ff16b17fdb2bd0 +#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 -#: c2c752b86bf94d6fb3751f4dd81bc7a7 +#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 -#: 2c38cc58cbb340bc935a5f00e96ba95c -msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their input " +"binding makes use of `self`. Below is an example workaround for this, " +"pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 -#: ce6db54bd0f54839a5beb948530a21f0 +#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 -#: d06cbf89028b4638ad54c2529bcbfa25 -msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +msgid "" +"Below is an example showing how to specify different strings to be added to " +"a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 -#: d53fb28dcad04e7788cba9e280a2343c +#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 -#: d9e30e11533b4d53a144f5df7041268d -msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +msgid "" +"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 -#: 941077158ec54ae19bfa2e2ad6662da1 +#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 -#: 937cb94a370640c788fbc3fe0b19f2e5 -msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +msgid "" +"The input must be an array consisting of exactly one entry for each input " +"link. If \"merge_nested\" is specified with a single link, the value from " +"the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 -#: a1d57e15656548128a76a8b975c564c9 +#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 -#: c8c235a9bf6240628f0b5493ffebf7e0 -msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " +"add `linkMerge: merge_nested` under the appropriate `in` entry of the " +"destination step." msgstr "" -#: ../../src/faq.md:229 -#: 3da4dcb043eb4423a53a14182949d9cd +#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 -#: 89b90d3bf1ea4ebd88482d435241fac5 -msgid "To make an input parameter optional, add a question mark to the type declaration." +#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." msgstr "" -#: ../../src/faq.md:247 -#: a854006054ce4ffe94bbfa73bdbecbf2 +#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 msgid "" msgstr "" -#: ../../src/faq.md:248 -#: f80eb714e9df417fbba555b5dd5f4d8c +#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 -#: 10af80fa13af4158aec7060550485350 -msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +msgid "" +"For command line flags that require a specific input as the argument an enum " +"type can be declared in CWL. **Specifying null here is known as long form " +"style. It does the same thing as the question mark on the other inputs.**" msgstr "" -#: ../../src/faq.md:267 -#: ad1c26711ccd4efd8fdb25f9293d33fd +#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd msgid "" msgstr "" -#: ../../src/faq.md:268 -#: 49e2095b51f84f609f5d4bc088ad9745 +#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 -#: 52b8538177c64090af51f5f6a696c28c -msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 -#: f96c9257e3734b8aa0cc5e065f74f944 +#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 -#: 7dc0540508084a3495ff3b2ac90fd323 -msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +msgid "" +"To properly set fields in a record input type, you need to pass a dictionary " +"to the input to properly set the parameters. This is done by using inline " +"JavaScript and returning the dictionary with the key of the field you want " +"to set. The source field is set to indicate the input from the workflow to " +"be used as the value." msgstr "" -#: ../../src/faq.md:342 -#: b53dc77466b24a67b52b8aadf4fab724 +#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 -#: cf4e7f3977ae4f9b877072c2b1c4b533 +#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 -#: 99b37739ef18443ca7c0e715a131e0c7 +#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 -#: 9b00b5a55ee941e1adbfe89e133791e3 +#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 -#: 07922147f7ab487ba2a1e7c43c9f410c +#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 -#: 7a11806f0c7045b48fe58a271f814797 +#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 -#: fdaec25650ab4b0fb1c527610e24ae5a -msgid "For example, the filename `a space is here.txt` includes 3 space characters." +#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +msgid "" +"For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" -#: ../../src/faq.md:371 -#: 182959fc9f4746d082994e07d05c8cde -msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 -#: cc7752e9989e4a6d957682f479d6fc60 +#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 -#: 6db1ebd2d6c74ceca889662cd7df5cd5 +#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 -#: 3de2513c7d7b4569ba63f7e6d29137b7 +#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 -#: ae3a9188706649e28f97bc4ec34c0821 +#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 -#: e1ac97ab6ad3449b8c54933d25257f73 +#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 -#: f6c402f7f6974edbbb5582c8e22f3869 +#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 -#: 190099a242a645c9b9f8bc3ce89d920d -msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +msgid "" +"If it is not possible to change the input identifier, then you can use an " +"alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 -#: 06a4f6ffc2da4d43b453d4784b42efd3 +#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 -#: 1901c34201054a9cae199b0dbb8b945e -msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +msgid "" +"The CWL standards are built around (optional) Docker format containers. The " +"reference runner and several other CWL implementations support running those " +"Docker format containers using the Singularity engine. Directly specifying a " +"Singularity format container is not part of the CWL standards." msgstr "" -#: ../../src/faq.md:450 -#: 2d498470524d47f18f9936ace6acebb0 +#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 -#: d7b044f5224a48eda09bc949cf645193 -msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +msgid "" +"You can use the --js-console option of cwltool, or " +"you can try creating a JavaScript or TypeScript project for your code, and " +"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 -#: 2754519265eb426b940bbbd2b8d64e1e +#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" msgstr "Common Workflow Language ユーザーガイド" -#: ../../src/index.md:3 -#: f8d6e4cd54cb42c88182a43171d97bab -msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +msgid "" +"This guide will introduce you to writing workflows using the [Common " +"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " +"guide describes the latest specification {{ cwl_version }}." msgstr "" -"本ガイドは、オープンスタンダードである [Common Workflow Language](https://www" -".commonwl.org/) (CWL) " -"を使用したワークフローの書き方を紹介するものです。本ガイドは、最新仕様{{ " -"cwl_version }}を解説しています。" +"本ガイドは、オープンスタンダードである [Common Workflow Language](https://" +"www.commonwl.org/) (CWL) を使用したワークフローの書き方を紹介するものです。本" +"ガイドは、最新仕様{{ cwl_version }}を解説しています。" -#: ../../src/index.md:7 -#: 132d40fee3b84469afa80d5ff613bf77 +#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 -#: 0f47157605a34ea58770ea898deebae4 -msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +msgid "" +"If you find that something is missing from this guide, or if you would like " +"to provide other feedback, file an Issue on the [project repository for this " +"guide][repo]. You can also suggest changes directly in a Pull Request by " +"clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" -#: ../../src/index.md:16 -#: 6d269e8d70184034bcb56385a6ca198f +#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 -#: ed74c9a4b623464480e2c184668fcec0 -msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +msgid "" +"If you are a beginner user get started with the [Introduction](/introduction/" +"index.md) section. For advanced users the subsections of the [Topics](/" +"topics/index.md) have detailed information about the most common topics for " +"CWL." msgstr "" -#: ../../src/index.md:23 -#: cfa67cf5521b414da6f7d34cbed283f7 -msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +msgid "" +"The Table of Contents is displayed at the top menu and also on the left " +"sidebar. It also appears further down this page but with links to " +"subsections. The right sidebar contains links to the sections of each page, " +"and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 -#: ee6b82bd86264e4bb1e8e4065b1e6b9c +#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 -#: e208c8a7506e41dcac9a403c5d2850c1 +#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 -#: ac62d326a68145b695e46b714d4e8156 -msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are expected " +"to be familiar with workflow managers, YAML, and comfortable with following " +"instructions for the command-line. The other sections of the user guide " +"cover the same concepts, but in more detail. If you are already familiar " +"with CWL or you are looking for more advanced content, you may want to skip " +"this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 -#: 984e6676b9d04c7092bc492f195dfb91 +#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 -#: cbe1d761da5b403d9605fa1fb8e62fdf -msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered in " +"this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 -#: 3a71b269bd3c49eb913cf69b60373c24 -msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes that " +"are backward-compatible. The last number is used for bug fixes, like typos " +"and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 -#: b171b72c48d44050a3416a7a42c4021d -msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +msgid "" +"The model used for the specification version is called Semantic Versioning. " +"See the end of this section to [learn more](#learn-more) about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 -#: b3df1607e9d242d78b22dc44335fbe2d +#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 -#: 078b58ffc1cc4d25a7c4eea3bb76e025 -msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "" +"An implementation of the CWL specification is any software written following " +"what is defined in a version of the specification document. However, " +"implementations may not implement every aspect of the specification. CWL " +"implementations are licensed under both Open Source and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 -#: c3869b4ec5ff47d99e8da79770722e04 -msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud " +"and high performance computing environments where tasks are scheduled in " +"parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 -#: 2482c84831fc4dfab629e7bfcfb41cbf +#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." msgstr "" @@ -495,7 +544,11 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:107 #: 86e6a06992dc4228bfda7add48e28ca3 -msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The " +"behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification " +"{{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 @@ -525,27 +578,44 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:119 #: cf2922f645904ac7955428ecddc37b8a -msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 #: 5f47aae608c041aeb4134d59dad314d2 -msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be used " +"to simplify workflows and command-line tools, moving common parts of a " +"workflow execution into reusable JavaScript code that takes inputs and " +"produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 #: f6f589481d0c4891beaccb63160619ef -msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgid "" +"Operation is an abstract process that also takes inputs, produces outputs, " +"and can be used in a workflow. But it is a special operation not so commonly " +"used. It is discussed in the [Operations section](../topics/operations.md) " +"of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 #: 73b0c1ccb18c4b74a2c0fdf9706eca85 -msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgid "" +"The workflow is a process that contains steps. Steps can be other workflows " +"(nested workflows), command-line tools, or expression tools. The inputs of a " +"workflow can be passed to any of its steps, while the outputs produced by " +"its steps can be used in the final output of the workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 #: 4ace6b92f4e04a07aa202840ebe36417 -msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through *requirements*. " +"There are many requirements defined in the CWL specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 @@ -560,17 +630,26 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:143 #: 907674a4ecff4826a2b880e28fc38f33 -msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgid "" +"`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 #: 037cd0e5ceda482eaeaca03d51745aee -msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgid "" +"Some CWL runners may provide requirements that are not in the specification. " +"For example, GPU requirements are supported in `cwltool` through the " +"`cwltool:CUDARequirement` requirement, but it is not part of the " +"{{ cwl_version }} specification and may not be supported by other CWL " +"runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 #: e4643938445b48cc80eb8973ceeb126e -msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgid "" +"Hints are similar to requirements, but while requirements list features that " +"are required, hints list optional features. Requirements are explained in " +"detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 @@ -580,17 +659,33 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:157 #: 3eb6a013a2a4478ca2ad134661f65c58 -msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created. It " +"is thus important that workflows support the creation of FAIR data and " +"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" +"workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 #: 074af9633627470485e5225326d5f20a -msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\", " +"CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 #: 847951c055b94a83b1e081594cef22ee -msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, and " +"scalability; tools and workflows described with CWL can transparently " +"leverage technologies such as Docker and be used with CWL implementations " +"from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 @@ -600,10 +695,8 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 -#: 65c24244713741e196da08cb9ba237b2 -#: f059896039524095b4deb65d693f8ddf -#: 3439764fab0e49d2bcb7c9fbae556e65 +#: ../../src/introduction/quick-start.md:94 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf 3439764fab0e49d2bcb7c9fbae556e65 msgid "Learn More" msgstr "" @@ -614,17 +707,23 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:181 #: 36eb4b3b966640af90faa55db3789cb6 -msgid "The CWL Specification page in the CWL website: " +msgid "" +"The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 #: 2ccb956baa6b4376a04ad9fcc4654631 -msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 #: 72889b830c514afe9a7cb1e64b5666a0 -msgid "The list of Implementations in the CWL website: " +msgid "" +"The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 @@ -634,397 +733,461 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:185 #: c377a7f5dbe645cebbb6c7eccf831a0b -msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 -#: 1769a0cbf4de4d77879c1f202cd11af9 +#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 -#: 950370f0a36048b38e1bde9b78f80816 -msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that " +"are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 -#: f01faaf1b253407cbbc2f353c24774f3 +#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 -#: 353b14f06ee845d0a06a829643e31534 -msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +msgid "" +"The software and configurations listed in this section are prerequisites for " +"following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements focuses " +"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " +"runner or workflow system, but the results and interface may look different " +"(though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 -#: b5a0607096814c0aa577f977c3b57c54 +#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 -#: ff2bb4c6504b456bac7ca9c514414dbf -msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +msgid "" +"There are many implementations of the CWL standards. Some are complete CWL " +"runners, while others could be plug-ins or extensions to workflow engines. " +"We have a better explanation in the [Implementations](basic-concepts." +"md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 -#: cbbcce4c2a96471b8b0ae3593ad59de4 +#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 -#: 5089fdba8aed4113983fa86e698df98b -msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +msgid "" +"We recommend using an up-to-date operating system. You can choose any of the " +"following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 -#: dbaa4bae22fe4d05b18d7351967ddbc3 +#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 -#: c05187af85be41b782678b79627f8fbf +#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 -#: beb6cf4d7c154eb9b6d7fe024a318ed7 +#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 -#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 -msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "" +"If you are using Windows, you will have to install the [Windows Subsystem " +"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " +"installing WSL2. Your operating system also needs internet access and a " +"recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 -#: 56d78c95daa54135b6aa9b2bfdc34d01 +#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 -#: 0f2704bf1f7148be95e999e312899f11 -msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL community. " +"It is also the CWL reference runner, which means it must support everything " +"in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 -#: 86264c9e56104ecea9146407c379aae2 -msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +msgid "" +"`cwltool` can be installed with `pip`. We recommend using a virtual " +"environment like `venv` or `conda`. The following commands will create and " +"activate a Python virtual environment using the `venv` module, and install " +"`cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 -#: 0a0f0e5151ab4c498b4f8a12c016f28d +#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 -#: f7aaafeee230400da056464c853582c2 -msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +msgid "" +"Visit the `cwltool` [documentation](https://github.com/common-workflow-" +"language/cwltool#install) for other ways to install `cwltool` with `apt` and " +"`conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 -#: 5eced7e4cd084e8a806b1d3b12d0c000 +#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 -#: 040c019b6e844eda8c8c2b210852516b +#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" msgstr "`true.cwl`" -#: ../../src/introduction/prerequisites.md:73 -#: 6391e08e0bde49f4b21286d8fdb97433 -msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the CWL " +"standards. However, these actions will be performed without running the " +"document. To validate CWL workflows (or even a standalone command line tool " +"description like the above) pass the `--validate` option to the `cwltool` " +"command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 -#: cdef47fca304479c9a9df75afc0afb35 +#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." msgstr "`cwltool` を使って `true.cwl` を検証します。" -#: ../../src/introduction/prerequisites.md:84 -#: d41c4bc740aa474ea09a7cbd267c8840 -msgid "You can run the CWL tool description by omitting the `--validate` option:" +#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 +msgid "" +"You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 -#: 24d7be55d3994f0b82c38da47918e0c9 +#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." msgstr "`cwltool` を使って `true.cwl` を実行します。" -#: ../../src/introduction/prerequisites.md:91 -#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 -#: 096d0a50f69e48bd9915238d1b4264c1 -msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be invoked " +"independently, and is not reliant on a particular CWL runner program name. " +"Users can invoke `cwl-runner` instead of invoking a CWL runner like " +"`cwltool` directly. The `cwl-runner` is installed by a system administrator " +"or user to point to the preferred CWL implementation. This is convenient for " +"environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 -#: f9df974a8e2645a6918e67466bd1fdc2 -msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +msgid "" +"The CWL community publishes a Python package with the name `cwlref-runner` " +"that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 -#: 71ebe91d4bda473abe87578929433212 +#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 -#: 746c6fc9c29d466494458a08d4c96672 -msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` executable, " +"which will invoke `cwltool`. You should have the same results and output as " +"in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 -#: b9cc5a843a0f49daad56e9303657bdd5 +#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "検証`true.cwl` with`cwl-runner`." -#: ../../src/introduction/prerequisites.md:120 -#: 34ab40437ab646488ba3ee86cd7fe071 +#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." msgstr "`true.cwl` を `cwl-runner` で実行します。" -#: ../../src/introduction/prerequisites.md:125 -#: 705807fae182425dbf4244dbf2be1226 -msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For " +"that, the first thing you need to do is copy `true.cwl` workflow into a new " +"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 -#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 -#: 164c438baab54ec19bbb4584a10dd411 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 +msgid "" +"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 -#: bf8be77af6154326b28442c5d2e2b852 +#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 -#: 695184d1b45a42f393e2da99c3721773 -msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +msgid "" +"And finally, you can execute it directly in the command-line. On execution, " +"the program specified in the shebang (`cwl-runner`) will be used to execute " +"the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 -#: 7c4f45b3e7b549e186126693aa4a3d4f +#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 -#: 3ba23b4ea01c46848e4e43bbeff5f5a1 -msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute the " +"script using the executable specified after the shebang. It is considered a " +"good practice to use `/usr/bin/env ` rather than using a hard-" +"coded location, since `/usr/bin/env ` looks for the " +"`` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 -#: eec6c07455384630809ff1c532bfe7d4 +#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 -#: f6b39b12bd5c495cb53e2795bf9200ed -msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 -#: 2fdb62a13f9447bc89183426260ce781 -msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting " +"and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 -#: 1f07135156254f74a6b043bf33d00cc3 -msgid "Visual Studio Code with the Benten (CWL) plugin - " +#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " msgstr "" -#: ../../src/introduction/prerequisites.md:172 -#: de344f356b1c466d9131cdbd4d7353a3 -msgid "cwl-plugin for IntelliJ - " +#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +msgid "" +"cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 -#: 3f9324ede11441f58d93875867034cf0 -msgid "The CWL community also maintains a list of editors and viewers: " +#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +msgid "" +"The CWL community also maintains a list of editors and viewers: " msgstr "" -#: ../../src/introduction/prerequisites.md:177 -#: 6ce8b81560e341c580d316d69202b268 +#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 msgid "Docker" msgstr "Docker" -#: ../../src/introduction/prerequisites.md:181 -#: 40cfd559d6a848d1aae354d3bdaa8e9c -msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: ." msgstr "" -#: ../../src/introduction/prerequisites.md:185 -#: 8a9a50b0ebe847ce90593881ffe0d69c -msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models with " +"and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 -#: 923cf9dd6d6c417aabe42f9fa62ffa35 -msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for pulling " +"images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 -#: 9390b03889de44638141d705e0ef8322 -msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the next " +"section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 -#: 12042e411482458f8c35a2491f9433e0 +#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 -#: cdd4196f9aa34beba115901ec97913b6 +#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" msgstr "クイックスタート" -#: ../../src/introduction/quick-start.md:3 -#: c43d9675ed134b78b02acb5a102a764a -msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +msgid "" +"This section will show you a brief overview of what CWL is, and where you " +"can learn more about it. No previous knowledge of CWL is required, but you " +"must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 -#: 280936bb2a22469799b2c9e9ba22adee +#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 -#: cb203354977d42a58112d09357f62565 -msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " +"example below shows a simple CWL “Hello World” workflow annotated with " +"comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 -#: 9e51962a7e5c47248f3e20703ae101eb +#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 -#: 7e475e3f3c4a4404bb0236124c0f7ce7 -msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the " +"same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 -#: 82613ca4e32b4ccab1b7735f5ba2d5a1 -msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "" +"In CWL, there is a distinction between a command-line tool and a workflow. " +"But for the sake of simplicity, we are using the term “workflow” here. You " +"will learn more about this in the [basic concepts](basic-concepts.md) " +"section." msgstr "" -#: ../../src/introduction/quick-start.md:32 -#: 498a43362a4749f3b8b433709d34a1d5 +#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 -#: f3e56aedd56b4b93bdc3894273e8c144 -msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the CWL " +"*Reference Runner* for the specification, and it is compliant with the " +"latest version of the specification: {{ cwl_version }}. You can install " +"`cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 -#: 81481f5b82e4488398f87f0a169bd359 +#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." msgstr "`cwltool` を`pip` でインストールします。" -#: ../../src/introduction/quick-start.md:47 -#: a81342e756d24c40acc15835d0a768f2 -msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the " +"[prerequisites](prerequisites.md) section contains other ways to install " +"`cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 -#: c12cf89f8b9a421ebd05330326e219b3 +#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 -#: 9b68bcb1a41849dc9601ab47c5bbb0fe -msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " +"workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 -#: ce04027dfcfe4b7b91ea3c2136b18b23 +#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 -#: 0d8a788402914ebd8f09a5ca80650011 -msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 -#: 6d0b679efab24813a7a3b709ade940d1 +#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 -#: 2ea056ab04b6419a9faf350de22a17f2 -msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +msgid "" +"Another way of passing values to your workflow input parameters is via an " +"*Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 -#: 1a44a545434b448aa956005deeed90a8 +#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 -#: e76bfcc0c9f84bcdb3f6d5277869a88c -msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 -#: d4cdbe870a6f4a68b542ca719d989062 +#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 -#: b6d59e4b9c854abab1b3f7a0fa26f504 -msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but it " +"is not a requirement. You can choose any name for your workflows and Inputs " +"Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 -#: 5535b98e8b1342f09f003ec6db2b44b1 +#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 -#: 77e43c7117fd4c52b140f0dd52cc3963 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 +msgid "" +"[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 -#: 7282abfa7155497ca47c30f9abfb6474 -msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 -#: 176d8d47830f4031bb95dc231ebf1303 -msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +msgid "" +"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 -#: 82a7ca3703bc4f0daa18942a1ac8943b -msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." +"org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 -#: d039a9d6461c44628d4660c00d9ce6ff -msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +msgid "" +"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." +"replace('VERSION', cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 -#: fbc3383d9e1c4eaca7931c3cc4f1752b -msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "" +"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 -#: 1330bd38c4b5495f890b98c669f81a9d -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +msgid "" +"This page is out-of-date and was kept here to preserve the links of the old " +"User Guide. The information on this page has been migrated to the [FAQ](/faq." +"md) section of the new user guide." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 @@ -1034,12 +1197,19 @@ msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 #: ad00d94d4fb64bbdac356e64dd3803b9 -msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 #: d8110ed19da94ad8a9f56e7006c4a2cf -msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files in " +"the same directory as the source file. However, CWL input files (and the " +"directories in which they appear) may be read-only, so we need to instruct " +"\"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 @@ -1048,8 +1218,7 @@ msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 -#: 0a8065edd8af4eaea08989a1060ce48f +#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f #: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "" @@ -1061,182 +1230,248 @@ msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 #: 9643449da1da46d7861866dce490cbcb -msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgid "" +"And now invoke `cwltool` providing the tool description and the input object " +"on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 #: 713666580a0a4466b4ba6e3eb2b54f0a -msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 #: d50574c8b9694f83aa376d39b9a6fcd6 -msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" +"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." +"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " +"specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 -#: 612c4a66c36a43d4ac5d74c1757d6845 +#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 -#: 939cd9e9eaff4e3ab74fe707a5d4eb21 -msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." -msgstr "" - -#: ../../src/topics/best-practices.md:8 -#: 4bcb84707acb40a0bfe2ea0853cb10b7 -msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "" +"The following are a set of recommended good practices to keep in mind when " +"writing a Common Workflow Language description for a tool or workflow. These " +"guidelines are presented for consideration on a scale of usefulness: " +"although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:11 -#: 4dee8504a8e5496081dadc386ab45540 -msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "" +"No `type: string` parameters for names of input or reference files/" +"directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:20 -#: 674c238b25e240eda05e22e399f2f78f -msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that " +"the usual rules of software licensing apply to this document. For example, " +"if the workflow is shared publicly, licensing terms must be clear so that a " +"future user understands under what conditions they can run the workflow, " +"modify it and/or combine it with other workflows. For this reason, please " +"consider including a license field in the document. The authors of this " +"guide urge you to choose a pre-existing license rather than trying to write " +"your own (see the link below to learn more about choosing a license), and " +"our recommended practice is to choose a license that allows for re-use by " +"anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +msgid "" +"If possible, the license should be specified with its corresponding [SPDX " +"identifier][spdx]. Construct the metadata field for the license by providing " +"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " +"taken from the list of identifiers linked above. See the example snippet " +"below for guidance. For non-standard licenses without an SPDX identifier, " +"provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 -#: b651f80f47b4442fbf29454a233697fc -msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 -#: 263a127a77cf4c41af76854f22f1f260 +#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 -#: 3a87a0fb2a364e3da5aaa4017e430b19 -msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "" +"For more examples of providing metadata within CWL descriptions, see [the " +"Metadata and Authorship section of this User Guide](../topics/metadata-and-" +"authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 -#: ecf2b9c0b1664afe9c4e180610610021 -msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +msgid "" +"Include [attribution information][license-example] for the author(s) of the " +"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" +"[orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 -#: e24cb13d98014e558b6a6946758359e0 -msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 -#: f2b14a92374e449d9fb1e8c86ae0dd61 -msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" +"identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 -#: 928e3df7ca3e479ca6474a8e72cf36eb -msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 -#: d355f035676446c88b028f327aeb4829 -msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 -#: 339b852df24242189d6efcd2898a3396 -msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" +"$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " +"[Full IANA media type list][iana-types] (also known as MIME types). For non-" +"bioinformatics tools, use or build an appropriate ontology/controlled " +"vocabulary in the same way. Please edit this page to let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 -#: 3ef57e6862f240bebcf193a52397af0a -msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." msgstr "" -#: ../../src/topics/best-practices.md:69 -#: f1a7c4f896a04a80b0c5f6a1db61ff8c -msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "" +"Each `CommandLineTool` description should focus on a single operation only, " +"even if the (sub)command is capable of more. Don't overcomplicate your tool " +"descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 -#: 1ac4c3d8c3e44bd1af3fc5df70051926 -msgid "Custom types should be defined with one external YAML per type definition for re-use." +#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "" +"Custom types should be defined with one external YAML per type definition " +"for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 -#: c858f64e66f048a5b0032ef3e4d83694 +#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 -#: fae385da16aa443da996fa23ac03d6ae -msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +msgid "" +"If useful, include a top-level `doc` as well. This should provide a longer, " +"more detailed description than was provided in the top-level `label` (see " +"above)." msgstr "" -#: ../../src/topics/best-practices.md:82 -#: 92430be71ecc40e18bbbb80d5576c613 -msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list of " +"valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 -#: 387d83db81024f65aa9a890c2d07874a -msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. One " +"common example: manipulating `File` names and paths? Consider whether one of " +"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 -#: d8e2280a75a74916a1630afaa2fe2ae3 -msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 -#: f1c1340f9745458980e0fbd641738687 -msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +msgid "" +"Complex workflows with individual components which can be abstracted should " +"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " +"workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 -#: 5424e5472c3d466fa2a3d2022c6cb475 -msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics " +"software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 -#: 3f4e98f6bfa141feba8c4b120e3d03e8 +#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 -#: 12f57b2ba76b492abe1816e06bfb1417 -msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +msgid "" +"A command-line tool is a type of Process object that can be run by itself or " +"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " +"etc. The command-line tool is defined in the `baseCommand` attribute of the " +"command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 -#: e1f657a46ce94a0d83671540e2cc2dab -msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The following " +"example contains a minimal example of a CWL command-line tool for the `echo` " +"Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 -#: abb83f0097654a43bd78639d3dbb2bc8 +#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 -#: 3b1a9ae3412f4d6e96a39b9a16934232 +#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 -#: a5eacdbc9aa142c890b177869da4143d -msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +msgid "" +"The example above uses a simplified form to define inputs and outputs. You " +"will learn more about in the [Inputs](../topics/inputs.md) and in the " +"[Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 -#: 1849b8f3ae1c4a84ae59a78ffd6b371e +#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 -#: e3bdaceae8784ab0807b2cf356a98580 -msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network access. " +"If a command-line tool is written manually in CWL v1.1+, there is a need to " +"specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 -#: ed521ac365db4a6ba5a1051fbaa2932e -msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " +"Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 @@ -1246,7 +1481,10 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 #: 0cf51b6da6884065ae42032abc20eb0d -msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgid "" +"Sometimes you need to create a file on the fly from input parameters, such " +"as tools that expect to read their input configuration from a file rather " +"than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 @@ -1261,879 +1499,982 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 #: cfffc518ba6e4ed1a80762ed6f7d25df -msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the value " +"at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 #: 9454a330b9324744b89448f2694b1b03 -msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later " +"during command line tool invocation. That means that any genuine need for " +"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " +"above is expanded to `${PREFIX}` in the generated file to be evaluated by " +"the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 #: 7f8d99a30b644457a62ac1523d0c72aa -msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 -#: ../../src/topics/outputs.md:77 -#: 2d2ef4769b2347e79db827655f1bcdeb -#: 2699fbc4376148af91b7a5a6cdac467c +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb 2699fbc4376148af91b7a5a6cdac467c #: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 #: 10d1373bb14a4a3cacd3b92a2f83382d -msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgid "" +"Before we run this, let us look at each step in a little more detail. The " +"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 #: 70e257091bdb456e8957f90a8fa90e8c -msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " +"array, we need a `-` on the first line of each element of the array, in this " +"case we have just one element. `entryname:` can have any value, but it must " +"match what was specified in the `baseCommand`. The final part is `entry:`, " +"this is followed by `|-` which is YAML quoting syntax, and means that you " +"are using a multiline string (without it, we would need to write the whole " +"script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 #: 1741804e33aa43ce88b4320c11ae5973 -msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:54 #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 -#: ../../src/topics/staging-input-files.md:20 -#: ../../src/topics/workflows.md:198 -#: b372f33c65bb4707b2a462a960bb1373 -#: 293fb1d428b849aebccad598a932992d -#: f924d65fed0c4cb5b0a019b084a8b535 -#: d6255506eebe44be94c5ce703c44a513 +#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 d6255506eebe44be94c5ce703c44a513 #: 7bbd2d738fc54649aeb10f8d2bc38b6f -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgid "" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 -#: cb34fd4c8cb04053ada491a227651048 +#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 -#: 67573252cc064b27ab13eebc468ac58a -msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +msgid "" +"Sometimes you may want to write your own custom types for use and reuse in " +"CWL descriptions. Use of such custom types can reduce redundancy between " +"multiple descriptions that all use the same type, and also allow for " +"additional customisation/configuration of a tool/analysis without the need " +"to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 -#: 73e68b3af9cf41338d843c0c40e50cdc -msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +msgid "" +"The example below is a CWL description of the [biom convert format][biom] " +"tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 -#: ef5f35acb97f4ddfad7b688712f53484 +#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 -#: 7015dfa99a6f4cfb87ebf0ed61e8043c +#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 -#: a999b1acda2641598086648c64aa3831 -msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +msgid "" +"___Note:___ To follow the example below, you need to [download the example " +"input file](https://github.com/common-workflow-language/user_guide/blob/main/" +"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " +"*rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 -#: f8c12a58cb0b46a488823c6ae95f25ea -msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to be " +"used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 -#: f25a63e0926d4932bbe64b2e4bdabf9e -msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +msgid "" +"The reference to a custom type is a combination of the name of the file in " +"which the object is defined (`biom-convert-table.yaml`) and the name of the " +"object within that file (`table_type`) that defines the custom type. In this " +"case the `symbols` array from the imported `biom-convert-table.yaml` file " +"define the allowable table options. For example, in `custom-types.yml`, we " +"pass `OTU table` as an `input` that tells the tool to create an OTU table in " +"hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 -#: b0a4df0fd3ca42338cff4689235dcf4e -msgid "The contents of the YAML file describing the custom type are given below:" +#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e +msgid "" +"The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 -#: fecfbb44456640d8ba05e519bf2ff564 +#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 -#: d718630a296545f3a989c8c71e9ddc77 -msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +msgid "" +"In order for the custom type to be used in the CWL description, it must be " +"imported. Imports are described in `requirements:SchemaDefRequirement`, as " +"below in the example `custom-types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 -#: 9a97acd430064710bcdf76edbd9f711c -msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +msgid "" +"Note also that the author of this CWL description has also included " +"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " +"cores required for the tool to run successfully, as well as details of the " +"version of the software that the description was written for and other " +"useful metadata. These features are discussed further in other chapters of " +"this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 -#: 59014808cbef4c02aaef03129d8a29b0 +#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 -#: 3c821c9c46d841ec89b8a5b1018f3af8 -msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "" +"Tools run in a restricted environment and do not inherit most environment " +"variables from the parent process. You can set environment variables for " +"the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 -#: bfdebb32440a4034beb42135e38884e8 +#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 -#: 777d4a52f7554eff84db2df6d4d0f729 +#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 -#: 48deb71f361a43e48a56ed483075bca8 -msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +msgid "" +"An expression tool is a type of Process that can be run by itself or as a " +"Workflow step. It executes a pure JavaScript expression. It is meant to be " +"used as a way to isolate complex JavaScript expressions that need to operate " +"on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 -#: 716b56506ca7470299899c5d820a9ea2 -msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 -#: b63e6f5a2e89431c8fc7d04f47fd69fe +#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 -#: 39727e9058f24b62b8746a46d3f812c2 +#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 -#: e3ecac0a8e604f2b98a2a12b0579990a -msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +msgid "" +"We had to use an `InlineJavascriptRequirement` as our expression contains a " +"JavaScript call in `.toUpperCase()`. This means to tools using the " +"expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 -#: c8d648b765ec499a8e9c464590838492 +#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 -#: 007a345b4bad49cf996c4301b8386473 -msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +msgid "" +"If you need to manipulate input parameters, include the requirement " +"`InlineJavascriptRequirement` and then anywhere a parameter reference is " +"legal you can provide a fragment of Javascript that will be evaluated by the " +"CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 -#: 2edbd398eadb458b8eacd5fa5496f0a2 -msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "" +"JavaScript expressions should only be used when absolutely necessary. When " +"manipulating file names, extensions, paths etc, consider whether one of the " +"[built in `File` properties][file-prop] like `basename`, `nameroot`, " +"`nameext`, etc, could be used instead. See the [list of best practices](best-" +"practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 -#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 -#: efb5fd14988c4e2a8f834ee5369d4102 -msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost) " +"empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 -#: e833649b951841c49397796f996d29f3 +#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 -#: 276f688ba7cc471a842f085ca852b1d9 -msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object is " +"represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 -#: ebf399ea4d5f47b9be03e24f04c69f2d +#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 -#: 65e0cdd505b944caa40f65e612cdddfc +#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 -#: 8b70a1ad70514039b97164fa630c12e4 -msgid "Note that requirements can be provided with the map syntax, as in the example above:" +#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" msgstr "" -#: ../../src/topics/expressions.md:54 -#: 2f28ab412d2843ffa5f14acdc01fc732 -msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " +"describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 -#: d957f55a6377422c9834f85d45e35009 +#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 -#: cbec9277b5004e50af2728cbda0df740 -msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 -#: e259f55f8000479bbd8009e25cf0ca6c -msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +msgid "" +"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 -#: 1acb064f7a4a482aa0174bdc847c6382 +#: ../../src/topics/parameter-references.md:64 1acb064f7a4a482aa0174bdc847c6382 #: 0222780b98ac48e89b1b4f57c9df8590 msgid "`arguments`" msgstr "" -#: ../../src/topics/expressions.md:68 -#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 -#: ef2b8433778a40408f179c3e6f0cf99e -#: 224732683a9c41f3ba1b778851e745a8 -#: 17b10d1e91b24dc582df98fcd2ac850e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 -#: e4e68011dc5f42e4918c747afa7d764b +#: ../../src/topics/parameter-references.md:86 ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 e4e68011dc5f42e4918c747afa7d764b #: d44e3cfa661840eb851782e24caf1b68 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 -#: 0bddedfe40e841f7878e09792531e6bf +#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf #: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 -#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 #: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 -#: 2437656e20354d63bede1b98d5348e2c +#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c #: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 -#: 8210b36347a749889450529ecdf4ff0e -msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +msgid "" +"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" -#: ../../src/topics/expressions.md:73 -#: ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 -#: ../../src/topics/expressions.md:93 +#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 -#: d0a92a3792b549e9b5ddce4667d168d2 -#: 801729c7c71b4109824b035437e69bf9 -#: 1bc510d525f0414e88692e356e67fbbc -#: d2e246ae56a24e4abdd6b7d9812a86e2 -#: b1446bab2732412e91f721a08067b0bd -#: e89dbeb22f41430ca39c923d9fdf68cb -#: bd61499b71e64164878dea08d6d7141e +#: ../../src/topics/parameter-references.md:90 d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb bd61499b71e64164878dea08d6d7141e #: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" -#: ../../src/topics/expressions.md:74 -#: ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 -#: ../../src/topics/expressions.md:94 +#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 -#: 8a1748579de14f0888d5ee9023e37c2d -#: f760465a49d64d4c8468ad9c4fea62b1 -#: 28b6b5ffa7524374aaa9525ebfafb762 -#: d11f6a19ddf34cf19ec856bacf998e29 -#: bcb7cd10cb5947bb9d85c040f57f954f -#: da5188d3bedc4997a35bdf417f2f643c -#: cd7a0190511d4613b09600a3b1e9d55f +#: ../../src/topics/parameter-references.md:91 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c cd7a0190511d4613b09600a3b1e9d55f #: 47def3b078e2402182039be0227090ae msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 -#: 23088850ad02459696f6bbd385109aac -msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +msgid "" +"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 -#: f02257a822ad46ac93c5981531cc85d5 -msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +msgid "" +"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 -#: 989a1c4aaa1143be9f53b90cd8b6d500 -msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "" +"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 -#: 582b03ac742745a89f4dfc86b7404db2 +#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 #: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 -#: d555a3d991e344a5a8e1289168d7c6d1 +#: ../../src/topics/parameter-references.md:79 d555a3d991e344a5a8e1289168d7c6d1 #: 44b3f123c9b04a308c1161b742a7b34b msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 -#: e9fa9430535c424fa3e8be5d460d2ba4 +#: ../../src/topics/parameter-references.md:80 e9fa9430535c424fa3e8be5d460d2ba4 #: 0e306cc923974d1db83fdfb45105a11c msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 -#: d289541e460147aa933f7878996f8649 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +msgid "" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 -#: b0290d1a477b48119e17cf1fed9d6dff +#: ../../src/topics/parameter-references.md:84 b0290d1a477b48119e17cf1fed9d6dff #: 446f1190af7a40a0913ff04ce7aa938c msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 -#: 81b4d1f23a3642bfa9bb395b94260cd1 -msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "" +"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 -#: e1cde4aa32c041238ed2596173c6d824 +#: ../../src/topics/parameter-references.md:87 e1cde4aa32c041238ed2596173c6d824 #: 557694f82e314baa9ccafba14d6ff2c9 -msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgid "" +"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." +"html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 -#: c2a92d3eca7f4ee39cec649170eeea53 +#: ../../src/topics/parameter-references.md:88 c2a92d3eca7f4ee39cec649170eeea53 #: 3c939769ede94602a67fc50c435741cf msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 -#: f495da32f05a4a5ba9539be0a54c1a59 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +msgid "" +"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](https://www." +"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 -#: bdb4c68a175047ddbe141ca24960127f -msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +msgid "" +"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 -#: 4b73495cf18a4d908525292b6f23c419 +#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 #: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 -#: 718ceee9973240ec9c100977bbcc8921 +#: ../../src/topics/parameter-references.md:94 718ceee9973240ec9c100977bbcc8921 #: 2b25152f6df5494a8632f3ce631c20d8 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 -#: c07ab08eb75d4528949c56a3d7c12b28 +#: ../../src/topics/parameter-references.md:95 c07ab08eb75d4528949c56a3d7c12b28 #: 846cd427ae25410eae7c920b237edcb0 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 -#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 #: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 -#: 700c57ccd5e347be86702c83a8af24b3 +#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 #: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 -#: 509a5e2ec52d413eb57754d359f133e4 +#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 #: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 -#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 #: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b -#: e3b76f42c924489f9a0bcf5a7b636d23 +#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 -#: 97b61352363f47cb890e8937c5613fa3 -msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +msgid "" +"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e -#: a258554d462f4f5f83ece28d5b2fc584 +#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 -#: 8d0b142bb7ed4e61b8fb03de197240ce +#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: effc0208cf4f4551958db6e526c0528b -#: 9d4889c8cec24351a7a9e3c547e331b6 +#: effc0208cf4f4551958db6e526c0528b 9d4889c8cec24351a7a9e3c547e331b6 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: be6c1e85c7b6495d8086c262daad20e7 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +#: be6c1e85c7b6495d8086c262daad20e7 af4f7f232a9d42388c0ba1cfc7c2cdf7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 -#: 6abeba392b0444b19f92a19f178a4682 +#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 -#: 0bc424ef2ca346099f29b937379908a0 -msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +msgid "" +"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd -#: 949c376120d8441796ec9c89364f8851 +#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 -#: 10d36a1adfd04144b401c993b12b4094 -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +msgid "" +"Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 -#: 29b73e1dd72744f68377f0a38c10f062 -msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +msgid "" +"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " +"attribute that allows users to load external JavaScript files, or to provide " +"inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 -#: 38a2afaf4a6c4d04909af22c93f2808d -msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts of " +"the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 -#: cd74f34b21af4de9be96fd897efc469b -msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +msgid "" +"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." +"org/v1.0/CommandLineTool.html#Expressions) that the only version of " +"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" +"international.org/5.1/). This means that any code that you include or write " +"in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 -#: f12e371f3f1a4b0cb2cff9800352d48c -msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " +"function inline in `expressionLib`. That function can then be used in other " +"parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 -#: 49d0fda2fc144e0b8b7c92afc1d8945e +#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 -#: 8f0e8f050e334ac08334e9215e1dcf61 -msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result in " +"the `echo` command printing the input message with capital initial letters:" msgstr "" -#: ../../src/topics/expressions.md:149 -#: 26c74b11bb1849cea0763bb74ec43e42 +#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 -#: 7a6be0005a6441feb67f036d005d7885 -msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 -#: ed590f9e6f4f425da886b110295c45db +#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 -#: 093235307d6f47d4858e559b780ef5e5 +#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 -#: 06635145b441418aaae84dc804f3d6ac -msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +msgid "" +"The `custom-functions.js` file is included in the CWL document with the `" +"$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 -#: 973a9b257b1a4f0dbd4444d4f11dadd7 +#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 -#: 04eaf1f7c630450db318dcd8b7626e15 -msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +msgid "" +"Finally, note that you can have both inline and external JavaScript code in " +"your CWL document. In this final example we have added another entry to the " +"`expressionLib` attribute with the new function `createHelloWorldMessage`, " +"that calls the `capitalizeWords` function from the external file `custom-" +"functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 -#: c4098489fbb049789f022cd3e5c3d49b +#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 -#: 5979e4ae5c424276bdbc47f69b379d0f +#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 -#: fd4579a3c9844492b314b5c3c1775fc7 -msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +msgid "" +"The `$include` statement can be used to include a file from the local disk " +"or from a remote location. It works with both relative and absolute paths. " +"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." +"html#Include) from the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 -#: 3f038e7371f84ed9b4547358dfb55a11 +#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 -#: e024bcb70e04412e90e1838426d1b69a -msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +msgid "" +"Tools and workflows can take `File` types as input and produce them as " +"output. We also recommend indicating the format for `File` types. This helps " +"document for others how to use your tool while allowing you to do some " +"simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 -#: a3db21c0b3114802a8a5b610e252ef13 -msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM in " +"our example), reference a local ontology for your institution, or do not add " +"a file format initially for quick development before sharing your tool with " +"others. You can browse existing [IANA file format listings][IANA] and [EDAM " +"file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 -#: 0f5bc8520d6a4dafa37c65343da9702a -msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` section " +"of the document in greater detail, so don't worry about these for now." msgstr "" -#: ../../src/topics/file-formats.md:17 -#: 5cb830da47464a8b9c3950983fa4d56f -msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 -#: 0535d5de416b4ea3b2f5996583deecc1 +#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 -#: fb47f73c38cf4ec59bd3021866a631f8 +#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 -#: 74b28c1b09c6429b82e462e4ec61808e +#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 -#: a2ce43b391864e8bbde16328cc19b32b -msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +msgid "" +"Below is an example of a parameter file for the example above. We encourage " +"checking in working examples of parameter files for your tool. This allows " +"others to quickly work with your tool, starting from a \"known good\" " +"parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 -#: aebee48b742c4145a600fd2daf8c75dc +#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 -#: 56ee4dcfff6141d5bef80eb96559876d -msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +msgid "" +"___Note:___ To follow the example below, you need to download the example " +"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 -#: 8d3a6d83e2e54c56995893c41590b7ff +#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 -#: 5abcdebfa1cb401bb8892553be285fd3 +#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 -#: d3a55f71dc244026a97902de9ed819ea +#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 -#: 96671c56523c4ea9992fb5dfcfa6490e -msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to run " +"the tool. Each parameter has an `id` for the name of parameter, and `type` " +"describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 -#: bcc6246742cb46bfb185e415c4a3431a -msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +msgid "" +"Available primitive types are *string*, *int*, *long*, *float*, *double*, " +"and *null*; complex types are *array* and *record*; in addition there are " +"special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 -#: 86dce36de687449c88fb5eb9d64eb045 -msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 -#: cd9cea15f57b492ba4098237cd7c5bed +#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 -#: 8bdb875b63104f699efe28ea0abb1e3d +#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 -#: c6a0151a68494c0cb0176781e65e252e +#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 -#: dc5e6b5e01d64226bd5dbbf3175fe010 +#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 -#: 36ab1d9edafc4831bb1bca5f123b04b0 -msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "" +"You can use `cwltool` to create a template input object. That saves you from " +"having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 -#: 7dc630ea86464b1dba3a4e5079260b3b -msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " +"> inp-job.yml`, and then modify the default values with your desired input " +"values." msgstr "" -#: ../../src/topics/inputs.md:44 -#: ae37901a8dbe48a59e27ab4e2e6e2d30 -msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 -#: 651e032007ea4a119d20c820bb61f86b -msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " +"command line." msgstr "" -#: ../../src/topics/inputs.md:53 -#: 0b056dde9e87428996e47870b12119da -msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +msgid "" +"Now invoke `cwltool` with the tool description and the input object on the " +"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " +"boxed text describes these two commands and the expected output from the " +"command line:" msgstr "" -#: ../../src/topics/inputs.md:64 -#: 628124a1670b4b058bb0fb6e495a099c -msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not explicitly " +"specified" msgstr "" -#: ../../src/topics/inputs.md:70 -#: 10ca6321ce3e4b08ab6a5bb380b19c11 -msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "" +"The field `inputBinding` is optional and indicates whether and how the input " +"parameter should appear on the tool's command line. If `inputBinding` is " +"missing, the parameter does not appear on the command line. Let's look at " +"each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 -#: ec2adb3912bc46e28891229e9e0d9a1c -msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +msgid "" +"Boolean types are treated as a flag. If the input parameter \"example_flag" +"\" is \"true\", then `prefix` will be added to the command line. If false, " +"no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 -#: a519be60726a44af9941fdce04735353 -msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +msgid "" +"String types appear on the command line as literal values. The `prefix` is " +"optional, if provided, it appears as a separate argument on the command line " +"before the parameter . In the example above, this is rendered as `--example-" +"string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 -#: cb8fc8c4c79e467eac5fab4ca685201e -msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +msgid "" +"Integer (and floating point) types appear on the command line with decimal " +"text representation. When the option `separate` is false (the default value " +"is true), the prefix and value are combined into a single argument. In the " +"example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 -#: a26cc105716f47cb807174c9003153b0 -msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the parameter " +"is optional. In the example above, this is rendered as `--file=/tmp/random/" +"path/whale.txt`. However, if the \"example_file\" parameter were not " +"provided in the input, nothing would appear on the command line." msgstr "" -#: ../../src/topics/inputs.md:131 -#: cc159dd5fe5748caac838862f5b8c4d1 -msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +msgid "" +"Input files are read-only. If you wish to update an input file, you must " +"[first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 -#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 -msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "" +"The value of `position` is used to determine where parameter should appear " +"on the command line. Positions are relative to one another, not absolute. " +"As a result, positions do not have to be sequential, three parameters with " +"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " +"than one parameter can have the same position (ties are broken using the " +"parameter name), and the position field itself is optional. The default " +"position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 -#: 6812698e9ad84d3385de5e88e9dde0b3 -msgid "The `baseCommand` field will always appear in the final command line before the parameters." +#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +msgid "" +"The `baseCommand` field will always appear in the final command line before " +"the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 -#: 9654e65b1c0642dbb5d4f34edb211989 +#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 -#: d1f02be278754267893dfce5a940997d -msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to provide " +"`type` field with `type: array` and `items` defining the valid data types " +"that may appear in the array. Alternatively, brackets `[]` may be added " +"after the type name to indicate that input parameter is array of that type." msgstr "" -#: ../../src/topics/inputs.md:154 -#: 01f30e38dfdd452dba3a996073936e16 +#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 -#: 787d4bfb093c4ad287b902084706b751 +#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:166 -#: ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 -#: 588f0f7f967f4d69af27c9729d6d3119 -#: 02adef8ee8204842b5b4a0408f3bac33 -#: 9db68837918a4a349f32f15f12697a1d -msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 9db68837918a4a349f32f15f12697a1d +msgid "" +"Now invoke `cwltool` providing the tool description and the input object on " +"the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 -#: 75d59e395c66416cae9b352db5081516 -msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +msgid "" +"The `inputBinding` can appear either on the outer array parameter definition " +"or the inner array element definition, and these produce different behavior " +"when constructing the command line, as shown above. In addition, the " +"`itemSeparator` field, if provided, specifies that array values should be " +"concatenated into a single argument separated by the item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 -#: 874c6f19abbf45d7ab7d30a378c4048d -msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` in " +"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " +"where array values that are not defined with an associated key are marked by " +"a leading `-`. This will be demonstrated in the next lesson and is discussed " +"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " +"arrays of arrays, arrays of records, and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 -#: 5d7d7a28cc5d4862803032aec78174d9 +#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 -#: dea0d4b681f94e73b13965dcfe75cf7d -msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be provided " +"together (they are exclusive). You can use records and type unions to group " +"parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 -#: ddf598abf4f34aca9fffa045860fbf96 +#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 -#: d52a8089920e45bd89d582533b50e3a1 +#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 -#: 750474486a84482292eeba45f118287f -msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 -#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 -#: 1eb0e39bb6d04b8cab300f44a79f3add -msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the first " +"matching item (`itemC`) is added to the command line and remaining item " +"(`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 -#: bc21ee10bff843689cc98ac6630edcea +#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 -#: 4b2ab812f62c4f949dd25c8527f2411c -msgid "In the third example, only `itemD` is provided, so it appears on the command line." +#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +msgid "" +"In the third example, only `itemD` is provided, so it appears on the command " +"line." msgstr "" -#: ../../src/topics/inputs.md:255 -#: b771302d1bec4050a9417b080eef76c9 +#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 -#: 2c3b884cb1c54521900cc90782e8a58d -msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +msgid "" +"If you use exclusive input parameters combined with expressions, you need to " +"be aware that the `inputs` JavaScript object will contain one of the " +"exclusive input values. This means that you might need to use an **or** " +"boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 -#: a1073b6306044dffb414319ae01f68bb -msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from an " +"enum." msgstr "" -#: ../../src/topics/inputs.md:265 -#: 4a31c733092142b1af834eab1747c224 +#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 -#: 9a1d92334685449386dfa3b3a899ed48 -msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you provide a " +"valid value, such as “fasta” (one of the values of the enum), your command " +"should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 -#: fb623af4c480411b8fde28d01c981411 -msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +msgid "" +"However, if you do not provide any input value, then `file_format` will be " +"evaluated to a `null` value, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your workflow." msgstr "" -#: ../../src/topics/inputs.md:289 -#: e98e165f6bba40809c90473d72f9d592 -msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +msgid "" +"To correct it, you must remember to use an or operator in your JavaScript " +"expression when using exclusive parameters, or any parameter that allows " +"`null`. For example, the expression could be changed to `$(inputs." +"file_format || 'auto')`, to have a default value if none was provided in the " +"command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 @@ -2143,12 +2484,25 @@ msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 #: cd64d2d828834cbbb24ea5358caf5405 -msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgid "" +"Implementation extensions not required for correct execution (for example, " +"fields related to GUI presentation) and metadata about the tool or workflow " +"itself (for example, authorship for use in citations) may be provided as " +"additional fields on any object. Such extensions fields (e.g. `format: edam:" +"format_2572`) can use a namespace prefix listed in the `$namespaces` section " +"of the document (e.g. edam: http://edamontology.org/) as described in the " +"[Schema Salad specification][schema-salad]. Once you add the namespace " +"prefix, you can access it anywhere in the document as shown below. " +"Otherwise, one must use full URLs: `format: http://edamontology.org/" +"format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 #: 80af387fe3ff4e2da999903385bd602b -msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to cite " +"your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 @@ -2163,7 +2517,12 @@ msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 #: cb9980db4e5f4c74b01c2dec6d5e92d0 -msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgid "" +"For those that are highly motivated, it is also possible to annotate your " +"tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints at " +"hardware requirements in order to use the tool, and a few more metadata " +"fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 @@ -2171,259 +2530,301 @@ msgstr "" msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 -#: 8acf361cf77c4d45ba3f2e344146259f +#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 -#: 83d3b9a0ed3148fda9ce72cd108cb9e1 -msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-line " +"tool, or an expression tool. It is a step of a workflow that specifies " +"inputs and outputs, but it does not provide enough information to be " +"executed." msgstr "" -#: ../../src/topics/operations.md:7 -#: 5565c1b2d8a349169a305a9b26b4574d -msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +msgid "" +"You can create operations to visualize a workflow during development, before " +"you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 -#: 49cf614893d8438299b3bca384eb40cf +#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 -#: 88160cef4cfa4add9020aa89511a5749 -msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +msgid "" +"The `uppercase` step of the workflow is an operation. It can be used like a " +"command line tool or an expression. You can also plot it with the CWL Viewer " +"or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 -#: 2f73a786b5d94dc0b23ed0cdd185afc8 -msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "" +"The output of the command above can be rendered with a Graphviz renderer. " +"The following image is rendered with the Sphinx Graphviz directive (this " +"user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 -#: 730ba1434a1445ae847ec6153b6a3b72 -msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +msgid "" +"If you try running it with `cwltool`, the command will fail since `cwltool` " +"does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 -#: 98d9b8d867594543890af99e77e24edb +#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 -#: a25d0b1e13324b40a6b8fcd227948c4f -msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A " +"CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 -#: da077da5eb8a4ffebfde041fc16300de +#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 -#: 1b3016f0462f42deb42ddaa33f28bf3d +#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 -#: d661df070e3040869da412d07a71f716 -msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name of " +"parameter, and `type` describing what types of values are valid for that " +"parameter." msgstr "" -#: ../../src/topics/outputs.md:10 -#: a11585474d3849cca5467512ed964743 -msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +msgid "" +"When a tool runs under CWL, the starting working directory is the designated " +"output directory. The underlying tool or script must record its results in " +"the form of files created in the output directory. The output parameters " +"returned by the CWL tool are either the output files themselves, or come " +"from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 -#: 2682f9ca8e604a0c9986f7746fdec960 -msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 -#: 7e3fa7baf0f549ec89457e7004ac9545 +#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 -#: 22447a560f6f4317bf67bd7c4336126c -msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string we can use an " +"_array of strings_. The first element is the command to run, and any " +"subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 -#: f1ee2e00b0cc4112b51c9df3a919b73f +#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 -#: ad8e1acb251246d2a47c39b20d4e483a +#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 -#: dc200c6960ae4476a772645d021f14b8 +#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 -#: 52703d6b7f914097934bfad13663abeb -msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +msgid "" +"And now invoke `cwltool` with the tool description and the input object on " +"the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 -#: 5e1c79df657d4a6e84e055dd6b300a5d -msgid "The field `outputBinding` describes how to set the value of each output parameter." +#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +msgid "" +"The field `outputBinding` describes how to set the value of each output " +"parameter." msgstr "" -#: ../../src/topics/outputs.md:62 -#: 329d2809dfae4f90bc638f5f03a47ee3 -msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +msgid "" +"The `glob` field consists of the name of a file in the output directory. If " +"you don't know name of the file in advance, you can use a wildcard pattern " +"like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 -#: 96df2d45e42441d49ce193ccbfab78a3 +#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 -#: c6bcf7c6a8774dd6be41cc775848c3b8 -msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "" +"To capture a tool's standard output stream, add the `stdout` field with the " +"name of the file where the output stream should go. Then add `type: stdout` " +"on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 -#: 9d86c03ab44841c785b924cc44727e31 +#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 -#: 2fb58c2feaa84970bb5274c49f4b5b64 +#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 -#: 9647019d8c37466886e7aab6f176634d -msgid "You can also capture multiple output files into an array of files using `glob`." +#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 -#: b9eaf21f5e014eefaae301c47dafd144 +#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 -#: cffff6c43b4945daa3b2a49763bc50ae +#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 -#: cc067051f22f433bbece08f60933e002 -msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions to " +"mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 -#: a190a6440ec34898990cdac05d809f22 +#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 -#: dbfe2c1123144316aa026374b0f353d3 -msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../src/topics/parameter-references.md:13 -#: 280f1a07d0ae41d7a4674504f832fcf0 +#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file we " +"were interested in was called \"hello.txt\", and this was written into the `." +"cwl` file. This is not the best way to do this, as the \"hello.txt\" " +"filename may vary or be dependent on the input file(s) used. To avoid this " +"we can specify the name of the file we want in the job parameters file (`." +"yml`). In this example, you will see how to reference the value of input " +"parameters dynamically from other fields, which will allow us to then " +"specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 -#: 5c64d938862747cb9fb52515a656ce27 +#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 -#: 074cf5d912854d8c864607cc24b15302 -msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +msgid "" +"Create your input files and invoke `cwltool` with the tool description and " +"the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 -#: 0290af3e3cbb4b32b0450c8771f3bf95 -msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "" +"Certain fields permit parameter references which are enclosed in `$(...)`. " +"These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 -#: b54240bb94f746bba7511633aa969db0 -msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" +"$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 -#: 8b70a072aa87414c88e89a3e19af0a51 -msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +msgid "" +"The value of the \"inputs\" variable is the input object provided when the " +"CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 -#: eea20f89c45f424a888178df53713b28 -msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +msgid "" +"Note that because `File` parameters are objects, to get the path to an input " +"file you must reference the path field on a file object; to reference the " +"path to the tar file in the above example you would write `$(inputs.tarfile." +"path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 -#: cb4ea13f5db84c0da43df3f7f2478d78 +#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 -#: 6d3fb423e6c4434697cd113fb27e28ad +#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 -#: 7647e0229a924f988cf02b7812a55c06 -msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +msgid "" +"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 -#: 9d663249666045618a0d3acddb85a9a9 -msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +msgid "" +"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 -#: 5fed4984f6784347b4cbe0630b1dd2c2 -msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "" +"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 -#: dbf6153cd02542a6a01c172803122b7f -msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +msgid "" +"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 -#: b6250cf6fa8a4a0c94b33302e0decca5 -msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +msgid "" +"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 -#: fa6ca3bbc6784380a03a950a6f49a180 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +msgid "" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 -#: b92b516e537a4773ad67b4af586e7a25 -msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +msgid "" +"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 -#: 467a701228504d06b971b79a59c69064 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +msgid "" +"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 -#: 2634f989eb304009a8568d70ed42786c -msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +msgid "" +"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 #: 5d8bed66282c408695292ea92a03b2c4 -msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgid "" +"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 @@ -2433,7 +2834,9 @@ msgstr "" #: ../../src/topics/parameter-references.md:107 #: 9a6b311ded8d4e43ae635b1b927dbdf2 -msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgid "" +"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 @@ -2448,690 +2851,899 @@ msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 #: 574d93d1d592458a985f259519c036cb -msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a `SoftwareRequirement` field in the `hints` section. This may also " +"help to avoid confusion about which version of a tool the description was " +"written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 #: 82e48b3e3c3f451480cc0b6a529271f6 -msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgid "" +"In this example, the software requirement being described is InterProScan " +"version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 #: 02e40154eac74ecc98d0447d03475b44 -msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the [dependency " +"resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 #: 8cb1c5d9b1a54c40924099494eb766c6 -msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 -#: b85eb83e05e845d7a179f1b1d74db444 +msgid "" +"As well as a version number, a unique resource identifier (URI) for the tool " +"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " +"up in the [SciCrunch][scicrunch] registry, which provides a portal for " +"finding, tracking, and referring to scientific resources consistently. If " +"you want to specify a tool as a `SoftwareRequirement`, search for the tool " +"on SciCrunch and use the RRID that it has been assigned in the registry. " +"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " +"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." +"org][identifiers]) in the `specs` field of your requirement description. " +"Other good choices, in order of preference, are to include the DOI for the " +"main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 -#: 35f97d37492b4c7ca3ad6cfc1e6fa366 -msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "" +"Normally, input files are located in a read-only directory separate from the " +"output directory. This causes problems if the underlying tool expects to " +"write its output files alongside the input file in the same directory. You " +"use `InitialWorkDirRequirement` to stage input files into the output " +"directory. In this example, we use a JavaScript expression to extract the " +"base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 -#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 -#: 0f7508ce59754a7eb230dea6042244c6 +#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 -#: fbe0c65b444441f785d0054176d036a6 -msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +msgid "" +"In this section you will find ways to troubleshoot when you have problems " +"executing CWL. We focus on `cwltool` here but some of these techniques may " +"apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 -#: 1b6b7a75cc754775bf9dd80c0941e8da +#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 -#: 9a710602e00c4934ae3a3b471aa68458 -msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor output " +"files, but created while your workflow is running). By default, these files " +"are created in a temporary directory but writing them to a separate " +"directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 -#: 21b5be7270a14f0987240c81d1ec879b -msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " +"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " +"olleH\". However, the second step, `step_b`, **has a typo**, where instead " +"of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 -#: 0490b1fab86749e49b473949c52bbe8b +#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 -#: cfe9d8241fe84bd5b74042a5625d933f -msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " +"(`cwltool` will create the directory for you if it does not exist already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 -#: 764d933cc4da446abd8dd8f913f05dac -msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. You " +"can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 -#: c93efc6d4e004859981ee7f5fa28ed03 -msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +msgid "" +"Each workflow step has received a unique ID (the long value that looks like " +"a hash). The `${HASH}.status` files display the status of each step executed " +"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " +"output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 -#: 546601da44cb49bd9611b1c85807fd90 -msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " +"the `step_b`). After fixing the typo, when you execute `cwltool` with the " +"same arguments as the previous time, note that now `cwltool` output contains " +"information about pre-cached outputs for `step_a`, and about a new cache " +"entry for the output of `step_b`. Also note that the status of `step_b` is " +"now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 -#: 7e0bf00f8ce542b9b009cdcf1945a9e5 -msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had " +"been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for " +"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " +"re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 -#: eff5f28ca83c458a9b07faf7a81f7e91 +#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 -#: 2e634f3737d04d279ae78ceee4b0a664 +#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 -#: e07f33d01b804663a25ffb08aad74821 -msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 -#: 7a644506619a4f08958ec7d4540cd557 -msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +msgid "" +"[Docker][docker] containers simplify software installation by providing a " +"complete known-good runtime for software and its dependencies. However, " +"containers are also purposefully isolated from the host system, so in order " +"to run a tool inside a Docker container there is additional work to ensure " +"that input files are available inside the container and output files can be " +"recovered from the container. A CWL runner can perform this work " +"automatically, allowing you to use Docker to simplify your software " +"management while avoiding the complexity of invoking and managing Docker " +"containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the container." msgstr "" -#: ../../src/topics/using-containers.md:18 -#: b5195b7d8eaa419fb2b90cb33a57783a -msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +msgid "" +"This example runs a simple Node.js script inside a Docker container which " +"will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 -#: 7921a837ee744c5aa9a5bda04b0c8db1 +#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 -#: 387e9bc9381a4450af54aff77e4df6a2 +#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 -#: 2713594c937d4c528fc8d04d9e9819ed -msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 -#: cf94c1424fc2413c85647fd1ee73d951 -msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that is " +"really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:52 -#: dc0452107c604e29bdf32bb289fe5db8 -msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using the " +"Node Js runtime that is meant for Javascript files. We then need to specify " +"some `hints` for how to find the container we want. In this case we list " +"just our requirements for the docker container in `DockerRequirements`. The " +"`dockerPull:` parameter takes the same value that you would pass to a " +"`docker pull` command. That is, the name of the container image (you can " +"even specify the tag, which is good idea for best practices when using " +"containers for reproducible research). In this case we have used a container " +"called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " +"the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 -#: 1a5596243cec4c948d9b6bf0bb12fad0 +#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 -#: 483181f498fc4d968b5fe6ef427709f7 -msgid "Notice the CWL runner has constructed a Docker command line to run the script." +#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." msgstr "" -#: ../../src/topics/using-containers.md:72 -#: 7487485d6aa4458089a4b4bdf107ea64 -msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +msgid "" +"In this example, the path to the script `hello.js` is `/home/me/cwl/" +"user_guide/hello.js` outside the container but `/var/lib/cwl/" +"job369354770_examples/hello.js` inside the container, as reflected in the " +"invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 -#: 7394e7690f934043af617436b40845f0 +#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 -#: b9ae9e9a896048caad7e6c38a5bc1bd1 -msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 -#: f228fb7953ea48ed99d89880205f4620 +#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 -#: 5870ac44e4c24b8daf5f06c49f95ce04 -msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier examples." msgstr "" -#: ../../src/topics/workflows.md:51 -#: a913c76d06164fa18718a8a6a7dcf0d6 +#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 -#: 93188ed43ee949cc98b3ea679ce14feb -msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +msgid "" +"A command-line tool or expression tool can also be written directly in the " +"same CWL document as the workflow. For example, we can rewrite the `echo-" +"uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 -#: 36618126a4df4326b236ebe2ea42cffa +#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 -#: 1cc17ad26e9c474b895ba5cd20c8b66a -msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "" +"Having separate files helps with modularity and code organization. But it " +"can be helpful writing everything in a single file for development. There " +"are other ways to combine multiple files into a single file (e.g. `cwltool --" +"pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 -#: 24aca0bea4d94e3593b844cf0586cffe -msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this " +"user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 -#: 46cc4859856e4367a9e5e68eecd48b73 +#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 -#: 9c56528acd5f49deb139e034dfbfac7c -msgid "This workflow extracts a java source file from a tar file and then compiles it." +#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +msgid "" +"This workflow extracts a java source file from a tar file and then compiles " +"it." msgstr "" -#: ../../src/topics/workflows.md:170 -#: 55ab007d472f43388e4c77aae8f165e7 +#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:179 -#: ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa -#: 307b6618a92948fca4203ccb497c77e6 +#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 -#: a2dd833fdca4443181648e41051a5232 -msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +msgid "" +"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" +"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 -#: 7e40cc9f9e1341c195e843c009575b94 -msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a " +"run:" msgstr "" -#: ../../src/topics/workflows.md:185 -#: 26c51dcb76364ed780376aecb7cbacda +#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 -#: 6fcf8ad3d1bd49afa4a105622437bd59 -msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 -#: 71cb81fa4511495b80422244849979e4 +#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 -#: def35d6021394def80a53ae49a2cdbde -msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a workflow." msgstr "" -#: ../../src/topics/workflows.md:221 -#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 -msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a list " +"of input parameters where each parameter consists of an identifier and a " +"data type. These parameters can be used as sources for input to specific " +"workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 -#: c84d4450bc6a475dbf34e0b22cea9130 -msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a list " +"of output parameters where each parameter consists of an identifier and a " +"data type. The `outputSource` connects the output parameter `classfile` of " +"the `compile` step to the workflow output parameter `compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 -#: cca9665f6daa44b49233baf34ab9fcc7 -msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second step " +"compiles the file from the first step using the java compiler. Workflow " +"steps are not necessarily run in the order they are listed, instead the " +"order is determined by the dependencies between steps (using `source`). In " +"addition, workflow steps which do not depend on one another may run in " +"parallel." msgstr "" -#: ../../src/topics/workflows.md:256 -#: 547edbf5fa424b8286cc21674ff159b0 -msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input " +"parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 -#: 7ca248888b9d484cb544cd76ba538662 -msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +msgid "" +"The ``in`` section of the workflow step connects these two input parameters " +"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " +"`source`. This means that when the workflow step is executed, the values " +"assigned to `tarball` and `name_of_file_to_extract` will be used for the " +"parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 -#: ae6b240718104380b08db5552d7355ea -msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +msgid "" +"The `out` section of the workflow step lists the output parameters that are " +"expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 -#: e5a8b7f84be64020b191099f3fad30ed -msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " +"in [Additional Arguments and Parameters](additional-arguments-and-parameters." +"md)). The output of this step `classfile` is connected to the `outputs` " +"section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 -#: f0b04849253c4693904512ddd7f9ce84 +#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 -#: 12a06d8358534102b202965d4258c18e -msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +msgid "" +"Workflows are ways to combine multiple tools to perform a larger operations. " +"We can also think of a workflow as being a tool itself; a CWL workflow can " +"be used as a step in another CWL workflow, if the workflow engine supports " +"the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 -#: 1658cac0de1b47e9b60f6d4a4ad9bb19 -msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 -#: 49ed137fe996452a8534c68d100db941 +#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 -#: b7f93705e5b8416696be01850072e8c0 -msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 -#: e87045829b344089ab59dc27063ddd7a -msgid "\"Visualization \"Visualization" +#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +msgid "" +"This two-step workflow starts with the `create-tar` step which is connected " +"to the `compile` step in orange; `compile` is another workflow, diagrammed " +"on the right. In purple we see the fixed string `\"Hello.java\"` being " +"supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:322 -#: 42ef2f145b824d69b63abc1da175c216 -msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +msgid "" +" \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " +"CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " +"to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 -#: c61cedf543664d388183e04b3939cc39 -msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and `*.java` " +"filename. This is generally best-practice, as it means it can be reused in " +"multiple parent workflows, or even in multiple steps within the same " +"workflow." msgstr "" -#: ../../src/topics/workflows.md:341 -#: 9e39e3f1501c4fcaab3e8962e090f6be -msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar " +"file at `tarball`, which we will prepare in the `create-tar` step. At this " +"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " +"specific input/output names, as those also appear in its usage as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 -#: 03e2f767c4da461982fc3c0f3ba94762 -msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 -#: 3bea5822b8694e2aa32c446e1c54a045 -msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +msgid "" +"In this case our step can assume `Hello.java` rather than be parameterized, " +"so we can use hardcoded values `hello.tar` and `Hello.java` in a " +"`baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 -#: 426023bd6e3a471cbb30dbda3d6f9e57 -msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This is " +"generally not best practice, as the tool then can't be reused. The reason " +"for doing it in this case is because the command line is hard-coded with " +"filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 -#: 0d498cd4caf54c15891ca1afe58e2727 -msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +msgid "" +"In this example we had to prepare a tar file outside, but only because our " +"inner workflow was designed to take that as an input. A better refactoring " +"of the inner workflow would be to take a list of Java files to compile, " +"which would simplify its usage as a tool step in other workflows." msgstr "" -#: ../../src/topics/workflows.md:394 -#: b2d75045e02741b4850f5ff1243f7858 -msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL " +"Tool description, care must be taken to improve its usability in multiple " +"workflows." msgstr "" -#: ../../src/topics/workflows.md:398 -#: cfa765264a27411ab914de569aa3dac4 +#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 -#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 -msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " +"run a tool or workflow multiple times over a list of inputs. The workflow " +"then takes the input(s) as an array and will run the specified step(s) on " +"each element of the array as if it were a single input. This allows you to " +"run the same workflow on multiple inputs without having to generate many " +"different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 -#: 5fa79c62049a447c8328ebf9db54ebf4 -msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +msgid "" +"The most common reason a new user might want to use scatter is to perform " +"the same analysis on different samples. Let's start with a simple workflow " +"that calls our first example (`hello_world.cwl`) and takes an array of " +"strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 -#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 -#: 3a67d77a2e7b4c0bb61cc3585ceae942 -msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "" +"Aside from the `requirements` section including `ScatterFeatureRequirement`, " +"what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 -#: f1cb55fc59824cc18a95fd6dcb32cf4c -msgid "First of all, notice that the main workflow level input here requires an array of strings." +#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 -#: d947c54933d64aad90df392a1cedd63f -msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This field " +"tells the runner that we'd like to scatter over this input for this " +"particular step. Note that the input name listed after scatter is the one of " +"the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 -#: 651d35997332404186aa6d5711da4a3d -msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if you " +"expect that the final output of your workflow will now have multiple outputs " +"to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 -#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 -#: 842b926ae34542cb9023021f137b08be +#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 -#: b662c1a5a4424c8d8350a806356acc61 -msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " +"calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 -#: 04d6babfd87343d7a5f13867ea02b65f -msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +msgid "" +"You can see that the workflow calls echo multiple times on each element of " +"our `message_array`. Ok, so how about if we want to scatter over two steps " +"in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 -#: 2eaacf1a90204a2b9bd621344560f2a1 -msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding the " +"following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 -#: 242993d42b164ee5abe7ca10d45856de +#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 -#: 4a94e5f7e1bc4d628702140e4e51d6d3 -msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "" +"And add a second step that uses `wc` to count the characters in each file. " +"See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 -#: e61d93b848184c8e8e573928427b4d0a +#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 -#: e3a7182f00f440b8b5461da91194a64b -msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under each " +"step:" msgstr "" -#: ../../src/topics/workflows.md:491 -#: 99fa96caacaa45cb97aded9a24fcac6d +#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 -#: b5338f39e8c74ff28e139da68089a742 -msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 -#: f6d92156d67c4a339bcfd194cff897df -msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +msgid "" +"Here we have placed the scatter field under each step. This is fine for this " +"example since it runs quickly, but if you're running many samples for a more " +"complex workflow, you may wish to consider an alternative. Here we are " +"running scatter on each step independently, but since the second step is not " +"dependent on the first step completing all languages, we aren't using the " +"scatter functionality efficiently. The second step expects an array as input " +"from the first step, so it will wait until everything in step one is " +"finished before doing anything. Pretend that `echo Hello World!` takes 1 " +"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " +"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " +"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " +"actually finish in 8 minutes because the first step must wait on `echo Hallo " +"welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can " +"make an entire workflow a single step in another workflow! Convert our two-" +"step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 -#: 1c9e386922324ec8a59306572c19fb8b +#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 -#: d80ab383eec9402faba997b548fe42eb -msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +msgid "" +"Now the scatter acts on a single step, but that step consists of two steps " +"so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 -#: f7d2827d97db4bf4ab84b5d6621c3b48 +#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 -#: 49217c02f58c43ff9ec00f10da8d4e84 -msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 -#: 20b9f181420c401d8615c17a10027517 +#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 -#: 8dbd56473f8c40c0bb12a48be06117e3 -msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +msgid "" +"The first thing you'll notice is that this workflow is only compatible for " +"version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 -#: 78d7f3ede2c746d482042adef050b2c4 -msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when` is " +"where the condition validation takes place. In this case only when `in1` " +"from the workflow contains a value `< 1` this step will be executed." msgstr "" -#: ../../src/topics/workflows.md:587 -#: cbbf93c70fe04ba7932ba25758ddc611 -msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " +"will pass the first conditional step and will therefore be executed and is " +"shown in the log by `INFO [step step1] start` whereas the second step is " +"skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 -#: cfa1c1fde4454df283f87cc54a9c59ec -msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +msgid "" +"When a value of 3 is given the first conditional step will not be executed " +"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 -#: 1a8be2950cbb475bbb2617e005f0fac9 -msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +msgid "" +"If no conditions are met for example when using `--val 2` the workflow will " +"raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 -#: 5f09d4d897cf457d80b9a11b8c01747e +#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 -#: 5d83c56102e141cc978500f678dd0c1c -msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers and " +"humans. This guide introduces the features of YAML that are relevant when " +"writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 -#: c38438fbf9a04e729ec2e3c962435289 +#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 -#: fdb9cc750cec43ee962517e637dc5fea +#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 -#: 08da9cd8056b4ddd8f5150cc85ba72ee +#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 -#: b027fc234ed943bbb00d4c6bc03c040a +#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 -#: b8befec0d8684638aaa616a659e0100c +#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 -#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 -#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 -#: 98056c5cfd5640ad9de0679360797cc7 +#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 -#: cda73485875d4c8e9464679a20558616 -msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " +"is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have special " +"meaning in the CWL specification and underscored key names otherwise. For " +"example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 -#: 98cae24919b74c088a5d89706aec581b -msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " +"and `home` - with their four respective values. Values can be character " +"strings, numeric (integer, floating point, or scientific representation), " +"Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 -#: b4b0940b4b5743c09637b36b964202d0 -msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may change " +"the way that they are interpreted i.e. `\"1234\"` will be treated as a " +"character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a " +"command: in CWL all parts of `baseCommand` must be strings so, if you want " +"to specify a fixed numeric value to a command, make sure that you wrap that " +"numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 -#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 -#: 9ca3554d771d45998e88aaede525b227 -msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program interpreting " +"the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 -#: 3fca839cede94cfd8e4f605c73ba699d -msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +msgid "" +"If there is anything on the line before the comment, be sure to add at least " +"one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 -#: da34c635707345b2a5e85a2fcd30bbaf +#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 -#: 3ded0f125249485c921994b6e6b93ac9 -msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, these " +"hierarchical structures are described in YAML by providing additional key-" +"value pairs as the value of any key. These pairs (sometimes referred to as " +"\"children\") are written on new lines under the key to which they belong " +"(the \"parent\"), and should be indented with two spaces (⇥tab characters " +"are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 -#: 53ece35d309a4c8d99f1efb2122a7092 -msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " +"while one of these children, `inputBinding`, contains a further two key-" +"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " +"below for more information about providing multiple values/key-value pairs " +"for a single key. For comparison with the example YAML above, here is a " +"graphical representation of the `inputs` object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 -#: d74321b111d84ae7a515f2f17dd39e23 +#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 -#: 7fc0bdf2489a44f2a29e71b86f7c0055 -msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) section " +"above, more than one key-value pair can be mapped to a single key. However, " +"it is also possible to define multiple values for a key without having to " +"provide a unique key for each value. We can achieve this with an _array_, " +"where each value is defined on its own line and preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 -#: fd64dd818ec64bb6aa9a11586a5747f6 +#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 -#: 8c06e542dd4144fa83388d8142552c8d +#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 -#: 87bafb845c714b109874f6137b84462d -msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " +"can also be defined in YAML using the native JSON syntax. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 -#: 5ab9ddf613a540a2b8228e37600cc5dc +#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 -#: fcd05b1ef31a4046946a2399c7fc5575 -msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +msgid "" +"Native JSON can be useful in indicating where a field is intentionally left " +"empty (such as `[]` for an empty array), as well as where it makes more " +"sense for the values to be located on the same line (For example, when " +"providing option flags and their values in a shell command). However, as the " +"second example above shows, it can severely affect the readability of a YAML " +"file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 -#: f4b8fc8236044fada420def13a02813d +#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 -#: 859368c1f25c4a4aad57abfd046c63f5 -msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " +"while we wrote this guide, though it also covers features that are not valid " +"in CWL." msgstr "" -#: ../../src/tutorials.md:1 -#: 2203c93f02ac4514a43508ecb98dfcc5 +#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 -#: 5d92464923c245818c070fbef102be89 -msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to the " +"list." msgstr "" -#: ../../src/tutorials.md:7 -#: 8a5cd557dab5456bb41cdc24af73b50c +#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 -#: 13d7e2e92e96432787c712cf6a595424 -msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +msgid "" +"[Introduction to Workflows with Common Workflow Language: For Contributors.]" +"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" -"[Common Workflow " -"Languageによるワークフロー入門：コントリビューターのために](https" -"://carpentries-incubator.github.io/cwl-novice-tutorial/)" +"[Common Workflow Languageによるワークフロー入門：コントリビューターのために]" +"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" -#: ../../src/tutorials.md:11 -#: 0abdd85c9b964a4e89ba3d80a6c78d6f +#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 -#: 3cbf1f69a5514fd3bee90e68b201190f +#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "[CWLでのTypeScript](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -#: ../../src/tutorials.md:15 -#: 68c97a7065634d02956f3f5c1d4eeb9f +#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 -#: a67c7e0eaf4e4d27b3e5db303333a088 +#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "[CWLでrnaseq](https://arvados.github.io/rnaseq-cwl-training/)" diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 5f3d463a..41a1d23f 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -8,8 +8,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-07-01 03:53+0000\n" -"Last-Translator: Zoë Ma \n" +"PO-Revision-Date: 2023-07-05 09:51+0000\n" +"Last-Translator: Michael Crusoe \n" "Language-Team: Chinese (Simplified) \n" "Language: zh_Hans\n" @@ -3018,7 +3018,7 @@ msgstr "" #: ../../src/topics/staging-input-files.md:9 #: c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" -msgstr "" +msgstr "`linkfile.cwl`" #: ../../src/topics/troubleshooting.md:1 #: 0f7508ce59754a7eb230dea6042244c6 @@ -3103,12 +3103,12 @@ msgstr "" #: ../../src/topics/using-containers.md:21 #: 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" -msgstr "" +msgstr "`docker.cwl`" #: ../../src/topics/using-containers.md:27 #: 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" -msgstr "" +msgstr "`docker-job.yml`" #: ../../src/topics/using-containers.md:33 #: 2713594c937d4c528fc8d04d9e9819ed @@ -3128,7 +3128,7 @@ msgstr "" #: ../../src/topics/using-containers.md:55 #: 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" -msgstr "" +msgstr "`hello.js`" #: ../../src/topics/using-containers.md:69 #: 483181f498fc4d968b5fe6ef427709f7 @@ -3163,7 +3163,7 @@ msgstr "" #: ../../src/topics/workflows.md:51 #: a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" -msgstr "" +msgstr "`echo-uppercase.cwl`" #: ../../src/topics/workflows.md:81 #: 93188ed43ee949cc98b3ea679ce14feb @@ -3173,7 +3173,7 @@ msgstr "" #: ../../src/topics/workflows.md:91 #: 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" -msgstr "" +msgstr "`echo-uppercase-single-file.cwl`" #: ../../src/topics/workflows.md:150 #: 1cc17ad26e9c474b895ba5cd20c8b66a @@ -3198,7 +3198,7 @@ msgstr "" #: ../../src/topics/workflows.md:170 #: 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" -msgstr "" +msgstr "`1st-workflow.cwl`" #: ../../src/topics/workflows.md:179 #: ../../src/topics/workflows.md:180 @@ -3220,7 +3220,7 @@ msgstr "" #: ../../src/topics/workflows.md:185 #: 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" -msgstr "" +msgstr "`1st-workflow-job.yml`" #: ../../src/topics/workflows.md:191 #: 6fcf8ad3d1bd49afa4a105622437bd59 @@ -3360,7 +3360,7 @@ msgstr "" #: ../../src/topics/workflows.md:415 #: 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" -msgstr "" +msgstr "`scatter-workflow.cwl`" #: ../../src/topics/workflows.md:421 #: 3a67d77a2e7b4c0bb61cc3585ceae942 @@ -3390,7 +3390,7 @@ msgstr "" #: ../../src/topics/workflows.md:452 #: 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" -msgstr "" +msgstr "`scatter-job.yml`" #: ../../src/topics/workflows.md:458 #: b662c1a5a4424c8d8350a806356acc61 @@ -3410,7 +3410,7 @@ msgstr "" #: ../../src/topics/workflows.md:472 #: 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" -msgstr "" +msgstr "`hello_world_to_stdout.cwl`" #: ../../src/topics/workflows.md:480 #: 4a94e5f7e1bc4d628702140e4e51d6d3 @@ -3420,7 +3420,7 @@ msgstr "" #: ../../src/topics/workflows.md:483 #: e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" -msgstr "" +msgstr "`wc-tool.cwl`" #: ../../src/topics/workflows.md:489 #: e3a7182f00f440b8b5461da91194a64b @@ -3430,7 +3430,7 @@ msgstr "" #: ../../src/topics/workflows.md:491 #: 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" -msgstr "" +msgstr "`scatter-two-steps.cwl`" #: ../../src/topics/workflows.md:497 #: b5338f39e8c74ff28e139da68089a742 @@ -3445,7 +3445,7 @@ msgstr "" #: ../../src/topics/workflows.md:513 #: 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" -msgstr "" +msgstr "`scatter-nested-workflow.cwl`" #: ../../src/topics/workflows.md:519 #: d80ab383eec9402faba997b548fe42eb @@ -3465,7 +3465,7 @@ msgstr "" #: ../../src/topics/workflows.md:527 #: 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" -msgstr "" +msgstr "`conditional-workflow.cwl`" #: ../../src/topics/workflows.md:566 #: 8dbd56473f8c40c0bb12a48be06117e3 From 789df1902b09cce03cdf3c738aaedd5815082a60 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Wed, 12 Jul 2023 12:19:10 +0200 Subject: [PATCH 080/179] Translated using Weblate (Japanese) (#412) Currently translated at 5.8% (35 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 31 ++++++++++++++-------------- 1 file changed, 16 insertions(+), 15 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 70df9bb6..a3025635 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,10 +8,10 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-07-01 03:53+0000\n" -"Last-Translator: Michael Crusoe \n" -"Language-Team: Japanese \n" +"PO-Revision-Date: 2023-07-11 22:53+0000\n" +"Last-Translator: Manabu ISHII \n" +"Language-Team: Japanese \n" "Language: ja\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" @@ -234,7 +234,7 @@ msgstr "" #: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" -msgstr "" +msgstr "「一か八か」のパラメータをモデル化する" #: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 msgid "" @@ -255,7 +255,7 @@ msgstr "" #: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" -msgstr "" +msgstr "merge_nested" #: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 msgid "" @@ -279,21 +279,21 @@ msgstr "" #: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" -msgstr "" +msgstr "オプション入力 💯" #: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." -msgstr "" +msgstr "入力パラメータをオプションにするには、型宣言に疑問符を付けます。" #: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 msgid "" -msgstr "" +msgstr "" #: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c msgid "Enum Inputs ⚜️" -msgstr "" +msgstr "列挙型入力 ⚜️" #: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 msgid "" @@ -304,11 +304,11 @@ msgstr "" #: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd msgid "" -msgstr "" +msgstr "" #: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 msgid "Record Inputs 📀" -msgstr "" +msgstr "レコード入力 📀" #: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c msgid "" @@ -348,16 +348,17 @@ msgstr "" #: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "" +msgstr "`cwltool` ファイル名の中に空白文字があるために起こるエラー" #: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "" +msgstr "`cwltool` は、デフォルトではファイル名に一部の文字を許可していません。" #: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a msgid "" "For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "" +msgstr "例えば、`a space is here.txt` " +"というファイル名には、3つの空白文字が含まれています。" #: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde msgid "" From 8abf537144d7b63c3561c1ff2b660543effd0eb0 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Thu, 13 Jul 2023 11:02:52 +0200 Subject: [PATCH 081/179] Translated using Weblate (Japanese) (#413) Currently translated at 6.6% (40 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index a3025635..edb79104 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-07-11 22:53+0000\n" +"PO-Revision-Date: 2023-07-13 02:28+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -451,7 +451,7 @@ msgstr "" #: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" -msgstr "" +msgstr "ユーザーガイドの使い方" #: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 msgid "" @@ -471,11 +471,11 @@ msgstr "" #: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" -msgstr "" +msgstr "目次" #: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" -msgstr "" +msgstr "基本コンセプト" #: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 msgid "" @@ -490,7 +490,7 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" -msgstr "" +msgstr "CWLの仕様" #: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf msgid "" @@ -517,7 +517,7 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" -msgstr "" +msgstr "実装" #: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 msgid "" From edc381739e6933abb6a140cbc8ddf4bd38a35881 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Tue, 15 Aug 2023 10:52:22 +0200 Subject: [PATCH 082/179] Translated using Weblate (Japanese) (#416) Currently translated at 8.3% (50 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index edb79104..03c4e309 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-07-13 02:28+0000\n" +"PO-Revision-Date: 2023-08-15 01:54+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -219,7 +219,7 @@ msgstr "" #: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." -msgstr "" +msgstr "CWLでは、すべてを直接的に記述する必要があります。。" #: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" @@ -319,7 +319,7 @@ msgstr "" #: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" -msgstr "" +msgstr "相互に排他的なパラメータを設定する" #: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 msgid "" @@ -332,19 +332,19 @@ msgstr "" #: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" -msgstr "" +msgstr "ブール値の設定" #: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" -msgstr "" +msgstr "デフォルトフィールドを使って、これらを設定します" #: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" -msgstr "" +msgstr "入力された文字列を連結する" #: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." -msgstr "" +msgstr "defaultフィールドの代わりにvalueFromフィールドを使用する必要があります。" #: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" @@ -364,7 +364,8 @@ msgstr "例えば、`a space is here.txt` " msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." -msgstr "" +msgstr "これらの危険な文字を避けられない場合は、`--relax-path-checks` を`cwltool` " +"に渡してください。" #: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" @@ -410,7 +411,7 @@ msgstr "" #: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" -msgstr "" +msgstr "JavaScriptの式をデバッグする" #: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 msgid "" @@ -439,7 +440,7 @@ msgstr "" #: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" -msgstr "" +msgstr "ご意見、ご感想、貢献をお待ちしております!" #: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 msgid "" @@ -498,6 +499,9 @@ msgid "" "community. The specification has different versions. The version covered in " "this user guide is the {{ cwl_version }}." msgstr "" +"CWL仕様は、CWLコミュニティによって書かれ、維持されている文書です。この仕様に" +"は異なるバージョンが存在します。このユーザーガイドで扱うバージョンは{{ " +"cwl_version }}です。" #: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 msgid "" From 80e91490f19f79d267a7e2f92ff1a66034f136d9 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Tue, 15 Aug 2023 15:34:30 +0200 Subject: [PATCH 083/179] Translated using Weblate (Japanese) (#417) Currently translated at 10.0% (60 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 03c4e309..ea602852 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-08-15 01:54+0000\n" +"PO-Revision-Date: 2023-08-15 12:33+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -559,27 +559,27 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:112 #: 8c9772f96caf4169924d22eb929a4f0f msgid "A command-line tool." -msgstr "" +msgstr "コマンドラインツール。" #: ../../src/introduction/basic-concepts.md:113 #: 4fac209a62114798b79e4810f7a0148b msgid "An expression tool." -msgstr "" +msgstr "Expression ツール。" #: ../../src/introduction/basic-concepts.md:114 #: b97ba368fd664caab0494e2392795697 msgid "An operation." -msgstr "" +msgstr "Operation。" #: ../../src/introduction/basic-concepts.md:115 #: 903a6796e3304a19ad885b2428b0e80f msgid "A workflow." -msgstr "" +msgstr "ワークフロー。" #: ../../src/introduction/basic-concepts.md:118 #: 6e352ac1f8e144c392ac5adf18c28298 msgid "The processing units available in the CWL objects model." -msgstr "" +msgstr "CWLオブジェクトモデルで使用可能な処理単位です。" #: ../../src/introduction/basic-concepts.md:119 #: cf2922f645904ac7955428ecddc37b8a @@ -587,6 +587,8 @@ msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" +"コマンドラインツールは、`echo` 、`ls` 、`tar` のようなコマンドラインユーティ" +"リティのラッパーです。コマンドラインツールは、ワークフローから呼び出せます。" #: ../../src/introduction/basic-concepts.md:122 #: 5f47aae608c041aeb4134d59dad314d2 @@ -626,18 +628,19 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:141 #: cc6cd8cb81564cadb8e6a4c49423b7f7 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" +msgstr "`InlineJavascriptWorkflow` - でJavaScriptを有効にします。" #: ../../src/introduction/basic-concepts.md:142 #: 2d9f53b6ed5041dbb6c0b54835897856 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" +msgstr "`SubworkflowFeatureRequirement` - ネストしたワークフローを有効にします。" #: ../../src/introduction/basic-concepts.md:143 #: 907674a4ecff4826a2b880e28fc38f33 msgid "" "`InitialWorkDirRequirement` - controls staging files in the input directory." -msgstr "" +msgstr "`InitialWorkDirRequirement` - " +"入力ディレクトリのステージングファイルを制御します。" #: ../../src/introduction/basic-concepts.md:145 #: 037cd0e5ceda482eaeaca03d51745aee @@ -660,7 +663,7 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:155 #: c4c3315c96714e81b364f8cc003b87e6 msgid "FAIR Workflows" -msgstr "" +msgstr "FAIRワークフロー" #: ../../src/introduction/basic-concepts.md:157 #: 3eb6a013a2a4478ca2ad134661f65c58 From fe9ef46442e115664ce530246b70254fa1019ae9 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Thu, 17 Aug 2023 08:08:19 +0200 Subject: [PATCH 084/179] Translated using Weblate (Japanese) (#418) Currently translated at 12.2% (73 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 29 +++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index ea602852..178636e3 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-08-15 12:33+0000\n" +"PO-Revision-Date: 2023-08-17 01:56+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -706,19 +706,19 @@ msgstr "" #: ../../src/introduction/quick-start.md:94 65c24244713741e196da08cb9ba237b2 #: f059896039524095b4deb65d693f8ddf 3439764fab0e49d2bcb7c9fbae556e65 msgid "Learn More" -msgstr "" +msgstr "さらなる学習" #: ../../src/introduction/basic-concepts.md:180 #: 9d5100c7d0a040aea1020bf633ad17de msgid "Semantic Versioning - " -msgstr "" +msgstr "セマンティック・バージョニング -" #: ../../src/introduction/basic-concepts.md:181 #: 36eb4b3b966640af90faa55db3789cb6 msgid "" "The CWL Specification page in the CWL website: " -msgstr "" +msgstr "CWLサイト内の「CWL仕様」ページ：" #: ../../src/introduction/basic-concepts.md:182 #: 2ccb956baa6b4376a04ad9fcc4654631 @@ -726,13 +726,15 @@ msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" +"GitHubにある現在のCWL仕様：{{ ''.format(cwl_version_text) }}" #: ../../src/introduction/basic-concepts.md:183 #: 72889b830c514afe9a7cb1e64b5666a0 msgid "" "The list of Implementations in the CWL website: " -msgstr "" +msgstr "CWLサイト内の実装のリスト：" #: ../../src/introduction/basic-concepts.md:184 #: e29bd7f973544600be589c3b3f84cf63 @@ -748,7 +750,7 @@ msgstr "" #: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" -msgstr "" +msgstr "はじめに" #: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 msgid "" @@ -759,7 +761,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" -msgstr "" +msgstr "前提条件" #: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 msgid "" @@ -773,7 +775,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" -msgstr "" +msgstr "CWL実装" #: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf msgid "" @@ -785,25 +787,26 @@ msgstr "" #: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" -msgstr "" +msgstr "オペレーティングシステム" #: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b msgid "" "We recommend using an up-to-date operating system. You can choose any of the " "following options for your operating system:" -msgstr "" +msgstr "最新のオペレーティングシステムを使用することをお勧めします。OSは、以下のいず" +"れかをお選びいただけます：" #: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" -msgstr "" +msgstr "Linux" #: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf msgid "macOS" -msgstr "" +msgstr "macOS" #: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" -msgstr "" +msgstr "Windows" #: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 msgid "" From 14ecb8addb54c5e02f302a4d51a9a755a6c24ded Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Tue, 22 Aug 2023 10:12:03 +0200 Subject: [PATCH 085/179] Translated using Weblate (Japanese) (#419) Currently translated at 19.8% (119 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 107 ++++++++++++++++++--------- 1 file changed, 71 insertions(+), 36 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 178636e3..b6ca836e 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-08-17 01:56+0000\n" +"PO-Revision-Date: 2023-08-22 00:00+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -901,10 +901,13 @@ msgid "" "The CWL community publishes a Python package with the name `cwlref-runner` " "that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" +"CWLコミュニティは、`cwlref-runner` " +"という名前のPythonパッケージを公開しており、`cwltool` のエイリアスを`cwl-" +"runner` という名前でインストールします。" #: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" +msgstr "cwltool のエイリアス `cwl-runner` を `pip` でインストールします。" #: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 msgid "" @@ -912,6 +915,9 @@ msgid "" "which will invoke `cwltool`. You should have the same results and output as " "in the previous section." msgstr "" +"これで `cwl-runner` 実行ファイルを用いてワークフローを検証・実行し、`cwltool`" +" を呼び出すことができるようになりました。前のセクションと同じ結果と出力が得ら" +"れるはずです。" #: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." @@ -930,16 +936,17 @@ msgstr "" #: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" -msgstr "" +msgstr "`true_shebang.cwl`" #: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 msgid "" "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" +msgstr "`chmod u+x` を実行することで、 `true_shebang.cwl` " +"を実行可能なファイルにすることができます。" #: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." -msgstr "" +msgstr "`true.cwl` 実行可能なものにする。" #: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 msgid "" @@ -950,7 +957,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" +msgstr "`true_shebang.cwl` をシェバングで実行する。" #: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 msgid "" @@ -964,7 +971,7 @@ msgstr "" #: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" -msgstr "" +msgstr "テキストエディタ" #: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed msgid "" @@ -997,6 +1004,8 @@ msgid "" "The CWL community also maintains a list of editors and viewers: " msgstr "" +"CWLコミュニティでは、エディターやビューアーのリストも管理しています：" #: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 msgid "Docker" @@ -1029,11 +1038,12 @@ msgstr "" msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the next " "section, Basic Concepts." -msgstr "" +msgstr "次項の「基本コンセプト」の[実装](basic-concepts." +"md#implementations)のトピックを参照してください。" #: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " -msgstr "" +msgstr "Python`venv` モジュール:" #: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" @@ -1048,7 +1058,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" -msgstr "" +msgstr "\"Hello World\"" #: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 msgid "" @@ -1059,7 +1069,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" -msgstr "" +msgstr "`hello_world.cwl`" #: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 msgid "" @@ -1145,7 +1155,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" +msgstr "`cwltool` に Inputs Object ファイルをします。" #: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 msgid "" @@ -1157,30 +1167,36 @@ msgstr "" #: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" -msgstr "" +msgstr "このユーザーガイドの次のセクションを読み進めてください！" #: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 msgid "" "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" +msgstr "[CWL 実装一覧](https://www.commonwl.org/implementations)。" #: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" +"GitHubの[`common-workflow-language` organization](https://github.com/common-" +"workflow-language)です。" #: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 msgid "" "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" "Common_Workflow_Language)." msgstr "" +"[Wikipedia上のCommon Workflow Language](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)。" #: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b msgid "" "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." "org/wiki/YAML)." msgstr "" +"[YAML.org](http://yaml.org/) と [WikipediaにあるYAML](https://en.wikipedia." +"org/wiki/YAML) です。" #: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff msgid "" @@ -1193,6 +1209,8 @@ msgid "" "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" "Workflow_management_system)." msgstr "" +"[Wikipediaの項目としてのワークフロー管理システム](https://en.wikipedia.org/" +"wiki/Workflow_management_system)。" #: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d msgid "" @@ -1244,7 +1262,8 @@ msgstr "" msgid "" "And now invoke `cwltool` providing the tool description and the input object " "on the command line:" -msgstr "" +msgstr "そして、コマンドラインでツール定義と入力オブジェクトを渡して`cwltool` " +"を起動します：" #: ../../src/topics/additional-arguments-and-parameters.md:36 #: 713666580a0a4466b4ba6e3eb2b54f0a @@ -1267,7 +1286,7 @@ msgstr "" #: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" -msgstr "" +msgstr "ベストプラクティス" #: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "" @@ -1312,7 +1331,8 @@ msgstr "" msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" -msgstr "" +msgstr "参考文献：\"[科学者・プログラマーのためのソフトウェアライセンス " +"クイックガイド][sci-license]\"" #: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" @@ -1336,7 +1356,8 @@ msgstr "" msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." -msgstr "" +msgstr "ツール定義では、`SoftwareRequirement` " +"の下に、短い名前を使用して依存関係をリストアップします。" #: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 msgid "" @@ -1357,6 +1378,8 @@ msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" +"ツール定義では、`SoftwareRequirement` の下に、このツール定義で動作することが" +"確認されているツールのバージョンのリストを含めるます。" #: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 msgid "" @@ -1399,12 +1422,15 @@ msgid "" "more detailed description than was provided in the top-level `label` (see " "above)." msgstr "" +"有用であれば、トップレベル`doc` も含めてください。これは、トップレベル`label`" +" （上記参照）で提供されたものより長く詳細な説明を記述します。" #: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list of " "valid values." -msgstr "" +msgstr "有効な値のリストが決まっている要素には、`type: string` の代わりに、`type: " +"enum` を使用してください。" #: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a msgid "" @@ -1418,7 +1444,8 @@ msgstr "" msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." -msgstr "" +msgstr "ツール定義を同僚（できれば別の機関の人）に渡し、テストしてもらい、フィードバ" +"ックをもらいましょう。" #: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 msgid "" @@ -1436,7 +1463,7 @@ msgstr "" #: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" -msgstr "" +msgstr "コマンドラインツール" #: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 msgid "" @@ -1452,14 +1479,17 @@ msgid "" "example contains a minimal example of a CWL command-line tool for the `echo` " "Linux command, using inputs and outputs." msgstr "" +"CWLコマンドラインツールは、`inputs` と`outputs` " +"も持っていなければなりません。次の例は、Linuxコマンド `echo` " +"のためのCWLコマンドラインツールの最小限の例で、inputsとoutputsを使用します。" #: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." -msgstr "" +msgstr "CWLコマンドラインツール。" #: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" -msgstr "" +msgstr "`echo.cwl`" #: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d msgid "" @@ -1506,7 +1536,7 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 #: d3f74c3b094a427fbec831afab657d50 msgid "`createfile.cwl`" -msgstr "" +msgstr "`createfile.cwl`" #: ../../src/topics/creating-files-at-runtime.md:15 #: cfffc518ba6e4ed1a80762ed6f7d25df @@ -1531,14 +1561,15 @@ msgstr "" msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" -msgstr "" +msgstr "上記のCWLツールをテストするために、このジョブを使用して、入力値`message` " +"を与えます：" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 #: 2d2ef4769b2347e79db827655f1bcdeb 2699fbc4376148af91b7a5a6cdac467c #: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" -msgstr "" +msgstr "`echo-job.yml`" #: ../../src/topics/creating-files-at-runtime.md:35 #: 10d1373bb14a4a3cacd3b92a2f83382d @@ -1565,7 +1596,8 @@ msgstr "" msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." -msgstr "" +msgstr "フォーマットについては、[YAMLガイド](../topics/yaml-guide." +"md#maps)を参照してください。" #: ../../src/topics/creating-files-at-runtime.md:54 #: ../../src/topics/environment-variables.md:18 @@ -1577,11 +1609,12 @@ msgstr "" msgid "" "Now invoke `cwltool` with the tool description and the input object on the " "command line:" -msgstr "" +msgstr "ここで、コマンドラインにツール定義と入力オブジェクトを指定して、`cwltool` " +"を起動します：" #: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" -msgstr "" +msgstr "カスタムタイプ" #: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a msgid "" @@ -1597,14 +1630,16 @@ msgid "" "The example below is a CWL description of the [biom convert format][biom] " "tool for converting a standard biom table file to hdf5 format." msgstr "" +"以下の例は、標準的なbiomテーブルファイルをhdf5形式に変換する[biom convert " +"format][biom] ツールのCWL定義です。" #: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" -msgstr "" +msgstr "`custom-types.cwl`" #: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" -msgstr "" +msgstr "`custom-types.yml`" #: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 msgid "" @@ -1634,11 +1669,11 @@ msgstr "" #: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e msgid "" "The contents of the YAML file describing the custom type are given below:" -msgstr "" +msgstr "カスタムタイプを記述するYAMLファイルの内容を以下に示します：" #: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" -msgstr "" +msgstr "`biom-convert-table.yaml`" #: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 msgid "" @@ -1659,7 +1694,7 @@ msgstr "" #: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" -msgstr "" +msgstr "環境変数" #: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 msgid "" @@ -1670,11 +1705,11 @@ msgstr "" #: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" -msgstr "" +msgstr "`env.cwl`" #: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" -msgstr "" +msgstr "Expression Tool" #: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 msgid "" From 5c63b0c948482c5995c4dc56d7760f066dd1980f Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Fri, 25 Aug 2023 09:23:02 +0200 Subject: [PATCH 086/179] Translated using Weblate (Japanese) (#420) Currently translated at 26.0% (156 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 113 ++++++++++++++++++--------- 1 file changed, 75 insertions(+), 38 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index b6ca836e..fa48a092 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-08-22 00:00+0000\n" +"PO-Revision-Date: 2023-08-25 00:56+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.0-dev\n" +"X-Generator: Weblate 5.0\n" #: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" @@ -1794,7 +1794,7 @@ msgstr "" msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" -msgstr "" +msgstr "なお、上の例のように、map構文で requirements を指定することも可能です：" #: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 msgid "" @@ -1805,7 +1805,7 @@ msgstr "" #: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" -msgstr "" +msgstr "JavaScriptはどこで使えますか？" #: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 msgid "" @@ -1814,16 +1814,19 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +#, fuzzy msgid "" "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineTool)" msgstr "" +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)から" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 1acb064f7a4a482aa0174bdc847c6382 #: 0222780b98ac48e89b1b4f57c9df8590 msgid "`arguments`" -msgstr "" +msgstr "`arguments`" #: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 #: ../../src/topics/expressions.md:89 @@ -1834,31 +1837,34 @@ msgstr "" #: ffd3ca1f97cf4d3a892ef4f4b04771e4 e4e68011dc5f42e4918c747afa7d764b #: d44e3cfa661840eb851782e24caf1b68 msgid "`valueFrom`" -msgstr "" +msgstr "`valueFrom`" #: ../../src/topics/expressions.md:69 #: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf #: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" -msgstr "" +msgstr "`stdin`" #: ../../src/topics/expressions.md:70 #: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 #: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" -msgstr "" +msgstr "`stdout`" #: ../../src/topics/expressions.md:71 #: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c #: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" -msgstr "" +msgstr "`stderr`" #: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +#, fuzzy msgid "" "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandInputParameter)" msgstr "" +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)から" #: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 #: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 @@ -1871,7 +1877,7 @@ msgstr "" #: e89dbeb22f41430ca39c923d9fdf68cb bd61499b71e64164878dea08d6d7141e #: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" -msgstr "" +msgstr "`format`" #: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 #: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 @@ -1884,76 +1890,94 @@ msgstr "" #: da5188d3bedc4997a35bdf417f2f643c cd7a0190511d4613b09600a3b1e9d55f #: 47def3b078e2402182039be0227090ae msgid "`secondaryFiles`" -msgstr "" +msgstr "`secondaryFiles`" #: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac msgid "" "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineBinding)" msgstr "" +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding)から" #: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 msgid "" "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputParameter)" msgstr "" +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter)から" #: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 msgid "" "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputBinding)" msgstr "" +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding)から" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 #: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" -msgstr "" +msgstr "`glob`" #: ../../src/topics/expressions.md:82 #: ../../src/topics/parameter-references.md:79 d555a3d991e344a5a8e1289168d7c6d1 #: 44b3f123c9b04a308c1161b742a7b34b msgid "`outputEval`" -msgstr "" +msgstr "`outputEval`" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 e9fa9430535c424fa3e8be5d460d2ba4 #: 0e306cc923974d1db83fdfb45105a11c +#, fuzzy msgid "From `Workflow`" -msgstr "" +msgstr "`Workflow`から" #: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +#, fuzzy msgid "" "From [InputParameter](https://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" "v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) " +"と [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowOutputParameter)から" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 b0290d1a477b48119e17cf1fed9d6dff #: 446f1190af7a40a0913ff04ce7aa938c +#, fuzzy msgid "From `steps`" -msgstr "" +msgstr "`steps`から" #: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +#, fuzzy msgid "" "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." "html#WorkflowStepInput)" msgstr "" +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)から" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 e1cde4aa32c041238ed2596173c6d824 #: 557694f82e314baa9ccafba14d6ff2c9 +#, fuzzy msgid "" "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." "html#ExpressionTool)" msgstr "" +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow." +"html#ExpressionTool)から" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 c2a92d3eca7f4ee39cec649170eeea53 #: 3c939769ede94602a67fc50c435741cf msgid "`expression`" -msgstr "" +msgstr "`expression`" #: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 msgid "" @@ -1961,106 +1985,119 @@ msgid "" "html#InputParameter) and [ExpressionToolOutputParameter](https://www." "commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) " +"と [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#ExpressionToolOutputParameter)から" #: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +#, fuzzy msgid "" "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." "html#ResourceRequirement)" msgstr "" +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)から" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 #: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" -msgstr "" +msgstr "`coresMin`" #: ../../src/topics/expressions.md:97 #: ../../src/topics/parameter-references.md:94 718ceee9973240ec9c100977bbcc8921 #: 2b25152f6df5494a8632f3ce631c20d8 msgid "`coresMax`" -msgstr "" +msgstr "`coresMax`" #: ../../src/topics/expressions.md:98 #: ../../src/topics/parameter-references.md:95 c07ab08eb75d4528949c56a3d7c12b28 #: 846cd427ae25410eae7c920b237edcb0 msgid "`ramMin`" -msgstr "" +msgstr "`ramMin`" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 #: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" -msgstr "" +msgstr "`ramMax`" #: ../../src/topics/expressions.md:100 #: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 #: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" -msgstr "" +msgstr "`tmpdirMin`" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 #: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" -msgstr "" +msgstr "`tmpdirMax`" #: ../../src/topics/expressions.md:102 #: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 #: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" -msgstr "" +msgstr "`outdirMin`" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 #: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" -msgstr "" +msgstr "`outdirMax`" #: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 msgid "" "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" "CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#InitialWorkDirRequirement)から" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 #: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" -msgstr "" +msgstr "`listing`" #: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +#, fuzzy msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" +msgstr "[Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)に" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 #: effc0208cf4f4551958db6e526c0528b 9d4889c8cec24351a7a9e3c547e331b6 msgid "`entry`" -msgstr "" +msgstr "`entry`" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 #: be6c1e85c7b6495d8086c262daad20e7 af4f7f232a9d42388c0ba1cfc7c2cdf7 msgid "`entryname`" -msgstr "" +msgstr "`entryname`" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 #: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +#, fuzzy msgid "From `EnvVarRequirement`" -msgstr "" +msgstr "`EnvVarRequirement`から" #: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +#, fuzzy msgid "" "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." "html#EnvironmentDef)" msgstr "" +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)から" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 #: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 msgid "`envValue`" -msgstr "" +msgstr "`envValue`" #: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 msgid "" @@ -2100,7 +2137,7 @@ msgstr "" #: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" -msgstr "" +msgstr "`hello-world-expressionlib-inline.cwl`" #: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 msgid "" @@ -2197,17 +2234,17 @@ msgstr "" #: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" -msgstr "" +msgstr "`metadata_example.cwl`" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 #: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" -msgstr "" +msgstr "このCWL定義に相当するものをコマンドライン形式にすると" #: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" -msgstr "" +msgstr "サンプルパラメーターファイル" #: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b msgid "" @@ -2219,7 +2256,7 @@ msgstr "" #: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" -msgstr "" +msgstr "`sample.yml`" #: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d msgid "" @@ -2231,15 +2268,15 @@ msgstr "" #: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" -msgstr "" +msgstr "トピックス" #: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" -msgstr "" +msgstr "Inputs" #: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" -msgstr "" +msgstr "必須入力パラメータ" #: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e msgid "" From 3c673b50e440a3f5e7bce0e7789e659174ca3e8d Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Mon, 28 Aug 2023 11:04:49 +0200 Subject: [PATCH 087/179] Translated using Weblate (Japanese) (#421) Currently translated at 28.0% (168 of 598 strings) Translated using Weblate (Japanese) Currently translated at 27.9% (167 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 32 +++++++++++++++++----------- 1 file changed, 19 insertions(+), 13 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index fa48a092..da099cdb 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-08-25 00:56+0000\n" +"PO-Revision-Date: 2023-08-26 23:56+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.0\n" +"X-Generator: Weblate 5.0.1-dev\n" #: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" @@ -2337,7 +2337,8 @@ msgstr "" msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " "command line." -msgstr "" +msgstr "次に、コマンドラインで`touch whale.txt` と入力し、[touch]" +"をコマンドを使用して whale.txt を作成します。" #: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da msgid "" @@ -2400,6 +2401,9 @@ msgid "" "Input files are read-only. If you wish to update an input file, you must " "[first copy it to the output directory](staging-input-files.md)." msgstr "" +"入力ファイルは読み取り専用です。 " +"入力ファイルを更新したい場合は、[まず出力ディレクトリにコピーする](staging-" +"input-files.md)必要があります。" #: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "" @@ -2416,11 +2420,12 @@ msgstr "" msgid "" "The `baseCommand` field will always appear in the final command line before " "the parameters." -msgstr "" +msgstr "`baseCommand` " +"フィールドは、常にパラメータの前の最終コマンド行に表示されます。" #: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" -msgstr "" +msgstr "配列入力" #: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d msgid "" @@ -2433,11 +2438,11 @@ msgstr "" #: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" -msgstr "" +msgstr "`array-inputs.cwl`" #: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" -msgstr "" +msgstr "`array-inputs-job.yml`" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 #: ../../src/topics/outputs.md:105 588f0f7f967f4d69af27c9729d6d3119 @@ -2480,21 +2485,21 @@ msgstr "" #: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" -msgstr "" +msgstr "`record.cwl`" #: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" -msgstr "" +msgstr "`record-job1.yml`" #: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." -msgstr "" +msgstr "最初の例では、`itemB` も与えずに、`itemA` を与えることはできません。" #: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" -msgstr "" +msgstr "`record-job2.yml`" #: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add msgid "" @@ -2505,13 +2510,14 @@ msgstr "" #: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" -msgstr "" +msgstr "`record-job3.yml`" #: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c msgid "" "In the third example, only `itemD` is provided, so it appears on the command " "line." -msgstr "" +msgstr "3番目の例では、`itemD` " +"のみが提供されているので、コマンドラインに表示されます。" #: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" From 545cef8bdc4e7897989a7c1abab77486bdaa1d29 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Tue, 29 Aug 2023 08:33:08 +0200 Subject: [PATCH 088/179] Translated using Weblate (Japanese) (#422) Currently translated at 31.1% (186 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 83 +++++++++++++++++++++------- 1 file changed, 62 insertions(+), 21 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index da099cdb..9f1819c6 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-08-26 23:56+0000\n" +"PO-Revision-Date: 2023-08-29 01:18+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -2620,8 +2620,9 @@ msgid "`metadata_example3.cwl`" msgstr "" #: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +#, fuzzy msgid "Operations" -msgstr "" +msgstr "Operations" #: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "" @@ -2635,11 +2636,12 @@ msgstr "" msgid "" "You can create operations to visualize a workflow during development, before " "you are ready to submit the workflow to a CWL runner:" -msgstr "" +msgstr "CWLランナーにワークフローを送信する前に、開発中のワークフローを可視化すること" +"ができます：" #: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" -msgstr "" +msgstr "`operations.cwl`" #: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 msgid "" @@ -2659,11 +2661,12 @@ msgstr "" msgid "" "If you try running it with `cwltool`, the command will fail since `cwltool` " "does not have enough information to know how to execute it:" -msgstr "" +msgstr "`cwltool` だけで実行しようとすると、`cwltool` " +"は実行するのに必要な情報がないため、コマンドは失敗します：" #: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" -msgstr "" +msgstr "`cwltool` は、どうやってoperationsを実行するかを知りません。" #: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f msgid "" @@ -2674,11 +2677,12 @@ msgstr "" #: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de msgid "Outputs" -msgstr "" +msgstr "Outputs" #: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +#, fuzzy msgid "Returning Output Files" -msgstr "" +msgstr "出力ファイルの回収" #: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 msgid "" @@ -2701,11 +2705,11 @@ msgstr "" msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." -msgstr "" +msgstr "次の例は、tarファイルから抽出されたファイルを返す方法を示しています。" #: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "" +msgstr "`baseCommand` に必須引数を渡します。" #: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c msgid "" @@ -2717,21 +2721,23 @@ msgstr "" #: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" -msgstr "" +msgstr "`tar.cwl`" #: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" -msgstr "" +msgstr "`tar-job.yml`" #: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +#, fuzzy msgid "Next, create a tar file for the example." -msgstr "" +msgstr "次に、サンプルとなるtarファイルを作成します。" #: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb msgid "" "And now invoke `cwltool` with the tool description and the input object on " "the command line:" -msgstr "" +msgstr "そして、今度はコマンドラインにツール定義と入力オブジェクトを指定して`cwltool`" +" を呼び出します：" #: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d msgid "" @@ -2810,13 +2816,15 @@ msgstr "" #: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" -msgstr "" +msgstr "`tar-param-job.yml`" #: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +#, fuzzy msgid "" "Create your input files and invoke `cwltool` with the tool description and " "the input object on the command line:" -msgstr "" +msgstr "入力ファイル(入力オブジェクト)を作成し、コマンドラインでツール定義と入力オブ" +"ジェクトを指定して`cwltool` を呼び出します：" #: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 msgid "" @@ -2835,7 +2843,7 @@ msgstr "" msgid "" "The value of the \"inputs\" variable is the input object provided when the " "CWL tool was invoked." -msgstr "" +msgstr "変数 \"inputs \"の値は、CWLツールの起動時に提供された入力オブジェクトです。" #: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 msgid "" @@ -2847,96 +2855,129 @@ msgstr "" #: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" -msgstr "" +msgstr "パラメータ参照はどこで許されるのですか？" #: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" #: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +#, fuzzy msgid "" "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineTool)" msgstr "" +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool) から" #: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 msgid "" "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandInputParameter)" msgstr "" +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter) から" #: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 msgid "" "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandLineBinding)" msgstr "" +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineBinding) から" #: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +#, fuzzy msgid "" "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputParameter)" msgstr "" +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter) から" #: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +#, fuzzy msgid "" "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." "html#CommandOutputBinding)" msgstr "" +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding) から" #: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +#, fuzzy msgid "" "From [InputParameter](http://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" "v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) " +"と [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowOutputParameter) から" #: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 msgid "" "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." "html#WorkflowStepInput)" msgstr "" +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput) から" #: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +#, fuzzy msgid "" "From [InputParameter](http://www.commonwl.org/v1.0/Workflow." "html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." "org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) " +"と [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#ExpressionToolOutputParameter) から" #: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +#, fuzzy msgid "" "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." "html#ResourceRequirement)" msgstr "" +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement) から" #: ../../src/topics/parameter-references.md:101 #: 5d8bed66282c408695292ea92a03b2c4 +#, fuzzy msgid "" "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" "CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#InitialWorkDirRequirement) から" #: ../../src/topics/parameter-references.md:103 #: 958178d1fa8843aaa0541e2bb115cfd4 +#, fuzzy msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" +msgstr "[Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent) の中に" #: ../../src/topics/parameter-references.md:107 #: 9a6b311ded8d4e43ae635b1b927dbdf2 +#, fuzzy msgid "" "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." "html#EnvironmentDef)" msgstr "" +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef) から" #: ../../src/topics/requirements-and-hints.md:5 #: aac74f957774479a83aab4c6ff1390ae msgid "Requirements and Hints" -msgstr "" +msgstr "Requirements と Hints" #: ../../src/topics/specifying-software-requirements.md:1 #: b75d29d1d55d44488338f9689f156855 msgid "Specifying Software Requirements" -msgstr "" +msgstr "ソフトウェア要求事項の指定" #: ../../src/topics/specifying-software-requirements.md:3 #: 574d93d1d592458a985f259519c036cb From 931fadb2ff3492bba7c548c9b137e2e03a9bdc62 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Mon, 4 Sep 2023 09:07:41 +0200 Subject: [PATCH 089/179] Translated using Weblate (Japanese) (#423) Currently translated at 33.9% (203 of 598 strings) Translated using Weblate (Japanese) Currently translated at 32.7% (196 of 598 strings) Translated using Weblate (Japanese) Currently translated at 31.9% (191 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 68 ++++++++++++++++++++-------- 1 file changed, 48 insertions(+), 20 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 9f1819c6..3a28102e 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-08-29 01:18+0000\n" +"PO-Revision-Date: 2023-09-03 01:58+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -3120,11 +3120,11 @@ msgstr "" #: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" -msgstr "" +msgstr "コンテナの使用" #: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" -msgstr "" +msgstr "Dockerの内部でツールを実行する" #: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 msgid "" @@ -3149,15 +3149,16 @@ msgstr "" msgid "" "This example runs a simple Node.js script inside a Docker container which " "will then print \"Hello World\" to the standard output." -msgstr "" +msgstr "この例では、Dockerコンテナ内で簡単なNode.jsスクリプトを実行し、標準出力に「" +"Hello World」と表示します。" #: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" -msgstr "" +msgstr "`docker.cwl`" #: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" -msgstr "" +msgstr "`docker-job.yml`" #: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed msgid "" @@ -3184,16 +3185,19 @@ msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " "the tool description and the input object on the command line:" msgstr "" +"Javascriptで \"hello.js \"というファイルを作成し、`cwltool` " +"コマンドラインでツール定義と入力オブジェクトを指定して呼び出します：" #: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" -msgstr "" +msgstr "`hello.js`" #: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." -msgstr "" +msgstr "CWLランナーがスクリプトを実行するためにDockerコマンドラインを構築していること" +"に注目してください。" #: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 msgid "" @@ -3202,10 +3206,14 @@ msgid "" "job369354770_examples/hello.js` inside the container, as reflected in the " "invocation of the `node` command." msgstr "" +"この例では、スクリプト`hello.js` のパスは、コンテナの外側では `/home/me/cwl/" +"user_guide/hello.js` が、コンテナの内側では`/var/lib/cwl/" +"job369354770_examples/hello.js` です。これは`node` " +"コマンドの呼び出しに反映されているためです。" #: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 msgid "Workflows" -msgstr "" +msgstr "ワークフロー" #: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 msgid "" @@ -3215,29 +3223,38 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +#, fuzzy msgid "CWL workflow." -msgstr "" +msgstr "CWLのワークフローです。" #: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +#, fuzzy msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier examples." msgstr "" +"CWL定義`echo-uppercase.cwl` は、コマンドラインツール、および先の例で示したExp" +"ressionToolを実行するワークフローを定義しています。" #: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" -msgstr "" +msgstr "`echo-uppercase.cwl`" #: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +#, fuzzy msgid "" "A command-line tool or expression tool can also be written directly in the " "same CWL document as the workflow. For example, we can rewrite the `echo-" "uppercase.cwl` workflow as a single file:" msgstr "" +"コマンドラインツールやExpressionToolは、ワークフローと同じCWLドキュメントに直" +"接記述することも可能です。例えば、`echo-uppercase.cwl` " +"ワークフローを1つのファイルとして書き換えることができます：" #: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +#, fuzzy msgid "`echo-uppercase-single-file.cwl`" -msgstr "" +msgstr "`echo-uppercase-single-file.cwl`" #: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a msgid "" @@ -3271,7 +3288,7 @@ msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 #: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" -msgstr "" +msgstr "1st-workflow.cwlの可視化。" #: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 msgid "" @@ -3287,27 +3304,32 @@ msgstr "" msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a " "run:" -msgstr "" +msgstr "Runの入力データを記述するために、別ファイルのYAMLまたはJSONオブジェクトを使用" +"します：" #: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" -msgstr "" +msgstr "`1st-workflow-job.yml`" #: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." -msgstr "" +msgstr "次に、サンプルとなるJavaファイルを作成し、コマンドラインツールで使用するため" +"にtarファイルに追加します。" #: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" -msgstr "" +msgstr "どうなっているのでしょう？ 分解してみましょう：" #: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +#, fuzzy msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a workflow." msgstr "" +"`cwlVersion` フィールドは、この文書が使用するCWL仕様のバージョンを示します。" +" ` class` フィールドは、この文書がワークフローを記述していることを示します。" #: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 msgid "" @@ -3480,8 +3502,9 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +#, fuzzy msgid "Scattering Steps" -msgstr "" +msgstr "Scatter ステップ" #: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 msgid "" @@ -3504,19 +3527,24 @@ msgstr "" #: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" -msgstr "" +msgstr "`scatter-workflow.cwl`" #: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +#, fuzzy msgid "" "Aside from the `requirements` section including `ScatterFeatureRequirement`, " "what is going on here?" msgstr "" +"`requirements` セクションの`ScatterFeatureRequirement` " +"などを含めて、ここはどうなっているのでしょうか。" #: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +#, fuzzy msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." -msgstr "" +msgstr "まず、ここでのメインワークフローの入力には、文字列の配列が必要であることに注" +"目してください。" #: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f msgid "" From 009b6899d5dd2a38264fd29f309eefedd261ca79 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Thu, 7 Sep 2023 09:16:26 +0200 Subject: [PATCH 090/179] Translated using Weblate (Japanese) (#424) Currently translated at 35.9% (215 of 598 strings) Translated using Weblate (Japanese) Currently translated at 34.4% (206 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 54 +++++++++++++++++----------- 1 file changed, 34 insertions(+), 20 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 3a28102e..eec9ce20 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-09-03 01:58+0000\n" +"PO-Revision-Date: 2023-09-07 04:57+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -3583,26 +3583,32 @@ msgid "" "our `message_array`. Ok, so how about if we want to scatter over two steps " "in a workflow?" msgstr "" +"ワークフローは、`message_array` の各要素毎に、echo を呼び出していることがわか" +"ります。では、ワークフローの2つのステップに分散させたい場合はどうでしょうか？" #: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding the " "following lines instead of `outputs: []`" -msgstr "" +msgstr "上記のような簡単なエコーを実行します、`outputs: " +"[]`の代わりに次の行を追加して`stdout` をキャプチャしてみましょう" #: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +#, fuzzy msgid "`hello_world_to_stdout.cwl`" -msgstr "" +msgstr "`hello_world_to_stdout.cwl`" #: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 msgid "" "And add a second step that uses `wc` to count the characters in each file. " "See the tool below:" -msgstr "" +msgstr "そして、`wc` を使って各ファイルの文字数をカウントする第2ステップを追加します" +"。以下のツールを見てください：" #: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +#, fuzzy msgid "`wc-tool.cwl`" -msgstr "" +msgstr "`wc-tool.cwl`" #: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b msgid "" @@ -3611,8 +3617,9 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +#, fuzzy msgid "`scatter-two-steps.cwl`" -msgstr "" +msgstr "`scatter-two-steps.cwl`" #: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 msgid "" @@ -3640,18 +3647,22 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +#, fuzzy msgid "`scatter-nested-workflow.cwl`" -msgstr "" +msgstr "`scatter-nested-workflow.cwl`" #: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +#, fuzzy msgid "" "Now the scatter acts on a single step, but that step consists of two steps " "so each step is performed in parallel." -msgstr "" +msgstr "今、scatter は1つのステップに作用しますが、そのステップは2つのステップで構成" +"されているので、各ステップは並行して実行されます。" #: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +#, fuzzy msgid "Conditional Workflows" -msgstr "" +msgstr "条件分岐ワークフロー" #: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 msgid "" @@ -3711,35 +3722,35 @@ msgstr "" #: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" +msgstr "すでにYAMLに慣れている方は、このセクションを読み飛ばしてもかまいません。" #: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea msgid "Contents" -msgstr "" +msgstr "目次" #: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "" +msgstr "[キーバリューペア](#key-value-pairs)" #: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" -msgstr "" +msgstr "[コメント](#comments)" #: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" -msgstr "" +msgstr "[マップ](#maps)" #: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" -msgstr "" +msgstr "[配列](#arrays)" #: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" -msgstr "" +msgstr "[JSON 形式](#json-style)" #: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" -msgstr "" +msgstr "キーバリューペア" #: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 msgid "" @@ -3772,7 +3783,7 @@ msgstr "" #: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" -msgstr "" +msgstr "コメント" #: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 msgid "" @@ -3782,14 +3793,17 @@ msgid "" msgstr "" #: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +#, fuzzy msgid "" "If there is anything on the line before the comment, be sure to add at least " "one space before the `#`!" -msgstr "" +msgstr "同じ行内のコメントの前に何かある場合は、必ず`#` " +"の前に少なくとも1つのスペースを追加してください！" #: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +#, fuzzy msgid "Maps" -msgstr "" +msgstr "マップ" #: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 msgid "" From bee8e419c2d870743e8e218c52ebc2d5eca10297 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Thu, 14 Sep 2023 09:16:29 +0200 Subject: [PATCH 091/179] Translated using Weblate (Japanese) (#425) Currently translated at 39.6% (237 of 598 strings) Translated using Weblate (Japanese) Currently translated at 38.7% (232 of 598 strings) Translated using Weblate (Japanese) Currently translated at 38.4% (230 of 598 strings) Translated using Weblate (Japanese) Currently translated at 38.1% (228 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 154 +++++++++++++++++++++++---- 1 file changed, 132 insertions(+), 22 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index eec9ce20..ab3d0378 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-09-07 04:57+0000\n" +"PO-Revision-Date: 2023-09-14 04:51+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -24,8 +24,9 @@ msgid "Licenses" msgstr "ライセンス" #: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +#, fuzzy msgid "Instructional Material" -msgstr "" +msgstr "指導資料" #: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d msgid "" @@ -113,12 +114,17 @@ msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 #: eab02dc13915490bb3c9ba744d78b6a7 d4f35995b0f6494d9771a4be0a82538f #: d6ccd4b546254f56a597d67dd4fdc5d6 +#, fuzzy msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece of " "software, tools and workflows described using CWL are portable across a " "variety of platforms that support the CWL standard." msgstr "" +"CWLは、コマンドラインツールを定義し、それらを結びつけてワークフローを作成する" +"ための方法です。CWLは仕様であり、特定のソフトウェアではないため、CWLを使用し" +"て記述されたツールやワークフローは、CWL標準をサポートするさまざまなプラットフ" +"ォームで利用可能です。" #: ../../src/episodes.md:5 ../../src/setup.md:5 #: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f @@ -131,6 +137,9 @@ msgid "" "User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" +"このページは古いもので、旧ユーザーガイドのリンクを保存するためにここに残され" +"ています。ユーザーガイドの閲覧には、新しい[目次](index.md#table-of-" +"contents)をご利用ください。" #: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" @@ -203,27 +212,32 @@ msgstr "" #: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be msgid "" "Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "" +msgstr "これで、`baseCommand: scriptname.sh` " +"を使って、スクリプトを直接実行できるようになりました。" #: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +#, fuzzy msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." -msgstr "" +msgstr "後で作ったものを共有したいときは、スクリプトをDockerコンテナに入れることがで" +"きます。" #: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +#, fuzzy msgid "" "The second method involves including an input of `type: File` in the script " "itself:" -msgstr "" +msgstr "2つ目の方法は、`type: File` をスクリプト自体に含める方法です：" #: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." msgstr "CWLでは、すべてを直接的に記述する必要があります。。" #: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +#, fuzzy msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "" +msgstr "オプショナル入力のために `self`-形式のInput Bindings を設定します" #: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c msgid "" @@ -240,18 +254,25 @@ msgstr "「一か八か」のパラメータをモデル化する" msgid "" "Below is an example showing how to specify different strings to be added to " "a command line, based on the value given to a Boolean parameter." -msgstr "" +msgstr "以下は、Booleanパラメータの値によって、コマンドラインに追加する文字列を変える" +"例を示しています。" #: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +#, fuzzy msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "" +msgstr "ある型の配列を期待する入力に１つの値を与える" #: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +#, fuzzy msgid "" "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" "Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow." +"html#MultipleInputFeatureRequirement) と [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)を一緒に使います。" #: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" @@ -372,34 +393,38 @@ msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +#, fuzzy msgid "If `cwltool --validate` returns valid" -msgstr "" +msgstr "`cwltool --validate` の結果が問題ない場合" #: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" -msgstr "" +msgstr "しかし、実行すると以下のようなエラーが発生します：" #: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" -msgstr "" +msgstr "ファイルはこちらです" #: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +#, fuzzy msgid "Problem caused by `-` (hyphen character)." -msgstr "" +msgstr "`-` (ハイフン文字、引き算の記号)が原因で発生した問題です。" #: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" +msgstr "このエラーを修正するには、`-` (ハイフン) を`_` (アンダースコア) " +"に変更してください。" #: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d msgid "" "If it is not possible to change the input identifier, then you can use an " "alternative CWL Parameter Reference syntax:" -msgstr "" +msgstr "入力識別子を変更することができない場合は、別のCWLパラメータリファレンス構文を" +"使用することができます：" #: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" -msgstr "" +msgstr "CWLとcwltoolをSingularityで使う" #: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e msgid "" @@ -449,18 +474,26 @@ msgid "" "guide][repo]. You can also suggest changes directly in a Pull Request by " "clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" +"このガイドに足りないものがある場合、またはその他のフィードバックを提供したい" +"場合は、[このユーザーガイドのプロジェクトリポジトリ][repo]にIssueを作成してく" +"ださい。また、各ページの右サイドバーにある「このページを編集する」ボタンをク" +"リックすると、Pull Requestで直接変更を提案することができます。" #: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" msgstr "ユーザーガイドの使い方" #: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +#, fuzzy msgid "" "If you are a beginner user get started with the [Introduction](/introduction/" "index.md) section. For advanced users the subsections of the [Topics](/" "topics/index.md) have detailed information about the most common topics for " "CWL." msgstr "" +"初心者の方は、[はじめに](/introduction/index." +"md)のセクションから始めてください。上級者向けには、[Topics](/topics/index." +"md)のサブセクションに、CWLで最も一般的なトピックに関する詳細情報があります。" #: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 msgid "" @@ -592,30 +625,43 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:122 #: 5f47aae608c041aeb4134d59dad314d2 +#, fuzzy msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be used " "to simplify workflows and command-line tools, moving common parts of a " "workflow execution into reusable JavaScript code that takes inputs and " "produces outputs like a command-line tool." msgstr "" +"ExpressionToolは、JavaScriptの式のラッパーです。WorkflowやCommandLineToolの簡" +"略化に使用でき、ワークフロー実行の共通部分を、CommandLineToolのように入力を受" +"けて出力を生成する再利用可能なJavaScriptコードに移動させることができます。" #: ../../src/introduction/basic-concepts.md:127 #: f6f589481d0c4891beaccb63160619ef +#, fuzzy msgid "" "Operation is an abstract process that also takes inputs, produces outputs, " "and can be used in a workflow. But it is a special operation not so commonly " "used. It is discussed in the [Operations section](../topics/operations.md) " "of this user guide." msgstr "" +"Operationは、入力を受け、出力を出す抽象的なプロセスでもあり、ワークフローで使" +"用することができます。しかし、あまり一般的に使われていない特別な処理です。こ" +"のユーザーガイドの[Operation編](../topics/operations.md)で説明します。" #: ../../src/introduction/basic-concepts.md:131 #: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#, fuzzy msgid "" "The workflow is a process that contains steps. Steps can be other workflows " "(nested workflows), command-line tools, or expression tools. The inputs of a " "workflow can be passed to any of its steps, while the outputs produced by " "its steps can be used in the final output of the workflow." msgstr "" +"Workflowは、ステップを含むプロセスである。ステップには、他のWorkflow（ネスト" +"されたWorkflow）、CommandLineTool、またはExpressionToolを使用することができま" +"す。Workflowの入力は、そのステップのいずれかに渡すことができ、ステップによっ" +"て生成された出力は、Workflowの最終出力に使用することができます。" #: ../../src/introduction/basic-concepts.md:137 #: 4ace6b92f4e04a07aa202840ebe36417 @@ -624,6 +670,9 @@ msgid "" "functionality and specify prerequisites to workflows through *requirements*. " "There are many requirements defined in the CWL specification, for instance:" msgstr "" +"CWL 仕様では、*requirements* を通じて、実装が追加機能を提供し、ワークフローの" +"前提条件を指定することができます。CWL仕様には、例えば、以下のような多くの要件" +"が定義されています：" #: ../../src/introduction/basic-concepts.md:141 #: cc6cd8cb81564cadb8e6a4c49423b7f7 @@ -644,6 +693,7 @@ msgstr "`InitialWorkDirRequirement` - " #: ../../src/introduction/basic-concepts.md:145 #: 037cd0e5ceda482eaeaca03d51745aee +#, fuzzy msgid "" "Some CWL runners may provide requirements that are not in the specification. " "For example, GPU requirements are supported in `cwltool` through the " @@ -651,14 +701,22 @@ msgid "" "{{ cwl_version }} specification and may not be supported by other CWL " "runners." msgstr "" +"いくつかのCWLランナーは、仕様にないrequirementsを提供することがあります。例え" +"ば、GPUに関するrequirementsは`cwltool` で`cwltool:CUDARequirement` " +"を通してサポートされていますが、{{ cwl_version }}仕様の一部ではないので、他の" +"CWLランナーではサポートされていないかもしれません。" #: ../../src/introduction/basic-concepts.md:151 #: e4643938445b48cc80eb8973ceeb126e +#, fuzzy msgid "" "Hints are similar to requirements, but while requirements list features that " "are required, hints list optional features. Requirements are explained in " "detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" +"Hintsはrequirementsと似ていますが、requirementsが必須の機能を列挙するのに対し" +"、hintsはオプションの機能を列挙します。requirementsについては、[requirements]" +"(../topics/requirements-and-hints.md) セクションで詳しく説明しています。" #: ../../src/introduction/basic-concepts.md:155 #: c4c3315c96714e81b364f8cc003b87e6 @@ -680,26 +738,34 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:167 #: 074af9633627470485e5225326d5f20a +#, fuzzy msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\", " "CWL tasks are isolated, and you must be explicit about your inputs and " "outputs." msgstr "" +"CWLのルーツは、タスク間の依存関係に基づき、実行順序を決定する \"make\" " +"や多くの類似ツールにあります。しかし、\"make\" " +"とは異なり、CWLのタスクは分離されており、入力と出力を明示する必要があります。" #: ../../src/introduction/basic-concepts.md:171 #: 847951c055b94a83b1e081594cef22ee +#, fuzzy msgid "" "The benefit of explicitness and isolation are flexibility, portability, and " "scalability; tools and workflows described with CWL can transparently " "leverage technologies such as Docker and be used with CWL implementations " "from different vendors." msgstr "" +"CWLで定義されたツールやワークフローは、Dockerなどの技術を透過的に活用し、異な" +"るベンダーのCWL実装と組み合わせて使用することができるためです。" #: ../../src/introduction/basic-concepts.md:176 #: 44bde1fae06b4678bcac4f3224601296 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" +msgstr "`cwltool` " +"はまた、データプロベナンスのためのPROV-O標準オントロジーを使用しています。" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 @@ -739,7 +805,7 @@ msgstr "CWLサイト内の実装のリスト：" -msgstr "" +msgstr "PROV-O: PROVオントロジー -" #: ../../src/introduction/basic-concepts.md:185 #: c377a7f5dbe645cebbb6c7eccf831a0b @@ -747,17 +813,23 @@ msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" +"CWLのOperationsについては、本ユーザーガイドの[Operations](../topics/" +"operations.md)セクションで説明します。" #: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" msgstr "はじめに" #: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +#, fuzzy msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that " "are useful to know before reading the rest of the user guide." msgstr "" +"このセクションでは、CWLの簡単な紹介、このユーザーガイドに従うための前提条件、" +"そしてユーザーガイドの他の部分を読む前に知っておくと便利な基本概念について案" +"内します。" #: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" @@ -778,12 +850,16 @@ msgid "CWL Implementations" msgstr "CWL実装" #: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +#, fuzzy msgid "" "There are many implementations of the CWL standards. Some are complete CWL " "runners, while others could be plug-ins or extensions to workflow engines. " "We have a better explanation in the [Implementations](basic-concepts." "md#implementations) section." msgstr "" +"CWL規格の実装は数多く存在します。あるものは完全なCWL実装であり、他のものはワ" +"ークフローエンジンのプラグインや拡張になり得ます。[実装](basic-concepts." +"md#implementations)のセクションでより詳しいをしています。" #: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" @@ -875,15 +951,17 @@ msgstr "`cwltool` を使って `true.cwl` を検証します。" #: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 msgid "" "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" +msgstr "`--validate` " +"オプションを省略することで、CWLツール定義を実行することができます：" #: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." msgstr "`cwltool` を使って `true.cwl` を実行します。" #: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +#, fuzzy msgid "Cwl-runner Python Module" -msgstr "" +msgstr "Cwl-runner Pythonモジュール" #: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 msgid "" @@ -933,6 +1011,9 @@ msgid "" "that, the first thing you need to do is copy `true.cwl` workflow into a new " "file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" +"`cwl-runner` を実行するもう一つの方法は、ファイルを直接起動することです。その" +"ためには、まず`true.cwl` ワークフローを新しいファイル`true_shebang.cwl` " +"にコピーし、特別な最初の行、*shebang* を含める必要があります：" #: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" @@ -954,6 +1035,9 @@ msgid "" "the program specified in the shebang (`cwl-runner`) will be used to execute " "the rest of the file." msgstr "" +"そして最後に、コマンドラインで直接実行することができます。実行時には、shebang" +"で指定されたプログラム(`cwl-" +"runner`)が、ファイルの残りの部分を実行するために使用されます。" #: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." @@ -998,6 +1082,8 @@ msgid "" "cwl-plugin for IntelliJ - " msgstr "" +"IntelliJ 用 cwl-plugin -" #: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 msgid "" @@ -1012,27 +1098,40 @@ msgid "Docker" msgstr "Docker" #: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +#, fuzzy msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " "documentation to install it for your operating system: ." msgstr "" +"`cwltool` は、ツール、ワークフロー、およびワークフロー " +"ステップで指定されたソフトウェアコンテナをDockerを使用して実行します。Docker " +"ドキュメントの指示に従って、お使いのオペレーティングシステム用にインストール" +"してください：." #: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +#, fuzzy msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " "examples, and to clarify the differences between the execution models with " "and without containers." msgstr "" +"Dockerコンテナの書き方や構築方法を知っておく必要はありません。このユーザーガ" +"イドの残りの部分では、実行例として既存のDockerイメージを使用し、コンテナのあ" +"る実行モデルとない実行モデルの違いを明確にすることにします。" #: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +#, fuzzy msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for pulling " "images." msgstr "" +"`cwltool` Docker、Podman、udocker、Singularityによるコンテナの実行をサポート" +"しています。また、コンテナイメージを取得するために代替のコンテナレジストリを" +"使用することもできます。" #: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 msgid "" @@ -1050,11 +1149,15 @@ msgid "Quick Start" msgstr "クイックスタート" #: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +#, fuzzy msgid "" "This section will show you a brief overview of what CWL is, and where you " "can learn more about it. No previous knowledge of CWL is required, but you " "must be comfortable following instructions for the command-line." msgstr "" +"このセクションでは、CWLとは何か、またCWLについてもっと詳しく知ることができる" +"場所について、簡単に紹介します。CWLに関する予備知識は必要ありませんが、コマン" +"ドラインを使用することに慣れていると良いです。" #: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" @@ -1066,6 +1169,10 @@ msgid "" "example below shows a simple CWL “Hello World” workflow annotated with " "comments. Note that comments start with `#`:" msgstr "" +"CWLドキュメントは[YAML](../topics/index." +"md)(および/またはJSON)で書かれています。以下の例は、" +"コメントで注釈されたシンプルなCWL \"Hello World\" " +"ワークフローを示しています。コメントは`#` で始まることに注意してください：" #: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" @@ -3891,10 +3998,13 @@ msgid "" "this page` link in the menu if you would like to add another tutorial to the " "list." msgstr "" +"これは、CWL コミュニティによって提供されたチュートリアルのリストです。リスト" +"に他のチュートリアルを追加したい場合は、メニューの`Edit this page` " +"リンクを使用してください。" #: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" -msgstr "" +msgstr "初心者向けチュートリアル" #: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 msgid "" @@ -3906,7 +4016,7 @@ msgstr "" #: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" -msgstr "" +msgstr "上級者向けチュートリアル" #: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" @@ -3914,7 +4024,7 @@ msgstr "[CWLでのTypeScript](https://github.com/umccr/cwl-ica/wiki/TypeScript)" #: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" -msgstr "" +msgstr "バイオインフォマティクス・チュートリアル" #: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" From 977b9a51dae495c20193aa9fc4d3b6ebf3b802f1 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Sat, 23 Sep 2023 10:14:01 +0200 Subject: [PATCH 092/179] Translated using Weblate (Japanese) (#426) Currently translated at 42.1% (252 of 598 strings) Translated using Weblate (Japanese) Currently translated at 41.9% (251 of 598 strings) Translated using Weblate (Japanese) Currently translated at 41.3% (247 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 107 ++++++++++++++++++++------- 1 file changed, 81 insertions(+), 26 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index ab3d0378..0778358e 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-09-14 04:51+0000\n" +"PO-Revision-Date: 2023-09-23 04:03+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.0.1-dev\n" +"X-Generator: Weblate 5.1-dev\n" #: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" @@ -1230,7 +1230,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" +msgstr "`hello_world.cwl` を `cwltool` で実行します。" #: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 msgid "" @@ -1240,7 +1240,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" +msgstr "`hello_world.cwl` を`cwltool` で入力パラメータを渡して実行する。" #: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 msgid "" @@ -1252,13 +1252,14 @@ msgstr "" #: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" -msgstr "" +msgstr "`hello_world-job.json`" #: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" -msgstr "" +msgstr "このInputs Objectファイルを使用して、「Hello " +"World」ワークフローを実行することができるようになりました：" #: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." @@ -1306,10 +1307,13 @@ msgstr "" "org/wiki/YAML) です。" #: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +#, fuzzy msgid "" "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." "replace('VERSION', cwl_version_text) }}." msgstr "" +"{{'[CWL 仕様 VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }} のことです。" #: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b msgid "" @@ -1328,8 +1332,9 @@ msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 #: 9c87c76c690948ac8e18088a0fffe679 +#, fuzzy msgid "Additional Arguments and Parameters" -msgstr "" +msgstr "追加の引数とパラメータ" #: ../../src/topics/additional-arguments-and-parameters.md:3 #: ad00d94d4fb64bbdac356e64dd3803b9 @@ -1351,18 +1356,18 @@ msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 #: a74935dc31664e979ca8f90a6a4ba53c msgid "`arguments.cwl`" -msgstr "" +msgstr "`arguments.cwl`" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f #: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" -msgstr "" +msgstr "`arguments-job.yml`" #: ../../src/topics/additional-arguments-and-parameters.md:24 #: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "" +msgstr "次に、CommandLineToolで使用するサンプルJavaファイルを作成します。" #: ../../src/topics/additional-arguments-and-parameters.md:30 #: 9643449da1da46d7861866dce490cbcb @@ -1377,7 +1382,8 @@ msgstr "そして、コマンドラインでツール定義と入力オブジェ msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." -msgstr "" +msgstr "ここでは、`arguments` フィールドを使用して、特定の入力パラメータに結びつかな" +"い追加の引数をコマンドラインに追加しています。" #: ../../src/topics/additional-arguments-and-parameters.md:43 #: d50574c8b9694f83aa376d39b9a6fcd6 @@ -1396,18 +1402,24 @@ msgid "Best Practices" msgstr "ベストプラクティス" #: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +#, fuzzy msgid "" "The following are a set of recommended good practices to keep in mind when " "writing a Common Workflow Language description for a tool or workflow. These " "guidelines are presented for consideration on a scale of usefulness: " "although more is better, not all are required." msgstr "" +"以下は、ツールやワークフローのCWL定義を書く際に留意すべき推奨グッドプラクティ" +"スのセットです。これらのガイドラインは、有用性の尺度で検討するために提示され" +"ています：多ければ多いほど良いが、すべてが必要なわけではありません。" #: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "" "No `type: string` parameters for names of input or reference files/" "directories; use `type: File` or `type: Directory` as appropriate." msgstr "" +"入力または参照のファイルやディレクトリの名前に `type: string` " +"を使用しません。 `type:File` または `type: Direcotry` を適宜使用します。" #: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 msgid "" @@ -1451,6 +1463,8 @@ msgid "" "Metadata and Authorship section of this User Guide](../topics/metadata-and-" "authorship.md)." msgstr "" +"CW定義にメタデータを与える例については、［このユーザーガイドのメタデータと著" +"者名のセクション］(../topics/metadata-and-authorship.md)を参照してください。" #: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 msgid "" @@ -1610,22 +1624,29 @@ msgid "Network Access" msgstr "" #: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +#, fuzzy msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network access. " "If a command-line tool is written manually in CWL v1.1+, there is a need to " "specify when network access is required." msgstr "" +"これは、プロセスが発信IPv4/" +"IPv6ネットワークアクセスを必要とするかどうかを示します。CWL v1.1+でCommandLin" +"eToolを手動で記述する場合、ネットワークアクセスが必要なタイミングを指定する必" +"要があります。" #: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " "Access automatically." -msgstr "" +msgstr "CWL v1.0のコマンドラインツールをv1.1またはv1." +"2にアップグレードすると、自動的にネットワークアクセスを取得します。" #: ../../src/topics/creating-files-at-runtime.md:1 #: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#, fuzzy msgid "Creating Files at Runtime" -msgstr "" +msgstr "実行時にファイルを作成する" #: ../../src/topics/creating-files-at-runtime.md:3 #: 0cf51b6da6884065ae42032abc20eb0d @@ -1638,7 +1659,8 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 #: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "" +msgstr "このようなファイルを生成するために、`InitialWorkDirRequirement` " +"を利用することができます。" #: ../../src/topics/creating-files-at-runtime.md:9 #: d3f74c3b094a427fbec831afab657d50 @@ -1809,6 +1831,9 @@ msgid "" "variables from the parent process. You can set environment variables for " "the tool using `EnvVarRequirement`." msgstr "" +"ツールは制限された環境で実行されるため、親プロセスからほとんどの環境変数を引" +"き継ぎません。 ツールの環境変数は、`EnvVarRequirement` " +"を使って設定できます。" #: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" @@ -1819,37 +1844,52 @@ msgid "Expression Tool" msgstr "Expression Tool" #: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +#, fuzzy msgid "" "An expression tool is a type of Process that can be run by itself or as a " "Workflow step. It executes a pure JavaScript expression. It is meant to be " "used as a way to isolate complex JavaScript expressions that need to operate " "on input data and produce some result as output." msgstr "" +"ExpressionToolは、それ自体またはワークフローのステップとして実行することがで" +"きるProcessの一種です。純粋な JavaScript 式を実行します。入力データを操作し、" +"出力として結果を生成する必要がある複雑な JavaScript " +"式を分離する方法として使用されることを意図しています。" #: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" +"CommandLinetToolと同様に、`inputs` と`outputs` " +"が必要です。しかし、`baseCommand` の代わりに、`expression` " +"属性を必要とします。" #: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +#, fuzzy msgid "CWL expression tool." -msgstr "" +msgstr "CWL expression tool." #: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +#, fuzzy msgid "`uppercase.cwl`" -msgstr "" +msgstr "`uppercase.cwl`" #: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +#, fuzzy msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains a " "JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" +"`InlineJavascriptRequirement` を使用する必要がありました。この式には`." +"toUpperCase()` で JavaScript の呼び出しが含まれているからです。これは、Expres" +"sionToolを使用するツールにとって、JavaScriptが必要であることを意味します。" #: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +#, fuzzy msgid "Expressions" -msgstr "" +msgstr "Expressions" #: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 msgid "" @@ -1869,18 +1909,22 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +#, fuzzy msgid "`expression.cwl`" -msgstr "" +msgstr "`expression.cwl`" #: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +#, fuzzy msgid "" "As this tool does not require any `inputs` we can run it with an (almost) " "empty job file:" -msgstr "" +msgstr "このツールは`inputs` " +"を必要としないので、（ほとんど）空のジョブファイルで実行することができます：" #: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +#, fuzzy msgid "`empty.yml`" -msgstr "" +msgstr "`empty.yml`" #: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 msgid "" @@ -2247,14 +2291,17 @@ msgid "`hello-world-expressionlib-inline.cwl`" msgstr "`hello-world-expressionlib-inline.cwl`" #: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +#, fuzzy msgid "" "Running this CWL workflow will invoke the JavaScript function and result in " "the `echo` command printing the input message with capital initial letters:" -msgstr "" +msgstr "このCWLワークフローを実行すると、JavaScript関数が起動し、`echo` " +"コマンドが入力メッセージを大文字の頭文字で表示します：" #: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +#, fuzzy msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "" +msgstr "`hello-world-expressionlib-inline.cwl` 実行しています。" #: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 msgid "" @@ -2263,23 +2310,30 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +#, fuzzy msgid "`custom-functions.js`" -msgstr "" +msgstr "`custom-functions.js`" #: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +#, fuzzy msgid "`hello-world-expressionlib-external.cwl`" -msgstr "" +msgstr "`hello-world-expressionlib-external.cwl`" #: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +#, fuzzy msgid "" "The `custom-functions.js` file is included in the CWL document with the `" "$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" +"`custom-functions.js` ファイルは、`$include: custom-functions.js` という記述" +"でCWL定義に含まれます。これにより、関数と変数がCWL定義の他の部分で使用できる" +"ようになります。" #: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +#, fuzzy msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "" +msgstr "`hello-world-expressionlib-external.cwl`実行しています。" #: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 msgid "" @@ -2331,7 +2385,8 @@ msgstr "" msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` section " "of the document in greater detail, so don't worry about these for now." -msgstr "" +msgstr "次のチュートリアルで、`$namespaces` と`$schemas` " +"の部分をより詳しく説明しますので、今は気にしないでください。" #: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f msgid "" From 9d9d16228d1462eb2de8d64092e7e6056cc13204 Mon Sep 17 00:00:00 2001 From: maxalbert Date: Thu, 28 Sep 2023 11:00:38 +0100 Subject: [PATCH 093/179] Add 'boolean' the list of available primitive types (#427) --- src/topics/inputs.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/topics/inputs.md b/src/topics/inputs.md index 7cc5c7d2..a5356a7a 100644 --- a/src/topics/inputs.md +++ b/src/topics/inputs.md @@ -6,7 +6,7 @@ The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter. -Available primitive types are *string*, *int*, *long*, *float*, *double*, +Available primitive types are *string*, *boolean*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*. From 50f13d24c95000cabe7d3e02530de007a0c75a31 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Sun, 8 Oct 2023 11:12:41 +0200 Subject: [PATCH 094/179] Translated using Weblate (Japanese) (#428) Currently translated at 44.6% (267 of 598 strings) Translated using Weblate (Japanese) Currently translated at 44.4% (266 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 97 ++++++++++++++++++++++------ 1 file changed, 79 insertions(+), 18 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 0778358e..57573c55 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-09-23 04:03+0000\n" +"PO-Revision-Date: 2023-10-08 04:10+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -2441,46 +2441,59 @@ msgid "Essential Input Parameters" msgstr "必須入力パラメータ" #: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +#, fuzzy msgid "" "The `inputs` of a tool is a list of input parameters that control how to run " "the tool. Each parameter has an `id` for the name of parameter, and `type` " "describing what types of values are valid for that parameter." msgstr "" +"ツールの`inputs` は、ツールの実行に関わる入力パラメーターのリストです。 " +"各パラメーターには、パラメーター名を示す`id` " +"と、そのパラメーターに有効な値の種類を示す`type` があります。" #: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +#, fuzzy msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*, " "and *null*; complex types are *array* and *record*; in addition there are " "special types *File*, *Directory* and *Any*." msgstr "" +"利用可能なプリミティブ型は*string*,*int*,*long*,*float*,*double*, *null*; " +"複合型は*array* and*record*; さらに特殊型*File*,*Directory* ,*Any* " +"があります。" #: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." -msgstr "" +msgstr "次の例では、異なる型の入力パラメーターが、異なる方法でコマンドライン上に表示" +"されることを示します。" #: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "" +msgstr "まず、以下の内容を含む`inp.cwl` というファイルを作成します：" #: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" -msgstr "" +msgstr "`inp.cwl`" #: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" -msgstr "" +msgstr "`inp-job.yml` というファイルを作成します：" #: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" -msgstr "" +msgstr "`inp-job.yml`" #: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +#, fuzzy msgid "" "You can use `cwltool` to create a template input object. That saves you from " "having to type all the input parameters in a input object file:" msgstr "" +"`cwltool` を使って、テンプレートとなる入力オブジェクトを作成することができま" +"す。これにより、入力オブジェクトファイルにすべての入力パラメータを入力する手" +"間を省くことができます：" #: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b msgid "" @@ -2609,10 +2622,12 @@ msgstr "`array-inputs-job.yml`" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 #: ../../src/topics/outputs.md:105 588f0f7f967f4d69af27c9729d6d3119 #: 02adef8ee8204842b5b4a0408f3bac33 9db68837918a4a349f32f15f12697a1d +#, fuzzy msgid "" "Now invoke `cwltool` providing the tool description and the input object on " "the command line:" -msgstr "" +msgstr "ここで、コマンドラインにツール定義と入力オブジェクトを指定し `cwltool` " +"を起動します：" #: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 msgid "" @@ -2669,6 +2684,9 @@ msgid "" "matching item (`itemC`) is added to the command line and remaining item " "(`itemD`) is ignored." msgstr "" +"2番目の例では、`itemC` と`itemD` が排他的であるため、最初に一致した項目 " +"(`itemC`) のみがコマンドラインに追加され、残りの項目 (`itemD`) " +"は無視されます。" #: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" @@ -2682,8 +2700,9 @@ msgstr "3番目の例では、`itemD` " "のみが提供されているので、コマンドラインに表示されます。" #: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +#, fuzzy msgid "Exclusive Input Parameters with Expressions" -msgstr "" +msgstr "式で入力パラメータを排他的に指定する" #: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d msgid "" @@ -2694,30 +2713,41 @@ msgid "" msgstr "" #: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +#, fuzzy msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from an " "enum." msgstr "" +"`file_format` 入力パラメータに、`null` (つまり、値が提供されていない)、" +"または enum の任意の値を受け入れる排他的なものを含む例を使ってみましょう。" #: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" +msgstr "`exclusive-parameter-expressions.cwl`" #: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +#, fuzzy msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you provide a " "valid value, such as “fasta” (one of the values of the enum), your command " "should execute successfully:" msgstr "" +"JavaScriptの式では、`null` の値を考慮せずに、排他的入力パラメータの値を使用し" +"ていることに注意してください。\"fasta\"（enumの値の1つ）のような有効な値を指" +"定すると、コマンドは正常に実行されるはずです：" #: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +#, fuzzy msgid "" "However, if you do not provide any input value, then `file_format` will be " "evaluated to a `null` value, which does not match the expected type for the " "output field (a `string`), resulting in failure when running your workflow." msgstr "" +"しかし、入力値を提供しない場合、`file_format` は、`null` " +"の値として評価されます。これは、出力フィールドが期待する型（`string` " +"）と一致しないため、ワークフロー実行時に失敗することになります。" #: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 msgid "" @@ -2779,7 +2809,7 @@ msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 #: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" -msgstr "" +msgstr "`metadata_example3.cwl`" #: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f #, fuzzy @@ -2787,12 +2817,16 @@ msgid "Operations" msgstr "Operations" #: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +#, fuzzy msgid "" "An Operation is a type of CWL process, just like a workflow, a command-line " "tool, or an expression tool. It is a step of a workflow that specifies " "inputs and outputs, but it does not provide enough information to be " "executed." msgstr "" +"Operationは、Workflow、CommandLineTool、ExpressionToolと同様に、CWL Processの" +"一種です。Workflowのステップで、入力と出力を指定しますが、実行するのに十分な" +"情報を提供しません。" #: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d msgid "" @@ -2806,11 +2840,15 @@ msgid "`operations.cwl`" msgstr "`operations.cwl`" #: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +#, fuzzy msgid "" "The `uppercase` step of the workflow is an operation. It can be used like a " "command line tool or an expression. You can also plot it with the CWL Viewer " "or `cwltool`:" msgstr "" +"ワークフローの`uppercase` ステップは Operation " +"です。CommandLineToolやExpressionToolのように使用することができます。また、" +"CWL Viewerや`cwltool` を使ってプロットすることもできます：" #: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "" @@ -2818,6 +2856,9 @@ msgid "" "The following image is rendered with the Sphinx Graphviz directive (this " "user guide is built with Sphinx):" msgstr "" +"上記のコマンドの出力は、Graphvizレンダラーでレンダリングすることができます。" +"以下の画像は、SphinxのGraphvizディレクティブでレンダリングしたものです（この" +"ユーザーガイドはSphinxで構築されています）：" #: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 msgid "" @@ -2847,12 +2888,17 @@ msgid "Returning Output Files" msgstr "出力ファイルの回収" #: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +#, fuzzy msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name of " "parameter, and `type` describing what types of values are valid for that " "parameter." msgstr "" +"ツールの`outputs` " +"は、ツールの実行後に返されるべき出力パラメータのリストです。 " +"各パラメーターには、パラメーター名を示す`id` " +"と、そのパラメーターに有効な値の型を示す`type` があります。" #: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 msgid "" @@ -2919,33 +2965,39 @@ msgid "Capturing Standard Output" msgstr "" #: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +#, fuzzy msgid "" "To capture a tool's standard output stream, add the `stdout` field with the " "name of the file where the output stream should go. Then add `type: stdout` " "on the corresponding output parameter." msgstr "" +"ツールの標準出力をキャプチャするには、`stdout` " +"フィールドに、標準出力を保存したいファイル名を追加します。 " +"次に、対応する出力パラメータに`type: stdout` を追加します。" #: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +#, fuzzy msgid "`stdout.cwl`" -msgstr "" +msgstr "`stdout.cwl`" #: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" -msgstr "" +msgstr "出力の配列" #: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d msgid "" "You can also capture multiple output files into an array of files using " "`glob`." -msgstr "" +msgstr "また、`glob` を使って、複数の出力ファイルを配列に取り込むことができます。" #: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +#, fuzzy msgid "`array-outputs.cwl`" -msgstr "" +msgstr "`array-outputs.cwl`" #: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" -msgstr "" +msgstr "`array-outputs-job.yml`" #: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 msgid "" @@ -2957,7 +3009,7 @@ msgstr "" #: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 msgid "Parameter References" -msgstr "" +msgstr "パラメータリファレンス" #: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 msgid "" @@ -2974,7 +3026,7 @@ msgstr "" #: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" -msgstr "" +msgstr "`tar-param.cwl`" #: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" @@ -2989,17 +3041,23 @@ msgstr "入力ファイル(入力オブジェクト)を作成し、コマンド "ジェクトを指定して`cwltool` を呼び出します：" #: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +#, fuzzy msgid "" "Certain fields permit parameter references which are enclosed in `$(...)`. " "These are evaluated and replaced with value being referenced." -msgstr "" +msgstr "`$(...)` で囲まれたパラメータ参照を許可するフィールドもあります。これらは評価" +"され、参照されている値に置き換えられます。" #: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +#, fuzzy msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" "$(inputs['extractfile'])` are equivalent." msgstr "" +"パラメータリファレンスは、Javascriptの構文のサブセットを使用して記述します。" +" この例では、`$(inputs.extractfile)` 、`$(inputs[\"extractfile\"])` " +"、`$(inputs['extractfile'])` は同等です。" #: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 msgid "" @@ -3211,6 +3269,9 @@ msgid "" "executing CWL. We focus on `cwltool` here but some of these techniques may " "apply to other CWL Runners." msgstr "" +"このセクションでは、CWLの実行に問題がある場合にトラブルシューティングを行う方" +"法を説明します。ここでは、`cwltool` に焦点を当てますが、これらのテクニックの" +"いくつかは他のCWLランナーにも適用されるかもしれません。" #: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" From 15a07378755f1ae60557cbcd4e90a24f50b0127c Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Fri, 13 Oct 2023 10:30:25 +0200 Subject: [PATCH 095/179] Translated using Weblate (Japanese) (#429) Currently translated at 45.1% (270 of 598 strings) Translated using Weblate (Japanese) Currently translated at 45.1% (270 of 598 strings) Translated using Weblate (Japanese) Currently translated at 44.8% (268 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 54 +++++++++++++++++++++++----- 1 file changed, 46 insertions(+), 8 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 57573c55..b371732f 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-10-08 04:10+0000\n" +"PO-Revision-Date: 2023-10-13 08:02+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -3274,8 +3274,9 @@ msgstr "" "いくつかは他のCWLランナーにも適用されるかもしれません。" #: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +#, fuzzy msgid "Run `cwltool` with `cachedir`" -msgstr "" +msgstr "`cwltool` を`cachedir` で実行する。" #: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 msgid "" @@ -3297,13 +3298,17 @@ msgstr "" #: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" -msgstr "" +msgstr "`troubleshooting-wf1.cwl`" #: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +#, fuzzy msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " "(`cwltool` will create the directory for you if it does not exist already):" msgstr "" +"`--cachedir` に `/tmp/cachedir/` " +"を指定して、このワークフローを実行してみましょう（`cwltool` " +"は、ディレクトリがまだ存在しない場合、新規作成します）：" #: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac msgid "" @@ -3363,10 +3368,12 @@ msgid "" msgstr "" #: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +#, fuzzy msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the container." -msgstr "" +msgstr "CWLランナーの役割のひとつに、入力ファイルのパスをコンテナ内のでの配置位置に合" +"わせて調整することがあります。" #: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a msgid "" @@ -3496,17 +3503,19 @@ msgstr "" #: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" -msgstr "" +msgstr "ワークフローを書く" #: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c msgid "" "This workflow extracts a java source file from a tar file and then compiles " "it." -msgstr "" +msgstr "このワークフローでは、tarファイルからJavaのソースファイルを取り出し、コンパイ" +"ルします。" #: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +#, fuzzy msgid "`1st-workflow.cwl`" -msgstr "" +msgstr "`1st-workflow.cwl`" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 #: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 @@ -3514,6 +3523,7 @@ msgid "Visualization of 1st-workflow.cwl" msgstr "1st-workflow.cwlの可視化。" #: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +#, fuzzy msgid "" "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" "github.com/common-workflow-language/user_guide/blob/" @@ -3522,6 +3532,13 @@ msgid "" "workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" "_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" +"[[1st-workflow.cwlを可視化したもの]](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/" +"common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)" #: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 msgid "" @@ -3555,20 +3572,30 @@ msgstr "" " ` class` フィールドは、この文書がワークフローを記述していることを示します。" #: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#, fuzzy msgid "" "The `inputs` section describes the inputs of the workflow. This is a list " "of input parameters where each parameter consists of an identifier and a " "data type. These parameters can be used as sources for input to specific " "workflows steps." msgstr "" +"`inputs` セクションでは、ワークフローの入力について記述します。 これは入力パ" +"ラメータのリストであり、各パラメータは識別子とデータ型から構成されます。 こ" +"れらのパラメータは、特定のワークフロー・ステップへの入力ソースとして使用でき" +"ます。" #: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +#, fuzzy msgid "" "The `outputs` section describes the outputs of the workflow. This is a list " "of output parameters where each parameter consists of an identifier and a " "data type. The `outputSource` connects the output parameter `classfile` of " "the `compile` step to the workflow output parameter `compiled_class`." msgstr "" +"`outputs` セクションでは、ワークフローの出力について記述します。 これは出力" +"パラメータのリストであり、各パラメータは識別子とデータ型から構成されます。 `" +" outputSource` は、`compile` ステップの出力パラメータ`classfile` " +"を、ワークフロー出力パラメータ`compiled_class` に接続します。" #: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 msgid "" @@ -3582,12 +3609,17 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +#, fuzzy msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input " "parameters, `tarfile` and `extractfile` and one output parameter " "`extracted_file`." msgstr "" +"最初のステップである`untar` は、`tar-param.cwl` を実行します（[パラメータ参照" +"](parameter-references." +"md)で以前説明しました）。このツールは、2つの入力パラメータ、`tarfile` " +"と`extractfile` と1つの出力パラメータ`extracted_file` を持ちます。" #: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 msgid "" @@ -3599,10 +3631,12 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +#, fuzzy msgid "" "The `out` section of the workflow step lists the output parameters that are " "expected from the tool." -msgstr "" +msgstr "ワークフローステップの`out` " +"セクションには、ツールから期待される出力パラメータが記載されています。" #: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed msgid "" @@ -3693,11 +3727,15 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +#, fuzzy msgid "" "In this case our step can assume `Hello.java` rather than be parameterized, " "so we can use hardcoded values `hello.tar` and `Hello.java` in a " "`baseCommand` and the resulting `outputs`:" msgstr "" +"この場合、ステップではパラメータ化するのではなく、`Hello.java` " +"を想定することができるので、`baseCommand` で直接書かれた値`hello.tar` " +"と`Hello.java` を使用でき、結果として`outputs` が得られます：" #: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 msgid "" From cb51d0a70830fddd8bd14658ad3a2840f8bf8b7d Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Fri, 20 Oct 2023 08:42:19 +0200 Subject: [PATCH 096/179] Translated using Weblate (Japanese) (#430) Currently translated at 48.6% (291 of 598 strings) Translated using Weblate (Japanese) Currently translated at 47.8% (286 of 598 strings) Translated using Weblate (Japanese) Currently translated at 47.6% (285 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 267 +++++++++++++++++++++++---- 1 file changed, 234 insertions(+), 33 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index b371732f..347064da 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-10-13 08:02+0000\n" +"PO-Revision-Date: 2023-10-20 04:13+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.1-dev\n" +"X-Generator: Weblate 5.1\n" #: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" @@ -146,8 +146,9 @@ msgid "FAQ" msgstr "よくある質問" #: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 +#, fuzzy msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "" +msgstr "\"`File`\" 型をつかわず `evalFrom`を使う方法" #: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" @@ -187,10 +188,13 @@ msgid "" "`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" +"最初の方法は、スクリプトの入ったフォルダを`PATH` " +"環境変数に追加する方法です。これにより、`sh` や`bash` " +"コマンドを使用せずに、シェルスクリプトを直接実行することができます。" #: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" +msgstr "まず、ファイルの先頭に_shebang_ を追加します：" #: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 msgid "" @@ -240,11 +244,15 @@ msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "オプショナル入力のために `self`-形式のInput Bindings を設定します" #: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +#, fuzzy msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their input " "binding makes use of `self`. Below is an example workaround for this, " "pending a more sophisticated fix." msgstr "" +"現在、`cwltool` は、入力バインディングが`self` を使用している場合、見つからな" +"いオプション入力に対処することができません。以下は、より洗練された修正を待つ" +"間の回避策の例です。" #: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" @@ -279,17 +287,23 @@ msgid "merge_nested" msgstr "merge_nested" #: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +#, fuzzy msgid "" "The input must be an array consisting of exactly one entry for each input " "link. If \"merge_nested\" is specified with a single link, the value from " "the link must be wrapped in a single-item list." msgstr "" +"入力は、各入力リンクに対して正確に1つのエントリで構成される配列でなければなり" +"ません。\"merge_nested\"が1つのリンクで指定された場合" +"、リンクからの値は1つのアイテムリストでラップされなければなりません。" #: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 +#, fuzzy msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "" +msgstr "つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです。" #: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +#, fuzzy msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -297,6 +311,10 @@ msgid "" "add `linkMerge: merge_nested` under the appropriate `in` entry of the " "destination step." msgstr "" +"`File[]` (`File`の配列) で、ソースが単一の`File` " +"の場合、`MultipleInputFeatureRequirement` " +"をワークフローレベルの`requirements` に追加し、`linkMerge: merge_nested` " +"を目的ステップのエントリの該当`in`に追加します。" #: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" @@ -317,11 +335,16 @@ msgid "Enum Inputs ⚜️" msgstr "列挙型入力 ⚜️" #: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +#, fuzzy msgid "" "For command line flags that require a specific input as the argument an enum " "type can be declared in CWL. **Specifying null here is known as long form " "style. It does the same thing as the question mark on the other inputs.**" msgstr "" +"引数として特定の入力を必要とするコマンドラインフラグについては、CWLで列挙型を" +"宣言することで実現できます。**ここでnullを指定することは、ロングフォーム・ス" +"タイルとして知られています。他の入力のクエスチョンマークと同じ働きをします。*" +"*" #: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd msgid "" @@ -332,11 +355,15 @@ msgid "Record Inputs 📀" msgstr "レコード入力 📀" #: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +#, fuzzy msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" +"**相互排他的** または**依存的** のいずれかのコマンドラインフラグについては、" +"特別なレコードタイプを定義することができます。また、ここにnullを指定すること" +"で、オプションの入力を作成することができます。" #: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" @@ -389,8 +416,9 @@ msgstr "これらの危険な文字を避けられない場合は、`--relax-pat "に渡してください。" #: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +#, fuzzy msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -msgstr "" +msgstr "入力識別子の中のハイフンに起因するCWLパラメータリファレンスエラー" #: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 #, fuzzy @@ -502,6 +530,10 @@ msgid "" "subsections. The right sidebar contains links to the sections of each page, " "and the Search form is on the left sidebar." msgstr "" +"目次は、トップメニューと左サイドバーに表示されています。また、このページのさ" +"らに下にも表示されますが、サブセクションへのリンクがあります。右サイドバーに" +"は各ページのセクションへのリンクがあり、左サイドバーには「検索フォーム」があ" +"ります。" #: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" @@ -547,10 +579,14 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +#, fuzzy msgid "" "The model used for the specification version is called Semantic Versioning. " "See the end of this section to [learn more](#learn-more) about it." msgstr "" +"仕様のバージョンアップに使われるモデルは、セマンティックバージョニングを利用" +"しています。それについて[もっと知りたい](#learn-" +"more)方は、このセクションの最後をご覧ください。" #: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" @@ -565,29 +601,38 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +#, fuzzy msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud " "and high performance computing environments where tasks are scheduled in " "parallel across many nodes." msgstr "" +"CWLは、多くのノードでタスクが並列にスケジューリングされるクラスタ、クラウド、" +"ハイパフォーマンスコンピューティング環境における大規模なワークフローを記述す" +"るのに適しています。" #: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." -msgstr "" +msgstr "CWL仕様、実装、その他ツール。" #: ../../src/introduction/basic-concepts.md:105 #: a5ebc727fb3443f78e81d6b7ed5ac750 +#, fuzzy msgid "Processes and Requirements" -msgstr "" +msgstr "Processes 及び Requirements" #: ../../src/introduction/basic-concepts.md:107 #: 86e6a06992dc4228bfda7add48e28ca3 +#, fuzzy msgid "" "A process is a computing unit that takes inputs and produces outputs. The " "behavior of a process can be affected by the inputs, requirements, and " "hints. There are four types of processes defined in the CWL specification " "{{ cwl_version }}:" msgstr "" +"Processとは、入力を受けて出力を生成する計算のユニットです。Processの動作は、i" +"nputs、requirements、hintsに影響されることがあります。CWL仕様{{ cwl_version " +"}}では、4種類のProcessが定義されています：" #: ../../src/introduction/basic-concepts.md:112 #: 8c9772f96caf4169924d22eb929a4f0f @@ -895,8 +940,9 @@ msgid "" msgstr "" #: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +#, fuzzy msgid "CWL Runner" -msgstr "" +msgstr "CWL Runner" #: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 msgid "" @@ -913,21 +959,32 @@ msgid "" "activate a Python virtual environment using the `venv` module, and install " "`cwltool` in that environment:" msgstr "" +"`cwltool` は、`pip` でインストールすることができます。`venv` または`conda` " +"のような仮想環境を使用することをお勧めします。以下のコマンドは、`venv` " +"モジュールを使用して Python " +"仮想環境を作成およびアクティブ化し、その環境内に`cwltool` " +"をインストールします：" #: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d +#, fuzzy msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" +msgstr "`pip` と `venv` での `cwltool` のインストール" #: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +#, fuzzy msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` and " "`conda`." msgstr "" +"`cwltool` を`apt` と`conda` " +"とともにインストールする他の方法については、`cwltool` " +"[documentation](https://github.com/common-workflow-language/cwltool#install) " +"を参照してください。" #: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" +msgstr "簡単なCWLツール定義`true.cwl` で`cwltool` を使ってみましょう。" #: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" @@ -1195,15 +1252,19 @@ msgstr "" #: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" -msgstr "" +msgstr "CWL Runnerのインストール" #: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +#, fuzzy msgid "" "`cwltool` is an implementation of the CWL specification. It is also the CWL " "*Reference Runner* for the specification, and it is compliant with the " "latest version of the specification: {{ cwl_version }}. You can install " "`cwltool` using `pip`:" msgstr "" +"`cwltool` は、CWL仕様の実装の１つです。また、同仕様のCWL*Reference Runner* " +"でもあり、同仕様の最新バージョンに準拠しています：{cwl_version " +"}}に準拠しています。`cwltool` は、`pip` を使ってインストールできます：" #: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." @@ -1236,7 +1297,8 @@ msgstr "`hello_world.cwl` を `cwltool` で実行します。" msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" -msgstr "" +msgstr "また、`echo` base コマンドの引数を変更するのと同様に、入力パラメータ`message`" +" のデフォルト値を上書きすることもできます：" #: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." @@ -1249,6 +1311,10 @@ msgid "" "corresponding values. The Inputs Objects file can be written in JSON or " "YAML. For example:" msgstr "" +"ワークフロー入力パラメータに値を渡すもう一つの方法は、*Inputs Object* " +"を介する方法です。これは、入力フィールドとその対応する値を含むファイルです。" +"Inputs Objects ファイルは、JSON または YAML " +"で記述することができます。例えば、以下のようになります：" #: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" @@ -1266,12 +1332,18 @@ msgid "Passing an Inputs Object file to `cwltool`." msgstr "`cwltool` に Inputs Object ファイルをします。" #: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +#, fuzzy msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but it " "is not a requirement. You can choose any name for your workflows and Inputs " "Object files." msgstr "" +"ワークフローとInputs " +"Objectファイルには、同様のファイル名を使用しました。*-job.json* " +"という接尾辞は、Inputs Object " +"ファイルでは非常に一般的ですが必須ではありません。ワークフローとInputs " +"Objectファイルには、任意の名前を付けることができます。" #: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" @@ -1324,11 +1396,15 @@ msgstr "" "wiki/Workflow_management_system)。" #: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +#, fuzzy msgid "" "This page is out-of-date and was kept here to preserve the links of the old " "User Guide. The information on this page has been migrated to the [FAQ](/faq." "md) section of the new user guide." msgstr "" +"このページは古いもので、旧ユーザーガイドのリンクを保存するためにここに残され" +"ていました。このページの情報は、新しいユーザーガイドの [FAQ](/faq.md) " +"セクションに移行されました。" #: ../../src/topics/additional-arguments-and-parameters.md:1 #: 9c87c76c690948ac8e18088a0fffe679 @@ -1338,10 +1414,12 @@ msgstr "追加の引数とパラメータ" #: ../../src/topics/additional-arguments-and-parameters.md:3 #: ad00d94d4fb64bbdac356e64dd3803b9 +#, fuzzy msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." -msgstr "" +msgstr "ツールには、入力パラメータに正確に対応しない追加のコマンドラインオプションが" +"必要な場合があります。" #: ../../src/topics/additional-arguments-and-parameters.md:6 #: d8110ed19da94ad8a9f56e7006c4a2cf @@ -1467,11 +1545,14 @@ msgstr "" "者名のセクション］(../topics/metadata-and-authorship.md)を参照してください。" #: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +#, fuzzy msgid "" "Include [attribution information][license-example] for the author(s) of the " "CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" "[orcid]." msgstr "" +"CWLツールやワークフローの定義の著者の[帰属情報][ライセンス例]を含みます。[ORC" +"ID][orcid]のような曖昧でない識別子を使用してください。" #: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 msgid "" @@ -1481,10 +1562,13 @@ msgstr "ツール定義では、`SoftwareRequirement` " "の下に、短い名前を使用して依存関係をリストアップします。" #: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +#, fuzzy msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" "identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` " +"フォーマットで依存関係のための [SciCrunch][scicrunch] 識別子を含みます。" #: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb msgid "" @@ -1514,28 +1598,38 @@ msgid "" msgstr "" #: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +#, fuzzy msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" +"`File`の入出力のうち、ストリーミング互換の方法（一度だけ、ランダムアクセスな" +"し）で読み書きされるものを、`streamable: true` としてマークします。" #: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +#, fuzzy msgid "" "Each `CommandLineTool` description should focus on a single operation only, " "even if the (sub)command is capable of more. Don't overcomplicate your tool " "descriptions with options that you don't need or use." msgstr "" +"各`CommandLineTool` の定義は、たとえ（サブ）コマンドがそれ以上の機能を備えて" +"いたとしても、単一の操作のみに焦点を当てるべきです。必要でない、または使用し" +"ないオプションでツールの定義を複雑にし過ぎないようにしましょう。" #: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +#, fuzzy msgid "" "Custom types should be defined with one external YAML per type definition " "for re-use." -msgstr "" +msgstr "カスタム型は、再利用のため、タイプ定義ごとに1つの外部YAMLで定義する必要があり" +"ます。" #: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +#, fuzzy msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "" +msgstr "ツール/ワークフローを要約したトップレベルの短い`label` を含めます。" #: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae msgid "" @@ -1569,30 +1663,44 @@ msgstr "ツール定義を同僚（できれば別の機関の人）に渡し、 "ックをもらいましょう。" #: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +#, fuzzy msgid "" "Complex workflows with individual components which can be abstracted should " "utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " "workflow modular and allow sections of them to be easily reused." msgstr "" +"抽象化できる個々のコンポーネントを持つ複雑なワークフローは、ワークフローをモ" +"ジュール化し、その一部を容易に再利用できるようにするために、[`SubworkflowFeat" +"ureRequirement`][サブワークフロー]を利用します。" #: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +#, fuzzy msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics " "software\"][containers] (also useful to other disciplines)." msgstr "" +"ソフトウェアのコンテナは、[\"Recommendations for packaging and " +"containerizing of bioinformatics software\"][containers] " +"に準拠するようにします（他の分野でも有用です）。" #: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "コマンドラインツール" #: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +#, fuzzy msgid "" "A command-line tool is a type of Process object that can be run by itself or " "as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " "etc. The command-line tool is defined in the `baseCommand` attribute of the " "command-line tool CWL document." msgstr "" +"コマンドラインツールは、Processオブジェクトの一種であり、" +"それ自体またはワークフローのステップとし " +"て実行することができます。`ls`,`echo`,`tar` などのコマンドのラッパーです。コ" +"マンドラインツールは、コマンドラインツールCWL文書の`baseCommand` " +"属性で定義されています。" #: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab msgid "" @@ -1613,15 +1721,19 @@ msgid "`echo.cwl`" msgstr "`echo.cwl`" #: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +#, fuzzy msgid "" "The example above uses a simplified form to define inputs and outputs. You " "will learn more about in the [Inputs](../topics/inputs.md) and in the " "[Outputs](../topics/outputs.md) sections." msgstr "" +"上記の例では、簡略化した形で入力と出力を定義しています。[Inputs](../topics/" +"inputs.md)と[Outputs](../topics/outputs." +"md)のセクションで、より詳しく説明する予定です。" #: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" -msgstr "" +msgstr "ネットワークアクセス" #: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 #, fuzzy @@ -1892,12 +2004,16 @@ msgid "Expressions" msgstr "Expressions" #: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +#, fuzzy msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " "legal you can provide a fragment of Javascript that will be evaluated by the " "CWL runner." msgstr "" +"入力パラメータを操作する必要がある場合は、`InlineJavascriptRequirement` " +"を含めると、パラメータ参照が合法な場所であれば、CWL " +"runnerによって評価されるJavascriptを使用できます。" #: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 msgid "" @@ -1932,14 +2048,17 @@ msgid "" "descriptions are contained inside curly brackets `{}`, so an empty object is " "represented simply by a set of empty brackets." msgstr "" +"`empty.yml` には、空のJSONオブジェクトの記述があります。JSONオブジェクトの記" +"述は、中括弧`{}` " +"の中に含まれるので、空のオブジェクトは、単に空の括弧のセットで表されます。" #: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" -msgstr "" +msgstr "次に、`expression.cwl` を実行することができます：" #: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" -msgstr "" +msgstr "`expression.cwl` を実行する。" #: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 msgid "" @@ -1948,21 +2067,28 @@ msgid "" msgstr "なお、上の例のように、map構文で requirements を指定することも可能です：" #: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +#, fuzzy msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " "describe the additional command line arguments." msgstr "" +"または配列として、各エントリ（この場合、`class: InlineJavascriptRequirement` " +"だけです）に`-` " +"を付けます。同じ構文で、追加のコマンドライン引数を定義します。" #: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "JavaScriptはどこで使えますか？" #: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +#, fuzzy msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" +"[パラメータ参照](parameter-references.md)と同様に、JavaScript " +"式は特定のフィールドにのみ使用できます。 以下はその例です：" #: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c #, fuzzy @@ -2251,9 +2377,10 @@ msgid "`envValue`" msgstr "`envValue`" #: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +#, fuzzy msgid "" "Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" +msgstr "`expressionLib` による外部ライブラリの利用とインラインJavaScriptコードの利用" #: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 msgid "" @@ -3755,12 +3882,16 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +#, fuzzy msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL " "Tool description, care must be taken to improve its usability in multiple " "workflows." msgstr "" +"ネストされたワークフローは、より高機能で再利用可能なワークフローユニットを生" +"成する強力な機能ですが、CWLツール定義の作成と同様に、複数のワークフローでの使" +"い勝手を向上させるための配慮が必要です。" #: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 #, fuzzy @@ -3785,6 +3916,10 @@ msgid "" "that calls our first example (`hello_world.cwl`) and takes an array of " "strings as input to the workflow:" msgstr "" +"新規ユーザーがscatterを使いたいと思う最も一般的な理由は、異なるサンプルに対し" +"て同じ分析を実行することです。最初の例（`hello_world.cwl` ）を呼び出し、ワー" +"クフローへの入力として文字列の配列を受け取る、簡単なワークフローから始めまし" +"ょう：" #: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" @@ -3808,35 +3943,50 @@ msgstr "まず、ここでのメインワークフローの入力には、文字 "目してください。" #: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +#, fuzzy msgid "" "Here we've added a new field to the step `echo` called `scatter`. This field " "tells the runner that we'd like to scatter over this input for this " "particular step. Note that the input name listed after scatter is the one of " "the step's input, not a workflow level input." msgstr "" +"ここでは、ステップ`echo` に、`scatter` という新しいフィールドを追加しました。" +"このフィールドは、CWLランナーに、この特定のステップのためにこの入力を分散した" +"いことを伝えます。scatterの後に記載されている入力名は、ワークフローレベルの入" +"力名ではなく、ステップの入力名であることに注意してください。" #: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +#, fuzzy msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if you " "expect that the final output of your workflow will now have multiple outputs " "to collect, be sure to update that to an array type as well!" msgstr "" +"最初のスキャッターでは、これと同じくらい簡単です！このツールは出力を回収しな" +"いので、`outputs: []` を使います。しかし、ワークフローの最終出力に収集する複" +"数の出力があることが予想される場合、それを配列型に更新するようにしてください" +"！" #: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" -msgstr "" +msgstr "以下の入力ファイルを使用します：" #: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" -msgstr "" +msgstr "`scatter-job.yml`" #: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +#, fuzzy msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " "calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" +"注意点として、[`hello_world.cwl`](../introduction/quick-start.md) " +"は単にメッセージに対して`echo` というコマンドを呼び出します。" +"コマンドラインで `cwltool scatter-workflow.cwl scatter-job.yml` " +"を呼び出すとします：" #: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f msgid "" @@ -3872,10 +4022,12 @@ msgid "`wc-tool.cwl`" msgstr "`wc-tool.cwl`" #: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +#, fuzzy msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under each " "step:" -msgstr "" +msgstr "さて、スキャッターはどのように取り入れるのでしょうか？スキャッターフィールド" +"は各ステップの下にあることを思い出してください：" #: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d #, fuzzy @@ -3926,60 +4078,85 @@ msgid "Conditional Workflows" msgstr "条件分岐ワークフロー" #: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +#, fuzzy msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" +"このワークフローは、条件付きステップを含み、入力に基づき実行されます。これに" +"より、ワークフローは、プログラムの開始時に与えられた入力パラメータや以前のス" +"テップによって、追加のステップをスキップすることができます。" #: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" -msgstr "" +msgstr "`conditional-workflow.cwl`" #: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +#, fuzzy msgid "" "The first thing you'll notice is that this workflow is only compatible for " "version 1.2 or greater of the CWL standards." -msgstr "" +msgstr "まず、このワークフローはCWL仕様のバージョン1." +"2以降でしか対応していないことがわかります。" #: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +#, fuzzy msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when` is " "where the condition validation takes place. In this case only when `in1` " "from the workflow contains a value `< 1` this step will be executed." msgstr "" +"ワークフローの最初のステップ（step1）には2つの入力プロパティがあり、条件を満" +"たしたときにfoo.cwlを実行します。新しいプロパティ`when` " +"は、条件の検証が行われる場所です。この場合、ワークフローから`in1` に値`< " +"1` が含まれるときのみ、このステップが実行されます。" #: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +#, fuzzy msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " "will pass the first conditional step and will therefore be executed and is " "shown in the log by `INFO [step step1] start` whereas the second step is " "skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" +"次のコマンドを実行します。`cwltool cond-wf-003.1.cwl --val 0` " +"この値は最初の条件ステップを通過するため実行され、ログには`INFO [step step1] " +"start` で示されています。一方、2番目のステップは`INFO [step step2] will be " +"skipped` で示されているようにスキップされ ます。" #: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +#, fuzzy msgid "" "When a value of 3 is given the first conditional step will not be executed " "but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" +"値3が与えられた場合、最初の条件ステップは実行されませんが、2番目の条件ステッ" +"プは実行されます`cwltool cond-wf-003.1.cwl --val 3`." #: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +#, fuzzy msgid "" "If no conditions are met for example when using `--val 2` the workflow will " "raise a permanentFail." -msgstr "" +msgstr "`--val 2` を使用した場合など、条件を満たさない場合は、ワークフローはpermanent" +"Failを発生させ、失敗となります。" #: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" -msgstr "" +msgstr "YAMLガイド" #: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +#, fuzzy msgid "" "[YAML][yaml] is a file format designed to be readable by both computers and " "humans. This guide introduces the features of YAML that are relevant when " "writing CWL descriptions and input parameter files." msgstr "" +"[YAML][yaml]は、コンピュータと人間の両方が読むことができるように設計されたフ" +"ァイル形式です。本ガイドでは、CWL定義や入力パラメータファイルを書く際に関連す" +"るYAMLの機能を紹介します。" #: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." @@ -4024,14 +4201,20 @@ msgid "" msgstr "" #: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +#, fuzzy msgid "" "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " "and `home` - with their four respective values. Values can be character " "strings, numeric (integer, floating point, or scientific representation), " "Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" +"上記のYAMLは4つのキー -`first_name`,`last_name`,`age_years`, `home` - と4つの" +"それぞれの値を定義しています。値は、文字列、数値（整数、浮動小数点、科学的表" +"現）、ブール値（`true` または`false` " +"）、またはより複雑な入れ子型（下記参照）にすることができます。" #: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +#, fuzzy msgid "" "Values may be wrapped in quotation marks, but be aware that this may change " "the way that they are interpreted i.e. `\"1234\"` will be treated as a " @@ -4041,17 +4224,25 @@ msgid "" "to specify a fixed numeric value to a command, make sure that you wrap that " "numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" +"値は引用符で括ることができますが、意味が変わってきます。例えば、`\"1234\"` " +"は文字列として扱われ、`1234` は整数値として扱われます。CWLでは、`baseCommand`" +" のすべての部分が文字列でなければならないので、コマンドに固定した数値を指定す" +"る場合は、その数値を引用符で囲むようにしてください：[echo, \"42\"]`." #: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "コメント" #: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +#, fuzzy msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program interpreting " "the YAML. For example:" msgstr "" +"`#` を使って、CWL定義と入力パラメータファイルにコメントを追加することができま" +"す。` #` の右側にある文字は、YAML " +"を解釈するプログラムによって無視されます。たとえば、次のようになります：" #: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d #, fuzzy @@ -4090,8 +4281,9 @@ msgid "" msgstr "" #: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +#, fuzzy msgid "Arrays" -msgstr "" +msgstr "配列" #: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 msgid "" @@ -4104,22 +4296,27 @@ msgid "" msgstr "" #: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +#, fuzzy msgid "and a more complex example combining maps and arrays:" -msgstr "" +msgstr "と、マップと配列を組み合わせたより複雑な例です：" #: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" -msgstr "" +msgstr "JSON形式" #: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +#, fuzzy msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " "can also be defined in YAML using the native JSON syntax. For example:" msgstr "" +"YAMLは[JavaScript Object Notation (JSON)][json]に基づいています。マップと配列" +"は、JSON構文を使ってYAMLで定義することもできます。例えば" #: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +#, fuzzy msgid "and:" -msgstr "" +msgstr "と：" #: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 msgid "" @@ -4133,18 +4330,22 @@ msgstr "" #: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d msgid "Reference" -msgstr "" +msgstr "リファレンス" #: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +#, fuzzy msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " "while we wrote this guide, though it also covers features that are not valid " "in CWL." msgstr "" +"[Learn YAML in Y Minutes][yaml-y-mins] リファレンスは、CWLでは有効でない機能" +"もカバーしていますが、このガイドを書く間、私たちにとって非常に役に立ちました" +"。" #: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" -msgstr "" +msgstr "チュートリアル" #: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 msgid "" From 59967d0cecf05f1e7848e133b48b90beca6810de Mon Sep 17 00:00:00 2001 From: Alexis Lucattini Date: Wed, 25 Oct 2023 17:48:40 +1100 Subject: [PATCH 097/179] 373 pr updates (#432) As discussed here: https://github.com/common-workflow-language/user_guide/pull/373#issuecomment-1772100153 1. Basic Concepts - Roll back changes to quote fair principles verbatim 2. Operations - Reword the operation file sentence - this is contrary to the discussion on https://github.com/common-workflow-language/user_guide/pull/373#issuecomment-1772100153 and instead have reworded this entirely - please discuss otherwise can go back to the 'then' addition. 3. FAQ - remove vague comment 'everything in CWL must be stated' Code 'note' is removed from the FAQ.md file --- src/faq.md | 4 ---- src/introduction/basic-concepts.md | 4 ++-- src/topics/operations.md | 4 ++-- 3 files changed, 4 insertions(+), 8 deletions(-) diff --git a/src/faq.md b/src/faq.md index 9e1cd870..72ad0151 100644 --- a/src/faq.md +++ b/src/faq.md @@ -131,10 +131,6 @@ baseCommand: sh outputs: [] ``` -```{note} -In CWL, everything must be directly stated. -``` - ## Setting `self`-based Input Bindings for Optional Inputs Currently, `cwltool` can't cope with missing optional inputs if their diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index 33f1ced7..f77a3c49 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -159,8 +159,8 @@ in detail in the [Requirements](../topics/requirements-and-hints.md) section. > machine accessibility and that all digital assets should be Findable, > Accessible, Interoperable, and Reusable. Workflows encode the methods > by which the scientific process is conducted and via which data are -> created. It is thus important that workflows support the creation -> of FAIR data and adhere to the FAIR principles. +> created. It is thus important that workflows both support the creation +> of FAIR data and themselves adhere to the FAIR principles. > — [FAIR Computational Workflows](https://workflows.community/groups/fair/), > Workflows Community Initiative. diff --git a/src/topics/operations.md b/src/topics/operations.md index b6afca2a..f6bd2f78 100644 --- a/src/topics/operations.md +++ b/src/topics/operations.md @@ -52,8 +52,8 @@ style=dashed; } ``` -If you try running it with `cwltool`, the command will fail since `cwltool` -does not have enough information to know how to execute it: +The operation file will fail to run with `cwltool` because `cwltool` +lacks the necessary information to execute it: ```{runcmd} cwltool operations.cwl --message Hello :working-directory: src/_includes/cwl/operations/ From 1585ac01c5052bcf9567dd9440d41a332116d2a4 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Fri, 27 Oct 2023 10:33:11 +0200 Subject: [PATCH 098/179] Grammer tweaks (#433) As inspired by https://hosted.weblate.org/translate/commonwl/user-guide/ja/?q=has:check --- src/faq.md | 8 ++++---- src/introduction/prerequisites.md | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/faq.md b/src/faq.md index 3e64ca74..ed19cccc 100644 --- a/src/faq.md +++ b/src/faq.md @@ -191,16 +191,16 @@ outputs: [] ## How do I connect a solo value to an input that expects an array of that type? -Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) +Add a [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with -[`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput) +[`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput): > merge_nested > > The input must be an array consisting of exactly one entry for each input link. > If "merge_nested" is specified with a single link, the value from the link must be wrapped in a single-item list. -Which means "create a list with exactly these sources as elements" +Which means "create a list with exactly these sources as elements". Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` @@ -424,7 +424,7 @@ inputs: ``` -To fix this error, change `-` (hyphen) to `_` (underscore) +To fix this error, change `-` (hyphen) to `_` (underscore): ```cwl valueFrom: $(inputs.sample_input) diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index 4ec6e183..7fce36a5 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -87,7 +87,7 @@ CWL implementation. This is convenient for environments with multiple CWL runners. The CWL community publishes a Python package with the name `cwlref-runner` that installs -an alias for `cwltool` under the name `cwl-runner` +an alias for `cwltool` under the name `cwl-runner`. ```{code-block} console :name: installing-cwlrunner-with-pip From 4805a9aefe60183e4e609f6797a0f056903290bc Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Mon, 13 Nov 2023 09:30:41 +0100 Subject: [PATCH 099/179] Translations update from Hosted Weblate (#434) * Translated using Weblate (Japanese) Currently translated at 49.1% (294 of 598 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide --------- Co-authored-by: Michael Crusoe Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 39 ++++++++++++++++++---------- 1 file changed, 26 insertions(+), 13 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 347064da..cfcb131f 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-10-20 04:13+0000\n" +"PO-Revision-Date: 2023-11-09 05:34+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.1\n" +"X-Generator: Weblate 5.2-dev\n" #: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" @@ -146,9 +146,8 @@ msgid "FAQ" msgstr "よくある質問" #: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 -#, fuzzy msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "\"`File`\" 型をつかわず `evalFrom`を使う方法" +msgstr "\"`File`\" 型をつかわず `evalFrom`を使う方法" #: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" @@ -194,7 +193,7 @@ msgstr "" #: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "まず、ファイルの先頭に_shebang_ を追加します：" +msgstr "まず、ファイルの先頭に _shebang_ を追加します：" #: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 msgid "" @@ -1541,18 +1540,18 @@ msgid "" "Metadata and Authorship section of this User Guide](../topics/metadata-and-" "authorship.md)." msgstr "" -"CW定義にメタデータを与える例については、［このユーザーガイドのメタデータと著" -"者名のセクション］(../topics/metadata-and-authorship.md)を参照してください。" +"CW定義にメタデータを与える例については、 " +"[このユーザーガイドのメタデータと著者名のセクション](../topics/metadata-and-" +"authorship.md)を参照してください。" #: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 -#, fuzzy msgid "" "Include [attribution information][license-example] for the author(s) of the " "CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" "[orcid]." msgstr "" -"CWLツールやワークフローの定義の著者の[帰属情報][ライセンス例]を含みます。[ORC" -"ID][orcid]のような曖昧でない識別子を使用してください。" +"CWLツールやワークフローの定義の著者の[帰属情報][license-example]を含みます。[" +"ORCID][orcid]のような曖昧でない識別子を使用してください。" #: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 msgid "" @@ -1663,7 +1662,6 @@ msgstr "ツール定義を同僚（できれば別の機関の人）に渡し、 "ックをもらいましょう。" #: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 -#, fuzzy msgid "" "Complex workflows with individual components which can be abstracted should " "utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " @@ -1671,7 +1669,7 @@ msgid "" msgstr "" "抽象化できる個々のコンポーネントを持つ複雑なワークフローは、ワークフローをモ" "ジュール化し、その一部を容易に再利用できるようにするために、[`SubworkflowFeat" -"ureRequirement`][サブワークフロー]を利用します。" +"ureRequirement`][subworkflow]を利用します。" #: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 #, fuzzy @@ -2516,10 +2514,12 @@ msgstr "次のチュートリアルで、`$namespaces` と`$schemas` " "の部分をより詳しく説明しますので、今は気にしないでください。" #: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +#, fuzzy msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." -msgstr "" +msgstr "なお、さらなる利点として`cwltool` は、ファイル形式に基づく基本的な推論を行い" +"、明らかな不一致があるようであれば警告を発します。" #: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" @@ -2536,24 +2536,34 @@ msgid "Sample Parameter Files" msgstr "サンプルパラメーターファイル" #: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +#, fuzzy msgid "" "Below is an example of a parameter file for the example above. We encourage " "checking in working examples of parameter files for your tool. This allows " "others to quickly work with your tool, starting from a \"known good\" " "parameterization." msgstr "" +"以下は、上記の例のパラメータファイルの例です。あなたのツールのパラメータファ" +"イルの実例をチェックすることをお勧めします。これにより、他の人が「既知の良い" +"」パラメータ化から始めて、あなたのツールで素早く作業することができます。" #: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "`sample.yml`" #: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +#, fuzzy msgid "" "___Note:___ To follow the example below, you need to download the example " "input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" +"___注：___ 以下の例に実行するには、例の入力ファイル、*file-formats.bam* " +"をダウンロードする必要があります。このファイルは から入手可能で、`wget` " +"などでダウンロードすることができます：" #: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" @@ -2623,11 +2633,14 @@ msgstr "" "間を省くことができます：" #: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +#, fuzzy msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " "> inp-job.yml`, and then modify the default values with your desired input " "values." msgstr "" +"`cwltool --make-template inp.cwl > inp-job.yml` のように、出力をファイルに" +"リダイレクトし、デフォルト値を希望の入力値で修正することができます。" #: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "" From d057fd9ce17a33c24bf8ac6a0018d2ebcbde71ad Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Mon, 13 Nov 2023 09:41:27 +0100 Subject: [PATCH 100/179] Translations update from Hosted Weblate (#435) * Added translation using Weblate (Portuguese) Added translation using Weblate (Portuguese) Co-authored-by: Weblate * Deleted translation using Weblate (Portuguese) Deleted translation using Weblate (Portuguese) Translated using Weblate (Japanese) Currently translated at 49.1% (294 of 598 strings) Co-authored-by: Michael Crusoe Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide --------- Co-authored-by: Michael Crusoe --- locales/ja/LC_MESSAGES/user_guide.po | 763 ++++++++++++++------------- 1 file changed, 408 insertions(+), 355 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index cfcb131f..83be4dd6 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -10,8 +10,8 @@ msgstr "" "POT-Creation-Date: 2023-01-25 14:33+0100\n" "PO-Revision-Date: 2023-11-09 05:34+0000\n" "Last-Translator: Manabu ISHII \n" -"Language-Team: Japanese \n" +"Language-Team: Japanese \n" "Language: ja\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" @@ -123,8 +123,8 @@ msgid "" msgstr "" "CWLは、コマンドラインツールを定義し、それらを結びつけてワークフローを作成する" "ための方法です。CWLは仕様であり、特定のソフトウェアではないため、CWLを使用し" -"て記述されたツールやワークフローは、CWL標準をサポートするさまざまなプラットフ" -"ォームで利用可能です。" +"て記述されたツールやワークフローは、CWL標準をサポートするさまざまなプラット" +"フォームで利用可能です。" #: ../../src/episodes.md:5 ../../src/setup.md:5 #: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f @@ -138,8 +138,8 @@ msgid "" "contents) to browse the User Guide." msgstr "" "このページは古いもので、旧ユーザーガイドのリンクを保存するためにここに残され" -"ています。ユーザーガイドの閲覧には、新しい[目次](index.md#table-of-" -"contents)をご利用ください。" +"ています。ユーザーガイドの閲覧には、新しい[目次](index.md#table-of-contents)" +"をご利用ください。" #: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" @@ -187,9 +187,9 @@ msgid "" "`PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -"最初の方法は、スクリプトの入ったフォルダを`PATH` " -"環境変数に追加する方法です。これにより、`sh` や`bash` " -"コマンドを使用せずに、シェルスクリプトを直接実行することができます。" +"最初の方法は、スクリプトの入ったフォルダを`PATH` 環境変数に追加する方法です。" +"これにより、`sh` や`bash` コマンドを使用せずに、シェルスクリプトを直接実行す" +"ることができます。" #: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" @@ -209,21 +209,23 @@ msgid "" "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -"最後に、`PATH` を変更し、スクリプトが置かれているディレクトリを追加します。(`" -"$HOME/bin` を自分のスクリプトを保存するために使用するのは良い習慣です）。" +"最後に、`PATH` を変更し、スクリプトが置かれているディレクトリを追加します。" +"(`$HOME/bin` を自分のスクリプトを保存するために使用するのは良い習慣です）。" #: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be msgid "" "Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "これで、`baseCommand: scriptname.sh` " -"を使って、スクリプトを直接実行できるようになりました。" +msgstr "" +"これで、`baseCommand: scriptname.sh` を使って、スクリプトを直接実行できるよう" +"になりました。" #: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 #, fuzzy msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." -msgstr "後で作ったものを共有したいときは、スクリプトをDockerコンテナに入れることがで" +msgstr "" +"後で作ったものを共有したいときは、スクリプトをDockerコンテナに入れることがで" "きます。" #: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 @@ -261,7 +263,8 @@ msgstr "「一か八か」のパラメータをモデル化する" msgid "" "Below is an example showing how to specify different strings to be added to " "a command line, based on the value given to a Boolean parameter." -msgstr "以下は、Booleanパラメータの値によって、コマンドラインに追加する文字列を変える" +msgstr "" +"以下は、Booleanパラメータの値によって、コマンドラインに追加する文字列を変える" "例を示しています。" #: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c @@ -277,9 +280,8 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow." -"html#MultipleInputFeatureRequirement) と [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)を一緒に使います。" +"html#MultipleInputFeatureRequirement) と [`linkMerge: merge_nested`](https://" +"www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)を一緒に使います。" #: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" @@ -293,13 +295,14 @@ msgid "" "the link must be wrapped in a single-item list." msgstr "" "入力は、各入力リンクに対して正確に1つのエントリで構成される配列でなければなり" -"ません。\"merge_nested\"が1つのリンクで指定された場合" -"、リンクからの値は1つのアイテムリストでラップされなければなりません。" +"ません。\"merge_nested\"が1つのリンクで指定された場合、リンクからの値は1つの" +"アイテムリストでラップされなければなりません。" #: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 #, fuzzy msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです。" +msgstr "" +"つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです。" #: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 #, fuzzy @@ -310,10 +313,10 @@ msgid "" "add `linkMerge: merge_nested` under the appropriate `in` entry of the " "destination step." msgstr "" -"`File[]` (`File`の配列) で、ソースが単一の`File` " -"の場合、`MultipleInputFeatureRequirement` " -"をワークフローレベルの`requirements` に追加し、`linkMerge: merge_nested` " -"を目的ステップのエントリの該当`in`に追加します。" +"`File[]` (`File`の配列) で、ソースが単一の`File` の場合、" +"`MultipleInputFeatureRequirement` をワークフローレベルの`requirements` に追加" +"し、`linkMerge: merge_nested` を目的ステップのエントリの該当`in`に追加しま" +"す。" #: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" @@ -342,8 +345,8 @@ msgid "" msgstr "" "引数として特定の入力を必要とするコマンドラインフラグについては、CWLで列挙型を" "宣言することで実現できます。**ここでnullを指定することは、ロングフォーム・ス" -"タイルとして知られています。他の入力のクエスチョンマークと同じ働きをします。*" -"*" +"タイルとして知られています。他の入力のクエスチョンマークと同じ働きをします。" +"**" #: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd msgid "" @@ -391,7 +394,8 @@ msgstr "入力された文字列を連結する" #: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." -msgstr "defaultフィールドの代わりにvalueFromフィールドを使用する必要があります。" +msgstr "" +"defaultフィールドの代わりにvalueFromフィールドを使用する必要があります。" #: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" @@ -404,15 +408,17 @@ msgstr "`cwltool` は、デフォルトではファイル名に一部の文字 #: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a msgid "" "For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "例えば、`a space is here.txt` " -"というファイル名には、3つの空白文字が含まれています。" +msgstr "" +"例えば、`a space is here.txt` というファイル名には、3つの空白文字が含まれてい" +"ます。" #: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." -msgstr "これらの危険な文字を避けられない場合は、`--relax-path-checks` を`cwltool` " -"に渡してください。" +msgstr "" +"これらの危険な文字を避けられない場合は、`--relax-path-checks` を`cwltool` に" +"渡してください。" #: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 #, fuzzy @@ -439,14 +445,16 @@ msgstr "`-` (ハイフン文字、引き算の記号)が原因で発生した問 #: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "このエラーを修正するには、`-` (ハイフン) を`_` (アンダースコア) " -"に変更してください。" +msgstr "" +"このエラーを修正するには、`-` (ハイフン) を`_` (アンダースコア) に変更してく" +"ださい。" #: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d msgid "" "If it is not possible to change the input identifier, then you can use an " "alternative CWL Parameter Reference syntax:" -msgstr "入力識別子を変更することができない場合は、別のCWLパラメータリファレンス構文を" +msgstr "" +"入力識別子を変更することができない場合は、別のCWLパラメータリファレンス構文を" "使用することができます：" #: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 @@ -518,9 +526,9 @@ msgid "" "topics/index.md) have detailed information about the most common topics for " "CWL." msgstr "" -"初心者の方は、[はじめに](/introduction/index." -"md)のセクションから始めてください。上級者向けには、[Topics](/topics/index." -"md)のサブセクションに、CWLで最も一般的なトピックに関する詳細情報があります。" +"初心者の方は、[はじめに](/introduction/index.md)のセクションから始めてくださ" +"い。上級者向けには、[Topics](/topics/index.md)のサブセクションに、CWLで最も一" +"般的なトピックに関する詳細情報があります。" #: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 msgid "" @@ -564,8 +572,8 @@ msgid "" "this user guide is the {{ cwl_version }}." msgstr "" "CWL仕様は、CWLコミュニティによって書かれ、維持されている文書です。この仕様に" -"は異なるバージョンが存在します。このユーザーガイドで扱うバージョンは{{ " -"cwl_version }}です。" +"は異なるバージョンが存在します。このユーザーガイドで扱うバージョンは" +"{{ cwl_version }}です。" #: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 msgid "" @@ -584,8 +592,8 @@ msgid "" "See the end of this section to [learn more](#learn-more) about it." msgstr "" "仕様のバージョンアップに使われるモデルは、セマンティックバージョニングを利用" -"しています。それについて[もっと知りたい](#learn-" -"more)方は、このセクションの最後をご覧ください。" +"しています。それについて[もっと知りたい](#learn-more)方は、このセクションの最" +"後をご覧ください。" #: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" @@ -629,9 +637,9 @@ msgid "" "hints. There are four types of processes defined in the CWL specification " "{{ cwl_version }}:" msgstr "" -"Processとは、入力を受けて出力を生成する計算のユニットです。Processの動作は、i" -"nputs、requirements、hintsに影響されることがあります。CWL仕様{{ cwl_version " -"}}では、4種類のProcessが定義されています：" +"Processとは、入力を受けて出力を生成する計算のユニットです。Processの動作は、" +"inputs、requirements、hintsに影響されることがあります。CWL仕様" +"{{ cwl_version }}では、4種類のProcessが定義されています：" #: ../../src/introduction/basic-concepts.md:112 #: 8c9772f96caf4169924d22eb929a4f0f @@ -726,14 +734,16 @@ msgstr "`InlineJavascriptWorkflow` - でJavaScriptを有効にします。" #: ../../src/introduction/basic-concepts.md:142 #: 2d9f53b6ed5041dbb6c0b54835897856 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "`SubworkflowFeatureRequirement` - ネストしたワークフローを有効にします。" +msgstr "" +"`SubworkflowFeatureRequirement` - ネストしたワークフローを有効にします。" #: ../../src/introduction/basic-concepts.md:143 #: 907674a4ecff4826a2b880e28fc38f33 msgid "" "`InitialWorkDirRequirement` - controls staging files in the input directory." -msgstr "`InitialWorkDirRequirement` - " -"入力ディレクトリのステージングファイルを制御します。" +msgstr "" +"`InitialWorkDirRequirement` - 入力ディレクトリのステージングファイルを制御し" +"ます。" #: ../../src/introduction/basic-concepts.md:145 #: 037cd0e5ceda482eaeaca03d51745aee @@ -746,9 +756,9 @@ msgid "" "runners." msgstr "" "いくつかのCWLランナーは、仕様にないrequirementsを提供することがあります。例え" -"ば、GPUに関するrequirementsは`cwltool` で`cwltool:CUDARequirement` " -"を通してサポートされていますが、{{ cwl_version }}仕様の一部ではないので、他の" -"CWLランナーではサポートされていないかもしれません。" +"ば、GPUに関するrequirementsは`cwltool` で`cwltool:CUDARequirement` を通してサ" +"ポートされていますが、{{ cwl_version }}仕様の一部ではないので、他のCWLラン" +"ナーではサポートされていないかもしれません。" #: ../../src/introduction/basic-concepts.md:151 #: e4643938445b48cc80eb8973ceeb126e @@ -758,9 +768,10 @@ msgid "" "are required, hints list optional features. Requirements are explained in " "detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" -"Hintsはrequirementsと似ていますが、requirementsが必須の機能を列挙するのに対し" -"、hintsはオプションの機能を列挙します。requirementsについては、[requirements]" -"(../topics/requirements-and-hints.md) セクションで詳しく説明しています。" +"Hintsはrequirementsと似ていますが、requirementsが必須の機能を列挙するのに対" +"し、hintsはオプションの機能を列挙します。requirementsについては、" +"[requirements](../topics/requirements-and-hints.md) セクションで詳しく説明し" +"ています。" #: ../../src/introduction/basic-concepts.md:155 #: c4c3315c96714e81b364f8cc003b87e6 @@ -789,9 +800,9 @@ msgid "" "CWL tasks are isolated, and you must be explicit about your inputs and " "outputs." msgstr "" -"CWLのルーツは、タスク間の依存関係に基づき、実行順序を決定する \"make\" " -"や多くの類似ツールにあります。しかし、\"make\" " -"とは異なり、CWLのタスクは分離されており、入力と出力を明示する必要があります。" +"CWLのルーツは、タスク間の依存関係に基づき、実行順序を決定する \"make\" や多く" +"の類似ツールにあります。しかし、\"make\" とは異なり、CWLのタスクは分離されて" +"おり、入力と出力を明示する必要があります。" #: ../../src/introduction/basic-concepts.md:171 #: 847951c055b94a83b1e081594cef22ee @@ -808,8 +819,9 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:176 #: 44bde1fae06b4678bcac4f3224601296 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "`cwltool` " -"はまた、データプロベナンスのためのPROV-O標準オントロジーを使用しています。" +msgstr "" +"`cwltool` はまた、データプロベナンスのためのPROV-O標準オントロジーを使用して" +"います。" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 @@ -828,7 +840,8 @@ msgstr "セマンティック・バージョニング -" msgid "" "The CWL Specification page in the CWL website: " -msgstr "CWLサイト内の「CWL仕様」ページ：" +msgstr "" +"CWLサイト内の「CWL仕様」ページ：" #: ../../src/introduction/basic-concepts.md:182 #: 2ccb956baa6b4376a04ad9fcc4654631 @@ -901,8 +914,8 @@ msgid "" "We have a better explanation in the [Implementations](basic-concepts." "md#implementations) section." msgstr "" -"CWL規格の実装は数多く存在します。あるものは完全なCWL実装であり、他のものはワ" -"ークフローエンジンのプラグインや拡張になり得ます。[実装](basic-concepts." +"CWL規格の実装は数多く存在します。あるものは完全なCWL実装であり、他のものは" +"ワークフローエンジンのプラグインや拡張になり得ます。[実装](basic-concepts." "md#implementations)のセクションでより詳しいをしています。" #: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 @@ -913,7 +926,8 @@ msgstr "オペレーティングシステム" msgid "" "We recommend using an up-to-date operating system. You can choose any of the " "following options for your operating system:" -msgstr "最新のオペレーティングシステムを使用することをお勧めします。OSは、以下のいず" +msgstr "" +"最新のオペレーティングシステムを使用することをお勧めします。OSは、以下のいず" "れかをお選びいただけます：" #: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 @@ -958,11 +972,10 @@ msgid "" "activate a Python virtual environment using the `venv` module, and install " "`cwltool` in that environment:" msgstr "" -"`cwltool` は、`pip` でインストールすることができます。`venv` または`conda` " -"のような仮想環境を使用することをお勧めします。以下のコマンドは、`venv` " -"モジュールを使用して Python " -"仮想環境を作成およびアクティブ化し、その環境内に`cwltool` " -"をインストールします：" +"`cwltool` は、`pip` でインストールすることができます。`venv` または`conda` の" +"ような仮想環境を使用することをお勧めします。以下のコマンドは、`venv` モジュー" +"ルを使用して Python 仮想環境を作成およびアクティブ化し、その環境内に" +"`cwltool` をインストールします：" #: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d #, fuzzy @@ -976,10 +989,9 @@ msgid "" "language/cwltool#install) for other ways to install `cwltool` with `apt` and " "`conda`." msgstr "" -"`cwltool` を`apt` と`conda` " -"とともにインストールする他の方法については、`cwltool` " -"[documentation](https://github.com/common-workflow-language/cwltool#install) " -"を参照してください。" +"`cwltool` を`apt` と`conda` とともにインストールする他の方法については、" +"`cwltool` [documentation](https://github.com/common-workflow-language/" +"cwltool#install) を参照してください。" #: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." @@ -1007,8 +1019,9 @@ msgstr "`cwltool` を使って `true.cwl` を検証します。" #: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 msgid "" "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "`--validate` " -"オプションを省略することで、CWLツール定義を実行することができます：" +msgstr "" +"`--validate` オプションを省略することで、CWLツール定義を実行することができま" +"す：" #: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." @@ -1035,9 +1048,8 @@ msgid "" "The CWL community publishes a Python package with the name `cwlref-runner` " "that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -"CWLコミュニティは、`cwlref-runner` " -"という名前のPythonパッケージを公開しており、`cwltool` のエイリアスを`cwl-" -"runner` という名前でインストールします。" +"CWLコミュニティは、`cwlref-runner` という名前のPythonパッケージを公開してお" +"り、`cwltool` のエイリアスを`cwl-runner` という名前でインストールします。" #: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." @@ -1049,9 +1061,9 @@ msgid "" "which will invoke `cwltool`. You should have the same results and output as " "in the previous section." msgstr "" -"これで `cwl-runner` 実行ファイルを用いてワークフローを検証・実行し、`cwltool`" -" を呼び出すことができるようになりました。前のセクションと同じ結果と出力が得ら" -"れるはずです。" +"これで `cwl-runner` 実行ファイルを用いてワークフローを検証・実行し、" +"`cwltool` を呼び出すことができるようになりました。前のセクションと同じ結果と" +"出力が得られるはずです。" #: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." @@ -1068,8 +1080,8 @@ msgid "" "file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" "`cwl-runner` を実行するもう一つの方法は、ファイルを直接起動することです。その" -"ためには、まず`true.cwl` ワークフローを新しいファイル`true_shebang.cwl` " -"にコピーし、特別な最初の行、*shebang* を含める必要があります：" +"ためには、まず`true.cwl` ワークフローを新しいファイル`true_shebang.cwl` にコ" +"ピーし、特別な最初の行、*shebang* を含める必要があります：" #: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" @@ -1078,8 +1090,9 @@ msgstr "`true_shebang.cwl`" #: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 msgid "" "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "`chmod u+x` を実行することで、 `true_shebang.cwl` " -"を実行可能なファイルにすることができます。" +msgstr "" +"`chmod u+x` を実行することで、 `true_shebang.cwl` を実行可能なファイルにする" +"ことができます。" #: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." @@ -1092,8 +1105,8 @@ msgid "" "the rest of the file." msgstr "" "そして最後に、コマンドラインで直接実行することができます。実行時には、shebang" -"で指定されたプログラム(`cwl-" -"runner`)が、ファイルの残りの部分を実行するために使用されます。" +"で指定されたプログラム(`cwl-runner`)が、ファイルの残りの部分を実行するために" +"使用されます。" #: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." @@ -1146,8 +1159,8 @@ msgid "" "The CWL community also maintains a list of editors and viewers: " msgstr "" -"CWLコミュニティでは、エディターやビューアーのリストも管理しています：" +"CWLコミュニティでは、エディターやビューアーのリストも管理しています：" +"" #: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 msgid "Docker" @@ -1161,10 +1174,10 @@ msgid "" "documentation to install it for your operating system: ." msgstr "" -"`cwltool` は、ツール、ワークフロー、およびワークフロー " -"ステップで指定されたソフトウェアコンテナをDockerを使用して実行します。Docker " -"ドキュメントの指示に従って、お使いのオペレーティングシステム用にインストール" -"してください：." +"`cwltool` は、ツール、ワークフロー、およびワークフロー ステップで指定されたソ" +"フトウェアコンテナをDockerを使用して実行します。Docker ドキュメントの指示に" +"従って、お使いのオペレーティングシステム用にインストールしてください：" +"." #: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c #, fuzzy @@ -1193,8 +1206,9 @@ msgstr "" msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the next " "section, Basic Concepts." -msgstr "次項の「基本コンセプト」の[実装](basic-concepts." -"md#implementations)のトピックを参照してください。" +msgstr "" +"次項の「基本コンセプト」の[実装](basic-concepts.md#implementations)のトピック" +"を参照してください。" #: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " @@ -1225,10 +1239,9 @@ msgid "" "example below shows a simple CWL “Hello World” workflow annotated with " "comments. Note that comments start with `#`:" msgstr "" -"CWLドキュメントは[YAML](../topics/index." -"md)(および/またはJSON)で書かれています。以下の例は、" -"コメントで注釈されたシンプルなCWL \"Hello World\" " -"ワークフローを示しています。コメントは`#` で始まることに注意してください：" +"CWLドキュメントは[YAML](../topics/index.md)(および/またはJSON)で書かれていま" +"す。以下の例は、コメントで注釈されたシンプルなCWL \"Hello World\" ワークフ" +"ローを示しています。コメントは`#` で始まることに注意してください：" #: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" @@ -1261,9 +1274,9 @@ msgid "" "latest version of the specification: {{ cwl_version }}. You can install " "`cwltool` using `pip`:" msgstr "" -"`cwltool` は、CWL仕様の実装の１つです。また、同仕様のCWL*Reference Runner* " -"でもあり、同仕様の最新バージョンに準拠しています：{cwl_version " -"}}に準拠しています。`cwltool` は、`pip` を使ってインストールできます：" +"`cwltool` は、CWL仕様の実装の１つです。また、同仕様のCWL*Reference Runner* で" +"もあり、同仕様の最新バージョンに準拠しています：{cwl_version }}に準拠していま" +"す。`cwltool` は、`pip` を使ってインストールできます：" #: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." @@ -1296,8 +1309,9 @@ msgstr "`hello_world.cwl` を `cwltool` で実行します。" msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" -msgstr "また、`echo` base コマンドの引数を変更するのと同様に、入力パラメータ`message`" -" のデフォルト値を上書きすることもできます：" +msgstr "" +"また、`echo` base コマンドの引数を変更するのと同様に、入力パラメータ" +"`message` のデフォルト値を上書きすることもできます：" #: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." @@ -1310,10 +1324,10 @@ msgid "" "corresponding values. The Inputs Objects file can be written in JSON or " "YAML. For example:" msgstr "" -"ワークフロー入力パラメータに値を渡すもう一つの方法は、*Inputs Object* " -"を介する方法です。これは、入力フィールドとその対応する値を含むファイルです。" -"Inputs Objects ファイルは、JSON または YAML " -"で記述することができます。例えば、以下のようになります：" +"ワークフロー入力パラメータに値を渡すもう一つの方法は、*Inputs Object* を介す" +"る方法です。これは、入力フィールドとその対応する値を含むファイルです。Inputs " +"Objects ファイルは、JSON または YAML で記述することができます。例えば、以下の" +"ようになります：" #: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" @@ -1323,8 +1337,9 @@ msgstr "`hello_world-job.json`" msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" -msgstr "このInputs Objectファイルを使用して、「Hello " -"World」ワークフローを実行することができるようになりました：" +msgstr "" +"このInputs Objectファイルを使用して、「Hello World」ワークフローを実行するこ" +"とができるようになりました：" #: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." @@ -1338,11 +1353,10 @@ msgid "" "is not a requirement. You can choose any name for your workflows and Inputs " "Object files." msgstr "" -"ワークフローとInputs " -"Objectファイルには、同様のファイル名を使用しました。*-job.json* " -"という接尾辞は、Inputs Object " -"ファイルでは非常に一般的ですが必須ではありません。ワークフローとInputs " -"Objectファイルには、任意の名前を付けることができます。" +"ワークフローとInputs Objectファイルには、同様のファイル名を使用しました。*-" +"job.json* という接尾辞は、Inputs Object ファイルでは非常に一般的ですが必須で" +"はありません。ワークフローとInputs Objectファイルには、任意の名前を付けること" +"ができます。" #: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" @@ -1402,8 +1416,8 @@ msgid "" "md) section of the new user guide." msgstr "" "このページは古いもので、旧ユーザーガイドのリンクを保存するためにここに残され" -"ていました。このページの情報は、新しいユーザーガイドの [FAQ](/faq.md) " -"セクションに移行されました。" +"ていました。このページの情報は、新しいユーザーガイドの [FAQ](/faq.md) セク" +"ションに移行されました。" #: ../../src/topics/additional-arguments-and-parameters.md:1 #: 9c87c76c690948ac8e18088a0fffe679 @@ -1417,7 +1431,8 @@ msgstr "追加の引数とパラメータ" msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." -msgstr "ツールには、入力パラメータに正確に対応しない追加のコマンドラインオプションが" +msgstr "" +"ツールには、入力パラメータに正確に対応しない追加のコマンドラインオプションが" "必要な場合があります。" #: ../../src/topics/additional-arguments-and-parameters.md:6 @@ -1451,15 +1466,17 @@ msgstr "次に、CommandLineToolで使用するサンプルJavaファイルを msgid "" "And now invoke `cwltool` providing the tool description and the input object " "on the command line:" -msgstr "そして、コマンドラインでツール定義と入力オブジェクトを渡して`cwltool` " -"を起動します：" +msgstr "" +"そして、コマンドラインでツール定義と入力オブジェクトを渡して`cwltool` を起動" +"します：" #: ../../src/topics/additional-arguments-and-parameters.md:36 #: 713666580a0a4466b4ba6e3eb2b54f0a msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." -msgstr "ここでは、`arguments` フィールドを使用して、特定の入力パラメータに結びつかな" +msgstr "" +"ここでは、`arguments` フィールドを使用して、特定の入力パラメータに結びつかな" "い追加の引数をコマンドラインに追加しています。" #: ../../src/topics/additional-arguments-and-parameters.md:43 @@ -1468,10 +1485,10 @@ msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" -"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." -"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " -"specification for details." +"designated output directory. Other parameters include `$(runtime.tmpdir)`, " +"`$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and " +"`$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of " +"the CWL specification for details." msgstr "" #: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 @@ -1495,8 +1512,8 @@ msgid "" "No `type: string` parameters for names of input or reference files/" "directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -"入力または参照のファイルやディレクトリの名前に `type: string` " -"を使用しません。 `type:File` または `type: Direcotry` を適宜使用します。" +"入力または参照のファイルやディレクトリの名前に `type: string` を使用しませ" +"ん。 `type:File` または `type: Direcotry` を適宜使用します。" #: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 msgid "" @@ -1527,8 +1544,9 @@ msgstr "" msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" -msgstr "参考文献：\"[科学者・プログラマーのためのソフトウェアライセンス " -"クイックガイド][sci-license]\"" +msgstr "" +"参考文献：\"[科学者・プログラマーのためのソフトウェアライセンス クイックガイ" +"ド][sci-license]\"" #: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" @@ -1540,9 +1558,8 @@ msgid "" "Metadata and Authorship section of this User Guide](../topics/metadata-and-" "authorship.md)." msgstr "" -"CW定義にメタデータを与える例については、 " -"[このユーザーガイドのメタデータと著者名のセクション](../topics/metadata-and-" -"authorship.md)を参照してください。" +"CW定義にメタデータを与える例については、 [このユーザーガイドのメタデータと著" +"者名のセクション](../topics/metadata-and-authorship.md)を参照してください。" #: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 msgid "" @@ -1550,15 +1567,16 @@ msgid "" "CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" "[orcid]." msgstr "" -"CWLツールやワークフローの定義の著者の[帰属情報][license-example]を含みます。[" -"ORCID][orcid]のような曖昧でない識別子を使用してください。" +"CWLツールやワークフローの定義の著者の[帰属情報][license-example]を含みます。" +"[ORCID][orcid]のような曖昧でない識別子を使用してください。" #: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." -msgstr "ツール定義では、`SoftwareRequirement` " -"の下に、短い名前を使用して依存関係をリストアップします。" +msgstr "" +"ツール定義では、`SoftwareRequirement` の下に、短い名前を使用して依存関係をリ" +"ストアップします。" #: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 #, fuzzy @@ -1566,8 +1584,8 @@ msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" "identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` " -"フォーマットで依存関係のための [SciCrunch][scicrunch] 識別子を含みます。" +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` フォーマットで依存関係のため" +"の [SciCrunch][scicrunch] 識別子を含みます。" #: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb msgid "" @@ -1589,8 +1607,8 @@ msgstr "" msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" -"$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with " +"`$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " "[Full IANA media type list][iana-types] (also known as MIME types). For non-" "bioinformatics tools, use or build an appropriate ontology/controlled " "vocabulary in the same way. Please edit this page to let us know about it." @@ -1622,7 +1640,8 @@ msgstr "" msgid "" "Custom types should be defined with one external YAML per type definition " "for re-use." -msgstr "カスタム型は、再利用のため、タイプ定義ごとに1つの外部YAMLで定義する必要があり" +msgstr "" +"カスタム型は、再利用のため、タイプ定義ごとに1つの外部YAMLで定義する必要があり" "ます。" #: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 @@ -1636,14 +1655,15 @@ msgid "" "more detailed description than was provided in the top-level `label` (see " "above)." msgstr "" -"有用であれば、トップレベル`doc` も含めてください。これは、トップレベル`label`" -" （上記参照）で提供されたものより長く詳細な説明を記述します。" +"有用であれば、トップレベル`doc` も含めてください。これは、トップレベル" +"`label` （上記参照）で提供されたものより長く詳細な説明を記述します。" #: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list of " "valid values." -msgstr "有効な値のリストが決まっている要素には、`type: string` の代わりに、`type: " +msgstr "" +"有効な値のリストが決まっている要素には、`type: string` の代わりに、`type: " "enum` を使用してください。" #: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a @@ -1658,8 +1678,9 @@ msgstr "" msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." -msgstr "ツール定義を同僚（できれば別の機関の人）に渡し、テストしてもらい、フィードバ" -"ックをもらいましょう。" +msgstr "" +"ツール定義を同僚（できれば別の機関の人）に渡し、テストしてもらい、フィード" +"バックをもらいましょう。" #: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 msgid "" @@ -1668,8 +1689,8 @@ msgid "" "workflow modular and allow sections of them to be easily reused." msgstr "" "抽象化できる個々のコンポーネントを持つ複雑なワークフローは、ワークフローをモ" -"ジュール化し、その一部を容易に再利用できるようにするために、[`SubworkflowFeat" -"ureRequirement`][subworkflow]を利用します。" +"ジュール化し、その一部を容易に再利用できるようにするために、" +"[`SubworkflowFeatureRequirement`][subworkflow]を利用します。" #: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 #, fuzzy @@ -1679,8 +1700,8 @@ msgid "" "software\"][containers] (also useful to other disciplines)." msgstr "" "ソフトウェアのコンテナは、[\"Recommendations for packaging and " -"containerizing of bioinformatics software\"][containers] " -"に準拠するようにします（他の分野でも有用です）。" +"containerizing of bioinformatics software\"][containers] に準拠するようにしま" +"す（他の分野でも有用です）。" #: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" @@ -1694,11 +1715,10 @@ msgid "" "etc. The command-line tool is defined in the `baseCommand` attribute of the " "command-line tool CWL document." msgstr "" -"コマンドラインツールは、Processオブジェクトの一種であり、" -"それ自体またはワークフローのステップとし " -"て実行することができます。`ls`,`echo`,`tar` などのコマンドのラッパーです。コ" -"マンドラインツールは、コマンドラインツールCWL文書の`baseCommand` " -"属性で定義されています。" +"コマンドラインツールは、Processオブジェクトの一種であり、それ自体またはワーク" +"フローのステップとし て実行することができます。`ls`,`echo`,`tar` などのコマン" +"ドのラッパーです。コマンドラインツールは、コマンドラインツールCWL文書の" +"`baseCommand` 属性で定義されています。" #: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab msgid "" @@ -1706,9 +1726,9 @@ msgid "" "example contains a minimal example of a CWL command-line tool for the `echo` " "Linux command, using inputs and outputs." msgstr "" -"CWLコマンドラインツールは、`inputs` と`outputs` " -"も持っていなければなりません。次の例は、Linuxコマンド `echo` " -"のためのCWLコマンドラインツールの最小限の例で、inputsとoutputsを使用します。" +"CWLコマンドラインツールは、`inputs` と`outputs` も持っていなければなりませ" +"ん。次の例は、Linuxコマンド `echo` のためのCWLコマンドラインツールの最小限の" +"例で、inputsとoutputsを使用します。" #: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." @@ -1726,8 +1746,8 @@ msgid "" "[Outputs](../topics/outputs.md) sections." msgstr "" "上記の例では、簡略化した形で入力と出力を定義しています。[Inputs](../topics/" -"inputs.md)と[Outputs](../topics/outputs." -"md)のセクションで、より詳しく説明する予定です。" +"inputs.md)と[Outputs](../topics/outputs.md)のセクションで、より詳しく説明する" +"予定です。" #: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" @@ -1740,17 +1760,17 @@ msgid "" "If a command-line tool is written manually in CWL v1.1+, there is a need to " "specify when network access is required." msgstr "" -"これは、プロセスが発信IPv4/" -"IPv6ネットワークアクセスを必要とするかどうかを示します。CWL v1.1+でCommandLin" -"eToolを手動で記述する場合、ネットワークアクセスが必要なタイミングを指定する必" -"要があります。" +"これは、プロセスが発信IPv4/IPv6ネットワークアクセスを必要とするかどうかを示し" +"ます。CWL v1.1+でCommandLineToolを手動で記述する場合、ネットワークアクセスが" +"必要なタイミングを指定する必要があります。" #: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " "Access automatically." -msgstr "CWL v1.0のコマンドラインツールをv1.1またはv1." -"2にアップグレードすると、自動的にネットワークアクセスを取得します。" +msgstr "" +"CWL v1.0のコマンドラインツールをv1.1またはv1.2にアップグレードすると、自動的" +"にネットワークアクセスを取得します。" #: ../../src/topics/creating-files-at-runtime.md:1 #: a2a0f0eb0f404eb3aaf19cfd3cdb559b @@ -1769,8 +1789,9 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 #: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "このようなファイルを生成するために、`InitialWorkDirRequirement` " -"を利用することができます。" +msgstr "" +"このようなファイルを生成するために、`InitialWorkDirRequirement` を利用するこ" +"とができます。" #: ../../src/topics/creating-files-at-runtime.md:9 #: d3f74c3b094a427fbec831afab657d50 @@ -1800,8 +1821,9 @@ msgstr "" msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" -msgstr "上記のCWLツールをテストするために、このジョブを使用して、入力値`message` " -"を与えます：" +msgstr "" +"上記のCWLツールをテストするために、このジョブを使用して、入力値`message` を与" +"えます：" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 @@ -1835,8 +1857,9 @@ msgstr "" msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." -msgstr "フォーマットについては、[YAMLガイド](../topics/yaml-guide." -"md#maps)を参照してください。" +msgstr "" +"フォーマットについては、[YAMLガイド](../topics/yaml-guide.md#maps)を参照して" +"ください。" #: ../../src/topics/creating-files-at-runtime.md:54 #: ../../src/topics/environment-variables.md:18 @@ -1848,8 +1871,9 @@ msgstr "フォーマットについては、[YAMLガイド](../topics/yaml-guide msgid "" "Now invoke `cwltool` with the tool description and the input object on the " "command line:" -msgstr "ここで、コマンドラインにツール定義と入力オブジェクトを指定して、`cwltool` " -"を起動します：" +msgstr "" +"ここで、コマンドラインにツール定義と入力オブジェクトを指定して、`cwltool` を" +"起動します：" #: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" @@ -1942,8 +1966,8 @@ msgid "" "the tool using `EnvVarRequirement`." msgstr "" "ツールは制限された環境で実行されるため、親プロセスからほとんどの環境変数を引" -"き継ぎません。 ツールの環境変数は、`EnvVarRequirement` " -"を使って設定できます。" +"き継ぎません。 ツールの環境変数は、`EnvVarRequirement` を使って設定できま" +"す。" #: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" @@ -1963,17 +1987,16 @@ msgid "" msgstr "" "ExpressionToolは、それ自体またはワークフローのステップとして実行することがで" "きるProcessの一種です。純粋な JavaScript 式を実行します。入力データを操作し、" -"出力として結果を生成する必要がある複雑な JavaScript " -"式を分離する方法として使用されることを意図しています。" +"出力として結果を生成する必要がある複雑な JavaScript 式を分離する方法として使" +"用されることを意図しています。" #: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -"CommandLinetToolと同様に、`inputs` と`outputs` " -"が必要です。しかし、`baseCommand` の代わりに、`expression` " -"属性を必要とします。" +"CommandLinetToolと同様に、`inputs` と`outputs` が必要です。しかし、" +"`baseCommand` の代わりに、`expression` 属性を必要とします。" #: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe #, fuzzy @@ -1993,8 +2016,9 @@ msgid "" "expression tool that JavaScript is a requirement." msgstr "" "`InlineJavascriptRequirement` を使用する必要がありました。この式には`." -"toUpperCase()` で JavaScript の呼び出しが含まれているからです。これは、Expres" -"sionToolを使用するツールにとって、JavaScriptが必要であることを意味します。" +"toUpperCase()` で JavaScript の呼び出しが含まれているからです。これは、" +"ExpressionToolを使用するツールにとって、JavaScriptが必要であることを意味しま" +"す。" #: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 #, fuzzy @@ -2009,9 +2033,9 @@ msgid "" "legal you can provide a fragment of Javascript that will be evaluated by the " "CWL runner." msgstr "" -"入力パラメータを操作する必要がある場合は、`InlineJavascriptRequirement` " -"を含めると、パラメータ参照が合法な場所であれば、CWL " -"runnerによって評価されるJavascriptを使用できます。" +"入力パラメータを操作する必要がある場合は、`InlineJavascriptRequirement` を含" +"めると、パラメータ参照が合法な場所であれば、CWL runnerによって評価される" +"Javascriptを使用できます。" #: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 msgid "" @@ -2032,8 +2056,9 @@ msgstr "`expression.cwl`" msgid "" "As this tool does not require any `inputs` we can run it with an (almost) " "empty job file:" -msgstr "このツールは`inputs` " -"を必要としないので、（ほとんど）空のジョブファイルで実行することができます：" +msgstr "" +"このツールは`inputs` を必要としないので、（ほとんど）空のジョブファイルで実行" +"することができます：" #: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 #, fuzzy @@ -2047,8 +2072,8 @@ msgid "" "represented simply by a set of empty brackets." msgstr "" "`empty.yml` には、空のJSONオブジェクトの記述があります。JSONオブジェクトの記" -"述は、中括弧`{}` " -"の中に含まれるので、空のオブジェクトは、単に空の括弧のセットで表されます。" +"述は、中括弧`{}` の中に含まれるので、空のオブジェクトは、単に空の括弧のセット" +"で表されます。" #: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" @@ -2062,7 +2087,8 @@ msgstr "`expression.cwl` を実行する。" msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" -msgstr "なお、上の例のように、map構文で requirements を指定することも可能です：" +msgstr "" +"なお、上の例のように、map構文で requirements を指定することも可能です：" #: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 #, fuzzy @@ -2072,8 +2098,8 @@ msgid "" "describe the additional command line arguments." msgstr "" "または配列として、各エントリ（この場合、`class: InlineJavascriptRequirement` " -"だけです）に`-` " -"を付けます。同じ構文で、追加のコマンドライン引数を定義します。" +"だけです）に`-` を付けます。同じ構文で、追加のコマンドライン引数を定義しま" +"す。" #: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" @@ -2085,8 +2111,8 @@ msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -"[パラメータ参照](parameter-references.md)と同様に、JavaScript " -"式は特定のフィールドにのみ使用できます。 以下はその例です：" +"[パラメータ参照](parameter-references.md)と同様に、JavaScript 式は特定の" +"フィールドにのみ使用できます。 以下はその例です：" #: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c #, fuzzy @@ -2245,8 +2271,8 @@ msgid "" "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." "html#ExpressionTool)" msgstr "" -"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow." -"html#ExpressionTool)から" +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +"から" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 c2a92d3eca7f4ee39cec649170eeea53 @@ -2378,7 +2404,8 @@ msgstr "`envValue`" #, fuzzy msgid "" "Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "`expressionLib` による外部ライブラリの利用とインラインJavaScriptコードの利用" +msgstr "" +"`expressionLib` による外部ライブラリの利用とインラインJavaScriptコードの利用" #: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 msgid "" @@ -2420,8 +2447,9 @@ msgstr "`hello-world-expressionlib-inline.cwl`" msgid "" "Running this CWL workflow will invoke the JavaScript function and result in " "the `echo` command printing the input message with capital initial letters:" -msgstr "このCWLワークフローを実行すると、JavaScript関数が起動し、`echo` " -"コマンドが入力メッセージを大文字の頭文字で表示します：" +msgstr "" +"このCWLワークフローを実行すると、JavaScript関数が起動し、`echo` コマンドが入" +"力メッセージを大文字の頭文字で表示します：" #: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 #, fuzzy @@ -2447,8 +2475,8 @@ msgstr "`hello-world-expressionlib-external.cwl`" #: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac #, fuzzy msgid "" -"The `custom-functions.js` file is included in the CWL document with the `" -"$include: custom-functions.js` statement. That makes the functions and " +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" "`custom-functions.js` ファイルは、`$include: custom-functions.js` という記述" @@ -2510,16 +2538,18 @@ msgstr "" msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` section " "of the document in greater detail, so don't worry about these for now." -msgstr "次のチュートリアルで、`$namespaces` と`$schemas` " -"の部分をより詳しく説明しますので、今は気にしないでください。" +msgstr "" +"次のチュートリアルで、`$namespaces` と`$schemas` の部分をより詳しく説明します" +"ので、今は気にしないでください。" #: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f #, fuzzy msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." -msgstr "なお、さらなる利点として`cwltool` は、ファイル形式に基づく基本的な推論を行い" -"、明らかな不一致があるようであれば警告を発します。" +msgstr "" +"なお、さらなる利点として`cwltool` は、ファイル形式に基づく基本的な推論を行" +"い、明らかな不一致があるようであれば警告を発します。" #: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" @@ -2544,8 +2574,8 @@ msgid "" "parameterization." msgstr "" "以下は、上記の例のパラメータファイルの例です。あなたのツールのパラメータファ" -"イルの実例をチェックすることをお勧めします。これにより、他の人が「既知の良い" -"」パラメータ化から始めて、あなたのツールで素早く作業することができます。" +"イルの実例をチェックすることをお勧めします。これにより、他の人が「既知の良" +"い」パラメータ化から始めて、あなたのツールで素早く作業することができます。" #: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" @@ -2559,11 +2589,10 @@ msgid "" "com/common-workflow-language/user_guide/raw/main/src/_includes/cwl/file-" "formats/file-formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -"___注：___ 以下の例に実行するには、例の入力ファイル、*file-formats.bam* " -"をダウンロードする必要があります。このファイルは から入手可能で、`wget` " -"などでダウンロードすることができます：" +"___注：___ 以下の例に実行するには、例の入力ファイル、*file-formats.bam* をダ" +"ウンロードする必要があります。このファイルは から入手可能で、`wget` などでダウンロードすることができます：" #: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" @@ -2584,9 +2613,9 @@ msgid "" "the tool. Each parameter has an `id` for the name of parameter, and `type` " "describing what types of values are valid for that parameter." msgstr "" -"ツールの`inputs` は、ツールの実行に関わる入力パラメーターのリストです。 " -"各パラメーターには、パラメーター名を示す`id` " -"と、そのパラメーターに有効な値の種類を示す`type` があります。" +"ツールの`inputs` は、ツールの実行に関わる入力パラメーターのリストです。 各パ" +"ラメーターには、パラメーター名を示す`id` と、そのパラメーターに有効な値の種類" +"を示す`type` があります。" #: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a #, fuzzy @@ -2595,15 +2624,15 @@ msgid "" "and *null*; complex types are *array* and *record*; in addition there are " "special types *File*, *Directory* and *Any*." msgstr "" -"利用可能なプリミティブ型は*string*,*int*,*long*,*float*,*double*, *null*; " -"複合型は*array* and*record*; さらに特殊型*File*,*Directory* ,*Any* " -"があります。" +"利用可能なプリミティブ型は*string*,*int*,*long*,*float*,*double*, *null*; 複" +"合型は*array* and*record*; さらに特殊型*File*,*Directory* ,*Any* があります。" #: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." -msgstr "次の例では、異なる型の入力パラメーターが、異なる方法でコマンドライン上に表示" +msgstr "" +"次の例では、異なる型の入力パラメーターが、異なる方法でコマンドライン上に表示" "されることを示します。" #: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed @@ -2652,8 +2681,9 @@ msgstr "" msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " "command line." -msgstr "次に、コマンドラインで`touch whale.txt` と入力し、[touch]" -"をコマンドを使用して whale.txt を作成します。" +msgstr "" +"次に、コマンドラインで`touch whale.txt` と入力し、[touch]をコマンドを使用し" +"て whale.txt を作成します。" #: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da msgid "" @@ -2681,9 +2711,9 @@ msgstr "" #: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c msgid "" -"Boolean types are treated as a flag. If the input parameter \"example_flag" -"\" is \"true\", then `prefix` will be added to the command line. If false, " -"no flag is added." +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." msgstr "" #: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 @@ -2716,9 +2746,8 @@ msgid "" "Input files are read-only. If you wish to update an input file, you must " "[first copy it to the output directory](staging-input-files.md)." msgstr "" -"入力ファイルは読み取り専用です。 " -"入力ファイルを更新したい場合は、[まず出力ディレクトリにコピーする](staging-" -"input-files.md)必要があります。" +"入力ファイルは読み取り専用です。 入力ファイルを更新したい場合は、[まず出力" +"ディレクトリにコピーする](staging-input-files.md)必要があります。" #: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "" @@ -2735,8 +2764,9 @@ msgstr "" msgid "" "The `baseCommand` field will always appear in the final command line before " "the parameters." -msgstr "`baseCommand` " -"フィールドは、常にパラメータの前の最終コマンド行に表示されます。" +msgstr "" +"`baseCommand` フィールドは、常にパラメータの前の最終コマンド行に表示されま" +"す。" #: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" @@ -2766,8 +2796,9 @@ msgstr "`array-inputs-job.yml`" msgid "" "Now invoke `cwltool` providing the tool description and the input object on " "the command line:" -msgstr "ここで、コマンドラインにツール定義と入力オブジェクトを指定し `cwltool` " -"を起動します：" +msgstr "" +"ここで、コマンドラインにツール定義と入力オブジェクトを指定し `cwltool` を起動" +"します：" #: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 msgid "" @@ -2825,8 +2856,8 @@ msgid "" "(`itemD`) is ignored." msgstr "" "2番目の例では、`itemC` と`itemD` が排他的であるため、最初に一致した項目 " -"(`itemC`) のみがコマンドラインに追加され、残りの項目 (`itemD`) " -"は無視されます。" +"(`itemC`) のみがコマンドラインに追加され、残りの項目 (`itemD`) は無視されま" +"す。" #: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" @@ -2836,8 +2867,9 @@ msgstr "`record-job3.yml`" msgid "" "In the third example, only `itemD` is provided, so it appears on the command " "line." -msgstr "3番目の例では、`itemD` " -"のみが提供されているので、コマンドラインに表示されます。" +msgstr "" +"3番目の例では、`itemD` のみが提供されているので、コマンドラインに表示されま" +"す。" #: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 #, fuzzy @@ -2859,8 +2891,8 @@ msgid "" "parameter that accepts `null` (i.e. no value provided), or any value from an " "enum." msgstr "" -"`file_format` 入力パラメータに、`null` (つまり、値が提供されていない)、" -"または enum の任意の値を受け入れる排他的なものを含む例を使ってみましょう。" +"`file_format` 入力パラメータに、`null` (つまり、値が提供されていない)、また" +"は enum の任意の値を受け入れる排他的なものを含む例を使ってみましょう。" #: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" @@ -2885,9 +2917,9 @@ msgid "" "evaluated to a `null` value, which does not match the expected type for the " "output field (a `string`), resulting in failure when running your workflow." msgstr "" -"しかし、入力値を提供しない場合、`file_format` は、`null` " -"の値として評価されます。これは、出力フィールドが期待する型（`string` " -"）と一致しないため、ワークフロー実行時に失敗することになります。" +"しかし、入力値を提供しない場合、`file_format` は、`null` の値として評価されま" +"す。これは、出力フィールドが期待する型（`string` ）と一致しないため、ワークフ" +"ロー実行時に失敗することになります。" #: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 msgid "" @@ -2972,7 +3004,8 @@ msgstr "" msgid "" "You can create operations to visualize a workflow during development, before " "you are ready to submit the workflow to a CWL runner:" -msgstr "CWLランナーにワークフローを送信する前に、開発中のワークフローを可視化すること" +msgstr "" +"CWLランナーにワークフローを送信する前に、開発中のワークフローを可視化すること" "ができます：" #: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf @@ -2986,9 +3019,9 @@ msgid "" "command line tool or an expression. You can also plot it with the CWL Viewer " "or `cwltool`:" msgstr "" -"ワークフローの`uppercase` ステップは Operation " -"です。CommandLineToolやExpressionToolのように使用することができます。また、" -"CWL Viewerや`cwltool` を使ってプロットすることもできます：" +"ワークフローの`uppercase` ステップは Operation です。CommandLineToolや" +"ExpressionToolのように使用することができます。また、CWL Viewerや`cwltool` を" +"使ってプロットすることもできます：" #: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "" @@ -3004,8 +3037,9 @@ msgstr "" msgid "" "If you try running it with `cwltool`, the command will fail since `cwltool` " "does not have enough information to know how to execute it:" -msgstr "`cwltool` だけで実行しようとすると、`cwltool` " -"は実行するのに必要な情報がないため、コマンドは失敗します：" +msgstr "" +"`cwltool` だけで実行しようとすると、`cwltool` は実行するのに必要な情報がない" +"ため、コマンドは失敗します：" #: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" @@ -3035,10 +3069,9 @@ msgid "" "parameter, and `type` describing what types of values are valid for that " "parameter." msgstr "" -"ツールの`outputs` " -"は、ツールの実行後に返されるべき出力パラメータのリストです。 " -"各パラメーターには、パラメーター名を示す`id` " -"と、そのパラメーターに有効な値の型を示す`type` があります。" +"ツールの`outputs` は、ツールの実行後に返されるべき出力パラメータのリストで" +"す。 各パラメーターには、パラメーター名を示す`id` と、そのパラメーターに有効" +"な値の型を示す`type` があります。" #: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 msgid "" @@ -3084,8 +3117,9 @@ msgstr "次に、サンプルとなるtarファイルを作成します。" msgid "" "And now invoke `cwltool` with the tool description and the input object on " "the command line:" -msgstr "そして、今度はコマンドラインにツール定義と入力オブジェクトを指定して`cwltool`" -" を呼び出します：" +msgstr "" +"そして、今度はコマンドラインにツール定義と入力オブジェクトを指定して" +"`cwltool` を呼び出します：" #: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d msgid "" @@ -3111,9 +3145,9 @@ msgid "" "name of the file where the output stream should go. Then add `type: stdout` " "on the corresponding output parameter." msgstr "" -"ツールの標準出力をキャプチャするには、`stdout` " -"フィールドに、標準出力を保存したいファイル名を追加します。 " -"次に、対応する出力パラメータに`type: stdout` を追加します。" +"ツールの標準出力をキャプチャするには、`stdout` フィールドに、標準出力を保存し" +"たいファイル名を追加します。 次に、対応する出力パラメータに`type: stdout` を" +"追加します。" #: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 #, fuzzy @@ -3128,7 +3162,8 @@ msgstr "出力の配列" msgid "" "You can also capture multiple output files into an array of files using " "`glob`." -msgstr "また、`glob` を使って、複数の出力ファイルを配列に取り込むことができます。" +msgstr "" +"また、`glob` を使って、複数の出力ファイルを配列に取り込むことができます。" #: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 #, fuzzy @@ -3177,7 +3212,8 @@ msgstr "`tar-param-job.yml`" msgid "" "Create your input files and invoke `cwltool` with the tool description and " "the input object on the command line:" -msgstr "入力ファイル(入力オブジェクト)を作成し、コマンドラインでツール定義と入力オブ" +msgstr "" +"入力ファイル(入力オブジェクト)を作成し、コマンドラインでツール定義と入力オブ" "ジェクトを指定して`cwltool` を呼び出します：" #: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 @@ -3185,25 +3221,27 @@ msgstr "入力ファイル(入力オブジェクト)を作成し、コマンド msgid "" "Certain fields permit parameter references which are enclosed in `$(...)`. " "These are evaluated and replaced with value being referenced." -msgstr "`$(...)` で囲まれたパラメータ参照を許可するフィールドもあります。これらは評価" +msgstr "" +"`$(...)` で囲まれたパラメータ参照を許可するフィールドもあります。これらは評価" "され、参照されている値に置き換えられます。" #: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 #, fuzzy msgid "" "References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" -"$(inputs['extractfile'])` are equivalent." +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." msgstr "" -"パラメータリファレンスは、Javascriptの構文のサブセットを使用して記述します。" -" この例では、`$(inputs.extractfile)` 、`$(inputs[\"extractfile\"])` " -"、`$(inputs['extractfile'])` は同等です。" +"パラメータリファレンスは、Javascriptの構文のサブセットを使用して記述しま" +"す。 この例では、`$(inputs.extractfile)` 、`$(inputs[\"extractfile\"])` 、" +"`$(inputs['extractfile'])` は同等です。" #: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 msgid "" "The value of the \"inputs\" variable is the input object provided when the " "CWL tool was invoked." -msgstr "変数 \"inputs \"の値は、CWLツールの起動時に提供された入力オブジェクトです。" +msgstr "" +"変数 \"inputs \"の値は、CWLツールの起動時に提供された入力オブジェクトです。" #: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 msgid "" @@ -3317,7 +3355,8 @@ msgstr "" #: 958178d1fa8843aaa0541e2bb115cfd4 #, fuzzy msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "[Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent) の中に" +msgstr "" +"[Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent) の中に" #: ../../src/topics/parameter-references.md:107 #: 9a6b311ded8d4e43ae635b1b927dbdf2 @@ -3446,9 +3485,8 @@ msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " "(`cwltool` will create the directory for you if it does not exist already):" msgstr "" -"`--cachedir` に `/tmp/cachedir/` " -"を指定して、このワークフローを実行してみましょう（`cwltool` " -"は、ディレクトリがまだ存在しない場合、新規作成します）：" +"`--cachedir` に `/tmp/cachedir/` を指定して、このワークフローを実行してみま" +"しょう（`cwltool` は、ディレクトリがまだ存在しない場合、新規作成します）：" #: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac msgid "" @@ -3512,15 +3550,17 @@ msgstr "" msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the container." -msgstr "CWLランナーの役割のひとつに、入力ファイルのパスをコンテナ内のでの配置位置に合" +msgstr "" +"CWLランナーの役割のひとつに、入力ファイルのパスをコンテナ内のでの配置位置に合" "わせて調整することがあります。" #: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a msgid "" "This example runs a simple Node.js script inside a Docker container which " "will then print \"Hello World\" to the standard output." -msgstr "この例では、Dockerコンテナ内で簡単なNode.jsスクリプトを実行し、標準出力に「" -"Hello World」と表示します。" +msgstr "" +"この例では、Dockerコンテナ内で簡単なNode.jsスクリプトを実行し、標準出力に" +"「Hello World」と表示します。" #: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" @@ -3555,8 +3595,8 @@ msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " "the tool description and the input object on the command line:" msgstr "" -"Javascriptで \"hello.js \"というファイルを作成し、`cwltool` " -"コマンドラインでツール定義と入力オブジェクトを指定して呼び出します：" +"Javascriptで \"hello.js \"というファイルを作成し、`cwltool` コマンドラインで" +"ツール定義と入力オブジェクトを指定して呼び出します：" #: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" @@ -3566,7 +3606,8 @@ msgstr "`hello.js`" msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." -msgstr "CWLランナーがスクリプトを実行するためにDockerコマンドラインを構築していること" +msgstr "" +"CWLランナーがスクリプトを実行するためにDockerコマンドラインを構築していること" "に注目してください。" #: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 @@ -3578,8 +3619,8 @@ msgid "" msgstr "" "この例では、スクリプト`hello.js` のパスは、コンテナの外側では `/home/me/cwl/" "user_guide/hello.js` が、コンテナの内側では`/var/lib/cwl/" -"job369354770_examples/hello.js` です。これは`node` " -"コマンドの呼び出しに反映されているためです。" +"job369354770_examples/hello.js` です。これは`node` コマンドの呼び出しに反映さ" +"れているためです。" #: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 msgid "Workflows" @@ -3603,8 +3644,8 @@ msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier examples." msgstr "" -"CWL定義`echo-uppercase.cwl` は、コマンドラインツール、および先の例で示したExp" -"ressionToolを実行するワークフローを定義しています。" +"CWL定義`echo-uppercase.cwl` は、コマンドラインツール、および先の例で示した" +"ExpressionToolを実行するワークフローを定義しています。" #: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" @@ -3618,8 +3659,8 @@ msgid "" "uppercase.cwl` workflow as a single file:" msgstr "" "コマンドラインツールやExpressionToolは、ワークフローと同じCWLドキュメントに直" -"接記述することも可能です。例えば、`echo-uppercase.cwl` " -"ワークフローを1つのファイルとして書き換えることができます：" +"接記述することも可能です。例えば、`echo-uppercase.cwl` ワークフローを1つの" +"ファイルとして書き換えることができます：" #: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa #, fuzzy @@ -3649,7 +3690,8 @@ msgstr "ワークフローを書く" msgid "" "This workflow extracts a java source file from a tar file and then compiles " "it." -msgstr "このワークフローでは、tarファイルからJavaのソースファイルを取り出し、コンパイ" +msgstr "" +"このワークフローでは、tarファイルからJavaのソースファイルを取り出し、コンパイ" "ルします。" #: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 @@ -3675,16 +3717,16 @@ msgstr "" "[[1st-workflow.cwlを可視化したもの]](https://view.commonwl.org/graph/png/" "github.com/common-workflow-language/user_guide/blob/" "a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" -"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/" -"common-workflow-language/user_guide/blob/" -"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" -"workflow.cwl)" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" +"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" #: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a " "run:" -msgstr "Runの入力データを記述するために、別ファイルのYAMLまたはJSONオブジェクトを使用" +msgstr "" +"Runの入力データを記述するために、別ファイルのYAMLまたはJSONオブジェクトを使用" "します：" #: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda @@ -3695,7 +3737,8 @@ msgstr "`1st-workflow-job.yml`" msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." -msgstr "次に、サンプルとなるJavaファイルを作成し、コマンドラインツールで使用するため" +msgstr "" +"次に、サンプルとなるJavaファイルを作成し、コマンドラインツールで使用するため" "にtarファイルに追加します。" #: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 @@ -3708,8 +3751,9 @@ msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a workflow." msgstr "" -"`cwlVersion` フィールドは、この文書が使用するCWL仕様のバージョンを示します。" -" ` class` フィールドは、この文書がワークフローを記述していることを示します。" +"`cwlVersion` フィールドは、この文書が使用するCWL仕様のバージョンを示しま" +"す。 ` class` フィールドは、この文書がワークフローを記述していることを示しま" +"す。" #: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 #, fuzzy @@ -3733,9 +3777,9 @@ msgid "" "the `compile` step to the workflow output parameter `compiled_class`." msgstr "" "`outputs` セクションでは、ワークフローの出力について記述します。 これは出力" -"パラメータのリストであり、各パラメータは識別子とデータ型から構成されます。 `" -" outputSource` は、`compile` ステップの出力パラメータ`classfile` " -"を、ワークフロー出力パラメータ`compiled_class` に接続します。" +"パラメータのリストであり、各パラメータは識別子とデータ型から構成されます。 " +"` outputSource` は、`compile` ステップの出力パラメータ`classfile` を、ワーク" +"フロー出力パラメータ`compiled_class` に接続します。" #: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 msgid "" @@ -3756,10 +3800,10 @@ msgid "" "parameters, `tarfile` and `extractfile` and one output parameter " "`extracted_file`." msgstr "" -"最初のステップである`untar` は、`tar-param.cwl` を実行します（[パラメータ参照" -"](parameter-references." -"md)で以前説明しました）。このツールは、2つの入力パラメータ、`tarfile` " -"と`extractfile` と1つの出力パラメータ`extracted_file` を持ちます。" +"最初のステップである`untar` は、`tar-param.cwl` を実行します（[パラメータ参" +"照](parameter-references.md)で以前説明しました）。このツールは、2つの入力パラ" +"メータ、`tarfile` と`extractfile` と1つの出力パラメータ`extracted_file` を持" +"ちます。" #: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 msgid "" @@ -3775,8 +3819,9 @@ msgstr "" msgid "" "The `out` section of the workflow step lists the output parameters that are " "expected from the tool." -msgstr "ワークフローステップの`out` " -"セクションには、ツールから期待される出力パラメータが記載されています。" +msgstr "" +"ワークフローステップの`out` セクションには、ツールから期待される出力パラメー" +"タが記載されています。" #: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed msgid "" @@ -3821,15 +3866,15 @@ msgstr "" #: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a msgid "" " \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/nestedworkflows." +"cwl\">\"Visualization \"Visualization" msgstr "" #: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 @@ -3873,9 +3918,9 @@ msgid "" "so we can use hardcoded values `hello.tar` and `Hello.java` in a " "`baseCommand` and the resulting `outputs`:" msgstr "" -"この場合、ステップではパラメータ化するのではなく、`Hello.java` " -"を想定することができるので、`baseCommand` で直接書かれた値`hello.tar` " -"と`Hello.java` を使用でき、結果として`outputs` が得られます：" +"この場合、ステップではパラメータ化するのではなく、`Hello.java` を想定すること" +"ができるので、`baseCommand` で直接書かれた値`hello.tar` と`Hello.java` を使用" +"でき、結果として`outputs` が得られます：" #: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 msgid "" @@ -3931,8 +3976,8 @@ msgid "" msgstr "" "新規ユーザーがscatterを使いたいと思う最も一般的な理由は、異なるサンプルに対し" "て同じ分析を実行することです。最初の例（`hello_world.cwl` ）を呼び出し、ワー" -"クフローへの入力として文字列の配列を受け取る、簡単なワークフローから始めまし" -"ょう：" +"クフローへの入力として文字列の配列を受け取る、簡単なワークフローから始めま" +"しょう：" #: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" @@ -3944,15 +3989,16 @@ msgid "" "Aside from the `requirements` section including `ScatterFeatureRequirement`, " "what is going on here?" msgstr "" -"`requirements` セクションの`ScatterFeatureRequirement` " -"などを含めて、ここはどうなっているのでしょうか。" +"`requirements` セクションの`ScatterFeatureRequirement` などを含めて、ここはど" +"うなっているのでしょうか。" #: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c #, fuzzy msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." -msgstr "まず、ここでのメインワークフローの入力には、文字列の配列が必要であることに注" +msgstr "" +"まず、ここでのメインワークフローの入力には、文字列の配列が必要であることに注" "目してください。" #: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f @@ -3978,8 +4024,8 @@ msgid "" msgstr "" "最初のスキャッターでは、これと同じくらい簡単です！このツールは出力を回収しな" "いので、`outputs: []` を使います。しかし、ワークフローの最終出力に収集する複" -"数の出力があることが予想される場合、それを配列型に更新するようにしてください" -"！" +"数の出力があることが予想される場合、それを配列型に更新するようにしてくださ" +"い！" #: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" @@ -3996,10 +4042,9 @@ msgid "" "calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -"注意点として、[`hello_world.cwl`](../introduction/quick-start.md) " -"は単にメッセージに対して`echo` というコマンドを呼び出します。" -"コマンドラインで `cwltool scatter-workflow.cwl scatter-job.yml` " -"を呼び出すとします：" +"注意点として、[`hello_world.cwl`](../introduction/quick-start.md) は単にメッ" +"セージに対して`echo` というコマンドを呼び出します。コマンドラインで `cwltool " +"scatter-workflow.cwl scatter-job.yml` を呼び出すとします：" #: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f msgid "" @@ -4014,8 +4059,9 @@ msgstr "" msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding the " "following lines instead of `outputs: []`" -msgstr "上記のような簡単なエコーを実行します、`outputs: " -"[]`の代わりに次の行を追加して`stdout` をキャプチャしてみましょう" +msgstr "" +"上記のような簡単なエコーを実行します、`outputs: []`の代わりに次の行を追加して" +"`stdout` をキャプチャしてみましょう" #: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de #, fuzzy @@ -4026,8 +4072,9 @@ msgstr "`hello_world_to_stdout.cwl`" msgid "" "And add a second step that uses `wc` to count the characters in each file. " "See the tool below:" -msgstr "そして、`wc` を使って各ファイルの文字数をカウントする第2ステップを追加します" -"。以下のツールを見てください：" +msgstr "" +"そして、`wc` を使って各ファイルの文字数をカウントする第2ステップを追加しま" +"す。以下のツールを見てください：" #: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a #, fuzzy @@ -4039,7 +4086,8 @@ msgstr "`wc-tool.cwl`" msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under each " "step:" -msgstr "さて、スキャッターはどのように取り入れるのでしょうか？スキャッターフィールド" +msgstr "" +"さて、スキャッターはどのように取り入れるのでしょうか？スキャッターフィールド" "は各ステップの下にあることを思い出してください：" #: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d @@ -4082,7 +4130,8 @@ msgstr "`scatter-nested-workflow.cwl`" msgid "" "Now the scatter acts on a single step, but that step consists of two steps " "so each step is performed in parallel." -msgstr "今、scatter は1つのステップに作用しますが、そのステップは2つのステップで構成" +msgstr "" +"今、scatter は1つのステップに作用しますが、そのステップは2つのステップで構成" "されているので、各ステップは並行して実行されます。" #: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 @@ -4110,8 +4159,9 @@ msgstr "`conditional-workflow.cwl`" msgid "" "The first thing you'll notice is that this workflow is only compatible for " "version 1.2 or greater of the CWL standards." -msgstr "まず、このワークフローはCWL仕様のバージョン1." -"2以降でしか対応していないことがわかります。" +msgstr "" +"まず、このワークフローはCWL仕様のバージョン1.2以降でしか対応していないことが" +"わかります。" #: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 #, fuzzy @@ -4122,9 +4172,9 @@ msgid "" "from the workflow contains a value `< 1` this step will be executed." msgstr "" "ワークフローの最初のステップ（step1）には2つの入力プロパティがあり、条件を満" -"たしたときにfoo.cwlを実行します。新しいプロパティ`when` " -"は、条件の検証が行われる場所です。この場合、ワークフローから`in1` に値`< " -"1` が含まれるときのみ、このステップが実行されます。" +"たしたときにfoo.cwlを実行します。新しいプロパティ`when` は、条件の検証が行わ" +"れる場所です。この場合、ワークフローから`in1` に値`< 1` が含まれるときの" +"み、このステップが実行されます。" #: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 #, fuzzy @@ -4134,10 +4184,10 @@ msgid "" "shown in the log by `INFO [step step1] start` whereas the second step is " "skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -"次のコマンドを実行します。`cwltool cond-wf-003.1.cwl --val 0` " -"この値は最初の条件ステップを通過するため実行され、ログには`INFO [step step1] " -"start` で示されています。一方、2番目のステップは`INFO [step step2] will be " -"skipped` で示されているようにスキップされ ます。" +"次のコマンドを実行します。`cwltool cond-wf-003.1.cwl --val 0` この値は最初の" +"条件ステップを通過するため実行され、ログには`INFO [step step1] start` で示さ" +"れています。一方、2番目のステップは`INFO [step step2] will be skipped` で示さ" +"れているようにスキップされ ます。" #: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec #, fuzzy @@ -4153,8 +4203,9 @@ msgstr "" msgid "" "If no conditions are met for example when using `--val 2` the workflow will " "raise a permanentFail." -msgstr "`--val 2` を使用した場合など、条件を満たさない場合は、ワークフローはpermanent" -"Failを発生させ、失敗となります。" +msgstr "" +"`--val 2` を使用した場合など、条件を満たさない場合は、ワークフローは" +"permanentFailを発生させ、失敗となります。" #: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" @@ -4167,13 +4218,14 @@ msgid "" "humans. This guide introduces the features of YAML that are relevant when " "writing CWL descriptions and input parameter files." msgstr "" -"[YAML][yaml]は、コンピュータと人間の両方が読むことができるように設計されたフ" -"ァイル形式です。本ガイドでは、CWL定義や入力パラメータファイルを書く際に関連す" -"るYAMLの機能を紹介します。" +"[YAML][yaml]は、コンピュータと人間の両方が読むことができるように設計された" +"ファイル形式です。本ガイドでは、CWL定義や入力パラメータファイルを書く際に関連" +"するYAMLの機能を紹介します。" #: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." -msgstr "すでにYAMLに慣れている方は、このセクションを読み飛ばしてもかまいません。" +msgstr "" +"すでにYAMLに慣れている方は、このセクションを読み飛ばしてもかまいません。" #: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea msgid "Contents" @@ -4223,8 +4275,8 @@ msgid "" msgstr "" "上記のYAMLは4つのキー -`first_name`,`last_name`,`age_years`, `home` - と4つの" "それぞれの値を定義しています。値は、文字列、数値（整数、浮動小数点、科学的表" -"現）、ブール値（`true` または`false` " -"）、またはより複雑な入れ子型（下記参照）にすることができます。" +"現）、ブール値（`true` または`false` ）、またはより複雑な入れ子型（下記参照）" +"にすることができます。" #: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 #, fuzzy @@ -4237,9 +4289,9 @@ msgid "" "to specify a fixed numeric value to a command, make sure that you wrap that " "numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -"値は引用符で括ることができますが、意味が変わってきます。例えば、`\"1234\"` " -"は文字列として扱われ、`1234` は整数値として扱われます。CWLでは、`baseCommand`" -" のすべての部分が文字列でなければならないので、コマンドに固定した数値を指定す" +"値は引用符で括ることができますが、意味が変わってきます。例えば、`\"1234\"` は" +"文字列として扱われ、`1234` は整数値として扱われます。CWLでは、`baseCommand` " +"のすべての部分が文字列でなければならないので、コマンドに固定した数値を指定す" "る場合は、その数値を引用符で囲むようにしてください：[echo, \"42\"]`." #: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 @@ -4254,16 +4306,17 @@ msgid "" "the YAML. For example:" msgstr "" "`#` を使って、CWL定義と入力パラメータファイルにコメントを追加することができま" -"す。` #` の右側にある文字は、YAML " -"を解釈するプログラムによって無視されます。たとえば、次のようになります：" +"す。` #` の右側にある文字は、YAML を解釈するプログラムによって無視されます。" +"たとえば、次のようになります：" #: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d #, fuzzy msgid "" "If there is anything on the line before the comment, be sure to add at least " "one space before the `#`!" -msgstr "同じ行内のコメントの前に何かある場合は、必ず`#` " -"の前に少なくとも1つのスペースを追加してください！" +msgstr "" +"同じ行内のコメントの前に何かある場合は、必ず`#` の前に少なくとも1つのスペース" +"を追加してください！" #: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf #, fuzzy @@ -4353,8 +4406,8 @@ msgid "" "in CWL." msgstr "" "[Learn YAML in Y Minutes][yaml-y-mins] リファレンスは、CWLでは有効でない機能" -"もカバーしていますが、このガイドを書く間、私たちにとって非常に役に立ちました" -"。" +"もカバーしていますが、このガイドを書く間、私たちにとって非常に役に立ちまし" +"た。" #: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" @@ -4367,8 +4420,8 @@ msgid "" "list." msgstr "" "これは、CWL コミュニティによって提供されたチュートリアルのリストです。リスト" -"に他のチュートリアルを追加したい場合は、メニューの`Edit this page` " -"リンクを使用してください。" +"に他のチュートリアルを追加したい場合は、メニューの`Edit this page` リンクを使" +"用してください。" #: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" From 480459a29c4e6375589ae3b1219b374c658ca336 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Sat, 18 Nov 2023 15:53:49 +0100 Subject: [PATCH 101/179] Translated using Weblate (Japanese) (#438) Currently translated at 51.3% (307 of 598 strings) Translated using Weblate (Japanese) Currently translated at 50.6% (303 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 100 ++++++++++++++++++--------- 1 file changed, 68 insertions(+), 32 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 83be4dd6..86996731 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,16 +8,16 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-11-09 05:34+0000\n" +"PO-Revision-Date: 2023-11-18 05:11+0000\n" "Last-Translator: Manabu ISHII \n" -"Language-Team: Japanese \n" +"Language-Team: Japanese \n" "Language: ja\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.2-dev\n" +"X-Generator: Weblate 5.2\n" #: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" @@ -273,15 +273,15 @@ msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "ある型の配列を期待する入力に１つの値を与える" #: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d -#, fuzzy msgid "" "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" "Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow." -"html#MultipleInputFeatureRequirement) と [`linkMerge: merge_nested`](https://" -"www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)を一緒に使います。" +"html#MultipleInputFeatureRequirement) と [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)を一緒に使います" #: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" @@ -299,10 +299,8 @@ msgstr "" "アイテムリストでラップされなければなりません。" #: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 -#, fuzzy msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "" -"つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです。" +msgstr "つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです" #: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 #, fuzzy @@ -445,9 +443,8 @@ msgstr "`-` (ハイフン文字、引き算の記号)が原因で発生した問 #: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" -"このエラーを修正するには、`-` (ハイフン) を`_` (アンダースコア) に変更してく" -"ださい。" +msgstr "このエラーを修正するには、`-` (ハイフン) を`_` (アンダースコア) " +"に変更してください" #: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d msgid "" @@ -958,12 +955,18 @@ msgid "CWL Runner" msgstr "CWL Runner" #: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +#, fuzzy msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL community. " "It is also the CWL reference runner, which means it must support everything " "in the current CWL specification, {{ cwl_version }}." msgstr "" +"CWL ワークフローを実行するために最初に必要なものは、CWL runnerです。`cwltool`" +" は、CWL コミュニティによって維持されている Python " +"オープンソース・プロジェクトです。これはCWL reference runner(訳注: " +"CWLの参照実装)でもあり、現在のCWL仕様{{ cwl_version " +"}}のすべてをサポートしなければならないことを意味します。" #: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 msgid "" @@ -978,9 +981,8 @@ msgstr "" "`cwltool` をインストールします：" #: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d -#, fuzzy msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "`pip` と `venv` での `cwltool` のインストール" +msgstr "`pip` と `venv` での `cwltool` のインストール。" #: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 #, fuzzy @@ -1048,8 +1050,9 @@ msgid "" "The CWL community publishes a Python package with the name `cwlref-runner` " "that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -"CWLコミュニティは、`cwlref-runner` という名前のPythonパッケージを公開してお" -"り、`cwltool` のエイリアスを`cwl-runner` という名前でインストールします。" +"CWLコミュニティは、`cwlref-runner` " +"という名前のPythonパッケージを公開しており、`cwltool` のエイリアスを`cwl-" +"runner` という名前でインストールします" #: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." @@ -2081,7 +2084,7 @@ msgstr "次に、`expression.cwl` を実行することができます：" #: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" -msgstr "`expression.cwl` を実行する。" +msgstr "`expression.cwl` を実行する" #: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 msgid "" @@ -2559,7 +2562,7 @@ msgstr "`metadata_example.cwl`" #: ../../src/topics/metadata-and-authorship.md:22 #: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" -msgstr "このCWL定義に相当するものをコマンドライン形式にすると" +msgstr "このCWL定義に相当するものをコマンドライン形式にすると:" #: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" @@ -2715,6 +2718,9 @@ msgid "" "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" +"ブール型はフラグとして扱われます。 入力パラメータ \"example_flag \"が \"true" +" \"の場合、コマンドラインに`prefix` が追加されます。 " +"falseの場合、フラグは付加されません。" #: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 msgid "" @@ -2723,6 +2729,9 @@ msgid "" "before the parameter . In the example above, this is rendered as `--example-" "string hello`." msgstr "" +"文字列型は、コマンドライン上ではリテラル値として与えられます。 ` prefix` は" +"オプションです。与えられた場合、コマンドライン上のパラメータの前に別の引数と" +"して与えられます。 上の例では、`--example-string hello` と与えられます。" #: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e msgid "" @@ -2820,8 +2829,9 @@ msgid "" msgstr "" #: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +#, fuzzy msgid "Inclusive and Exclusive Inputs" -msgstr "" +msgstr "包括的入力と排他的入力" #: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d msgid "" @@ -2877,12 +2887,17 @@ msgid "Exclusive Input Parameters with Expressions" msgstr "式で入力パラメータを排他的に指定する" #: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +#, fuzzy msgid "" "If you use exclusive input parameters combined with expressions, you need to " "be aware that the `inputs` JavaScript object will contain one of the " "exclusive input values. This means that you might need to use an **or** " "boolean operator to check which values are present." msgstr "" +"排他的入力パラメータを式と組み合わせて使用する場合、`inputs` JavaScript オブ" +"ジェクトに排他的入力値のいずれかが含まれることを意識する必要があります。つま" +"り、**or** のブーリアン演算子を使用して、どの値が存在するかをチェックする必要" +"がある場合があります。" #: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb #, fuzzy @@ -2922,6 +2937,7 @@ msgstr "" "ロー実行時に失敗することになります。" #: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +#, fuzzy msgid "" "To correct it, you must remember to use an or operator in your JavaScript " "expression when using exclusive parameters, or any parameter that allows " @@ -2929,11 +2945,16 @@ msgid "" "file_format || 'auto')`, to have a default value if none was provided in the " "command line or job input file." msgstr "" +"これを修正するには、排他的パラメータ、または`null` " +"を許可するパラメータを使用する場合、JavaScript 式で or " +"演算子を使用することを忘れてはなりません。たとえば、式を`$(" +"inputs.file_format || 'auto')` に変更すると、コマンドラインやジョブ入力ファイ" +"ルで何も指定されていない場合にデフォルト値を持つようになります。" #: ../../src/topics/metadata-and-authorship.md:1 #: d33aa2353ad44fb885d3a1ee48263dc4 msgid "Metadata and Authorship" -msgstr "" +msgstr "メタデータと著者" #: ../../src/topics/metadata-and-authorship.md:3 #: cd64d2d828834cbbb24ea5358caf5405 @@ -2970,6 +2991,7 @@ msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 #: cb9980db4e5f4c74b01c2dec6d5e92d0 +#, fuzzy msgid "" "For those that are highly motivated, it is also possible to annotate your " "tool with a much larger amount of metadata. This example includes EDAM " @@ -2977,6 +2999,10 @@ msgid "" "hardware requirements in order to use the tool, and a few more metadata " "fields." msgstr "" +"高いモチベーションを持つ人であれば、ツールにもっと多くのメタデータを付与する" +"ことも可能です。この例では、EDAMオントロジーのタグをキーワードとして含み（関" +"連するツールのグループ化が可能）、ツールを使用するために必要なハードウェアの" +"ヒントや、さらにいくつかのメタデータフィールドがあります。" #: ../../src/topics/metadata-and-authorship.md:35 #: 2dfbd4d580044ed083992f3ceb1bc64e @@ -3043,14 +3069,19 @@ msgstr "" #: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" -msgstr "`cwltool` は、どうやってoperationsを実行するかを知りません。" +msgstr "`cwltool` は、どうやってoperationsを実行するかを知りません" #: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +#, fuzzy msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A " "CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" +"CWL runnerは、操作を具体的なステップにバインドする方法を思いつくかもしれませ" +"ん。例えば、CWL runnerは、" +"異なるワークフローエンジンで実行されるステップに対応するIDを持つ抽象的な " +"operation を使用することができます。" #: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de msgid "Outputs" @@ -3099,6 +3130,10 @@ msgid "" "_array of strings_. The first element is the command to run, and any " "subsequent elements are mandatory command line arguments" msgstr "" +"これまでの例では、`baseCommand` " +"は単なる文字列で、引数はCWL入力として渡していました。単一の文字列の代わりに、" +"文字列の配列__ を使用することができます。 最初の要素は実行するコマンドで、そ" +"れ以降の要素は必須のコマンドライン引数です。" #: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" @@ -3125,7 +3160,8 @@ msgstr "" msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." -msgstr "" +msgstr "`outputBinding` " +"フィールドには、各出力パラメータの値の設定方法が記述されています。" #: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 msgid "" @@ -3133,10 +3169,13 @@ msgid "" "you don't know name of the file in advance, you can use a wildcard pattern " "like `glob: '*.txt'`." msgstr "" +"`glob` フィールドは、出力ディレクトリ内のファイル名で構成されます。ファイル名" +"が予め分からない場合は、`glob: '*.txt'` " +"のようにワイルドカードパターンを使用することができます。" #: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" -msgstr "" +msgstr "標準出力をキャプチャする" #: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 #, fuzzy @@ -3453,9 +3492,8 @@ msgstr "" "いくつかは他のCWLランナーにも適用されるかもしれません。" #: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da -#, fuzzy msgid "Run `cwltool` with `cachedir`" -msgstr "`cwltool` を`cachedir` で実行する。" +msgstr "`cwltool` を`cachedir` で実行する" #: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 msgid "" @@ -3702,7 +3740,7 @@ msgstr "`1st-workflow.cwl`" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 #: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" -msgstr "1st-workflow.cwlの可視化。" +msgstr "1st-workflow.cwlの可視化" #: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 #, fuzzy @@ -3984,13 +4022,12 @@ msgid "`scatter-workflow.cwl`" msgstr "`scatter-workflow.cwl`" #: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 -#, fuzzy msgid "" "Aside from the `requirements` section including `ScatterFeatureRequirement`, " "what is going on here?" msgstr "" -"`requirements` セクションの`ScatterFeatureRequirement` などを含めて、ここはど" -"うなっているのでしょうか。" +"`requirements` セクションの`ScatterFeatureRequirement` " +"などを含めて、ここはどうなっているのでしょうか？" #: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c #, fuzzy @@ -4371,13 +4408,12 @@ msgid "JSON Style" msgstr "JSON形式" #: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d -#, fuzzy msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " "can also be defined in YAML using the native JSON syntax. For example:" msgstr "" "YAMLは[JavaScript Object Notation (JSON)][json]に基づいています。マップと配列" -"は、JSON構文を使ってYAMLで定義することもできます。例えば" +"は、JSON構文を使ってYAMLで定義することもできます。例えば:" #: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc #, fuzzy From f04dfe31292cbffd6866e1829e6ab00289959055 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Fri, 24 Nov 2023 10:08:22 +0100 Subject: [PATCH 102/179] Translated using Weblate (Japanese) (#439) Currently translated at 52.6% (315 of 598 strings) Translated using Weblate (Japanese) Currently translated at 51.8% (310 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 38 ++++++++++++++++++++-------- 1 file changed, 28 insertions(+), 10 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 86996731..a00eac3a 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-11-18 05:11+0000\n" +"PO-Revision-Date: 2023-11-22 21:01+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.2\n" +"X-Generator: Weblate 5.2.1-rc\n" #: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" @@ -3132,8 +3132,8 @@ msgid "" msgstr "" "これまでの例では、`baseCommand` " "は単なる文字列で、引数はCWL入力として渡していました。単一の文字列の代わりに、" -"文字列の配列__ を使用することができます。 最初の要素は実行するコマンドで、そ" -"れ以降の要素は必須のコマンドライン引数です。" +"文字列の配列__ を使用することができます。 " +"最初の要素は実行するコマンドで、それ以降の要素は必須のコマンドライン引数です" #: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" @@ -3461,7 +3461,7 @@ msgstr "" #: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" -msgstr "" +msgstr "入力ファイルのステージング" #: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 msgid "" @@ -3475,11 +3475,11 @@ msgstr "" #: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" -msgstr "" +msgstr "`linkfile.cwl`" #: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" -msgstr "" +msgstr "トラブルシューティング" #: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 msgid "" @@ -3609,11 +3609,15 @@ msgid "`docker-job.yml`" msgstr "`docker-job.yml`" #: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +#, fuzzy msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that is " "really new is the `dockerRequirement` section." msgstr "" +"これを実行する前に、これを分解して、いくつか細かく何をするのかを見てみましょ" +"う。 この大部分は以前のセクションで説明したもので、本当に新しいのは`dockerRe" +"quirement` の部分だけです。" #: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 msgid "" @@ -3873,7 +3877,7 @@ msgstr "" #: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" -msgstr "" +msgstr "ネストされたワークフロー" #: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e msgid "" @@ -3882,16 +3886,20 @@ msgid "" "be used as a step in another CWL workflow, if the workflow engine supports " "the `SubworkflowFeatureRequirement`:" msgstr "" +"ワークフローは、複数のツールを組み合わせてより大きな処理を実行するための方法" +"です。ワークフローエンジンが`SubworkflowFeatureRequirement` " +"をサポートしている場合、CWL ワークフローを別の CWL " +"ワークフローのステップとすることができます ：" #: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" -msgstr "" +msgstr "`1st-workflow.cwl` をネストしたワークフローの例を紹介します：" #: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" -msgstr "" +msgstr "`nestedworkflows.cwl`" #: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 msgid "" @@ -3900,6 +3908,11 @@ msgid "" "on the right. In purple we see the fixed string `\"Hello.java\"` being " "supplied as the `name_of_file_to_extract`." msgstr "" +"この2ステップのワークフローは、`create-tar` " +"ステップから始まり、オレンジ色の`compile` " +"ステップに接続されています。`compile` " +"は、右図にある別のワークフローです。紫色では、固定文字列`\"Hello.java\"` " +"が`name_of_file_to_extract` として与えられているのがわかります。" #: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a msgid "" @@ -3916,12 +3929,17 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +#, fuzzy msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " "CWL file is included with `run`. The workflow inputs (`tarball` and " "`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " "to become the step's input/outputs." msgstr "" +"CWL`Workflow` は、`CommandLineTool` を`step` として使用することができ、その " +"CWL ファイルは`run` に記述されます。ワークフローの入力（`tarball` " +"および`name_of_file_to_extract` ）と出力（`compiled_class` " +"）は、ステップの入力/出力になるようにマッピングすることができます。" #: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 msgid "" From 3e4f3824578a3470095969d164e8bf3de5bb80de Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 24 Nov 2023 10:17:12 +0100 Subject: [PATCH 103/179] gh-actions: permission fix? --- .github/workflows/ci-tests.yml | 2 +- .github/workflows/gh-pages.yaml | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml index 9cb2de82..b29d0742 100644 --- a/.github/workflows/ci-tests.yml +++ b/.github/workflows/ci-tests.yml @@ -39,6 +39,6 @@ jobs: **/setup.cfg - run: pip install -U pip setuptools wheel typing - - run: pip install -e .[all] + - run: pip install -e ".[all]" - run: make RUNNER=cwltool unittest-examples diff --git a/.github/workflows/gh-pages.yaml b/.github/workflows/gh-pages.yaml index fcec7837..ed5fbed0 100644 --- a/.github/workflows/gh-pages.yaml +++ b/.github/workflows/gh-pages.yaml @@ -12,6 +12,8 @@ jobs: # Ref: https://stackoverflow.com/questions/57989790/using-github-actions-to-publish-documentation deploy: runs-on: ubuntu-latest + permissions: + contents: write steps: - uses: actions/checkout@v3 @@ -30,7 +32,7 @@ jobs: python3 -m pip install --upgrade pip - name: Get pip cache dir id: pip-cache - run: echo "::set-output name=dir::$(pip cache dir)" + run: echo "dir=$(pip cache dir)" >> "$GITHUB_OUTPUT" - name: Cache dependencies uses: actions/cache@v3 @@ -40,7 +42,7 @@ jobs: restore-keys: | ${{ runner.os }}-pip- - name: Install dependencies - run: python3 -m pip install -U -e .[all] + run: python3 -m pip install -U -e ".[all]" - name: pre-pull container images run: make container-pull From ff548f2ecd42f66a3948e7c6bc450b4c9e33d6da Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 24 Nov 2023 10:24:26 +0100 Subject: [PATCH 104/179] gh-pages: simplify --- .github/workflows/gh-pages.yaml | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/.github/workflows/gh-pages.yaml b/.github/workflows/gh-pages.yaml index ed5fbed0..40068c61 100644 --- a/.github/workflows/gh-pages.yaml +++ b/.github/workflows/gh-pages.yaml @@ -25,22 +25,8 @@ jobs: uses: actions/setup-python@v4 with: python-version: '3.9' + cache: pip - - name: Upgrade pip - run: | - # pip >= 20.1 so we can use ``pip cache dir`` - python3 -m pip install --upgrade pip - - name: Get pip cache dir - id: pip-cache - run: echo "dir=$(pip cache dir)" >> "$GITHUB_OUTPUT" - - - name: Cache dependencies - uses: actions/cache@v3 - with: - path: ${{ steps.pip-cache.outputs.dir }} - key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} - restore-keys: | - ${{ runner.os }}-pip- - name: Install dependencies run: python3 -m pip install -U -e ".[all]" From d0e191c622138eb0d5b6a7d3ebbd9db3bd37df10 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 24 Nov 2023 10:40:50 +0100 Subject: [PATCH 105/179] sphinx: fix warnings --- Makefile | 2 +- src/conf.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 183468f2..0c85e3bb 100644 --- a/Makefile +++ b/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line, and also # from the environment for the first two. -#SPHINXOPTS = # was "-W" (turn warnings into errors) +SPHINXOPTS = # was "-W" (turn warnings into errors) SPHINXBUILD = sphinx-build SOURCEDIR = src BUILDDIR = _build diff --git a/src/conf.py b/src/conf.py index 38617d94..600fcc04 100644 --- a/src/conf.py +++ b/src/conf.py @@ -218,7 +218,8 @@ "navigation_depth": 2, "collapse_navigation": True, "show_prev_next": True, - "footer_items": ["copyright"], + "footer_start": ["copyright", "sphinx-version"], + "footer_end": ["theme-version"], } html_context = { From c93e12fefa6f8cabacad62a44193cb1ad0702c75 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 24 Nov 2023 10:55:19 +0100 Subject: [PATCH 106/179] avoid things that look like HTML tags --- src/introduction/prerequisites.md | 4 ++-- src/introduction/quick-start.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/introduction/prerequisites.md b/src/introduction/prerequisites.md index 2a3b8603..1dc47954 100644 --- a/src/introduction/prerequisites.md +++ b/src/introduction/prerequisites.md @@ -141,8 +141,8 @@ rest of the file. The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is -considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` -looks for the `` program in the system `PATH`, +considered a good practice to use `/usr/bin/env [executable]` rather than using a hard-coded location, since `/usr/bin/env [executable]` +looks for the `[executable]` program in the system `PATH`, ``` ## Text Editor diff --git a/src/introduction/quick-start.md b/src/introduction/quick-start.md index 84d52dc9..0e18127b 100644 --- a/src/introduction/quick-start.md +++ b/src/introduction/quick-start.md @@ -51,7 +51,7 @@ of software and libraries used for following the rest of this user guide. ## Running "Hello World" The usage of the `cwltool` command-line executable is basically -`cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the +`cwltool [OPTIONS] [CWL_DOCUMENT] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option: ```{runcmd} cwltool hello_world.cwl From 904f87a2b15c97a1e85cfb24ad9c20aa5a9e1e1d Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 24 Nov 2023 11:08:18 +0100 Subject: [PATCH 107/179] gh-pages: render multiple langs --- .github/workflows/gh-pages.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/gh-pages.yaml b/.github/workflows/gh-pages.yaml index 40068c61..5bd84a2f 100644 --- a/.github/workflows/gh-pages.yaml +++ b/.github/workflows/gh-pages.yaml @@ -34,7 +34,11 @@ jobs: run: make container-pull - name: Build documentation - run: make html + run: | + make html + for lang in en es pt_BR pt_PT ja zh_Hans; do + make html BUILDDIR=_build/${lang} SPHINXOPTS="-D language=${lang}" + done - name: Deploy uses: peaceiris/actions-gh-pages@v3 From 047d71f04368466a8320b0126ec5c43779c7800f Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 24 Nov 2023 11:58:36 +0100 Subject: [PATCH 108/179] gh-pages: consolidate language builds into one directory --- .github/workflows/gh-pages.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/gh-pages.yaml b/.github/workflows/gh-pages.yaml index 5bd84a2f..2569a38a 100644 --- a/.github/workflows/gh-pages.yaml +++ b/.github/workflows/gh-pages.yaml @@ -35,9 +35,11 @@ jobs: - name: Build documentation run: | + mkdir -p _build/html make html for lang in en es pt_BR pt_PT ja zh_Hans; do - make html BUILDDIR=_build/${lang} SPHINXOPTS="-D language=${lang}" + make html BUILDDIR=_build/${lang} SPHINXOPTS="-D language=${lang} -j auto" + mv _build/${lang}/html _build/html/${lang} done - name: Deploy From 801d34c8c643e7489125f3e83a01e74d80563ed3 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Fri, 1 Dec 2023 08:39:26 +0100 Subject: [PATCH 109/179] Translations update from Hosted Weblate (#441) * Translated using Weblate (Japanese) Currently translated at 53.5% (320 of 598 strings) Translated using Weblate (Japanese) Currently translated at 53.0% (317 of 598 strings) Translated using Weblate (Japanese) Currently translated at 52.8% (316 of 598 strings) Translated using Weblate (Japanese) Currently translated at 52.6% (315 of 598 strings) Translated using Weblate (Japanese) Currently translated at 51.8% (310 of 598 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 53.6% (321 of 598 strings) Co-authored-by: Michael Crusoe Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 54.1% (324 of 598 strings) Translation: Common Workflow Language/CWL User Guide Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ * Translated using Weblate (Japanese) Currently translated at 56.1% (336 of 598 strings) Translation: Common Workflow Language/CWL User Guide Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ --------- Co-authored-by: Manabu ISHII Co-authored-by: Michael Crusoe --- locales/ja/LC_MESSAGES/user_guide.po | 208 ++++++++++++++++++++------- 1 file changed, 153 insertions(+), 55 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index a00eac3a..56c64d04 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-11-22 21:01+0000\n" +"PO-Revision-Date: 2023-12-01 01:10+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.2.1-rc\n" +"X-Generator: Weblate 5.3-dev\n" #: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" @@ -160,6 +160,10 @@ msgid "" "from another step in a workflow, and don't want to work with the default " "names that these files were given when they were created." msgstr "" +"この例では、ツール定義の一部として、入力ファイルの名前を変更する方法を説明し" +"ます。これは、ワークフローの別のステップで作成されたファイルを使用する場合に" +"、これらのファイルが作成されたときに与えられたデフォルトの名前を使用して作業" +"したくない場合に便利です。" #: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" @@ -279,9 +283,8 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow." -"html#MultipleInputFeatureRequirement) と [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)を一緒に使います" +"html#MultipleInputFeatureRequirement) と [`linkMerge: merge_nested`](https://" +"www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)を一緒に使います" #: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" @@ -300,7 +303,8 @@ msgstr "" #: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです" +msgstr "" +"つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです" #: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 #, fuzzy @@ -443,8 +447,9 @@ msgstr "`-` (ハイフン文字、引き算の記号)が原因で発生した問 #: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "このエラーを修正するには、`-` (ハイフン) を`_` (アンダースコア) " -"に変更してください" +msgstr "" +"このエラーを修正するには、`-` (ハイフン) を`_` (アンダースコア) に変更してく" +"ださい" #: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d msgid "" @@ -962,11 +967,11 @@ msgid "" "It is also the CWL reference runner, which means it must support everything " "in the current CWL specification, {{ cwl_version }}." msgstr "" -"CWL ワークフローを実行するために最初に必要なものは、CWL runnerです。`cwltool`" -" は、CWL コミュニティによって維持されている Python " -"オープンソース・プロジェクトです。これはCWL reference runner(訳注: " -"CWLの参照実装)でもあり、現在のCWL仕様{{ cwl_version " -"}}のすべてをサポートしなければならないことを意味します。" +"CWL ワークフローを実行するために最初に必要なものは、CWL runnerです。" +"`cwltool` は、CWL コミュニティによって維持されている Python オープンソース・" +"プロジェクトです。これはCWL reference runner(訳注: CWLの参照実装)でもあり、現" +"在のCWL仕様{{ cwl_version }}のすべてをサポートしなければならないことを意味し" +"ます。" #: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 msgid "" @@ -1013,6 +1018,12 @@ msgid "" "description like the above) pass the `--validate` option to the `cwltool` " "command:" msgstr "" +"`cwltool` コマンドには、CWL ツールおよびワークフロー定義を検証するオプション" +"があります。このオプションは、CWL文書を解析し、構文エラーを探し、ワークフロー" +"記述がCWL標準に準拠しているかどうかを検証します。ただし、これらの操作は、ド" +"キュメントを実行せずに行われます。CWLワークフロー（または上記のようなスタンド" +"アロンコマンドラインツールの記述も）を検証するには、`cwltool` コマンドに`--" +"validate` オプションを渡します：" #: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." @@ -1044,15 +1055,20 @@ msgid "" "or user to point to the preferred CWL implementation. This is convenient for " "environments with multiple CWL runners." msgstr "" +"`cwl-runner` は、CWL準拠のランナーに対する、実装にとらわれないエイリアスで" +"す。これは、`cwl-runner` エイリアスコマンドを独立して呼び出すことができ、特定" +"のCWLランナープログラム名に依存しないことを意味します。ユーザーは、`cwltool` " +"のようなCWLランナーを直接呼び出す代わりに、`cwl-runner` を呼び出すことができ" +"ます。`cwl-runner` は、システム管理者またはユーザーによってインストールされ、" +"好みのCWL実装を指し示す。これは、複数のCWLランナーがある環境では便利です。" #: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 msgid "" "The CWL community publishes a Python package with the name `cwlref-runner` " "that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -"CWLコミュニティは、`cwlref-runner` " -"という名前のPythonパッケージを公開しており、`cwltool` のエイリアスを`cwl-" -"runner` という名前でインストールします" +"CWLコミュニティは、`cwlref-runner` という名前のPythonパッケージを公開してお" +"り、`cwltool` のエイリアスを`cwl-runner` という名前でインストールします" #: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." @@ -1124,6 +1140,12 @@ msgid "" "coded location, since `/usr/bin/env ` looks for the " "`` program in the system `PATH`," msgstr "" +"*shebang* は、スクリプトの冒頭の2文字列`#!` のことです。スクリプトが実行可能" +"な場合、オペレーティングシステムは、shebangの後に指定された実行可能ファイルを" +"使用してスクリプトを実行します。`/usr/bin/env ` は` `" +" プログラムをシステムの`PATH` " +"で探すので、ハードコードされた場所を使うよりも`/usr/bin/env ` を" +"使うことが良い習慣と考えられています、" #: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" @@ -1135,6 +1157,9 @@ msgid "" "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" +"CWLではどんなテキストエディタでも使えますが、シンタックスハイライトのために、" +"YAMLをサポートするエディタをお勧めします。人気のあるエディタは、Visual " +"Studio Code、Sublime、WebStorm、vim/neovim、そしてEmacsです。" #: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 msgid "" @@ -1142,12 +1167,18 @@ msgid "" "integration with CWL, and features such as customized syntax highlighting " "and better auto-complete:" msgstr "" +"Visual Studio CodeとWebStormには、CWLとの統合を実現する拡張機能があり、カスタ" +"マイズされたシンタックスハイライトやより優れた自動補完などの機能が用意されて" +"います：" #: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +#, fuzzy msgid "" "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" +"Benten(弁天)（CWL）プラグインを使ったVisual Studio Code -" #: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 msgid "" @@ -1251,19 +1282,27 @@ msgid "`hello_world.cwl`" msgstr "`hello_world.cwl`" #: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +#, fuzzy msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the " "same result as the command-line `echo \"Hello World\"`." msgstr "" +"上記の例は、`echo` のコマンドラインツールのラッパーに過ぎません。デフォルトの" +"入力値で上記のワークフローを実行すると、コマンドラインと同じ結果が得られます`" +"echo \"Hello World\"`." #: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +#, fuzzy msgid "" "In CWL, there is a distinction between a command-line tool and a workflow. " "But for the sake of simplicity, we are using the term “workflow” here. You " "will learn more about this in the [basic concepts](basic-concepts.md) " "section." msgstr "" +"CWLでは、CommandLineToolとWorkflowは区別されています。しかし、ここでは簡略化" +"のため、「ワークフロー」という用語を使用しています。これについては、[基本概念" +"](basic-concepts.md)のセクションで詳しく説明します。" #: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" @@ -1292,10 +1331,14 @@ msgid "" "`cwltool` and a more detailed list of software and libraries used for " "following the rest of this user guide." msgstr "" +"pipコマンドを使用してcwltoolをインストールしてもうまくいかない場合は、[前提条" +"件](prerequisites.md)セクションに、`cwltool` をインストールする他の方法と、こ" +"のユーザーガイドの残りの部分を追うために使用するソフトウェアとライブラリのよ" +"り詳細なリストがあります。" #: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" -msgstr "" +msgstr "\"Hello World\"を実行する" #: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe msgid "" @@ -1303,6 +1346,9 @@ msgid "" "[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " "workflow without specifying any option:" msgstr "" +"`cwltool` コマンドライン実行ファイルの使い方は、基本的に`cwltool [OPTIONS] " +" [INPUTS_OBJECT]`です。`hello_world.cwl` " +"Workflowは、オプションを指定せずに実行することができます：" #: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." @@ -1440,6 +1486,7 @@ msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 #: d8110ed19da94ad8a9f56e7006c4a2cf +#, fuzzy msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files in " @@ -1447,6 +1494,12 @@ msgid "" "directories in which they appear) may be read-only, so we need to instruct " "\"javac\" to write the class file to the designated output directory instead." msgstr "" +"この例では、Javaコンパイラを使用して、javaソースファイルをクラスファイルにコ" +"ンパイルするようにラップします。 デフォルトでは、\"javac \"はソース" +"・ファイルと同じディレクトリにクラス・ファイルを作成します。 しかし、CWLの入" +"力ファイル（およびそのディレクトリ）は読み取り専用である場合があるので、代わ" +"りに指定された出力ディレクトリにクラスファイルを書き込むように「javac」に指示" +"する必要があります。" #: ../../src/topics/additional-arguments-and-parameters.md:13 #: a74935dc31664e979ca8f90a6a4ba53c @@ -1553,7 +1606,7 @@ msgstr "" #: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" +msgstr "_SPDX 識別子を持つライセンスのメタデータフィールドの例：_" #: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 msgid "" @@ -1783,11 +1836,15 @@ msgstr "実行時にファイルを作成する" #: ../../src/topics/creating-files-at-runtime.md:3 #: 0cf51b6da6884065ae42032abc20eb0d +#, fuzzy msgid "" "Sometimes you need to create a file on the fly from input parameters, such " "as tools that expect to read their input configuration from a file rather " "than the command line parameters, or need a small wrapper shell script." msgstr "" +"コマンドラインパラメーターではなく、ファイルから入力設定を読み込むことを期待" +"するツールや、小さなラッパーシェルスクリプトが必要な場合など、入力パラメータ" +"ーからその場でファイルを作成する必要があることがあります。" #: ../../src/topics/creating-files-at-runtime.md:7 #: 2df3a3a9094d4b79b1d5dd99195f3bff @@ -1803,11 +1860,15 @@ msgstr "`createfile.cwl`" #: ../../src/topics/creating-files-at-runtime.md:15 #: cfffc518ba6e4ed1a80762ed6f7d25df +#, fuzzy msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the value " "at the input `message`." msgstr "" +"`$(inputs.message)` のような [Expressions](../topics/expressions.md)は、ファ" +"イルを作成する前にCWLエンジンによって展開されます。ここでは、入力パラメータ`m" +"essage` に値を挿入します。" #: ../../src/topics/creating-files-at-runtime.md:20 #: 9454a330b9324744b89448f2694b1b03 @@ -1920,6 +1981,8 @@ msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to be " "used in the table conversion are imported as a custom object:" msgstr "" +"29行目の`inputs:table_type` で、テーブル変換で使用できるテーブルオプションの" +"リストがカスタムオブジェクトとしてインポートされます：" #: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e msgid "" @@ -1947,6 +2010,9 @@ msgid "" "imported. Imports are described in `requirements:SchemaDefRequirement`, as " "below in the example `custom-types.cwl` description:" msgstr "" +"カスタム型をCWL定義で使用するためには、インポートする必要があります。インポー" +"トについては、`requirements:SchemaDefRequirement` で定義されており、例として" +"`custom-types.cwl` の定義にあるように、インポートされます：" #: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c msgid "" @@ -2041,6 +2107,7 @@ msgstr "" "Javascriptを使用できます。" #: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +#, fuzzy msgid "" "JavaScript expressions should only be used when absolutely necessary. When " "manipulating file names, extensions, paths etc, consider whether one of the " @@ -2048,6 +2115,11 @@ msgid "" "`nameext`, etc, could be used instead. See the [list of best practices](best-" "practices.md)." msgstr "" +"JavaScript の式は、絶対に必要な場合のみ使用するようにしてください。ファイル名" +"、拡張子、パスなどを操作する場合は、`basename`,`nameroot`,`nameext`, などの " +"[`File` のビルトインプロパティ][file-prop] のいずれかを代わりに使用できるかど" +"うかを検討してください。[ベストプラクティスのリスト](best-practices." +"md)を参照してください。" #: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 #, fuzzy @@ -2416,6 +2488,9 @@ msgid "" "attribute that allows users to load external JavaScript files, or to provide " "inline JavaScript code." msgstr "" +"`InlineJavascriptRequirement` は、`expressionLib` 属性をサポートし、" +"ユーザーが外部 JavaScript ファイルを読み込んだり、インライン JavaScript " +"コードを提供したりできるようにします。" #: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d msgid "" @@ -2424,6 +2499,9 @@ msgid "" "files or to create JavaScript functions that can be called in other parts of " "the CWL document." msgstr "" +"`expressionLib` 属性に追加されたエントリーは、CWLランナーのJavaScriptエンジン" +"で解析されます。これは、外部ファイルをインクルードしたり、CWL定義の他の部分で" +"呼び出すことができるJavaScript関数を作成するために使用することができます。" #: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b msgid "" @@ -2440,6 +2518,9 @@ msgid "" "function inline in `expressionLib`. That function can then be used in other " "parts of the CWL document:" msgstr "" +"例えば、`InlineJavascriptRequirement` を使って、`expressionLib` に " +"JavaScript 関数をインラインで記述することができます。その関数は、CWL定義の他" +"の部分で使用することができます：" #: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" @@ -2464,6 +2545,8 @@ msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" +"`capitalizeWords` 関数を外部ファイル`custom-functions.js` に移動し、CWL " +"定義でインポートしてみましょう：" #: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db #, fuzzy @@ -2502,11 +2585,11 @@ msgstr "" #: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" -msgstr "" +msgstr "`hello-world-expressionlib.cwl`" #: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" +msgstr "`hello-world-expressionlib.cwl`を実行する。" #: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 msgid "" @@ -2518,7 +2601,7 @@ msgstr "" #: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" -msgstr "" +msgstr "ファイルフォーマット" #: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a msgid "" @@ -2679,6 +2762,8 @@ msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" +"\"example_file\" は `File` 型として、フィールド `class： File` と `path` " +"フィールドを持つオブジェクトとして提供されなければなりません。" #: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b msgid "" @@ -2718,9 +2803,9 @@ msgid "" "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -"ブール型はフラグとして扱われます。 入力パラメータ \"example_flag \"が \"true" -" \"の場合、コマンドラインに`prefix` が追加されます。 " -"falseの場合、フラグは付加されません。" +"ブール型はフラグとして扱われます。 入力パラメータ \"example_flag \"が " +"\"true \"の場合、コマンドラインに`prefix` が追加されます。 falseの場合、フラ" +"グは付加されません。" #: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 msgid "" @@ -2945,11 +3030,10 @@ msgid "" "file_format || 'auto')`, to have a default value if none was provided in the " "command line or job input file." msgstr "" -"これを修正するには、排他的パラメータ、または`null` " -"を許可するパラメータを使用する場合、JavaScript 式で or " -"演算子を使用することを忘れてはなりません。たとえば、式を`$(" -"inputs.file_format || 'auto')` に変更すると、コマンドラインやジョブ入力ファイ" -"ルで何も指定されていない場合にデフォルト値を持つようになります。" +"これを修正するには、排他的パラメータ、または`null` を許可するパラメータを使用" +"する場合、JavaScript 式で or 演算子を使用することを忘れてはなりません。たとえ" +"ば、式を`$(inputs.file_format || 'auto')` に変更すると、コマンドラインやジョ" +"ブ入力ファイルで何も指定されていない場合にデフォルト値を持つようになります。" #: ../../src/topics/metadata-and-authorship.md:1 #: d33aa2353ad44fb885d3a1ee48263dc4 @@ -3079,9 +3163,8 @@ msgid "" "correspond to steps executed by a different workflow engine." msgstr "" "CWL runnerは、操作を具体的なステップにバインドする方法を思いつくかもしれませ" -"ん。例えば、CWL runnerは、" -"異なるワークフローエンジンで実行されるステップに対応するIDを持つ抽象的な " -"operation を使用することができます。" +"ん。例えば、CWL runnerは、異なるワークフローエンジンで実行されるステップに対" +"応するIDを持つ抽象的な operation を使用することができます。" #: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de msgid "Outputs" @@ -3130,10 +3213,9 @@ msgid "" "_array of strings_. The first element is the command to run, and any " "subsequent elements are mandatory command line arguments" msgstr "" -"これまでの例では、`baseCommand` " -"は単なる文字列で、引数はCWL入力として渡していました。単一の文字列の代わりに、" -"文字列の配列__ を使用することができます。 " -"最初の要素は実行するコマンドで、それ以降の要素は必須のコマンドライン引数です" +"これまでの例では、`baseCommand` は単なる文字列で、引数はCWL入力として渡してい" +"ました。単一の文字列の代わりに、文字列の配列__ を使用することができます。 最" +"初の要素は実行するコマンドで、それ以降の要素は必須のコマンドライン引数です" #: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" @@ -3160,8 +3242,9 @@ msgstr "" msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." -msgstr "`outputBinding` " -"フィールドには、各出力パラメータの値の設定方法が記述されています。" +msgstr "" +"`outputBinding` フィールドには、各出力パラメータの値の設定方法が記述されてい" +"ます。" #: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 msgid "" @@ -3170,8 +3253,8 @@ msgid "" "like `glob: '*.txt'`." msgstr "" "`glob` フィールドは、出力ディレクトリ内のファイル名で構成されます。ファイル名" -"が予め分からない場合は、`glob: '*.txt'` " -"のようにワイルドカードパターンを使用することができます。" +"が予め分からない場合は、`glob: '*.txt'` のようにワイルドカードパターンを使用" +"することができます。" #: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" @@ -3616,8 +3699,8 @@ msgid "" "really new is the `dockerRequirement` section." msgstr "" "これを実行する前に、これを分解して、いくつか細かく何をするのかを見てみましょ" -"う。 この大部分は以前のセクションで説明したもので、本当に新しいのは`dockerRe" -"quirement` の部分だけです。" +"う。 この大部分は以前のセクションで説明したもので、本当に新しいのは" +"`dockerRequirement` の部分だけです。" #: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 msgid "" @@ -3887,9 +3970,9 @@ msgid "" "the `SubworkflowFeatureRequirement`:" msgstr "" "ワークフローは、複数のツールを組み合わせてより大きな処理を実行するための方法" -"です。ワークフローエンジンが`SubworkflowFeatureRequirement` " -"をサポートしている場合、CWL ワークフローを別の CWL " -"ワークフローのステップとすることができます ：" +"です。ワークフローエンジンが`SubworkflowFeatureRequirement` をサポートしてい" +"る場合、CWL ワークフローを別の CWL ワークフローのステップとすることができま" +"す ：" #: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "" @@ -3908,11 +3991,10 @@ msgid "" "on the right. In purple we see the fixed string `\"Hello.java\"` being " "supplied as the `name_of_file_to_extract`." msgstr "" -"この2ステップのワークフローは、`create-tar` " -"ステップから始まり、オレンジ色の`compile` " -"ステップに接続されています。`compile` " -"は、右図にある別のワークフローです。紫色では、固定文字列`\"Hello.java\"` " -"が`name_of_file_to_extract` として与えられているのがわかります。" +"この2ステップのワークフローは、`create-tar` ステップから始まり、オレンジ色の" +"`compile` ステップに接続されています。`compile` は、右図にある別のワークフ" +"ローです。紫色では、固定文字列`\"Hello.java\"` が`name_of_file_to_extract` と" +"して与えられているのがわかります。" #: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a msgid "" @@ -3937,9 +4019,9 @@ msgid "" "to become the step's input/outputs." msgstr "" "CWL`Workflow` は、`CommandLineTool` を`step` として使用することができ、その " -"CWL ファイルは`run` に記述されます。ワークフローの入力（`tarball` " -"および`name_of_file_to_extract` ）と出力（`compiled_class` " -"）は、ステップの入力/出力になるようにマッピングすることができます。" +"CWL ファイルは`run` に記述されます。ワークフローの入力（`tarball` および" +"`name_of_file_to_extract` ）と出力（`compiled_class` ）は、ステップの入力/出" +"力になるようにマッピングすることができます。" #: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 msgid "" @@ -4044,8 +4126,8 @@ msgid "" "Aside from the `requirements` section including `ScatterFeatureRequirement`, " "what is going on here?" msgstr "" -"`requirements` セクションの`ScatterFeatureRequirement` " -"などを含めて、ここはどうなっているのでしょうか？" +"`requirements` セクションの`ScatterFeatureRequirement` などを含めて、ここはど" +"うなっているのでしょうか？" #: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c #, fuzzy @@ -4174,6 +4256,10 @@ msgid "" "make an entire workflow a single step in another workflow! Convert our two-" "step workflow to a single step subworkflow:" msgstr "" +"では、他のサンプルと独立して進行できるステップを分散させるにはどうすればいい" +"のでしょうか？[Nested Workflows](#nested-workflows)で、ワークフロー全体を別の" +"ワークフローの1ステップにすることができることを思い出しましょう！2ステップの" +"ワークフローを1ステップのサブワークフローに変換してみましょう：" #: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b #, fuzzy @@ -4311,6 +4397,7 @@ msgid "Key-Value Pairs" msgstr "キーバリューペア" #: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +#, fuzzy msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the `:` " @@ -4319,6 +4406,11 @@ msgid "" "meaning in the CWL specification and underscored key names otherwise. For " "example:" msgstr "" +"基本的に、YAML で書かれたファイルは_キーと値のペア_ のセットで構成されていま" +"す。各ペアは`key: value` として記述され、`:` の後に空白が必要です。CWLファイ" +"ルのキー名には、空白を含めるべきではありません。[_camelCase_][camelCase] は、" +"CWL仕様で特別な意味を持つ複数語のキー名、それ以外はアンダースコアのキー名とし" +"て使用します。例えば" #: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b #, fuzzy @@ -4439,6 +4531,7 @@ msgid "and:" msgstr "と：" #: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +#, fuzzy msgid "" "Native JSON can be useful in indicating where a field is intentionally left " "empty (such as `[]` for an empty array), as well as where it makes more " @@ -4447,6 +4540,11 @@ msgid "" "second example above shows, it can severely affect the readability of a YAML " "file, and should be used sparingly." msgstr "" +"ネイティブ JSON は、フィールドが意図的に空のままになっている場所 (空の配列を" +"表す`[]` など) や、値が同じ行にあることがより理にかなっている場所 (たとえば、" +"シェルコマンドでオプションフラグとその値を提供する場合) を示すのに便利なこと" +"があります。しかし、上の2番目の例が示すように、YAMLファイルの可読性に深刻な影" +"響を与える可能性があるので、控えめに使用する必要があります。" #: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d msgid "Reference" From 62cdcbf622fc8b7c67f9de37e75f9de47b4554fe Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Fri, 1 Dec 2023 08:40:28 +0100 Subject: [PATCH 110/179] Translations update from Hosted Weblate (#441) (#444) * Translated using Weblate (Japanese) Currently translated at 53.5% (320 of 598 strings) Translated using Weblate (Japanese) Currently translated at 53.0% (317 of 598 strings) Translated using Weblate (Japanese) Currently translated at 52.8% (316 of 598 strings) Translated using Weblate (Japanese) Currently translated at 52.6% (315 of 598 strings) Translated using Weblate (Japanese) Currently translated at 51.8% (310 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 53.6% (321 of 598 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 54.1% (324 of 598 strings) Translation: Common Workflow Language/CWL User Guide Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ * Translated using Weblate (Japanese) Currently translated at 56.1% (336 of 598 strings) Translation: Common Workflow Language/CWL User Guide Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ --------- Co-authored-by: Weblate (bot) Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 208 ++++++++++++++++++++------- 1 file changed, 153 insertions(+), 55 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index a00eac3a..56c64d04 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-11-22 21:01+0000\n" +"PO-Revision-Date: 2023-12-01 01:10+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.2.1-rc\n" +"X-Generator: Weblate 5.3-dev\n" #: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" @@ -160,6 +160,10 @@ msgid "" "from another step in a workflow, and don't want to work with the default " "names that these files were given when they were created." msgstr "" +"この例では、ツール定義の一部として、入力ファイルの名前を変更する方法を説明し" +"ます。これは、ワークフローの別のステップで作成されたファイルを使用する場合に" +"、これらのファイルが作成されたときに与えられたデフォルトの名前を使用して作業" +"したくない場合に便利です。" #: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" @@ -279,9 +283,8 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow." -"html#MultipleInputFeatureRequirement) と [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)を一緒に使います" +"html#MultipleInputFeatureRequirement) と [`linkMerge: merge_nested`](https://" +"www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)を一緒に使います" #: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" @@ -300,7 +303,8 @@ msgstr "" #: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです" +msgstr "" +"つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです" #: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 #, fuzzy @@ -443,8 +447,9 @@ msgstr "`-` (ハイフン文字、引き算の記号)が原因で発生した問 #: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "このエラーを修正するには、`-` (ハイフン) を`_` (アンダースコア) " -"に変更してください" +msgstr "" +"このエラーを修正するには、`-` (ハイフン) を`_` (アンダースコア) に変更してく" +"ださい" #: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d msgid "" @@ -962,11 +967,11 @@ msgid "" "It is also the CWL reference runner, which means it must support everything " "in the current CWL specification, {{ cwl_version }}." msgstr "" -"CWL ワークフローを実行するために最初に必要なものは、CWL runnerです。`cwltool`" -" は、CWL コミュニティによって維持されている Python " -"オープンソース・プロジェクトです。これはCWL reference runner(訳注: " -"CWLの参照実装)でもあり、現在のCWL仕様{{ cwl_version " -"}}のすべてをサポートしなければならないことを意味します。" +"CWL ワークフローを実行するために最初に必要なものは、CWL runnerです。" +"`cwltool` は、CWL コミュニティによって維持されている Python オープンソース・" +"プロジェクトです。これはCWL reference runner(訳注: CWLの参照実装)でもあり、現" +"在のCWL仕様{{ cwl_version }}のすべてをサポートしなければならないことを意味し" +"ます。" #: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 msgid "" @@ -1013,6 +1018,12 @@ msgid "" "description like the above) pass the `--validate` option to the `cwltool` " "command:" msgstr "" +"`cwltool` コマンドには、CWL ツールおよびワークフロー定義を検証するオプション" +"があります。このオプションは、CWL文書を解析し、構文エラーを探し、ワークフロー" +"記述がCWL標準に準拠しているかどうかを検証します。ただし、これらの操作は、ド" +"キュメントを実行せずに行われます。CWLワークフロー（または上記のようなスタンド" +"アロンコマンドラインツールの記述も）を検証するには、`cwltool` コマンドに`--" +"validate` オプションを渡します：" #: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." @@ -1044,15 +1055,20 @@ msgid "" "or user to point to the preferred CWL implementation. This is convenient for " "environments with multiple CWL runners." msgstr "" +"`cwl-runner` は、CWL準拠のランナーに対する、実装にとらわれないエイリアスで" +"す。これは、`cwl-runner` エイリアスコマンドを独立して呼び出すことができ、特定" +"のCWLランナープログラム名に依存しないことを意味します。ユーザーは、`cwltool` " +"のようなCWLランナーを直接呼び出す代わりに、`cwl-runner` を呼び出すことができ" +"ます。`cwl-runner` は、システム管理者またはユーザーによってインストールされ、" +"好みのCWL実装を指し示す。これは、複数のCWLランナーがある環境では便利です。" #: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 msgid "" "The CWL community publishes a Python package with the name `cwlref-runner` " "that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -"CWLコミュニティは、`cwlref-runner` " -"という名前のPythonパッケージを公開しており、`cwltool` のエイリアスを`cwl-" -"runner` という名前でインストールします" +"CWLコミュニティは、`cwlref-runner` という名前のPythonパッケージを公開してお" +"り、`cwltool` のエイリアスを`cwl-runner` という名前でインストールします" #: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." @@ -1124,6 +1140,12 @@ msgid "" "coded location, since `/usr/bin/env ` looks for the " "`` program in the system `PATH`," msgstr "" +"*shebang* は、スクリプトの冒頭の2文字列`#!` のことです。スクリプトが実行可能" +"な場合、オペレーティングシステムは、shebangの後に指定された実行可能ファイルを" +"使用してスクリプトを実行します。`/usr/bin/env ` は` `" +" プログラムをシステムの`PATH` " +"で探すので、ハードコードされた場所を使うよりも`/usr/bin/env ` を" +"使うことが良い習慣と考えられています、" #: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" @@ -1135,6 +1157,9 @@ msgid "" "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" +"CWLではどんなテキストエディタでも使えますが、シンタックスハイライトのために、" +"YAMLをサポートするエディタをお勧めします。人気のあるエディタは、Visual " +"Studio Code、Sublime、WebStorm、vim/neovim、そしてEmacsです。" #: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 msgid "" @@ -1142,12 +1167,18 @@ msgid "" "integration with CWL, and features such as customized syntax highlighting " "and better auto-complete:" msgstr "" +"Visual Studio CodeとWebStormには、CWLとの統合を実現する拡張機能があり、カスタ" +"マイズされたシンタックスハイライトやより優れた自動補完などの機能が用意されて" +"います：" #: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +#, fuzzy msgid "" "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" +"Benten(弁天)（CWL）プラグインを使ったVisual Studio Code -" #: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 msgid "" @@ -1251,19 +1282,27 @@ msgid "`hello_world.cwl`" msgstr "`hello_world.cwl`" #: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +#, fuzzy msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the " "same result as the command-line `echo \"Hello World\"`." msgstr "" +"上記の例は、`echo` のコマンドラインツールのラッパーに過ぎません。デフォルトの" +"入力値で上記のワークフローを実行すると、コマンドラインと同じ結果が得られます`" +"echo \"Hello World\"`." #: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +#, fuzzy msgid "" "In CWL, there is a distinction between a command-line tool and a workflow. " "But for the sake of simplicity, we are using the term “workflow” here. You " "will learn more about this in the [basic concepts](basic-concepts.md) " "section." msgstr "" +"CWLでは、CommandLineToolとWorkflowは区別されています。しかし、ここでは簡略化" +"のため、「ワークフロー」という用語を使用しています。これについては、[基本概念" +"](basic-concepts.md)のセクションで詳しく説明します。" #: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" @@ -1292,10 +1331,14 @@ msgid "" "`cwltool` and a more detailed list of software and libraries used for " "following the rest of this user guide." msgstr "" +"pipコマンドを使用してcwltoolをインストールしてもうまくいかない場合は、[前提条" +"件](prerequisites.md)セクションに、`cwltool` をインストールする他の方法と、こ" +"のユーザーガイドの残りの部分を追うために使用するソフトウェアとライブラリのよ" +"り詳細なリストがあります。" #: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" -msgstr "" +msgstr "\"Hello World\"を実行する" #: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe msgid "" @@ -1303,6 +1346,9 @@ msgid "" "[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " "workflow without specifying any option:" msgstr "" +"`cwltool` コマンドライン実行ファイルの使い方は、基本的に`cwltool [OPTIONS] " +" [INPUTS_OBJECT]`です。`hello_world.cwl` " +"Workflowは、オプションを指定せずに実行することができます：" #: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." @@ -1440,6 +1486,7 @@ msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 #: d8110ed19da94ad8a9f56e7006c4a2cf +#, fuzzy msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files in " @@ -1447,6 +1494,12 @@ msgid "" "directories in which they appear) may be read-only, so we need to instruct " "\"javac\" to write the class file to the designated output directory instead." msgstr "" +"この例では、Javaコンパイラを使用して、javaソースファイルをクラスファイルにコ" +"ンパイルするようにラップします。 デフォルトでは、\"javac \"はソース" +"・ファイルと同じディレクトリにクラス・ファイルを作成します。 しかし、CWLの入" +"力ファイル（およびそのディレクトリ）は読み取り専用である場合があるので、代わ" +"りに指定された出力ディレクトリにクラスファイルを書き込むように「javac」に指示" +"する必要があります。" #: ../../src/topics/additional-arguments-and-parameters.md:13 #: a74935dc31664e979ca8f90a6a4ba53c @@ -1553,7 +1606,7 @@ msgstr "" #: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" +msgstr "_SPDX 識別子を持つライセンスのメタデータフィールドの例：_" #: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 msgid "" @@ -1783,11 +1836,15 @@ msgstr "実行時にファイルを作成する" #: ../../src/topics/creating-files-at-runtime.md:3 #: 0cf51b6da6884065ae42032abc20eb0d +#, fuzzy msgid "" "Sometimes you need to create a file on the fly from input parameters, such " "as tools that expect to read their input configuration from a file rather " "than the command line parameters, or need a small wrapper shell script." msgstr "" +"コマンドラインパラメーターではなく、ファイルから入力設定を読み込むことを期待" +"するツールや、小さなラッパーシェルスクリプトが必要な場合など、入力パラメータ" +"ーからその場でファイルを作成する必要があることがあります。" #: ../../src/topics/creating-files-at-runtime.md:7 #: 2df3a3a9094d4b79b1d5dd99195f3bff @@ -1803,11 +1860,15 @@ msgstr "`createfile.cwl`" #: ../../src/topics/creating-files-at-runtime.md:15 #: cfffc518ba6e4ed1a80762ed6f7d25df +#, fuzzy msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the value " "at the input `message`." msgstr "" +"`$(inputs.message)` のような [Expressions](../topics/expressions.md)は、ファ" +"イルを作成する前にCWLエンジンによって展開されます。ここでは、入力パラメータ`m" +"essage` に値を挿入します。" #: ../../src/topics/creating-files-at-runtime.md:20 #: 9454a330b9324744b89448f2694b1b03 @@ -1920,6 +1981,8 @@ msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to be " "used in the table conversion are imported as a custom object:" msgstr "" +"29行目の`inputs:table_type` で、テーブル変換で使用できるテーブルオプションの" +"リストがカスタムオブジェクトとしてインポートされます：" #: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e msgid "" @@ -1947,6 +2010,9 @@ msgid "" "imported. Imports are described in `requirements:SchemaDefRequirement`, as " "below in the example `custom-types.cwl` description:" msgstr "" +"カスタム型をCWL定義で使用するためには、インポートする必要があります。インポー" +"トについては、`requirements:SchemaDefRequirement` で定義されており、例として" +"`custom-types.cwl` の定義にあるように、インポートされます：" #: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c msgid "" @@ -2041,6 +2107,7 @@ msgstr "" "Javascriptを使用できます。" #: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +#, fuzzy msgid "" "JavaScript expressions should only be used when absolutely necessary. When " "manipulating file names, extensions, paths etc, consider whether one of the " @@ -2048,6 +2115,11 @@ msgid "" "`nameext`, etc, could be used instead. See the [list of best practices](best-" "practices.md)." msgstr "" +"JavaScript の式は、絶対に必要な場合のみ使用するようにしてください。ファイル名" +"、拡張子、パスなどを操作する場合は、`basename`,`nameroot`,`nameext`, などの " +"[`File` のビルトインプロパティ][file-prop] のいずれかを代わりに使用できるかど" +"うかを検討してください。[ベストプラクティスのリスト](best-practices." +"md)を参照してください。" #: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 #, fuzzy @@ -2416,6 +2488,9 @@ msgid "" "attribute that allows users to load external JavaScript files, or to provide " "inline JavaScript code." msgstr "" +"`InlineJavascriptRequirement` は、`expressionLib` 属性をサポートし、" +"ユーザーが外部 JavaScript ファイルを読み込んだり、インライン JavaScript " +"コードを提供したりできるようにします。" #: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d msgid "" @@ -2424,6 +2499,9 @@ msgid "" "files or to create JavaScript functions that can be called in other parts of " "the CWL document." msgstr "" +"`expressionLib` 属性に追加されたエントリーは、CWLランナーのJavaScriptエンジン" +"で解析されます。これは、外部ファイルをインクルードしたり、CWL定義の他の部分で" +"呼び出すことができるJavaScript関数を作成するために使用することができます。" #: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b msgid "" @@ -2440,6 +2518,9 @@ msgid "" "function inline in `expressionLib`. That function can then be used in other " "parts of the CWL document:" msgstr "" +"例えば、`InlineJavascriptRequirement` を使って、`expressionLib` に " +"JavaScript 関数をインラインで記述することができます。その関数は、CWL定義の他" +"の部分で使用することができます：" #: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" @@ -2464,6 +2545,8 @@ msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" +"`capitalizeWords` 関数を外部ファイル`custom-functions.js` に移動し、CWL " +"定義でインポートしてみましょう：" #: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db #, fuzzy @@ -2502,11 +2585,11 @@ msgstr "" #: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" -msgstr "" +msgstr "`hello-world-expressionlib.cwl`" #: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" +msgstr "`hello-world-expressionlib.cwl`を実行する。" #: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 msgid "" @@ -2518,7 +2601,7 @@ msgstr "" #: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" -msgstr "" +msgstr "ファイルフォーマット" #: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a msgid "" @@ -2679,6 +2762,8 @@ msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" +"\"example_file\" は `File` 型として、フィールド `class： File` と `path` " +"フィールドを持つオブジェクトとして提供されなければなりません。" #: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b msgid "" @@ -2718,9 +2803,9 @@ msgid "" "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -"ブール型はフラグとして扱われます。 入力パラメータ \"example_flag \"が \"true" -" \"の場合、コマンドラインに`prefix` が追加されます。 " -"falseの場合、フラグは付加されません。" +"ブール型はフラグとして扱われます。 入力パラメータ \"example_flag \"が " +"\"true \"の場合、コマンドラインに`prefix` が追加されます。 falseの場合、フラ" +"グは付加されません。" #: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 msgid "" @@ -2945,11 +3030,10 @@ msgid "" "file_format || 'auto')`, to have a default value if none was provided in the " "command line or job input file." msgstr "" -"これを修正するには、排他的パラメータ、または`null` " -"を許可するパラメータを使用する場合、JavaScript 式で or " -"演算子を使用することを忘れてはなりません。たとえば、式を`$(" -"inputs.file_format || 'auto')` に変更すると、コマンドラインやジョブ入力ファイ" -"ルで何も指定されていない場合にデフォルト値を持つようになります。" +"これを修正するには、排他的パラメータ、または`null` を許可するパラメータを使用" +"する場合、JavaScript 式で or 演算子を使用することを忘れてはなりません。たとえ" +"ば、式を`$(inputs.file_format || 'auto')` に変更すると、コマンドラインやジョ" +"ブ入力ファイルで何も指定されていない場合にデフォルト値を持つようになります。" #: ../../src/topics/metadata-and-authorship.md:1 #: d33aa2353ad44fb885d3a1ee48263dc4 @@ -3079,9 +3163,8 @@ msgid "" "correspond to steps executed by a different workflow engine." msgstr "" "CWL runnerは、操作を具体的なステップにバインドする方法を思いつくかもしれませ" -"ん。例えば、CWL runnerは、" -"異なるワークフローエンジンで実行されるステップに対応するIDを持つ抽象的な " -"operation を使用することができます。" +"ん。例えば、CWL runnerは、異なるワークフローエンジンで実行されるステップに対" +"応するIDを持つ抽象的な operation を使用することができます。" #: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de msgid "Outputs" @@ -3130,10 +3213,9 @@ msgid "" "_array of strings_. The first element is the command to run, and any " "subsequent elements are mandatory command line arguments" msgstr "" -"これまでの例では、`baseCommand` " -"は単なる文字列で、引数はCWL入力として渡していました。単一の文字列の代わりに、" -"文字列の配列__ を使用することができます。 " -"最初の要素は実行するコマンドで、それ以降の要素は必須のコマンドライン引数です" +"これまでの例では、`baseCommand` は単なる文字列で、引数はCWL入力として渡してい" +"ました。単一の文字列の代わりに、文字列の配列__ を使用することができます。 最" +"初の要素は実行するコマンドで、それ以降の要素は必須のコマンドライン引数です" #: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" @@ -3160,8 +3242,9 @@ msgstr "" msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." -msgstr "`outputBinding` " -"フィールドには、各出力パラメータの値の設定方法が記述されています。" +msgstr "" +"`outputBinding` フィールドには、各出力パラメータの値の設定方法が記述されてい" +"ます。" #: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 msgid "" @@ -3170,8 +3253,8 @@ msgid "" "like `glob: '*.txt'`." msgstr "" "`glob` フィールドは、出力ディレクトリ内のファイル名で構成されます。ファイル名" -"が予め分からない場合は、`glob: '*.txt'` " -"のようにワイルドカードパターンを使用することができます。" +"が予め分からない場合は、`glob: '*.txt'` のようにワイルドカードパターンを使用" +"することができます。" #: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" @@ -3616,8 +3699,8 @@ msgid "" "really new is the `dockerRequirement` section." msgstr "" "これを実行する前に、これを分解して、いくつか細かく何をするのかを見てみましょ" -"う。 この大部分は以前のセクションで説明したもので、本当に新しいのは`dockerRe" -"quirement` の部分だけです。" +"う。 この大部分は以前のセクションで説明したもので、本当に新しいのは" +"`dockerRequirement` の部分だけです。" #: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 msgid "" @@ -3887,9 +3970,9 @@ msgid "" "the `SubworkflowFeatureRequirement`:" msgstr "" "ワークフローは、複数のツールを組み合わせてより大きな処理を実行するための方法" -"です。ワークフローエンジンが`SubworkflowFeatureRequirement` " -"をサポートしている場合、CWL ワークフローを別の CWL " -"ワークフローのステップとすることができます ：" +"です。ワークフローエンジンが`SubworkflowFeatureRequirement` をサポートしてい" +"る場合、CWL ワークフローを別の CWL ワークフローのステップとすることができま" +"す ：" #: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "" @@ -3908,11 +3991,10 @@ msgid "" "on the right. In purple we see the fixed string `\"Hello.java\"` being " "supplied as the `name_of_file_to_extract`." msgstr "" -"この2ステップのワークフローは、`create-tar` " -"ステップから始まり、オレンジ色の`compile` " -"ステップに接続されています。`compile` " -"は、右図にある別のワークフローです。紫色では、固定文字列`\"Hello.java\"` " -"が`name_of_file_to_extract` として与えられているのがわかります。" +"この2ステップのワークフローは、`create-tar` ステップから始まり、オレンジ色の" +"`compile` ステップに接続されています。`compile` は、右図にある別のワークフ" +"ローです。紫色では、固定文字列`\"Hello.java\"` が`name_of_file_to_extract` と" +"して与えられているのがわかります。" #: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a msgid "" @@ -3937,9 +4019,9 @@ msgid "" "to become the step's input/outputs." msgstr "" "CWL`Workflow` は、`CommandLineTool` を`step` として使用することができ、その " -"CWL ファイルは`run` に記述されます。ワークフローの入力（`tarball` " -"および`name_of_file_to_extract` ）と出力（`compiled_class` " -"）は、ステップの入力/出力になるようにマッピングすることができます。" +"CWL ファイルは`run` に記述されます。ワークフローの入力（`tarball` および" +"`name_of_file_to_extract` ）と出力（`compiled_class` ）は、ステップの入力/出" +"力になるようにマッピングすることができます。" #: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 msgid "" @@ -4044,8 +4126,8 @@ msgid "" "Aside from the `requirements` section including `ScatterFeatureRequirement`, " "what is going on here?" msgstr "" -"`requirements` セクションの`ScatterFeatureRequirement` " -"などを含めて、ここはどうなっているのでしょうか？" +"`requirements` セクションの`ScatterFeatureRequirement` などを含めて、ここはど" +"うなっているのでしょうか？" #: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c #, fuzzy @@ -4174,6 +4256,10 @@ msgid "" "make an entire workflow a single step in another workflow! Convert our two-" "step workflow to a single step subworkflow:" msgstr "" +"では、他のサンプルと独立して進行できるステップを分散させるにはどうすればいい" +"のでしょうか？[Nested Workflows](#nested-workflows)で、ワークフロー全体を別の" +"ワークフローの1ステップにすることができることを思い出しましょう！2ステップの" +"ワークフローを1ステップのサブワークフローに変換してみましょう：" #: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b #, fuzzy @@ -4311,6 +4397,7 @@ msgid "Key-Value Pairs" msgstr "キーバリューペア" #: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +#, fuzzy msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the `:` " @@ -4319,6 +4406,11 @@ msgid "" "meaning in the CWL specification and underscored key names otherwise. For " "example:" msgstr "" +"基本的に、YAML で書かれたファイルは_キーと値のペア_ のセットで構成されていま" +"す。各ペアは`key: value` として記述され、`:` の後に空白が必要です。CWLファイ" +"ルのキー名には、空白を含めるべきではありません。[_camelCase_][camelCase] は、" +"CWL仕様で特別な意味を持つ複数語のキー名、それ以外はアンダースコアのキー名とし" +"て使用します。例えば" #: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b #, fuzzy @@ -4439,6 +4531,7 @@ msgid "and:" msgstr "と：" #: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +#, fuzzy msgid "" "Native JSON can be useful in indicating where a field is intentionally left " "empty (such as `[]` for an empty array), as well as where it makes more " @@ -4447,6 +4540,11 @@ msgid "" "second example above shows, it can severely affect the readability of a YAML " "file, and should be used sparingly." msgstr "" +"ネイティブ JSON は、フィールドが意図的に空のままになっている場所 (空の配列を" +"表す`[]` など) や、値が同じ行にあることがより理にかなっている場所 (たとえば、" +"シェルコマンドでオプションフラグとその値を提供する場合) を示すのに便利なこと" +"があります。しかし、上の2番目の例が示すように、YAMLファイルの可読性に深刻な影" +"響を与える可能性があるので、控えめに使用する必要があります。" #: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d msgid "Reference" From f173bcee8fea4241eb886670aa386a2716606054 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Thu, 7 Dec 2023 13:36:09 +0100 Subject: [PATCH 111/179] Translations update from Hosted Weblate (#443) * Translated using Weblate (Japanese) Currently translated at 56.5% (338 of 598 strings) Translated using Weblate (Japanese) Currently translated at 53.5% (320 of 598 strings) Translated using Weblate (Japanese) Currently translated at 53.0% (317 of 598 strings) Translated using Weblate (Japanese) Currently translated at 52.8% (316 of 598 strings) Translated using Weblate (Japanese) Currently translated at 52.6% (315 of 598 strings) Translated using Weblate (Japanese) Currently translated at 51.8% (310 of 598 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Added translation using Weblate (Russian) Co-authored-by: gfbdrgng * Added translation using Weblate (Russian) Co-authored-by: Weblate --------- Co-authored-by: Manabu ISHII Co-authored-by: gfbdrgng --- locales/ja/LC_MESSAGES/user_guide.po | 109 +- locales/ru/LC_MESSAGES/sphinx.po | 27 + locales/ru/LC_MESSAGES/user_guide.po | 3122 ++++++++++++++++++++++++++ 3 files changed, 3221 insertions(+), 37 deletions(-) create mode 100644 locales/ru/LC_MESSAGES/sphinx.po create mode 100644 locales/ru/LC_MESSAGES/user_guide.po diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 56c64d04..2fdfca1e 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-12-01 01:10+0000\n" +"PO-Revision-Date: 2023-12-07 05:06+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -161,9 +161,9 @@ msgid "" "names that these files were given when they were created." msgstr "" "この例では、ツール定義の一部として、入力ファイルの名前を変更する方法を説明し" -"ます。これは、ワークフローの別のステップで作成されたファイルを使用する場合に" -"、これらのファイルが作成されたときに与えられたデフォルトの名前を使用して作業" -"したくない場合に便利です。" +"ます。これは、ワークフローの別のステップで作成されたファイルを使用する場合" +"に、これらのファイルが作成されたときに与えられたデフォルトの名前を使用して作" +"業したくない場合に便利です。" #: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" @@ -476,6 +476,7 @@ msgid "Debug JavaScript Expressions" msgstr "JavaScriptの式をデバッグする" #: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +#, fuzzy msgid "" "You can use the --js-console option of cwltool, or " "you can try creating a JavaScript or TypeScript project for your code, and " @@ -485,6 +486,13 @@ msgid "" "common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" +"cwltool の --js-console " +"オプションを使用するか、または、あなたのコードのためのJavaScript または " +"TypeScript プロジェクトを作成し、expressionLib " +"を使用して読み込んでみてください（例： https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" #: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" @@ -1142,10 +1150,10 @@ msgid "" msgstr "" "*shebang* は、スクリプトの冒頭の2文字列`#!` のことです。スクリプトが実行可能" "な場合、オペレーティングシステムは、shebangの後に指定された実行可能ファイルを" -"使用してスクリプトを実行します。`/usr/bin/env ` は` `" -" プログラムをシステムの`PATH` " -"で探すので、ハードコードされた場所を使うよりも`/usr/bin/env ` を" -"使うことが良い習慣と考えられています、" +"使用してスクリプトを実行します。`/usr/bin/env ` は` " +"` プログラムをシステムの`PATH` で探すので、ハードコードされた場所" +"を使うよりも`/usr/bin/env ` を使うことが良い習慣と考えられていま" +"す、" #: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" @@ -1289,8 +1297,8 @@ msgid "" "same result as the command-line `echo \"Hello World\"`." msgstr "" "上記の例は、`echo` のコマンドラインツールのラッパーに過ぎません。デフォルトの" -"入力値で上記のワークフローを実行すると、コマンドラインと同じ結果が得られます`" -"echo \"Hello World\"`." +"入力値で上記のワークフローを実行すると、コマンドラインと同じ結果が得られます" +"`echo \"Hello World\"`." #: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 #, fuzzy @@ -1301,8 +1309,8 @@ msgid "" "section." msgstr "" "CWLでは、CommandLineToolとWorkflowは区別されています。しかし、ここでは簡略化" -"のため、「ワークフロー」という用語を使用しています。これについては、[基本概念" -"](basic-concepts.md)のセクションで詳しく説明します。" +"のため、「ワークフロー」という用語を使用しています。これについては、[基本概" +"念](basic-concepts.md)のセクションで詳しく説明します。" #: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" @@ -1347,8 +1355,8 @@ msgid "" "workflow without specifying any option:" msgstr "" "`cwltool` コマンドライン実行ファイルの使い方は、基本的に`cwltool [OPTIONS] " -" [INPUTS_OBJECT]`です。`hello_world.cwl` " -"Workflowは、オプションを指定せずに実行することができます：" +" [INPUTS_OBJECT]`です。`hello_world.cwl` Workflowは、オプション" +"を指定せずに実行することができます：" #: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." @@ -1495,11 +1503,11 @@ msgid "" "\"javac\" to write the class file to the designated output directory instead." msgstr "" "この例では、Javaコンパイラを使用して、javaソースファイルをクラスファイルにコ" -"ンパイルするようにラップします。 デフォルトでは、\"javac \"はソース" -"・ファイルと同じディレクトリにクラス・ファイルを作成します。 しかし、CWLの入" -"力ファイル（およびそのディレクトリ）は読み取り専用である場合があるので、代わ" -"りに指定された出力ディレクトリにクラスファイルを書き込むように「javac」に指示" -"する必要があります。" +"ンパイルするようにラップします。 デフォルトでは、\"javac \"はソース・ファイ" +"ルと同じディレクトリにクラス・ファイルを作成します。 しかし、CWLの入力ファイ" +"ル（およびそのディレクトリ）は読み取り専用である場合があるので、代わりに指定" +"された出力ディレクトリにクラスファイルを書き込むように「javac」に指示する必要" +"があります。" #: ../../src/topics/additional-arguments-and-parameters.md:13 #: a74935dc31664e979ca8f90a6a4ba53c @@ -1843,8 +1851,8 @@ msgid "" "than the command line parameters, or need a small wrapper shell script." msgstr "" "コマンドラインパラメーターではなく、ファイルから入力設定を読み込むことを期待" -"するツールや、小さなラッパーシェルスクリプトが必要な場合など、入力パラメータ" -"ーからその場でファイルを作成する必要があることがあります。" +"するツールや、小さなラッパーシェルスクリプトが必要な場合など、入力パラメー" +"ターからその場でファイルを作成する必要があることがあります。" #: ../../src/topics/creating-files-at-runtime.md:7 #: 2df3a3a9094d4b79b1d5dd99195f3bff @@ -1867,8 +1875,8 @@ msgid "" "at the input `message`." msgstr "" "`$(inputs.message)` のような [Expressions](../topics/expressions.md)は、ファ" -"イルを作成する前にCWLエンジンによって展開されます。ここでは、入力パラメータ`m" -"essage` に値を挿入します。" +"イルを作成する前にCWLエンジンによって展開されます。ここでは、入力パラメータ" +"`message` に値を挿入します。" #: ../../src/topics/creating-files-at-runtime.md:20 #: 9454a330b9324744b89448f2694b1b03 @@ -2115,11 +2123,11 @@ msgid "" "`nameext`, etc, could be used instead. See the [list of best practices](best-" "practices.md)." msgstr "" -"JavaScript の式は、絶対に必要な場合のみ使用するようにしてください。ファイル名" -"、拡張子、パスなどを操作する場合は、`basename`,`nameroot`,`nameext`, などの " -"[`File` のビルトインプロパティ][file-prop] のいずれかを代わりに使用できるかど" -"うかを検討してください。[ベストプラクティスのリスト](best-practices." -"md)を参照してください。" +"JavaScript の式は、絶対に必要な場合のみ使用するようにしてください。ファイル" +"名、拡張子、パスなどを操作する場合は、`basename`,`nameroot`,`nameext`, など" +"の [`File` のビルトインプロパティ][file-prop] のいずれかを代わりに使用できる" +"かどうかを検討してください。[ベストプラクティスのリスト](best-practices.md)を" +"参照してください。" #: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 #, fuzzy @@ -2488,9 +2496,9 @@ msgid "" "attribute that allows users to load external JavaScript files, or to provide " "inline JavaScript code." msgstr "" -"`InlineJavascriptRequirement` は、`expressionLib` 属性をサポートし、" -"ユーザーが外部 JavaScript ファイルを読み込んだり、インライン JavaScript " -"コードを提供したりできるようにします。" +"`InlineJavascriptRequirement` は、`expressionLib` 属性をサポートし、ユーザー" +"が外部 JavaScript ファイルを読み込んだり、インライン JavaScript コードを提供" +"したりできるようにします。" #: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d msgid "" @@ -2545,8 +2553,8 @@ msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -"`capitalizeWords` 関数を外部ファイル`custom-functions.js` に移動し、CWL " -"定義でインポートしてみましょう：" +"`capitalizeWords` 関数を外部ファイル`custom-functions.js` に移動し、CWL 定義" +"でインポートしてみましょう：" #: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db #, fuzzy @@ -3062,16 +3070,20 @@ msgid "" "tool and workflows. This example includes metadata allowing others to cite " "your tool." msgstr "" +"すべての開発者に対し、ツールおよびワークフローに関する以下の最小限のメタデー" +"タを推奨します。この例では、他の人があなたのツールを引用するためのメタデータ" +"を含んでいます。" #: ../../src/topics/metadata-and-authorship.md:16 #: 0d5200bbbfdc43e6a78b4e4c3096ebd7 msgid "`metadata_example2.cwl`" -msgstr "" +msgstr "`metadata_example2.cwl`" #: ../../src/topics/metadata-and-authorship.md:28 #: d402bf528c7f4eb69aaaa275be2bf1d4 +#, fuzzy msgid "Extended Example" -msgstr "" +msgstr "拡張された例" #: ../../src/topics/metadata-and-authorship.md:30 #: cb9980db4e5f4c74b01c2dec6d5e92d0 @@ -3188,6 +3200,7 @@ msgstr "" "な値の型を示す`type` があります。" #: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +#, fuzzy msgid "" "When a tool runs under CWL, the starting working directory is the designated " "output directory. The underlying tool or script must record its results in " @@ -3195,6 +3208,11 @@ msgid "" "returned by the CWL tool are either the output files themselves, or come " "from examining the content of those files." msgstr "" +"CWLでツールを実行する場合、開始時の作業ディレクトリは指定された出力ディレクト" +"リになります。 基礎となるツールやスクリプトは、出力ディレクトリに作成される" +"ファイルの形でその結果を記録しなければなりません。 CWLツールによって返される" +"出力パラメータは、出力ファイルそのものであるか、またはそれらのファイルの内容" +"を調べることによって得られるものです。" #: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 msgid "" @@ -3297,12 +3315,18 @@ msgid "`array-outputs-job.yml`" msgstr "`array-outputs-job.yml`" #: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +#, fuzzy msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " "marked by a leading `-`. This format can also be used in CWL descriptions to " "mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" +"[YAML Guide](yaml-guide.md#arrays) " +"で説明されているように、期待される出力の配列は`array-outputs-job.yml` " +"で指定され、それぞれのエントリーは先頭の`-` でマークされています。このフォー" +"マットは、CWL定義で配列のエントリーをマークするために使用することもでき、今後" +"のいくつかのセクションでデモがあります。" #: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 msgid "Parameter References" @@ -3366,20 +3390,26 @@ msgstr "" "変数 \"inputs \"の値は、CWLツールの起動時に提供された入力オブジェクトです。" #: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +#, fuzzy msgid "" "Note that because `File` parameters are objects, to get the path to an input " "file you must reference the path field on a file object; to reference the " "path to the tar file in the above example you would write `$(inputs.tarfile." "path)`." msgstr "" +"`File` パラメータはオブジェクトであるため、入力ファイルのパスを取得するには、" +"ファイルオブジェクトのpathフィールドを参照する必要があります。上記の例でtarフ" +"ァイルのパスを参照するには、`$(inputs.tarfile.path)`となります。" #: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "パラメータ参照はどこで許されるのですか？" #: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +#, fuzzy msgid "You can only use parameter references in certain fields. These are:" -msgstr "" +msgstr "パラメータ参照は、特定のフィールドにのみ使用することができます。 " +"以下はその例です：" #: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 #, fuzzy @@ -3512,10 +3542,11 @@ msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 #: 82e48b3e3c3f451480cc0b6a529271f6 +#, fuzzy msgid "" "In this example, the software requirement being described is InterProScan " "version 5.21-60." -msgstr "" +msgstr "この例では、定義されるソフトウェア要件はInterProScanバージョン5.21-60です。" #: ../../src/topics/specifying-software-requirements.md:25 #: 02e40154eac74ecc98d0447d03475b44 @@ -3752,11 +3783,15 @@ msgid "Workflows" msgstr "ワークフロー" #: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +#, fuzzy msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" +"Workflowは、CommandLineTool、ExpressionTool、またはWorkflow（サブワークフロー" +"）をステップ として実行する CWL 処理ユニットです。CWLドキュメントには`inputs`" +" 、`outputs` 、`steps` を定義する必要があります。" #: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 #, fuzzy diff --git a/locales/ru/LC_MESSAGES/sphinx.po b/locales/ru/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..13426aa9 --- /dev/null +++ b/locales/ru/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: ru\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "" diff --git a/locales/ru/LC_MESSAGES/user_guide.po b/locales/ru/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..c6f3ca0c --- /dev/null +++ b/locales/ru/LC_MESSAGES/user_guide.po @@ -0,0 +1,3122 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: ru\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 4dee8504a8e5496081dadc386ab45540 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 674c238b25e240eda05e22e399f2f78f +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: b651f80f47b4442fbf29454a233697fc +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: ecf2b9c0b1664afe9c4e180610610021 +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: e24cb13d98014e558b6a6946758359e0 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: 928e3df7ca3e479ca6474a8e72cf36eb +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: d355f035676446c88b028f327aeb4829 +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 339b852df24242189d6efcd2898a3396 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: 3ef57e6862f240bebcf193a52397af0a +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: fae385da16aa443da996fa23ac03d6ae +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: 92430be71ecc40e18bbbb80d5576c613 +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 387d83db81024f65aa9a890c2d07874a +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: d8e2280a75a74916a1630afaa2fe2ae3 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: f1c1340f9745458980e0fbd641738687 +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 5424e5472c3d466fa2a3d2022c6cb475 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: 12f57b2ba76b492abe1816e06bfb1417 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: e1f657a46ce94a0d83671540e2cc2dab +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a5eacdbc9aa142c890b177869da4143d +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: e3bdaceae8784ab0807b2cf356a98580 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: ed521ac365db4a6ba5a1051fbaa2932e +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 67573252cc064b27ab13eebc468ac58a +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 73e68b3af9cf41338d843c0c40e50cdc +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: a999b1acda2641598086648c64aa3831 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: f8c12a58cb0b46a488823c6ae95f25ea +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: f25a63e0926d4932bbe64b2e4bdabf9e +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: d718630a296545f3a989c8c71e9ddc77 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 9a97acd430064710bcdf76edbd9f711c +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: 48deb71f361a43e48a56ed483075bca8 +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 716b56506ca7470299899c5d820a9ea2 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: e3ecac0a8e604f2b98a2a12b0579990a +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 007a345b4bad49cf996c4301b8386473 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: efb5fd14988c4e2a8f834ee5369d4102 +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: 276f688ba7cc471a842f085ca852b1d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 8b70a1ad70514039b97164fa630c12e4 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 2f28ab412d2843ffa5f14acdc01fc732 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: cbec9277b5004e50af2728cbda0df740 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: e259f55f8000479bbd8009e25cf0ca6c +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 8210b36347a749889450529ecdf4ff0e +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 23088850ad02459696f6bbd385109aac +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: f02257a822ad46ac93c5981531cc85d5 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: d289541e460147aa933f7878996f8649 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: f495da32f05a4a5ba9539be0a54c1a59 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: bdb4c68a175047ddbe141ca24960127f +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 97b61352363f47cb890e8937c5613fa3 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: 0bc424ef2ca346099f29b937379908a0 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 29b73e1dd72744f68377f0a38c10f062 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 38a2afaf4a6c4d04909af22c93f2808d +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: cd74f34b21af4de9be96fd897efc469b +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: f12e371f3f1a4b0cb2cff9800352d48c +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 8f0e8f050e334ac08334e9215e1dcf61 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 7a6be0005a6441feb67f036d005d7885 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 06635145b441418aaae84dc804f3d6ac +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 04eaf1f7c630450db318dcd8b7626e15 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: fd4579a3c9844492b314b5c3c1775fc7 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: e024bcb70e04412e90e1838426d1b69a +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: a3db21c0b3114802a8a5b610e252ef13 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 0f5bc8520d6a4dafa37c65343da9702a +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 5cb830da47464a8b9c3950983fa4d56f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: a2ce43b391864e8bbde16328cc19b32b +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 56ee4dcfff6141d5bef80eb96559876d +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 96671c56523c4ea9992fb5dfcfa6490e +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: bcc6246742cb46bfb185e415c4a3431a +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 86dce36de687449c88fb5eb9d64eb045 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 7dc630ea86464b1dba3a4e5079260b3b +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: 651e032007ea4a119d20c820bb61f86b +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 0b056dde9e87428996e47870b12119da +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 628124a1670b4b058bb0fb6e495a099c +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: ec2adb3912bc46e28891229e9e0d9a1c +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: a519be60726a44af9941fdce04735353 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: cb8fc8c4c79e467eac5fab4ca685201e +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: a26cc105716f47cb807174c9003153b0 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: cc159dd5fe5748caac838862f5b8c4d1 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 6812698e9ad84d3385de5e88e9dde0b3 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: d1f02be278754267893dfce5a940997d +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: 75d59e395c66416cae9b352db5081516 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 874c6f19abbf45d7ab7d30a378c4048d +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: dea0d4b681f94e73b13965dcfe75cf7d +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: 750474486a84482292eeba45f118287f +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 1eb0e39bb6d04b8cab300f44a79f3add +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 4b2ab812f62c4f949dd25c8527f2411c +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 2c3b884cb1c54521900cc90782e8a58d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: a1073b6306044dffb414319ae01f68bb +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: 9a1d92334685449386dfa3b3a899ed48 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: fb623af4c480411b8fde28d01c981411 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: e98e165f6bba40809c90473d72f9d592 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 5565c1b2d8a349169a305a9b26b4574d +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: 88160cef4cfa4add9020aa89511a5749 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 730ba1434a1445ae847ec6153b6a3b72 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: a25d0b1e13324b40a6b8fcd227948c4f +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: d661df070e3040869da412d07a71f716 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: a11585474d3849cca5467512ed964743 +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 2682f9ca8e604a0c9986f7746fdec960 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 22447a560f6f4317bf67bd7c4336126c +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 52703d6b7f914097934bfad13663abeb +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 5e1c79df657d4a6e84e055dd6b300a5d +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 329d2809dfae4f90bc638f5f03a47ee3 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 9647019d8c37466886e7aab6f176634d +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: cc067051f22f433bbece08f60933e002 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: dbfe2c1123144316aa026374b0f353d3 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: 074cf5d912854d8c864607cc24b15302 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: b54240bb94f746bba7511633aa969db0 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 8b70a072aa87414c88e89a3e19af0a51 +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: eea20f89c45f424a888178df53713b28 +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7647e0229a924f988cf02b7812a55c06 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 9d663249666045618a0d3acddb85a9a9 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: dbf6153cd02542a6a01c172803122b7f +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: b6250cf6fa8a4a0c94b33302e0decca5 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: fa6ca3bbc6784380a03a950a6f49a180 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: b92b516e537a4773ad67b4af586e7a25 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: 467a701228504d06b971b79a59c69064 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: 2634f989eb304009a8568d70ed42786c +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: fbe0c65b444441f785d0054176d036a6 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 9a710602e00c4934ae3a3b471aa68458 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: 21b5be7270a14f0987240c81d1ec879b +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: cfe9d8241fe84bd5b74042a5625d933f +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 764d933cc4da446abd8dd8f913f05dac +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: c93efc6d4e004859981ee7f5fa28ed03 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: 546601da44cb49bd9611b1c85807fd90 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: e07f33d01b804663a25ffb08aad74821 +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: 7a644506619a4f08958ec7d4540cd557 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: b5195b7d8eaa419fb2b90cb33a57783a +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: 2713594c937d4c528fc8d04d9e9819ed +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: cf94c1424fc2413c85647fd1ee73d951 +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: dc0452107c604e29bdf32bb289fe5db8 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 483181f498fc4d968b5fe6ef427709f7 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 7487485d6aa4458089a4b4bdf107ea64 +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 93188ed43ee949cc98b3ea679ce14feb +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 24aca0bea4d94e3593b844cf0586cffe +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 9c56528acd5f49deb139e034dfbfac7c +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: a2dd833fdca4443181648e41051a5232 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: 7e40cc9f9e1341c195e843c009575b94 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: def35d6021394def80a53ae49a2cdbde +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: c84d4450bc6a475dbf34e0b22cea9130 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: cca9665f6daa44b49233baf34ab9fcc7 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: 547edbf5fa424b8286cc21674ff159b0 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 7ca248888b9d484cb544cd76ba538662 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: ae6b240718104380b08db5552d7355ea +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: e5a8b7f84be64020b191099f3fad30ed +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 12a06d8358534102b202965d4258c18e +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: b7f93705e5b8416696be01850072e8c0 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: e87045829b344089ab59dc27063ddd7a +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: 42ef2f145b824d69b63abc1da175c216 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: c61cedf543664d388183e04b3939cc39 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: 9e39e3f1501c4fcaab3e8962e090f6be +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: 03e2f767c4da461982fc3c0f3ba94762 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 3bea5822b8694e2aa32c446e1c54a045 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: 0d498cd4caf54c15891ca1afe58e2727 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: b2d75045e02741b4850f5ff1243f7858 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: 5fa79c62049a447c8328ebf9db54ebf4 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: d947c54933d64aad90df392a1cedd63f +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 651d35997332404186aa6d5711da4a3d +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: b662c1a5a4424c8d8350a806356acc61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 04d6babfd87343d7a5f13867ea02b65f +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 2eaacf1a90204a2b9bd621344560f2a1 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: e3a7182f00f440b8b5461da91194a64b +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: b5338f39e8c74ff28e139da68089a742 +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: f6d92156d67c4a339bcfd194cff897df +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: d80ab383eec9402faba997b548fe42eb +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: 49217c02f58c43ff9ec00f10da8d4e84 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 8dbd56473f8c40c0bb12a48be06117e3 +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 78d7f3ede2c746d482042adef050b2c4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: cbbf93c70fe04ba7932ba25758ddc611 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: cfa1c1fde4454df283f87cc54a9c59ec +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 1a8be2950cbb475bbb2617e005f0fac9 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: 5d83c56102e141cc978500f678dd0c1c +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: cda73485875d4c8e9464679a20558616 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 98cae24919b74c088a5d89706aec581b +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: b4b0940b4b5743c09637b36b964202d0 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 9ca3554d771d45998e88aaede525b227 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 3fca839cede94cfd8e4f605c73ba699d +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: 3ded0f125249485c921994b6e6b93ac9 +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 53ece35d309a4c8d99f1efb2122a7092 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 87bafb845c714b109874f6137b84462d +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: fcd05b1ef31a4046946a2399c7fc5575 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: 859368c1f25c4a4aad57abfd046c63f5 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" From 9f975db03e60e064a96a6333842701f5f5fc32d3 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 24 Nov 2023 11:58:36 +0100 Subject: [PATCH 112/179] gh-pages: consolidate language builds into one directory --- .github/workflows/gh-pages.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/gh-pages.yaml b/.github/workflows/gh-pages.yaml index 5bd84a2f..2569a38a 100644 --- a/.github/workflows/gh-pages.yaml +++ b/.github/workflows/gh-pages.yaml @@ -35,9 +35,11 @@ jobs: - name: Build documentation run: | + mkdir -p _build/html make html for lang in en es pt_BR pt_PT ja zh_Hans; do - make html BUILDDIR=_build/${lang} SPHINXOPTS="-D language=${lang}" + make html BUILDDIR=_build/${lang} SPHINXOPTS="-D language=${lang} -j auto" + mv _build/${lang}/html _build/html/${lang} done - name: Deploy From 4d506714a453a4f09b14d25197d7bf500e7168b5 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 8 Dec 2023 09:59:50 +0100 Subject: [PATCH 113/179] Add Dependabot --- .github/dependabot.yml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 00000000..c0a96e68 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,16 @@ +# To get started with Dependabot version updates, you'll need to specify which +# package ecosystems to update and where the package manifests are located. +# Please see the documentation for all configuration options: +# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates + +version: 2 +updates: + - package-ecosystem: "pip" # See documentation for possible values + directory: "/" # Location of package manifests + schedule: + interval: "daily" + # Maintain dependencies for GitHub Actions + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "daily" From 76ee7e2553cd39fef65cc681aadf6aade3cd602e Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Fri, 8 Dec 2023 10:04:57 +0100 Subject: [PATCH 114/179] convert to pyproject.toml Thank you https://pypi.org/project/ini2toml/ ! --- pyproject.toml | 69 ++++++++++++++++++++++++++++++++++++++++++++++++++ setup.cfg | 61 -------------------------------------------- 2 files changed, 69 insertions(+), 61 deletions(-) delete mode 100644 setup.cfg diff --git a/pyproject.toml b/pyproject.toml index e69de29b..00da5572 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -0,0 +1,69 @@ +[build-system] +requires = ["setuptools>=61.2"] +build-backend = "setuptools.build_meta" + +[project] +name = "cwl-user-guide" +description = "CWL User Guide" +license = {text = "GPL"} +classifiers = [ + "Environment :: Console", + "Environment :: Web Environment", + "Intended Audience :: Developers", + "Intended Audience :: System Administrators", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", + "Operating System :: POSIX :: Linux", + "Programming Language :: Python", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: Implementation :: CPython", +] +requires-python = ">=3.6" +dependencies = [ + "cwltool", + "cwlref-runner", + "cwl-utils==0.*", + "myst-parser==0.*", + "pydata-sphinx-theme==0.*", + "sphinx==5.*", + "sphinx-reredirects==0.1.*", + "sphinxcontrib-runcmd==0.2.*", + "sphinx-favicon", + "python-Levenshtein", + "sphinx-intl", +] +dynamic = ["version"] + +[project.readme] +file = "README.md" +content-type = "text/markdown" + +[project.urls] +Homepage = "https://www.commonwl.org/user_guide/" +Documentation = "https://www.commonwl.org/user_guide/" +Source = "https://github.com/common-workflow-language/user_guide" +Tracker = "https://github.com/common-workflow-language/user_guide/issues" + +[project.optional-dependencies] +test = [ + "cwltest==2.*", + "cwltool==3.1.*", +] +watch = ["sphinx-autobuild==2021.3.*"] +rtd = ["udocker"] +all = ["cwl-user-guide[test,watch,rtd]"] + +[tool.setuptools] +include-package-data = true +platforms = ["any"] + +[tool.setuptools.packages.find] +include = ["cwl*"] +namespaces = true + +[tool.setuptools.dynamic] +version = {attr = "cwl.doc.__version__"} diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 2afc5085..00000000 --- a/setup.cfg +++ /dev/null @@ -1,61 +0,0 @@ -[metadata] -name=cwl-user-guide -version=attr: cwl.doc.__version__ -url=https://www.commonwl.org/user_guide/ -description=CWL User Guide -long_description=file: README.md -long_description_content_type=text/markdown -project_urls= - Documentation=https://www.commonwl.org/user_guide/ - Source=https://github.com/common-workflow-language/user_guide - Tracker=https://github.com/common-workflow-language/user_guide/issues -license=GPL -platforms=any -classifiers= - Environment :: Console - Environment :: Web Environment - Intended Audience :: Developers - Intended Audience :: System Administrators - Intended Audience :: Science/Research - License :: OSI Approved :: GNU General Public License v3 (GPLv3) - Operating System :: POSIX :: Linux - Programming Language :: Python - Programming Language :: Python :: 3.6 - Programming Language :: Python :: 3.7 - Programming Language :: Python :: 3.8 - Programming Language :: Python :: 3.9 - Programming Language :: Python :: 3 :: Only - Programming Language :: Python :: Implementation :: CPython - -[options] -packages = find_namespace: -include_package_data = True -python_requires = >=3.6 -install_requires = - cwltool - cwlref-runner - cwl-utils==0.* - myst-parser==0.* - pydata-sphinx-theme==0.* - sphinx==5.* - sphinx-reredirects==0.1.* - sphinxcontrib-runcmd==0.2.* - sphinx-favicon - python-Levenshtein - sphinx-intl - -[options.packages.find] -include = cwl* - -[options.extras_require] -test = - cwltest==2.* - cwltool==3.1.* -watch = - sphinx-autobuild==2021.3.* -rtd = - udocker -all = - %(test)s - %(watch)s - %(rtd)s From 9dc613c94a9cae4716d5232e764a965e38e3a96d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 8 Dec 2023 11:17:26 +0100 Subject: [PATCH 115/179] Bump actions/setup-python from 4 to 5 (#447) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/ci-tests.yml | 2 +- .github/workflows/gh-pages.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml index b29d0742..d6b9e45c 100644 --- a/.github/workflows/ci-tests.yml +++ b/.github/workflows/ci-tests.yml @@ -31,7 +31,7 @@ jobs: - uses: actions/checkout@v3 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ env.py-semver }} cache: pip diff --git a/.github/workflows/gh-pages.yaml b/.github/workflows/gh-pages.yaml index 2569a38a..767c6d8e 100644 --- a/.github/workflows/gh-pages.yaml +++ b/.github/workflows/gh-pages.yaml @@ -22,7 +22,7 @@ jobs: sudo apt-get install -y graphviz tree - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: '3.9' cache: pip From 918f9fc21efeb1e06a0c4473ca971fa8256adb62 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 8 Dec 2023 11:33:41 +0100 Subject: [PATCH 116/179] Bump actions/checkout from 3 to 4 (#448) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/ci-tests.yml | 2 +- .github/workflows/codeql.yml | 2 +- .github/workflows/gh-pages.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml index d6b9e45c..e7c0d108 100644 --- a/.github/workflows/ci-tests.yml +++ b/.github/workflows/ci-tests.yml @@ -28,7 +28,7 @@ jobs: py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python uses: actions/setup-python@v5 diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index c880dca1..56e96b2c 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -24,7 +24,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Initialize CodeQL uses: github/codeql-action/init@v2 diff --git a/.github/workflows/gh-pages.yaml b/.github/workflows/gh-pages.yaml index 767c6d8e..79ebd7ec 100644 --- a/.github/workflows/gh-pages.yaml +++ b/.github/workflows/gh-pages.yaml @@ -15,7 +15,7 @@ jobs: permissions: contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Install apt packages run: | From c4fe947c35917de547c9618c9c86acf6984e39ce Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 8 Dec 2023 15:33:58 +0100 Subject: [PATCH 117/179] Update myst-parser requirement from ==0.* to ==2.* (#449) * Update myst-parser requirement from ==0.* to ==2.* Updates the requirements on [myst-parser](https://github.com/executablebooks/MyST-Parser) to permit the latest version. - [Release notes](https://github.com/executablebooks/MyST-Parser/releases) - [Changelog](https://github.com/executablebooks/MyST-Parser/blob/master/CHANGELOG.md) - [Commits](https://github.com/executablebooks/MyST-Parser/compare/v0.3.0...v2.0.0) --- updated-dependencies: - dependency-name: myst-parser dependency-type: direct:production ... Signed-off-by: dependabot[bot] * myst-parser 2.x needs sphinx >=6 --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com> --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 00da5572..10c98900 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,9 +27,9 @@ dependencies = [ "cwltool", "cwlref-runner", "cwl-utils==0.*", - "myst-parser==0.*", + "myst-parser==2.*", "pydata-sphinx-theme==0.*", - "sphinx==5.*", + "sphinx==6.*", "sphinx-reredirects==0.1.*", "sphinxcontrib-runcmd==0.2.*", "sphinx-favicon", From 7ebdcbd5e3885da5ab728d63cedbcc9b31721864 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 8 Dec 2023 16:55:00 +0100 Subject: [PATCH 118/179] Update sphinx requirement from ==5.* to ==7.* (#450) Updates the requirements on [sphinx](https://github.com/sphinx-doc/sphinx) to permit the latest version. - [Release notes](https://github.com/sphinx-doc/sphinx/releases) - [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES.rst) - [Commits](https://github.com/sphinx-doc/sphinx/compare/v5.0.0b1...v7.2.6) --- updated-dependencies: - dependency-name: sphinx dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 10c98900..b039f887 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,7 +29,7 @@ dependencies = [ "cwl-utils==0.*", "myst-parser==2.*", "pydata-sphinx-theme==0.*", - "sphinx==6.*", + "sphinx==7.*", "sphinx-reredirects==0.1.*", "sphinxcontrib-runcmd==0.2.*", "sphinx-favicon", From 3115dc61cbe3f185974094c0c0ced340d17bed77 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 14 Dec 2023 02:11:12 +0100 Subject: [PATCH 119/179] Bump github/codeql-action from 2 to 3 (#451) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/v2...v3) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/codeql.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index 56e96b2c..c4095636 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -27,16 +27,16 @@ jobs: uses: actions/checkout@v4 - name: Initialize CodeQL - uses: github/codeql-action/init@v2 + uses: github/codeql-action/init@v3 with: languages: ${{ matrix.language }} queries: +security-and-quality - name: Autobuild - uses: github/codeql-action/autobuild@v2 + uses: github/codeql-action/autobuild@v3 if: ${{ matrix.language == 'javascript' || matrix.language == 'python' }} - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v2 + uses: github/codeql-action/analyze@v3 with: category: "/language:${{ matrix.language }}" From 1b98346dfd54aa23f177ea2b7da385c5a605d195 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Sat, 16 Dec 2023 11:26:26 +0100 Subject: [PATCH 120/179] Translations update from Hosted Weblate (#445) * Translated using Weblate (Japanese) Currently translated at 57.3% (343 of 598 strings) Translated using Weblate (Japanese) Currently translated at 56.6% (339 of 598 strings) Translated using Weblate (Japanese) Currently translated at 56.6% (339 of 598 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 56.8% (340 of 598 strings) Co-authored-by: Michael Crusoe Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 57.6% (345 of 598 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide --------- Co-authored-by: Manabu ISHII Co-authored-by: Michael Crusoe --- locales/ja/LC_MESSAGES/user_guide.po | 119 +++++++++++++++++++++------ 1 file changed, 93 insertions(+), 26 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 2fdfca1e..5af7a3fd 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2023-12-07 05:06+0000\n" +"PO-Revision-Date: 2023-12-16 02:08+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.3-dev\n" +"X-Generator: Weblate 5.3\n" #: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" @@ -486,13 +486,13 @@ msgid "" "common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -"cwltool の --js-console " -"オプションを使用するか、または、あなたのコードのためのJavaScript または " -"TypeScript プロジェクトを作成し、expressionLib " -"を使用して読み込んでみてください（例： https://github.com/common-workflow-language/" -"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +"cwltool の --js-console オプションを使用するか、ま" +"たは、あなたのコードのためのJavaScript または TypeScript プロジェクトを作成" +"し、expressionLib を使用して読み込んでみてください（例： https://github.com/common-" +"workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-" +"tool.cwl#L6-L8" #: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" @@ -610,12 +610,17 @@ msgid "Implementations" msgstr "実装" #: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +#, fuzzy msgid "" "An implementation of the CWL specification is any software written following " "what is defined in a version of the specification document. However, " "implementations may not implement every aspect of the specification. CWL " "implementations are licensed under both Open Source and commercial licenses." msgstr "" +"CWL仕様の実装とは、あるバージョンの仕様書で定義された内容に従って書かれたソフ" +"トウェアのことです。ただし、実装は仕様のすべての側面を実装するわけではありま" +"せん。CWLの実装は、オープンソース・ライセンスと商用ライセンスの両方でライセン" +"スされています。" #: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 #, fuzzy @@ -1153,7 +1158,7 @@ msgstr "" "使用してスクリプトを実行します。`/usr/bin/env ` は` " "` プログラムをシステムの`PATH` で探すので、ハードコードされた場所" "を使うよりも`/usr/bin/env ` を使うことが良い習慣と考えられていま" -"す、" +"す" #: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" @@ -1356,7 +1361,7 @@ msgid "" msgstr "" "`cwltool` コマンドライン実行ファイルの使い方は、基本的に`cwltool [OPTIONS] " " [INPUTS_OBJECT]`です。`hello_world.cwl` Workflowは、オプション" -"を指定せずに実行することができます：" +"を指定せずに実行することができます：" #: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." @@ -1658,6 +1663,10 @@ msgid "" "`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" +"`input` および`output` の識別子はすべて、その概念的同一性を反映する必要があり" +"ます。`foo_input`,`foo_file`,`result`,`input`,`output`, などの代わりに" +"`unaligned_sequences`,`reference_genome`,`phylogeny`, または" +"`aligned_sequences` などの情報量の多い名称を使ってください。" #: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 msgid "" @@ -1731,12 +1740,17 @@ msgstr "" "enum` を使用してください。" #: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +#, fuzzy msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. One " "common example: manipulating `File` names and paths? Consider whether one of " "the [built in `File` properties][file-prop] like `basename`, `nameroot`, " "`nameext`, etc., could be used instead." msgstr "" +"JavaScriptのすべての使用について、削除または置換の可能性を評価します。よくあ" +"る例：`File` の名前とパスを操作する方法は？`basename`,`nameroot`,`nameext`, " +"などの [built in`File` properties][file-prop] のいずれかを代わりに使用できな" +"いか考えてみてください。" #: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 msgid "" @@ -1880,6 +1894,7 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 #: 9454a330b9324744b89448f2694b1b03 +#, fuzzy msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later " "during command line tool invocation. That means that any genuine need for " @@ -1887,6 +1902,11 @@ msgid "" "above is expanded to `${PREFIX}` in the generated file to be evaluated by " "the shell script instead of the CWL engine." msgstr "" +"_CWL expressions_ は、コマンドラインツール起動時に使用される_shell " +"variables_ とは無関係です。つまり、`$` という文字が本当に必要な場合は、** ` " +"\\` で** をエスケープする必要があります。例えば，上記の`\\${PREFIX}` は，CWL" +"エンジンの代わりにシェルスクリプトで評価されるように，生成されたファイルでは" +"`${PREFIX}` に展開されます．" #: ../../src/topics/creating-files-at-runtime.md:27 #: 7f8d99a30b644457a62ac1523d0c72aa @@ -1911,6 +1931,9 @@ msgid "" "base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " "command `sh example.sh`. This will run the file we create in the shell." msgstr "" +"これを実行する前に、各ステップをもう少し詳しく見てみましょう。ベースコマンド" +"`baseCommand: [\"sh\", \"example.sh\"]` は、`sh example.sh` というコマンドを" +"実行します。これで、作成したファイルがシェルで実行されます。" #: ../../src/topics/creating-files-at-runtime.md:40 #: 70e257091bdb456e8957f90a8fa90e8c @@ -2519,6 +2542,11 @@ msgid "" "international.org/5.1/). This means that any code that you include or write " "in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" +"CWL標準（バージョン1.0から1.2）は、CWL定義で有効なJavaScriptのバージョンは[" +"ECMAScript 5.1](https://262.ecma-international.org/5.1/" +")のみであると[明記しています](https://www.commonwl.org/v1.0/CommandLineTool." +"html#Expressions)。これは、CWLドキュメントに含める、または書くコードは、" +"ECMAScript 5.1に準拠していなければならないことを意味します。" #: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c msgid "" @@ -2590,6 +2618,10 @@ msgid "" "that calls the `capitalizeWords` function from the external file `custom-" "functions.js`." msgstr "" +"最後に、CWL定義にはインラインと外部JavaScriptコードの両方が存在できることに注" +"意してください。この最後の例では、`expressionLib` 属性に、新しい関数" +"`createHelloWorldMessage` を追加しました。この関数は、外部ファイル`custom-" +"functions.js` から`capitalizeWords` 関数を呼び出しています。" #: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" @@ -2600,12 +2632,17 @@ msgid "Running `hello-world-expressionlib.cwl`." msgstr "`hello-world-expressionlib.cwl`を実行する。" #: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +#, fuzzy msgid "" "The `$include` statement can be used to include a file from the local disk " "or from a remote location. It works with both relative and absolute paths. " "Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." "html#Include) from the CWL specification to learn more about it." msgstr "" +"`$include` ステートメントを使用すると、ローカルディスクまたはリモートロケー" +"ションからファイルをインクルードすることができます。相対パスと絶対パスの両方" +"で動作します。CWL仕様の[text about`$include`](https://www.commonwl.org/v1.0/" +"SchemaSalad.html#Include)を読むと、より詳しく知ることができます。" #: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" @@ -2618,6 +2655,11 @@ msgid "" "document for others how to use your tool while allowing you to do some " "simple type-checking when creating parameter files." msgstr "" +"ToolsやWorkflowsは、`File` " +"型を入力として受け取り、出力として生成することができます。また、`File` タイプ" +"のフォーマットを示すことをお勧めします。これにより、ツールの使用方法を他の人" +"に示すことができ、また、パラメータファイルを作成する際に簡単な型チェックを行" +"うことができるようになります。" #: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 msgid "" @@ -2788,14 +2830,22 @@ msgid "" "boxed text describes these two commands and the expected output from the " "command line:" msgstr "" +"次に、`cwltool inp.cwl inp-job.yml` というコマンドを使い、コマンドラインに" +"ツール定義と入力オブジェクトを指定して`cwltool` を起動します。次のボックステ" +"キストは、これら2つのコマンドと、コマンドラインから期待される出力について説明" +"しています：" #: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +#, fuzzy msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " "that the tools aren't accidentally accessing files that were not explicitly " "specified" msgstr "" +"CWLリファレンスランナー（cwltool）と他のランナーは、ツールが明示的に指定され" +"ていないファイルに誤ってアクセスしないように、入力ファイルへの（\"ソフト\"）" +"シンボリックリンクを持つ一時ディレクトリを作成します。" #: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "" @@ -3322,11 +3372,10 @@ msgid "" "marked by a leading `-`. This format can also be used in CWL descriptions to " "mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" -"[YAML Guide](yaml-guide.md#arrays) " -"で説明されているように、期待される出力の配列は`array-outputs-job.yml` " -"で指定され、それぞれのエントリーは先頭の`-` でマークされています。このフォー" -"マットは、CWL定義で配列のエントリーをマークするために使用することもでき、今後" -"のいくつかのセクションでデモがあります。" +"[YAML Guide](yaml-guide.md#arrays) で説明されているように、期待される出力の配" +"列は`array-outputs-job.yml` で指定され、それぞれのエントリーは先頭の`-` で" +"マークされています。このフォーマットは、CWL定義で配列のエントリーをマークする" +"ために使用することもでき、今後のいくつかのセクションでデモがあります。" #: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 msgid "Parameter References" @@ -3398,8 +3447,8 @@ msgid "" "path)`." msgstr "" "`File` パラメータはオブジェクトであるため、入力ファイルのパスを取得するには、" -"ファイルオブジェクトのpathフィールドを参照する必要があります。上記の例でtarフ" -"ァイルのパスを参照するには、`$(inputs.tarfile.path)`となります。" +"ファイルオブジェクトのpathフィールドを参照する必要があります。上記の例でtar" +"ファイルのパスを参照するには、`$(inputs.tarfile.path)`となります。" #: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" @@ -3408,8 +3457,9 @@ msgstr "パラメータ参照はどこで許されるのですか？" #: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad #, fuzzy msgid "You can only use parameter references in certain fields. These are:" -msgstr "パラメータ参照は、特定のフィールドにのみ使用することができます。 " -"以下はその例です：" +msgstr "" +"パラメータ参照は、特定のフィールドにのみ使用することができます。 以下はその" +"例です：" #: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 #, fuzzy @@ -3546,7 +3596,8 @@ msgstr "" msgid "" "In this example, the software requirement being described is InterProScan " "version 5.21-60." -msgstr "この例では、定義されるソフトウェア要件はInterProScanバージョン5.21-60です。" +msgstr "" +"この例では、定義されるソフトウェア要件はInterProScanバージョン5.21-60です。" #: ../../src/topics/specifying-software-requirements.md:25 #: 02e40154eac74ecc98d0447d03475b44 @@ -3789,9 +3840,9 @@ msgid "" "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -"Workflowは、CommandLineTool、ExpressionTool、またはWorkflow（サブワークフロー" -"）をステップ として実行する CWL 処理ユニットです。CWLドキュメントには`inputs`" -" 、`outputs` 、`steps` を定義する必要があります。" +"Workflowは、CommandLineTool、ExpressionTool、またはWorkflow（サブワークフ" +"ロー）をステップ として実行する CWL 処理ユニットです。CWLドキュメントには" +"`inputs` 、`outputs` 、`steps` を定義する必要があります。" #: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 #, fuzzy @@ -4077,12 +4128,17 @@ msgid "" msgstr "" #: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +#, fuzzy msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" "coded `Hello.java` file using the previously mentioned " "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" +"また、あまり一般的でない方法で、ジョブファイルの外部依存を回避することも可能" +"です。そこで、このワークフローでは、先に述べた`InitialWorkDirRequirement` の" +"要件を使用して、ハードコードされた`Hello.java` ファイルを生成してから、それ" +"を tar ファイルに追加することができます。" #: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 #, fuzzy @@ -4096,6 +4152,7 @@ msgstr "" "でき、結果として`outputs` が得られます：" #: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +#, fuzzy msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This is " @@ -4103,14 +4160,25 @@ msgid "" "for doing it in this case is because the command line is hard-coded with " "filenames that only make sense within this workflow." msgstr "" +"`tar --create` ツールを別のファイルに分割せず、CWL Workflow 定義の中に埋め込" +"んだことにお気づきでしょうか。これは一般的にベストプラクティスではありませ" +"ん。なぜなら、そのツールを再利用できないからです。このケースでそれを行う理由" +"は、コマンドラインに、このワークフロー定義内でしか意味をなさないファイル名が" +"ハードコーディングされているためです。" #: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +#, fuzzy msgid "" "In this example we had to prepare a tar file outside, but only because our " "inner workflow was designed to take that as an input. A better refactoring " "of the inner workflow would be to take a list of Java files to compile, " "which would simplify its usage as a tool step in other workflows." msgstr "" +"この例では、外部にtarファイルを用意する必要がありましたが、これは内部のワーク" +"フローがそれを入力として受け取るように設計されているためです。内部ワークフ" +"ローのリファクタリングとしては、コンパイルするJavaファイルのリストを受け取る" +"ようにすれば、他のワークフローにおけるツールステップとしての使い方が簡単にな" +"ります。" #: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 #, fuzzy @@ -4432,7 +4500,6 @@ msgid "Key-Value Pairs" msgstr "キーバリューペア" #: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 -#, fuzzy msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the `:` " @@ -4445,7 +4512,7 @@ msgstr "" "す。各ペアは`key: value` として記述され、`:` の後に空白が必要です。CWLファイ" "ルのキー名には、空白を含めるべきではありません。[_camelCase_][camelCase] は、" "CWL仕様で特別な意味を持つ複数語のキー名、それ以外はアンダースコアのキー名とし" -"て使用します。例えば" +"て使用します。例えば：" #: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b #, fuzzy From 45518ed7714f9ea4d88ff43d5a9c8b4293524e60 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Sat, 16 Dec 2023 11:52:45 +0100 Subject: [PATCH 121/179] Update translation files to changes in content `make update_translations` --- locales/es/LC_MESSAGES/user_guide.po | 3935 +++++++++------- locales/ja/LC_MESSAGES/user_guide.po | 5026 ++++++++++---------- locales/pt_BR/LC_MESSAGES/user_guide.po | 4117 ++++++++++------- locales/pt_PT/LC_MESSAGES/user_guide.po | 4114 ++++++++++------- locales/ru/LC_MESSAGES/user_guide.po | 4396 +++++++++++------- locales/zh_Hans/LC_MESSAGES/user_guide.po | 5124 ++++++++++++--------- 6 files changed, 15143 insertions(+), 11569 deletions(-) diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index ca09ccab..6f69499c 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -8,33 +8,33 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-27 16:02+0100\n" +"POT-Creation-Date: 2023-12-16 11:48+0100\n" "PO-Revision-Date: 2023-01-27 14:27+0000\n" "Last-Translator: Michael Crusoe \n" "Language: es\n" -"Language-Team: Spanish \n" +"Language-Team: Spanish \n" "Plural-Forms: nplurals=2; plural=n != 1;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" +"Generated-By: Babel 2.12.1\n" -#: ../../LICENSE.md:2 3eb955b4f3dd4c3188924b97ea6ab592 +#: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac msgid "Licenses" msgstr "Licencias" -#: ../../LICENSE.md:4 bf4480e7fff4460a87e8f43c11599f07 +#: ../../LICENSE.md:4 9dd9705700664b31a3f296d263b4028b msgid "Instructional Material" msgstr "Material didáctico" -#: ../../LICENSE.md:6 9e9eab12205d4e82b4fedca520370f4c +#: ../../LICENSE.md:6 e54324bd39cd431d91b32e338217b8c7 msgid "" -"All Common Workflow Language project instructional material and changes to " -"the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable summary " -"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" -"[cc-by-legal]." +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." msgstr "" "Todo el material instructivo del proyecto Common Workflow Language y los " "cambios en la estructura también están disponibles bajo la [licencia " @@ -42,1325 +42,1356 @@ msgstr "" "legible por humanos (y no un sustituto) del [texto legal completo de la " "licencia CC BY 4.0][cc-by-legal]." -#: ../../LICENSE.md:12 a8e98ad541c642e58e201afa625ec791 +#: ../../LICENSE.md:12 754f3f54aa4142ef9dac27f508dd0bca msgid "You are free:" msgstr "Usted es libre de:" -#: ../../LICENSE.md:14 b4cb4bc4261347fcb0d2c8a93995ab76 -msgid "" -"to **Share**---copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 d2b1d5e965ef4e71b64c359549919975 +msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" "**Compartir**---copiar y redistribuir el material en cualquier medio o " "formato" -#: ../../LICENSE.md:15 d66dcbf95ccc41aaa53be523487ec913 +#: ../../LICENSE.md:15 fe9551ffef8149bf8da50e70318e8de8 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" -#: ../../LICENSE.md:17 ca1c299a1b834b868bcdd4ca9f244696 +#: ../../LICENSE.md:17 247db3bcc7024c44a044886a29ef1414 msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.md:19 6133f79f93be4991a6f5290f72d1a63d +#: ../../LICENSE.md:19 c04d906124854afc917707b7b4e45bb2 msgid "" -"The licensor cannot revoke these freedoms as long as you follow the license " -"terms:" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " "términos de la licencia:" -#: ../../LICENSE.md:24 2d6ce81add1043629b676187f890288c +#: ../../LICENSE.md:24 551cb5ab59dd4737b1042a4ef79ffab7 msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow Language " -"project, and, where practical, linking to https://www.commonwl.org/ ), " -"provide a [link to the license][cc-by-human], and indicate if changes were " -"made. You may do so in any reasonable manner, but not in any way that " -"suggests the licensor endorses you or your use." -msgstr "" -"**Atribución**---Usted debe dar crédito de manera adecuada(mencionando que " -"su trabajo se deriva de un trabajo que tiene «Copyright © The Common " -"Workflow Language Project» y, cuando sea práctico, con un enlace a https://" -"www.commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e " -"indicar si se han realizado cambios. Puede hacerlo en cualquier forma " -"razonable, pero no de forma tal que sugiera que usted o su uso tienen el " -"apoyo de la licenciante." - -#: ../../LICENSE.md:32 f3f22597b6f845208a0cce3b3b2c8f5d +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." +msgstr "" +"**Atribución**---Usted debe dar crédito de manera adecuada(mencionando " +"que su trabajo se deriva de un trabajo que tiene «Copyright © The Common " +"Workflow Language Project» y, cuando sea práctico, con un enlace a " +"https://www.commonwl.org/%20),%20brindar%20un%20[enlace%20a%20la%20licencia][cc-by-" +"human], e indicar si se han realizado cambios. Puede hacerlo en cualquier" +" forma razonable, pero no de forma tal que sugiera que usted o su uso " +"tienen el apoyo de la licenciante." + +#: ../../LICENSE.md:32 f6c3b2ccad494ed6811a35537fc1fb0d msgid "" "**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything the " -"license permits. With the understanding that:" +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" msgstr "" -"**No hay restricciones adicionales**---No puede aplicar términos legales ni " -"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " -"permitido por la licencia. Con el entendimiento de que:" +"**No hay restricciones adicionales**---No puede aplicar términos legales " +"ni medidas tecnológicas que restrinjan legalmente a otras a hacer " +"cualquier uso permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.md:36 3cfedee64d4e46098a159cb2acdba4ef +#: ../../LICENSE.md:36 91c95248cd7f435c909ee263a9a8bf3f msgid "" -"You do not have to comply with the license for elements of the material in " -"the public domain or where your use is permitted by an applicable exception " -"or limitation." +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." msgstr "" "No tiene que cumplir con la licencia para elementos del materiale en el " "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.md:39 c836a570faaf449d9716da5f75556627 +#: ../../LICENSE.md:39 27f79b0b648b4de4b0eb3172b2dc4ae8 msgid "" -"No warranties are given. The license may not give you all of the permissions " -"necessary for your intended use. For example, other rights such as " -"publicity, privacy, or moral rights may limit how you use the material." +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." msgstr "" "No se dan garantías. La licencia podría no darle todos los permisos que " -"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como " -"publicidad, privacidad, o derechos morales pueden limitar la forma en que " -"utilice el material." +"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como" +" publicidad, privacidad, o derechos morales pueden limitar la forma en " +"que utilice el material." -#: ../../LICENSE.md:44 896f9966e5014e8a88b060be3063fe09 +#: ../../LICENSE.md:44 1e367d07720d4f9fb7ebc3149052e823 msgid "Software" msgstr "Software" -#: ../../LICENSE.md:46 007f8613dc234c3fa8d5d92b18af0eb1 +#: ../../LICENSE.md:46 cf8b58d02b6943a48cb70aa78a27bea4 msgid "" "Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the " -"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Excepto cuando se indique lo contrario, los programas de ejemplo y otro " "software proporcionado por el proyecto Common Workflow Language están " -"disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " -"la [OSI][osi]." +"disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada " +"por la [OSI][osi]." -#: ../../LICENSE.md:51 227bc635a06f49dbb771fd9b62157d00 +#: ../../LICENSE.md:51 96f1e5be3e1e48db8d9a4c7693008715 msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." msgstr "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 1861131d3df648ae9e74ce1c87f0be7b a2ffa927deb2451d95ec63528e8078dd -#: d6055d3f15604ce6940770c7b561d4c5 +#: 08aa9181d5304e0fa96b28db15718559 d37fc100eb6948bba8b5e757574b2aaf +#: ecdd0f28d5b048d69dd1ffae2fa1f6c0 msgid "" "CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece of " -"software, tools and workflows described using CWL are portable across a " -"variety of platforms that support the CWL standard." +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 38b062f219b34e08a46bd8f6525353ec 89e7e1dd05474344a1d929cb492e9caf +#: 1361ff6bf4924efc9ce9a85785a6b381 eb254514301c491e81f72ae19c407261 msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 d3357ff3c8874e368aea0d6062ef6190 +#: ../../src/episodes.md:9 f03d7cbe6670451db0896f1b674d56c7 msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. Please use the new [Table of Contents](index.md#table-of-" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 f2c4882e0e164c2b869e3eb969241061 +#: ../../src/faq.md:1 d65ad48ac6314bf0a74c34a6766561fc msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 41099ab64e0544d894bd9e3af2718bda -msgid "Non \"`File`\" Types Using `evalFrom`" +#: ../../src/faq.md:11 370a9659c7904ef6b5e1ae7480f82ef6 +msgid "How do I create non \"`File`\" types using `evalFrom`?" msgstr "" -#: ../../src/faq.md:41 bb6aff70534148fa8a4b01140f7be150 -msgid "Rename an Input File" +#: ../../src/faq.md:41 8333f51e3f5945fe8963adfc6685bcb1 +msgid "How do I rename an input file?" msgstr "" -#: ../../src/faq.md:43 70ebc653b0d54d60a866edc0dbf56b57 +#: ../../src/faq.md:43 f6b88d9154d049d7807afa9bb0f1ac98 msgid "" -"This example demonstrates how to change the name of an input file as part of " -"a tool description. This could be useful when you are taking files produced " -"from another step in a workflow, and don't want to work with the default " -"names that these files were given when they were created." +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 833510f5896b4a6eb5875d25eca5b047 +msgid "How do I rename an output file?" msgstr "" -#: ../../src/faq.md:59 38b687f707d2438b85df08a445ab816f -msgid "Rename an Output File" +#: ../../src/faq.md:61 207e2f97d1c44233ae3f109c5a6ec944 +msgid "" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:61 d48422c020004ef084ca11e6229b5450 +#: ../../src/faq.md:83 d66acc583da24273980a52be03e79e91 msgid "" -"This example demonstrates how to change the name of an output file from the " -"default name given to it by a tool:" +"By modifying the `basename` field in the `outputEval` field, CWL workflow" +" engines will rename the file using the new name for subsequent steps or " +"as a workflow-level output." msgstr "" -#: ../../src/faq.md:82 48765409ab9d48ccbcecceb46ddf2e91 -msgid "Referencing a Local Script" +#: ../../src/faq.md:86 8641f105131b4ac1bca7e0a46756ef79 +msgid "How do I reference a local script?" msgstr "" -#: ../../src/faq.md:84 a59b8acd72124e2c95d1905ae494d928 +#: ../../src/faq.md:88 d3e43b40d6994b32bc37067ee116418e msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 f36088ba90d24f9f9c7c1bd59deb6f49 +#: ../../src/faq.md:90 64b140a321ca4087945339c523cc24dd msgid "" -"The first method involves adding the folder containing your scripts to the " -"`PATH` environment variable. This allows you to run the shell script " -"directly without using `sh` or `bash` commands." +"The first method involves adding the path to a folder containing your " +"scripts to the `PATH` environment variable. This allows you to execute " +"the shell script directly (without explicitly using the `sh` or `bash` " +"commands)." msgstr "" -#: ../../src/faq.md:89 45ee965ee4a7494a8354b82208e2ab45 +#: ../../src/faq.md:93 34ebca4487a54ceab5d087105820e945 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 734cc1abe1c841ffac8d0895463d91fc +#: ../../src/faq.md:99 6b04a4dcdada4515b28d74aacff3537a msgid "" -"After that, make the script executable with the command `chmod +x scriptname." -"sh`" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 f01bc8c4d6134f0ea27dc7f5b39def24 +#: ../../src/faq.md:101 756ab4f7edcf42d3872bb86818e088c3 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 dd6fc2a04e3b476892f05bc5b746d0fa -msgid "" -"Now you can use `baseCommand: scriptname.sh` to run the script directly." +#: ../../src/faq.md:108 efb46b3a2d7c4c51b65998602bfa6f18 +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 e309eaad55144052866ce131eb80fd14 +#: ../../src/faq.md:117 844938d5d2304c6cb03184b4b4b0b024 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 f0d649a60a13404ebecd540789202b87 +#: ../../src/faq.md:119 796ce8155e32486d9651f8f13bfa3148 msgid "" -"The second method involves including an input of `type: File` in the script " -"itself:" -msgstr "" - -#: ../../src/faq.md:135 e2b782f88d494de398af0c9002a3ccdc -msgid "In CWL, everything must be directly stated." +"The second method involves including an input of `type: File` in the " +"script itself:" msgstr "" -#: ../../src/faq.md:138 b4a033731fcd4322bd2bb71c609a4cb7 -msgid "Setting `self`-based Input Bindings for Optional Inputs" +#: ../../src/faq.md:138 ba246320fdd94a1aab4736f83718d793 +msgid "How can I set `self`-based input bindings for optional inputs?" msgstr "" -#: ../../src/faq.md:140 43a64810b12b4c7d82a5803c3b910fe5 +#: ../../src/faq.md:140 6169b7be9af7448abcb57eaf91e1cc91 msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their input " -"binding makes use of `self`. Below is an example workaround for this, " -"pending a more sophisticated fix." +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 60f009e3714c405695da069204b196ea -msgid "Model a \"one-or-the-other\" Parameter" +#: ../../src/faq.md:165 6c98b7948059411b8e09cf03a552c5ab +msgid "How can I model a \"one-or-the-other\" parameter?" msgstr "" -#: ../../src/faq.md:167 98916ed9355842e49bef073430e10675 +#: ../../src/faq.md:167 d1424da3f43c4519a4c4735f4a720341 msgid "" -"Below is an example showing how to specify different strings to be added to " -"a command line, based on the value given to a Boolean parameter." +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 9b8f2d0b33db4bbc82aaf5836b6f7ed8 -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +#: ../../src/faq.md:188 5c9980839f404ba6aef92ef23034500f +msgid "" +"How do I connect a solo value to an input that expects an array of that " +"type?" msgstr "" -#: ../../src/faq.md:190 a251693354d24bf0bda4938c8890090a +#: ../../src/faq.md:190 2525baf16c1f4725b096f33fd99009cf msgid "" -"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" -"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +"Add a " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput):" msgstr "" -#: ../../src/faq.md:194 f46740ac0acb473583facb9f7528d03c +#: ../../src/faq.md:194 a00d5d96b15048a79ae099d22d63bb42 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 7de1f9e3175b4c2ab156192f28fd3535 +#: ../../src/faq.md:196 3a92c6cc5c2b40ffa0d692d03bad5c87 msgid "" -"The input must be an array consisting of exactly one entry for each input " -"link. If \"merge_nested\" is specified with a single link, the value from " -"the link must be wrapped in a single-item list." +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 225c6f08068e41f58eb62f99dc06210f -msgid "Which means \"create a list with exactly these sources as elements\"" +#: ../../src/faq.md:199 3af16c07e3f148ddb8849c94a3864158 +msgid "Which means \"create a list with exactly these sources as elements\"." msgstr "" -#: ../../src/faq.md:201 4e741f4e3bc74e10bd9568826e81c478 +#: ../../src/faq.md:201 0ea3de393d2f42aeb82658c85a19ec45 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " -"add `linkMerge: merge_nested` under the appropriate `in` entry of the " -"destination step." +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." msgstr "" -#: ../../src/faq.md:229 bfdb011cb81c4ef9b9e56b24f1e9ccd5 -msgid "Optional Inputs 💯" +#: ../../src/faq.md:229 2f1bbb611c9c4f80b7ae0566432f2f35 +msgid "How do make an input optional? 💯" msgstr "" -#: ../../src/faq.md:231 09f385e325f942afaa3dd195c16a18d2 +#: ../../src/faq.md:231 08a226efe5d141e68215ac77725033db msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 c5d087082bb2468483e7ccda3ca45a07 +#: ../../src/faq.md:247 06e70a855a8f455ca0536eead77073c2 msgid "" msgstr "" -#: ../../src/faq.md:248 41e30b0224a0492f9047b4f320f39a23 -msgid "Enum Inputs ⚜️" +#: ../../src/faq.md:248 7fda8eeb6a7f4689993ed0118c77f023 +msgid "" +"How do I specify an input that must come from a list of predefined values" +" (i.e. How do I use enum inputs) ?" msgstr "" -#: ../../src/faq.md:250 f06d073014a44f33a60d947a8c5b0e59 +#: ../../src/faq.md:250 b1934a82553b4da3b7f981e576245dd8 msgid "" -"For command line flags that require a specific input as the argument an enum " -"type can be declared in CWL. **Specifying null here is known as long form " -"style. It does the same thing as the question mark on the other inputs.**" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" msgstr "" -#: ../../src/faq.md:267 2fb74cd1b41e4fdb81a8f9b3b6c84373 +#: ../../src/faq.md:267 17fc34fad2094f5ea60e963dabd632b8 msgid "" msgstr "" -#: ../../src/faq.md:268 09e19f34d0fd4e388d4939cbc2be3436 -msgid "Record Inputs 📀" +#: ../../src/faq.md:268 4d7acfbeba5b4e9cb31f08ef4b280447 +msgid "" +"How do I describe dependent or exclusive input parameters(e.g. How do I " +"use record inputs)?" msgstr "" -#: ../../src/faq.md:270 1ecae448dfcf45a4ae0dd39bd011e449 +#: ../../src/faq.md:270 949ce95c082f4a05891a55fee25d4873 msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 6df3d4e918cc4bccb823859ce07b197a -msgid "Setting Mutually Exclusive Parameters" +#: ../../src/faq.md:322 6fd3c469d11d4d52b9fbb7a3d443a8db +msgid "How do I set mutually exclusive parameters?" msgstr "" -#: ../../src/faq.md:324 086db1a093e64caa88d958150accc19c +#: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f msgid "" -"To properly set fields in a record input type, you need to pass a dictionary " -"to the input to properly set the parameters. This is done by using inline " -"JavaScript and returning the dictionary with the key of the field you want " -"to set. The source field is set to indicate the input from the workflow to " -"be used as the value." +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 da77c818d8694ab99fb2eccf73083047 -msgid "Setting Booleans" +#: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 +msgid "How can I set Booleans?" msgstr "" -#: ../../src/faq.md:344 254259509ed6462d8ebc296b5f811f44 +#: ../../src/faq.md:344 8dcb88744e5840029de0e1bbf1c4b967 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 f7a44f76579d4709a61d2d61bc352b76 -msgid "Concatenating Strings in Inputs" +#: ../../src/faq.md:349 972b7a5551bb43e6b9fa30e0cb713ff7 +msgid "What should I do when concatenating strings in inputs?" msgstr "" -#: ../../src/faq.md:351 d67278e99c684f488f1e3418e1c8c207 +#: ../../src/faq.md:351 68f74afc21d846dd9070d45dec0cc1d8 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 f5e35ee06cd24edf831589ebaa6193d2 -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +#: ../../src/faq.md:359 53b633c6f8644106beb95ae567eb0708 +msgid "" +"I get `cwltool` errors due to filenames with space characters inside. " +"What should I do?" msgstr "" -#: ../../src/faq.md:361 2ffb67e547c446499625a8db9a102da6 +#: ../../src/faq.md:361 7101bb5cb69e4faca4e60eabb4eb258e msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 ee653ff9fefe4771b35e2e76199b536a +#: ../../src/faq.md:363 0eaf834b0ca847cca6736794895f5f81 msgid "" -"For example, the filename `a space is here.txt` includes 3 space characters." +"For example, the filename `a space is here.txt` includes 3 space " +"characters." msgstr "" -#: ../../src/faq.md:371 02b1eb159e934fd692929f7c30319ddd +#: ../../src/faq.md:371 7dabd8aab7a5423b842433616640bac0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 857024702f624885be706c405b7a088e -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +#: ../../src/faq.md:373 b7ec33f38ce74ceb890f4379e4c41054 +msgid "" +"What should I do when I get CWL Parameter Reference error due to hyphen " +"in an input identifier?" msgstr "" -#: ../../src/faq.md:375 d664e30899bd463bb48d38adec318dd4 +#: ../../src/faq.md:375 e39b65947b294b20a444f18d780246f4 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 9f3957bbe205454e8bffc4b5caac5970 +#: ../../src/faq.md:384 dcd42c65681b438bb541fb38ddebb536 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 6ec3bbc6a1ca4e23b47f025f0732e609 +#: ../../src/faq.md:396 2b96665acac449758b852bbe7600e007 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 3e727d79e65e4c6cb157550e80261c53 +#: ../../src/faq.md:410 f59751d2f0014e59af7879a748062cec msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 6e0705f4ab4b4e9093794cb4fccb6be9 -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +#: ../../src/faq.md:423 7780f461ca4c478b92fca893c0b0894a +msgid "To fix this error, change `-` (hyphen) to `_` (underscore):" msgstr "" -#: ../../src/faq.md:436 0047d039317349679fb6a66d18ec8487 +#: ../../src/faq.md:436 88df56dfff854fc68fb6ad3835a846e4 msgid "" -"If it is not possible to change the input identifier, then you can use an " -"alternative CWL Parameter Reference syntax:" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 8c39608ad0494bee9a4a422cbeb34387 -msgid "Use CWL and cwltool with Singularity" +#: ../../src/faq.md:442 fc407a9e8d8c4b699d9cd14b369343b5 +msgid "How do I use CWL and cwltool with Singularity?" msgstr "" -#: ../../src/faq.md:445 7dac53bca8c14a3f9af75cb162cba4f9 +#: ../../src/faq.md:445 239f5f81cef042b08fb8015c36b3ecad msgid "" -"The CWL standards are built around (optional) Docker format containers. The " -"reference runner and several other CWL implementations support running those " -"Docker format containers using the Singularity engine. Directly specifying a " -"Singularity format container is not part of the CWL standards." +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." msgstr "" -#: ../../src/faq.md:450 ffcc38ff98324d71bfeb8d66d4901da7 -msgid "Debug JavaScript Expressions" +#: ../../src/faq.md:450 61641314d82b43e982e54c64c73232c5 +msgid "How do I debug the JavaScript in my CWL tool?" msgstr "" -#: ../../src/faq.md:452 0d7bf2cefe4a4e22b186bdf4d0ed793d +#: ../../src/faq.md:452 5556d3c323664edea55cfb777f4efb3b msgid "" -"You can use the --js-console option of cwltool, or " -"you can try creating a JavaScript or TypeScript project for your code, and " -"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" -"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 1506b4e7ee014a01bfdb067489501a9e +#: ../../src/index.md:1 1c9fb72b83c9467a9672943fb47ffe32 msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 0ce058b5210d46a0b78eb78dbca07a9f +#: ../../src/index.md:3 aaa44578e27345e682ab44686b4da159 msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 3404c064950d453d8af446e8b6554cb6 +#: ../../src/index.md:7 0adfc2adb0c74372b25d197dd3a73b8b msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 1e239cad669648e48694eaf91284766a +#: ../../src/index.md:9 96c8dca812f1415db7c5c006b0c0e022 msgid "" -"If you find that something is missing from this guide, or if you would like " -"to provide other feedback, file an Issue on the [project repository for this " -"guide][repo]. You can also suggest changes directly in a Pull Request by " -"clicking the \"Edit this page\" button at the right sidebar of each page." +"If you find that something is missing from this guide, or if you would " +"like to provide other feedback, file an Issue on the [project repository " +"for this guide][repo]. You can also suggest changes directly in a Pull " +"Request by clicking the \"Edit this page\" button at the right sidebar of" +" each page." msgstr "" -#: ../../src/index.md:16 9dba2e06f1be4a50b1fabaaf216d02b4 +#: ../../src/index.md:16 35c50bb5c3a345b4a4ae66b2df065376 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 ba4074bbb69e4096a808001afaf2e0dc +#: ../../src/index.md:18 9431edcf4e344fb89b6a251e627279d2 msgid "" -"If you are a beginner user get started with the [Introduction](/introduction/" -"index.md) section. For advanced users the subsections of the [Topics](/" -"topics/index.md) have detailed information about the most common topics for " -"CWL." +"If you are a beginner user get started with the " +"[Introduction](/introduction/index.md) section. For advanced users the " +"subsections of the [Topics](/topics/index.md) have detailed information " +"about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 ad34a37bf4ec488bb825a34456f4fe8d +#: ../../src/index.md:23 61cf57e61a9f46e5a1bff6368c5ad5e3 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " -"subsections. The right sidebar contains links to the sections of each page, " -"and the Search form is on the left sidebar." +"subsections. The right sidebar contains links to the sections of each " +"page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 2bd8eb5957ed40f4a72a6b7408044c78 +#: ../../src/index.md:28 94381840d8a848c4a02fa97bfe83566d msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 8bb0df5531474301a185f1ba375320df +#: ../../src/introduction/basic-concepts.md:1 c1271d88e203454688a22e61ee88f02a msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 653373e1f11e4f81ad561378854a71fc +#: ../../src/introduction/basic-concepts.md:3 dd462818cc9a4205b38866d0c5137ece msgid "" "This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are expected " -"to be familiar with workflow managers, YAML, and comfortable with following " -"instructions for the command-line. The other sections of the user guide " -"cover the same concepts, but in more detail. If you are already familiar " -"with CWL or you are looking for more advanced content, you may want to skip " -"this section." +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 7766227bf91b48b2b9752b625e5a9084 +#: ../../src/introduction/basic-concepts.md:10 7a56d394fb244431aefce7ebbb834ecf msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 032d414ac29740aa9041d89d0ebf70e6 +#: ../../src/introduction/basic-concepts.md:21 35800ed2c56d489190d3702d9ad20fd7 msgid "" "The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered in " -"this user guide is the {{ cwl_version }}." +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 74e92eb0a4e64098b5aaf08d043e0641 +#: ../../src/introduction/basic-concepts.md:25 3ab6dd6b2f694afeb08f3984a74f3efb msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" "incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes that " -"are backward-compatible. The last number is used for bug fixes, like typos " -"and other corrections to the specification." +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 baa40b445f3c409b9a3e10a85fa38bfd +#: ../../src/introduction/basic-concepts.md:33 72ae1fb763a34c41b1b06adcbe1522c3 msgid "" -"The model used for the specification version is called Semantic Versioning. " -"See the end of this section to [learn more](#learn-more) about it." +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 648e94a9d368450dbdac706445254c9f +#: ../../src/introduction/basic-concepts.md:37 5aa7d3ee6cb048d888f1e1f49d0e08be msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 e9ae15124dcd408395fc67e16b50696a +#: ../../src/introduction/basic-concepts.md:39 c87e6daefda74579a39924777b2e6809 msgid "" -"An implementation of the CWL specification is any software written following " -"what is defined in a version of the specification document. However, " -"implementations may not implement every aspect of the specification. CWL " -"implementations are licensed under both Open Source and commercial licenses." +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 b1c864d6775048cab01eb3de641f6475 +#: ../../src/introduction/basic-concepts.md:44 c995e699ae2949219af252f9d802a43d msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud " -"and high performance computing environments where tasks are scheduled in " -"parallel across many nodes." +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 a05d24121e534d65947eb26e4dada5b7 +#: ../../src/introduction/basic-concepts.md:51 09171f48a3d841b2acb6d803b2340c8e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: ace0388fd04845e79d31ec99a48a8a3f +#: 1c1647a3496c4251a3193f94ee4e78c8 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 70ecd37237e14ae19539f2bf692882ed +#: 854633336f4d4fc394e62c53ce022c6b msgid "" -"A process is a computing unit that takes inputs and produces outputs. The " -"behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification " -"{{ cwl_version }}:" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 38121b4b00324bebb6499184b3dcb5c1 +#: 142a847f11d7462f8bf77bfe789410ca msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: e0c278f52e824673ac708885d985b7d2 +#: 7c7567fa690043f9b4b89bdf8ca60cad msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: 6b4d0f0651cc46f5abf195b281967913 +#: 7afcf087d3ea49dabf1a641a2bb71b35 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 88bdc9e046e4487cb0eee3f1d4819e57 +#: 6399939602334819a20b92b957352a8a msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 12eed3ef7d444585b150bbdab0665bc8 +#: 8c55b15cebf142899045f229ccc86b1e msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: dfc85226313d46f9868dc4de53546a69 +#: ec54c0e67e894bfba2d0fbb0f87ffdf4 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: f636b10c47734e589291de95443d8115 +#: c88ad26efa794cbeb6f0690aa0cad5ea msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be used " -"to simplify workflows and command-line tools, moving common parts of a " -"workflow execution into reusable JavaScript code that takes inputs and " -"produces outputs like a command-line tool." +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: bb51025d04444dd5b16000d5d6a3f41a +#: 946825a7ea2c450eb3e41b5548670fb7 msgid "" -"Operation is an abstract process that also takes inputs, produces outputs, " -"and can be used in a workflow. But it is a special operation not so commonly " -"used. It is discussed in the [Operations section](../topics/operations.md) " -"of this user guide." +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 93dbaa0aa2c6493ab22a937c6861fac4 +#: 44aac23f302c4178accf7e431cfbb96c msgid "" -"The workflow is a process that contains steps. Steps can be other workflows " -"(nested workflows), command-line tools, or expression tools. The inputs of a " -"workflow can be passed to any of its steps, while the outputs produced by " -"its steps can be used in the final output of the workflow." +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: fcde5ef65ebf45a3b4b67eec993a1729 +#: 5afdb7aaf0bf4c1abf4c22cdbdd58be9 msgid "" "The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through *requirements*. " -"There are many requirements defined in the CWL specification, for instance:" +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: c8ff34ff5d3b4a508e8c291196d08067 -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +#: 07c5789c59224ed78a3ecd03cfe872e9 +msgid "" +"[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement)" +" - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: fe25f15fc11c49ab827b884d081c3df0 -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +#: 6f9854ae1b884ad39f88d2f39d66cb98 +msgid "" +"[`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow.html#SubworkflowFeatureRequirement)" +" - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 2b93b6219142431ca748a404a56ced5d +#: 23fef6de073f4da18118e4d0512670fe msgid "" -"`InitialWorkDirRequirement` - controls staging files in the input directory." +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow.html#InitialWorkDirRequirement)" +" - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 0094b13b26014ba3be61769b422802f5 +#: fb3762f91177401ea624d1e716d67ae6 msgid "" -"Some CWL runners may provide requirements that are not in the specification. " -"For example, GPU requirements are supported in `cwltool` through the " -"`cwltool:CUDARequirement` requirement, but it is not part of the " -"{{ cwl_version }} specification and may not be supported by other CWL " -"runners." +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: 576a0778d3dd44f68cb241346f441660 +#: b6a5cd431c324078a9a4e1513a14ee28 msgid "" -"Hints are similar to requirements, but while requirements list features that " -"are required, hints list optional features. Requirements are explained in " -"detail in the [Requirements](../topics/requirements-and-hints.md) section." +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 7d98949fe97744158fad81f41d780de9 +#: 88d7bad84dd341d2abb33673b8b8f250 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: fc142b791aa1434aa75b0782248de988 +#: bcbf5d76cf5f47b2a9691b7d2d8ef891 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " "machine accessibility and that all digital assets should be Findable, " "Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created. It " -"is thus important that workflows support the creation of FAIR data and " -"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" -"workflows.community/groups/fair/), Workflows Community Initiative." +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows both support the creation of FAIR " +"data and themselves adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: c3fc91ae3bae4e3db60e8271e95135a2 +#: 4ea1d3bf04dc42f0bc6735a45b9e0dc0 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\", " -"CWL tasks are isolated, and you must be explicit about your inputs and " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " "outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 8f097ae5ff6a4be0b7428345362dc55e +#: c0f53138bf084939a54b0a576b44199f msgid "" -"The benefit of explicitness and isolation are flexibility, portability, and " -"scalability; tools and workflows described with CWL can transparently " -"leverage technologies such as Docker and be used with CWL implementations " -"from different vendors." +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 60c56fa6a67346d6966f0d841213e11b +#: 91d6eb4984a6410ba99616b6617ba9af msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 7377b155e8694798994bbc911a3f3152 -#: 7699685836064bd89db530a9c1918865 7d187a209ebd4e3ba6c6aeb05743041a +#: ../../src/introduction/prerequisites.md:183 +#: ../../src/introduction/quick-start.md:94 0d7e607b00b9485aa2e3c5fb0a931bc6 +#: 161697ed3e864155bb89d8be794fc139 b4a7563eabf547c3bf7eab2567a27b51 msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 3fcbf810c86f4cf7b8499de88147aa95 +#: 7221a89559944627b4c3db37f468f72c msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: e242228b6b3d440cbca8418050220267 +#: bccf086fc9514f76b60dc161e3a09da3 msgid "" -"The CWL Specification page in the CWL website: " +"The CWL Specification page in the CWL website: " +"" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 6e01963a01cb49e39692455256679bfc +#: a5b37924c7d04ab984ff2542847afc4a msgid "" -"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +"The Command Line Tool Description Standard: " +"<[https://www.commonwl.org/v1.2/CommandLineTool.html](https://w3id.org/cwl/CommandLineTool.html)>" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: ed81ea2234b041c79449dcd20f886cb6 +#: 44af015fa36644b99f07338d241d29c1 msgid "" -"The list of Implementations in the CWL website: " +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e8e3996f6a894b4f9cc266b46cb8d756 -msgid "PROV-O: The PROV Ontology - " +#: bffca993172048a4b7ab7c62637662e2 +msgid "" +"The list of Implementations in the CWL website: " +"" msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: 085e4d1a7a9744d2884f3003c64ca174 +#: 84c61946406347c8b138772909110d54 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:186 +#: eb0b6a62e06143eabc7b92acff9643ea msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 dcd96950854f47a6ad4169320c1dab34 +#: ../../src/introduction/index.md:1 48532f7701c54166859098e521a43db0 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 c4d17eec31874bf1ae9b49d73537d86c +#: ../../src/introduction/index.md:3 08db628a949b4513b824ee334e70a7df msgid "" "This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that " -"are useful to know before reading the rest of the user guide." +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 98a8bdfc7c91436d9cb46abbb7c19c57 +#: ../../src/introduction/prerequisites.md:1 d3f5749a76c14fdf8052f5f683d11b9e msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 244a716e267540c782e627adaea3a413 +#: ../../src/introduction/prerequisites.md:6 ab9e21b3e99641d096ba70012b4eb035 msgid "" -"The software and configurations listed in this section are prerequisites for " -"following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements focuses " -"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " -"runner or workflow system, but the results and interface may look different " -"(though the exact workflow outputs should be identical)." +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 2cdf453d2c8b4e2ea50555ef0b7364e5 +#: ../../src/introduction/prerequisites.md:12 8ed426ebcb744839915e7c414d69b1e9 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 53643a4f190c412d9552d1908f408318 +#: ../../src/introduction/prerequisites.md:14 ff74d48407464c4b9d451fa419137144 msgid "" -"There are many implementations of the CWL standards. Some are complete CWL " -"runners, while others could be plug-ins or extensions to workflow engines. " -"We have a better explanation in the [Implementations](basic-concepts." -"md#implementations) section." +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 1df6c63de3914af68f758054fe6955f4 +#: ../../src/introduction/prerequisites.md:19 eb98aa9c71d746a69e9610996ffc5b47 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 ceaa3a6bebab45a0907ee0cad01429a2 +#: ../../src/introduction/prerequisites.md:21 209a0018e7da48f09b27dc507ba14d24 msgid "" -"We recommend using an up-to-date operating system. You can choose any of the " -"following options for your operating system:" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 1506ac904c6345c5806704a0ccf235aa +#: ../../src/introduction/prerequisites.md:24 8baf869537ea478791356320280df928 msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 a616213ed24e427bb91ee33cb21ec131 +#: ../../src/introduction/prerequisites.md:25 248e9760ce60442eb10ab7247d6af23b msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 a4e9ae38103843739f13c62befd21f3e +#: ../../src/introduction/prerequisites.md:26 d89306bbadf44b6bba8959f1f68cc2f0 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 2cd231aac42c4a69a925cea369999a8b +#: ../../src/introduction/prerequisites.md:29 aeeb990abbbd42cca122c342054be29c msgid "" -"If you are using Windows, you will have to install the [Windows Subsystem " -"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " -"installing WSL2. Your operating system also needs internet access and a " -"recent version of Python (3.6+)." +"If you are using Windows, you will have to install the Windows Subsystem " +"for Linux 2 as documented in the [`cwltool` documentation for Microsoft " +"Windows users](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users). Your operating " +"system also needs internet access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 051d7cd7d3a94baa865d180afdd71688 +#: ../../src/introduction/prerequisites.md:34 21d1f29fb15745c480194eae6acdd031 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 1a93aaf5bd5e4862b15e0636b4478640 +#: ../../src/introduction/prerequisites.md:39 89f0bf6ff8544a6d87114085be8e0bb6 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL community. " -"It is also the CWL reference runner, which means it must support everything " -"in the current CWL specification, {{ cwl_version }}." +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 edd0613118a2493c876652bdcb9e0fbf +#: ../../src/introduction/prerequisites.md:44 068f09d4d66547448693f7b9dadef497 msgid "" -"`cwltool` can be installed with `pip`. We recommend using a virtual " -"environment like `venv` or `conda`. The following commands will create and " -"activate a Python virtual environment using the `venv` module, and install " -"`cwltool` in that environment:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:51 3448d215c2434866b8a4b340872ba81e -msgid "Installing `cwltool` with `pip` and `venv`." +"`cwltool` can be installed with `pip`, `apt`, or `conda`. We recommend " +"using a virtual environment like `venv` or `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 4c24d05f65794735b816024c78b63f1c +#: ../../src/introduction/prerequisites.md:48 1edf8b8438334ae29dc406dbfd711228 msgid "" -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool#install) for other ways to install `cwltool` with `apt` and " -"`conda`." +"Visit the `cwltool` " +"[documentation](https://cwltool.readthedocs.io/en/latest/#install) for " +"details on installing `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 3167f4a2a8394feda1f848334be62022 +#: ../../src/introduction/prerequisites.md:52 5e300141ce43435f9437507374987213 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 3c4b67d62c9c4d658ccaafcd1977ec08 +#: ../../src/introduction/prerequisites.md:54 282ac7ba2a2346feac2456bcda0f214a msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 30792f78348942e0acdde411342e8830 +#: ../../src/introduction/prerequisites.md:60 0b36f94f479a4bce9bd9be9983894421 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the CWL " -"standards. However, these actions will be performed without running the " -"document. To validate CWL workflows (or even a standalone command line tool " -"description like the above) pass the `--validate` option to the `cwltool` " -"command:" +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 4473e41281fb4e738e4eb26c2d178934 +#: ../../src/introduction/prerequisites.md:66 5fce122794e34892b430ca4bdba5ba50 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 548393974d4d4acc91738f9bc13a3a48 -msgid "" -"You can run the CWL tool description by omitting the `--validate` option:" +#: ../../src/introduction/prerequisites.md:71 73f074f47d1449dcb40ff960a84851fd +msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 2ab3963cf9504ec097eda2b14f3448c4 +#: ../../src/introduction/prerequisites.md:73 2dd5a67870ca41b48e17c468ba15888b msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 690882dcc29c48acbeb215a8be52eb9e -msgid "Cwl-runner Python Module" +#: ../../src/introduction/prerequisites.md:78 d2dc809318be49cc996d892e93ad84ac +msgid "Generic ``cwl-runner`` alias" msgstr "" -#: ../../src/introduction/prerequisites.md:93 6c3ba51b1e9a4add9203d62cec6ebae9 +#: ../../src/introduction/prerequisites.md:80 9809c2e262924ef286b0bd62e0b00995 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be invoked " -"independently, and is not reliant on a particular CWL runner program name. " -"Users can invoke `cwl-runner` instead of invoking a CWL runner like " -"`cwltool` directly. The `cwl-runner` is installed by a system administrator " -"or user to point to the preferred CWL implementation. This is convenient for " -"environments with multiple CWL runners." +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 b2360ef646854422ad6c0f90fa49306f +#: ../../src/introduction/prerequisites.md:88 6dd6aa836099469381fb564d63b84f3d msgid "" -"The CWL community publishes a Python package with the name `cwlref-runner` " -"that installs an alias for `cwltool` under the name `cwl-runner`" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:104 c9fadfa85a2641378e99a462e8e8d940 +#: ../../src/introduction/prerequisites.md:91 cc1a9b95508e44a1bf08ae75d990c301 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 abb8993ede4d4e479d88d2e848546f68 +#: ../../src/introduction/prerequisites.md:98 8f8c80f705d94d4899b250bbf9c54562 msgid "" -"Now you can validate and run your workflow with the `cwl-runner` executable, " -"which will invoke `cwltool`. You should have the same results and output as " -"in the previous section." +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 ba0f7606e6174e53a8bf23c1ccd99250 +#: ../../src/introduction/prerequisites.md:102 176e4214d18149f3ba0bda692bcf760f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 dd2e10f43e8f498cb01de5faa4fccb70 +#: ../../src/introduction/prerequisites.md:107 4890bf20bc3842d3a7421b555bcda94a msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 e500e9c71c7042169c25b31f21a09142 +#: ../../src/introduction/prerequisites.md:112 2475a83cf6ed4389bb680fa37e8fe69c msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For " -"that, the first thing you need to do is copy `true.cwl` workflow into a new " -"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 d989516c873f4446bba005f42796b8b9 +#: ../../src/introduction/prerequisites.md:116 24da787aa76c4480838a93ba0533898d msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 e9d8610478094a98b5b5a0f568a315de -msgid "" -"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +#: ../../src/introduction/prerequisites.md:122 4f3cb8d1f9ce4e3d852e81aa4e0f60be +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 d6d8131f91b740189e56ab9d90bee55a +#: ../../src/introduction/prerequisites.md:124 27693d62faa045d9b03143d9bd2afcdf msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 def7400a00e84070a4bd80c2367d3bde +#: ../../src/introduction/prerequisites.md:131 703531514abe4fd48015c472005dbffa msgid "" -"And finally, you can execute it directly in the command-line. On execution, " -"the program specified in the shebang (`cwl-runner`) will be used to execute " -"the rest of the file." +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 564e7be94d254e52a6c44b234d6ddc63 +#: ../../src/introduction/prerequisites.md:135 abba2e14c4e54252bb75983274663a7a msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 bb5fe42ddd814ad4ac1071c0b18f24c2 +#: ../../src/introduction/prerequisites.md:141 11fea992c00940d29eb29ccf4b9370e9 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute the " -"script using the executable specified after the shebang. It is considered a " -"good practice to use `/usr/bin/env ` rather than using a hard-" -"coded location, since `/usr/bin/env ` looks for the " -"`` program in the system `PATH`," +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env [executable]` rather than" +" using a hard-coded location, since `/usr/bin/env [executable]` looks for" +" the `[executable]` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 53bb712a68cd49fca4db11e9e507c9a4 +#: ../../src/introduction/prerequisites.md:148 854736eef2ac4b63b187a4cea9660ae4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 bdcf61cce5294e45a9f964628a8a66bd +#: ../../src/introduction/prerequisites.md:150 480fbb7a743046068c114fff5b396a9f msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 28d33daee6e246c8a6d1382208e19c39 +#: ../../src/introduction/prerequisites.md:154 28da3eea8fd245d1936013d021c25164 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting " -"and better auto-complete:" +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 b071d7c87b7a4817b871085a652cd580 +#: ../../src/introduction/prerequisites.md:158 73c08e11e90d4c7f952307a1cdaa360b msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " +"Visual Studio Code with the Benten (CWL) plugin - " +"" msgstr "" -#: ../../src/introduction/prerequisites.md:172 97658a1b16874ba8b0bb748242d0da64 +#: ../../src/introduction/prerequisites.md:159 a5b788252a924338963f0ed198fc22ca msgid "" -"cwl-plugin for IntelliJ - " +"cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 6198aa6769b74ef0a2a1ba539789f3ee +#: ../../src/introduction/prerequisites.md:161 ee705b919acd461a8d9622821da246b6 msgid "" -"The CWL community also maintains a list of editors and viewers: " +"The CWL community also maintains a list of editors and viewers: " +"" msgstr "" -#: ../../src/introduction/prerequisites.md:177 0c17235a374e40099be37b9b8ac8f1f0 +#: ../../src/introduction/prerequisites.md:164 7724b63db3cc45139379898d047c0f83 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 e3690e656b5a4348845c654689935a88 +#: ../../src/introduction/prerequisites.md:168 eff13997c1ce43d1ad2d7a4d927394fe msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: ." +"documentation to install it for your operating system: " +"." msgstr "" -#: ../../src/introduction/prerequisites.md:185 2db34e925a81422986ccb868463a7a42 +#: ../../src/introduction/prerequisites.md:172 2872503638624b7e904ae407375ac165 msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models with " -"and without containers." +"examples, and to clarify the differences between the execution models " +"with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 d677fb155b0343ba8771398cca967fed +#: ../../src/introduction/prerequisites.md:178 52ddcc9bc1554d809371fc0a503c40bc msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for pulling " -"images." +"Singularity. You can also use alternative container registries for " +"pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 22ed0b55de38408393af4a8309a995ea +#: ../../src/introduction/prerequisites.md:185 f3bbfa17f31a459386461951de157dd2 msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the next " -"section, Basic Concepts." +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 5ded73cae5db40ad840c3022e7cd447f +#: ../../src/introduction/prerequisites.md:186 e22b9e7c56104e018e6d2f3d547c01ea msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 23e5613df7c94e5f938c85b14f5441e4 +#: ../../src/introduction/quick-start.md:1 9ca367e3ca754a0fa88dab64724b95b6 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 3b425afc63d841d4be57c92b25b4ed2d +#: ../../src/introduction/quick-start.md:3 733db5702c774f32b8c91d13f74f3720 msgid "" -"This section will show you a brief overview of what CWL is, and where you " -"can learn more about it. No previous knowledge of CWL is required, but you " -"must be comfortable following instructions for the command-line." +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 75a26c48d3e04e24abb96d81cb31c94e +#: ../../src/introduction/quick-start.md:7 0b164074dd0849c3b2c8d2f78ea99e95 msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 88b4ecd45ea44dd4befe3ce89b30f6c2 +#: ../../src/introduction/quick-start.md:12 6485f96f638548fbb7addc57f6cde92b msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " -"example below shows a simple CWL “Hello World” workflow annotated with " -"comments. Note that comments start with `#`:" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 e1789ef78bd64332a18d8601094a0f72 +#: ../../src/introduction/quick-start.md:16 5e06f9c4754347b8bac88d24c21e0f67 msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 196ceef96c27434eb4b0b7222c2fe73c +#: ../../src/introduction/quick-start.md:22 6a13fb9112ab41acb60dc65b3656f63e msgid "" "The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the " -"same result as the command-line `echo \"Hello World\"`." +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 e6a44130c6b44d5bb6451a147f28dd8c +#: ../../src/introduction/quick-start.md:27 7b2ae93353184faea0ae4f4acdfc3350 msgid "" -"In CWL, there is a distinction between a command-line tool and a workflow. " -"But for the sake of simplicity, we are using the term “workflow” here. You " -"will learn more about this in the [basic concepts](basic-concepts.md) " -"section." +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 340b46acc7a34b7b978f5a734f529553 +#: ../../src/introduction/quick-start.md:32 1ed30b04073d47a9893774746479fb5d msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 139e48dcf0474fea932ca07a0001d208 +#: ../../src/introduction/quick-start.md:34 73a42cd9e0e54296985088b7221a8a93 msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the CWL " -"*Reference Runner* for the specification, and it is compliant with the " -"latest version of the specification: {{ cwl_version }}. You can install " -"`cwltool` using `pip`:" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 d6f6e061c0f4434eb6d70f9d84759042 +#: ../../src/introduction/quick-start.md:39 57aea587ade24610be62f5d993b0b755 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 cb2b548489df45ee9d49b36116440eea +#: ../../src/introduction/quick-start.md:47 51183fc986014edbb026a53f222e6c2e msgid "" -"If installing the cwltool using the pip command doesn't work for you, the " -"[prerequisites](prerequisites.md) section contains other ways to install " -"`cwltool` and a more detailed list of software and libraries used for " +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 aa751bda67ec44ba988642b061e2a094 +#: ../../src/introduction/quick-start.md:51 a7582c3ae37a462a8ae1e72b3f321534 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 a7e0209af0544b0ab31012864a43886c +#: ../../src/introduction/quick-start.md:53 0595e96912dc40e5a09f2ced2d2b7bcd msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " -"workflow without specifying any option:" +"[OPTIONS] [CWL_DOCUMENT] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 d0f424f0041c4635a0559fa32a76c86f +#: ../../src/introduction/quick-start.md:57 5b393c69816549b084516dda4d4274f5 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 eeee96c4e59447aea6b239c63e4bb3e5 +#: ../../src/introduction/quick-start.md:62 4306d8ad802f45c18487d932d04492fa msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 961a385b340141e980aa4f8791fa2f12 +#: ../../src/introduction/quick-start.md:65 8339ec411ad04c70ab8d795eb154fc38 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 c48cd1be543d4ccbab964b28c2e08584 +#: ../../src/introduction/quick-start.md:70 3ecca6985e754951aee00c93effe9517 msgid "" -"Another way of passing values to your workflow input parameters is via an " -"*Inputs Object*. This is a file containing the input fields with their " +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " "corresponding values. The Inputs Objects file can be written in JSON or " "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 e5619164bdf242f0b09cac668adc0ef7 +#: ../../src/introduction/quick-start.md:74 d05e8e016b1d40c28c4b6091103fe920 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 9f80772a53154bbeb27895d35435de10 +#: ../../src/introduction/quick-start.md:80 c5983ba6c86f4b749522c11cb3843911 msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 98b6d400cb274d08ad6489adbef08c4b +#: ../../src/introduction/quick-start.md:82 4065124edf3a4678a37c82e3070595cb msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 4faabaab56f1444da290cf64cc389f37 +#: ../../src/introduction/quick-start.md:88 52b1602b5c8d48db88d0b16f788e7703 msgid "" "We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but it " -"is not a requirement. You can choose any name for your workflows and Inputs " -"Object files." +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 48beaccb16a24427bd015c63f9e06d37 +#: ../../src/introduction/quick-start.md:96 3b06faf5f3194bd8a96118d9f050f61e msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 68035ead1c6844128011ca32c04fd20f -msgid "" -"[List of CWL Implementations](https://www.commonwl.org/implementations)." +#: ../../src/introduction/quick-start.md:97 669b8ac154e74181830a430b1dc7684b +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 8fc1ebf21a6f4894a4acfba74a80602b +#: ../../src/introduction/quick-start.md:98 1c888f1b771d49b3a257ed534b5afa0a msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 27fbad579d8b4ebeacc6fd3ef7e85a39 +#: ../../src/introduction/quick-start.md:99 dbce82b7a930493486a585ecb8891121 msgid "" -"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" -"Common_Workflow_Language)." +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 a8791b670848474da292a467f01f8c45 +#: ../../src/introduction/quick-start.md:100 dc714ffd4278421b9f2417f41627722c msgid "" -"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." -"org/wiki/YAML)." +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 fc20fa4c04104417b541a67ada2ab9a9 +#: ../../src/introduction/quick-start.md:101 2bf7b924182f4f2bab88edef5ef85baa msgid "" -"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." -"replace('VERSION', cwl_version_text) }}." +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 a93a7797a12b48dfa5bc3a7c50ab88e7 +#: ../../src/introduction/quick-start.md:102 936a7dfab11a4f2c82c0b59964e3ea28 msgid "" -"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" -"Workflow_management_system)." +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 6f02fa47aca14c59a35b3ab750f5f236 +#: ../../src/setup.md:9 24ea9c5144664d9599d7aca767b4730a msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. The information on this page has been migrated to the [FAQ](/faq." -"md) section of the new user guide." +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 3821c2d16b254672a494522e47386cb0 +#: 3843684b039a40dea163de951ca56738 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: 412a05f3492349a7bd26ea0c30e9bd80 +#: a6fd1842b938435aa2a3c889019eec71 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 1232f6c81da141cb8482294eee5955dc +#: dfed0747ed544547afd364086d828c9b msgid "" "In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files in " -"the same directory as the source file. However, CWL input files (and the " -"directories in which they appear) may be read-only, so we need to instruct " -"\"javac\" to write the class file to the designated output directory instead." +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 485bb71673144e3f90f05b420b7079ac +#: e690b567eae34f3f8dbdd7760e51449a msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0beb10c3133643f6b62c7d4aeec33709 -#: 5d48d9a2e977431f9a3625abaa466f5f +#: ../../src/topics/staging-input-files.md:15 4cee519b108143be89a0e47a75d7d649 +#: 79585673fd654bab9ba7c1927d7e153b msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: fcc1151a2e8b4a84b8595c7f913781a1 +#: ef070ebe5f7245489b05660fb6d7c178 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 4a291c7ac7c84257b7402567d8364a36 +#: 4ae43e3e841442039e4bb8c740096c56 msgid "" -"And now invoke `cwltool` providing the tool description and the input object " -"on the command line:" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 3b1ae26038fd498ca0ae23aa70a35d3f +#: 8497291577914eb3a172c1ffb736d95d msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: 40388ebefb6947089c4a0f6d5d6e92e8 +#: dc9fa5f2cbb147b1853c4042c54010f3 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include `$(runtime.tmpdir)`, " -"`$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and " -"`$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of " -"the CWL specification for details." +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 a417fdd330db47a3aac07f7006c83ca9 +#: ../../src/topics/best-practices.md:1 964bf8276dd04b65887448e1386e63fe msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 99bad0fd9bee428a8d936d5a8e84d97d +#: ../../src/topics/best-practices.md:3 7b59377bd56c47b8a71c18acfba4d3bb msgid "" -"The following are a set of recommended good practices to keep in mind when " -"writing a Common Workflow Language description for a tool or workflow. These " -"guidelines are presented for consideration on a scale of usefulness: " -"although more is better, not all are required." +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 935500b0e6e249eba585644cddbd0253 +#: ../../src/topics/best-practices.md:8 2292670347cd4549bc6a51e972de0ef4 msgid "" -"No `type: string` parameters for names of input or reference files/" -"directories; use `type: File` or `type: Directory` as appropriate." +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 96f924d6e02f4005b35d463e49be2982 +#: ../../src/topics/best-practices.md:11 ae127b776eed4894af8cb680377703e0 msgid "" "A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that " -"the usual rules of software licensing apply to this document. For example, " -"if the workflow is shared publicly, licensing terms must be clear so that a " -"future user understands under what conditions they can run the workflow, " -"modify it and/or combine it with other workflows. For this reason, please " -"consider including a license field in the document. The authors of this " -"guide urge you to choose a pre-existing license rather than trying to write " -"your own (see the link below to learn more about choosing a license), and " -"our recommended practice is to choose a license that allows for re-use by " -"anyone, e.g. [Apache 2.0][apache-license]." +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." msgstr "" -#: ../../src/topics/best-practices.md:20 25e0a5c93ccc49bc8b6206c7c2e3de5c +#: ../../src/topics/best-practices.md:20 384eb620dc31468e8c3f5f33a3436200 msgid "" -"If possible, the license should be specified with its corresponding [SPDX " -"identifier][spdx]. Construct the metadata field for the license by providing " -"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " -"taken from the list of identifiers linked above. See the example snippet " -"below for guidance. For non-standard licenses without an SPDX identifier, " -"provide a URL to the license." +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 34ad53bc5a40446daa0dac4571600d1e +#: ../../src/topics/best-practices.md:26 e8259b43fa6944eda73eae381db6b97b msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 4c397ffd2e9148e39bdd614683a98a78 +#: ../../src/topics/best-practices.md:28 5b976a5aec7d44bda55b0a019e955416 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 1ed7f7e73afb4bd2ad2e29b65d020ff1 +#: ../../src/topics/best-practices.md:37 924b8df24deb4c82b32732f491c9a246 msgid "" -"For more examples of providing metadata within CWL descriptions, see [the " -"Metadata and Authorship section of this User Guide](../topics/metadata-and-" -"authorship.md)." +"For more examples of providing metadata within CWL descriptions, see [the" +" Metadata and Authorship section of this User Guide](../topics/metadata-" +"and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 13b058dfa3cd4bbea54ae7d5a56c4c50 +#: ../../src/topics/best-practices.md:40 9e64a9fc89cb45cfbff0e925cc91b1be msgid "" -"Include [attribution information][license-example] for the author(s) of the " -"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" -"[orcid]." +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 69369b917c1a45199343266650b1b220 +#: ../../src/topics/best-practices.md:44 87030aef02044b8283c76debab4772bf msgid "" "In tool descriptions, list dependencies using short name(s) under " -"`SoftwareRequirement`." +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "" -#: ../../src/topics/best-practices.md:47 0245a61fd2ef4fb69cbb8d732086fb8f +#: ../../src/topics/best-practices.md:47 6c9eaae099fa4ca4b0986b1c4146df50 msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" -"identifiers.org/rrid/RRID:SCR_NNNNNN` format." +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 e9a56e3634a042279cae1745b7820658 +#: ../../src/topics/best-practices.md:50 5ae8950fd31541399c2fe59096581dbc msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1368,216 +1399,224 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 8a180861a66c4aaa9e8fdefd929ed829 +#: ../../src/topics/best-practices.md:55 b0493895105e43849bff2026763e472a msgid "" "In tool descriptions, include a list of version(s) of the tool that are " -"known to work with this description under `SoftwareRequirement`." +"known to work with this description under " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "" -#: ../../src/topics/best-practices.md:58 00f333a383b64578b32c687b42924a77 +#: ../../src/topics/best-practices.md:58 88806cb0462f4359801c1fa0ff0ebcc0 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with " -"`$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " -"[Full IANA media type list][iana-types] (also known as MIME types). For non-" -"bioinformatics tools, use or build an appropriate ontology/controlled " -"vocabulary in the same way. Please edit this page to let us know about it." +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 6b960d362bb540299f0560c14c5f2d8c +#: ../../src/topics/best-practices.md:66 b178c7296ed5491782a4180c76883c14 msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 9cf9342bf0864e87b495913d8e06d021 +#: ../../src/topics/best-practices.md:69 886d15c1972243acadccff5760f842f1 msgid "" -"Each `CommandLineTool` description should focus on a single operation only, " -"even if the (sub)command is capable of more. Don't overcomplicate your tool " +"Each " +"[`CommandLineTool`](https://w3id.org/cwl/CommandLineTool.html#CommandLineTool)" +" description should focus on a single operation only, even if the " +"(sub)command is capable of more. Don't overcomplicate your tool " "descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 587b048324e447cb85844d8c64ae9a1e +#: ../../src/topics/best-practices.md:73 ef5a5f9b253c4ca3916802a695fb7c6d msgid "" -"Custom types should be defined with one external YAML per type definition " -"for re-use." +"Custom types should be defined with one external YAML per type definition" +" for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 d8df6bbd5d324f7c9f48edb33e113b75 +#: ../../src/topics/best-practices.md:76 ff59f40e84004523904e3094be07cc80 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 2235174088ad48a89d4fc21223e627b7 +#: ../../src/topics/best-practices.md:78 78d73fde24e24beeab541a623d9530b6 msgid "" -"If useful, include a top-level `doc` as well. This should provide a longer, " -"more detailed description than was provided in the top-level `label` (see " -"above)." +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 a0f0953a1a9f40cebd4dbe028784ff96 +#: ../../src/topics/best-practices.md:82 d92013d662b44dbf8875e06c9dfbfd79 msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list of " -"valid values." +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 0ec380c683534892b6b8b8fcea84f765 +#: ../../src/topics/best-practices.md:85 c100d5192a52497fb6a890b81a388fcf msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. One " -"common example: manipulating `File` names and paths? Consider whether one of " -"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " -"`nameext`, etc., could be used instead." +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 65f23741db4e4a6abda8e5f7e036753a +#: ../../src/topics/best-practices.md:90 e22fbacdb2fb4202b1bd69cfc24af5cd msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 34c2caee8eb84e01a37033b67eb4aaba +#: ../../src/topics/best-practices.md:93 0060a863362140f6bb3932cb5da1df04 msgid "" -"Complex workflows with individual components which can be abstracted should " -"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " -"workflow modular and allow sections of them to be easily reused." +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 d7c7484b2f1048aea9802400410f0858 +#: ../../src/topics/best-practices.md:97 93f6d6b544c24ce780184272f66bacab msgid "" "Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics " -"software\"][containers] (also useful to other disciplines)." +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 a905abc2eead4dbaa035235936025499 +#: ../../src/topics/command-line-tool.md:1 a378a2f7d268401abfbbbe6e5090a952 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 eb91b6dab34d4d5f9854ac580a6cbde2 +#: ../../src/topics/command-line-tool.md:3 cf0f1c00c0b34c94a8e2460a700c303e msgid "" -"A command-line tool is a type of Process object that can be run by itself or " -"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " -"etc. The command-line tool is defined in the `baseCommand` attribute of the " -"command-line tool CWL document." +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 7caeb91564634091a932f1270c4f5ef9 +#: ../../src/topics/command-line-tool.md:8 7a180ba1f2d746a78b79be7e899cbad6 msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The following " -"example contains a minimal example of a CWL command-line tool for the `echo` " -"Linux command, using inputs and outputs." +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 c6ac4a60d102407991f40b892fb60560 +#: ../../src/topics/command-line-tool.md:19 128bd8cd6788431da54fa07a8dc87f99 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 51d3ce421db345f5ab19e02fbbc51df2 +#: ../../src/topics/command-line-tool.md:50 d742e9e59ea44ca1a1df2de85059343f msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 8311d1430e624435b7b04bf2574a90c5 +#: ../../src/topics/command-line-tool.md:57 e3a06ebe51b64b0183673a8acc04969f msgid "" -"The example above uses a simplified form to define inputs and outputs. You " -"will learn more about in the [Inputs](../topics/inputs.md) and in the " -"[Outputs](../topics/outputs.md) sections." +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 d1c03e5f19d64ea89276d126de6e4bda +#: ../../src/topics/command-line-tool.md:68 2bab464d19d14562a6501373aff13905 msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 8494b43e98dd424db7d57aa1d731f7b4 +#: ../../src/topics/command-line-tool.md:69 201712f3ceee4d4ea56ab96d3fef97b0 msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network access. " -"If a command-line tool is written manually in CWL v1.1+, there is a need to " -"specify when network access is required." +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. Starting with CWL v1.1, programs are not granted network access " +"by default, so you must include the requirement for network access in the" +" specification of your tool." msgstr "" -#: ../../src/topics/command-line-tool.md:83 8c4573fb120149269a0fe3a1ba6c9ef8 +#: ../../src/topics/command-line-tool.md:84 3282a357799f4a72a6b8bace206144c4 msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " -"Access automatically." +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 or v1.2 " +"will have `networkAccess: true` set automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: e1c709ac0fb249928d14aeced6551ae0 +#: 17c5b4ee43cc4a979676ad27e473d046 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: c26c9c640e0747c8b2c2977c860c9d82 +#: cd0dff10471c4ad2b84e3a0e4d7767ea msgid "" -"Sometimes you need to create a file on the fly from input parameters, such " -"as tools that expect to read their input configuration from a file rather " -"than the command line parameters, or need a small wrapper shell script." +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: edbe918d7df14cafb440e171e46c6de3 -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +#: bf4aea0a22334a1ca75cc20e937e6581 +msgid "" +"To generate such files, we can use the " +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 6d457d9b4ae746d384e65d9a37ca3591 +#: 008f768d56b8465bb4e8f4fde15853a7 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 868394c1b8374ee6bbd43463e73d7edc +#: 252f8e897b0942a8be098481890005f3 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the value " -"at the input `message`." +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 08a9e08cba674db09c9bfbef37e9579f +#: aca24b72687c4d4d84bf9de8b71413f7 msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later " -"during command line tool invocation. That means that any genuine need for " -"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " -"above is expanded to `${PREFIX}` in the generated file to be evaluated by " -"the shell script instead of the CWL engine." +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 6f6f437753dd4eddae0b2ea62046fe39 +#: 750b3232e8754448bc2b5913539495b8 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 096b17907bc3452d9927ef2fb6f5c11f 78ed5d8fb9bd4e068023d2c717e20f62 -#: c3a2e9e6b4414597a17db6d55d98e9d1 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:81 +#: 687c8a84bade43269f3cd767d32f9f47 81da7a18fe8d4659abc883cf43009f1f +#: d5d67eae63304ebb9b242133feacb0d1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: ac783e6415a44cb59d4b425bac5087b7 +#: c4f964450d014734877fb3c968353a74 msgid "" -"Before we run this, let us look at each step in a little more detail. The " -"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " "command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: b9e6e15b541149c6a2d3922c11405267 +#: 9aeea5a6a4244bc7a1626e0cb7351068 msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " -"array, we need a `-` on the first line of each element of the array, in this " -"case we have just one element. `entryname:` can have any value, but it must " -"match what was specified in the `baseCommand`. The final part is `entry:`, " -"this is followed by `|-` which is YAML quoting syntax, and means that you " -"are using a multiline string (without it, we would need to write the whole " -"script on one line)." +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 87088899567a4402aeb34605d3c6b06b +#: 867239e9ad3d4187a2703662a0ca3976 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1587,222 +1626,228 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 304c1bfe5ecd4d26b5dfaf9ad2e2c7f8 3ef7f0e3099147d78fd2d30bfa73cc6b -#: 4fef79a30282456eb9b5dd34a5eec0b1 afe775762ed348e5982b99bcf1451606 -#: f0689cd0e5b34414b6693331186ee4a3 +#: 0d7151b9f0194197bd686fe6c9c47afd 78bb40eeeda24d7b923162daa45d51a7 +#: 7b341a317347482ca86fc56119c3686f 7c637fa62cab4d0dbe670a3b72737cc9 +#: cfb4605a01dd4475aabcc086a4e65957 msgid "" -"Now invoke `cwltool` with the tool description and the input object on the " -"command line:" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 9f1967411aa7497fa43a4851f0645d6e +#: ../../src/topics/custom-types.md:1 252a3a17b1ec4d5a9a82ebbf6c2f314c msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 90bd62e4ef8b41e398a5c9b31f132774 +#: ../../src/topics/custom-types.md:3 e0275ddda8f84207a58d10c17ca99a45 msgid "" -"Sometimes you may want to write your own custom types for use and reuse in " -"CWL descriptions. Use of such custom types can reduce redundancy between " -"multiple descriptions that all use the same type, and also allow for " -"additional customisation/configuration of a tool/analysis without the need " -"to fiddle with the CWL description directly." +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 3465527b8ff4407587f7c46fa9fa2a98 +#: ../../src/topics/custom-types.md:9 8367e38e5e7c4a298d1d87b9001aaddc msgid "" -"The example below is a CWL description of the [biom convert format][biom] " -"tool for converting a standard biom table file to hdf5 format." +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 c0cc869690804ada96a5c1813d17b895 +#: ../../src/topics/custom-types.md:12 18b802f45ce0454ab7aa2a21812863c6 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 01f369931c8142c08fe821a0ca31bf92 +#: ../../src/topics/custom-types.md:18 66d1953f5dd54d448bddd0f30c330402 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 0b3ff704cdea44e28aee3c704ca98e27 +#: ../../src/topics/custom-types.md:24 56b8912a1ea84f28adeb8beaf92ab563 msgid "" -"___Note:___ To follow the example below, you need to [download the example " -"input file](https://github.com/common-workflow-language/user_guide/blob/main/" -"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " -"*rich_sparse_otu_table.biom* e.g. via `wget`:" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 cb456bcae0dd41ffbc514eeea283e130 +#: ../../src/topics/custom-types.md:30 a48539920c4944898918bc90b2d4e3c9 msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to be " -"used in the table conversion are imported as a custom object:" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 c610173365d04c57900b22f4024b47b4 +#: ../../src/topics/custom-types.md:46 c791096f537141e8bd7cc941d711d108 msgid "" -"The reference to a custom type is a combination of the name of the file in " -"which the object is defined (`biom-convert-table.yaml`) and the name of the " -"object within that file (`table_type`) that defines the custom type. In this " -"case the `symbols` array from the imported `biom-convert-table.yaml` file " -"define the allowable table options. For example, in `custom-types.yml`, we " -"pass `OTU table` as an `input` that tells the tool to create an OTU table in " -"hdf5 format." +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 c2b2e18d55c94721812431583cfc4725 -msgid "" -"The contents of the YAML file describing the custom type are given below:" +#: ../../src/topics/custom-types.md:53 5f6bc6ed72334a74b9a4c46c29ddda46 +msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 3e61c3920a7a45db8917c348bd44384d +#: ../../src/topics/custom-types.md:55 3b55419088e8446994703220bd8e8480 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 cd87d210b03c4da2a7608b40a6bbcca0 +#: ../../src/topics/custom-types.md:61 fe6f4ce5e7344af0abea9d5c03e32ecd msgid "" -"In order for the custom type to be used in the CWL description, it must be " -"imported. Imports are described in `requirements:SchemaDefRequirement`, as " -"below in the example `custom-types.cwl` description:" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 7af9ba3219e44ed49b8da781db5d6fb5 +#: ../../src/topics/custom-types.md:76 dce43b138ba24b22bfa9fa5692a17009 msgid "" "Note also that the author of this CWL description has also included " -"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " -"cores required for the tool to run successfully, as well as details of the " -"version of the software that the description was written for and other " -"useful metadata. These features are discussed further in other chapters of " -"this user guide." +"[`ResourceRequirement`](https://w3id.org/cwl/CommandLineTool.html#ResourceRequirement)s," +" specifying the minimum amount of RAM and number of cores required for " +"the tool to run successfully, as well as details of the version of the " +"software that the description was written for and other useful metadata. " +"These features are discussed further in other chapters of this user " +"guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 eae1994f3a4d481b863b5125c7f4a383 +#: ../../src/topics/environment-variables.md:1 19737f89f2994815969fa4a88346f49a msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 8bd8c06d416740b69d126eb9f5f24ad3 +#: ../../src/topics/environment-variables.md:3 ad965f75aa0c41cda8b82c46af49774d msgid "" -"Tools run in a restricted environment and do not inherit most environment " -"variables from the parent process. You can set environment variables for " -"the tool using `EnvVarRequirement`." +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 11c6bffc620b4c789b29ab4034a8bfbd +#: ../../src/topics/environment-variables.md:7 38b276f9b0114a0bb87734f0a07a736f msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 89888b1b994546ce8a93f9630b4bb07e +#: ../../src/topics/expression-tool.md:1 9f33532119dc47ffb6ade20fb1d950bd msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 191d3010b9244b39bc3bc50246ac7ad7 +#: ../../src/topics/expression-tool.md:3 b267056eae704737af5aaada3ea7e6e2 msgid "" -"An expression tool is a type of Process that can be run by itself or as a " -"Workflow step. It executes a pure JavaScript expression. It is meant to be " -"used as a way to isolate complex JavaScript expressions that need to operate " -"on input data and produce some result as output." +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 3437ed6e184748e4af1ef62f32c8cef1 +#: ../../src/topics/expression-tool.md:8 7e930144163e4d6e9f0bcaa764497ccf msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " -"instead of `baseCommand`, it requires an `expression` attribute." +"instead of `baseCommand`, it requires an " +"[`expression`](https://w3id.org/cwl/CommandLineTool.html#Expressions_(Optional))" +" attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 c3ae1ef318bb4e0fada76c353dd5f6f1 +#: ../../src/topics/expression-tool.md:17 f172488c19a94d688036197117d30b38 msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 a7f5e04d242c48a7b3deffb5ff6528be +#: ../../src/topics/expression-tool.md:48 ef978c951f1a4b7d9280d31367e5bae7 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 32b6841faed044409bc618cba54a22f0 +#: ../../src/topics/expression-tool.md:67 0b63da31bc274b3cad798b07149592ab msgid "" -"We had to use an `InlineJavascriptRequirement` as our expression contains a " -"JavaScript call in `.toUpperCase()`. This means to tools using the " -"expression tool that JavaScript is a requirement." +"We had to use an " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" as our expression contains a JavaScript call in `.toUpperCase()`. This " +"means to tools using the expression tool that JavaScript is a " +"requirement." msgstr "" -#: ../../src/topics/expressions.md:1 6821ba7a84a44d309d245c429948ad09 +#: ../../src/topics/expressions.md:1 b0e567a985f748538552bdb486a47998 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 8167269bc3a64c72bd6c909362350a15 +#: ../../src/topics/expressions.md:3 24d05cbbab8e460e99f2edc97ab0dcec msgid "" "If you need to manipulate input parameters, include the requirement " -"`InlineJavascriptRequirement` and then anywhere a parameter reference is " -"legal you can provide a fragment of Javascript that will be evaluated by the " -"CWL runner." +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" and then anywhere a parameter reference is legal you can provide a " +"fragment of Javascript that will be evaluated by the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 c0f75603a6024063a6911f17c70908cc +#: ../../src/topics/expressions.md:9 3d48d1a8f7f74bc1886e41653cb53a22 msgid "" -"JavaScript expressions should only be used when absolutely necessary. When " -"manipulating file names, extensions, paths etc, consider whether one of the " -"[built in `File` properties][file-prop] like `basename`, `nameroot`, " -"`nameext`, etc, could be used instead. See the [list of best practices](best-" -"practices.md)." +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 7faec63b389a4c07b6929b7a78f0cc70 +#: ../../src/topics/expressions.md:16 7d444aacd418466bbe588fa964b45179 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 d7dca89942f949d58cb18cb94bb7de72 +#: ../../src/topics/expressions.md:22 72a0558a83964796a8c1a0eb55fd78e8 msgid "" -"As this tool does not require any `inputs` we can run it with an (almost) " -"empty job file:" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 1abc1a21c0764415b138099e0e21432b +#: ../../src/topics/expressions.md:25 d679fd1363b24c81979c68e7342159cf msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 b8b5a50a82e44e49a37c6396f1ff9464 +#: ../../src/topics/expressions.md:31 d2ee4fcece744b6681f29322b5305111 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object is " -"represented simply by a set of empty brackets." +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 b38d66c12ab74dfc9395e69d9c04bbf5 +#: ../../src/topics/expressions.md:35 624e4a270e374b1699b780df508b9184 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 8417aa7a9d034361a41def6b71e93413 +#: ../../src/topics/expressions.md:37 c252eac9a35e46aab08bd07bc1cdb57d msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 c1f672b377da4605b9c5098ebb6e1147 +#: ../../src/topics/expressions.md:47 f6f64d57a50742b19b801c14806ee18a msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 af52f5197e8545d2be22cc0f7f03648c +#: ../../src/topics/expressions.md:54 052e24e2ad044cc28f04d7f39be871d6 msgid "" "Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " -"describe the additional command line arguments." +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 5e12ce15018942bf9010ce6519c17b00 +#: ../../src/topics/expressions.md:62 84b31c076d4b4826aae35e8c23fe6a25 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 e2e9c5f7b681427a9589476649e5a9d8 +#: ../../src/topics/expressions.md:64 8c3b402c40f64880a4bd42c47b910254 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 8a74763ead0147bbaf3892e552fad546 +#: ../../src/topics/expressions.md:66 9bf5ca0e769147c6a9705bc40bd1febc msgid "" -"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 0aab7de8d69f49438d4eeed17316df68 -#: 75f90cb870d14d0dbb4c4ee80d32a65e +#: ../../src/topics/parameter-references.md:64 7ab0dbd54c1441539673fa12ef96b89e +#: e76c6ece0c594fefa86b190879c5acaa msgid "`arguments`" msgstr "" @@ -1810,35 +1855,35 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 0b9d8268c177489b86b8eaa638dfa063 -#: 204cd6d8375a4462a8247863a96df906 2b7e56ceb4ad49a8b29a58b10bad7c0a -#: 81f15c64379941d8ac2a681b3879761c f11ae7d801db45989b598864dc6291c9 -#: fc4534b475334f7281d1740c9a78f640 +#: ../../src/topics/parameter-references.md:86 0209558b1013471eb708698537edaf06 +#: 4458393fdb0e451f9806e91122ea2534 594a163e08f04aa5a04a44a303a1c643 +#: a6fddc160afc4ef09717f69de72c11ce a9ec99ddcb344bcbbe5c1f59af0bcff2 +#: af2cdb5f66ac4fd5b8f91258f005cc62 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 70e9085b21f640d6893309a3375c0511 -#: f529003dd7a64bc7be0ccef8dbfa84b3 +#: ../../src/topics/parameter-references.md:66 afb175f182354cb19e23b1cad241437e +#: f9a6718845e24f46b76fcc8ab26eec7a msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 3fceb522ba6245129b826c342eaf31b4 -#: a5f71add5b8345a4bfa02853ef8a6d35 +#: ../../src/topics/parameter-references.md:67 3bce21dcc2da439daca80c4fcdf4c343 +#: 7f5ce097ca0442a6a200599342a6e24b msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 018300196ea24550988a0156894b5e85 -#: 2c799286e8204ed9a83c3fc006988139 +#: ../../src/topics/parameter-references.md:68 3397e8816f6a4d4b9af728c175f04917 +#: 7b14686e16eb4f488659b22d67ec3bfa msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 25d91d6624bd42e7948e29c684e8e441 +#: ../../src/topics/expressions.md:72 7a2d74aa018f4cab8c68e8775d83dd01 msgid "" -"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter)" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" #: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 @@ -1846,11 +1891,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 0944d6525c3c460aa4b5a0e72552ca4d -#: 1187b0d330cb470fbea82a8b8c95aa28 265602307ccd42458ba47ac1b689242c -#: 2febce1b1ad74b18af3a9b3fa137c780 3215ee41f96541cbbda60a1167386c2f -#: 80efeab6ec0e447bbe158cbaa57f83d8 8d2bbd91b4ab4faa923fc1a14ec49dd5 -#: b4a6e640275b4fc7a18e3083e86b72a1 +#: ../../src/topics/parameter-references.md:90 24f27702d0684bc98e3232103510232e +#: 26a8dff7b80c4e059f1e20eef9da6203 476aa37af5214bcf963c7aab1f859273 +#: 4b0a0cd934bd41b4b55c034b91392bc7 5182e2165e44429287b4d924c2f896a4 +#: 7de500d3be6b4c3e8f274fd6a092109f 953d824a494947a3ab0ca2988717ee01 +#: b301751f90af4700bbada5e5b166be35 msgid "`format`" msgstr "" @@ -1859,1484 +1904,1538 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 480b2e4207574b27b8d33dfe5e9ab64e -#: 4b4149a3b97a4de5b2d7fd84bd547ffe 7af1a82df41e40d0a430babafe1bc5e2 -#: be01787b66e34074af32bb45dcce8657 be099ab533504a7596fd56ec1ce7ca5d -#: c8b96271665444608f601a460dd28fb3 cb6dfa7bc68b41929a5247d929c2f94a -#: f7f452e92f6d4a14ba3912c62699019a +#: ../../src/topics/parameter-references.md:91 2c2b8db396b04ace8aa396c0a5a4858f +#: 33a9b77ce15b4910962a7f08bd2f47a3 57cba0191de3470bbe112ed2a0d3f252 +#: 6efe998094b3469eae61cfff551b1eb1 776de1ecfafc41ada7e916addd7229fd +#: 8595d62eb0274b3a8a7f0adf058b51d3 988966a2d4844e73961b0358aff8f6e1 +#: faa7d521fec240748407d03ffdb93aa0 msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 4811c1b9867b44caa70dec4b91970484 +#: ../../src/topics/expressions.md:75 d737a9e9bf1c45d695bf584bc3241d9a msgid "" -"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding)" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 0b1f2a8986e0419a90e484d3a945a037 +#: ../../src/topics/expressions.md:77 0e2052e16f6a41b8983dc64b4b3a7586 msgid "" -"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 dbc02876870d49d2b9e39db4133a0f62 +#: ../../src/topics/expressions.md:80 dff31dd961d540e3b8cd1247e978d60e msgid "" -"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding)" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 97339a3fa43849f7b292f4643b5fe35c -#: da8b81b1e1884406a188fb04825ef90e +#: ../../src/topics/parameter-references.md:78 249aba7c38ce49379b9d35e7ad81a0bf +#: 5a354eb4883948e0a2b5c96b5ae12da7 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 077e7b0d2dde443699050af8c63ab912 -#: c8cbe3dfd0984221ae72012ea26edc6f +#: ../../src/topics/parameter-references.md:79 2325a310f2bc4d09b53b32c54efae2df +#: 9e477e2cfab24861b517fe2fb52962f4 msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 3f07f4a8594640c2b2da4da521872b59 -#: 573f7e4b72ec4c47ab2e54e2c4877d9c -msgid "From `Workflow`" +#: ../../src/topics/parameter-references.md:80 9448462d104b4be5904623c85a9e16b7 +#: bf11a7a72147445c9b8e44b541e09f36 +msgid "From [`Workflow`](https://w3id.org/cwl/Workflow.html)" msgstr "" -#: ../../src/topics/expressions.md:84 f03011b3479b47c690604c508d95c263 +#: ../../src/topics/expressions.md:84 0d54a777a33d4f17a2f3390384a3c0c5 msgid "" -"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" -"v1.0/Workflow.html#WorkflowOutputParameter)" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 1ec3f913909b4e04bb602767d23bd85d -#: 2f7130500b8c450fa4af226b18e38407 +#: ../../src/topics/parameter-references.md:84 7918d0661be746faaddf25ad49172f30 +#: b8439dbaa949427097e25ccb48fe15ee msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 a5849a856a374cda807ecf48034af915 +#: ../../src/topics/expressions.md:88 7b37eb600c9b4847a58a7e5077bef4c3 msgid "" -"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 bd8bbd60aaff4e7aacec91bcbad500f4 -#: f0c99004211e4adf8c0b524d5bbcc12b +#: ../../src/topics/parameter-references.md:87 368ef005c2ca4b8599f76242f7178375 +#: ab1ba7626eae483a8b614ee4cd5bab6f msgid "" -"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." -"html#ExpressionTool)" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 96c544cf213245cfb3d1f5196223c6cc -#: c6a04d4f3ef24104b0a86f9093935c13 +#: ../../src/topics/parameter-references.md:88 595b9ddcee734d6595c1b4b2d169dcb8 +#: 80b55c77a4384644acfc9472c3cedee0 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 946e0437a48b4d5da2a29d489250cbaa +#: ../../src/topics/expressions.md:92 fd504478a6c641e0a72321fa80ad1c9c msgid "" -"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [ExpressionToolOutputParameter](https://www." -"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 1f287ebf87ae4e93bd1ac65cc1d01bf4 +#: ../../src/topics/expressions.md:95 32b1a39cca1a4402af9bdc0abc4d70c8 msgid "" -"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement)" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 0d0f4f0e12174d588c131afef70efc5f -#: a74e0e3499d644b4a9d999d3555f03de +#: ../../src/topics/parameter-references.md:93 2518d499801e4bcf82e9e4666280504d +#: 98a511d138e9497c923963c2ca5f0a0b msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 b2e31c38f7cb4ecabd6b9b89ef051c0e -#: ddc9d9ae72a64a76a2a8e2bba22584ee +#: ../../src/topics/parameter-references.md:94 57a055b125f742dc8842b798b034161b +#: e84bc5505a6549ae9aacde8cb9225403 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 12f86817dfc14f2bb39509886d56017f -#: 8a94f2c3b1674162a268f67935a3025b +#: ../../src/topics/parameter-references.md:95 98cd455e080f43749090270e7a61cb42 +#: e698ea756fe94e99837312fb30c9f9bf msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 a800acfefb3f433fae2cdda9ac4a795a -#: bcb58fc2447a4472b86913871b8c12ee +#: ../../src/topics/parameter-references.md:96 8dfae10004a641fdb95c456c90a48d94 +#: bef90c153d4f4397b1f69f9beb38f7e6 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 5be337d412ba4d48877e991d535e810c -#: e6cf2f8498db4f549193be20d87e16f9 +#: ../../src/topics/parameter-references.md:97 47fddc711ce44086a7811bdfbd9167dd +#: e2bdf4fe676346cbb4443ee54fb7419b msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 3bc61c8197664f12a98d1ac38b421b38 -#: 9973a87f747445ad89ce959420cac5fd +#: ../../src/topics/parameter-references.md:98 7d143ba98f1f4dfcbe08b70389d43092 +#: 8f1665baca2e4e3b96026b50d132709a msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 0f5dc4f5a4c64f818e2e22f20472ae84 -#: 2ec9d1f191f44686b1cb8622336d6b92 +#: ../../src/topics/parameter-references.md:99 79bea45c2a484eda92c8578130b0b982 +#: d169949866a24e31947dffcb94620c5f msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 5382ff97ad2f419dbe1bed266997aa84 74406f77013443f28d4d6306c54b0df1 +#: 8d2e01f2aa314f1cb1231f2e08f89ce5 d5417397b1e242ef9878ac77d2f65005 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 f594a20dc038457e815dc17bae6e031d +#: ../../src/topics/expressions.md:104 08a66b2ab271494d810ff5834ca5c1bc msgid "" -"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" -"CommandLineTool.html#InitialWorkDirRequirement)" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 5814f96ee4ec4822aecad33c8eda0473 c46c44268b2a4b96b1df13e53e82e54c +#: 21e9582891cf4b87a7ee4693663040fa 51bc6d1ccef14729a0d5e63b56d73d20 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 b9824103ef8745bab30b65887c82f62f +#: ../../src/topics/expressions.md:106 7d8755f05d6541439f72ec9d6806d3fc msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 28b23f84c64549e7a0fe444ccc3e1b05 fdd5d742a6764e5db2281ed844bf3475 +#: 29c2424fc7dc43e68c9bfee179167bb3 30f25141bcce4670882e4a5bbe4fc3e2 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: b6123c911c804f3c8cb596d2aa495b2b d81a7d8b7db444409b286e5f1d863968 +#: 02cfd4f1c3014e1eaa598a329dc5a95d d76fb015595e4194a7e15d714baaaf98 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: eb6255a0f8d748588d87e7ad38e507bd fffc5a80bd68495396d32b7a1821eb4e +#: 408f69a2df1343a78f93ff2ac0a994ea d37c78309e8b427f835af4fbd367e643 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 b00a8a2a572742e0929470550433e929 +#: ../../src/topics/expressions.md:110 53752bdff0974e39b2a86e8f2d96455f msgid "" -"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef)" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 9b34c95e483e47f3828e79bf929a23b4 c968eebaf0114b23b789e9ce68e7588d +#: 242a12ec757947db894195c9aefba818 7b26b9972f7141bf950b3bb024b0e369 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 7c8fb996d1af4cfdb0d49d8ed2696745 -msgid "" -"Using External Libraries and Inline JavaScript Code with `expressionLib`" +#: ../../src/topics/expressions.md:116 93d6c90b49d8424f9283c384062ce333 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 75a29e9ff2cf4b5bb6afa87a741a111b +#: ../../src/topics/expressions.md:118 ea6cbaa5dae647538c0bd9a4d5cad3f9 msgid "" -"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " -"attribute that allows users to load external JavaScript files, or to provide " -"inline JavaScript code." +"The requirement " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" supports an `expressionLib` attribute that allows users to load external" +" JavaScript files, or to provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 5233d8baa8b74391bf8fee5ae2324234 +#: ../../src/topics/expressions.md:122 484dc17440524cfda4dc486a7c5d5f63 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts of " -"the CWL document." +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 343e8b78a1f94b8cbafac05212e5a333 +#: ../../src/topics/expressions.md:128 5b2336cae1ef4cae8ed187d3f33cff25 msgid "" -"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." -"org/v1.0/CommandLineTool.html#Expressions) that the only version of " -"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" -"international.org/5.1/). This means that any code that you include or write " -"in your CWL Document must be compliant with ECMAScript 5.1." +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 0657ee8f03d8462ca6ca6fc538386b0d +#: ../../src/topics/expressions.md:135 32eca3a47efc4685bf7be706e123adbe msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " -"function inline in `expressionLib`. That function can then be used in other " -"parts of the CWL document:" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 e3c593cf50da426f8d9df215c7db0bc9 +#: ../../src/topics/expressions.md:139 6839a02fb82d45c29ae518f2b00cb9d5 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 b971e53c3ed847f1b7c7a6d50e344baf +#: ../../src/topics/expressions.md:146 5b5e59fa1688499ea4560ee6f8023227 msgid "" -"Running this CWL workflow will invoke the JavaScript function and result in " -"the `echo` command printing the input message with capital initial letters:" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" msgstr "" -#: ../../src/topics/expressions.md:149 d2315d46369f4e9d9c871d7f88f7006e +#: ../../src/topics/expressions.md:149 a1e57c6833c848d3974cf448493ab924 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 04fdaa45a7ed47d5830181611bda924e +#: ../../src/topics/expressions.md:155 1a4dfef06b5c4402bdb7e7dbd79eeb5d msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 8d7686f62f314d98aae8c262befd5283 +#: ../../src/topics/expressions.md:158 71ac99c65d15451cbbf58d1e81934010 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 e68ee17607be4a06a66f9fc67624aff5 +#: ../../src/topics/expressions.md:164 60918e53189243d3872e61c7a4de20fc msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 76b85d3729274fc08adfadcbf1172650 +#: ../../src/topics/expressions.md:171 ad2a74bd983b47869dc78b2eb7b6fce1 msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 29f334957fa940c289f385160cca6d63 +#: ../../src/topics/expressions.md:175 82c02dd2446b4de9a4c4b87736107b30 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 6d255ae6b92a48fa9b7b98443cc2f5bb +#: ../../src/topics/expressions.md:181 6fa7ebeffc7b44c6a12cd84897d186a1 msgid "" -"Finally, note that you can have both inline and external JavaScript code in " -"your CWL document. In this final example we have added another entry to the " -"`expressionLib` attribute with the new function `createHelloWorldMessage`, " -"that calls the `capitalizeWords` function from the external file `custom-" -"functions.js`." +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 89734e7855654b2e8bfddeea96241539 +#: ../../src/topics/expressions.md:186 d34f3e688d2d49b6bfcda4c962895d8c msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 1915f8e68f624027827d28f8e17d2dec +#: ../../src/topics/expressions.md:193 9e2774fc35b14832a0f92b7afaafd537 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 750f94edb4f84e45a276f6ab28fad95e +#: ../../src/topics/expressions.md:200 8b797cfb232f4e5da51f6c21e9a8e7e3 msgid "" -"The `$include` statement can be used to include a file from the local disk " -"or from a remote location. It works with both relative and absolute paths. " -"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." -"html#Include) from the CWL specification to learn more about it." +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 2e9e8cfaf48a43a88c31a855dac4f748 +#: ../../src/topics/file-formats.md:1 ac906f26116c45d882e1afa42ae38e34 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 c574b54d998243f28d2caa91434968a7 +#: ../../src/topics/file-formats.md:3 d99dab4f2f264c68b839b59b80d570e0 msgid "" -"Tools and workflows can take `File` types as input and produce them as " -"output. We also recommend indicating the format for `File` types. This helps " -"document for others how to use your tool while allowing you to do some " -"simple type-checking when creating parameter files." +"Tools and workflows can take " +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types as input " +"and produce them as output. We also recommend indicating the format for " +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 b0ec34507eea473c91d6ada09a1c5c09 +#: ../../src/topics/file-formats.md:8 23ba3dd26f5543119e2c152105b58e98 msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM in " -"our example), reference a local ontology for your institution, or do not add " -"a file format initially for quick development before sharing your tool with " -"others. You can browse existing [IANA file format listings][IANA] and [EDAM " -"file format listings][EDAM] on their websites." +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 a688e39859734a518c0fcc19f532a432 +#: ../../src/topics/file-formats.md:14 81c441846fc249c58607bacf97095eb8 msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` section " -"of the document in greater detail, so don't worry about these for now." +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." msgstr "" -#: ../../src/topics/file-formats.md:17 e068422ad9b84ca1b27008127928cc0f +#: ../../src/topics/file-formats.md:17 c04841dbf4be4cf8a22cceca8b08bd14 msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 8c3ef5e145b14299bf3671add0da56ac +#: ../../src/topics/file-formats.md:20 c5f6f6e4c23e4bf19dee69acb8ebed8e msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 0d92f1c0f1ce448fb698e9b390b45c15 fc4773204ebc4e3789bb076dff0d0393 +#: 20e97d58596a4a959ad76ec6128ac414 4e070ae9110d437bbf008b0c60a00cd5 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 900abc5aa6a940f48f9c93e79cd1c47f +#: ../../src/topics/file-formats.md:32 632e441919094610b97afc17e9c5e625 msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 0390555b96c84aadbd9325c152972087 +#: ../../src/topics/file-formats.md:34 afd8633db1904897aa3e499354b1c376 msgid "" -"Below is an example of a parameter file for the example above. We encourage " -"checking in working examples of parameter files for your tool. This allows " -"others to quickly work with your tool, starting from a \"known good\" " -"parameterization." +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 d5752ee5437b496ca10f4f12b76fc5dc +#: ../../src/topics/file-formats.md:39 bb69d6963c174191bf527335c3f665b7 msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 91dc76bb4565473ab948eecf628a405c +#: ../../src/topics/file-formats.md:45 ddb4f6f81c7d462b974e98c88dd3f558 msgid "" -"___Note:___ To follow the example below, you need to download the example " -"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 0b8b9b7f533543a49f876421ce6057d9 +#: ../../src/topics/index.md:1 2995cd4fb85c423dba021611dac4a137 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 1b6cfac3a92347d4b98bb54de1e26870 +#: ../../src/topics/inputs.md:1 3bac021fe7614d74ae701fb3c3765b93 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 53dd5f476f064cbf9b9826d1e80eb830 +#: ../../src/topics/inputs.md:3 8bb3ee0cd0fc4d85ba007431fc541973 msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 420b33d143fc44d1b237bc678f0af663 +#: ../../src/topics/inputs.md:5 17365707f58242369dd6aa73fc8d7242 msgid "" -"The `inputs` of a tool is a list of input parameters that control how to run " -"the tool. Each parameter has an `id` for the name of parameter, and `type` " -"describing what types of values are valid for that parameter." +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 55136332e3bb48f892cf6a74c67a4ac6 +#: ../../src/topics/inputs.md:9 521cb5dead5d4e9ab5ff037fb4b683cb msgid "" -"Available primitive types are *string*, *int*, *long*, *float*, *double*, " -"and *null*; complex types are *array* and *record*; in addition there are " -"special types *File*, *Directory* and *Any*." +"Available primitive types are *string*, *boolean*, *int*, *long*, " +"*float*, *double*, and *null*; complex types are *array* and *record*; in" +" addition there are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 cb2527899cc04b6d8060c4d57883beb5 +#: ../../src/topics/inputs.md:13 fbdf2c1bed3e41d7a41ec6b14d134a98 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 c79668b856b14243b4fad0f46dc5d6d7 +#: ../../src/topics/inputs.md:16 008f79cdf0074c73948bf50deb0a8a47 msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 ed6f3e5c7b3f403a9a94359983107645 +#: ../../src/topics/inputs.md:18 94cd3f10e94f4735bd3ae7dc168e5deb msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 034075eb09db4897a96d3332408427db +#: ../../src/topics/inputs.md:24 b339be370e8742b69400c8040ad7d15b msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 08181d391cc543a5a81d3257654df213 +#: ../../src/topics/inputs.md:26 78974fb2475947ccb8b8c55e34df5fa6 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 15215522e38242c4b17ec3aa089269d4 +#: ../../src/topics/inputs.md:33 9cc4a60d01f945aa9b4c43afcf20098b msgid "" -"You can use `cwltool` to create a template input object. That saves you from " -"having to type all the input parameters in a input object file:" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in an input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 64bd3382ec234ec8a50217b794b96916 +#: ../../src/topics/inputs.md:40 5ac6da11d56446de97c251a37d997671 msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " -"> inp-job.yml`, and then modify the default values with your desired input " -"values." +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 3611c1ca498a4197a4a6612c60f5f565 +#: ../../src/topics/inputs.md:44 6a3edb0d259d4d7c900dd9811f978d4e msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 da924e8142d34e86bcb5de1cd1da71ca +#: ../../src/topics/inputs.md:47 f1d76be7ba0b48f4b605581d0a9a5c72 msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " -"command line." +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." msgstr "" -#: ../../src/topics/inputs.md:53 13c97256a5ee49c99f4010edf9dbc9bf +#: ../../src/topics/inputs.md:53 8cabfa0cbcfd4a5aa30d1aabd412136d msgid "" -"Now invoke `cwltool` with the tool description and the input object on the " -"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " -"boxed text describes these two commands and the expected output from the " -"command line:" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 dcc3f2a47a6449efb857af63ed4b65d0 +#: ../../src/topics/inputs.md:64 5c78d7824ef34636ae2ed68d524d79e8 msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not explicitly " -"specified" +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 cf54a30ae24f4013bb19f379a7ca67be +#: ../../src/topics/inputs.md:70 5bdf77c45346445d8f93353c1e73f768 msgid "" -"The field `inputBinding` is optional and indicates whether and how the input " -"parameter should appear on the tool's command line. If `inputBinding` is " -"missing, the parameter does not appear on the command line. Let's look at " -"each example in detail." +"The field " +"[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)" +" is optional and indicates whether and how the input parameter should " +"appear on the tool's command line. If `inputBinding` is missing, the " +"parameter does not appear on the command line. Let's look at each " +"example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 ff75644bae9c46af8379d78360d4c696 +#: ../../src/topics/inputs.md:83 d783fe52e86f4feda33ea0eecb622603 msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 e90abe59a84e48d4b8d6caa737e087aa +#: ../../src/topics/inputs.md:95 f99fb9a6d0374ef78503815d4db9006d msgid "" -"String types appear on the command line as literal values. The `prefix` is " -"optional, if provided, it appears as a separate argument on the command line " -"before the parameter . In the example above, this is rendered as `--example-" -"string hello`." +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 9275236d87b646cab1058dd750e11a50 +#: ../../src/topics/inputs.md:109 b106eed01c1744a792368f91f547e553 msgid "" -"Integer (and floating point) types appear on the command line with decimal " -"text representation. When the option `separate` is false (the default value " -"is true), the prefix and value are combined into a single argument. In the " -"example above, this is rendered as `-i42`." +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 6a39929af73f4ba9b6455ed9fd287e08 +#: ../../src/topics/inputs.md:124 1c70336741a842a5b16b687642d1d9b4 msgid "" "File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the parameter " -"is optional. In the example above, this is rendered as `--file=/tmp/random/" -"path/whale.txt`. However, if the \"example_file\" parameter were not " -"provided in the input, nothing would appear on the command line." +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." msgstr "" -#: ../../src/topics/inputs.md:131 44ce716561cc4dff8fef1ca59f816c7c +#: ../../src/topics/inputs.md:131 9294c07c672b414f9c3895ed70b9b4ee msgid "" -"Input files are read-only. If you wish to update an input file, you must " -"[first copy it to the output directory](staging-input-files.md)." +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 9f1da592350f40ee88920465e2004148 +#: ../../src/topics/inputs.md:134 a07137c36e63495f836c483fd472904f msgid "" -"The value of `position` is used to determine where parameter should appear " -"on the command line. Positions are relative to one another, not absolute. " -"As a result, positions do not have to be sequential, three parameters with " -"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " -"than one parameter can have the same position (ties are broken using the " -"parameter name), and the position field itself is optional. The default " -"position is 0." +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 5116d91f247f44518eb21840415f6eaa +#: ../../src/topics/inputs.md:142 7513adabd3ae4701b17f578ac9f321d7 msgid "" -"The `baseCommand` field will always appear in the final command line before " -"the parameters." +"The `baseCommand` field will always appear in the final command line " +"before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 08b26d1688e3470288e73d587f052d88 +#: ../../src/topics/inputs.md:146 c3c82d25a75941b0b50a4a6bb826568f msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 f91994a4279a41bda3de41fe79008c62 +#: ../../src/topics/inputs.md:148 b11a5c7a13b345939e4ae15e1e2c0786 msgid "" "It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to provide " -"`type` field with `type: array` and `items` defining the valid data types " -"that may appear in the array. Alternatively, brackets `[]` may be added " -"after the type name to indicate that input parameter is array of that type." +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." msgstr "" -#: ../../src/topics/inputs.md:154 4b93a4f980634e88a8f34a38703fc906 +#: ../../src/topics/inputs.md:154 aa00bcfc6c0f4085ae52621a2f4ae8d9 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 de3e760ebb0e4ae099deddb978046a2c +#: ../../src/topics/inputs.md:160 e730b2b9bace4427bdd045556963634f msgid "`array-inputs-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 06ec811e8f0e43b8b929198533ac8082 -#: 797c06f0605d4e4ba306c2803a7834f9 d76d42c490a24b6daed944f45fe7a351 +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:86 +#: ../../src/topics/outputs.md:109 015a0f00c2b245e2b0e87735926da736 +#: 390384208d7b4771888f164b587c7b9a edb3ae59c48945f29c3086b16a5265d3 msgid "" -"Now invoke `cwltool` providing the tool description and the input object on " -"the command line:" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 49406f30f62346968bb1250efc940f70 +#: ../../src/topics/inputs.md:178 13e59751d43b49f0ac366538a14f9c84 msgid "" -"The `inputBinding` can appear either on the outer array parameter definition " -"or the inner array element definition, and these produce different behavior " -"when constructing the command line, as shown above. In addition, the " -"`itemSeparator` field, if provided, specifies that array values should be " -"concatenated into a single argument separated by the item separator string." +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 3d8711f0135e4ab1b59fce94c83b97c0 +#: ../../src/topics/inputs.md:185 bb31c6784ea843ec88f185523cfa25df msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` in " -"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " -"where array values that are not defined with an associated key are marked by " -"a leading `-`. This will be demonstrated in the next lesson and is discussed " -"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " -"arrays of arrays, arrays of records, and other complex types." +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 6f146779d6a84888948751b8b1fd0515 +#: ../../src/topics/inputs.md:191 53817379078548b2aeb6195cae9cbab7 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 e5970a83876e4b5e9a02f2ab0030eb83 +#: ../../src/topics/inputs.md:193 e163c0cfe9694a85b2e42682f42970a5 msgid "" "Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be provided " -"together (they are exclusive). You can use records and type unions to group " -"parameters together to describe these two conditions." +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 0db71b22173846d7b8d4aeb66d2ed8ed +#: ../../src/topics/inputs.md:198 84e1ab25511c49d1baabb1f80f247b49 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 f90fd48656a7424aac304987adf1b068 +#: ../../src/topics/inputs.md:204 3d5dfc8ee47b458db638a9eed84b4938 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 3c8bd9134a1c4bda9461362df3257d6b +#: ../../src/topics/inputs.md:215 ecfb1d911a84400ba3db12fd0adf9279 msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 63bd06780bb949e5b1a1d10389c8c23f +#: ../../src/topics/inputs.md:217 24ba804374b4471d8e925d80670f9dff msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 0d448baa57f14e7783d3167611e8c659 +#: ../../src/topics/inputs.md:233 436707d9c7634732ad1e60d8294bd4ba msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the first " -"matching item (`itemC`) is added to the command line and remaining item " -"(`itemD`) is ignored." +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 202239a6e90044e39b676d641aa6d58a +#: ../../src/topics/inputs.md:236 01b168c5faf94ead8d836dfe39e4c592 msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 512ecb3349b0450cb741de4ed2d2e850 +#: ../../src/topics/inputs.md:252 e6d81d6549984689bae4533c6d01bd5b msgid "" -"In the third example, only `itemD` is provided, so it appears on the command " -"line." +"In the third example, only `itemD` is provided, so it appears on the " +"command line." msgstr "" -#: ../../src/topics/inputs.md:255 185ff0bb49e841c592b29112eb171bdc +#: ../../src/topics/inputs.md:255 ffddeeda8f04408ba73f7a59a4618da5 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 6cd5df09e4594d78a526f199ac577881 +#: ../../src/topics/inputs.md:257 cf22f21ec44c483986979316544a7c3b msgid "" -"If you use exclusive input parameters combined with expressions, you need to " -"be aware that the `inputs` JavaScript object will contain one of the " -"exclusive input values. This means that you might need to use an **or** " -"boolean operator to check which values are present." +"If you use exclusive input parameters and reference them in expressions, " +"you need to be aware that the `inputs` JavaScript object will contain one" +" of the possible, mutually-exclusive input values. Because the types of " +"these exclusive values may differ, you may need to check which type is in" +" use when you reference the properties of the `input` object." msgstr "" -#: ../../src/topics/inputs.md:262 9db9f784a5cd4ca5b90691d1e2e827ea +#: ../../src/topics/inputs.md:263 0fecb128b19b44d796b6c1b6de4f7166 msgid "" "Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from an " -"enum." +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." msgstr "" -#: ../../src/topics/inputs.md:265 09b1db3cc6c845058cf0ad4c24d71733 +#: ../../src/topics/inputs.md:266 7f1941698a6046e9b9e8a53736af949a msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 84aa6e0c479f4528836691005129056e +#: ../../src/topics/inputs.md:272 60b585142f06489d9f48090b664b6d32 msgid "" "Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you provide a " -"valid value, such as “fasta” (one of the values of the enum), your command " -"should execute successfully:" +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as `fasta` (one of the possible values of the" +" enum), your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 76611ebb19764bdc8a1f6eacfb76138f +#: ../../src/topics/inputs.md:281 11fdeb057d674f118830f431ff019c15 msgid "" -"However, if you do not provide any input value, then `file_format` will be " -"evaluated to a `null` value, which does not match the expected type for the " -"output field (a `string`), resulting in failure when running your workflow." +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to `null`, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your " +"workflow." msgstr "" -#: ../../src/topics/inputs.md:289 bf9750d215be4294b1cf1e0490a0796a +#: ../../src/topics/inputs.md:290 8594cca9d93b4280b6cfee64c8a7c578 msgid "" -"To correct it, you must remember to use an or operator in your JavaScript " -"expression when using exclusive parameters, or any parameter that allows " -"`null`. For example, the expression could be changed to `$(inputs." -"file_format || 'auto')`, to have a default value if none was provided in the " -"command line or job input file." +"To correct it, you should explicitly handle the possibility of a `null` " +"value. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value `\"auto\"` if " +"none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/inputs.md:295 b5055c77f85e43609fe3e9b9839778e3 +msgid "" +"Here, the boolean “or” operator `||` in JavaScript is used for its " +"_short-circuiting_ property. If `inputs.file_format` is “true” in a " +"boolean context (e.g. a valid non-empty string from the enum), the " +"evaluation of the expression stops at the first operand of `||`; it " +"“short-circuits”. If however `inputs.file_format` is `null`, the whole " +"expression’s value becomes that of the second operand, which is why a " +"reasonable default can be provided there." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 612f9efa0ed04559a174c37958def6f7 +#: 723c2232310c4276aeac2bd6728d2912 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: 57eb990c11f044dfb60c012a92a30eb1 +#: 4d81aac1830045229e5c60c7959074d8 msgid "" -"Implementation extensions not required for correct execution (for example, " -"fields related to GUI presentation) and metadata about the tool or workflow " -"itself (for example, authorship for use in citations) may be provided as " -"additional fields on any object. Such extensions fields (e.g. `format: edam:" -"format_2572`) can use a namespace prefix listed in the `$namespaces` section " -"of the document (e.g. edam: http://edamontology.org/) as described in the " -"[Schema Salad specification][schema-salad]. Once you add the namespace " -"prefix, you can access it anywhere in the document as shown below. " -"Otherwise, one must use full URLs: `format: http://edamontology.org/" -"format_2572`." +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: a6e6155cb8ff40fb9d8b1fff3e94fb02 +#: 368f8993ae9d401488081d74ae5acd49 msgid "" "For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to cite " -"your tool." +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 063c28fc9e654dfd91c66da164ac1d3d +#: c80f2b180ca74afb8a1fc18f8686304b msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 8fcd2ae1ce8d4c7f951281ced81ab32d +#: 37b07ea9b7124842b8ba3040f70308e9 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: 639533652456427480fa311da7beb4f0 +#: 1cd5989ade6741aabe625c13bed3c8ed msgid "" -"For those that are highly motivated, it is also possible to annotate your " -"tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints at " -"hardware requirements in order to use the tool, and a few more metadata " -"fields." +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 266808daf2004bbd9830045fbc67a541 +#: ae7369ba14404d23b72d1ef30dcd4153 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 fd9b715bfa3243b19a919ad19843232d +#: ../../src/topics/operations.md:1 a79974b2f4534fcd8c7a04401e8a5556 msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 fb568063fa7a4cbe83c271772d3d62bc +#: ../../src/topics/operations.md:3 b6507c8e1625476b97708423acb4fd0e msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-line " -"tool, or an expression tool. It is a step of a workflow that specifies " -"inputs and outputs, but it does not provide enough information to be " -"executed." +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." msgstr "" -#: ../../src/topics/operations.md:7 981486166754435cbcd8152e93679405 +#: ../../src/topics/operations.md:7 047b09455db64524a71c47ab5192039f msgid "" -"You can create operations to visualize a workflow during development, before " -"you are ready to submit the workflow to a CWL runner:" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 7b165718ffeb42e793c97fad807f216f +#: ../../src/topics/operations.md:10 e9b2b97f3059460b867577a49934a338 msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 5e31cddd14414d31b7bd0a6c2745d272 +#: ../../src/topics/operations.md:16 d21e9444182d4e27bae934db4573ae99 msgid "" -"The `uppercase` step of the workflow is an operation. It can be used like a " -"command line tool or an expression. You can also plot it with the CWL Viewer " -"or `cwltool`:" +"The `uppercase` step of the workflow is an operation. It can appear where" +" a command line tool or an expression is expected. You can also plot it " +"with the CWL Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 02c372245dc9453ea0841026335e405b +#: ../../src/topics/operations.md:24 61e4ae6ed18e41708270eb358cd55277 msgid "" -"The output of the command above can be rendered with a Graphviz renderer. " -"The following image is rendered with the Sphinx Graphviz directive (this " -"user guide is built with Sphinx):" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx `{graphviz}` directive " +"(this user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 d331327285d1434e8c17187737345919 +#: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd msgid "" -"If you try running it with `cwltool`, the command will fail since `cwltool` " -"does not have enough information to know how to execute it:" +"The operation file will fail to run with `cwltool` because `cwltool` " +"lacks the necessary information to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 72705f8940bb4194bc5554fcc29eed49 +#: ../../src/topics/operations.md:59 e184470550e645f6b9ce658af7e65ecf msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 76b7c63107e94323859904415d07d31c +#: ../../src/topics/operations.md:67 3b90445d3428444cafd7d5c0e5884980 msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A " -"CWL runner could, for instance, use abstract operations with ID's that " +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 ebf56d267612461799bf801136e61b69 +#: ../../src/topics/outputs.md:1 35e7bad6fdc04bcf9bbfbb2d8d42cfa5 msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 f9cff6b272a24ef6ada90e263c1b1784 +#: ../../src/topics/outputs.md:3 6d912d40359c4d33a4f08abca83c00be msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 e482821911004cdd8c3ff1539c69368a +#: ../../src/topics/outputs.md:5 a6bd3f9e23de488394958fe7b59a61e0 msgid "" "The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name of " -"parameter, and `type` describing what types of values are valid for that " -"parameter." +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 e11fcfe1e84b476ea879810b76ff2cb8 +#: ../../src/topics/outputs.md:10 a229d8d983344e51a231edb5f667d84b msgid "" -"When a tool runs under CWL, the starting working directory is the designated " -"output directory. The underlying tool or script must record its results in " -"the form of files created in the output directory. The output parameters " -"returned by the CWL tool are either the output files themselves, or come " -"from examining the content of those files." +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or the result of examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 65c73a37f06a4782bf43f4acf4f1c77e +#: ../../src/topics/outputs.md:16 9845e517f7d848e5b59a97880ca6999f msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 e172dde545164fefac826d910ddd399e +#: ../../src/topics/outputs.md:19 0bf1ad2c43174e57a3ba8dd86f7c96b2 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 225f4d04c28149898f06bd771f741358 +#: ../../src/topics/outputs.md:21 553d535b023e4d69a888fe5b24bb8c5b msgid "" "In previous examples, the `baseCommand` was just a string, with any " -"arguments passed as CWL inputs. Instead of a single string we can use an " -"_array of strings_. The first element is the command to run, and any " -"subsequent elements are mandatory command line arguments" +"arguments passed as CWL inputs. Instead of a single string, we can use an" +" _array of strings_ as the value of `baseCommand`. The first element of " +"the array is the command to run, and any subsequent elements are " +"mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 14e9e446768a454ea786b3256b49632e +#: ../../src/topics/outputs.md:28 9b65071222c94951bed12ac53e964ee3 msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 4bd659cee1904868a7c33345f94f1300 +#: ../../src/topics/outputs.md:34 759ab0847b97479fb4a15e4b7d4e6565 msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 8803a28ccff846eea7d06f4bd908c763 +#: ../../src/topics/outputs.md:40 f9752ec303ab419c8db8adef3fa2466f msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 661b62e554d64e449c69e475e5188f99 +#: ../../src/topics/outputs.md:47 4f96576528684f28a72b805f777769e6 msgid "" -"And now invoke `cwltool` with the tool description and the input object on " -"the command line:" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 44cdca5b777441baa246c87940df7264 +#: ../../src/topics/outputs.md:53 707803bec0cb42919905c7c321bd9d30 msgid "" -"The field `outputBinding` describes how to set the value of each output " -"parameter." +"The field " +"[`outputBinding`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding)" +" describes how to set the value of each output parameter." msgstr "" -#: ../../src/topics/outputs.md:62 edb34af3b22d418d9a6178c0ecbb8b80 +#: ../../src/topics/outputs.md:64 cbaec50871e04718883c8c91ff475d20 msgid "" -"The `glob` field consists of the name of a file in the output directory. If " -"you don't know name of the file in advance, you can use a wildcard pattern " -"like `glob: '*.txt'`." +"The " +"[`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) " +"field consists of the pattern to match file names in the output " +"directory. This can simply be the file's exact name. But if you don't " +"know the name of the file in advance, you can use a wildcard pattern like" +" `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 10e68fad866f4187981f0b365b957b03 +#: ../../src/topics/outputs.md:69 8a6e9173198241429effd911c3a7c4d7 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 77e1261484964ba9ac67d9fc9139a1d6 +#: ../../src/topics/outputs.md:71 a7c4fdaeda3e411fbeb802c5fa529ce9 msgid "" -"To capture a tool's standard output stream, add the `stdout` field with the " -"name of the file where the output stream should go. Then add `type: stdout` " -"on the corresponding output parameter." +"To capture a tool's standard output stream, add the " +"[`stdout`](https://w3id.org/cwl/CommandLineTool.html#stdout) field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 c66bd08354d54ccb9e3e1da89634a816 +#: ../../src/topics/outputs.md:75 cf2ef8dc7fda49308c09efe4f4ef5d7b msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 7d4056355da1451dbed6733fba8c3c38 +#: ../../src/topics/outputs.md:93 cbe236266dd148aaa96355e490a87cbe msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 8fed80f9633a4e87a67c651dc3160ce6 +#: ../../src/topics/outputs.md:95 77f86a7b94924a08b6ea2660218fe3c5 msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 6cba36e037d54f93add05fb16d2359bd +#: ../../src/topics/outputs.md:97 b34e30481fbd489d95fb7f8d5b5ab50c msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 08862892ecf849a1ba2f25ecc9e98227 +#: ../../src/topics/outputs.md:103 3aab0e0c9a78430f9caaa29a93303b56 msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 c5dcc68bb28041b3b96ac1af716b0db8 +#: ../../src/topics/outputs.md:116 9a14271c3180429988aaa14869f783a0 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions to " -"mark entries in arrays, as demonstrated in several of the upcoming sections." +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 53b95fd10d61462daf153d45e5517dad +#: ../../src/topics/parameter-references.md:1 c8a6ea340e6a43398e97b68e03a8bb3b msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 0702e71de81e493dac08a91d667569e3 +#: ../../src/topics/parameter-references.md:3 f5c0592ca28c46c2a89943f4f6f69a27 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file we " -"were interested in was called \"hello.txt\", and this was written into the `." -"cwl` file. This is not the best way to do this, as the \"hello.txt\" " -"filename may vary or be dependent on the input file(s) used. To avoid this " -"we can specify the name of the file we want in the job parameters file (`." -"yml`). In this example, you will see how to reference the value of input " -"parameters dynamically from other fields, which will allow us to then " -"specify the name of the file to extract." +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 a1703da32ad64fd2b8bdd423605b50bd +#: ../../src/topics/parameter-references.md:13 50db8add9b1942d986e581b8d21c2ee4 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 2f32531e47b4465594d41ddd218fb2fd +#: ../../src/topics/parameter-references.md:19 d01ad5fd9fea462cab0d4d776824b4e1 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 501dd6f9dbb1438f9a59f6a025639f35 +#: ../../src/topics/parameter-references.md:25 9b1e2f1a23ea4fe2af97ef5108f33376 msgid "" -"Create your input files and invoke `cwltool` with the tool description and " -"the input object on the command line:" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 1bcdd99111bd4bc5b75a8297bb61d9bb +#: ../../src/topics/parameter-references.md:36 06926a516ae6432d96e3eaa62202cd86 msgid "" -"Certain fields permit parameter references which are enclosed in `$(...)`. " -"These are evaluated and replaced with value being referenced." +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 32eae36c593e43a9a6b4e103a0c2028a +#: ../../src/topics/parameter-references.md:47 384fe8188f414eafbbb8d6b81bdfd779 msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 1d785e8a450140a982142aa0fa906257 +#: ../../src/topics/parameter-references.md:51 56ead1c8d45c43bdbcbc6f7cbb8e1e92 msgid "" -"The value of the \"inputs\" variable is the input object provided when the " -"CWL tool was invoked." +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 e862bb8bc3e84e24a2aa5ec34298cfd5 +#: ../../src/topics/parameter-references.md:54 56bca89e314c4223b33d7fe63c9b771d msgid "" -"Note that because `File` parameters are objects, to get the path to an input " -"file you must reference the path field on a file object; to reference the " -"path to the tar file in the above example you would write `$(inputs.tarfile." -"path)`." +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 46ffaab11be040cea96a294d9a814738 +#: ../../src/topics/parameter-references.md:59 1c1ab240c4114572bb4e42955baad361 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 890d619c415741179c83ffcd56833fbe +#: ../../src/topics/parameter-references.md:61 055d3268859c46c4b7db5005608bae05 msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 373e1847d9f745d7a749928642c8e0e3 +#: ../../src/topics/parameter-references.md:63 2ed66835bd9044adbfdd0b5097787f22 msgid "" -"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 90d3624e062c41c7a6d1a9824515d0df +#: ../../src/topics/parameter-references.md:69 f592619e4b2c497e80cd75da0548cf07 msgid "" -"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter)" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 76d09490bd464b708c28991dbff0104e +#: ../../src/topics/parameter-references.md:72 81ea71a35020421187dc18ddd151c62f msgid "" -"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding)" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 f33c76e590dd4feaac1e3cf568069d33 +#: ../../src/topics/parameter-references.md:74 ea0117748adc4324901024f21eed04ac msgid "" -"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 74ed4a06c1984c58826ddceb1a45a4ea +#: ../../src/topics/parameter-references.md:77 3a30e73176cf4e4eb9f26770a176b9c9 msgid "" -"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding)" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 eba3362d34354daa89dc516722c6fbd0 +#: ../../src/topics/parameter-references.md:81 551c199c9a6344fca9bfacfb69fc4e53 msgid "" -"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" -"v1.0/Workflow.html#WorkflowOutputParameter)" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 e924874af32d4be19c5e8446768226dd +#: ../../src/topics/parameter-references.md:85 7008a1ff1af54fda827637e787e5c7dd msgid "" -"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 b162113f364445af9ff1bfc8a6610e13 +#: ../../src/topics/parameter-references.md:89 45743e1b261c4195856de0c2e30ea72e msgid "" -"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." -"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 aa721077e16948c3a5bb8ef5bd7aff04 +#: ../../src/topics/parameter-references.md:92 0ae32d1db5f9452bbfcbbc4719b0b9f1 msgid "" -"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement)" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 2fad0c2bc2834350826b22c454d33cf0 +#: 7e1907ff15c74f488187531de336eccf msgid "" -"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" -"CommandLineTool.html#InitialWorkDirRequirement)" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 9e303aa89a9b4447b0dbdc5ac0a0eb9e +#: 678874668fed4f4d80a1b0990e183e2f msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 7a4eb47c25a54d11a00eb73e9333ad1c +#: e2882880886046ac88ae1c0d414366d1 msgid "" -"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef)" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: 8a957bc8e577476bb59647661b3c0990 +#: 05324169d8ae48d4a1abe3a0ac07c891 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: 2b31f1dec3f5498e9e363a4f1f50dc8d +#: 1f5b72d7ec82442ba29baa14a03f061b msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 5a5f84ecc2f449bf9f037dc9da0ac670 +#: e708866921ea49d69d3c2a32d63ea468 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " -"include a `SoftwareRequirement` field in the `hints` section. This may also " -"help to avoid confusion about which version of a tool the description was " -"written for." +"include a " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)" +" field in the `hints` section. This may also help to avoid confusion " +"about which version of a tool the description was written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: ee89f1526c1f4452b4e36ba67bb59747 +#: 6f722d6fd54f485fa964076c8d08938b msgid "" -"In this example, the software requirement being described is InterProScan " -"version 5.21-60." +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: c76cec44f5424f6087df28aa33c521a2 +#: 5c1236ec57c64079bfb7c779524b12ad msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the [dependency " -"resolvers configuration][dependencies]." +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 072d7b3ce3284ed994ff0736b43bbb86 -msgid "" -"As well as a version number, a unique resource identifier (URI) for the tool " -"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " -"up in the [SciCrunch][scicrunch] registry, which provides a portal for " -"finding, tracking, and referring to scientific resources consistently. If " -"you want to specify a tool as a `SoftwareRequirement`, search for the tool " -"on SciCrunch and use the RRID that it has been assigned in the registry. " -"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " -"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." -"org][identifiers]) in the `specs` field of your requirement description. " -"Other good choices, in order of preference, are to include the DOI for the " -"main tool citation and the URL to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 395d611104604a28b78e11b112a95027 +#: 1a8b8aadf1c64e87b8b670e288bc14bc +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)," +" search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 d10c792550e8498c8ee384d3093da306 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 811b4db0b1794fa89dc870f6cb59a3cd +#: ../../src/topics/staging-input-files.md:3 ac2ef1fced5f4044861761a11c35e78a msgid "" -"Normally, input files are located in a read-only directory separate from the " -"output directory. This causes problems if the underlying tool expects to " -"write its output files alongside the input file in the same directory. You " -"use `InitialWorkDirRequirement` to stage input files into the output " -"directory. In this example, we use a JavaScript expression to extract the " -"base name of the input file from its leading directory path." +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use " +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)" +" to stage input files into the output directory. In this example, we use " +"a JavaScript expression to extract the base name of the input file from " +"its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 7159b5c5023c47128057c4116cce69f4 +#: ../../src/topics/staging-input-files.md:9 d8ca16f5321e486ebe8ea9f9752b3737 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 3bfa6791d78f43629de90345f4441ebb +#: ../../src/topics/troubleshooting.md:1 aa3eddcaa0684f86ba67aafcd57872e7 msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 9a6bd5b684a740ed9e8993d9f8607774 +#: ../../src/topics/troubleshooting.md:3 3207f476afa04158bd26db39a16a2df5 msgid "" -"In this section you will find ways to troubleshoot when you have problems " -"executing CWL. We focus on `cwltool` here but some of these techniques may " -"apply to other CWL Runners." +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 6db8a02139644598894220d538c590b9 +#: ../../src/topics/troubleshooting.md:6 1d47f4ce04554cabb1ccf40a13ee42ec msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 f0da0f6283d44bcc95224eb9fe2d1764 +#: ../../src/topics/troubleshooting.md:8 0c25602a83e441b48b536eb49568f2b6 msgid "" "You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor output " -"files, but created while your workflow is running). By default, these files " -"are created in a temporary directory but writing them to a separate " -"directory makes accessing them easier." +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 e2fc28b44ffe4254892a7c7973dc80c4 +#: ../../src/topics/troubleshooting.md:14 36ec60b80c714357a4274217274136ff msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " -"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " -"olleH\". However, the second step, `step_b`, **has a typo**, where instead " -"of executing the `rev` command it tries to execute `revv`, which fails." +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 505c7cf9ee9c4af1aeed29002eed1b33 +#: ../../src/topics/troubleshooting.md:20 6f34038054ac4f4fa0b0ad9cbc3ecdc7 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 4c31fd11a28943538690d04baa2b5dd0 +#: ../../src/topics/troubleshooting.md:27 b777877c88024c9fb06a6614029ef8d6 msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " -"(`cwltool` will create the directory for you if it does not exist already):" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 a8532ac700014db4bd8ef690a27fb844 +#: ../../src/topics/troubleshooting.md:35 8654b7f2f4464d13be4b47729e1f07e5 msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. You " -"can inspect the intermediate files created:" +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 94a6148512b24b90b87fd1312a926d75 +#: ../../src/topics/troubleshooting.md:44 04e80f7ce14d4d73bc5d290dcf01bcdb msgid "" -"Each workflow step has received a unique ID (the long value that looks like " -"a hash). The `${HASH}.status` files display the status of each step executed " -"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " -"output of the command above." +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 ec4165b7c25c449db6a8804161805e80 +#: ../../src/topics/troubleshooting.md:48 719917cb0fd849f5a328671df8726189 msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " -"the `step_b`). After fixing the typo, when you execute `cwltool` with the " -"same arguments as the previous time, note that now `cwltool` output contains " -"information about pre-cached outputs for `step_a`, and about a new cache " -"entry for the output of `step_b`. Also note that the status of `step_b` is " -"now of success." +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 5c0b71a6376848d4aa491854ea2d185d +#: ../../src/topics/troubleshooting.md:59 2a9dbb3ad7564f5aa103349c45ee7925 msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had " -"been cached, and there was no change in its execution or output. " +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " "Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for " -"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " -"re-evaluate steps unnecessarily." +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 95b832552e8443ea9c652f8c95afc01e +#: ../../src/topics/using-containers.md:1 7439fe097aa4459ba1e4c0e28fc59b9a msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 561fc9c561bc492ea82c17784dfd439c +#: ../../src/topics/using-containers.md:3 eff5c6ac1cad44f9862585daf0a91298 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 2420b16855cf4b25af5bcb87413f6dd9 +#: ../../src/topics/using-containers.md:5 50d1a644bc8c49f78c453e4e0f3c07c8 msgid "" -"[Docker][docker] containers simplify software installation by providing a " -"complete known-good runtime for software and its dependencies. However, " -"containers are also purposefully isolated from the host system, so in order " -"to run a tool inside a Docker container there is additional work to ensure " -"that input files are available inside the container and output files can be " -"recovered from the container. A CWL runner can perform this work " -"automatically, allowing you to use Docker to simplify your software " -"management while avoiding the complexity of invoking and managing Docker " -"containers." +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." msgstr "" -#: ../../src/topics/using-containers.md:15 f5266ee2c2b34170bc89cb501b869893 +#: ../../src/topics/using-containers.md:15 4b0f6cfc8a774c77bfbc99e568af2ece msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the container." +"input files to reflect the location where they appear inside the " +"container." msgstr "" -#: ../../src/topics/using-containers.md:18 728166bf41504e1d89b755400742a1b4 +#: ../../src/topics/using-containers.md:18 27c02a5d479a420eab7d14888d9fb288 msgid "" -"This example runs a simple Node.js script inside a Docker container which " -"will then print \"Hello World\" to the standard output." +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 104351ac29d247cb8e017228e2c9b3d8 +#: ../../src/topics/using-containers.md:21 1a62a93ab20b4f2ca1e13ded3a767dc5 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 e11a38bfb30b404c99d223647960cb16 +#: ../../src/topics/using-containers.md:27 ccc2874840c3476bb714ddf4bdbf0f3e msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 7ed0bd21e998417cb02fdcb8e44734b6 +#: ../../src/topics/using-containers.md:33 d766b66de4714a5da0cd87ed886cc32f msgid "" "Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that is " -"really new is the `dockerRequirement` section." +"Most of this has been explained in previous sections, the only part that " +"is really new is the " +"[`dockerRequirement`](https://w3id.org/cwl/CommandLineTool.html#DockerRequirement)" +" section." msgstr "" -#: ../../src/topics/using-containers.md:44 9dcddf6812ba4bc2a7d6c5fcdb978a68 +#: ../../src/topics/using-containers.md:44 1f02618ab6254459ae71f72844e3cc18 msgid "" -"`baseCommand: node` tells CWL that we will be running this command using the " -"Node Js runtime that is meant for Javascript files. We then need to specify " -"some `hints` for how to find the container we want. In this case we list " -"just our requirements for the docker container in `DockerRequirements`. The " -"`dockerPull:` parameter takes the same value that you would pass to a " -"`docker pull` command. That is, the name of the container image (you can " -"even specify the tag, which is good idea for best practices when using " -"containers for reproducible research). In this case we have used a container " -"called `node:slim`." +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 bc1a09475f154562a4db445bf81ac92f +#: ../../src/topics/using-containers.md:52 54cade4978ec463bbb5c0d8c08e27adb msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " -"the tool description and the input object on the command line:" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 2e117019ace84604a8ed5a31214c2587 +#: ../../src/topics/using-containers.md:55 6541d0cd9f6c4c43b8601715cc35e585 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 d0d5b2a1a008411e92859a72101088c1 +#: ../../src/topics/using-containers.md:69 6abf220b7fa4479394ed33447cdd070e msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 591d1cd0282b4095a267b44da7d59804 +#: ../../src/topics/using-containers.md:72 d2dd89a5edde4f2eab4c2baf0cc78745 msgid "" -"In this example, the path to the script `hello.js` is `/home/me/cwl/" -"user_guide/hello.js` outside the container but `/var/lib/cwl/" -"job369354770_examples/hello.js` inside the container, as reflected in the " -"invocation of the `node` command." +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 9f989fff165448ecbcaad6adc0f58d6b +#: ../../src/topics/workflows.md:1 06281a10592d42509566c8fc51f8d4da msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 212c82dca23645e89d8b5bb7599f2d25 +#: ../../src/topics/workflows.md:3 325a656f9b8e4c1fa6f699cd8c447d00 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 7530029ec04746f2a888dcbc10aa5ce4 +#: ../../src/topics/workflows.md:13 b92275181c9e480da64e660b7aca0745 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 c1f1d644b37b4f018b87e15249d8758d +#: ../../src/topics/workflows.md:41 be2540315f854b8e9a1d257bcabd78db msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier examples." +"command-line tool, and the expression tool showed in the earlier " +"examples." msgstr "" -#: ../../src/topics/workflows.md:51 2d07232b7d9c415b8ad971e8cbcd9577 +#: ../../src/topics/workflows.md:51 3be900594bb743399854b95baa9ae2f9 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 fa1f770ffeba4b74bcb200cd3949e070 +#: ../../src/topics/workflows.md:81 5133c4e062bc4e479ce1dc8abbb08107 msgid "" -"A command-line tool or expression tool can also be written directly in the " -"same CWL document as the workflow. For example, we can rewrite the `echo-" -"uppercase.cwl` workflow as a single file:" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 570020792e824c2ba732bcc2c0134aa1 +#: ../../src/topics/workflows.md:91 83bc2796889f4dccb713764ac1b3c3ad msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 8a50c511004941d0917a8f0d471467f0 +#: ../../src/topics/workflows.md:150 5a9a1dd6ed1f4ca6803f1d235c4fd392 msgid "" -"Having separate files helps with modularity and code organization. But it " -"can be helpful writing everything in a single file for development. There " -"are other ways to combine multiple files into a single file (e.g. `cwltool --" -"pack`) discussed further in other sections of this user guide." +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 4d2bf0341836405d9729c47d8020faea +#: ../../src/topics/workflows.md:160 277ed30d4b3a4156a4523e8d10e6ce60 msgid "" "For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this " -"user guide in more detail." +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 dd6fc85f74984517b284853a0d46c122 +#: ../../src/topics/workflows.md:165 82818ab17aa4403eb982fd81a14a5865 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 f857d80cd5d84622a560c895ab260a92 +#: ../../src/topics/workflows.md:167 3d8b98e8d03548699fadb22198de9b20 msgid "" -"This workflow extracts a java source file from a tar file and then compiles " -"it." +"This workflow extracts a java source file from a tar file and then " +"compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 02e7e81cdf7e4226973f910cd57b8ccf +#: ../../src/topics/workflows.md:170 c61097c695424f7195e8205a23b6ecff msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 3a88d92f41aa4daaad4f4cc6829184b3 646367f222ea41e5987561941d17c4f9 +#: 6660c48f51d94d4fbcc05656e154059e bd2bab6c11614fa983ca8dab1408e1d8 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 aaba75eb272245db82d072fed97b311c +#: ../../src/topics/workflows.md:180 f0831481a43548039fbc4fd17555af57 msgid "" -"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" -"github.com/common-workflow-language/user_guide/blob/" -"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" "workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" -"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 f8a6e1af5f0349a5a384be0629c37ac8 +#: ../../src/topics/workflows.md:183 5ff059fc8ae6471c8ea86dab7e5a93f5 msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a " -"run:" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" msgstr "" -#: ../../src/topics/workflows.md:185 c4f854c7a279404da3688bdf424c7c5e +#: ../../src/topics/workflows.md:185 822e5d0a097b4109960d621a72a3c009 msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 d383ce45139944cb85768627965d9467 +#: ../../src/topics/workflows.md:191 4a4db7da861547639524083bf35ccfc0 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 84293afa7a6c40f2af0b980c89581fc7 +#: ../../src/topics/workflows.md:205 ed16b30eaa4747f79b6dd10a19188d8c msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 e66daf8af53849109936c36ca7d2b2c9 +#: ../../src/topics/workflows.md:212 6428bd7bd3be4393bfe5675f8e45ff94 msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a workflow." +"document. The `class` field indicates this document describes a " +"workflow." msgstr "" -#: ../../src/topics/workflows.md:221 8fbfbb587b264dcf98a3cea16dd36ef3 +#: ../../src/topics/workflows.md:221 d6abec8805f649fca668292412263f78 msgid "" -"The `inputs` section describes the inputs of the workflow. This is a list " -"of input parameters where each parameter consists of an identifier and a " -"data type. These parameters can be used as sources for input to specific " -"workflows steps." +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 5cdbc4771ea841b4960362b930de2af6 +#: ../../src/topics/workflows.md:233 22bf3e4910ef4f86a2e8f6d5a6cf0d42 msgid "" -"The `outputs` section describes the outputs of the workflow. This is a list " -"of output parameters where each parameter consists of an identifier and a " -"data type. The `outputSource` connects the output parameter `classfile` of " -"the `compile` step to the workflow output parameter `compiled_class`." +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 2e8a41fe43984dc6b4cf430e1ff66b28 +#: ../../src/topics/workflows.md:248 e0429688fce445da8083e69323e5b020 msgid "" "The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second step " -"compiles the file from the first step using the java compiler. Workflow " -"steps are not necessarily run in the order they are listed, instead the " -"order is determined by the dependencies between steps (using `source`). In " -"addition, workflow steps which do not depend on one another may run in " -"parallel." +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 78c20aa5a5724da6a4c908849c571334 +#: ../../src/topics/workflows.md:256 980f5eada57c4fadbb783838ded1fa0b msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input " -"parameters, `tarfile` and `extractfile` and one output parameter " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 1606a2f059eb4b0c9e90f2f0cbbe779b +#: ../../src/topics/workflows.md:261 3532e165842f4ebb8db0c78208071555 msgid "" -"The ``in`` section of the workflow step connects these two input parameters " -"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " -"`source`. This means that when the workflow step is executed, the values " -"assigned to `tarball` and `name_of_file_to_extract` will be used for the " -"parameters `tarfile` and `extractfile` in order to run the tool." +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 b456b11e2760479bbf81a773a3e1f8ee +#: ../../src/topics/workflows.md:267 04a4db2f3da94ce29e7999039ee13fde msgid "" -"The `out` section of the workflow step lists the output parameters that are " -"expected from the tool." +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 0fa01fcec32049c989ad1d68841c74de +#: ../../src/topics/workflows.md:278 2651ee113a3d4b79b138854ebe729f48 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " -"in [Additional Arguments and Parameters](additional-arguments-and-parameters." -"md)). The output of this step `classfile` is connected to the `outputs` " -"section for the Workflow, described above." +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 2bc9829f95584a269eb577c610b2a80c +#: ../../src/topics/workflows.md:285 177040bf9c0045f2878f42bcdd8cbd2d msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 0e5e6445bfcb42a4bd03612316dd7225 +#: ../../src/topics/workflows.md:287 e8adc2f7c5ac4464b0711712617b8bbe msgid "" -"Workflows are ways to combine multiple tools to perform a larger operations. " -"We can also think of a workflow as being a tool itself; a CWL workflow can " -"be used as a step in another CWL workflow, if the workflow engine supports " -"the `SubworkflowFeatureRequirement`:" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 0b83c1028b0e43ba972609e4302bc8a2 +#: ../../src/topics/workflows.md:297 44d281d99cd944478db98446a984c001 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 cbe1ef068b0c417b953655e132333447 +#: ../../src/topics/workflows.md:300 d7b60ce81ea741ffa08f2c2d9d7cca69 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 a691c36a15044b11a6d037d16f818a6d +#: ../../src/topics/workflows.md:309 a5b7a1ab16e34bda8744ffadacdda3e8 msgid "" -"This two-step workflow starts with the `create-tar` step which is connected " -"to the `compile` step in orange; `compile` is another workflow, diagrammed " -"on the right. In purple we see the fixed string `\"Hello.java\"` being " -"supplied as the `name_of_file_to_extract`." +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 2e9797fcd4f04f56b5d2b2f1a3e306d5 +#: ../../src/topics/workflows.md:314 8654f2d86b644609aaa5b9b73db30bda msgid "" "\"Visualization \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/1st-" +"workflow.cwl\">\"Visualization" msgstr "" -#: ../../src/topics/workflows.md:322 28f4139911b44eeeb7afd31e9f7cae7b +#: ../../src/topics/workflows.md:322 7ce847ab54224452b6425de2a55ec893 msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " -"CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " -"to become the step's input/outputs." +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 4a6cb397a20241beab24d956920a8379 +#: ../../src/topics/workflows.md:336 d621821d2c1b403cb7415b381dd883f6 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and `*.java` " -"filename. This is generally best-practice, as it means it can be reused in " -"multiple parent workflows, or even in multiple steps within the same " -"workflow." +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 dccb5472a5dc42b7946dd9245a71ecf0 +#: ../../src/topics/workflows.md:341 358c612f175241f7bf148a04d75e00c9 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar " -"file at `tarball`, which we will prepare in the `create-tar` step. At this " -"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " -"specific input/output names, as those also appear in its usage as a tool." +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 de1e18b69f654cabb75e52b47058030a +#: ../../src/topics/workflows.md:347 c6297c120e004ae8b52d5b519fbc04d2 msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3344,431 +3443,929 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 b947e62f4b3b4c10b95737f1839bcc5a +#: ../../src/topics/workflows.md:366 66f76677f4ce42baa8a8813410ea5aee msgid "" -"In this case our step can assume `Hello.java` rather than be parameterized, " -"so we can use hardcoded values `hello.tar` and `Hello.java` in a " -"`baseCommand` and the resulting `outputs`:" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 2ed0258a3a104ed5ba3b6b95ad998839 +#: ../../src/topics/workflows.md:383 a8ccb9f9ab4448e087ea8448d620d33c msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This is " -"generally not best practice, as the tool then can't be reused. The reason " -"for doing it in this case is because the command line is hard-coded with " -"filenames that only make sense within this workflow." +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 6584c0995288450b8a01c35fa231afb6 +#: ../../src/topics/workflows.md:389 afe43b9e92e949a589f493293eff2903 msgid "" -"In this example we had to prepare a tar file outside, but only because our " -"inner workflow was designed to take that as an input. A better refactoring " -"of the inner workflow would be to take a list of Java files to compile, " -"which would simplify its usage as a tool step in other workflows." +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." msgstr "" -#: ../../src/topics/workflows.md:394 19237513fd134c33801a7af08f74e70c +#: ../../src/topics/workflows.md:394 239eef3a740d42a69208a8f4e716d2b3 msgid "" "Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL " -"Tool description, care must be taken to improve its usability in multiple " -"workflows." +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 b66e0d0a36994b3182a3784bda8ffc19 +#: ../../src/topics/workflows.md:398 96d1ca78cc324f40b61c4b7330447db2 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 3bfb9851302248568bb4535ddc87a27f +#: ../../src/topics/workflows.md:400 eab4437bf9994b649954221375e3dd6d msgid "" "Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " -"run a tool or workflow multiple times over a list of inputs. The workflow " -"then takes the input(s) as an array and will run the specified step(s) on " -"each element of the array as if it were a single input. This allows you to " -"run the same workflow on multiple inputs without having to generate many " -"different commands or input yaml files." +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 78a5a600f8cc49ce8055c77a596ad833 +#: ../../src/topics/workflows.md:411 c245ba0ae2074fa388ad6c35695033c8 msgid "" -"The most common reason a new user might want to use scatter is to perform " -"the same analysis on different samples. Let's start with a simple workflow " -"that calls our first example (`hello_world.cwl`) and takes an array of " -"strings as input to the workflow:" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 f9618882e0a14a0b84ff9751346dc291 +#: ../../src/topics/workflows.md:415 83537938ce1244709f9b72269b048d63 msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 4fe03daddd304a9b828fdd1c29f0d072 +#: ../../src/topics/workflows.md:421 4f507925766e48ae8f713d56051a5e29 msgid "" -"Aside from the `requirements` section including `ScatterFeatureRequirement`, " -"what is going on here?" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 7ab022708a9642ab8aa2e79ea7810381 +#: ../../src/topics/workflows.md:429 ccbbba3189404241a44736c970249b84 msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 fe144641fc8040b283f15b2b99ecb5a2 +#: ../../src/topics/workflows.md:441 31eff13bb8334fc7b6d48ef6c5b1ce33 msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This field " -"tells the runner that we'd like to scatter over this input for this " -"particular step. Note that the input name listed after scatter is the one of " -"the step's input, not a workflow level input." +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 f13d1b071a7f4a75a4cdee40ecef14fa +#: ../../src/topics/workflows.md:445 0d5cf8b82dbd47f2abd1ed16b9b3eb61 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if you " -"expect that the final output of your workflow will now have multiple outputs " -"to collect, be sure to update that to an array type as well!" +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 b0b2e63d2b8a4fd0983e976c16440da4 +#: ../../src/topics/workflows.md:450 38b7042a270043ba82c11cf2e758f0c8 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 47ac993a90fe46ca92e97d6b67b3276b +#: ../../src/topics/workflows.md:452 b3fc75c262fe4a3a8e8bfba1abb07b3d msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 f5b8681b3c3b4890a86d7b9fb812d958 +#: ../../src/topics/workflows.md:458 f9fa7046c89c417db51dc7c8a026fd5d msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " -"calls the command `echo` on a message. If we invoke `cwltool scatter-" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 74e70fec6d2447bbbd2a5bc8af1fa58c +#: ../../src/topics/workflows.md:466 b6a33410ee9a45d7bf7b2ba56f786f8f msgid "" -"You can see that the workflow calls echo multiple times on each element of " -"our `message_array`. Ok, so how about if we want to scatter over two steps " -"in a workflow?" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 76fed9e7ad1d4792b7bb364bb684eeb2 +#: ../../src/topics/workflows.md:469 99b5c8a845ab4beb8524a69c051e2d42 msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding the " -"following lines instead of `outputs: []`" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 bef387d9be1f4ca19a97023cfdd1c910 +#: ../../src/topics/workflows.md:472 97bf58937d3f4e98af702e3c1a418992 msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 eea1be83da574f39914566d835701b4a +#: ../../src/topics/workflows.md:480 173bd28708834f11a2a1366b579b7ad7 msgid "" -"And add a second step that uses `wc` to count the characters in each file. " -"See the tool below:" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 2043f12eb2ce4424b133e0dc0b62aafc +#: ../../src/topics/workflows.md:483 4afccfe982ff4be2be96cbe5889e5014 msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 87ba95507fc44dbca4cb6c5283ce50f9 +#: ../../src/topics/workflows.md:489 63595d35dded4911aab0be3a165eec0c msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under each " -"step:" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" msgstr "" -#: ../../src/topics/workflows.md:491 e6e1a79638d74547b00c64e3c8b05710 +#: ../../src/topics/workflows.md:491 a7f96ec6e4f24c62ac0f5b6edcc9734b msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 03fb16e74bf14c49b43e35ef6cb45030 +#: ../../src/topics/workflows.md:497 122452b7d7114c3fa53cbea286703023 msgid "" -"Here we have placed the scatter field under each step. This is fine for this " -"example since it runs quickly, but if you're running many samples for a more " -"complex workflow, you may wish to consider an alternative. Here we are " -"running scatter on each step independently, but since the second step is not " -"dependent on the first step completing all languages, we aren't using the " -"scatter functionality efficiently. The second step expects an array as input " -"from the first step, so it will wait until everything in step one is " -"finished before doing anything. Pretend that `echo Hello World!` takes 1 " -"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " -"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " -"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " -"actually finish in 8 minutes because the first step must wait on `echo Hallo " -"welt!`. You can see how this might not scale well." +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 eca3380c60094df2b91b44b5f7718fae +#: ../../src/topics/workflows.md:509 85dd63daf04546b78bdcb68c1d985fa9 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can " -"make an entire workflow a single step in another workflow! Convert our two-" -"step workflow to a single step subworkflow:" +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 6c61733fe4284f51a6b46e89cafe78c4 +#: ../../src/topics/workflows.md:513 fac138ba275745898b763a7d719a8235 msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 0585f83162c349969391c9456a884f28 +#: ../../src/topics/workflows.md:519 508ef2240879445594b0f262ed11a01d msgid "" -"Now the scatter acts on a single step, but that step consists of two steps " -"so each step is performed in parallel." +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 f209343966db4d46b4611d3620c3b496 +#: ../../src/topics/workflows.md:522 b0bf01dad1234a1db3c87b10953e42ef msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 5a2661ce35dc4d79a15da1e17c0a95ec +#: ../../src/topics/workflows.md:524 8d933ed1ec6e408589f781e3a425b869 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 8f7ee09c9d6b491195e2d80315dae398 +#: ../../src/topics/workflows.md:527 9ac7b4f71621411da9a4ca3bc277dcb0 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 966acff0d3d24104ae9673df8a790fb1 +#: ../../src/topics/workflows.md:566 4a4a2b2b99b44d449adb246cebce0a26 msgid "" -"The first thing you'll notice is that this workflow is only compatible for " -"version 1.2 or greater of the CWL standards." +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 d60e1df759654f1b873276cf0296f234 +#: ../../src/topics/workflows.md:573 4742fe09a4264fb8be6f092519de5d72 msgid "" "The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when` is " -"where the condition validation takes place. In this case only when `in1` " -"from the workflow contains a value `< 1` this step will be executed." +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." msgstr "" -#: ../../src/topics/workflows.md:587 69aa8d3c9d9a4fe4a62875827648d95f +#: ../../src/topics/workflows.md:587 b33ecd2b8af042feb08687e32d4b6bbf msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " -"will pass the first conditional step and will therefore be executed and is " -"shown in the log by `INFO [step step1] start` whereas the second step is " -"skipped as indicated by `INFO [step step2] will be skipped`." +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 fee34c880e964e08b040adf2d3831803 +#: ../../src/topics/workflows.md:607 7cd80b31a94543358ece7a2d413adce9 msgid "" -"When a value of 3 is given the first conditional step will not be executed " -"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 cb9e82cf4b484ca7be19612b14fbdf33 +#: ../../src/topics/workflows.md:627 9679e32f65e0482a8b083387e4a18c1f msgid "" -"If no conditions are met for example when using `--val 2` the workflow will " -"raise a permanentFail." +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 8e7c3365f0f94038930f71666f05170f +#: ../../src/topics/yaml-guide.md:1 4fa76441f95d45fab76ab7eef8d7d4d2 msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 cbe6f35c21044054a010767f2f0cae46 +#: ../../src/topics/yaml-guide.md:6 705765787eb84ecaae004194225924cb msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers and " -"humans. This guide introduces the features of YAML that are relevant when " -"writing CWL descriptions and input parameter files." +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 2cc21093311548cd837aa7b3f0939093 +#: ../../src/topics/yaml-guide.md:13 cb243f6ab11f48ffb5c91945c4e0d101 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 6e7ea76e8aeb477cbb8197efed33e53d +#: ../../src/topics/yaml-guide.md:16 cfc95d15e33a492f842649f92ced941d msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 482e121a6e74428dbe6ad1f772f14684 +#: ../../src/topics/yaml-guide.md:18 f618d44d202f4c2ea6ff72a1dca2c659 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 179290eee12343dd9aa4d49207cf7c68 +#: ../../src/topics/yaml-guide.md:19 36bfa6ed40c54bd99826bedff12c759d msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 7880db40e98e4aaabdc96def3d9f515d +#: ../../src/topics/yaml-guide.md:20 61913753eb0c4c728889b47f1110be24 msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 75f3b499494b445f9f9a532d178cbc10 +#: ../../src/topics/yaml-guide.md:21 0de824a05eea46209aafa6f9e2e8623c msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 2b900b2779c84de5bbd3c933c56e5922 +#: ../../src/topics/yaml-guide.md:22 95627bc476b3415ca4d77246125137d2 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 189db6d0e54a400eb5615e259354827e +#: ../../src/topics/yaml-guide.md:24 3f64a6d33d9a4c22a8a839a8def82686 msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 e689c0e1dcd645348ceed51e91eb9ad0 +#: ../../src/topics/yaml-guide.md:26 2f74f6eaa8d84dc9b4d0a166844dedbe msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " -"is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have special " -"meaning in the CWL specification and underscored key names otherwise. For " -"example:" +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 9532ac8e1dda479e890bf970323a0a32 +#: ../../src/topics/yaml-guide.md:42 514365e59d9648deb896e2068d967a64 msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " -"and `home` - with their four respective values. Values can be character " -"strings, numeric (integer, floating point, or scientific representation), " -"Boolean (`true` or `false`), or more complex nested types (see below)." +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 91a057a7d10f438fad10338dd44c013c +#: ../../src/topics/yaml-guide.md:51 6939eb7e783744d7bcf75ea0a7cae129 msgid "" -"Values may be wrapped in quotation marks, but be aware that this may change " -"the way that they are interpreted i.e. `\"1234\"` will be treated as a " -"character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a " -"command: in CWL all parts of `baseCommand` must be strings so, if you want " -"to specify a fixed numeric value to a command, make sure that you wrap that " -"numeric value in quotes: `baseCommand: [echo, \"42\"]`." +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 d18c1f5ef55d4bb6b8334438fcbc96b8 +#: ../../src/topics/yaml-guide.md:61 96e1776b09e840ebbc9b4b7e01da0e43 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 dc6869049fc143b4af91d172a419a125 +#: ../../src/topics/yaml-guide.md:63 8b17f7557c3540b2b0d0beca0fe4ebc7 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program interpreting " -"the YAML. For example:" +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 c3c7f5ecfedb4884ad5e91bb79ba2a7c +#: ../../src/topics/yaml-guide.md:76 13da997c82c04023a4b7bb36b76e969d msgid "" -"If there is anything on the line before the comment, be sure to add at least " -"one space before the `#`!" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 84f16419237a4789ac0f3c682b3a11ee +#: ../../src/topics/yaml-guide.md:79 b9fc191166a64450b64a8182adabad75 msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 269ca8e05ce14e899fc8b2a00b1e458e +#: ../../src/topics/yaml-guide.md:81 aedf8c4f615845ad91a7947217005d6e msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, these " -"hierarchical structures are described in YAML by providing additional key-" -"value pairs as the value of any key. These pairs (sometimes referred to as " -"\"children\") are written on new lines under the key to which they belong " -"(the \"parent\"), and should be indented with two spaces (⇥tab characters " -"are not allowed). For example:" +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 ce790af50da540eb9108ad89eae037cf +#: ../../src/topics/yaml-guide.md:104 f0f1f414f74342a89065ba5ded8668e5 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " -"while one of these children, `inputBinding`, contains a further two key-" -"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " -"below for more information about providing multiple values/key-value pairs " -"for a single key. For comparison with the example YAML above, here is a " -"graphical representation of the `inputs` object it describes." +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 c3c9ef616b5d472a894ad6330267bcd2 +#: ../../src/topics/yaml-guide.md:127 965405e2a45a4cbb8f227bc8ceeb05df msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 b8a7360f6e0640aa9a2c4907c1ba3fe8 +#: ../../src/topics/yaml-guide.md:129 5aca9a90fb6149529ed717992746a2f3 msgid "" "In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) section " -"above, more than one key-value pair can be mapped to a single key. However, " -"it is also possible to define multiple values for a key without having to " -"provide a unique key for each value. We can achieve this with an _array_, " -"where each value is defined on its own line and preceded by `-`. For example:" +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 363da878600a4d229efe0ba79835d73c +#: ../../src/topics/yaml-guide.md:146 d1c9e72e004b4fb4a6efb7748a15ab6f msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 209dfb0d0a1148ed962dbb33890a3160 +#: ../../src/topics/yaml-guide.md:167 9a3d6879404745a48cd394bf86865dbc msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 cd3a174dae334d0d977a3234e258bd25 +#: ../../src/topics/yaml-guide.md:169 6a7cca0339794e679329b00d89e29d2b msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " -"can also be defined in YAML using the native JSON syntax. For example:" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 b0f0b10de8f54e1e951e480f696976f1 +#: ../../src/topics/yaml-guide.md:177 d8feed2d36d04fe283b9de9784d91941 msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 b5597e8984ad4e0bad33433c1dab89bd +#: ../../src/topics/yaml-guide.md:184 5156ad32791048f8ace51475d7689575 msgid "" -"Native JSON can be useful in indicating where a field is intentionally left " -"empty (such as `[]` for an empty array), as well as where it makes more " -"sense for the values to be located on the same line (For example, when " -"providing option flags and their values in a shell command). However, as the " -"second example above shows, it can severely affect the readability of a YAML " -"file, and should be used sparingly." +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 5ad7d551d3d347a097508a8488f9d15c +#: ../../src/topics/yaml-guide.md:194 ce49f80e6fc0498b8ad298fb1f0268f3 msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 58f80e6944f9402a810b9b02ba3ad917 +#: ../../src/topics/yaml-guide.md:196 180d261392a644fcb8ff47d7a4a160c0 msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " -"while we wrote this guide, though it also covers features that are not valid " -"in CWL." +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 8fdcc745f4684fa7816c62782507438e +#: ../../src/tutorials.md:1 d682035afebf4c128755bd4e58780dd2 msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 3c933ac074ee4d94b7aeacb7abeaf388 +#: ../../src/tutorials.md:5 d9adeab63ec54084bc41fb90f264d3ae msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to the " -"list." +"this page` link in the menu if you would like to add another tutorial to " +"the list." msgstr "" -#: ../../src/tutorials.md:7 1d6cdf13aa834cb4a682553227d9f725 +#: ../../src/tutorials.md:7 23c81edb650b4f86a60c5e0bcedeac1d msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 606cc939c5014e2abdab163e4d726f1b +#: ../../src/tutorials.md:9 87ddaa1e5f57445c8f13803722aa146e msgid "" -"[Introduction to Workflows with Common Workflow Language: For Contributors.]" -"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 3505468d39c34a20bc55f431a3c697f7 +#: ../../src/tutorials.md:11 b8ee193ba533498db6263e0f5f4ec45f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 e5731a11b89e492d8d751100a46c5226 +#: ../../src/tutorials.md:13 67c4b3923fce46fdab025495125c91d4 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 cdfeabb88f6245d9a687197d242ed3f9 +#: ../../src/tutorials.md:15 e640316669104239970794191b6da38b msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 997679b781a84add9b6d8b1900deec35 +#: ../../src/tutorials.md:17 efe94af44b874f9b81b245fbdee43f7f msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" + +#~ msgid "Non \"`File`\" Types Using `evalFrom`" +#~ msgstr "" + +#~ msgid "Rename an Input File" +#~ msgstr "" + +#~ msgid "Rename an Output File" +#~ msgstr "" + +#~ msgid "Referencing a Local Script" +#~ msgstr "" + +#~ msgid "" +#~ "The first method involves adding the " +#~ "folder containing your scripts to the" +#~ " `PATH` environment variable. This allows" +#~ " you to run the shell script " +#~ "directly without using `sh` or `bash`" +#~ " commands." +#~ msgstr "" + +#~ msgid "In CWL, everything must be directly stated." +#~ msgstr "" + +#~ msgid "Setting `self`-based Input Bindings for Optional Inputs" +#~ msgstr "" + +#~ msgid "Model a \"one-or-the-other\" Parameter" +#~ msgstr "" + +#~ msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +#~ msgstr "" + +#~ msgid "" +#~ "Using " +#~ "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +#~ " along with [`linkMerge: " +#~ "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#~ msgstr "" + +#~ msgid "Which means \"create a list with exactly these sources as elements\"" +#~ msgstr "" + +#~ msgid "Optional Inputs 💯" +#~ msgstr "" + +#~ msgid "Enum Inputs ⚜️" +#~ msgstr "" + +#~ msgid "Record Inputs 📀" +#~ msgstr "" + +#~ msgid "Setting Mutually Exclusive Parameters" +#~ msgstr "" + +#~ msgid "Setting Booleans" +#~ msgstr "" + +#~ msgid "Concatenating Strings in Inputs" +#~ msgstr "" + +#~ msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +#~ msgstr "" + +#~ msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +#~ msgstr "" + +#~ msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +#~ msgstr "" + +#~ msgid "Use CWL and cwltool with Singularity" +#~ msgstr "" + +#~ msgid "Debug JavaScript Expressions" +#~ msgstr "" + +#~ msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +#~ msgstr "" + +#~ msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +#~ msgstr "" + +#~ msgid "" +#~ "`InitialWorkDirRequirement` - controls staging " +#~ "files in the input directory." +#~ msgstr "" + +#~ msgid "" +#~ "The FAIR principles have laid a " +#~ "foundation for sharing and publishing " +#~ "digital assets, and in particular, data." +#~ " The FAIR principles emphasize machine " +#~ "accessibility and that all digital " +#~ "assets should be Findable, Accessible, " +#~ "Interoperable, and Reusable. Workflows encode" +#~ " the methods by which the scientific" +#~ " process is conducted and via which" +#~ " data are created. It is thus " +#~ "important that workflows support the " +#~ "creation of FAIR data and adhere " +#~ "to the FAIR principles. — [FAIR " +#~ "Computational " +#~ "Workflows](https://workflows.community/groups/fair/), Workflows" +#~ " Community Initiative." +#~ msgstr "" + +#~ msgid "" +#~ "If you are using Windows, you will" +#~ " have to install the [Windows " +#~ "Subsystem for Linux 2](https://learn.microsoft.com" +#~ "/en-us/windows/wsl/install) (WSL2). Visit the " +#~ "`cwltool` [documentation](https://github.com/common-" +#~ "workflow-language/cwltool/blob/main/README.rst#ms-windows-" +#~ "users) for details on installing WSL2." +#~ " Your operating system also needs " +#~ "internet access and a recent version " +#~ "of Python (3.6+)." +#~ msgstr "" + +#~ msgid "" +#~ "`cwltool` can be installed with `pip`." +#~ " We recommend using a virtual " +#~ "environment like `venv` or `conda`. The" +#~ " following commands will create and " +#~ "activate a Python virtual environment " +#~ "using the `venv` module, and install " +#~ "`cwltool` in that environment:" +#~ msgstr "" + +#~ msgid "Installing `cwltool` with `pip` and `venv`." +#~ msgstr "" + +#~ msgid "" +#~ "Visit the `cwltool` " +#~ "[documentation](https://github.com/common-workflow-" +#~ "language/cwltool#install) for other ways to" +#~ " install `cwltool` with `apt` and " +#~ "`conda`." +#~ msgstr "" + +#~ msgid "Cwl-runner Python Module" +#~ msgstr "" + +#~ msgid "" +#~ "The CWL community publishes a Python " +#~ "package with the name `cwlref-runner`" +#~ " that installs an alias for `cwltool`" +#~ " under the name `cwl-runner`" +#~ msgstr "" + +#~ msgid "" +#~ "The *shebang* is the two-character " +#~ "sequence `#!` at the beginning of " +#~ "a script. When the script is " +#~ "executable, the operating system will " +#~ "execute the script using the executable" +#~ " specified after the shebang. It is" +#~ " considered a good practice to use" +#~ " `/usr/bin/env ` rather than " +#~ "using a hard-coded location, since " +#~ "`/usr/bin/env ` looks for the " +#~ "`` program in the system " +#~ "`PATH`," +#~ msgstr "" + +#~ msgid "" +#~ "The usage of the `cwltool` command-" +#~ "line executable is basically `cwltool " +#~ "[OPTIONS] [INPUTS_OBJECT]`. You " +#~ "can run the `hello_world.cwl` workflow " +#~ "without specifying any option:" +#~ msgstr "" + +#~ msgid "" +#~ "For more examples of providing metadata" +#~ " within CWL descriptions, see [the " +#~ "Metadata and Authorship section of this" +#~ " User Guide](../topics/metadata-and-" +#~ "authorship.md)." +#~ msgstr "" + +#~ msgid "" +#~ "In tool descriptions, list dependencies " +#~ "using short name(s) under " +#~ "`SoftwareRequirement`." +#~ msgstr "" + +#~ msgid "" +#~ "In tool descriptions, include a list " +#~ "of version(s) of the tool that are" +#~ " known to work with this description" +#~ " under `SoftwareRequirement`." +#~ msgstr "" + +#~ msgid "" +#~ "Each `CommandLineTool` description should " +#~ "focus on a single operation only, " +#~ "even if the (sub)command is capable " +#~ "of more. Don't overcomplicate your tool" +#~ " descriptions with options that you " +#~ "don't need or use." +#~ msgstr "" + +#~ msgid "" +#~ "This indicates whether a process " +#~ "requires outgoing IPv4/IPv6 network access." +#~ " If a command-line tool is " +#~ "written manually in CWL v1.1+, there " +#~ "is a need to specify when network" +#~ " access is required." +#~ msgstr "" + +#~ msgid "" +#~ "CWL v1.0 command-line tools that " +#~ "are upgraded to v1.1 or v1.2 get" +#~ " Network Access automatically." +#~ msgstr "" + +#~ msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +#~ msgstr "" + +#~ msgid "" +#~ "Note also that the author of this" +#~ " CWL description has also included " +#~ "`ResourceRequirement`s, specifying the minimum " +#~ "amount of RAM and number of cores" +#~ " required for the tool to run " +#~ "successfully, as well as details of " +#~ "the version of the software that " +#~ "the description was written for and " +#~ "other useful metadata. These features " +#~ "are discussed further in other chapters" +#~ " of this user guide." +#~ msgstr "" + +#~ msgid "" +#~ "Similar to the command-line tool " +#~ "it requires `inputs` and `outputs`. But" +#~ " instead of `baseCommand`, it requires " +#~ "an `expression` attribute." +#~ msgstr "" + +#~ msgid "" +#~ "We had to use an " +#~ "`InlineJavascriptRequirement` as our expression " +#~ "contains a JavaScript call in " +#~ "`.toUpperCase()`. This means to tools " +#~ "using the expression tool that " +#~ "JavaScript is a requirement." +#~ msgstr "" + +#~ msgid "" +#~ "If you need to manipulate input " +#~ "parameters, include the requirement " +#~ "`InlineJavascriptRequirement` and then anywhere " +#~ "a parameter reference is legal you " +#~ "can provide a fragment of Javascript " +#~ "that will be evaluated by the CWL" +#~ " runner." +#~ msgstr "" + +#~ msgid "From `Workflow`" +#~ msgstr "" + +#~ msgid "" +#~ "The requirement `InlineJavascriptRequirement` " +#~ "supports an `expressionLib` attribute that " +#~ "allows users to load external JavaScript" +#~ " files, or to provide inline " +#~ "JavaScript code." +#~ msgstr "" + +#~ msgid "" +#~ "Tools and workflows can take `File` " +#~ "types as input and produce them as" +#~ " output. We also recommend indicating " +#~ "the format for `File` types. This " +#~ "helps document for others how to " +#~ "use your tool while allowing you " +#~ "to do some simple type-checking " +#~ "when creating parameter files." +#~ msgstr "" + +#~ msgid "" +#~ "Available primitive types are *string*, " +#~ "*int*, *long*, *float*, *double*, and " +#~ "*null*; complex types are *array* and" +#~ " *record*; in addition there are " +#~ "special types *File*, *Directory* and " +#~ "*Any*." +#~ msgstr "" + +#~ msgid "" +#~ "You can use `cwltool` to create a" +#~ " template input object. That saves " +#~ "you from having to type all the" +#~ " input parameters in a input object" +#~ " file:" +#~ msgstr "" + +#~ msgid "" +#~ "The field `inputBinding` is optional and" +#~ " indicates whether and how the input" +#~ " parameter should appear on the " +#~ "tool's command line. If `inputBinding` " +#~ "is missing, the parameter does not " +#~ "appear on the command line. Let's " +#~ "look at each example in detail." +#~ msgstr "" + +#~ msgid "" +#~ "If you use exclusive input parameters" +#~ " combined with expressions, you need " +#~ "to be aware that the `inputs` " +#~ "JavaScript object will contain one of" +#~ " the exclusive input values. This " +#~ "means that you might need to use" +#~ " an **or** boolean operator to check" +#~ " which values are present." +#~ msgstr "" + +#~ msgid "" +#~ "Note how the JavaScript expression uses" +#~ " the value of the exclusive input " +#~ "parameter without taking into consideration" +#~ " a `null` value. If you provide " +#~ "a valid value, such as “fasta” " +#~ "(one of the values of the enum)," +#~ " your command should execute successfully:" +#~ msgstr "" + +#~ msgid "" +#~ "However, if you do not provide any" +#~ " input value, then `file_format` will " +#~ "be evaluated to a `null` value, " +#~ "which does not match the expected " +#~ "type for the output field (a " +#~ "`string`), resulting in failure when " +#~ "running your workflow." +#~ msgstr "" + +#~ msgid "" +#~ "To correct it, you must remember " +#~ "to use an or operator in your " +#~ "JavaScript expression when using exclusive " +#~ "parameters, or any parameter that allows" +#~ " `null`. For example, the expression " +#~ "could be changed to `$(inputs.file_format " +#~ "|| 'auto')`, to have a default " +#~ "value if none was provided in the" +#~ " command line or job input file." +#~ msgstr "" + +#~ msgid "" +#~ "The `uppercase` step of the workflow " +#~ "is an operation. It can be used" +#~ " like a command line tool or an" +#~ " expression. You can also plot it " +#~ "with the CWL Viewer or `cwltool`:" +#~ msgstr "" + +#~ msgid "" +#~ "The output of the command above " +#~ "can be rendered with a Graphviz " +#~ "renderer. The following image is " +#~ "rendered with the Sphinx Graphviz " +#~ "directive (this user guide is built " +#~ "with Sphinx):" +#~ msgstr "" + +#~ msgid "" +#~ "If you try running it with " +#~ "`cwltool`, the command will fail since" +#~ " `cwltool` does not have enough " +#~ "information to know how to execute " +#~ "it:" +#~ msgstr "" + +#~ msgid "" +#~ "When a tool runs under CWL, the" +#~ " starting working directory is the " +#~ "designated output directory. The underlying" +#~ " tool or script must record its " +#~ "results in the form of files " +#~ "created in the output directory. The" +#~ " output parameters returned by the " +#~ "CWL tool are either the output " +#~ "files themselves, or come from examining" +#~ " the content of those files." +#~ msgstr "" + +#~ msgid "" +#~ "In previous examples, the `baseCommand` " +#~ "was just a string, with any " +#~ "arguments passed as CWL inputs. Instead" +#~ " of a single string we can use" +#~ " an _array of strings_. The first" +#~ " element is the command to run, " +#~ "and any subsequent elements are " +#~ "mandatory command line arguments" +#~ msgstr "" + +#~ msgid "" +#~ "The field `outputBinding` describes how " +#~ "to set the value of each output" +#~ " parameter." +#~ msgstr "" + +#~ msgid "" +#~ "The `glob` field consists of the " +#~ "name of a file in the output " +#~ "directory. If you don't know name " +#~ "of the file in advance, you can" +#~ " use a wildcard pattern like `glob:" +#~ " '*.txt'`." +#~ msgstr "" + +#~ msgid "" +#~ "To capture a tool's standard output " +#~ "stream, add the `stdout` field with " +#~ "the name of the file where the " +#~ "output stream should go. Then add " +#~ "`type: stdout` on the corresponding " +#~ "output parameter." +#~ msgstr "" + +#~ msgid "" +#~ "Often, tool descriptions will be written" +#~ " for a specific version of a " +#~ "software. To make it easier for " +#~ "others to use your descriptions, you " +#~ "can include a `SoftwareRequirement` field " +#~ "in the `hints` section. This may " +#~ "also help to avoid confusion about " +#~ "which version of a tool the " +#~ "description was written for." +#~ msgstr "" + +#~ msgid "" +#~ "As well as a version number, a " +#~ "unique resource identifier (URI) for the" +#~ " tool is given in the form of" +#~ " an [RRID][rrid]. Resources with RRIDs " +#~ "can be looked up in the " +#~ "[SciCrunch][scicrunch] registry, which provides " +#~ "a portal for finding, tracking, and " +#~ "referring to scientific resources " +#~ "consistently. If you want to specify " +#~ "a tool as a `SoftwareRequirement`, " +#~ "search for the tool on SciCrunch " +#~ "and use the RRID that it has " +#~ "been assigned in the registry. (Follow" +#~ " this [Adding a Resource Tutorial" +#~ "][scicrunch-add-tool] to add a tool" +#~ " to SciCrunch). You can use this " +#~ "RRID to refer to the tool (via " +#~ "[identifiers.org][identifiers]) in the `specs` " +#~ "field of your requirement description. " +#~ "Other good choices, in order of " +#~ "preference, are to include the DOI " +#~ "for the main tool citation and the" +#~ " URL to the tool." +#~ msgstr "" + +#~ msgid "" +#~ "Normally, input files are located in " +#~ "a read-only directory separate from " +#~ "the output directory. This causes " +#~ "problems if the underlying tool expects" +#~ " to write its output files alongside" +#~ " the input file in the same " +#~ "directory. You use `InitialWorkDirRequirement` " +#~ "to stage input files into the " +#~ "output directory. In this example, we" +#~ " use a JavaScript expression to " +#~ "extract the base name of the input" +#~ " file from its leading directory " +#~ "path." +#~ msgstr "" + +#~ msgid "" +#~ "Before we run this, let's just " +#~ "break it down and see what some" +#~ " bits do. Most of this has " +#~ "been explained in previous sections, the" +#~ " only part that is really new " +#~ "is the `dockerRequirement` section." +#~ msgstr "" + diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 5af7a3fd..ce4d41ef 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -1,2237 +1,2102 @@ # SOME DESCRIPTIVE TITLE. # Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. # msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"POT-Creation-Date: 2023-12-16 11:48+0100\n" "PO-Revision-Date: 2023-12-16 02:08+0000\n" "Last-Translator: Manabu ISHII \n" -"Language-Team: Japanese \n" "Language: ja\n" +"Language-Team: Japanese \n" +"Plural-Forms: nplurals=1; plural=0;\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" +"Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.3\n" +"Generated-By: Babel 2.12.1\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac msgid "Licenses" msgstr "ライセンス" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.md:4 9dd9705700664b31a3f296d263b4028b #, fuzzy msgid "Instructional Material" msgstr "指導資料" -#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +#: ../../LICENSE.md:6 e54324bd39cd431d91b32e338217b8c7 msgid "" -"All Common Workflow Language project instructional material and changes to " -"the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable summary " -"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" -"[cc-by-legal]." +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." msgstr "" -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.md:12 754f3f54aa4142ef9dac27f508dd0bca msgid "You are free:" msgstr "" -#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb -msgid "" -"to **Share**---copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 d2b1d5e965ef4e71b64c359549919975 +msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" -#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +#: ../../LICENSE.md:15 fe9551ffef8149bf8da50e70318e8de8 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.md:17 247db3bcc7024c44a044886a29ef1414 msgid "for any purpose, even commercially." msgstr "" -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +#: ../../LICENSE.md:19 c04d906124854afc917707b7b4e45bb2 msgid "" -"The licensor cannot revoke these freedoms as long as you follow the license " -"terms:" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" msgstr "" -#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +#: ../../LICENSE.md:24 551cb5ab59dd4737b1042a4ef79ffab7 msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow Language " -"project, and, where practical, linking to https://www.commonwl.org/ ), " -"provide a [link to the license][cc-by-human], and indicate if changes were " -"made. You may do so in any reasonable manner, but not in any way that " -"suggests the licensor endorses you or your use." +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." msgstr "" -#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +#: ../../LICENSE.md:32 f6c3b2ccad494ed6811a35537fc1fb0d msgid "" "**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything the " -"license permits. With the understanding that:" +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" msgstr "" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +#: ../../LICENSE.md:36 91c95248cd7f435c909ee263a9a8bf3f msgid "" -"You do not have to comply with the license for elements of the material in " -"the public domain or where your use is permitted by an applicable exception " -"or limitation." +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." msgstr "" -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +#: ../../LICENSE.md:39 27f79b0b648b4de4b0eb3172b2dc4ae8 msgid "" -"No warranties are given. The license may not give you all of the permissions " -"necessary for your intended use. For example, other rights such as " -"publicity, privacy, or moral rights may limit how you use the material." +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." msgstr "" -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.md:44 1e367d07720d4f9fb7ebc3149052e823 msgid "Software" msgstr "ソフトウェア" -#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +#: ../../LICENSE.md:46 cf8b58d02b6943a48cb70aa78a27bea4 msgid "" "Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the " -"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" -#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +#: ../../LICENSE.md:51 96f1e5be3e1e48db8d9a4c7693008715 msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: eab02dc13915490bb3c9ba744d78b6a7 d4f35995b0f6494d9771a4be0a82538f -#: d6ccd4b546254f56a597d67dd4fdc5d6 +#: 08aa9181d5304e0fa96b28db15718559 d37fc100eb6948bba8b5e757574b2aaf +#: ecdd0f28d5b048d69dd1ffae2fa1f6c0 #, fuzzy msgid "" "CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece of " -"software, tools and workflows described using CWL are portable across a " -"variety of platforms that support the CWL standard." -msgstr "" -"CWLは、コマンドラインツールを定義し、それらを結びつけてワークフローを作成する" -"ための方法です。CWLは仕様であり、特定のソフトウェアではないため、CWLを使用し" -"て記述されたツールやワークフローは、CWL標準をサポートするさまざまなプラット" -"フォームで利用可能です。" +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "CWLは、コマンドラインツールを定義し、それらを結びつけてワークフローを作成するための方法です。CWLは仕様であり、特定のソフトウェアではないため、CWLを使用して記述されたツールやワークフローは、CWL標準をサポートするさまざまなプラットフォームで利用可能です。" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +#: 1361ff6bf4924efc9ce9a85785a6b381 eb254514301c491e81f72ae19c407261 msgid "This page has moved" msgstr "このページは移動しました" -#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +#: ../../src/episodes.md:9 f03d7cbe6670451db0896f1b674d56c7 msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. Please use the new [Table of Contents](index.md#table-of-" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -"このページは古いもので、旧ユーザーガイドのリンクを保存するためにここに残され" -"ています。ユーザーガイドの閲覧には、新しい[目次](index.md#table-of-contents)" -"をご利用ください。" +"このページは古いもので、旧ユーザーガイドのリンクを保存するためにここに残されています。ユーザーガイドの閲覧には、新しい[目次](index.md" +"#table-of-contents)をご利用ください。" -#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +#: ../../src/faq.md:1 d65ad48ac6314bf0a74c34a6766561fc msgid "FAQ" msgstr "よくある質問" -#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 -msgid "Non \"`File`\" Types Using `evalFrom`" +#: ../../src/faq.md:11 370a9659c7904ef6b5e1ae7480f82ef6 +#, fuzzy +msgid "How do I create non \"`File`\" types using `evalFrom`?" msgstr "\"`File`\" 型をつかわず `evalFrom`を使う方法" -#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 -msgid "Rename an Input File" +#: ../../src/faq.md:41 8333f51e3f5945fe8963adfc6685bcb1 +#, fuzzy +msgid "How do I rename an input file?" msgstr "入力ファイルの名前を変更する" -#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +#: ../../src/faq.md:43 f6b88d9154d049d7807afa9bb0f1ac98 msgid "" -"This example demonstrates how to change the name of an input file as part of " -"a tool description. This could be useful when you are taking files produced " -"from another step in a workflow, and don't want to work with the default " -"names that these files were given when they were created." -msgstr "" -"この例では、ツール定義の一部として、入力ファイルの名前を変更する方法を説明し" -"ます。これは、ワークフローの別のステップで作成されたファイルを使用する場合" -"に、これらのファイルが作成されたときに与えられたデフォルトの名前を使用して作" -"業したくない場合に便利です。" +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." +msgstr "この例では、ツール定義の一部として、入力ファイルの名前を変更する方法を説明します。これは、ワークフローの別のステップで作成されたファイルを使用する場合に、これらのファイルが作成されたときに与えられたデフォルトの名前を使用して作業したくない場合に便利です。" -#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f -msgid "Rename an Output File" +#: ../../src/faq.md:59 833510f5896b4a6eb5875d25eca5b047 +#, fuzzy +msgid "How do I rename an output file?" msgstr "出力ファイルの名前を変更する" -#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +#: ../../src/faq.md:61 207e2f97d1c44233ae3f109c5a6ec944 +msgid "" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" +msgstr "この例では、出力ファイルの名前を、ツールから与えられたデフォルトの名前から変更する方法を示します：" + +#: ../../src/faq.md:83 d66acc583da24273980a52be03e79e91 msgid "" -"This example demonstrates how to change the name of an output file from the " -"default name given to it by a tool:" +"By modifying the `basename` field in the `outputEval` field, CWL workflow" +" engines will rename the file using the new name for subsequent steps or " +"as a workflow-level output." msgstr "" -"この例では、出力ファイルの名前を、ツールから与えられたデフォルトの名前から変" -"更する方法を示します：" -#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 -msgid "Referencing a Local Script" +#: ../../src/faq.md:86 8641f105131b4ac1bca7e0a46756ef79 +#, fuzzy +msgid "How do I reference a local script?" msgstr "ローカルスクリプトを参照する" -#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +#: ../../src/faq.md:88 d3e43b40d6994b32bc37067ee116418e msgid "There are two ways to reference a local script:" msgstr "ローカルスクリプトを参照するには、2つの方法があります：" -#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +#: ../../src/faq.md:90 64b140a321ca4087945339c523cc24dd +#, fuzzy msgid "" -"The first method involves adding the folder containing your scripts to the " -"`PATH` environment variable. This allows you to run the shell script " -"directly without using `sh` or `bash` commands." +"The first method involves adding the path to a folder containing your " +"scripts to the `PATH` environment variable. This allows you to execute " +"the shell script directly (without explicitly using the `sh` or `bash` " +"commands)." msgstr "" -"最初の方法は、スクリプトの入ったフォルダを`PATH` 環境変数に追加する方法です。" -"これにより、`sh` や`bash` コマンドを使用せずに、シェルスクリプトを直接実行す" -"ることができます。" +"最初の方法は、スクリプトの入ったフォルダを`PATH` 環境変数に追加する方法です。これにより、`sh` や`bash` " +"コマンドを使用せずに、シェルスクリプトを直接実行することができます。" -#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +#: ../../src/faq.md:93 34ebca4487a54ceab5d087105820e945 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "まず、ファイルの先頭に _shebang_ を追加します：" -#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +#: ../../src/faq.md:99 6b04a4dcdada4515b28d74aacff3537a msgid "" -"After that, make the script executable with the command `chmod +x scriptname." -"sh`" -msgstr "" -"その後、`chmod +x scriptname.sh` というコマンドでスクリプトを実行可能な状態に" -"します" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" +msgstr "その後、`chmod +x scriptname.sh` というコマンドでスクリプトを実行可能な状態にします" -#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +#: ../../src/faq.md:101 756ab4f7edcf42d3872bb86818e088c3 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -"最後に、`PATH` を変更し、スクリプトが置かれているディレクトリを追加します。" -"(`$HOME/bin` を自分のスクリプトを保存するために使用するのは良い習慣です）。" +"最後に、`PATH` を変更し、スクリプトが置かれているディレクトリを追加します。(`$HOME/bin` " +"を自分のスクリプトを保存するために使用するのは良い習慣です）。" -#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be -msgid "" -"Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "" -"これで、`baseCommand: scriptname.sh` を使って、スクリプトを直接実行できるよう" -"になりました。" +#: ../../src/faq.md:108 efb46b3a2d7c4c51b65998602bfa6f18 +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "これで、`baseCommand: scriptname.sh` を使って、スクリプトを直接実行できるようになりました。" -#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +#: ../../src/faq.md:117 844938d5d2304c6cb03184b4b4b0b024 #, fuzzy msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." -msgstr "" -"後で作ったものを共有したいときは、スクリプトをDockerコンテナに入れることがで" -"きます。" +msgstr "後で作ったものを共有したいときは、スクリプトをDockerコンテナに入れることができます。" -#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +#: ../../src/faq.md:119 796ce8155e32486d9651f8f13bfa3148 #, fuzzy msgid "" -"The second method involves including an input of `type: File` in the script " -"itself:" +"The second method involves including an input of `type: File` in the " +"script itself:" msgstr "2つ目の方法は、`type: File` をスクリプト自体に含める方法です：" -#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 -msgid "In CWL, everything must be directly stated." -msgstr "CWLでは、すべてを直接的に記述する必要があります。。" - -#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 +#: ../../src/faq.md:138 ba246320fdd94a1aab4736f83718d793 #, fuzzy -msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgid "How can I set `self`-based input bindings for optional inputs?" msgstr "オプショナル入力のために `self`-形式のInput Bindings を設定します" -#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +#: ../../src/faq.md:140 6169b7be9af7448abcb57eaf91e1cc91 #, fuzzy msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their input " -"binding makes use of `self`. Below is an example workaround for this, " -"pending a more sophisticated fix." +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." msgstr "" -"現在、`cwltool` は、入力バインディングが`self` を使用している場合、見つからな" -"いオプション入力に対処することができません。以下は、より洗練された修正を待つ" -"間の回避策の例です。" +"現在、`cwltool` は、入力バインディングが`self` " +"を使用している場合、見つからないオプション入力に対処することができません。以下は、より洗練された修正を待つ間の回避策の例です。" -#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 -msgid "Model a \"one-or-the-other\" Parameter" +#: ../../src/faq.md:165 6c98b7948059411b8e09cf03a552c5ab +#, fuzzy +msgid "How can I model a \"one-or-the-other\" parameter?" msgstr "「一か八か」のパラメータをモデル化する" -#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +#: ../../src/faq.md:167 d1424da3f43c4519a4c4735f4a720341 msgid "" -"Below is an example showing how to specify different strings to be added to " -"a command line, based on the value given to a Boolean parameter." -msgstr "" -"以下は、Booleanパラメータの値によって、コマンドラインに追加する文字列を変える" -"例を示しています。" +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." +msgstr "以下は、Booleanパラメータの値によって、コマンドラインに追加する文字列を変える例を示しています。" -#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c +#: ../../src/faq.md:188 5c9980839f404ba6aef92ef23034500f #, fuzzy -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgid "" +"How do I connect a solo value to an input that expects an array of that " +"type?" msgstr "ある型の配列を期待する入力に１つの値を与える" -#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +#: ../../src/faq.md:190 2525baf16c1f4725b096f33fd99009cf +#, fuzzy msgid "" -"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" -"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +"Add a " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput):" msgstr "" -"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow." -"html#MultipleInputFeatureRequirement) と [`linkMerge: merge_nested`](https://" -"www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)を一緒に使います" +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" と [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)を一緒に使います" -#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +#: ../../src/faq.md:194 a00d5d96b15048a79ae099d22d63bb42 msgid "merge_nested" msgstr "merge_nested" -#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +#: ../../src/faq.md:196 3a92c6cc5c2b40ffa0d692d03bad5c87 #, fuzzy msgid "" -"The input must be an array consisting of exactly one entry for each input " -"link. If \"merge_nested\" is specified with a single link, the value from " -"the link must be wrapped in a single-item list." -msgstr "" -"入力は、各入力リンクに対して正確に1つのエントリで構成される配列でなければなり" -"ません。\"merge_nested\"が1つのリンクで指定された場合、リンクからの値は1つの" -"アイテムリストでラップされなければなりません。" +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." +msgstr "入力は、各入力リンクに対して正確に1つのエントリで構成される配列でなければなりません。\"merge_nested\"が1つのリンクで指定された場合、リンクからの値は1つのアイテムリストでラップされなければなりません。" -#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 -msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "" -"つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです" +#: ../../src/faq.md:199 3af16c07e3f148ddb8849c94a3864158 +#, fuzzy +msgid "Which means \"create a list with exactly these sources as elements\"." +msgstr "つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです" -#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +#: ../../src/faq.md:201 0ea3de393d2f42aeb82658c85a19ec45 #, fuzzy msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " -"add `linkMerge: merge_nested` under the appropriate `in` entry of the " -"destination step." +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." msgstr "" -"`File[]` (`File`の配列) で、ソースが単一の`File` の場合、" -"`MultipleInputFeatureRequirement` をワークフローレベルの`requirements` に追加" -"し、`linkMerge: merge_nested` を目的ステップのエントリの該当`in`に追加しま" -"す。" +"`File[]` (`File`の配列) で、ソースが単一の`File` " +"の場合、`MultipleInputFeatureRequirement` をワークフローレベルの`requirements` " +"に追加し、`linkMerge: merge_nested` を目的ステップのエントリの該当`in`に追加します。" -#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd -msgid "Optional Inputs 💯" -msgstr "オプション入力 💯" +#: ../../src/faq.md:229 2f1bbb611c9c4f80b7ae0566432f2f35 +msgid "How do make an input optional? 💯" +msgstr "" -#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +#: ../../src/faq.md:231 08a226efe5d141e68215ac77725033db msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "入力パラメータをオプションにするには、型宣言に疑問符を付けます。" -#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +#: ../../src/faq.md:247 06e70a855a8f455ca0536eead77073c2 msgid "" msgstr "" -#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c -msgid "Enum Inputs ⚜️" -msgstr "列挙型入力 ⚜️" +#: ../../src/faq.md:248 7fda8eeb6a7f4689993ed0118c77f023 +msgid "" +"How do I specify an input that must come from a list of predefined values" +" (i.e. How do I use enum inputs) ?" +msgstr "" -#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +#: ../../src/faq.md:250 b1934a82553b4da3b7f981e576245dd8 #, fuzzy msgid "" -"For command line flags that require a specific input as the argument an enum " -"type can be declared in CWL. **Specifying null here is known as long form " -"style. It does the same thing as the question mark on the other inputs.**" -msgstr "" -"引数として特定の入力を必要とするコマンドラインフラグについては、CWLで列挙型を" -"宣言することで実現できます。**ここでnullを指定することは、ロングフォーム・ス" -"タイルとして知られています。他の入力のクエスチョンマークと同じ働きをします。" -"**" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" +msgstr "引数として特定の入力を必要とするコマンドラインフラグについては、CWLで列挙型を宣言することで実現できます。**ここでnullを指定することは、ロングフォーム・スタイルとして知られています。他の入力のクエスチョンマークと同じ働きをします。**" -#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +#: ../../src/faq.md:267 17fc34fad2094f5ea60e963dabd632b8 msgid "" msgstr "" -#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 -msgid "Record Inputs 📀" -msgstr "レコード入力 📀" +#: ../../src/faq.md:268 4d7acfbeba5b4e9cb31f08ef4b280447 +msgid "" +"How do I describe dependent or exclusive input parameters(e.g. How do I " +"use record inputs)?" +msgstr "" -#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +#: ../../src/faq.md:270 949ce95c082f4a05891a55fee25d4873 #, fuzzy msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -"**相互排他的** または**依存的** のいずれかのコマンドラインフラグについては、" -"特別なレコードタイプを定義することができます。また、ここにnullを指定すること" -"で、オプションの入力を作成することができます。" +"**相互排他的** または**依存的** " +"のいずれかのコマンドラインフラグについては、特別なレコードタイプを定義することができます。また、ここにnullを指定することで、オプションの入力を作成することができます。" -#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 -msgid "Setting Mutually Exclusive Parameters" +#: ../../src/faq.md:322 6fd3c469d11d4d52b9fbb7a3d443a8db +#, fuzzy +msgid "How do I set mutually exclusive parameters?" msgstr "相互に排他的なパラメータを設定する" -#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +#: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f msgid "" -"To properly set fields in a record input type, you need to pass a dictionary " -"to the input to properly set the parameters. This is done by using inline " -"JavaScript and returning the dictionary with the key of the field you want " -"to set. The source field is set to indicate the input from the workflow to " -"be used as the value." +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 -msgid "Setting Booleans" +#: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 +#, fuzzy +msgid "How can I set Booleans?" msgstr "ブール値の設定" -#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +#: ../../src/faq.md:344 8dcb88744e5840029de0e1bbf1c4b967 msgid "These can be set by using the default field" msgstr "デフォルトフィールドを使って、これらを設定します" -#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 -msgid "Concatenating Strings in Inputs" +#: ../../src/faq.md:349 972b7a5551bb43e6b9fa30e0cb713ff7 +#, fuzzy +msgid "What should I do when concatenating strings in inputs?" msgstr "入力された文字列を連結する" -#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +#: ../../src/faq.md:351 68f74afc21d846dd9070d45dec0cc1d8 msgid "The valueFrom field must be used instead of default." -msgstr "" -"defaultフィールドの代わりにvalueFromフィールドを使用する必要があります。" +msgstr "defaultフィールドの代わりにvalueFromフィールドを使用する必要があります。" -#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +#: ../../src/faq.md:359 53b633c6f8644106beb95ae567eb0708 +#, fuzzy +msgid "" +"I get `cwltool` errors due to filenames with space characters inside. " +"What should I do?" msgstr "`cwltool` ファイル名の中に空白文字があるために起こるエラー" -#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +#: ../../src/faq.md:361 7101bb5cb69e4faca4e60eabb4eb258e msgid "`cwltool` does not allow some characters in filenames by default." msgstr "`cwltool` は、デフォルトではファイル名に一部の文字を許可していません。" -#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +#: ../../src/faq.md:363 0eaf834b0ca847cca6736794895f5f81 msgid "" -"For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "" -"例えば、`a space is here.txt` というファイル名には、3つの空白文字が含まれてい" -"ます。" +"For example, the filename `a space is here.txt` includes 3 space " +"characters." +msgstr "例えば、`a space is here.txt` というファイル名には、3つの空白文字が含まれています。" -#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +#: ../../src/faq.md:371 7dabd8aab7a5423b842433616640bac0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." -msgstr "" -"これらの危険な文字を避けられない場合は、`--relax-path-checks` を`cwltool` に" -"渡してください。" +msgstr "これらの危険な文字を避けられない場合は、`--relax-path-checks` を`cwltool` に渡してください。" -#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 +#: ../../src/faq.md:373 b7ec33f38ce74ceb890f4379e4c41054 #, fuzzy -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgid "" +"What should I do when I get CWL Parameter Reference error due to hyphen " +"in an input identifier?" msgstr "入力識別子の中のハイフンに起因するCWLパラメータリファレンスエラー" -#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +#: ../../src/faq.md:375 e39b65947b294b20a444f18d780246f4 #, fuzzy msgid "If `cwltool --validate` returns valid" msgstr "`cwltool --validate` の結果が問題ない場合" -#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +#: ../../src/faq.md:384 dcd42c65681b438bb541fb38ddebb536 msgid "But executing it causes an error like:" msgstr "しかし、実行すると以下のようなエラーが発生します：" -#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +#: ../../src/faq.md:396 2b96665acac449758b852bbe7600e007 msgid "The file is here" msgstr "ファイルはこちらです" -#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +#: ../../src/faq.md:410 f59751d2f0014e59af7879a748062cec #, fuzzy msgid "Problem caused by `-` (hyphen character)." msgstr "`-` (ハイフン文字、引き算の記号)が原因で発生した問題です。" -#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" -"このエラーを修正するには、`-` (ハイフン) を`_` (アンダースコア) に変更してく" -"ださい" +#: ../../src/faq.md:423 7780f461ca4c478b92fca893c0b0894a +#, fuzzy +msgid "To fix this error, change `-` (hyphen) to `_` (underscore):" +msgstr "このエラーを修正するには、`-` (ハイフン) を`_` (アンダースコア) に変更してください" -#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +#: ../../src/faq.md:436 88df56dfff854fc68fb6ad3835a846e4 msgid "" -"If it is not possible to change the input identifier, then you can use an " -"alternative CWL Parameter Reference syntax:" -msgstr "" -"入力識別子を変更することができない場合は、別のCWLパラメータリファレンス構文を" -"使用することができます：" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" +msgstr "入力識別子を変更することができない場合は、別のCWLパラメータリファレンス構文を使用することができます：" -#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 -msgid "Use CWL and cwltool with Singularity" +#: ../../src/faq.md:442 fc407a9e8d8c4b699d9cd14b369343b5 +#, fuzzy +msgid "How do I use CWL and cwltool with Singularity?" msgstr "CWLとcwltoolをSingularityで使う" -#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +#: ../../src/faq.md:445 239f5f81cef042b08fb8015c36b3ecad msgid "" -"The CWL standards are built around (optional) Docker format containers. The " -"reference runner and several other CWL implementations support running those " -"Docker format containers using the Singularity engine. Directly specifying a " -"Singularity format container is not part of the CWL standards." +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." msgstr "" -#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 -msgid "Debug JavaScript Expressions" -msgstr "JavaScriptの式をデバッグする" +#: ../../src/faq.md:450 61641314d82b43e982e54c64c73232c5 +msgid "How do I debug the JavaScript in my CWL tool?" +msgstr "" -#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +#: ../../src/faq.md:452 5556d3c323664edea55cfb777f4efb3b #, fuzzy msgid "" -"You can use the --js-console option of cwltool, or " -"you can try creating a JavaScript or TypeScript project for your code, and " -"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" -"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -"cwltool の --js-console オプションを使用するか、ま" -"たは、あなたのコードのためのJavaScript または TypeScript プロジェクトを作成" -"し、expressionLib を使用して読み込んでみてください（例： https://github.com/common-" -"workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-" -"tool.cwl#L6-L8" +"cwltool の --js-console " +"オプションを使用するか、または、あなたのコードのためのJavaScript または TypeScript " +"プロジェクトを作成し、expressionLib を使用して読み込んでみてください（例： " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" -#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +#: ../../src/index.md:1 1c9fb72b83c9467a9672943fb47ffe32 msgid "Common Workflow Language User Guide" msgstr "Common Workflow Language ユーザーガイド" -#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +#: ../../src/index.md:3 aaa44578e27345e682ab44686b4da159 msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -"本ガイドは、オープンスタンダードである [Common Workflow Language](https://" -"www.commonwl.org/) (CWL) を使用したワークフローの書き方を紹介するものです。本" -"ガイドは、最新仕様{{ cwl_version }}を解説しています。" +"本ガイドは、オープンスタンダードである [Common Workflow Language](https://www.commonwl.org/)" +" (CWL) を使用したワークフローの書き方を紹介するものです。本ガイドは、最新仕様{{ cwl_version }}を解説しています。" -#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +#: ../../src/index.md:7 0adfc2adb0c74372b25d197dd3a73b8b msgid "Contributions and Feedback are Welcome!" msgstr "ご意見、ご感想、貢献をお待ちしております!" -#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +#: ../../src/index.md:9 96c8dca812f1415db7c5c006b0c0e022 msgid "" -"If you find that something is missing from this guide, or if you would like " -"to provide other feedback, file an Issue on the [project repository for this " -"guide][repo]. You can also suggest changes directly in a Pull Request by " -"clicking the \"Edit this page\" button at the right sidebar of each page." +"If you find that something is missing from this guide, or if you would " +"like to provide other feedback, file an Issue on the [project repository " +"for this guide][repo]. You can also suggest changes directly in a Pull " +"Request by clicking the \"Edit this page\" button at the right sidebar of" +" each page." msgstr "" -"このガイドに足りないものがある場合、またはその他のフィードバックを提供したい" -"場合は、[このユーザーガイドのプロジェクトリポジトリ][repo]にIssueを作成してく" -"ださい。また、各ページの右サイドバーにある「このページを編集する」ボタンをク" -"リックすると、Pull Requestで直接変更を提案することができます。" +"このガイドに足りないものがある場合、またはその他のフィードバックを提供したい場合は、[このユーザーガイドのプロジェクトリポジトリ][repo]にIssueを作成してください。また、各ページの右サイドバーにある「このページを編集する」ボタンをクリックすると、Pull" +" Requestで直接変更を提案することができます。" -#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +#: ../../src/index.md:16 35c50bb5c3a345b4a4ae66b2df065376 msgid "Navigating the User Guide" msgstr "ユーザーガイドの使い方" -#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +#: ../../src/index.md:18 9431edcf4e344fb89b6a251e627279d2 #, fuzzy msgid "" -"If you are a beginner user get started with the [Introduction](/introduction/" -"index.md) section. For advanced users the subsections of the [Topics](/" -"topics/index.md) have detailed information about the most common topics for " -"CWL." -msgstr "" -"初心者の方は、[はじめに](/introduction/index.md)のセクションから始めてくださ" -"い。上級者向けには、[Topics](/topics/index.md)のサブセクションに、CWLで最も一" -"般的なトピックに関する詳細情報があります。" +"If you are a beginner user get started with the " +"[Introduction](/introduction/index.md) section. For advanced users the " +"subsections of the [Topics](/topics/index.md) have detailed information " +"about the most common topics for CWL." +msgstr "初心者の方は、[はじめに](/introduction/index.md)のセクションから始めてください。上級者向けには、[Topics](/topics/index.md)のサブセクションに、CWLで最も一般的なトピックに関する詳細情報があります。" -#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +#: ../../src/index.md:23 61cf57e61a9f46e5a1bff6368c5ad5e3 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " -"subsections. The right sidebar contains links to the sections of each page, " -"and the Search form is on the left sidebar." -msgstr "" -"目次は、トップメニューと左サイドバーに表示されています。また、このページのさ" -"らに下にも表示されますが、サブセクションへのリンクがあります。右サイドバーに" -"は各ページのセクションへのリンクがあり、左サイドバーには「検索フォーム」があ" -"ります。" +"subsections. The right sidebar contains links to the sections of each " +"page, and the Search form is on the left sidebar." +msgstr "目次は、トップメニューと左サイドバーに表示されています。また、このページのさらに下にも表示されますが、サブセクションへのリンクがあります。右サイドバーには各ページのセクションへのリンクがあり、左サイドバーには「検索フォーム」があります。" -#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +#: ../../src/index.md:28 94381840d8a848c4a02fa97bfe83566d msgid "Table of Contents" msgstr "目次" -#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +#: ../../src/introduction/basic-concepts.md:1 c1271d88e203454688a22e61ee88f02a msgid "Basic Concepts" msgstr "基本コンセプト" -#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +#: ../../src/introduction/basic-concepts.md:3 dd462818cc9a4205b38866d0c5137ece msgid "" "This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are expected " -"to be familiar with workflow managers, YAML, and comfortable with following " -"instructions for the command-line. The other sections of the user guide " -"cover the same concepts, but in more detail. If you are already familiar " -"with CWL or you are looking for more advanced content, you may want to skip " -"this section." +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +#: ../../src/introduction/basic-concepts.md:10 7a56d394fb244431aefce7ebbb834ecf msgid "The CWL Specification" msgstr "CWLの仕様" -#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +#: ../../src/introduction/basic-concepts.md:21 35800ed2c56d489190d3702d9ad20fd7 msgid "" "The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered in " -"this user guide is the {{ cwl_version }}." +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." msgstr "" -"CWL仕様は、CWLコミュニティによって書かれ、維持されている文書です。この仕様に" -"は異なるバージョンが存在します。このユーザーガイドで扱うバージョンは" -"{{ cwl_version }}です。" +"CWL仕様は、CWLコミュニティによって書かれ、維持されている文書です。この仕様には異なるバージョンが存在します。このユーザーガイドで扱うバージョンは{{" +" cwl_version }}です。" -#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +#: ../../src/introduction/basic-concepts.md:25 3ab6dd6b2f694afeb08f3984a74f3efb msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" "incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes that " -"are backward-compatible. The last number is used for bug fixes, like typos " -"and other corrections to the specification." +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +#: ../../src/introduction/basic-concepts.md:33 72ae1fb763a34c41b1b06adcbe1522c3 #, fuzzy msgid "" -"The model used for the specification version is called Semantic Versioning. " -"See the end of this section to [learn more](#learn-more) about it." +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." msgstr "" -"仕様のバージョンアップに使われるモデルは、セマンティックバージョニングを利用" -"しています。それについて[もっと知りたい](#learn-more)方は、このセクションの最" -"後をご覧ください。" +"仕様のバージョンアップに使われるモデルは、セマンティックバージョニングを利用しています。それについて[もっと知りたい](#learn-" +"more)方は、このセクションの最後をご覧ください。" -#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +#: ../../src/introduction/basic-concepts.md:37 5aa7d3ee6cb048d888f1e1f49d0e08be msgid "Implementations" msgstr "実装" -#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +#: ../../src/introduction/basic-concepts.md:39 c87e6daefda74579a39924777b2e6809 #, fuzzy msgid "" -"An implementation of the CWL specification is any software written following " -"what is defined in a version of the specification document. However, " -"implementations may not implement every aspect of the specification. CWL " -"implementations are licensed under both Open Source and commercial licenses." -msgstr "" -"CWL仕様の実装とは、あるバージョンの仕様書で定義された内容に従って書かれたソフ" -"トウェアのことです。ただし、実装は仕様のすべての側面を実装するわけではありま" -"せん。CWLの実装は、オープンソース・ライセンスと商用ライセンスの両方でライセン" -"スされています。" +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." +msgstr "CWL仕様の実装とは、あるバージョンの仕様書で定義された内容に従って書かれたソフトウェアのことです。ただし、実装は仕様のすべての側面を実装するわけではありません。CWLの実装は、オープンソース・ライセンスと商用ライセンスの両方でライセンスされています。" -#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +#: ../../src/introduction/basic-concepts.md:44 c995e699ae2949219af252f9d802a43d #, fuzzy msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud " -"and high performance computing environments where tasks are scheduled in " -"parallel across many nodes." -msgstr "" -"CWLは、多くのノードでタスクが並列にスケジューリングされるクラスタ、クラウド、" -"ハイパフォーマンスコンピューティング環境における大規模なワークフローを記述す" -"るのに適しています。" +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." +msgstr "CWLは、多くのノードでタスクが並列にスケジューリングされるクラスタ、クラウド、ハイパフォーマンスコンピューティング環境における大規模なワークフローを記述するのに適しています。" -#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +#: ../../src/introduction/basic-concepts.md:51 09171f48a3d841b2acb6d803b2340c8e msgid "CWL specification, implementations, and other tools." msgstr "CWL仕様、実装、その他ツール。" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: 1c1647a3496c4251a3193f94ee4e78c8 #, fuzzy msgid "Processes and Requirements" msgstr "Processes 及び Requirements" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 +#: 854633336f4d4fc394e62c53ce022c6b #, fuzzy msgid "" -"A process is a computing unit that takes inputs and produces outputs. The " -"behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification " -"{{ cwl_version }}:" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" msgstr "" -"Processとは、入力を受けて出力を生成する計算のユニットです。Processの動作は、" -"inputs、requirements、hintsに影響されることがあります。CWL仕様" -"{{ cwl_version }}では、4種類のProcessが定義されています：" +"Processとは、入力を受けて出力を生成する計算のユニットです。Processの動作は、inputs、requirements、hintsに影響されることがあります。CWL仕様{{" +" cwl_version }}では、4種類のProcessが定義されています：" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 142a847f11d7462f8bf77bfe789410ca msgid "A command-line tool." msgstr "コマンドラインツール。" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 7c7567fa690043f9b4b89bdf8ca60cad msgid "An expression tool." msgstr "Expression ツール。" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: 7afcf087d3ea49dabf1a641a2bb71b35 msgid "An operation." msgstr "Operation。" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: 6399939602334819a20b92b957352a8a msgid "A workflow." msgstr "ワークフロー。" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 8c55b15cebf142899045f229ccc86b1e msgid "The processing units available in the CWL objects model." msgstr "CWLオブジェクトモデルで使用可能な処理単位です。" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a +#: ec54c0e67e894bfba2d0fbb0f87ffdf4 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" -"コマンドラインツールは、`echo` 、`ls` 、`tar` のようなコマンドラインユーティ" -"リティのラッパーです。コマンドラインツールは、ワークフローから呼び出せます。" +"コマンドラインツールは、`echo` 、`ls` 、`tar` " +"のようなコマンドラインユーティリティのラッパーです。コマンドラインツールは、ワークフローから呼び出せます。" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 +#: c88ad26efa794cbeb6f0690aa0cad5ea #, fuzzy msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be used " -"to simplify workflows and command-line tools, moving common parts of a " -"workflow execution into reusable JavaScript code that takes inputs and " -"produces outputs like a command-line tool." -msgstr "" -"ExpressionToolは、JavaScriptの式のラッパーです。WorkflowやCommandLineToolの簡" -"略化に使用でき、ワークフロー実行の共通部分を、CommandLineToolのように入力を受" -"けて出力を生成する再利用可能なJavaScriptコードに移動させることができます。" +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." +msgstr "ExpressionToolは、JavaScriptの式のラッパーです。WorkflowやCommandLineToolの簡略化に使用でき、ワークフロー実行の共通部分を、CommandLineToolのように入力を受けて出力を生成する再利用可能なJavaScriptコードに移動させることができます。" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef +#: 946825a7ea2c450eb3e41b5548670fb7 #, fuzzy msgid "" -"Operation is an abstract process that also takes inputs, produces outputs, " -"and can be used in a workflow. But it is a special operation not so commonly " -"used. It is discussed in the [Operations section](../topics/operations.md) " -"of this user guide." -msgstr "" -"Operationは、入力を受け、出力を出す抽象的なプロセスでもあり、ワークフローで使" -"用することができます。しかし、あまり一般的に使われていない特別な処理です。こ" -"のユーザーガイドの[Operation編](../topics/operations.md)で説明します。" +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." +msgstr "Operationは、入力を受け、出力を出す抽象的なプロセスでもあり、ワークフローで使用することができます。しかし、あまり一般的に使われていない特別な処理です。このユーザーガイドの[Operation編](../topics/operations.md)で説明します。" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#: 44aac23f302c4178accf7e431cfbb96c #, fuzzy msgid "" -"The workflow is a process that contains steps. Steps can be other workflows " -"(nested workflows), command-line tools, or expression tools. The inputs of a " -"workflow can be passed to any of its steps, while the outputs produced by " -"its steps can be used in the final output of the workflow." -msgstr "" -"Workflowは、ステップを含むプロセスである。ステップには、他のWorkflow（ネスト" -"されたWorkflow）、CommandLineTool、またはExpressionToolを使用することができま" -"す。Workflowの入力は、そのステップのいずれかに渡すことができ、ステップによっ" -"て生成された出力は、Workflowの最終出力に使用することができます。" +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." +msgstr "Workflowは、ステップを含むプロセスである。ステップには、他のWorkflow（ネストされたWorkflow）、CommandLineTool、またはExpressionToolを使用することができます。Workflowの入力は、そのステップのいずれかに渡すことができ、ステップによって生成された出力は、Workflowの最終出力に使用することができます。" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 +#: 5afdb7aaf0bf4c1abf4c22cdbdd58be9 msgid "" "The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through *requirements*. " -"There are many requirements defined in the CWL specification, for instance:" +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" msgstr "" -"CWL 仕様では、*requirements* を通じて、実装が追加機能を提供し、ワークフローの" -"前提条件を指定することができます。CWL仕様には、例えば、以下のような多くの要件" -"が定義されています：" +"CWL 仕様では、*requirements* " +"を通じて、実装が追加機能を提供し、ワークフローの前提条件を指定することができます。CWL仕様には、例えば、以下のような多くの要件が定義されています：" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +#: 07c5789c59224ed78a3ecd03cfe872e9 +#, fuzzy +msgid "" +"[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement)" +" - enables JavaScript in expressions." msgstr "`InlineJavascriptWorkflow` - でJavaScriptを有効にします。" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" -"`SubworkflowFeatureRequirement` - ネストしたワークフローを有効にします。" +#: 6f9854ae1b884ad39f88d2f39d66cb98 +#, fuzzy +msgid "" +"[`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow.html#SubworkflowFeatureRequirement)" +" - enables nested workflows." +msgstr "`SubworkflowFeatureRequirement` - ネストしたワークフローを有効にします。" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 +#: 23fef6de073f4da18118e4d0512670fe +#, fuzzy msgid "" -"`InitialWorkDirRequirement` - controls staging files in the input directory." -msgstr "" -"`InitialWorkDirRequirement` - 入力ディレクトリのステージングファイルを制御し" -"ます。" +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow.html#InitialWorkDirRequirement)" +" - controls staging files in the input directory." +msgstr "`InitialWorkDirRequirement` - 入力ディレクトリのステージングファイルを制御します。" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee +#: fb3762f91177401ea624d1e716d67ae6 #, fuzzy msgid "" -"Some CWL runners may provide requirements that are not in the specification. " -"For example, GPU requirements are supported in `cwltool` through the " -"`cwltool:CUDARequirement` requirement, but it is not part of the " -"{{ cwl_version }} specification and may not be supported by other CWL " -"runners." +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." msgstr "" -"いくつかのCWLランナーは、仕様にないrequirementsを提供することがあります。例え" -"ば、GPUに関するrequirementsは`cwltool` で`cwltool:CUDARequirement` を通してサ" -"ポートされていますが、{{ cwl_version }}仕様の一部ではないので、他のCWLラン" -"ナーではサポートされていないかもしれません。" +"いくつかのCWLランナーは、仕様にないrequirementsを提供することがあります。例えば、GPUに関するrequirementsは`cwltool`" +" で`cwltool:CUDARequirement` を通してサポートされていますが、{{ cwl_version " +"}}仕様の一部ではないので、他のCWLランナーではサポートされていないかもしれません。" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e +#: b6a5cd431c324078a9a4e1513a14ee28 #, fuzzy msgid "" -"Hints are similar to requirements, but while requirements list features that " -"are required, hints list optional features. Requirements are explained in " -"detail in the [Requirements](../topics/requirements-and-hints.md) section." +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." msgstr "" -"Hintsはrequirementsと似ていますが、requirementsが必須の機能を列挙するのに対" -"し、hintsはオプションの機能を列挙します。requirementsについては、" -"[requirements](../topics/requirements-and-hints.md) セクションで詳しく説明し" -"ています。" +"Hintsはrequirementsと似ていますが、requirementsが必須の機能を列挙するのに対し、hintsはオプションの機能を列挙します。requirementsについては、[requirements](../topics" +"/requirements-and-hints.md) セクションで詳しく説明しています。" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: 88d7bad84dd341d2abb33673b8b8f250 msgid "FAIR Workflows" msgstr "FAIRワークフロー" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 +#: bcbf5d76cf5f47b2a9691b7d2d8ef891 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " "machine accessibility and that all digital assets should be Findable, " "Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created. It " -"is thus important that workflows support the creation of FAIR data and " -"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" -"workflows.community/groups/fair/), Workflows Community Initiative." +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows both support the creation of FAIR " +"data and themselves adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a +#: 4ea1d3bf04dc42f0bc6735a45b9e0dc0 #, fuzzy msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\", " -"CWL tasks are isolated, and you must be explicit about your inputs and " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " "outputs." msgstr "" -"CWLのルーツは、タスク間の依存関係に基づき、実行順序を決定する \"make\" や多く" -"の類似ツールにあります。しかし、\"make\" とは異なり、CWLのタスクは分離されて" -"おり、入力と出力を明示する必要があります。" +"CWLのルーツは、タスク間の依存関係に基づき、実行順序を決定する \"make\" や多くの類似ツールにあります。しかし、\"make\" " +"とは異なり、CWLのタスクは分離されており、入力と出力を明示する必要があります。" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee +#: c0f53138bf084939a54b0a576b44199f #, fuzzy msgid "" -"The benefit of explicitness and isolation are flexibility, portability, and " -"scalability; tools and workflows described with CWL can transparently " -"leverage technologies such as Docker and be used with CWL implementations " -"from different vendors." -msgstr "" -"CWLで定義されたツールやワークフローは、Dockerなどの技術を透過的に活用し、異な" -"るベンダーのCWL実装と組み合わせて使用することができるためです。" +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." +msgstr "CWLで定義されたツールやワークフローは、Dockerなどの技術を透過的に活用し、異なるベンダーのCWL実装と組み合わせて使用することができるためです。" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: 91d6eb4984a6410ba99616b6617ba9af msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" -"`cwltool` はまた、データプロベナンスのためのPROV-O標準オントロジーを使用して" -"います。" +msgstr "`cwltool` はまた、データプロベナンスのためのPROV-O標準オントロジーを使用しています。" #: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 65c24244713741e196da08cb9ba237b2 -#: f059896039524095b4deb65d693f8ddf 3439764fab0e49d2bcb7c9fbae556e65 +#: ../../src/introduction/prerequisites.md:183 +#: ../../src/introduction/quick-start.md:94 0d7e607b00b9485aa2e3c5fb0a931bc6 +#: 161697ed3e864155bb89d8be794fc139 b4a7563eabf547c3bf7eab2567a27b51 msgid "Learn More" msgstr "さらなる学習" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 7221a89559944627b4c3db37f468f72c msgid "Semantic Versioning - " msgstr "セマンティック・バージョニング -" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 +#: bccf086fc9514f76b60dc161e3a09da3 msgid "" -"The CWL Specification page in the CWL website: " -msgstr "" -"CWLサイト内の「CWL仕様」ページ：" +"The CWL Specification page in the CWL website: " +"" +msgstr "CWLサイト内の「CWL仕様」ページ：" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 +#: a5b37924c7d04ab984ff2542847afc4a +#, fuzzy +msgid "" +"The Command Line Tool Description Standard: " +"<[https://www.commonwl.org/v1.2/CommandLineTool.html](https://w3id.org/cwl/CommandLineTool.html)>" +msgstr "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)から" + +#: ../../src/introduction/basic-concepts.md:183 +#: 44af015fa36644b99f07338d241d29c1 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" -"GitHubにある現在のCWL仕様：{{ ''.format(cwl_version_text) }}" +"GitHubにある現在のCWL仕様：{{ ''.format(cwl_version_text) }}" -#: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 +#: ../../src/introduction/basic-concepts.md:184 +#: bffca993172048a4b7ab7c62637662e2 msgid "" -"The list of Implementations in the CWL website: " +"The list of Implementations in the CWL website: " +"" msgstr "CWLサイト内の実装のリスト：" -#: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: ../../src/introduction/basic-concepts.md:185 +#: 84c61946406347c8b138772909110d54 msgid "PROV-O: The PROV Ontology - " msgstr "PROV-O: PROVオントロジー -" -#: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b +#: ../../src/introduction/basic-concepts.md:186 +#: eb0b6a62e06143eabc7b92acff9643ea msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." -msgstr "" -"CWLのOperationsについては、本ユーザーガイドの[Operations](../topics/" -"operations.md)セクションで説明します。" +msgstr "CWLのOperationsについては、本ユーザーガイドの[Operations](../topics/operations.md)セクションで説明します。" -#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +#: ../../src/introduction/index.md:1 48532f7701c54166859098e521a43db0 msgid "Introduction" msgstr "はじめに" -#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +#: ../../src/introduction/index.md:3 08db628a949b4513b824ee334e70a7df #, fuzzy msgid "" "This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that " -"are useful to know before reading the rest of the user guide." -msgstr "" -"このセクションでは、CWLの簡単な紹介、このユーザーガイドに従うための前提条件、" -"そしてユーザーガイドの他の部分を読む前に知っておくと便利な基本概念について案" -"内します。" +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." +msgstr "このセクションでは、CWLの簡単な紹介、このユーザーガイドに従うための前提条件、そしてユーザーガイドの他の部分を読む前に知っておくと便利な基本概念について案内します。" -#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +#: ../../src/introduction/prerequisites.md:1 d3f5749a76c14fdf8052f5f683d11b9e msgid "Prerequisites" msgstr "前提条件" -#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +#: ../../src/introduction/prerequisites.md:6 ab9e21b3e99641d096ba70012b4eb035 msgid "" -"The software and configurations listed in this section are prerequisites for " -"following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements focuses " -"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " -"runner or workflow system, but the results and interface may look different " -"(though the exact workflow outputs should be identical)." +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +#: ../../src/introduction/prerequisites.md:12 8ed426ebcb744839915e7c414d69b1e9 msgid "CWL Implementations" msgstr "CWL実装" -#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +#: ../../src/introduction/prerequisites.md:14 ff74d48407464c4b9d451fa419137144 #, fuzzy msgid "" -"There are many implementations of the CWL standards. Some are complete CWL " -"runners, while others could be plug-ins or extensions to workflow engines. " -"We have a better explanation in the [Implementations](basic-concepts." -"md#implementations) section." +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." msgstr "" -"CWL規格の実装は数多く存在します。あるものは完全なCWL実装であり、他のものは" -"ワークフローエンジンのプラグインや拡張になり得ます。[実装](basic-concepts." -"md#implementations)のセクションでより詳しいをしています。" +"CWL規格の実装は数多く存在します。あるものは完全なCWL実装であり、他のものはワークフローエンジンのプラグインや拡張になり得ます。[実装" +"](basic-concepts.md#implementations)のセクションでより詳しいをしています。" -#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +#: ../../src/introduction/prerequisites.md:19 eb98aa9c71d746a69e9610996ffc5b47 msgid "Operating System" msgstr "オペレーティングシステム" -#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +#: ../../src/introduction/prerequisites.md:21 209a0018e7da48f09b27dc507ba14d24 msgid "" -"We recommend using an up-to-date operating system. You can choose any of the " -"following options for your operating system:" -msgstr "" -"最新のオペレーティングシステムを使用することをお勧めします。OSは、以下のいず" -"れかをお選びいただけます：" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" +msgstr "最新のオペレーティングシステムを使用することをお勧めします。OSは、以下のいずれかをお選びいただけます：" -#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +#: ../../src/introduction/prerequisites.md:24 8baf869537ea478791356320280df928 msgid "Linux" msgstr "Linux" -#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +#: ../../src/introduction/prerequisites.md:25 248e9760ce60442eb10ab7247d6af23b msgid "macOS" msgstr "macOS" -#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +#: ../../src/introduction/prerequisites.md:26 d89306bbadf44b6bba8959f1f68cc2f0 msgid "Windows" msgstr "Windows" -#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +#: ../../src/introduction/prerequisites.md:29 aeeb990abbbd42cca122c342054be29c msgid "" -"If you are using Windows, you will have to install the [Windows Subsystem " -"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " -"installing WSL2. Your operating system also needs internet access and a " -"recent version of Python (3.6+)." +"If you are using Windows, you will have to install the Windows Subsystem " +"for Linux 2 as documented in the [`cwltool` documentation for Microsoft " +"Windows users](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users). Your operating " +"system also needs internet access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +#: ../../src/introduction/prerequisites.md:34 21d1f29fb15745c480194eae6acdd031 #, fuzzy msgid "CWL Runner" msgstr "CWL Runner" -#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +#: ../../src/introduction/prerequisites.md:39 89f0bf6ff8544a6d87114085be8e0bb6 #, fuzzy msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL community. " -"It is also the CWL reference runner, which means it must support everything " -"in the current CWL specification, {{ cwl_version }}." +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -"CWL ワークフローを実行するために最初に必要なものは、CWL runnerです。" -"`cwltool` は、CWL コミュニティによって維持されている Python オープンソース・" -"プロジェクトです。これはCWL reference runner(訳注: CWLの参照実装)でもあり、現" -"在のCWL仕様{{ cwl_version }}のすべてをサポートしなければならないことを意味し" -"ます。" +"CWL ワークフローを実行するために最初に必要なものは、CWL runnerです。`cwltool` は、CWL " +"コミュニティによって維持されている Python オープンソース・プロジェクトです。これはCWL reference runner(訳注: " +"CWLの参照実装)でもあり、現在のCWL仕様{{ cwl_version }}のすべてをサポートしなければならないことを意味します。" -#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +#: ../../src/introduction/prerequisites.md:44 068f09d4d66547448693f7b9dadef497 msgid "" -"`cwltool` can be installed with `pip`. We recommend using a virtual " -"environment like `venv` or `conda`. The following commands will create and " -"activate a Python virtual environment using the `venv` module, and install " -"`cwltool` in that environment:" +"`cwltool` can be installed with `pip`, `apt`, or `conda`. We recommend " +"using a virtual environment like `venv` or `conda`." msgstr "" -"`cwltool` は、`pip` でインストールすることができます。`venv` または`conda` の" -"ような仮想環境を使用することをお勧めします。以下のコマンドは、`venv` モジュー" -"ルを使用して Python 仮想環境を作成およびアクティブ化し、その環境内に" -"`cwltool` をインストールします：" - -#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "`pip` と `venv` での `cwltool` のインストール。" -#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +#: ../../src/introduction/prerequisites.md:48 1edf8b8438334ae29dc406dbfd711228 #, fuzzy msgid "" -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool#install) for other ways to install `cwltool` with `apt` and " -"`conda`." +"Visit the `cwltool` " +"[documentation](https://cwltool.readthedocs.io/en/latest/#install) for " +"details on installing `cwltool`." msgstr "" -"`cwltool` を`apt` と`conda` とともにインストールする他の方法については、" -"`cwltool` [documentation](https://github.com/common-workflow-language/" -"cwltool#install) を参照してください。" +"`cwltool` を`apt` と`conda` とともにインストールする他の方法については、`cwltool` " +"[documentation](https://github.com/common-workflow-" +"language/cwltool#install) を参照してください。" -#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +#: ../../src/introduction/prerequisites.md:52 5e300141ce43435f9437507374987213 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "簡単なCWLツール定義`true.cwl` で`cwltool` を使ってみましょう。" -#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +#: ../../src/introduction/prerequisites.md:54 282ac7ba2a2346feac2456bcda0f214a msgid "`true.cwl`" msgstr "`true.cwl`" -#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +#: ../../src/introduction/prerequisites.md:60 0b36f94f479a4bce9bd9be9983894421 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the CWL " -"standards. However, these actions will be performed without running the " -"document. To validate CWL workflows (or even a standalone command line tool " -"description like the above) pass the `--validate` option to the `cwltool` " -"command:" -msgstr "" -"`cwltool` コマンドには、CWL ツールおよびワークフロー定義を検証するオプション" -"があります。このオプションは、CWL文書を解析し、構文エラーを探し、ワークフロー" -"記述がCWL標準に準拠しているかどうかを検証します。ただし、これらの操作は、ド" -"キュメントを実行せずに行われます。CWLワークフロー（または上記のようなスタンド" -"アロンコマンドラインツールの記述も）を検証するには、`cwltool` コマンドに`--" -"validate` オプションを渡します：" - -#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" +msgstr "" +"`cwltool` コマンドには、CWL " +"ツールおよびワークフロー定義を検証するオプションがあります。このオプションは、CWL文書を解析し、構文エラーを探し、ワークフロー記述がCWL標準に準拠しているかどうかを検証します。ただし、これらの操作は、ドキュメントを実行せずに行われます。CWLワークフロー（または上記のようなスタンドアロンコマンドラインツールの記述も）を検証するには、`cwltool`" +" コマンドに`--validate` オプションを渡します：" + +#: ../../src/introduction/prerequisites.md:66 5fce122794e34892b430ca4bdba5ba50 msgid "Validating `true.cwl` with `cwltool`." msgstr "`cwltool` を使って `true.cwl` を検証します。" -#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 -msgid "" -"You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" -"`--validate` オプションを省略することで、CWLツール定義を実行することができま" -"す：" +#: ../../src/introduction/prerequisites.md:71 73f074f47d1449dcb40ff960a84851fd +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "`--validate` オプションを省略することで、CWLツール定義を実行することができます：" -#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +#: ../../src/introduction/prerequisites.md:73 2dd5a67870ca41b48e17c468ba15888b msgid "Running `true.cwl` with `cwltool`." msgstr "`cwltool` を使って `true.cwl` を実行します。" -#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 -#, fuzzy -msgid "Cwl-runner Python Module" -msgstr "Cwl-runner Pythonモジュール" +#: ../../src/introduction/prerequisites.md:78 d2dc809318be49cc996d892e93ad84ac +msgid "Generic ``cwl-runner`` alias" +msgstr "" -#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +#: ../../src/introduction/prerequisites.md:80 9809c2e262924ef286b0bd62e0b00995 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be invoked " -"independently, and is not reliant on a particular CWL runner program name. " -"Users can invoke `cwl-runner` instead of invoking a CWL runner like " -"`cwltool` directly. The `cwl-runner` is installed by a system administrator " -"or user to point to the preferred CWL implementation. This is convenient for " -"environments with multiple CWL runners." +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." msgstr "" -"`cwl-runner` は、CWL準拠のランナーに対する、実装にとらわれないエイリアスで" -"す。これは、`cwl-runner` エイリアスコマンドを独立して呼び出すことができ、特定" -"のCWLランナープログラム名に依存しないことを意味します。ユーザーは、`cwltool` " -"のようなCWLランナーを直接呼び出す代わりに、`cwl-runner` を呼び出すことができ" -"ます。`cwl-runner` は、システム管理者またはユーザーによってインストールされ、" -"好みのCWL実装を指し示す。これは、複数のCWLランナーがある環境では便利です。" +"`cwl-runner` は、CWL準拠のランナーに対する、実装にとらわれないエイリアスです。これは、`cwl-runner` " +"エイリアスコマンドを独立して呼び出すことができ、特定のCWLランナープログラム名に依存しないことを意味します。ユーザーは、`cwltool` " +"のようなCWLランナーを直接呼び出す代わりに、`cwl-runner` を呼び出すことができます。`cwl-runner` " +"は、システム管理者またはユーザーによってインストールされ、好みのCWL実装を指し示す。これは、複数のCWLランナーがある環境では便利です。" -#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +#: ../../src/introduction/prerequisites.md:88 6dd6aa836099469381fb564d63b84f3d +#, fuzzy msgid "" -"The CWL community publishes a Python package with the name `cwlref-runner` " -"that installs an alias for `cwltool` under the name `cwl-runner`" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`." msgstr "" -"CWLコミュニティは、`cwlref-runner` という名前のPythonパッケージを公開してお" -"り、`cwltool` のエイリアスを`cwl-runner` という名前でインストールします" +"CWLコミュニティは、`cwlref-runner` という名前のPythonパッケージを公開しており、`cwltool` のエイリアスを" +"`cwl-runner` という名前でインストールします" -#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +#: ../../src/introduction/prerequisites.md:91 cc1a9b95508e44a1bf08ae75d990c301 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "cwltool のエイリアス `cwl-runner` を `pip` でインストールします。" -#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +#: ../../src/introduction/prerequisites.md:98 8f8c80f705d94d4899b250bbf9c54562 msgid "" -"Now you can validate and run your workflow with the `cwl-runner` executable, " -"which will invoke `cwltool`. You should have the same results and output as " -"in the previous section." +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." msgstr "" -"これで `cwl-runner` 実行ファイルを用いてワークフローを検証・実行し、" -"`cwltool` を呼び出すことができるようになりました。前のセクションと同じ結果と" -"出力が得られるはずです。" +"これで `cwl-runner` 実行ファイルを用いてワークフローを検証・実行し、`cwltool` " +"を呼び出すことができるようになりました。前のセクションと同じ結果と出力が得られるはずです。" -#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +#: ../../src/introduction/prerequisites.md:102 176e4214d18149f3ba0bda692bcf760f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "検証`true.cwl` with`cwl-runner`." -#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +#: ../../src/introduction/prerequisites.md:107 4890bf20bc3842d3a7421b555bcda94a msgid "Running `true.cwl` with `cwl-runner`." msgstr "`true.cwl` を `cwl-runner` で実行します。" -#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +#: ../../src/introduction/prerequisites.md:112 2475a83cf6ed4389bb680fa37e8fe69c msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For " -"that, the first thing you need to do is copy `true.cwl` workflow into a new " -"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" msgstr "" -"`cwl-runner` を実行するもう一つの方法は、ファイルを直接起動することです。その" -"ためには、まず`true.cwl` ワークフローを新しいファイル`true_shebang.cwl` にコ" -"ピーし、特別な最初の行、*shebang* を含める必要があります：" +"`cwl-runner` を実行するもう一つの方法は、ファイルを直接起動することです。そのためには、まず`true.cwl` " +"ワークフローを新しいファイル`true_shebang.cwl` にコピーし、特別な最初の行、*shebang* を含める必要があります：" -#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: ../../src/introduction/prerequisites.md:116 24da787aa76c4480838a93ba0533898d msgid "`true_shebang.cwl`" msgstr "`true_shebang.cwl`" -#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 -msgid "" -"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" -"`chmod u+x` を実行することで、 `true_shebang.cwl` を実行可能なファイルにする" -"ことができます。" +#: ../../src/introduction/prerequisites.md:122 4f3cb8d1f9ce4e3d852e81aa4e0f60be +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "`chmod u+x` を実行することで、 `true_shebang.cwl` を実行可能なファイルにすることができます。" -#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +#: ../../src/introduction/prerequisites.md:124 27693d62faa045d9b03143d9bd2afcdf msgid "Making `true.cwl` executable." msgstr "`true.cwl` 実行可能なものにする。" -#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +#: ../../src/introduction/prerequisites.md:131 703531514abe4fd48015c472005dbffa msgid "" -"And finally, you can execute it directly in the command-line. On execution, " -"the program specified in the shebang (`cwl-runner`) will be used to execute " -"the rest of the file." +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." msgstr "" -"そして最後に、コマンドラインで直接実行することができます。実行時には、shebang" -"で指定されたプログラム(`cwl-runner`)が、ファイルの残りの部分を実行するために" -"使用されます。" +"そして最後に、コマンドラインで直接実行することができます。実行時には、shebangで指定されたプログラム(`cwl-" +"runner`)が、ファイルの残りの部分を実行するために使用されます。" -#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +#: ../../src/introduction/prerequisites.md:135 abba2e14c4e54252bb75983274663a7a msgid "Running `true_shebang.cwl` with a shebang." msgstr "`true_shebang.cwl` をシェバングで実行する。" -#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +#: ../../src/introduction/prerequisites.md:141 11fea992c00940d29eb29ccf4b9370e9 +#, fuzzy msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute the " -"script using the executable specified after the shebang. It is considered a " -"good practice to use `/usr/bin/env ` rather than using a hard-" -"coded location, since `/usr/bin/env ` looks for the " -"`` program in the system `PATH`," -msgstr "" -"*shebang* は、スクリプトの冒頭の2文字列`#!` のことです。スクリプトが実行可能" -"な場合、オペレーティングシステムは、shebangの後に指定された実行可能ファイルを" -"使用してスクリプトを実行します。`/usr/bin/env ` は` " -"` プログラムをシステムの`PATH` で探すので、ハードコードされた場所" -"を使うよりも`/usr/bin/env ` を使うことが良い習慣と考えられていま" -"す" - -#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env [executable]` rather than" +" using a hard-coded location, since `/usr/bin/env [executable]` looks for" +" the `[executable]` program in the system `PATH`," +msgstr "" +"*shebang* は、スクリプトの冒頭の2文字列`#!` " +"のことです。スクリプトが実行可能な場合、オペレーティングシステムは、shebangの後に指定された実行可能ファイルを使用してスクリプトを実行します。`/usr/bin/env" +" ` は` ` プログラムをシステムの`PATH` " +"で探すので、ハードコードされた場所を使うよりも`/usr/bin/env ` を使うことが良い習慣と考えられています" + +#: ../../src/introduction/prerequisites.md:148 854736eef2ac4b63b187a4cea9660ae4 msgid "Text Editor" msgstr "テキストエディタ" -#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +#: ../../src/introduction/prerequisites.md:150 480fbb7a743046068c114fff5b396a9f msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -"CWLではどんなテキストエディタでも使えますが、シンタックスハイライトのために、" -"YAMLをサポートするエディタをお勧めします。人気のあるエディタは、Visual " -"Studio Code、Sublime、WebStorm、vim/neovim、そしてEmacsです。" +"CWLではどんなテキストエディタでも使えますが、シンタックスハイライトのために、YAMLをサポートするエディタをお勧めします。人気のあるエディタは、Visual" +" Studio Code、Sublime、WebStorm、vim/neovim、そしてEmacsです。" -#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +#: ../../src/introduction/prerequisites.md:154 28da3eea8fd245d1936013d021c25164 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting " -"and better auto-complete:" +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" msgstr "" -"Visual Studio CodeとWebStormには、CWLとの統合を実現する拡張機能があり、カスタ" -"マイズされたシンタックスハイライトやより優れた自動補完などの機能が用意されて" -"います：" +"Visual Studio " +"CodeとWebStormには、CWLとの統合を実現する拡張機能があり、カスタマイズされたシンタックスハイライトやより優れた自動補完などの機能が用意されています：" -#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +#: ../../src/introduction/prerequisites.md:158 73c08e11e90d4c7f952307a1cdaa360b #, fuzzy msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " +"Visual Studio Code with the Benten (CWL) plugin - " +"" msgstr "" -"Benten(弁天)（CWL）プラグインを使ったVisual Studio Code -" +"Benten(弁天)（CWL）プラグインを使ったVisual Studio Code " +"-" -#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +#: ../../src/introduction/prerequisites.md:159 a5b788252a924338963f0ed198fc22ca msgid "" -"cwl-plugin for IntelliJ - " +"cwl-plugin for IntelliJ - " msgstr "" "IntelliJ 用 cwl-plugin -" -#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +#: ../../src/introduction/prerequisites.md:161 ee705b919acd461a8d9622821da246b6 msgid "" -"The CWL community also maintains a list of editors and viewers: " -msgstr "" -"CWLコミュニティでは、エディターやビューアーのリストも管理しています：" +"The CWL community also maintains a list of editors and viewers: " "" +msgstr "CWLコミュニティでは、エディターやビューアーのリストも管理しています：" -#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +#: ../../src/introduction/prerequisites.md:164 7724b63db3cc45139379898d047c0f83 msgid "Docker" msgstr "Docker" -#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +#: ../../src/introduction/prerequisites.md:168 eff13997c1ce43d1ad2d7a4d927394fe #, fuzzy msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: ." -msgstr "" -"`cwltool` は、ツール、ワークフロー、およびワークフロー ステップで指定されたソ" -"フトウェアコンテナをDockerを使用して実行します。Docker ドキュメントの指示に" -"従って、お使いのオペレーティングシステム用にインストールしてください：" +"documentation to install it for your operating system: " "." +msgstr "" +"`cwltool` は、ツール、ワークフロー、およびワークフロー " +"ステップで指定されたソフトウェアコンテナをDockerを使用して実行します。Docker " +"ドキュメントの指示に従って、お使いのオペレーティングシステム用にインストールしてください：." -#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +#: ../../src/introduction/prerequisites.md:172 2872503638624b7e904ae407375ac165 #, fuzzy msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models with " -"and without containers." -msgstr "" -"Dockerコンテナの書き方や構築方法を知っておく必要はありません。このユーザーガ" -"イドの残りの部分では、実行例として既存のDockerイメージを使用し、コンテナのあ" -"る実行モデルとない実行モデルの違いを明確にすることにします。" +"examples, and to clarify the differences between the execution models " +"with and without containers." +msgstr "Dockerコンテナの書き方や構築方法を知っておく必要はありません。このユーザーガイドの残りの部分では、実行例として既存のDockerイメージを使用し、コンテナのある実行モデルとない実行モデルの違いを明確にすることにします。" -#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +#: ../../src/introduction/prerequisites.md:178 52ddcc9bc1554d809371fc0a503c40bc #, fuzzy msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for pulling " -"images." +"Singularity. You can also use alternative container registries for " +"pulling images." msgstr "" -"`cwltool` Docker、Podman、udocker、Singularityによるコンテナの実行をサポート" -"しています。また、コンテナイメージを取得するために代替のコンテナレジストリを" -"使用することもできます。" +"`cwltool` " +"Docker、Podman、udocker、Singularityによるコンテナの実行をサポートしています。また、コンテナイメージを取得するために代替のコンテナレジストリを使用することもできます。" -#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +#: ../../src/introduction/prerequisites.md:185 f3bbfa17f31a459386461951de157dd2 msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the next " -"section, Basic Concepts." -msgstr "" -"次項の「基本コンセプト」の[実装](basic-concepts.md#implementations)のトピック" -"を参照してください。" +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." +msgstr "次項の「基本コンセプト」の[実装](basic-concepts.md#implementations)のトピックを参照してください。" -#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +#: ../../src/introduction/prerequisites.md:186 e22b9e7c56104e018e6d2f3d547c01ea msgid "The Python `venv` module: " msgstr "Python`venv` モジュール:" -#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +#: ../../src/introduction/quick-start.md:1 9ca367e3ca754a0fa88dab64724b95b6 msgid "Quick Start" msgstr "クイックスタート" -#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +#: ../../src/introduction/quick-start.md:3 733db5702c774f32b8c91d13f74f3720 #, fuzzy msgid "" -"This section will show you a brief overview of what CWL is, and where you " -"can learn more about it. No previous knowledge of CWL is required, but you " -"must be comfortable following instructions for the command-line." -msgstr "" -"このセクションでは、CWLとは何か、またCWLについてもっと詳しく知ることができる" -"場所について、簡単に紹介します。CWLに関する予備知識は必要ありませんが、コマン" -"ドラインを使用することに慣れていると良いです。" +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." +msgstr "このセクションでは、CWLとは何か、またCWLについてもっと詳しく知ることができる場所について、簡単に紹介します。CWLに関する予備知識は必要ありませんが、コマンドラインを使用することに慣れていると良いです。" -#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +#: ../../src/introduction/quick-start.md:7 0b164074dd0849c3b2c8d2f78ea99e95 msgid "“Hello World”" msgstr "\"Hello World\"" -#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +#: ../../src/introduction/quick-start.md:12 6485f96f638548fbb7addc57f6cde92b msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " -"example below shows a simple CWL “Hello World” workflow annotated with " -"comments. Note that comments start with `#`:" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" msgstr "" -"CWLドキュメントは[YAML](../topics/index.md)(および/またはJSON)で書かれていま" -"す。以下の例は、コメントで注釈されたシンプルなCWL \"Hello World\" ワークフ" -"ローを示しています。コメントは`#` で始まることに注意してください：" +"CWLドキュメントは[YAML](../topics/index.md)(および/またはJSON)で書かれています。以下の例は、コメントで注釈されたシンプルなCWL" +" \"Hello World\" ワークフローを示しています。コメントは`#` で始まることに注意してください：" -#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +#: ../../src/introduction/quick-start.md:16 5e06f9c4754347b8bac88d24c21e0f67 msgid "`hello_world.cwl`" msgstr "`hello_world.cwl`" -#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +#: ../../src/introduction/quick-start.md:22 6a13fb9112ab41acb60dc65b3656f63e #, fuzzy msgid "" "The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the " -"same result as the command-line `echo \"Hello World\"`." +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." msgstr "" -"上記の例は、`echo` のコマンドラインツールのラッパーに過ぎません。デフォルトの" -"入力値で上記のワークフローを実行すると、コマンドラインと同じ結果が得られます" -"`echo \"Hello World\"`." +"上記の例は、`echo` " +"のコマンドラインツールのラッパーに過ぎません。デフォルトの入力値で上記のワークフローを実行すると、コマンドラインと同じ結果が得られます`echo " +"\"Hello World\"`." -#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +#: ../../src/introduction/quick-start.md:27 7b2ae93353184faea0ae4f4acdfc3350 #, fuzzy msgid "" -"In CWL, there is a distinction between a command-line tool and a workflow. " -"But for the sake of simplicity, we are using the term “workflow” here. You " -"will learn more about this in the [basic concepts](basic-concepts.md) " -"section." +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." msgstr "" -"CWLでは、CommandLineToolとWorkflowは区別されています。しかし、ここでは簡略化" -"のため、「ワークフロー」という用語を使用しています。これについては、[基本概" -"念](basic-concepts.md)のセクションで詳しく説明します。" +"CWLでは、CommandLineToolとWorkflowは区別されています。しかし、ここでは簡略化のため、「ワークフロー」という用語を使用しています。これについては、[基本概念" +"](basic-concepts.md)のセクションで詳しく説明します。" -#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +#: ../../src/introduction/quick-start.md:32 1ed30b04073d47a9893774746479fb5d msgid "Installing a CWL Runner" msgstr "CWL Runnerのインストール" -#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +#: ../../src/introduction/quick-start.md:34 73a42cd9e0e54296985088b7221a8a93 #, fuzzy msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the CWL " -"*Reference Runner* for the specification, and it is compliant with the " -"latest version of the specification: {{ cwl_version }}. You can install " -"`cwltool` using `pip`:" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" msgstr "" -"`cwltool` は、CWL仕様の実装の１つです。また、同仕様のCWL*Reference Runner* で" -"もあり、同仕様の最新バージョンに準拠しています：{cwl_version }}に準拠していま" -"す。`cwltool` は、`pip` を使ってインストールできます：" +"`cwltool` は、CWL仕様の実装の１つです。また、同仕様のCWL*Reference Runner* " +"でもあり、同仕様の最新バージョンに準拠しています：{cwl_version }}に準拠しています。`cwltool` は、`pip` " +"を使ってインストールできます：" -#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +#: ../../src/introduction/quick-start.md:39 57aea587ade24610be62f5d993b0b755 msgid "Installing `cwltool` with `pip`." msgstr "`cwltool` を`pip` でインストールします。" -#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +#: ../../src/introduction/quick-start.md:47 51183fc986014edbb026a53f222e6c2e msgid "" -"If installing the cwltool using the pip command doesn't work for you, the " -"[prerequisites](prerequisites.md) section contains other ways to install " -"`cwltool` and a more detailed list of software and libraries used for " +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " "following the rest of this user guide." msgstr "" -"pipコマンドを使用してcwltoolをインストールしてもうまくいかない場合は、[前提条" -"件](prerequisites.md)セクションに、`cwltool` をインストールする他の方法と、こ" -"のユーザーガイドの残りの部分を追うために使用するソフトウェアとライブラリのよ" -"り詳細なリストがあります。" +"pipコマンドを使用してcwltoolをインストールしてもうまくいかない場合は、[前提条件](prerequisites.md)セクションに、`cwltool`" +" をインストールする他の方法と、このユーザーガイドの残りの部分を追うために使用するソフトウェアとライブラリのより詳細なリストがあります。" -#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +#: ../../src/introduction/quick-start.md:51 a7582c3ae37a462a8ae1e72b3f321534 msgid "Running \"Hello World\"" msgstr "\"Hello World\"を実行する" -#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +#: ../../src/introduction/quick-start.md:53 0595e96912dc40e5a09f2ced2d2b7bcd +#, fuzzy msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " -"workflow without specifying any option:" +"[OPTIONS] [CWL_DOCUMENT] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" msgstr "" -"`cwltool` コマンドライン実行ファイルの使い方は、基本的に`cwltool [OPTIONS] " -" [INPUTS_OBJECT]`です。`hello_world.cwl` Workflowは、オプション" -"を指定せずに実行することができます：" +"`cwltool` コマンドライン実行ファイルの使い方は、基本的に`cwltool [OPTIONS] " +"[INPUTS_OBJECT]`です。`hello_world.cwl` Workflowは、オプションを指定せずに実行することができます：" -#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +#: ../../src/introduction/quick-start.md:57 5b393c69816549b084516dda4d4274f5 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "`hello_world.cwl` を `cwltool` で実行します。" -#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +#: ../../src/introduction/quick-start.md:62 4306d8ad802f45c18487d932d04492fa msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" -msgstr "" -"また、`echo` base コマンドの引数を変更するのと同様に、入力パラメータ" -"`message` のデフォルト値を上書きすることもできます：" +msgstr "また、`echo` base コマンドの引数を変更するのと同様に、入力パラメータ`message` のデフォルト値を上書きすることもできます：" -#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +#: ../../src/introduction/quick-start.md:65 8339ec411ad04c70ab8d795eb154fc38 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "`hello_world.cwl` を`cwltool` で入力パラメータを渡して実行する。" -#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +#: ../../src/introduction/quick-start.md:70 3ecca6985e754951aee00c93effe9517 msgid "" -"Another way of passing values to your workflow input parameters is via an " -"*Inputs Object*. This is a file containing the input fields with their " +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " "corresponding values. The Inputs Objects file can be written in JSON or " "YAML. For example:" msgstr "" -"ワークフロー入力パラメータに値を渡すもう一つの方法は、*Inputs Object* を介す" -"る方法です。これは、入力フィールドとその対応する値を含むファイルです。Inputs " -"Objects ファイルは、JSON または YAML で記述することができます。例えば、以下の" -"ようになります：" +"ワークフロー入力パラメータに値を渡すもう一つの方法は、*Inputs Object* " +"を介する方法です。これは、入力フィールドとその対応する値を含むファイルです。Inputs Objects ファイルは、JSON または YAML " +"で記述することができます。例えば、以下のようになります：" -#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +#: ../../src/introduction/quick-start.md:74 d05e8e016b1d40c28c4b6091103fe920 msgid "`hello_world-job.json`" msgstr "`hello_world-job.json`" -#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +#: ../../src/introduction/quick-start.md:80 c5983ba6c86f4b749522c11cb3843911 msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" -msgstr "" -"このInputs Objectファイルを使用して、「Hello World」ワークフローを実行するこ" -"とができるようになりました：" +msgstr "このInputs Objectファイルを使用して、「Hello World」ワークフローを実行することができるようになりました：" -#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +#: ../../src/introduction/quick-start.md:82 4065124edf3a4678a37c82e3070595cb msgid "Passing an Inputs Object file to `cwltool`." msgstr "`cwltool` に Inputs Object ファイルをします。" -#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +#: ../../src/introduction/quick-start.md:88 52b1602b5c8d48db88d0b16f788e7703 #, fuzzy msgid "" "We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but it " -"is not a requirement. You can choose any name for your workflows and Inputs " -"Object files." +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." msgstr "" -"ワークフローとInputs Objectファイルには、同様のファイル名を使用しました。*-" -"job.json* という接尾辞は、Inputs Object ファイルでは非常に一般的ですが必須で" -"はありません。ワークフローとInputs Objectファイルには、任意の名前を付けること" -"ができます。" +"ワークフローとInputs Objectファイルには、同様のファイル名を使用しました。*-job.json* という接尾辞は、Inputs " +"Object ファイルでは非常に一般的ですが必須ではありません。ワークフローとInputs " +"Objectファイルには、任意の名前を付けることができます。" -#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +#: ../../src/introduction/quick-start.md:96 3b06faf5f3194bd8a96118d9f050f61e msgid "Continue reading the next sections of this User Guide!" msgstr "このユーザーガイドの次のセクションを読み進めてください！" -#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 -msgid "" -"[List of CWL Implementations](https://www.commonwl.org/implementations)." +#: ../../src/introduction/quick-start.md:97 669b8ac154e74181830a430b1dc7684b +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "[CWL 実装一覧](https://www.commonwl.org/implementations)。" -#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +#: ../../src/introduction/quick-start.md:98 1c888f1b771d49b3a257ed534b5afa0a msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -"GitHubの[`common-workflow-language` organization](https://github.com/common-" -"workflow-language)です。" +"GitHubの[`common-workflow-language` organization](https://github.com" +"/common-workflow-language)です。" -#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +#: ../../src/introduction/quick-start.md:99 dbce82b7a930493486a585ecb8891121 msgid "" -"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" -"Common_Workflow_Language)." +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -"[Wikipedia上のCommon Workflow Language](https://en.wikipedia.org/wiki/" -"Common_Workflow_Language)。" +"[Wikipedia上のCommon Workflow " +"Language](https://en.wikipedia.org/wiki/Common_Workflow_Language)。" -#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +#: ../../src/introduction/quick-start.md:100 dc714ffd4278421b9f2417f41627722c msgid "" -"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." -"org/wiki/YAML)." +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -"[YAML.org](http://yaml.org/) と [WikipediaにあるYAML](https://en.wikipedia." -"org/wiki/YAML) です。" +"[YAML.org](http://yaml.org/) と " +"[WikipediaにあるYAML](https://en.wikipedia.org/wiki/YAML) です。" -#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +#: ../../src/introduction/quick-start.md:101 2bf7b924182f4f2bab88edef5ef85baa #, fuzzy msgid "" -"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." -"replace('VERSION', cwl_version_text) }}." +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." msgstr "" -"{{'[CWL 仕様 VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " -"cwl_version_text) }} のことです。" +"{{'[CWL 仕様 VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION'," +" cwl_version_text) }} のことです。" -#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +#: ../../src/introduction/quick-start.md:102 936a7dfab11a4f2c82c0b59964e3ea28 msgid "" -"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" -"Workflow_management_system)." -msgstr "" -"[Wikipediaの項目としてのワークフロー管理システム](https://en.wikipedia.org/" -"wiki/Workflow_management_system)。" +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "[Wikipediaの項目としてのワークフロー管理システム](https://en.wikipedia.org/wiki/Workflow_management_system)。" -#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +#: ../../src/setup.md:9 24ea9c5144664d9599d7aca767b4730a #, fuzzy msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. The information on this page has been migrated to the [FAQ](/faq." -"md) section of the new user guide." +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." msgstr "" -"このページは古いもので、旧ユーザーガイドのリンクを保存するためにここに残され" -"ていました。このページの情報は、新しいユーザーガイドの [FAQ](/faq.md) セク" -"ションに移行されました。" +"このページは古いもので、旧ユーザーガイドのリンクを保存するためにここに残されていました。このページの情報は、新しいユーザーガイドの " +"[FAQ](/faq.md) セクションに移行されました。" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 3843684b039a40dea163de951ca56738 #, fuzzy msgid "Additional Arguments and Parameters" msgstr "追加の引数とパラメータ" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 +#: a6fd1842b938435aa2a3c889019eec71 #, fuzzy msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." -msgstr "" -"ツールには、入力パラメータに正確に対応しない追加のコマンドラインオプションが" -"必要な場合があります。" +msgstr "ツールには、入力パラメータに正確に対応しない追加のコマンドラインオプションが必要な場合があります。" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf +#: dfed0747ed544547afd364086d828c9b #, fuzzy msgid "" "In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files in " -"the same directory as the source file. However, CWL input files (and the " -"directories in which they appear) may be read-only, so we need to instruct " -"\"javac\" to write the class file to the designated output directory instead." -msgstr "" -"この例では、Javaコンパイラを使用して、javaソースファイルをクラスファイルにコ" -"ンパイルするようにラップします。 デフォルトでは、\"javac \"はソース・ファイ" -"ルと同じディレクトリにクラス・ファイルを作成します。 しかし、CWLの入力ファイ" -"ル（およびそのディレクトリ）は読み取り専用である場合があるので、代わりに指定" -"された出力ディレクトリにクラスファイルを書き込むように「javac」に指示する必要" -"があります。" +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." +msgstr "" +"この例では、Javaコンパイラを使用して、javaソースファイルをクラスファイルにコンパイルするようにラップします。 " +"デフォルトでは、\"javac \"はソース・ファイルと同じディレクトリにクラス・ファイルを作成します。 " +"しかし、CWLの入力ファイル（およびそのディレクトリ）は読み取り専用である場合があるので、代わりに指定された出力ディレクトリにクラスファイルを書き込むように「javac」に指示する必要があります。" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: e690b567eae34f3f8dbdd7760e51449a msgid "`arguments.cwl`" msgstr "`arguments.cwl`" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: ../../src/topics/staging-input-files.md:15 4cee519b108143be89a0e47a75d7d649 +#: 79585673fd654bab9ba7c1927d7e153b msgid "`arguments-job.yml`" msgstr "`arguments-job.yml`" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: ef070ebe5f7245489b05660fb6d7c178 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "次に、CommandLineToolで使用するサンプルJavaファイルを作成します。" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb +#: 4ae43e3e841442039e4bb8c740096c56 msgid "" -"And now invoke `cwltool` providing the tool description and the input object " -"on the command line:" -msgstr "" -"そして、コマンドラインでツール定義と入力オブジェクトを渡して`cwltool` を起動" -"します：" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" +msgstr "そして、コマンドラインでツール定義と入力オブジェクトを渡して`cwltool` を起動します：" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a +#: 8497291577914eb3a172c1ffb736d95d msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." -msgstr "" -"ここでは、`arguments` フィールドを使用して、特定の入力パラメータに結びつかな" -"い追加の引数をコマンドラインに追加しています。" +msgstr "ここでは、`arguments` フィールドを使用して、特定の入力パラメータに結びつかない追加の引数をコマンドラインに追加しています。" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 +#: dc9fa5f2cbb147b1853c4042c54010f3 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include `$(runtime.tmpdir)`, " -"`$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and " -"`$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of " -"the CWL specification for details." +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +#: ../../src/topics/best-practices.md:1 964bf8276dd04b65887448e1386e63fe msgid "Best Practices" msgstr "ベストプラクティス" -#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +#: ../../src/topics/best-practices.md:3 7b59377bd56c47b8a71c18acfba4d3bb #, fuzzy msgid "" -"The following are a set of recommended good practices to keep in mind when " -"writing a Common Workflow Language description for a tool or workflow. These " -"guidelines are presented for consideration on a scale of usefulness: " -"although more is better, not all are required." -msgstr "" -"以下は、ツールやワークフローのCWL定義を書く際に留意すべき推奨グッドプラクティ" -"スのセットです。これらのガイドラインは、有用性の尺度で検討するために提示され" -"ています：多ければ多いほど良いが、すべてが必要なわけではありません。" +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." +msgstr "以下は、ツールやワークフローのCWL定義を書く際に留意すべき推奨グッドプラクティスのセットです。これらのガイドラインは、有用性の尺度で検討するために提示されています：多ければ多いほど良いが、すべてが必要なわけではありません。" -#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +#: ../../src/topics/best-practices.md:8 2292670347cd4549bc6a51e972de0ef4 msgid "" -"No `type: string` parameters for names of input or reference files/" -"directories; use `type: File` or `type: Directory` as appropriate." +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -"入力または参照のファイルやディレクトリの名前に `type: string` を使用しませ" -"ん。 `type:File` または `type: Direcotry` を適宜使用します。" +"入力または参照のファイルやディレクトリの名前に `type: string` を使用しません。 `type:File` または `type: " +"Direcotry` を適宜使用します。" -#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +#: ../../src/topics/best-practices.md:11 ae127b776eed4894af8cb680377703e0 msgid "" "A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that " -"the usual rules of software licensing apply to this document. For example, " -"if the workflow is shared publicly, licensing terms must be clear so that a " -"future user understands under what conditions they can run the workflow, " -"modify it and/or combine it with other workflows. For this reason, please " -"consider including a license field in the document. The authors of this " -"guide urge you to choose a pre-existing license rather than trying to write " -"your own (see the link below to learn more about choosing a license), and " -"our recommended practice is to choose a license that allows for re-use by " -"anyone, e.g. [Apache 2.0][apache-license]." +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." msgstr "" -#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +#: ../../src/topics/best-practices.md:20 384eb620dc31468e8c3f5f33a3436200 msgid "" -"If possible, the license should be specified with its corresponding [SPDX " -"identifier][spdx]. Construct the metadata field for the license by providing " -"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " -"taken from the list of identifiers linked above. See the example snippet " -"below for guidance. For non-standard licenses without an SPDX identifier, " -"provide a URL to the license." +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +#: ../../src/topics/best-practices.md:26 e8259b43fa6944eda73eae381db6b97b msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" -msgstr "" -"参考文献：\"[科学者・プログラマーのためのソフトウェアライセンス クイックガイ" -"ド][sci-license]\"" +msgstr "参考文献：\"[科学者・プログラマーのためのソフトウェアライセンス クイックガイド][sci-license]\"" -#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +#: ../../src/topics/best-practices.md:28 5b976a5aec7d44bda55b0a019e955416 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "_SPDX 識別子を持つライセンスのメタデータフィールドの例：_" -#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +#: ../../src/topics/best-practices.md:37 924b8df24deb4c82b32732f491c9a246 +#, fuzzy msgid "" -"For more examples of providing metadata within CWL descriptions, see [the " -"Metadata and Authorship section of this User Guide](../topics/metadata-and-" -"authorship.md)." +"For more examples of providing metadata within CWL descriptions, see [the" +" Metadata and Authorship section of this User Guide](../topics/metadata-" +"and-authorship.md)." msgstr "" -"CW定義にメタデータを与える例については、 [このユーザーガイドのメタデータと著" -"者名のセクション](../topics/metadata-and-authorship.md)を参照してください。" +"CW定義にメタデータを与える例については、 [このユーザーガイドのメタデータと著者名のセクション](../topics/metadata-and-" +"authorship.md)を参照してください。" -#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +#: ../../src/topics/best-practices.md:40 9e64a9fc89cb45cfbff0e925cc91b1be msgid "" -"Include [attribution information][license-example] for the author(s) of the " -"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" -"[orcid]." +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." msgstr "" -"CWLツールやワークフローの定義の著者の[帰属情報][license-example]を含みます。" -"[ORCID][orcid]のような曖昧でない識別子を使用してください。" +"CWLツールやワークフローの定義の著者の[帰属情報][license-" +"example]を含みます。[ORCID][orcid]のような曖昧でない識別子を使用してください。" -#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +#: ../../src/topics/best-practices.md:44 87030aef02044b8283c76debab4772bf +#, fuzzy msgid "" "In tool descriptions, list dependencies using short name(s) under " -"`SoftwareRequirement`." -msgstr "" -"ツール定義では、`SoftwareRequirement` の下に、短い名前を使用して依存関係をリ" -"ストアップします。" +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." +msgstr "ツール定義では、`SoftwareRequirement` の下に、短い名前を使用して依存関係をリストアップします。" -#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +#: ../../src/topics/best-practices.md:47 6c9eaae099fa4ca4b0986b1c4146df50 #, fuzzy msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" -"identifiers.org/rrid/RRID:SCR_NNNNNN` format." +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` フォーマットで依存関係のため" -"の [SciCrunch][scicrunch] 識別子を含みます。" +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` フォーマットで依存関係のための " +"[SciCrunch][scicrunch] 識別子を含みます。" -#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +#: ../../src/topics/best-practices.md:50 5ae8950fd31541399c2fe59096581dbc msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " "`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -"`input` および`output` の識別子はすべて、その概念的同一性を反映する必要があり" -"ます。`foo_input`,`foo_file`,`result`,`input`,`output`, などの代わりに" -"`unaligned_sequences`,`reference_genome`,`phylogeny`, または" -"`aligned_sequences` などの情報量の多い名称を使ってください。" +"`input` および`output` " +"の識別子はすべて、その概念的同一性を反映する必要があります。`foo_input`,`foo_file`,`result`,`input`,`output`," +" などの代わりに`unaligned_sequences`,`reference_genome`,`phylogeny`, " +"または`aligned_sequences` などの情報量の多い名称を使ってください。" -#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +#: ../../src/topics/best-practices.md:55 b0493895105e43849bff2026763e472a +#, fuzzy msgid "" "In tool descriptions, include a list of version(s) of the tool that are " -"known to work with this description under `SoftwareRequirement`." +"known to work with this description under " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "" -"ツール定義では、`SoftwareRequirement` の下に、このツール定義で動作することが" -"確認されているツールのバージョンのリストを含めるます。" +"ツール定義では、`SoftwareRequirement` " +"の下に、このツール定義で動作することが確認されているツールのバージョンのリストを含めるます。" -#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +#: ../../src/topics/best-practices.md:58 88806cb0462f4359801c1fa0ff0ebcc0 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with " -"`$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " -"[Full IANA media type list][iana-types] (also known as MIME types). For non-" -"bioinformatics tools, use or build an appropriate ontology/controlled " -"vocabulary in the same way. Please edit this page to let us know about it." +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +#: ../../src/topics/best-practices.md:66 b178c7296ed5491782a4180c76883c14 #, fuzzy msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -"`File`の入出力のうち、ストリーミング互換の方法（一度だけ、ランダムアクセスな" -"し）で読み書きされるものを、`streamable: true` としてマークします。" +"`File`の入出力のうち、ストリーミング互換の方法（一度だけ、ランダムアクセスなし）で読み書きされるものを、`streamable: true`" +" としてマークします。" -#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +#: ../../src/topics/best-practices.md:69 886d15c1972243acadccff5760f842f1 #, fuzzy msgid "" -"Each `CommandLineTool` description should focus on a single operation only, " -"even if the (sub)command is capable of more. Don't overcomplicate your tool " +"Each " +"[`CommandLineTool`](https://w3id.org/cwl/CommandLineTool.html#CommandLineTool)" +" description should focus on a single operation only, even if the " +"(sub)command is capable of more. Don't overcomplicate your tool " "descriptions with options that you don't need or use." msgstr "" -"各`CommandLineTool` の定義は、たとえ（サブ）コマンドがそれ以上の機能を備えて" -"いたとしても、単一の操作のみに焦点を当てるべきです。必要でない、または使用し" -"ないオプションでツールの定義を複雑にし過ぎないようにしましょう。" +"各`CommandLineTool` " +"の定義は、たとえ（サブ）コマンドがそれ以上の機能を備えていたとしても、単一の操作のみに焦点を当てるべきです。必要でない、または使用しないオプションでツールの定義を複雑にし過ぎないようにしましょう。" -#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +#: ../../src/topics/best-practices.md:73 ef5a5f9b253c4ca3916802a695fb7c6d #, fuzzy msgid "" -"Custom types should be defined with one external YAML per type definition " -"for re-use." -msgstr "" -"カスタム型は、再利用のため、タイプ定義ごとに1つの外部YAMLで定義する必要があり" -"ます。" +"Custom types should be defined with one external YAML per type definition" +" for re-use." +msgstr "カスタム型は、再利用のため、タイプ定義ごとに1つの外部YAMLで定義する必要があります。" -#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +#: ../../src/topics/best-practices.md:76 ff59f40e84004523904e3094be07cc80 #, fuzzy msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "ツール/ワークフローを要約したトップレベルの短い`label` を含めます。" -#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +#: ../../src/topics/best-practices.md:78 78d73fde24e24beeab541a623d9530b6 msgid "" -"If useful, include a top-level `doc` as well. This should provide a longer, " -"more detailed description than was provided in the top-level `label` (see " -"above)." +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." msgstr "" -"有用であれば、トップレベル`doc` も含めてください。これは、トップレベル" -"`label` （上記参照）で提供されたものより長く詳細な説明を記述します。" +"有用であれば、トップレベル`doc` も含めてください。これは、トップレベル`label` " +"（上記参照）で提供されたものより長く詳細な説明を記述します。" -#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +#: ../../src/topics/best-practices.md:82 d92013d662b44dbf8875e06c9dfbfd79 msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list of " -"valid values." -msgstr "" -"有効な値のリストが決まっている要素には、`type: string` の代わりに、`type: " -"enum` を使用してください。" +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." +msgstr "有効な値のリストが決まっている要素には、`type: string` の代わりに、`type: enum` を使用してください。" -#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +#: ../../src/topics/best-practices.md:85 c100d5192a52497fb6a890b81a388fcf #, fuzzy msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. One " -"common example: manipulating `File` names and paths? Consider whether one of " -"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " -"`nameext`, etc., could be used instead." +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." msgstr "" -"JavaScriptのすべての使用について、削除または置換の可能性を評価します。よくあ" -"る例：`File` の名前とパスを操作する方法は？`basename`,`nameroot`,`nameext`, " -"などの [built in`File` properties][file-prop] のいずれかを代わりに使用できな" -"いか考えてみてください。" +"JavaScriptのすべての使用について、削除または置換の可能性を評価します。よくある例：`File` " +"の名前とパスを操作する方法は？`basename`,`nameroot`,`nameext`, などの [built in`File` " +"properties][file-prop] のいずれかを代わりに使用できないか考えてみてください。" -#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +#: ../../src/topics/best-practices.md:90 e22fbacdb2fb4202b1bd69cfc24af5cd msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." -msgstr "" -"ツール定義を同僚（できれば別の機関の人）に渡し、テストしてもらい、フィード" -"バックをもらいましょう。" +msgstr "ツール定義を同僚（できれば別の機関の人）に渡し、テストしてもらい、フィードバックをもらいましょう。" -#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +#: ../../src/topics/best-practices.md:93 0060a863362140f6bb3932cb5da1df04 msgid "" -"Complex workflows with individual components which can be abstracted should " -"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " -"workflow modular and allow sections of them to be easily reused." -msgstr "" -"抽象化できる個々のコンポーネントを持つ複雑なワークフローは、ワークフローをモ" -"ジュール化し、その一部を容易に再利用できるようにするために、" -"[`SubworkflowFeatureRequirement`][subworkflow]を利用します。" +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." +msgstr "抽象化できる個々のコンポーネントを持つ複雑なワークフローは、ワークフローをモジュール化し、その一部を容易に再利用できるようにするために、[`SubworkflowFeatureRequirement`][subworkflow]を利用します。" -#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +#: ../../src/topics/best-practices.md:97 93f6d6b544c24ce780184272f66bacab #, fuzzy msgid "" "Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics " -"software\"][containers] (also useful to other disciplines)." +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." msgstr "" -"ソフトウェアのコンテナは、[\"Recommendations for packaging and " -"containerizing of bioinformatics software\"][containers] に準拠するようにしま" -"す（他の分野でも有用です）。" +"ソフトウェアのコンテナは、[\"Recommendations for packaging and containerizing of " +"bioinformatics software\"][containers] に準拠するようにします（他の分野でも有用です）。" -#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +#: ../../src/topics/command-line-tool.md:1 a378a2f7d268401abfbbbe6e5090a952 msgid "Command Line Tool" msgstr "コマンドラインツール" -#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +#: ../../src/topics/command-line-tool.md:3 cf0f1c00c0b34c94a8e2460a700c303e #, fuzzy msgid "" -"A command-line tool is a type of Process object that can be run by itself or " -"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " -"etc. The command-line tool is defined in the `baseCommand` attribute of the " -"command-line tool CWL document." +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." msgstr "" -"コマンドラインツールは、Processオブジェクトの一種であり、それ自体またはワーク" -"フローのステップとし て実行することができます。`ls`,`echo`,`tar` などのコマン" -"ドのラッパーです。コマンドラインツールは、コマンドラインツールCWL文書の" -"`baseCommand` 属性で定義されています。" +"コマンドラインツールは、Processオブジェクトの一種であり、それ自体またはワークフローのステップとし " +"て実行することができます。`ls`,`echo`,`tar` " +"などのコマンドのラッパーです。コマンドラインツールは、コマンドラインツールCWL文書の`baseCommand` 属性で定義されています。" -#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +#: ../../src/topics/command-line-tool.md:8 7a180ba1f2d746a78b79be7e899cbad6 msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The following " -"example contains a minimal example of a CWL command-line tool for the `echo` " -"Linux command, using inputs and outputs." +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." msgstr "" -"CWLコマンドラインツールは、`inputs` と`outputs` も持っていなければなりませ" -"ん。次の例は、Linuxコマンド `echo` のためのCWLコマンドラインツールの最小限の" -"例で、inputsとoutputsを使用します。" +"CWLコマンドラインツールは、`inputs` と`outputs` も持っていなければなりません。次の例は、Linuxコマンド `echo` " +"のためのCWLコマンドラインツールの最小限の例で、inputsとoutputsを使用します。" -#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +#: ../../src/topics/command-line-tool.md:19 128bd8cd6788431da54fa07a8dc87f99 msgid "CWL command-line tool." msgstr "CWLコマンドラインツール。" -#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +#: ../../src/topics/command-line-tool.md:50 d742e9e59ea44ca1a1df2de85059343f msgid "`echo.cwl`" msgstr "`echo.cwl`" -#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +#: ../../src/topics/command-line-tool.md:57 e3a06ebe51b64b0183673a8acc04969f #, fuzzy msgid "" -"The example above uses a simplified form to define inputs and outputs. You " -"will learn more about in the [Inputs](../topics/inputs.md) and in the " -"[Outputs](../topics/outputs.md) sections." -msgstr "" -"上記の例では、簡略化した形で入力と出力を定義しています。[Inputs](../topics/" -"inputs.md)と[Outputs](../topics/outputs.md)のセクションで、より詳しく説明する" -"予定です。" +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." +msgstr "上記の例では、簡略化した形で入力と出力を定義しています。[Inputs](../topics/inputs.md)と[Outputs](../topics/outputs.md)のセクションで、より詳しく説明する予定です。" -#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +#: ../../src/topics/command-line-tool.md:68 2bab464d19d14562a6501373aff13905 msgid "Network Access" msgstr "ネットワークアクセス" -#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 -#, fuzzy +#: ../../src/topics/command-line-tool.md:69 201712f3ceee4d4ea56ab96d3fef97b0 msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network access. " -"If a command-line tool is written manually in CWL v1.1+, there is a need to " -"specify when network access is required." +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. Starting with CWL v1.1, programs are not granted network access " +"by default, so you must include the requirement for network access in the" +" specification of your tool." msgstr "" -"これは、プロセスが発信IPv4/IPv6ネットワークアクセスを必要とするかどうかを示し" -"ます。CWL v1.1+でCommandLineToolを手動で記述する場合、ネットワークアクセスが" -"必要なタイミングを指定する必要があります。" -#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +#: ../../src/topics/command-line-tool.md:84 3282a357799f4a72a6b8bace206144c4 +#, fuzzy msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " -"Access automatically." -msgstr "" -"CWL v1.0のコマンドラインツールをv1.1またはv1.2にアップグレードすると、自動的" -"にネットワークアクセスを取得します。" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 or v1.2 " +"will have `networkAccess: true` set automatically." +msgstr "CWL v1.0のコマンドラインツールをv1.1またはv1.2にアップグレードすると、自動的にネットワークアクセスを取得します。" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: 17c5b4ee43cc4a979676ad27e473d046 #, fuzzy msgid "Creating Files at Runtime" msgstr "実行時にファイルを作成する" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d +#: cd0dff10471c4ad2b84e3a0e4d7767ea #, fuzzy msgid "" -"Sometimes you need to create a file on the fly from input parameters, such " -"as tools that expect to read their input configuration from a file rather " -"than the command line parameters, or need a small wrapper shell script." -msgstr "" -"コマンドラインパラメーターではなく、ファイルから入力設定を読み込むことを期待" -"するツールや、小さなラッパーシェルスクリプトが必要な場合など、入力パラメー" -"ターからその場でファイルを作成する必要があることがあります。" +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." +msgstr "コマンドラインパラメーターではなく、ファイルから入力設定を読み込むことを期待するツールや、小さなラッパーシェルスクリプトが必要な場合など、入力パラメーターからその場でファイルを作成する必要があることがあります。" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "" -"このようなファイルを生成するために、`InitialWorkDirRequirement` を利用するこ" -"とができます。" +#: bf4aea0a22334a1ca75cc20e937e6581 +#, fuzzy +msgid "" +"To generate such files, we can use the " +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)." +msgstr "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)から" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: 008f768d56b8465bb4e8f4fde15853a7 msgid "`createfile.cwl`" msgstr "`createfile.cwl`" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df +#: 252f8e897b0942a8be098481890005f3 #, fuzzy msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the value " -"at the input `message`." +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." msgstr "" -"`$(inputs.message)` のような [Expressions](../topics/expressions.md)は、ファ" -"イルを作成する前にCWLエンジンによって展開されます。ここでは、入力パラメータ" -"`message` に値を挿入します。" +"`$(inputs.message)` のような " +"[Expressions](../topics/expressions.md)は、ファイルを作成する前にCWLエンジンによって展開されます。ここでは、入力パラメータ`message`" +" に値を挿入します。" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 +#: aca24b72687c4d4d84bf9de8b71413f7 #, fuzzy msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later " -"during command line tool invocation. That means that any genuine need for " -"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " -"above is expanded to `${PREFIX}` in the generated file to be evaluated by " -"the shell script instead of the CWL engine." +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." msgstr "" -"_CWL expressions_ は、コマンドラインツール起動時に使用される_shell " -"variables_ とは無関係です。つまり、`$` という文字が本当に必要な場合は、** ` " -"\\` で** をエスケープする必要があります。例えば，上記の`\\${PREFIX}` は，CWL" -"エンジンの代わりにシェルスクリプトで評価されるように，生成されたファイルでは" -"`${PREFIX}` に展開されます．" +"_CWL expressions_ は、コマンドラインツール起動時に使用される_shell variables_ とは無関係です。つまり、`$` " +"という文字が本当に必要な場合は、** ` \\` で** をエスケープする必要があります。例えば，上記の`\\${PREFIX}` " +"は，CWLエンジンの代わりにシェルスクリプトで評価されるように，生成されたファイルでは`${PREFIX}` に展開されます．" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa +#: 750b3232e8754448bc2b5913539495b8 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" -msgstr "" -"上記のCWLツールをテストするために、このジョブを使用して、入力値`message` を与" -"えます：" +msgstr "上記のCWLツールをテストするために、このジョブを使用して、入力値`message` を与えます：" #: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 2d2ef4769b2347e79db827655f1bcdeb 2699fbc4376148af91b7a5a6cdac467c -#: ca03defa3ad14cf698171cb09e3055c1 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:81 +#: 687c8a84bade43269f3cd767d32f9f47 81da7a18fe8d4659abc883cf43009f1f +#: d5d67eae63304ebb9b242133feacb0d1 msgid "`echo-job.yml`" msgstr "`echo-job.yml`" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d +#: c4f964450d014734877fb3c968353a74 msgid "" -"Before we run this, let us look at each step in a little more detail. The " -"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " "command `sh example.sh`. This will run the file we create in the shell." msgstr "" -"これを実行する前に、各ステップをもう少し詳しく見てみましょう。ベースコマンド" -"`baseCommand: [\"sh\", \"example.sh\"]` は、`sh example.sh` というコマンドを" -"実行します。これで、作成したファイルがシェルで実行されます。" +"これを実行する前に、各ステップをもう少し詳しく見てみましょう。ベースコマンド`baseCommand: [\"sh\", " +"\"example.sh\"]` は、`sh example.sh` というコマンドを実行します。これで、作成したファイルがシェルで実行されます。" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c +#: 9aeea5a6a4244bc7a1626e0cb7351068 msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " -"array, we need a `-` on the first line of each element of the array, in this " -"case we have just one element. `entryname:` can have any value, but it must " -"match what was specified in the `baseCommand`. The final part is `entry:`, " -"this is followed by `|-` which is YAML quoting syntax, and means that you " -"are using a multiline string (without it, we would need to write the whole " -"script on one line)." +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 +#: 867239e9ad3d4187a2703662a0ca3976 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." -msgstr "" -"フォーマットについては、[YAMLガイド](../topics/yaml-guide.md#maps)を参照して" -"ください。" +msgstr "フォーマットについては、[YAMLガイド](../topics/yaml-guide.md#maps)を参照してください。" #: ../../src/topics/creating-files-at-runtime.md:54 #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: b372f33c65bb4707b2a462a960bb1373 293fb1d428b849aebccad598a932992d -#: f924d65fed0c4cb5b0a019b084a8b535 d6255506eebe44be94c5ce703c44a513 -#: 7bbd2d738fc54649aeb10f8d2bc38b6f +#: 0d7151b9f0194197bd686fe6c9c47afd 78bb40eeeda24d7b923162daa45d51a7 +#: 7b341a317347482ca86fc56119c3686f 7c637fa62cab4d0dbe670a3b72737cc9 +#: cfb4605a01dd4475aabcc086a4e65957 msgid "" -"Now invoke `cwltool` with the tool description and the input object on the " -"command line:" -msgstr "" -"ここで、コマンドラインにツール定義と入力オブジェクトを指定して、`cwltool` を" -"起動します：" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "ここで、コマンドラインにツール定義と入力オブジェクトを指定して、`cwltool` を起動します：" -#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +#: ../../src/topics/custom-types.md:1 252a3a17b1ec4d5a9a82ebbf6c2f314c msgid "Custom Types" msgstr "カスタムタイプ" -#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +#: ../../src/topics/custom-types.md:3 e0275ddda8f84207a58d10c17ca99a45 msgid "" -"Sometimes you may want to write your own custom types for use and reuse in " -"CWL descriptions. Use of such custom types can reduce redundancy between " -"multiple descriptions that all use the same type, and also allow for " -"additional customisation/configuration of a tool/analysis without the need " -"to fiddle with the CWL description directly." +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +#: ../../src/topics/custom-types.md:9 8367e38e5e7c4a298d1d87b9001aaddc msgid "" -"The example below is a CWL description of the [biom convert format][biom] " -"tool for converting a standard biom table file to hdf5 format." -msgstr "" -"以下の例は、標準的なbiomテーブルファイルをhdf5形式に変換する[biom convert " -"format][biom] ツールのCWL定義です。" +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." +msgstr "以下の例は、標準的なbiomテーブルファイルをhdf5形式に変換する[biom convert format][biom] ツールのCWL定義です。" -#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +#: ../../src/topics/custom-types.md:12 18b802f45ce0454ab7aa2a21812863c6 msgid "`custom-types.cwl`" msgstr "`custom-types.cwl`" -#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +#: ../../src/topics/custom-types.md:18 66d1953f5dd54d448bddd0f30c330402 msgid "`custom-types.yml`" msgstr "`custom-types.yml`" -#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +#: ../../src/topics/custom-types.md:24 56b8912a1ea84f28adeb8beaf92ab563 msgid "" -"___Note:___ To follow the example below, you need to [download the example " -"input file](https://github.com/common-workflow-language/user_guide/blob/main/" -"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " -"*rich_sparse_otu_table.biom* e.g. via `wget`:" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +#: ../../src/topics/custom-types.md:30 a48539920c4944898918bc90b2d4e3c9 msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to be " -"used in the table conversion are imported as a custom object:" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" msgstr "" -"29行目の`inputs:table_type` で、テーブル変換で使用できるテーブルオプションの" -"リストがカスタムオブジェクトとしてインポートされます：" +"29行目の`inputs:table_type` " +"で、テーブル変換で使用できるテーブルオプションのリストがカスタムオブジェクトとしてインポートされます：" -#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +#: ../../src/topics/custom-types.md:46 c791096f537141e8bd7cc941d711d108 msgid "" -"The reference to a custom type is a combination of the name of the file in " -"which the object is defined (`biom-convert-table.yaml`) and the name of the " -"object within that file (`table_type`) that defines the custom type. In this " -"case the `symbols` array from the imported `biom-convert-table.yaml` file " -"define the allowable table options. For example, in `custom-types.yml`, we " -"pass `OTU table` as an `input` that tells the tool to create an OTU table in " -"hdf5 format." +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e -msgid "" -"The contents of the YAML file describing the custom type are given below:" +#: ../../src/topics/custom-types.md:53 5f6bc6ed72334a74b9a4c46c29ddda46 +msgid "The contents of the YAML file describing the custom type are given below:" msgstr "カスタムタイプを記述するYAMLファイルの内容を以下に示します：" -#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +#: ../../src/topics/custom-types.md:55 3b55419088e8446994703220bd8e8480 msgid "`biom-convert-table.yaml`" msgstr "`biom-convert-table.yaml`" -#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +#: ../../src/topics/custom-types.md:61 fe6f4ce5e7344af0abea9d5c03e32ecd msgid "" -"In order for the custom type to be used in the CWL description, it must be " -"imported. Imports are described in `requirements:SchemaDefRequirement`, as " -"below in the example `custom-types.cwl` description:" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" msgstr "" -"カスタム型をCWL定義で使用するためには、インポートする必要があります。インポー" -"トについては、`requirements:SchemaDefRequirement` で定義されており、例として" -"`custom-types.cwl` の定義にあるように、インポートされます：" +"カスタム型をCWL定義で使用するためには、インポートする必要があります。インポートについては、`requirements:SchemaDefRequirement`" +" で定義されており、例として`custom-types.cwl` の定義にあるように、インポートされます：" -#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +#: ../../src/topics/custom-types.md:76 dce43b138ba24b22bfa9fa5692a17009 msgid "" "Note also that the author of this CWL description has also included " -"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " -"cores required for the tool to run successfully, as well as details of the " -"version of the software that the description was written for and other " -"useful metadata. These features are discussed further in other chapters of " -"this user guide." +"[`ResourceRequirement`](https://w3id.org/cwl/CommandLineTool.html#ResourceRequirement)s," +" specifying the minimum amount of RAM and number of cores required for " +"the tool to run successfully, as well as details of the version of the " +"software that the description was written for and other useful metadata. " +"These features are discussed further in other chapters of this user " +"guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +#: ../../src/topics/environment-variables.md:1 19737f89f2994815969fa4a88346f49a msgid "Environment Variables" msgstr "環境変数" -#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +#: ../../src/topics/environment-variables.md:3 ad965f75aa0c41cda8b82c46af49774d msgid "" -"Tools run in a restricted environment and do not inherit most environment " -"variables from the parent process. You can set environment variables for " -"the tool using `EnvVarRequirement`." +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." msgstr "" -"ツールは制限された環境で実行されるため、親プロセスからほとんどの環境変数を引" -"き継ぎません。 ツールの環境変数は、`EnvVarRequirement` を使って設定できま" -"す。" +"ツールは制限された環境で実行されるため、親プロセスからほとんどの環境変数を引き継ぎません。 " +"ツールの環境変数は、`EnvVarRequirement` を使って設定できます。" -#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +#: ../../src/topics/environment-variables.md:7 38b276f9b0114a0bb87734f0a07a736f msgid "`env.cwl`" msgstr "`env.cwl`" -#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +#: ../../src/topics/expression-tool.md:1 9f33532119dc47ffb6ade20fb1d950bd msgid "Expression Tool" msgstr "Expression Tool" -#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +#: ../../src/topics/expression-tool.md:3 b267056eae704737af5aaada3ea7e6e2 #, fuzzy msgid "" -"An expression tool is a type of Process that can be run by itself or as a " -"Workflow step. It executes a pure JavaScript expression. It is meant to be " -"used as a way to isolate complex JavaScript expressions that need to operate " -"on input data and produce some result as output." +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." msgstr "" -"ExpressionToolは、それ自体またはワークフローのステップとして実行することがで" -"きるProcessの一種です。純粋な JavaScript 式を実行します。入力データを操作し、" -"出力として結果を生成する必要がある複雑な JavaScript 式を分離する方法として使" -"用されることを意図しています。" +"ExpressionToolは、それ自体またはワークフローのステップとして実行することができるProcessの一種です。純粋な " +"JavaScript 式を実行します。入力データを操作し、出力として結果を生成する必要がある複雑な JavaScript " +"式を分離する方法として使用されることを意図しています。" -#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +#: ../../src/topics/expression-tool.md:8 7e930144163e4d6e9f0bcaa764497ccf +#, fuzzy msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " -"instead of `baseCommand`, it requires an `expression` attribute." +"instead of `baseCommand`, it requires an " +"[`expression`](https://w3id.org/cwl/CommandLineTool.html#Expressions_(Optional))" +" attribute." msgstr "" -"CommandLinetToolと同様に、`inputs` と`outputs` が必要です。しかし、" -"`baseCommand` の代わりに、`expression` 属性を必要とします。" +"CommandLinetToolと同様に、`inputs` と`outputs` が必要です。しかし、`baseCommand` " +"の代わりに、`expression` 属性を必要とします。" -#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +#: ../../src/topics/expression-tool.md:17 f172488c19a94d688036197117d30b38 #, fuzzy msgid "CWL expression tool." msgstr "CWL expression tool." -#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +#: ../../src/topics/expression-tool.md:48 ef978c951f1a4b7d9280d31367e5bae7 #, fuzzy msgid "`uppercase.cwl`" msgstr "`uppercase.cwl`" -#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +#: ../../src/topics/expression-tool.md:67 0b63da31bc274b3cad798b07149592ab #, fuzzy msgid "" -"We had to use an `InlineJavascriptRequirement` as our expression contains a " -"JavaScript call in `.toUpperCase()`. This means to tools using the " -"expression tool that JavaScript is a requirement." +"We had to use an " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" as our expression contains a JavaScript call in `.toUpperCase()`. This " +"means to tools using the expression tool that JavaScript is a " +"requirement." msgstr "" -"`InlineJavascriptRequirement` を使用する必要がありました。この式には`." -"toUpperCase()` で JavaScript の呼び出しが含まれているからです。これは、" -"ExpressionToolを使用するツールにとって、JavaScriptが必要であることを意味しま" -"す。" +"`InlineJavascriptRequirement` を使用する必要がありました。この式には`.toUpperCase()` で " +"JavaScript " +"の呼び出しが含まれているからです。これは、ExpressionToolを使用するツールにとって、JavaScriptが必要であることを意味します。" -#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +#: ../../src/topics/expressions.md:1 b0e567a985f748538552bdb486a47998 #, fuzzy msgid "Expressions" msgstr "Expressions" -#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +#: ../../src/topics/expressions.md:3 24d05cbbab8e460e99f2edc97ab0dcec #, fuzzy msgid "" "If you need to manipulate input parameters, include the requirement " -"`InlineJavascriptRequirement` and then anywhere a parameter reference is " -"legal you can provide a fragment of Javascript that will be evaluated by the " -"CWL runner." +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" and then anywhere a parameter reference is legal you can provide a " +"fragment of Javascript that will be evaluated by the CWL runner." msgstr "" -"入力パラメータを操作する必要がある場合は、`InlineJavascriptRequirement` を含" -"めると、パラメータ参照が合法な場所であれば、CWL runnerによって評価される" -"Javascriptを使用できます。" +"入力パラメータを操作する必要がある場合は、`InlineJavascriptRequirement` " +"を含めると、パラメータ参照が合法な場所であれば、CWL runnerによって評価されるJavascriptを使用できます。" -#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +#: ../../src/topics/expressions.md:9 3d48d1a8f7f74bc1886e41653cb53a22 #, fuzzy msgid "" -"JavaScript expressions should only be used when absolutely necessary. When " -"manipulating file names, extensions, paths etc, consider whether one of the " -"[built in `File` properties][file-prop] like `basename`, `nameroot`, " -"`nameext`, etc, could be used instead. See the [list of best practices](best-" -"practices.md)." +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." msgstr "" -"JavaScript の式は、絶対に必要な場合のみ使用するようにしてください。ファイル" -"名、拡張子、パスなどを操作する場合は、`basename`,`nameroot`,`nameext`, など" -"の [`File` のビルトインプロパティ][file-prop] のいずれかを代わりに使用できる" -"かどうかを検討してください。[ベストプラクティスのリスト](best-practices.md)を" -"参照してください。" +"JavaScript " +"の式は、絶対に必要な場合のみ使用するようにしてください。ファイル名、拡張子、パスなどを操作する場合は、`basename`,`nameroot`,`nameext`," +" などの [`File` のビルトインプロパティ][file-prop] " +"のいずれかを代わりに使用できるかどうかを検討してください。[ベストプラクティスのリスト](best-practices.md)を参照してください。" -#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: ../../src/topics/expressions.md:16 7d444aacd418466bbe588fa964b45179 #, fuzzy msgid "`expression.cwl`" msgstr "`expression.cwl`" -#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +#: ../../src/topics/expressions.md:22 72a0558a83964796a8c1a0eb55fd78e8 #, fuzzy msgid "" -"As this tool does not require any `inputs` we can run it with an (almost) " -"empty job file:" -msgstr "" -"このツールは`inputs` を必要としないので、（ほとんど）空のジョブファイルで実行" -"することができます：" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" +msgstr "このツールは`inputs` を必要としないので、（ほとんど）空のジョブファイルで実行することができます：" -#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +#: ../../src/topics/expressions.md:25 d679fd1363b24c81979c68e7342159cf #, fuzzy msgid "`empty.yml`" msgstr "`empty.yml`" -#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +#: ../../src/topics/expressions.md:31 d2ee4fcece744b6681f29322b5305111 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object is " -"represented simply by a set of empty brackets." +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." msgstr "" -"`empty.yml` には、空のJSONオブジェクトの記述があります。JSONオブジェクトの記" -"述は、中括弧`{}` の中に含まれるので、空のオブジェクトは、単に空の括弧のセット" -"で表されます。" +"`empty.yml` には、空のJSONオブジェクトの記述があります。JSONオブジェクトの記述は、中括弧`{}` " +"の中に含まれるので、空のオブジェクトは、単に空の括弧のセットで表されます。" -#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +#: ../../src/topics/expressions.md:35 624e4a270e374b1699b780df508b9184 msgid "We can then run `expression.cwl`:" msgstr "次に、`expression.cwl` を実行することができます：" -#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +#: ../../src/topics/expressions.md:37 c252eac9a35e46aab08bd07bc1cdb57d msgid "Running `expression.cwl`" msgstr "`expression.cwl` を実行する" -#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +#: ../../src/topics/expressions.md:47 f6f64d57a50742b19b801c14806ee18a msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" -msgstr "" -"なお、上の例のように、map構文で requirements を指定することも可能です：" +msgstr "なお、上の例のように、map構文で requirements を指定することも可能です：" -#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +#: ../../src/topics/expressions.md:54 052e24e2ad044cc28f04d7f39be871d6 #, fuzzy msgid "" "Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " -"describe the additional command line arguments." +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." msgstr "" -"または配列として、各エントリ（この場合、`class: InlineJavascriptRequirement` " -"だけです）に`-` を付けます。同じ構文で、追加のコマンドライン引数を定義しま" -"す。" +"または配列として、各エントリ（この場合、`class: InlineJavascriptRequirement` だけです）に`-` " +"を付けます。同じ構文で、追加のコマンドライン引数を定義します。" -#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +#: ../../src/topics/expressions.md:62 84b31c076d4b4826aae35e8c23fe6a25 msgid "Where are JavaScript expressions allowed?" msgstr "JavaScriptはどこで使えますか？" -#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +#: ../../src/topics/expressions.md:64 8c3b402c40f64880a4bd42c47b910254 #, fuzzy msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -"[パラメータ参照](parameter-references.md)と同様に、JavaScript 式は特定の" -"フィールドにのみ使用できます。 以下はその例です：" +"[パラメータ参照](parameter-references.md)と同様に、JavaScript 式は特定のフィールドにのみ使用できます。 " +"以下はその例です：" -#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +#: ../../src/topics/expressions.md:66 9bf5ca0e769147c6a9705bc40bd1febc #, fuzzy msgid "" -"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)" -msgstr "" -"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)から" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)から" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 1acb064f7a4a482aa0174bdc847c6382 -#: 0222780b98ac48e89b1b4f57c9df8590 +#: ../../src/topics/parameter-references.md:64 7ab0dbd54c1441539673fa12ef96b89e +#: e76c6ece0c594fefa86b190879c5acaa msgid "`arguments`" msgstr "`arguments`" @@ -2239,50 +2104,48 @@ msgstr "`arguments`" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 ef2b8433778a40408f179c3e6f0cf99e -#: 224732683a9c41f3ba1b778851e745a8 17b10d1e91b24dc582df98fcd2ac850e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 e4e68011dc5f42e4918c747afa7d764b -#: d44e3cfa661840eb851782e24caf1b68 +#: ../../src/topics/parameter-references.md:86 0209558b1013471eb708698537edaf06 +#: 4458393fdb0e451f9806e91122ea2534 594a163e08f04aa5a04a44a303a1c643 +#: a6fddc160afc4ef09717f69de72c11ce a9ec99ddcb344bcbbe5c1f59af0bcff2 +#: af2cdb5f66ac4fd5b8f91258f005cc62 msgid "`valueFrom`" msgstr "`valueFrom`" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: ../../src/topics/parameter-references.md:66 afb175f182354cb19e23b1cad241437e +#: f9a6718845e24f46b76fcc8ab26eec7a msgid "`stdin`" msgstr "`stdin`" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: ../../src/topics/parameter-references.md:67 3bce21dcc2da439daca80c4fcdf4c343 +#: 7f5ce097ca0442a6a200599342a6e24b msgid "`stdout`" msgstr "`stdout`" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: ../../src/topics/parameter-references.md:68 3397e8816f6a4d4b9af728c175f04917 +#: 7b14686e16eb4f488659b22d67ec3bfa msgid "`stderr`" msgstr "`stderr`" -#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +#: ../../src/topics/expressions.md:72 7a2d74aa018f4cab8c68e8775d83dd01 #, fuzzy msgid "" -"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter)" -msgstr "" -"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter)から" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)から" #: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 #: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 d0a92a3792b549e9b5ddce4667d168d2 -#: 801729c7c71b4109824b035437e69bf9 1bc510d525f0414e88692e356e67fbbc -#: d2e246ae56a24e4abdd6b7d9812a86e2 b1446bab2732412e91f721a08067b0bd -#: e89dbeb22f41430ca39c923d9fdf68cb bd61499b71e64164878dea08d6d7141e -#: ed875a006df64f9e8a55fa5e9fa87404 +#: ../../src/topics/parameter-references.md:90 24f27702d0684bc98e3232103510232e +#: 26a8dff7b80c4e059f1e20eef9da6203 476aa37af5214bcf963c7aab1f859273 +#: 4b0a0cd934bd41b4b55c034b91392bc7 5182e2165e44429287b4d924c2f896a4 +#: 7de500d3be6b4c3e8f274fd6a092109f 953d824a494947a3ab0ca2988717ee01 +#: b301751f90af4700bbada5e5b166be35 msgid "`format`" msgstr "`format`" @@ -2291,523 +2154,493 @@ msgstr "`format`" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 8a1748579de14f0888d5ee9023e37c2d -#: f760465a49d64d4c8468ad9c4fea62b1 28b6b5ffa7524374aaa9525ebfafb762 -#: d11f6a19ddf34cf19ec856bacf998e29 bcb7cd10cb5947bb9d85c040f57f954f -#: da5188d3bedc4997a35bdf417f2f643c cd7a0190511d4613b09600a3b1e9d55f -#: 47def3b078e2402182039be0227090ae +#: ../../src/topics/parameter-references.md:91 2c2b8db396b04ace8aa396c0a5a4858f +#: 33a9b77ce15b4910962a7f08bd2f47a3 57cba0191de3470bbe112ed2a0d3f252 +#: 6efe998094b3469eae61cfff551b1eb1 776de1ecfafc41ada7e916addd7229fd +#: 8595d62eb0274b3a8a7f0adf058b51d3 988966a2d4844e73961b0358aff8f6e1 +#: faa7d521fec240748407d03ffdb93aa0 msgid "`secondaryFiles`" msgstr "`secondaryFiles`" -#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +#: ../../src/topics/expressions.md:75 d737a9e9bf1c45d695bf584bc3241d9a msgid "" -"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding)" -msgstr "" -"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding)から" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)から" -#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +#: ../../src/topics/expressions.md:77 0e2052e16f6a41b8983dc64b4b3a7586 msgid "" -"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)" -msgstr "" -"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)から" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)から" -#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +#: ../../src/topics/expressions.md:80 dff31dd961d540e3b8cd1247e978d60e msgid "" -"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding)" -msgstr "" -"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding)から" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)から" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: ../../src/topics/parameter-references.md:78 249aba7c38ce49379b9d35e7ad81a0bf +#: 5a354eb4883948e0a2b5c96b5ae12da7 msgid "`glob`" msgstr "`glob`" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 d555a3d991e344a5a8e1289168d7c6d1 -#: 44b3f123c9b04a308c1161b742a7b34b +#: ../../src/topics/parameter-references.md:79 2325a310f2bc4d09b53b32c54efae2df +#: 9e477e2cfab24861b517fe2fb52962f4 msgid "`outputEval`" msgstr "`outputEval`" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 e9fa9430535c424fa3e8be5d460d2ba4 -#: 0e306cc923974d1db83fdfb45105a11c +#: ../../src/topics/parameter-references.md:80 9448462d104b4be5904623c85a9e16b7 +#: bf11a7a72147445c9b8e44b541e09f36 #, fuzzy -msgid "From `Workflow`" -msgstr "`Workflow`から" +msgid "From [`Workflow`](https://w3id.org/cwl/Workflow.html)" +msgstr "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)から" -#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +#: ../../src/topics/expressions.md:84 0d54a777a33d4f17a2f3390384a3c0c5 #, fuzzy msgid "" -"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" -"v1.0/Workflow.html#WorkflowOutputParameter)" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) " -"と [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#WorkflowOutputParameter)から" +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" と " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)から" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 b0290d1a477b48119e17cf1fed9d6dff -#: 446f1190af7a40a0913ff04ce7aa938c +#: ../../src/topics/parameter-references.md:84 7918d0661be746faaddf25ad49172f30 +#: b8439dbaa949427097e25ccb48fe15ee #, fuzzy msgid "From `steps`" msgstr "`steps`から" -#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +#: ../../src/topics/expressions.md:88 7b37eb600c9b4847a58a7e5077bef4c3 #, fuzzy msgid "" -"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" -msgstr "" -"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)から" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)から" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 e1cde4aa32c041238ed2596173c6d824 -#: 557694f82e314baa9ccafba14d6ff2c9 +#: ../../src/topics/parameter-references.md:87 368ef005c2ca4b8599f76242f7178375 +#: ab1ba7626eae483a8b614ee4cd5bab6f #, fuzzy msgid "" -"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." -"html#ExpressionTool)" -msgstr "" +"From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -"から" +msgstr "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)から" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 c2a92d3eca7f4ee39cec649170eeea53 -#: 3c939769ede94602a67fc50c435741cf +#: ../../src/topics/parameter-references.md:88 595b9ddcee734d6595c1b4b2d169dcb8 +#: 80b55c77a4384644acfc9472c3cedee0 msgid "`expression`" msgstr "`expression`" -#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +#: ../../src/topics/expressions.md:92 fd504478a6c641e0a72321fa80ad1c9c msgid "" -"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [ExpressionToolOutputParameter](https://www." -"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) " -"と [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#ExpressionToolOutputParameter)から" +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" と " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)から" -#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +#: ../../src/topics/expressions.md:95 32b1a39cca1a4402af9bdc0abc4d70c8 #, fuzzy msgid "" -"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement)" -msgstr "" -"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement)から" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)から" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: ../../src/topics/parameter-references.md:93 2518d499801e4bcf82e9e4666280504d +#: 98a511d138e9497c923963c2ca5f0a0b msgid "`coresMin`" msgstr "`coresMin`" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 718ceee9973240ec9c100977bbcc8921 -#: 2b25152f6df5494a8632f3ce631c20d8 +#: ../../src/topics/parameter-references.md:94 57a055b125f742dc8842b798b034161b +#: e84bc5505a6549ae9aacde8cb9225403 msgid "`coresMax`" msgstr "`coresMax`" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 c07ab08eb75d4528949c56a3d7c12b28 -#: 846cd427ae25410eae7c920b237edcb0 +#: ../../src/topics/parameter-references.md:95 98cd455e080f43749090270e7a61cb42 +#: e698ea756fe94e99837312fb30c9f9bf msgid "`ramMin`" msgstr "`ramMin`" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: ../../src/topics/parameter-references.md:96 8dfae10004a641fdb95c456c90a48d94 +#: bef90c153d4f4397b1f69f9beb38f7e6 msgid "`ramMax`" msgstr "`ramMax`" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: ../../src/topics/parameter-references.md:97 47fddc711ce44086a7811bdfbd9167dd +#: e2bdf4fe676346cbb4443ee54fb7419b msgid "`tmpdirMin`" msgstr "`tmpdirMin`" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: ../../src/topics/parameter-references.md:98 7d143ba98f1f4dfcbe08b70389d43092 +#: 8f1665baca2e4e3b96026b50d132709a msgid "`tmpdirMax`" msgstr "`tmpdirMax`" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: ../../src/topics/parameter-references.md:99 79bea45c2a484eda92c8578130b0b982 +#: d169949866a24e31947dffcb94620c5f msgid "`outdirMin`" msgstr "`outdirMin`" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +#: 8d2e01f2aa314f1cb1231f2e08f89ce5 d5417397b1e242ef9878ac77d2f65005 msgid "`outdirMax`" msgstr "`outdirMax`" -#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +#: ../../src/topics/expressions.md:104 08a66b2ab271494d810ff5834ca5c1bc msgid "" -"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" -"CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" -"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#InitialWorkDirRequirement)から" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)から" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +#: 21e9582891cf4b87a7ee4693663040fa 51bc6d1ccef14729a0d5e63b56d73d20 msgid "`listing`" msgstr "`listing`" -#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +#: ../../src/topics/expressions.md:106 7d8755f05d6541439f72ec9d6806d3fc #, fuzzy msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "[Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)に" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: effc0208cf4f4551958db6e526c0528b 9d4889c8cec24351a7a9e3c547e331b6 +#: 29c2424fc7dc43e68c9bfee179167bb3 30f25141bcce4670882e4a5bbe4fc3e2 msgid "`entry`" msgstr "`entry`" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: be6c1e85c7b6495d8086c262daad20e7 af4f7f232a9d42388c0ba1cfc7c2cdf7 +#: 02cfd4f1c3014e1eaa598a329dc5a95d d76fb015595e4194a7e15d714baaaf98 msgid "`entryname`" msgstr "`entryname`" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +#: 408f69a2df1343a78f93ff2ac0a994ea d37c78309e8b427f835af4fbd367e643 #, fuzzy msgid "From `EnvVarRequirement`" msgstr "`EnvVarRequirement`から" -#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +#: ../../src/topics/expressions.md:110 53752bdff0974e39b2a86e8f2d96455f #, fuzzy msgid "" -"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef)" -msgstr "" -"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef)から" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)から" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +#: 242a12ec757947db894195c9aefba818 7b26b9972f7141bf950b3bb024b0e369 msgid "`envValue`" msgstr "`envValue`" -#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 +#: ../../src/topics/expressions.md:116 93d6c90b49d8424f9283c384062ce333 #, fuzzy -msgid "" -"Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" -"`expressionLib` による外部ライブラリの利用とインラインJavaScriptコードの利用" +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "`expressionLib` による外部ライブラリの利用とインラインJavaScriptコードの利用" -#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +#: ../../src/topics/expressions.md:118 ea6cbaa5dae647538c0bd9a4d5cad3f9 +#, fuzzy msgid "" -"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " -"attribute that allows users to load external JavaScript files, or to provide " -"inline JavaScript code." +"The requirement " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" supports an `expressionLib` attribute that allows users to load external" +" JavaScript files, or to provide inline JavaScript code." msgstr "" -"`InlineJavascriptRequirement` は、`expressionLib` 属性をサポートし、ユーザー" -"が外部 JavaScript ファイルを読み込んだり、インライン JavaScript コードを提供" -"したりできるようにします。" +"`InlineJavascriptRequirement` は、`expressionLib` 属性をサポートし、ユーザーが外部 " +"JavaScript ファイルを読み込んだり、インライン JavaScript コードを提供したりできるようにします。" -#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +#: ../../src/topics/expressions.md:122 484dc17440524cfda4dc486a7c5d5f63 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts of " -"the CWL document." +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." msgstr "" -"`expressionLib` 属性に追加されたエントリーは、CWLランナーのJavaScriptエンジン" -"で解析されます。これは、外部ファイルをインクルードしたり、CWL定義の他の部分で" -"呼び出すことができるJavaScript関数を作成するために使用することができます。" +"`expressionLib` " +"属性に追加されたエントリーは、CWLランナーのJavaScriptエンジンで解析されます。これは、外部ファイルをインクルードしたり、CWL定義の他の部分で呼び出すことができるJavaScript関数を作成するために使用することができます。" -#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +#: ../../src/topics/expressions.md:128 5b2336cae1ef4cae8ed187d3f33cff25 msgid "" -"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." -"org/v1.0/CommandLineTool.html#Expressions) that the only version of " -"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" -"international.org/5.1/). This means that any code that you include or write " -"in your CWL Document must be compliant with ECMAScript 5.1." +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." msgstr "" -"CWL標準（バージョン1.0から1.2）は、CWL定義で有効なJavaScriptのバージョンは[" -"ECMAScript 5.1](https://262.ecma-international.org/5.1/" -")のみであると[明記しています](https://www.commonwl.org/v1.0/CommandLineTool." -"html#Expressions)。これは、CWLドキュメントに含める、または書くコードは、" -"ECMAScript 5.1に準拠していなければならないことを意味します。" +"CWL標準（バージョン1.0から1.2）は、CWL定義で有効なJavaScriptのバージョンは[ECMAScript " +"5.1](https://262.ecma-" +"international.org/5.1/)のみであると[明記しています](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)。これは、CWLドキュメントに含める、または書くコードは、ECMAScript" +" 5.1に準拠していなければならないことを意味します。" -#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +#: ../../src/topics/expressions.md:135 32eca3a47efc4685bf7be706e123adbe msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " -"function inline in `expressionLib`. That function can then be used in other " -"parts of the CWL document:" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" msgstr "" -"例えば、`InlineJavascriptRequirement` を使って、`expressionLib` に " -"JavaScript 関数をインラインで記述することができます。その関数は、CWL定義の他" -"の部分で使用することができます：" +"例えば、`InlineJavascriptRequirement` を使って、`expressionLib` に JavaScript " +"関数をインラインで記述することができます。その関数は、CWL定義の他の部分で使用することができます：" -#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +#: ../../src/topics/expressions.md:139 6839a02fb82d45c29ae518f2b00cb9d5 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "`hello-world-expressionlib-inline.cwl`" -#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +#: ../../src/topics/expressions.md:146 5b5e59fa1688499ea4560ee6f8023227 #, fuzzy msgid "" -"Running this CWL workflow will invoke the JavaScript function and result in " -"the `echo` command printing the input message with capital initial letters:" -msgstr "" -"このCWLワークフローを実行すると、JavaScript関数が起動し、`echo` コマンドが入" -"力メッセージを大文字の頭文字で表示します：" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" +msgstr "このCWLワークフローを実行すると、JavaScript関数が起動し、`echo` コマンドが入力メッセージを大文字の頭文字で表示します：" -#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +#: ../../src/topics/expressions.md:149 a1e57c6833c848d3974cf448493ab924 #, fuzzy msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "`hello-world-expressionlib-inline.cwl` 実行しています。" -#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +#: ../../src/topics/expressions.md:155 1a4dfef06b5c4402bdb7e7dbd79eeb5d msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" -msgstr "" -"`capitalizeWords` 関数を外部ファイル`custom-functions.js` に移動し、CWL 定義" -"でインポートしてみましょう：" +msgstr "`capitalizeWords` 関数を外部ファイル`custom-functions.js` に移動し、CWL 定義でインポートしてみましょう：" -#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +#: ../../src/topics/expressions.md:158 71ac99c65d15451cbbf58d1e81934010 #, fuzzy msgid "`custom-functions.js`" msgstr "`custom-functions.js`" -#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +#: ../../src/topics/expressions.md:164 60918e53189243d3872e61c7a4de20fc #, fuzzy msgid "`hello-world-expressionlib-external.cwl`" msgstr "`hello-world-expressionlib-external.cwl`" -#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +#: ../../src/topics/expressions.md:171 ad2a74bd983b47869dc78b2eb7b6fce1 #, fuzzy msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -"`custom-functions.js` ファイルは、`$include: custom-functions.js` という記述" -"でCWL定義に含まれます。これにより、関数と変数がCWL定義の他の部分で使用できる" -"ようになります。" +"`custom-functions.js` ファイルは、`$include: custom-functions.js` " +"という記述でCWL定義に含まれます。これにより、関数と変数がCWL定義の他の部分で使用できるようになります。" -#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +#: ../../src/topics/expressions.md:175 82c02dd2446b4de9a4c4b87736107b30 #, fuzzy msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "`hello-world-expressionlib-external.cwl`実行しています。" -#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +#: ../../src/topics/expressions.md:181 6fa7ebeffc7b44c6a12cd84897d186a1 msgid "" -"Finally, note that you can have both inline and external JavaScript code in " -"your CWL document. In this final example we have added another entry to the " -"`expressionLib` attribute with the new function `createHelloWorldMessage`, " -"that calls the `capitalizeWords` function from the external file `custom-" -"functions.js`." +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." msgstr "" -"最後に、CWL定義にはインラインと外部JavaScriptコードの両方が存在できることに注" -"意してください。この最後の例では、`expressionLib` 属性に、新しい関数" -"`createHelloWorldMessage` を追加しました。この関数は、外部ファイル`custom-" +"最後に、CWL定義にはインラインと外部JavaScriptコードの両方が存在できることに注意してください。この最後の例では、`expressionLib`" +" 属性に、新しい関数`createHelloWorldMessage` を追加しました。この関数は、外部ファイル`custom-" "functions.js` から`capitalizeWords` 関数を呼び出しています。" -#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +#: ../../src/topics/expressions.md:186 d34f3e688d2d49b6bfcda4c962895d8c msgid "`hello-world-expressionlib.cwl`" msgstr "`hello-world-expressionlib.cwl`" -#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +#: ../../src/topics/expressions.md:193 9e2774fc35b14832a0f92b7afaafd537 msgid "Running `hello-world-expressionlib.cwl`." msgstr "`hello-world-expressionlib.cwl`を実行する。" -#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +#: ../../src/topics/expressions.md:200 8b797cfb232f4e5da51f6c21e9a8e7e3 #, fuzzy msgid "" -"The `$include` statement can be used to include a file from the local disk " -"or from a remote location. It works with both relative and absolute paths. " -"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." -"html#Include) from the CWL specification to learn more about it." +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." msgstr "" -"`$include` ステートメントを使用すると、ローカルディスクまたはリモートロケー" -"ションからファイルをインクルードすることができます。相対パスと絶対パスの両方" -"で動作します。CWL仕様の[text about`$include`](https://www.commonwl.org/v1.0/" -"SchemaSalad.html#Include)を読むと、より詳しく知ることができます。" +"`$include` " +"ステートメントを使用すると、ローカルディスクまたはリモートロケーションからファイルをインクルードすることができます。相対パスと絶対パスの両方で動作します。CWL仕様の[text" +" " +"about`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include)を読むと、より詳しく知ることができます。" -#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +#: ../../src/topics/file-formats.md:1 ac906f26116c45d882e1afa42ae38e34 msgid "File Formats" msgstr "ファイルフォーマット" -#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +#: ../../src/topics/file-formats.md:3 d99dab4f2f264c68b839b59b80d570e0 +#, fuzzy msgid "" -"Tools and workflows can take `File` types as input and produce them as " -"output. We also recommend indicating the format for `File` types. This helps " -"document for others how to use your tool while allowing you to do some " -"simple type-checking when creating parameter files." +"Tools and workflows can take " +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types as input " +"and produce them as output. We also recommend indicating the format for " +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." msgstr "" -"ToolsやWorkflowsは、`File` " -"型を入力として受け取り、出力として生成することができます。また、`File` タイプ" -"のフォーマットを示すことをお勧めします。これにより、ツールの使用方法を他の人" -"に示すことができ、また、パラメータファイルを作成する際に簡単な型チェックを行" -"うことができるようになります。" +"ToolsやWorkflowsは、`File` 型を入力として受け取り、出力として生成することができます。また、`File` " +"タイプのフォーマットを示すことをお勧めします。これにより、ツールの使用方法を他の人に示すことができ、また、パラメータファイルを作成する際に簡単な型チェックを行うことができるようになります。" -#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +#: ../../src/topics/file-formats.md:8 23ba3dd26f5543119e2c152105b58e98 msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM in " -"our example), reference a local ontology for your institution, or do not add " -"a file format initially for quick development before sharing your tool with " -"others. You can browse existing [IANA file format listings][IANA] and [EDAM " -"file format listings][EDAM] on their websites." +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +#: ../../src/topics/file-formats.md:14 81c441846fc249c58607bacf97095eb8 msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` section " -"of the document in greater detail, so don't worry about these for now." -msgstr "" -"次のチュートリアルで、`$namespaces` と`$schemas` の部分をより詳しく説明します" -"ので、今は気にしないでください。" +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." +msgstr "次のチュートリアルで、`$namespaces` と`$schemas` の部分をより詳しく説明しますので、今は気にしないでください。" -#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +#: ../../src/topics/file-formats.md:17 c04841dbf4be4cf8a22cceca8b08bd14 #, fuzzy msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." -msgstr "" -"なお、さらなる利点として`cwltool` は、ファイル形式に基づく基本的な推論を行" -"い、明らかな不一致があるようであれば警告を発します。" +msgstr "なお、さらなる利点として`cwltool` は、ファイル形式に基づく基本的な推論を行い、明らかな不一致があるようであれば警告を発します。" -#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +#: ../../src/topics/file-formats.md:20 c5f6f6e4c23e4bf19dee69acb8ebed8e msgid "`metadata_example.cwl`" msgstr "`metadata_example.cwl`" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +#: 20e97d58596a4a959ad76ec6128ac414 4e070ae9110d437bbf008b0c60a00cd5 msgid "The equivalent of this CWL description in command line format is:" msgstr "このCWL定義に相当するものをコマンドライン形式にすると:" -#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +#: ../../src/topics/file-formats.md:32 632e441919094610b97afc17e9c5e625 msgid "Sample Parameter Files" msgstr "サンプルパラメーターファイル" -#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +#: ../../src/topics/file-formats.md:34 afd8633db1904897aa3e499354b1c376 #, fuzzy msgid "" -"Below is an example of a parameter file for the example above. We encourage " -"checking in working examples of parameter files for your tool. This allows " -"others to quickly work with your tool, starting from a \"known good\" " -"parameterization." -msgstr "" -"以下は、上記の例のパラメータファイルの例です。あなたのツールのパラメータファ" -"イルの実例をチェックすることをお勧めします。これにより、他の人が「既知の良" -"い」パラメータ化から始めて、あなたのツールで素早く作業することができます。" +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." +msgstr "以下は、上記の例のパラメータファイルの例です。あなたのツールのパラメータファイルの実例をチェックすることをお勧めします。これにより、他の人が「既知の良い」パラメータ化から始めて、あなたのツールで素早く作業することができます。" -#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +#: ../../src/topics/file-formats.md:39 bb69d6963c174191bf527335c3f665b7 msgid "`sample.yml`" msgstr "`sample.yml`" -#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +#: ../../src/topics/file-formats.md:45 ddb4f6f81c7d462b974e98c88dd3f558 #, fuzzy msgid "" -"___Note:___ To follow the example below, you need to download the example " -"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" msgstr "" -"___注：___ 以下の例に実行するには、例の入力ファイル、*file-formats.bam* をダ" -"ウンロードする必要があります。このファイルは から入手可能で、`wget` などでダウンロードすることができます：" -#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +#: ../../src/topics/index.md:1 2995cd4fb85c423dba021611dac4a137 msgid "Topics" msgstr "トピックス" -#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +#: ../../src/topics/inputs.md:1 3bac021fe7614d74ae701fb3c3765b93 msgid "Inputs" msgstr "Inputs" -#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +#: ../../src/topics/inputs.md:3 8bb3ee0cd0fc4d85ba007431fc541973 msgid "Essential Input Parameters" msgstr "必須入力パラメータ" -#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +#: ../../src/topics/inputs.md:5 17365707f58242369dd6aa73fc8d7242 #, fuzzy msgid "" -"The `inputs` of a tool is a list of input parameters that control how to run " -"the tool. Each parameter has an `id` for the name of parameter, and `type` " -"describing what types of values are valid for that parameter." +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." msgstr "" -"ツールの`inputs` は、ツールの実行に関わる入力パラメーターのリストです。 各パ" -"ラメーターには、パラメーター名を示す`id` と、そのパラメーターに有効な値の種類" -"を示す`type` があります。" +"ツールの`inputs` は、ツールの実行に関わる入力パラメーターのリストです。 各パラメーターには、パラメーター名を示す`id` " +"と、そのパラメーターに有効な値の種類を示す`type` があります。" -#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +#: ../../src/topics/inputs.md:9 521cb5dead5d4e9ab5ff037fb4b683cb #, fuzzy msgid "" -"Available primitive types are *string*, *int*, *long*, *float*, *double*, " -"and *null*; complex types are *array* and *record*; in addition there are " -"special types *File*, *Directory* and *Any*." +"Available primitive types are *string*, *boolean*, *int*, *long*, " +"*float*, *double*, and *null*; complex types are *array* and *record*; in" +" addition there are special types *File*, *Directory* and *Any*." msgstr "" -"利用可能なプリミティブ型は*string*,*int*,*long*,*float*,*double*, *null*; 複" -"合型は*array* and*record*; さらに特殊型*File*,*Directory* ,*Any* があります。" +"利用可能なプリミティブ型は*string*,*int*,*long*,*float*,*double*, *null*; 複合型は*array* " +"and*record*; さらに特殊型*File*,*Directory* ,*Any* があります。" -#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +#: ../../src/topics/inputs.md:13 fbdf2c1bed3e41d7a41ec6b14d134a98 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." -msgstr "" -"次の例では、異なる型の入力パラメーターが、異なる方法でコマンドライン上に表示" -"されることを示します。" +msgstr "次の例では、異なる型の入力パラメーターが、異なる方法でコマンドライン上に表示されることを示します。" -#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +#: ../../src/topics/inputs.md:16 008f79cdf0074c73948bf50deb0a8a47 msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "まず、以下の内容を含む`inp.cwl` というファイルを作成します：" -#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +#: ../../src/topics/inputs.md:18 94cd3f10e94f4735bd3ae7dc168e5deb msgid "`inp.cwl`" msgstr "`inp.cwl`" -#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +#: ../../src/topics/inputs.md:24 b339be370e8742b69400c8040ad7d15b msgid "Create a file called `inp-job.yml`:" msgstr "`inp-job.yml` というファイルを作成します：" -#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +#: ../../src/topics/inputs.md:26 78974fb2475947ccb8b8c55e34df5fa6 msgid "`inp-job.yml`" msgstr "`inp-job.yml`" -#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +#: ../../src/topics/inputs.md:33 9cc4a60d01f945aa9b4c43afcf20098b #, fuzzy msgid "" -"You can use `cwltool` to create a template input object. That saves you from " -"having to type all the input parameters in a input object file:" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in an input object file:" msgstr "" -"`cwltool` を使って、テンプレートとなる入力オブジェクトを作成することができま" -"す。これにより、入力オブジェクトファイルにすべての入力パラメータを入力する手" -"間を省くことができます：" +"`cwltool` " +"を使って、テンプレートとなる入力オブジェクトを作成することができます。これにより、入力オブジェクトファイルにすべての入力パラメータを入力する手間を省くことができます：" -#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +#: ../../src/topics/inputs.md:40 5ac6da11d56446de97c251a37d997671 #, fuzzy msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " -"> inp-job.yml`, and then modify the default values with your desired input " -"values." +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." msgstr "" -"`cwltool --make-template inp.cwl > inp-job.yml` のように、出力をファイルに" -"リダイレクトし、デフォルト値を希望の入力値で修正することができます。" +"`cwltool --make-template inp.cwl > inp-job.yml` " +"のように、出力をファイルにリダイレクトし、デフォルト値を希望の入力値で修正することができます。" -#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +#: ../../src/topics/inputs.md:44 6a3edb0d259d4d7c900dd9811f978d4e msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." @@ -2815,1319 +2648,1291 @@ msgstr "" "\"example_file\" は `File` 型として、フィールド `class： File` と `path` " "フィールドを持つオブジェクトとして提供されなければなりません。" -#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +#: ../../src/topics/inputs.md:47 f1d76be7ba0b48f4b605581d0a9a5c72 msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " -"command line." -msgstr "" -"次に、コマンドラインで`touch whale.txt` と入力し、[touch]をコマンドを使用し" -"て whale.txt を作成します。" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." +msgstr "次に、コマンドラインで`touch whale.txt` と入力し、[touch]をコマンドを使用して whale.txt を作成します。" -#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +#: ../../src/topics/inputs.md:53 8cabfa0cbcfd4a5aa30d1aabd412136d msgid "" -"Now invoke `cwltool` with the tool description and the input object on the " -"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " -"boxed text describes these two commands and the expected output from the " -"command line:" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" msgstr "" -"次に、`cwltool inp.cwl inp-job.yml` というコマンドを使い、コマンドラインに" -"ツール定義と入力オブジェクトを指定して`cwltool` を起動します。次のボックステ" -"キストは、これら2つのコマンドと、コマンドラインから期待される出力について説明" -"しています：" +"次に、`cwltool inp.cwl inp-job.yml` " +"というコマンドを使い、コマンドラインにツール定義と入力オブジェクトを指定して`cwltool` " +"を起動します。次のボックステキストは、これら2つのコマンドと、コマンドラインから期待される出力について説明しています：" -#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +#: ../../src/topics/inputs.md:64 5c78d7824ef34636ae2ed68d524d79e8 #, fuzzy msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not explicitly " -"specified" -msgstr "" -"CWLリファレンスランナー（cwltool）と他のランナーは、ツールが明示的に指定され" -"ていないファイルに誤ってアクセスしないように、入力ファイルへの（\"ソフト\"）" -"シンボリックリンクを持つ一時ディレクトリを作成します。" +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" +msgstr "CWLリファレンスランナー（cwltool）と他のランナーは、ツールが明示的に指定されていないファイルに誤ってアクセスしないように、入力ファイルへの（\"ソフト\"）シンボリックリンクを持つ一時ディレクトリを作成します。" -#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +#: ../../src/topics/inputs.md:70 5bdf77c45346445d8f93353c1e73f768 msgid "" -"The field `inputBinding` is optional and indicates whether and how the input " -"parameter should appear on the tool's command line. If `inputBinding` is " -"missing, the parameter does not appear on the command line. Let's look at " -"each example in detail." +"The field " +"[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)" +" is optional and indicates whether and how the input parameter should " +"appear on the tool's command line. If `inputBinding` is missing, the " +"parameter does not appear on the command line. Let's look at each " +"example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +#: ../../src/topics/inputs.md:83 d783fe52e86f4feda33ea0eecb622603 msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -"ブール型はフラグとして扱われます。 入力パラメータ \"example_flag \"が " -"\"true \"の場合、コマンドラインに`prefix` が追加されます。 falseの場合、フラ" -"グは付加されません。" +"ブール型はフラグとして扱われます。 入力パラメータ \"example_flag \"が \"true " +"\"の場合、コマンドラインに`prefix` が追加されます。 falseの場合、フラグは付加されません。" -#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +#: ../../src/topics/inputs.md:95 f99fb9a6d0374ef78503815d4db9006d msgid "" -"String types appear on the command line as literal values. The `prefix` is " -"optional, if provided, it appears as a separate argument on the command line " -"before the parameter . In the example above, this is rendered as `--example-" -"string hello`." +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." msgstr "" -"文字列型は、コマンドライン上ではリテラル値として与えられます。 ` prefix` は" -"オプションです。与えられた場合、コマンドライン上のパラメータの前に別の引数と" -"して与えられます。 上の例では、`--example-string hello` と与えられます。" +"文字列型は、コマンドライン上ではリテラル値として与えられます。 ` prefix` " +"はオプションです。与えられた場合、コマンドライン上のパラメータの前に別の引数として与えられます。 上の例では、`--example-string" +" hello` と与えられます。" -#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +#: ../../src/topics/inputs.md:109 b106eed01c1744a792368f91f547e553 msgid "" -"Integer (and floating point) types appear on the command line with decimal " -"text representation. When the option `separate` is false (the default value " -"is true), the prefix and value are combined into a single argument. In the " -"example above, this is rendered as `-i42`." +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +#: ../../src/topics/inputs.md:124 1c70336741a842a5b16b687642d1d9b4 msgid "" "File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the parameter " -"is optional. In the example above, this is rendered as `--file=/tmp/random/" -"path/whale.txt`. However, if the \"example_file\" parameter were not " -"provided in the input, nothing would appear on the command line." +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." msgstr "" -#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +#: ../../src/topics/inputs.md:131 9294c07c672b414f9c3895ed70b9b4ee msgid "" -"Input files are read-only. If you wish to update an input file, you must " -"[first copy it to the output directory](staging-input-files.md)." +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." msgstr "" -"入力ファイルは読み取り専用です。 入力ファイルを更新したい場合は、[まず出力" -"ディレクトリにコピーする](staging-input-files.md)必要があります。" +"入力ファイルは読み取り専用です。 入力ファイルを更新したい場合は、[まず出力ディレクトリにコピーする](staging-input-" +"files.md)必要があります。" -#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +#: ../../src/topics/inputs.md:134 a07137c36e63495f836c483fd472904f msgid "" -"The value of `position` is used to determine where parameter should appear " -"on the command line. Positions are relative to one another, not absolute. " -"As a result, positions do not have to be sequential, three parameters with " -"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " -"than one parameter can have the same position (ties are broken using the " -"parameter name), and the position field itself is optional. The default " -"position is 0." +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +#: ../../src/topics/inputs.md:142 7513adabd3ae4701b17f578ac9f321d7 msgid "" -"The `baseCommand` field will always appear in the final command line before " -"the parameters." -msgstr "" -"`baseCommand` フィールドは、常にパラメータの前の最終コマンド行に表示されま" -"す。" +"The `baseCommand` field will always appear in the final command line " +"before the parameters." +msgstr "`baseCommand` フィールドは、常にパラメータの前の最終コマンド行に表示されます。" -#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +#: ../../src/topics/inputs.md:146 c3c82d25a75941b0b50a4a6bb826568f msgid "Array Inputs" msgstr "配列入力" -#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +#: ../../src/topics/inputs.md:148 b11a5c7a13b345939e4ae15e1e2c0786 msgid "" "It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to provide " -"`type` field with `type: array` and `items` defining the valid data types " -"that may appear in the array. Alternatively, brackets `[]` may be added " -"after the type name to indicate that input parameter is array of that type." +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." msgstr "" -#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +#: ../../src/topics/inputs.md:154 aa00bcfc6c0f4085ae52621a2f4ae8d9 msgid "`array-inputs.cwl`" msgstr "`array-inputs.cwl`" -#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +#: ../../src/topics/inputs.md:160 e730b2b9bace4427bdd045556963634f msgid "`array-inputs-job.yml`" msgstr "`array-inputs-job.yml`" -#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 588f0f7f967f4d69af27c9729d6d3119 -#: 02adef8ee8204842b5b4a0408f3bac33 9db68837918a4a349f32f15f12697a1d +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:86 +#: ../../src/topics/outputs.md:109 015a0f00c2b245e2b0e87735926da736 +#: 390384208d7b4771888f164b587c7b9a edb3ae59c48945f29c3086b16a5265d3 #, fuzzy msgid "" -"Now invoke `cwltool` providing the tool description and the input object on " -"the command line:" -msgstr "" -"ここで、コマンドラインにツール定義と入力オブジェクトを指定し `cwltool` を起動" -"します：" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" +msgstr "ここで、コマンドラインにツール定義と入力オブジェクトを指定し `cwltool` を起動します：" -#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +#: ../../src/topics/inputs.md:178 13e59751d43b49f0ac366538a14f9c84 msgid "" -"The `inputBinding` can appear either on the outer array parameter definition " -"or the inner array element definition, and these produce different behavior " -"when constructing the command line, as shown above. In addition, the " -"`itemSeparator` field, if provided, specifies that array values should be " -"concatenated into a single argument separated by the item separator string." +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +#: ../../src/topics/inputs.md:185 bb31c6784ea843ec88f185523cfa25df msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` in " -"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " -"where array values that are not defined with an associated key are marked by " -"a leading `-`. This will be demonstrated in the next lesson and is discussed " -"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " -"arrays of arrays, arrays of records, and other complex types." +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +#: ../../src/topics/inputs.md:191 53817379078548b2aeb6195cae9cbab7 #, fuzzy msgid "Inclusive and Exclusive Inputs" msgstr "包括的入力と排他的入力" -#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +#: ../../src/topics/inputs.md:193 e163c0cfe9694a85b2e42682f42970a5 msgid "" "Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be provided " -"together (they are exclusive). You can use records and type unions to group " -"parameters together to describe these two conditions." +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +#: ../../src/topics/inputs.md:198 84e1ab25511c49d1baabb1f80f247b49 msgid "`record.cwl`" msgstr "`record.cwl`" -#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +#: ../../src/topics/inputs.md:204 3d5dfc8ee47b458db638a9eed84b4938 msgid "`record-job1.yml`" msgstr "`record-job1.yml`" -#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +#: ../../src/topics/inputs.md:215 ecfb1d911a84400ba3db12fd0adf9279 msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "最初の例では、`itemB` も与えずに、`itemA` を与えることはできません。" -#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: ../../src/topics/inputs.md:217 24ba804374b4471d8e925d80670f9dff msgid "`record-job2.yml`" msgstr "`record-job2.yml`" -#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +#: ../../src/topics/inputs.md:233 436707d9c7634732ad1e60d8294bd4ba msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the first " -"matching item (`itemC`) is added to the command line and remaining item " -"(`itemD`) is ignored." +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." msgstr "" -"2番目の例では、`itemC` と`itemD` が排他的であるため、最初に一致した項目 " -"(`itemC`) のみがコマンドラインに追加され、残りの項目 (`itemD`) は無視されま" -"す。" +"2番目の例では、`itemC` と`itemD` が排他的であるため、最初に一致した項目 (`itemC`) " +"のみがコマンドラインに追加され、残りの項目 (`itemD`) は無視されます。" -#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +#: ../../src/topics/inputs.md:236 01b168c5faf94ead8d836dfe39e4c592 msgid "`record-job3.yml`" msgstr "`record-job3.yml`" -#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +#: ../../src/topics/inputs.md:252 e6d81d6549984689bae4533c6d01bd5b msgid "" -"In the third example, only `itemD` is provided, so it appears on the command " -"line." -msgstr "" -"3番目の例では、`itemD` のみが提供されているので、コマンドラインに表示されま" -"す。" +"In the third example, only `itemD` is provided, so it appears on the " +"command line." +msgstr "3番目の例では、`itemD` のみが提供されているので、コマンドラインに表示されます。" -#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +#: ../../src/topics/inputs.md:255 ffddeeda8f04408ba73f7a59a4618da5 #, fuzzy msgid "Exclusive Input Parameters with Expressions" msgstr "式で入力パラメータを排他的に指定する" -#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +#: ../../src/topics/inputs.md:257 cf22f21ec44c483986979316544a7c3b #, fuzzy msgid "" -"If you use exclusive input parameters combined with expressions, you need to " -"be aware that the `inputs` JavaScript object will contain one of the " -"exclusive input values. This means that you might need to use an **or** " -"boolean operator to check which values are present." +"If you use exclusive input parameters and reference them in expressions, " +"you need to be aware that the `inputs` JavaScript object will contain one" +" of the possible, mutually-exclusive input values. Because the types of " +"these exclusive values may differ, you may need to check which type is in" +" use when you reference the properties of the `input` object." msgstr "" -"排他的入力パラメータを式と組み合わせて使用する場合、`inputs` JavaScript オブ" -"ジェクトに排他的入力値のいずれかが含まれることを意識する必要があります。つま" -"り、**or** のブーリアン演算子を使用して、どの値が存在するかをチェックする必要" -"がある場合があります。" +"排他的入力パラメータを式と組み合わせて使用する場合、`inputs` JavaScript " +"オブジェクトに排他的入力値のいずれかが含まれることを意識する必要があります。つまり、**or** " +"のブーリアン演算子を使用して、どの値が存在するかをチェックする必要がある場合があります。" -#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +#: ../../src/topics/inputs.md:263 0fecb128b19b44d796b6c1b6de4f7166 #, fuzzy msgid "" "Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from an " -"enum." +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." msgstr "" -"`file_format` 入力パラメータに、`null` (つまり、値が提供されていない)、また" -"は enum の任意の値を受け入れる排他的なものを含む例を使ってみましょう。" +"`file_format` 入力パラメータに、`null` (つまり、値が提供されていない)、または enum " +"の任意の値を受け入れる排他的なものを含む例を使ってみましょう。" -#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +#: ../../src/topics/inputs.md:266 7f1941698a6046e9b9e8a53736af949a msgid "`exclusive-parameter-expressions.cwl`" msgstr "`exclusive-parameter-expressions.cwl`" -#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +#: ../../src/topics/inputs.md:272 60b585142f06489d9f48090b664b6d32 #, fuzzy msgid "" "Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you provide a " -"valid value, such as “fasta” (one of the values of the enum), your command " -"should execute successfully:" +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as `fasta` (one of the possible values of the" +" enum), your command should execute successfully:" msgstr "" -"JavaScriptの式では、`null` の値を考慮せずに、排他的入力パラメータの値を使用し" -"ていることに注意してください。\"fasta\"（enumの値の1つ）のような有効な値を指" -"定すると、コマンドは正常に実行されるはずです：" +"JavaScriptの式では、`null` " +"の値を考慮せずに、排他的入力パラメータの値を使用していることに注意してください。\"fasta\"（enumの値の1つ）のような有効な値を指定すると、コマンドは正常に実行されるはずです：" -#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +#: ../../src/topics/inputs.md:281 11fdeb057d674f118830f431ff019c15 #, fuzzy msgid "" -"However, if you do not provide any input value, then `file_format` will be " -"evaluated to a `null` value, which does not match the expected type for the " -"output field (a `string`), resulting in failure when running your workflow." +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to `null`, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your " +"workflow." msgstr "" -"しかし、入力値を提供しない場合、`file_format` は、`null` の値として評価されま" -"す。これは、出力フィールドが期待する型（`string` ）と一致しないため、ワークフ" -"ロー実行時に失敗することになります。" +"しかし、入力値を提供しない場合、`file_format` は、`null` " +"の値として評価されます。これは、出力フィールドが期待する型（`string` ）と一致しないため、ワークフロー実行時に失敗することになります。" -#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +#: ../../src/topics/inputs.md:290 8594cca9d93b4280b6cfee64c8a7c578 #, fuzzy msgid "" -"To correct it, you must remember to use an or operator in your JavaScript " -"expression when using exclusive parameters, or any parameter that allows " -"`null`. For example, the expression could be changed to `$(inputs." -"file_format || 'auto')`, to have a default value if none was provided in the " -"command line or job input file." +"To correct it, you should explicitly handle the possibility of a `null` " +"value. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value `\"auto\"` if " +"none was provided in the command line or job input file." +msgstr "" +"これを修正するには、排他的パラメータ、または`null` を許可するパラメータを使用する場合、JavaScript 式で or " +"演算子を使用することを忘れてはなりません。たとえば、式を`$(inputs.file_format || 'auto')` " +"に変更すると、コマンドラインやジョブ入力ファイルで何も指定されていない場合にデフォルト値を持つようになります。" + +#: ../../src/topics/inputs.md:295 b5055c77f85e43609fe3e9b9839778e3 +msgid "" +"Here, the boolean “or” operator `||` in JavaScript is used for its " +"_short-circuiting_ property. If `inputs.file_format` is “true” in a " +"boolean context (e.g. a valid non-empty string from the enum), the " +"evaluation of the expression stops at the first operand of `||`; it " +"“short-circuits”. If however `inputs.file_format` is `null`, the whole " +"expression’s value becomes that of the second operand, which is why a " +"reasonable default can be provided there." msgstr "" -"これを修正するには、排他的パラメータ、または`null` を許可するパラメータを使用" -"する場合、JavaScript 式で or 演算子を使用することを忘れてはなりません。たとえ" -"ば、式を`$(inputs.file_format || 'auto')` に変更すると、コマンドラインやジョ" -"ブ入力ファイルで何も指定されていない場合にデフォルト値を持つようになります。" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: 723c2232310c4276aeac2bd6728d2912 msgid "Metadata and Authorship" msgstr "メタデータと著者" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 +#: 4d81aac1830045229e5c60c7959074d8 msgid "" -"Implementation extensions not required for correct execution (for example, " -"fields related to GUI presentation) and metadata about the tool or workflow " -"itself (for example, authorship for use in citations) may be provided as " -"additional fields on any object. Such extensions fields (e.g. `format: edam:" -"format_2572`) can use a namespace prefix listed in the `$namespaces` section " -"of the document (e.g. edam: http://edamontology.org/) as described in the " -"[Schema Salad specification][schema-salad]. Once you add the namespace " -"prefix, you can access it anywhere in the document as shown below. " -"Otherwise, one must use full URLs: `format: http://edamontology.org/" -"format_2572`." +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b +#: 368f8993ae9d401488081d74ae5acd49 msgid "" "For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to cite " -"your tool." -msgstr "" -"すべての開発者に対し、ツールおよびワークフローに関する以下の最小限のメタデー" -"タを推奨します。この例では、他の人があなたのツールを引用するためのメタデータ" -"を含んでいます。" +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." +msgstr "すべての開発者に対し、ツールおよびワークフローに関する以下の最小限のメタデータを推奨します。この例では、他の人があなたのツールを引用するためのメタデータを含んでいます。" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: c80f2b180ca74afb8a1fc18f8686304b msgid "`metadata_example2.cwl`" msgstr "`metadata_example2.cwl`" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: 37b07ea9b7124842b8ba3040f70308e9 #, fuzzy msgid "Extended Example" msgstr "拡張された例" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 +#: 1cd5989ade6741aabe625c13bed3c8ed #, fuzzy msgid "" -"For those that are highly motivated, it is also possible to annotate your " -"tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints at " -"hardware requirements in order to use the tool, and a few more metadata " -"fields." -msgstr "" -"高いモチベーションを持つ人であれば、ツールにもっと多くのメタデータを付与する" -"ことも可能です。この例では、EDAMオントロジーのタグをキーワードとして含み（関" -"連するツールのグループ化が可能）、ツールを使用するために必要なハードウェアの" -"ヒントや、さらにいくつかのメタデータフィールドがあります。" +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." +msgstr "高いモチベーションを持つ人であれば、ツールにもっと多くのメタデータを付与することも可能です。この例では、EDAMオントロジーのタグをキーワードとして含み（関連するツールのグループ化が可能）、ツールを使用するために必要なハードウェアのヒントや、さらにいくつかのメタデータフィールドがあります。" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: ae7369ba14404d23b72d1ef30dcd4153 msgid "`metadata_example3.cwl`" msgstr "`metadata_example3.cwl`" -#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +#: ../../src/topics/operations.md:1 a79974b2f4534fcd8c7a04401e8a5556 #, fuzzy msgid "Operations" msgstr "Operations" -#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +#: ../../src/topics/operations.md:3 b6507c8e1625476b97708423acb4fd0e #, fuzzy msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-line " -"tool, or an expression tool. It is a step of a workflow that specifies " -"inputs and outputs, but it does not provide enough information to be " -"executed." +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." msgstr "" -"Operationは、Workflow、CommandLineTool、ExpressionToolと同様に、CWL Processの" -"一種です。Workflowのステップで、入力と出力を指定しますが、実行するのに十分な" -"情報を提供しません。" +"Operationは、Workflow、CommandLineTool、ExpressionToolと同様に、CWL " +"Processの一種です。Workflowのステップで、入力と出力を指定しますが、実行するのに十分な情報を提供しません。" -#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +#: ../../src/topics/operations.md:7 047b09455db64524a71c47ab5192039f msgid "" -"You can create operations to visualize a workflow during development, before " -"you are ready to submit the workflow to a CWL runner:" -msgstr "" -"CWLランナーにワークフローを送信する前に、開発中のワークフローを可視化すること" -"ができます：" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" +msgstr "CWLランナーにワークフローを送信する前に、開発中のワークフローを可視化することができます：" -#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +#: ../../src/topics/operations.md:10 e9b2b97f3059460b867577a49934a338 msgid "`operations.cwl`" msgstr "`operations.cwl`" -#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +#: ../../src/topics/operations.md:16 d21e9444182d4e27bae934db4573ae99 #, fuzzy msgid "" -"The `uppercase` step of the workflow is an operation. It can be used like a " -"command line tool or an expression. You can also plot it with the CWL Viewer " -"or `cwltool`:" +"The `uppercase` step of the workflow is an operation. It can appear where" +" a command line tool or an expression is expected. You can also plot it " +"with the CWL Viewer or `cwltool`:" msgstr "" -"ワークフローの`uppercase` ステップは Operation です。CommandLineToolや" -"ExpressionToolのように使用することができます。また、CWL Viewerや`cwltool` を" -"使ってプロットすることもできます：" +"ワークフローの`uppercase` ステップは Operation " +"です。CommandLineToolやExpressionToolのように使用することができます。また、CWL Viewerや`cwltool` " +"を使ってプロットすることもできます：" -#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +#: ../../src/topics/operations.md:24 61e4ae6ed18e41708270eb358cd55277 +#, fuzzy msgid "" -"The output of the command above can be rendered with a Graphviz renderer. " -"The following image is rendered with the Sphinx Graphviz directive (this " -"user guide is built with Sphinx):" -msgstr "" -"上記のコマンドの出力は、Graphvizレンダラーでレンダリングすることができます。" -"以下の画像は、SphinxのGraphvizディレクティブでレンダリングしたものです（この" -"ユーザーガイドはSphinxで構築されています）：" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx `{graphviz}` directive " +"(this user guide is built with Sphinx):" +msgstr "上記のコマンドの出力は、Graphvizレンダラーでレンダリングすることができます。以下の画像は、SphinxのGraphvizディレクティブでレンダリングしたものです（このユーザーガイドはSphinxで構築されています）：" -#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +#: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd msgid "" -"If you try running it with `cwltool`, the command will fail since `cwltool` " -"does not have enough information to know how to execute it:" +"The operation file will fail to run with `cwltool` because `cwltool` " +"lacks the necessary information to execute it:" msgstr "" -"`cwltool` だけで実行しようとすると、`cwltool` は実行するのに必要な情報がない" -"ため、コマンドは失敗します：" -#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +#: ../../src/topics/operations.md:59 e184470550e645f6b9ce658af7e65ecf msgid "`cwltool` does not know how to run operations" msgstr "`cwltool` は、どうやってoperationsを実行するかを知りません" -#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +#: ../../src/topics/operations.md:67 3b90445d3428444cafd7d5c0e5884980 #, fuzzy msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A " -"CWL runner could, for instance, use abstract operations with ID's that " +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -"CWL runnerは、操作を具体的なステップにバインドする方法を思いつくかもしれませ" -"ん。例えば、CWL runnerは、異なるワークフローエンジンで実行されるステップに対" -"応するIDを持つ抽象的な operation を使用することができます。" +"CWL runnerは、操作を具体的なステップにバインドする方法を思いつくかもしれません。例えば、CWL " +"runnerは、異なるワークフローエンジンで実行されるステップに対応するIDを持つ抽象的な operation を使用することができます。" -#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +#: ../../src/topics/outputs.md:1 35e7bad6fdc04bcf9bbfbb2d8d42cfa5 msgid "Outputs" msgstr "Outputs" -#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +#: ../../src/topics/outputs.md:3 6d912d40359c4d33a4f08abca83c00be #, fuzzy msgid "Returning Output Files" msgstr "出力ファイルの回収" -#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +#: ../../src/topics/outputs.md:5 a6bd3f9e23de488394958fe7b59a61e0 #, fuzzy msgid "" "The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name of " -"parameter, and `type` describing what types of values are valid for that " -"parameter." +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." msgstr "" -"ツールの`outputs` は、ツールの実行後に返されるべき出力パラメータのリストで" -"す。 各パラメーターには、パラメーター名を示す`id` と、そのパラメーターに有効" -"な値の型を示す`type` があります。" +"ツールの`outputs` は、ツールの実行後に返されるべき出力パラメータのリストです。 各パラメーターには、パラメーター名を示す`id` " +"と、そのパラメーターに有効な値の型を示す`type` があります。" -#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +#: ../../src/topics/outputs.md:10 a229d8d983344e51a231edb5f667d84b #, fuzzy msgid "" -"When a tool runs under CWL, the starting working directory is the designated " -"output directory. The underlying tool or script must record its results in " -"the form of files created in the output directory. The output parameters " -"returned by the CWL tool are either the output files themselves, or come " -"from examining the content of those files." +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or the result of examining the content of those files." msgstr "" -"CWLでツールを実行する場合、開始時の作業ディレクトリは指定された出力ディレクト" -"リになります。 基礎となるツールやスクリプトは、出力ディレクトリに作成される" -"ファイルの形でその結果を記録しなければなりません。 CWLツールによって返される" -"出力パラメータは、出力ファイルそのものであるか、またはそれらのファイルの内容" -"を調べることによって得られるものです。" +"CWLでツールを実行する場合、開始時の作業ディレクトリは指定された出力ディレクトリになります。 " +"基礎となるツールやスクリプトは、出力ディレクトリに作成されるファイルの形でその結果を記録しなければなりません。 " +"CWLツールによって返される出力パラメータは、出力ファイルそのものであるか、またはそれらのファイルの内容を調べることによって得られるものです。" -#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +#: ../../src/topics/outputs.md:16 9845e517f7d848e5b59a97880ca6999f msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "次の例は、tarファイルから抽出されたファイルを返す方法を示しています。" -#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +#: ../../src/topics/outputs.md:19 0bf1ad2c43174e57a3ba8dd86f7c96b2 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "`baseCommand` に必須引数を渡します。" -#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +#: ../../src/topics/outputs.md:21 553d535b023e4d69a888fe5b24bb8c5b +#, fuzzy msgid "" "In previous examples, the `baseCommand` was just a string, with any " -"arguments passed as CWL inputs. Instead of a single string we can use an " -"_array of strings_. The first element is the command to run, and any " -"subsequent elements are mandatory command line arguments" +"arguments passed as CWL inputs. Instead of a single string, we can use an" +" _array of strings_ as the value of `baseCommand`. The first element of " +"the array is the command to run, and any subsequent elements are " +"mandatory command line arguments" msgstr "" -"これまでの例では、`baseCommand` は単なる文字列で、引数はCWL入力として渡してい" -"ました。単一の文字列の代わりに、文字列の配列__ を使用することができます。 最" -"初の要素は実行するコマンドで、それ以降の要素は必須のコマンドライン引数です" +"これまでの例では、`baseCommand` は単なる文字列で、引数はCWL入力として渡していました。単一の文字列の代わりに、文字列の配列__ " +"を使用することができます。 最初の要素は実行するコマンドで、それ以降の要素は必須のコマンドライン引数です" -#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +#: ../../src/topics/outputs.md:28 9b65071222c94951bed12ac53e964ee3 msgid "`tar.cwl`" msgstr "`tar.cwl`" -#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +#: ../../src/topics/outputs.md:34 759ab0847b97479fb4a15e4b7d4e6565 msgid "`tar-job.yml`" msgstr "`tar-job.yml`" -#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +#: ../../src/topics/outputs.md:40 f9752ec303ab419c8db8adef3fa2466f #, fuzzy msgid "Next, create a tar file for the example." msgstr "次に、サンプルとなるtarファイルを作成します。" -#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +#: ../../src/topics/outputs.md:47 4f96576528684f28a72b805f777769e6 msgid "" -"And now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" -"そして、今度はコマンドラインにツール定義と入力オブジェクトを指定して" -"`cwltool` を呼び出します：" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" +msgstr "そして、今度はコマンドラインにツール定義と入力オブジェクトを指定して`cwltool` を呼び出します：" -#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +#: ../../src/topics/outputs.md:53 707803bec0cb42919905c7c321bd9d30 +#, fuzzy msgid "" -"The field `outputBinding` describes how to set the value of each output " -"parameter." -msgstr "" -"`outputBinding` フィールドには、各出力パラメータの値の設定方法が記述されてい" -"ます。" +"The field " +"[`outputBinding`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding)" +" describes how to set the value of each output parameter." +msgstr "`outputBinding` フィールドには、各出力パラメータの値の設定方法が記述されています。" -#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +#: ../../src/topics/outputs.md:64 cbaec50871e04718883c8c91ff475d20 +#, fuzzy msgid "" -"The `glob` field consists of the name of a file in the output directory. If " -"you don't know name of the file in advance, you can use a wildcard pattern " -"like `glob: '*.txt'`." +"The " +"[`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) " +"field consists of the pattern to match file names in the output " +"directory. This can simply be the file's exact name. But if you don't " +"know the name of the file in advance, you can use a wildcard pattern like" +" `glob: '*.txt'`." msgstr "" -"`glob` フィールドは、出力ディレクトリ内のファイル名で構成されます。ファイル名" -"が予め分からない場合は、`glob: '*.txt'` のようにワイルドカードパターンを使用" -"することができます。" +"`glob` フィールドは、出力ディレクトリ内のファイル名で構成されます。ファイル名が予め分からない場合は、`glob: '*.txt'` " +"のようにワイルドカードパターンを使用することができます。" -#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +#: ../../src/topics/outputs.md:69 8a6e9173198241429effd911c3a7c4d7 msgid "Capturing Standard Output" msgstr "標準出力をキャプチャする" -#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +#: ../../src/topics/outputs.md:71 a7c4fdaeda3e411fbeb802c5fa529ce9 #, fuzzy msgid "" -"To capture a tool's standard output stream, add the `stdout` field with the " -"name of the file where the output stream should go. Then add `type: stdout` " -"on the corresponding output parameter." +"To capture a tool's standard output stream, add the " +"[`stdout`](https://w3id.org/cwl/CommandLineTool.html#stdout) field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." msgstr "" -"ツールの標準出力をキャプチャするには、`stdout` フィールドに、標準出力を保存し" -"たいファイル名を追加します。 次に、対応する出力パラメータに`type: stdout` を" -"追加します。" +"ツールの標準出力をキャプチャするには、`stdout` フィールドに、標準出力を保存したいファイル名を追加します。 " +"次に、対応する出力パラメータに`type: stdout` を追加します。" -#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +#: ../../src/topics/outputs.md:75 cf2ef8dc7fda49308c09efe4f4ef5d7b #, fuzzy msgid "`stdout.cwl`" msgstr "`stdout.cwl`" -#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +#: ../../src/topics/outputs.md:93 cbe236266dd148aaa96355e490a87cbe msgid "Array Outputs" msgstr "出力の配列" -#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +#: ../../src/topics/outputs.md:95 77f86a7b94924a08b6ea2660218fe3c5 msgid "" "You can also capture multiple output files into an array of files using " "`glob`." -msgstr "" -"また、`glob` を使って、複数の出力ファイルを配列に取り込むことができます。" +msgstr "また、`glob` を使って、複数の出力ファイルを配列に取り込むことができます。" -#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +#: ../../src/topics/outputs.md:97 b34e30481fbd489d95fb7f8d5b5ab50c #, fuzzy msgid "`array-outputs.cwl`" msgstr "`array-outputs.cwl`" -#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +#: ../../src/topics/outputs.md:103 3aab0e0c9a78430f9caaa29a93303b56 msgid "`array-outputs-job.yml`" msgstr "`array-outputs-job.yml`" -#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +#: ../../src/topics/outputs.md:116 9a14271c3180429988aaa14869f783a0 #, fuzzy msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions to " -"mark entries in arrays, as demonstrated in several of the upcoming sections." +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." msgstr "" -"[YAML Guide](yaml-guide.md#arrays) で説明されているように、期待される出力の配" -"列は`array-outputs-job.yml` で指定され、それぞれのエントリーは先頭の`-` で" -"マークされています。このフォーマットは、CWL定義で配列のエントリーをマークする" -"ために使用することもでき、今後のいくつかのセクションでデモがあります。" +"[YAML Guide](yaml-guide.md#arrays) で説明されているように、期待される出力の配列は`array-outputs-" +"job.yml` で指定され、それぞれのエントリーは先頭の`-` " +"でマークされています。このフォーマットは、CWL定義で配列のエントリーをマークするために使用することもでき、今後のいくつかのセクションでデモがあります。" -#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +#: ../../src/topics/parameter-references.md:1 c8a6ea340e6a43398e97b68e03a8bb3b msgid "Parameter References" msgstr "パラメータリファレンス" -#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +#: ../../src/topics/parameter-references.md:3 f5c0592ca28c46c2a89943f4f6f69a27 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file we " -"were interested in was called \"hello.txt\", and this was written into the `." -"cwl` file. This is not the best way to do this, as the \"hello.txt\" " -"filename may vary or be dependent on the input file(s) used. To avoid this " -"we can specify the name of the file we want in the job parameters file (`." -"yml`). In this example, you will see how to reference the value of input " -"parameters dynamically from other fields, which will allow us to then " -"specify the name of the file to extract." +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +#: ../../src/topics/parameter-references.md:13 50db8add9b1942d986e581b8d21c2ee4 msgid "`tar-param.cwl`" msgstr "`tar-param.cwl`" -#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +#: ../../src/topics/parameter-references.md:19 d01ad5fd9fea462cab0d4d776824b4e1 msgid "`tar-param-job.yml`" msgstr "`tar-param-job.yml`" -#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +#: ../../src/topics/parameter-references.md:25 9b1e2f1a23ea4fe2af97ef5108f33376 #, fuzzy msgid "" -"Create your input files and invoke `cwltool` with the tool description and " -"the input object on the command line:" -msgstr "" -"入力ファイル(入力オブジェクト)を作成し、コマンドラインでツール定義と入力オブ" -"ジェクトを指定して`cwltool` を呼び出します：" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" +msgstr "入力ファイル(入力オブジェクト)を作成し、コマンドラインでツール定義と入力オブジェクトを指定して`cwltool` を呼び出します：" -#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +#: ../../src/topics/parameter-references.md:36 06926a516ae6432d96e3eaa62202cd86 #, fuzzy msgid "" -"Certain fields permit parameter references which are enclosed in `$(...)`. " -"These are evaluated and replaced with value being referenced." -msgstr "" -"`$(...)` で囲まれたパラメータ参照を許可するフィールドもあります。これらは評価" -"され、参照されている値に置き換えられます。" +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." +msgstr "`$(...)` で囲まれたパラメータ参照を許可するフィールドもあります。これらは評価され、参照されている値に置き換えられます。" -#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +#: ../../src/topics/parameter-references.md:47 384fe8188f414eafbbb8d6b81bdfd779 #, fuzzy msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -"パラメータリファレンスは、Javascriptの構文のサブセットを使用して記述しま" -"す。 この例では、`$(inputs.extractfile)` 、`$(inputs[\"extractfile\"])` 、" -"`$(inputs['extractfile'])` は同等です。" +"パラメータリファレンスは、Javascriptの構文のサブセットを使用して記述します。 " +"この例では、`$(inputs.extractfile)` 、`$(inputs[\"extractfile\"])` " +"、`$(inputs['extractfile'])` は同等です。" -#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +#: ../../src/topics/parameter-references.md:51 56ead1c8d45c43bdbcbc6f7cbb8e1e92 msgid "" -"The value of the \"inputs\" variable is the input object provided when the " -"CWL tool was invoked." -msgstr "" -"変数 \"inputs \"の値は、CWLツールの起動時に提供された入力オブジェクトです。" +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." +msgstr "変数 \"inputs \"の値は、CWLツールの起動時に提供された入力オブジェクトです。" -#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +#: ../../src/topics/parameter-references.md:54 56bca89e314c4223b33d7fe63c9b771d #, fuzzy msgid "" -"Note that because `File` parameters are objects, to get the path to an input " -"file you must reference the path field on a file object; to reference the " -"path to the tar file in the above example you would write `$(inputs.tarfile." -"path)`." +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." msgstr "" -"`File` パラメータはオブジェクトであるため、入力ファイルのパスを取得するには、" -"ファイルオブジェクトのpathフィールドを参照する必要があります。上記の例でtar" -"ファイルのパスを参照するには、`$(inputs.tarfile.path)`となります。" +"`File` " +"パラメータはオブジェクトであるため、入力ファイルのパスを取得するには、ファイルオブジェクトのpathフィールドを参照する必要があります。上記の例でtarファイルのパスを参照するには、`$(inputs.tarfile.path)`となります。" -#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +#: ../../src/topics/parameter-references.md:59 1c1ab240c4114572bb4e42955baad361 msgid "Where are parameter references allowed?" msgstr "パラメータ参照はどこで許されるのですか？" -#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +#: ../../src/topics/parameter-references.md:61 055d3268859c46c4b7db5005608bae05 #, fuzzy msgid "You can only use parameter references in certain fields. These are:" -msgstr "" -"パラメータ参照は、特定のフィールドにのみ使用することができます。 以下はその" -"例です：" +msgstr "パラメータ参照は、特定のフィールドにのみ使用することができます。 以下はその例です：" -#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +#: ../../src/topics/parameter-references.md:63 2ed66835bd9044adbfdd0b5097787f22 #, fuzzy msgid "" -"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool) から" +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +" から" -#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +#: ../../src/topics/parameter-references.md:69 f592619e4b2c497e80cd75da0548cf07 msgid "" -"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter)" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter) から" +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +" から" -#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +#: ../../src/topics/parameter-references.md:72 81ea71a35020421187dc18ddd151c62f msgid "" -"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding)" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding) から" +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +" から" -#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +#: ../../src/topics/parameter-references.md:74 ea0117748adc4324901024f21eed04ac #, fuzzy msgid "" -"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter) から" +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +" から" -#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +#: ../../src/topics/parameter-references.md:77 3a30e73176cf4e4eb9f26770a176b9c9 #, fuzzy msgid "" -"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding)" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding) から" +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +" から" -#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +#: ../../src/topics/parameter-references.md:81 551c199c9a6344fca9bfacfb69fc4e53 #, fuzzy msgid "" -"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" -"v1.0/Workflow.html#WorkflowOutputParameter)" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) " -"と [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#WorkflowOutputParameter) から" +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" と " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +" から" -#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +#: ../../src/topics/parameter-references.md:85 7008a1ff1af54fda827637e787e5c7dd msgid "" -"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput) から" +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +" から" -#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +#: ../../src/topics/parameter-references.md:89 45743e1b261c4195856de0c2e30ea72e #, fuzzy msgid "" -"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." -"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) " -"と [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#ExpressionToolOutputParameter) から" +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" と " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +" から" -#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +#: ../../src/topics/parameter-references.md:92 0ae32d1db5f9452bbfcbbc4719b0b9f1 #, fuzzy msgid "" -"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement)" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" -"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement) から" +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +" から" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 +#: 7e1907ff15c74f488187531de336eccf #, fuzzy msgid "" -"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" -"CommandLineTool.html#InitialWorkDirRequirement)" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" -"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#InitialWorkDirRequirement) から" +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +" から" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: 678874668fed4f4d80a1b0990e183e2f #, fuzzy msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" -"[Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent) の中に" +msgstr "[Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent) の中に" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 +#: e2882880886046ac88ae1c0d414366d1 #, fuzzy msgid "" -"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef)" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" -"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef) から" +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +" から" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: 05324169d8ae48d4a1abe3a0ac07c891 msgid "Requirements and Hints" msgstr "Requirements と Hints" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: 1f5b72d7ec82442ba29baa14a03f061b msgid "Specifying Software Requirements" msgstr "ソフトウェア要求事項の指定" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb +#: e708866921ea49d69d3c2a32d63ea468 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " -"include a `SoftwareRequirement` field in the `hints` section. This may also " -"help to avoid confusion about which version of a tool the description was " -"written for." +"include a " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)" +" field in the `hints` section. This may also help to avoid confusion " +"about which version of a tool the description was written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 +#: 6f722d6fd54f485fa964076c8d08938b #, fuzzy msgid "" -"In this example, the software requirement being described is InterProScan " -"version 5.21-60." -msgstr "" -"この例では、定義されるソフトウェア要件はInterProScanバージョン5.21-60です。" +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." +msgstr "この例では、定義されるソフトウェア要件はInterProScanバージョン5.21-60です。" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 +#: 5c1236ec57c64079bfb7c779524b12ad msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the [dependency " -"resolvers configuration][dependencies]." +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 -msgid "" -"As well as a version number, a unique resource identifier (URI) for the tool " -"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " -"up in the [SciCrunch][scicrunch] registry, which provides a portal for " -"finding, tracking, and referring to scientific resources consistently. If " -"you want to specify a tool as a `SoftwareRequirement`, search for the tool " -"on SciCrunch and use the RRID that it has been assigned in the registry. " -"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " -"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." -"org][identifiers]) in the `specs` field of your requirement description. " -"Other good choices, in order of preference, are to include the DOI for the " -"main tool citation and the URL to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +#: 1a8b8aadf1c64e87b8b670e288bc14bc +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)," +" search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 d10c792550e8498c8ee384d3093da306 msgid "Staging Input Files" msgstr "入力ファイルのステージング" -#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +#: ../../src/topics/staging-input-files.md:3 ac2ef1fced5f4044861761a11c35e78a msgid "" -"Normally, input files are located in a read-only directory separate from the " -"output directory. This causes problems if the underlying tool expects to " -"write its output files alongside the input file in the same directory. You " -"use `InitialWorkDirRequirement` to stage input files into the output " -"directory. In this example, we use a JavaScript expression to extract the " -"base name of the input file from its leading directory path." +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use " +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)" +" to stage input files into the output directory. In this example, we use " +"a JavaScript expression to extract the base name of the input file from " +"its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: ../../src/topics/staging-input-files.md:9 d8ca16f5321e486ebe8ea9f9752b3737 msgid "`linkfile.cwl`" msgstr "`linkfile.cwl`" -#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +#: ../../src/topics/troubleshooting.md:1 aa3eddcaa0684f86ba67aafcd57872e7 msgid "Troubleshooting" msgstr "トラブルシューティング" -#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +#: ../../src/topics/troubleshooting.md:3 3207f476afa04158bd26db39a16a2df5 msgid "" -"In this section you will find ways to troubleshoot when you have problems " -"executing CWL. We focus on `cwltool` here but some of these techniques may " -"apply to other CWL Runners." +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." msgstr "" -"このセクションでは、CWLの実行に問題がある場合にトラブルシューティングを行う方" -"法を説明します。ここでは、`cwltool` に焦点を当てますが、これらのテクニックの" -"いくつかは他のCWLランナーにも適用されるかもしれません。" +"このセクションでは、CWLの実行に問題がある場合にトラブルシューティングを行う方法を説明します。ここでは、`cwltool` " +"に焦点を当てますが、これらのテクニックのいくつかは他のCWLランナーにも適用されるかもしれません。" -#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +#: ../../src/topics/troubleshooting.md:6 1d47f4ce04554cabb1ccf40a13ee42ec msgid "Run `cwltool` with `cachedir`" msgstr "`cwltool` を`cachedir` で実行する" -#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +#: ../../src/topics/troubleshooting.md:8 0c25602a83e441b48b536eb49568f2b6 msgid "" "You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor output " -"files, but created while your workflow is running). By default, these files " -"are created in a temporary directory but writing them to a separate " -"directory makes accessing them easier." +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +#: ../../src/topics/troubleshooting.md:14 36ec60b80c714357a4274217274136ff msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " -"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " -"olleH\". However, the second step, `step_b`, **has a typo**, where instead " -"of executing the `rev` command it tries to execute `revv`, which fails." +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +#: ../../src/topics/troubleshooting.md:20 6f34038054ac4f4fa0b0ad9cbc3ecdc7 msgid "`troubleshooting-wf1.cwl`" msgstr "`troubleshooting-wf1.cwl`" -#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +#: ../../src/topics/troubleshooting.md:27 b777877c88024c9fb06a6614029ef8d6 #, fuzzy msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " -"(`cwltool` will create the directory for you if it does not exist already):" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" msgstr "" -"`--cachedir` に `/tmp/cachedir/` を指定して、このワークフローを実行してみま" -"しょう（`cwltool` は、ディレクトリがまだ存在しない場合、新規作成します）：" +"`--cachedir` に `/tmp/cachedir/` を指定して、このワークフローを実行してみましょう（`cwltool` " +"は、ディレクトリがまだ存在しない場合、新規作成します）：" -#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +#: ../../src/topics/troubleshooting.md:35 8654b7f2f4464d13be4b47729e1f07e5 msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. You " -"can inspect the intermediate files created:" +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +#: ../../src/topics/troubleshooting.md:44 04e80f7ce14d4d73bc5d290dcf01bcdb msgid "" -"Each workflow step has received a unique ID (the long value that looks like " -"a hash). The `${HASH}.status` files display the status of each step executed " -"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " -"output of the command above." +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +#: ../../src/topics/troubleshooting.md:48 719917cb0fd849f5a328671df8726189 msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " -"the `step_b`). After fixing the typo, when you execute `cwltool` with the " -"same arguments as the previous time, note that now `cwltool` output contains " -"information about pre-cached outputs for `step_a`, and about a new cache " -"entry for the output of `step_b`. Also note that the status of `step_b` is " -"now of success." +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +#: ../../src/topics/troubleshooting.md:59 2a9dbb3ad7564f5aa103349c45ee7925 msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had " -"been cached, and there was no change in its execution or output. " +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " "Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for " -"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " -"re-evaluate steps unnecessarily." +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +#: ../../src/topics/using-containers.md:1 7439fe097aa4459ba1e4c0e28fc59b9a msgid "Using Containers" msgstr "コンテナの使用" -#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +#: ../../src/topics/using-containers.md:3 eff5c6ac1cad44f9862585daf0a91298 msgid "Running Tools Inside Docker" msgstr "Dockerの内部でツールを実行する" -#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +#: ../../src/topics/using-containers.md:5 50d1a644bc8c49f78c453e4e0f3c07c8 msgid "" -"[Docker][docker] containers simplify software installation by providing a " -"complete known-good runtime for software and its dependencies. However, " -"containers are also purposefully isolated from the host system, so in order " -"to run a tool inside a Docker container there is additional work to ensure " -"that input files are available inside the container and output files can be " -"recovered from the container. A CWL runner can perform this work " -"automatically, allowing you to use Docker to simplify your software " -"management while avoiding the complexity of invoking and managing Docker " -"containers." +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." msgstr "" -#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +#: ../../src/topics/using-containers.md:15 4b0f6cfc8a774c77bfbc99e568af2ece #, fuzzy msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the container." -msgstr "" -"CWLランナーの役割のひとつに、入力ファイルのパスをコンテナ内のでの配置位置に合" -"わせて調整することがあります。" +"input files to reflect the location where they appear inside the " +"container." +msgstr "CWLランナーの役割のひとつに、入力ファイルのパスをコンテナ内のでの配置位置に合わせて調整することがあります。" -#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +#: ../../src/topics/using-containers.md:18 27c02a5d479a420eab7d14888d9fb288 msgid "" -"This example runs a simple Node.js script inside a Docker container which " -"will then print \"Hello World\" to the standard output." -msgstr "" -"この例では、Dockerコンテナ内で簡単なNode.jsスクリプトを実行し、標準出力に" -"「Hello World」と表示します。" +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." +msgstr "この例では、Dockerコンテナ内で簡単なNode.jsスクリプトを実行し、標準出力に「Hello World」と表示します。" -#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +#: ../../src/topics/using-containers.md:21 1a62a93ab20b4f2ca1e13ded3a767dc5 msgid "`docker.cwl`" msgstr "`docker.cwl`" -#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +#: ../../src/topics/using-containers.md:27 ccc2874840c3476bb714ddf4bdbf0f3e msgid "`docker-job.yml`" msgstr "`docker-job.yml`" -#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +#: ../../src/topics/using-containers.md:33 d766b66de4714a5da0cd87ed886cc32f #, fuzzy msgid "" "Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that is " -"really new is the `dockerRequirement` section." +"Most of this has been explained in previous sections, the only part that " +"is really new is the " +"[`dockerRequirement`](https://w3id.org/cwl/CommandLineTool.html#DockerRequirement)" +" section." msgstr "" -"これを実行する前に、これを分解して、いくつか細かく何をするのかを見てみましょ" -"う。 この大部分は以前のセクションで説明したもので、本当に新しいのは" -"`dockerRequirement` の部分だけです。" +"これを実行する前に、これを分解して、いくつか細かく何をするのかを見てみましょう。 " +"この大部分は以前のセクションで説明したもので、本当に新しいのは`dockerRequirement` の部分だけです。" -#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +#: ../../src/topics/using-containers.md:44 1f02618ab6254459ae71f72844e3cc18 msgid "" -"`baseCommand: node` tells CWL that we will be running this command using the " -"Node Js runtime that is meant for Javascript files. We then need to specify " -"some `hints` for how to find the container we want. In this case we list " -"just our requirements for the docker container in `DockerRequirements`. The " -"`dockerPull:` parameter takes the same value that you would pass to a " -"`docker pull` command. That is, the name of the container image (you can " -"even specify the tag, which is good idea for best practices when using " -"containers for reproducible research). In this case we have used a container " -"called `node:slim`." +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +#: ../../src/topics/using-containers.md:52 54cade4978ec463bbb5c0d8c08e27adb msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " -"the tool description and the input object on the command line:" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" msgstr "" -"Javascriptで \"hello.js \"というファイルを作成し、`cwltool` コマンドラインで" -"ツール定義と入力オブジェクトを指定して呼び出します：" +"Javascriptで \"hello.js \"というファイルを作成し、`cwltool` " +"コマンドラインでツール定義と入力オブジェクトを指定して呼び出します：" -#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +#: ../../src/topics/using-containers.md:55 6541d0cd9f6c4c43b8601715cc35e585 msgid "`hello.js`" msgstr "`hello.js`" -#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +#: ../../src/topics/using-containers.md:69 6abf220b7fa4479394ed33447cdd070e msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." -msgstr "" -"CWLランナーがスクリプトを実行するためにDockerコマンドラインを構築していること" -"に注目してください。" +msgstr "CWLランナーがスクリプトを実行するためにDockerコマンドラインを構築していることに注目してください。" -#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +#: ../../src/topics/using-containers.md:72 d2dd89a5edde4f2eab4c2baf0cc78745 msgid "" -"In this example, the path to the script `hello.js` is `/home/me/cwl/" -"user_guide/hello.js` outside the container but `/var/lib/cwl/" -"job369354770_examples/hello.js` inside the container, as reflected in the " -"invocation of the `node` command." +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." msgstr "" -"この例では、スクリプト`hello.js` のパスは、コンテナの外側では `/home/me/cwl/" -"user_guide/hello.js` が、コンテナの内側では`/var/lib/cwl/" -"job369354770_examples/hello.js` です。これは`node` コマンドの呼び出しに反映さ" -"れているためです。" +"この例では、スクリプト`hello.js` のパスは、コンテナの外側では `/home/me/cwl/user_guide/hello.js` " +"が、コンテナの内側では`/var/lib/cwl/job369354770_examples/hello.js` です。これは`node` " +"コマンドの呼び出しに反映されているためです。" -#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +#: ../../src/topics/workflows.md:1 06281a10592d42509566c8fc51f8d4da msgid "Workflows" msgstr "ワークフロー" -#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +#: ../../src/topics/workflows.md:3 325a656f9b8e4c1fa6f699cd8c447d00 #, fuzzy msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -"Workflowは、CommandLineTool、ExpressionTool、またはWorkflow（サブワークフ" -"ロー）をステップ として実行する CWL 処理ユニットです。CWLドキュメントには" -"`inputs` 、`outputs` 、`steps` を定義する必要があります。" +"Workflowは、CommandLineTool、ExpressionTool、またはWorkflow（サブワークフロー）をステップ " +"として実行する CWL 処理ユニットです。CWLドキュメントには`inputs` 、`outputs` 、`steps` " +"を定義する必要があります。" -#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +#: ../../src/topics/workflows.md:13 b92275181c9e480da64e660b7aca0745 #, fuzzy msgid "CWL workflow." msgstr "CWLのワークフローです。" -#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +#: ../../src/topics/workflows.md:41 be2540315f854b8e9a1d257bcabd78db #, fuzzy msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier examples." +"command-line tool, and the expression tool showed in the earlier " +"examples." msgstr "" -"CWL定義`echo-uppercase.cwl` は、コマンドラインツール、および先の例で示した" -"ExpressionToolを実行するワークフローを定義しています。" +"CWL定義`echo-uppercase.cwl` " +"は、コマンドラインツール、および先の例で示したExpressionToolを実行するワークフローを定義しています。" -#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +#: ../../src/topics/workflows.md:51 3be900594bb743399854b95baa9ae2f9 msgid "`echo-uppercase.cwl`" msgstr "`echo-uppercase.cwl`" -#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +#: ../../src/topics/workflows.md:81 5133c4e062bc4e479ce1dc8abbb08107 #, fuzzy msgid "" -"A command-line tool or expression tool can also be written directly in the " -"same CWL document as the workflow. For example, we can rewrite the `echo-" -"uppercase.cwl` workflow as a single file:" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" msgstr "" -"コマンドラインツールやExpressionToolは、ワークフローと同じCWLドキュメントに直" -"接記述することも可能です。例えば、`echo-uppercase.cwl` ワークフローを1つの" -"ファイルとして書き換えることができます：" +"コマンドラインツールやExpressionToolは、ワークフローと同じCWLドキュメントに直接記述することも可能です。例えば、`echo-" +"uppercase.cwl` ワークフローを1つのファイルとして書き換えることができます：" -#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +#: ../../src/topics/workflows.md:91 83bc2796889f4dccb713764ac1b3c3ad #, fuzzy msgid "`echo-uppercase-single-file.cwl`" msgstr "`echo-uppercase-single-file.cwl`" -#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +#: ../../src/topics/workflows.md:150 5a9a1dd6ed1f4ca6803f1d235c4fd392 msgid "" -"Having separate files helps with modularity and code organization. But it " -"can be helpful writing everything in a single file for development. There " -"are other ways to combine multiple files into a single file (e.g. `cwltool --" -"pack`) discussed further in other sections of this user guide." +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +#: ../../src/topics/workflows.md:160 277ed30d4b3a4156a4523e8d10e6ce60 msgid "" "For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this " -"user guide in more detail." +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +#: ../../src/topics/workflows.md:165 82818ab17aa4403eb982fd81a14a5865 msgid "Writing Workflows" msgstr "ワークフローを書く" -#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +#: ../../src/topics/workflows.md:167 3d8b98e8d03548699fadb22198de9b20 msgid "" -"This workflow extracts a java source file from a tar file and then compiles " -"it." -msgstr "" -"このワークフローでは、tarファイルからJavaのソースファイルを取り出し、コンパイ" -"ルします。" +"This workflow extracts a java source file from a tar file and then " +"compiles it." +msgstr "このワークフローでは、tarファイルからJavaのソースファイルを取り出し、コンパイルします。" -#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +#: ../../src/topics/workflows.md:170 c61097c695424f7195e8205a23b6ecff #, fuzzy msgid "`1st-workflow.cwl`" msgstr "`1st-workflow.cwl`" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +#: 6660c48f51d94d4fbcc05656e154059e bd2bab6c11614fa983ca8dab1408e1d8 msgid "Visualization of 1st-workflow.cwl" msgstr "1st-workflow.cwlの可視化" -#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +#: ../../src/topics/workflows.md:180 f0831481a43548039fbc4fd17555af57 #, fuzzy msgid "" -"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" -"github.com/common-workflow-language/user_guide/blob/" -"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" "workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" -"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" -msgstr "" -"[[1st-workflow.cwlを可視化したもの]](https://view.commonwl.org/graph/png/" -"github.com/common-workflow-language/user_guide/blob/" -"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" +msgstr "" +"[[1st-" +"workflow.cwlを可視化したもの]](https://view.commonwl.org/graph/png/github.com" +"/common-workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" "workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" -"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" -#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +#: ../../src/topics/workflows.md:183 5ff059fc8ae6471c8ea86dab7e5a93f5 msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a " -"run:" -msgstr "" -"Runの入力データを記述するために、別ファイルのYAMLまたはJSONオブジェクトを使用" -"します：" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" +msgstr "Runの入力データを記述するために、別ファイルのYAMLまたはJSONオブジェクトを使用します：" -#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +#: ../../src/topics/workflows.md:185 822e5d0a097b4109960d621a72a3c009 msgid "`1st-workflow-job.yml`" msgstr "`1st-workflow-job.yml`" -#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +#: ../../src/topics/workflows.md:191 4a4db7da861547639524083bf35ccfc0 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." -msgstr "" -"次に、サンプルとなるJavaファイルを作成し、コマンドラインツールで使用するため" -"にtarファイルに追加します。" +msgstr "次に、サンプルとなるJavaファイルを作成し、コマンドラインツールで使用するためにtarファイルに追加します。" -#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +#: ../../src/topics/workflows.md:205 ed16b30eaa4747f79b6dd10a19188d8c msgid "What's going on here? Let's break it down:" msgstr "どうなっているのでしょう？ 分解してみましょう：" -#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +#: ../../src/topics/workflows.md:212 6428bd7bd3be4393bfe5675f8e45ff94 #, fuzzy msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a workflow." +"document. The `class` field indicates this document describes a " +"workflow." msgstr "" -"`cwlVersion` フィールドは、この文書が使用するCWL仕様のバージョンを示しま" -"す。 ` class` フィールドは、この文書がワークフローを記述していることを示しま" -"す。" +"`cwlVersion` フィールドは、この文書が使用するCWL仕様のバージョンを示します。 ` class` " +"フィールドは、この文書がワークフローを記述していることを示します。" -#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#: ../../src/topics/workflows.md:221 d6abec8805f649fca668292412263f78 #, fuzzy msgid "" -"The `inputs` section describes the inputs of the workflow. This is a list " -"of input parameters where each parameter consists of an identifier and a " -"data type. These parameters can be used as sources for input to specific " -"workflows steps." +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." msgstr "" -"`inputs` セクションでは、ワークフローの入力について記述します。 これは入力パ" -"ラメータのリストであり、各パラメータは識別子とデータ型から構成されます。 こ" -"れらのパラメータは、特定のワークフロー・ステップへの入力ソースとして使用でき" -"ます。" +"`inputs` セクションでは、ワークフローの入力について記述します。 " +"これは入力パラメータのリストであり、各パラメータは識別子とデータ型から構成されます。 " +"これらのパラメータは、特定のワークフロー・ステップへの入力ソースとして使用できます。" -#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +#: ../../src/topics/workflows.md:233 22bf3e4910ef4f86a2e8f6d5a6cf0d42 #, fuzzy msgid "" -"The `outputs` section describes the outputs of the workflow. This is a list " -"of output parameters where each parameter consists of an identifier and a " -"data type. The `outputSource` connects the output parameter `classfile` of " -"the `compile` step to the workflow output parameter `compiled_class`." +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." msgstr "" -"`outputs` セクションでは、ワークフローの出力について記述します。 これは出力" -"パラメータのリストであり、各パラメータは識別子とデータ型から構成されます。 " -"` outputSource` は、`compile` ステップの出力パラメータ`classfile` を、ワーク" -"フロー出力パラメータ`compiled_class` に接続します。" +"`outputs` セクションでは、ワークフローの出力について記述します。 " +"これは出力パラメータのリストであり、各パラメータは識別子とデータ型から構成されます。 ` outputSource` は、`compile` " +"ステップの出力パラメータ`classfile` を、ワークフロー出力パラメータ`compiled_class` に接続します。" -#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +#: ../../src/topics/workflows.md:248 e0429688fce445da8083e69323e5b020 msgid "" "The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second step " -"compiles the file from the first step using the java compiler. Workflow " -"steps are not necessarily run in the order they are listed, instead the " -"order is determined by the dependencies between steps (using `source`). In " -"addition, workflow steps which do not depend on one another may run in " -"parallel." +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +#: ../../src/topics/workflows.md:256 980f5eada57c4fadbb783838ded1fa0b #, fuzzy msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input " -"parameters, `tarfile` and `extractfile` and one output parameter " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " "`extracted_file`." msgstr "" -"最初のステップである`untar` は、`tar-param.cwl` を実行します（[パラメータ参" -"照](parameter-references.md)で以前説明しました）。このツールは、2つの入力パラ" -"メータ、`tarfile` と`extractfile` と1つの出力パラメータ`extracted_file` を持" -"ちます。" +"最初のステップである`untar` は、`tar-param.cwl` を実行します（[パラメータ参照](parameter-" +"references.md)で以前説明しました）。このツールは、2つの入力パラメータ、`tarfile` と`extractfile` " +"と1つの出力パラメータ`extracted_file` を持ちます。" -#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +#: ../../src/topics/workflows.md:261 3532e165842f4ebb8db0c78208071555 msgid "" -"The ``in`` section of the workflow step connects these two input parameters " -"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " -"`source`. This means that when the workflow step is executed, the values " -"assigned to `tarball` and `name_of_file_to_extract` will be used for the " -"parameters `tarfile` and `extractfile` in order to run the tool." +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +#: ../../src/topics/workflows.md:267 04a4db2f3da94ce29e7999039ee13fde #, fuzzy msgid "" -"The `out` section of the workflow step lists the output parameters that are " -"expected from the tool." -msgstr "" -"ワークフローステップの`out` セクションには、ツールから期待される出力パラメー" -"タが記載されています。" +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." +msgstr "ワークフローステップの`out` セクションには、ツールから期待される出力パラメータが記載されています。" -#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +#: ../../src/topics/workflows.md:278 2651ee113a3d4b79b138854ebe729f48 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " -"in [Additional Arguments and Parameters](additional-arguments-and-parameters." -"md)). The output of this step `classfile` is connected to the `outputs` " -"section for the Workflow, described above." +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +#: ../../src/topics/workflows.md:285 177040bf9c0045f2878f42bcdd8cbd2d msgid "Nested Workflows" msgstr "ネストされたワークフロー" -#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +#: ../../src/topics/workflows.md:287 e8adc2f7c5ac4464b0711712617b8bbe msgid "" -"Workflows are ways to combine multiple tools to perform a larger operations. " -"We can also think of a workflow as being a tool itself; a CWL workflow can " -"be used as a step in another CWL workflow, if the workflow engine supports " -"the `SubworkflowFeatureRequirement`:" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -"ワークフローは、複数のツールを組み合わせてより大きな処理を実行するための方法" -"です。ワークフローエンジンが`SubworkflowFeatureRequirement` をサポートしてい" -"る場合、CWL ワークフローを別の CWL ワークフローのステップとすることができま" -"す ：" +"ワークフローは、複数のツールを組み合わせてより大きな処理を実行するための方法です。ワークフローエンジンが`SubworkflowFeatureRequirement`" +" をサポートしている場合、CWL ワークフローを別の CWL ワークフローのステップとすることができます ：" -#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +#: ../../src/topics/workflows.md:297 44d281d99cd944478db98446a984c001 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "`1st-workflow.cwl` をネストしたワークフローの例を紹介します：" -#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +#: ../../src/topics/workflows.md:300 d7b60ce81ea741ffa08f2c2d9d7cca69 msgid "`nestedworkflows.cwl`" msgstr "`nestedworkflows.cwl`" -#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +#: ../../src/topics/workflows.md:309 a5b7a1ab16e34bda8744ffadacdda3e8 msgid "" -"This two-step workflow starts with the `create-tar` step which is connected " -"to the `compile` step in orange; `compile` is another workflow, diagrammed " -"on the right. In purple we see the fixed string `\"Hello.java\"` being " -"supplied as the `name_of_file_to_extract`." +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -"この2ステップのワークフローは、`create-tar` ステップから始まり、オレンジ色の" -"`compile` ステップに接続されています。`compile` は、右図にある別のワークフ" -"ローです。紫色では、固定文字列`\"Hello.java\"` が`name_of_file_to_extract` と" -"して与えられているのがわかります。" +"この2ステップのワークフローは、`create-tar` ステップから始まり、オレンジ色の`compile` " +"ステップに接続されています。`compile` は、右図にある別のワークフローです。紫色では、固定文字列`\"Hello.java\"` " +"が`name_of_file_to_extract` として与えられているのがわかります。" -#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +#: ../../src/topics/workflows.md:314 8654f2d86b644609aaa5b9b73db30bda msgid "" "\"Visualization \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/1st-" +"workflow.cwl\">\"Visualization" msgstr "" -#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +#: ../../src/topics/workflows.md:322 7ce847ab54224452b6425de2a55ec893 #, fuzzy msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " -"CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " -"to become the step's input/outputs." +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." msgstr "" -"CWL`Workflow` は、`CommandLineTool` を`step` として使用することができ、その " -"CWL ファイルは`run` に記述されます。ワークフローの入力（`tarball` および" -"`name_of_file_to_extract` ）と出力（`compiled_class` ）は、ステップの入力/出" -"力になるようにマッピングすることができます。" +"CWL`Workflow` は、`CommandLineTool` を`step` として使用することができ、その CWL ファイルは`run` " +"に記述されます。ワークフローの入力（`tarball` および`name_of_file_to_extract` " +"）と出力（`compiled_class` ）は、ステップの入力/出力になるようにマッピングすることができます。" -#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +#: ../../src/topics/workflows.md:336 d621821d2c1b403cb7415b381dd883f6 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and `*.java` " -"filename. This is generally best-practice, as it means it can be reused in " -"multiple parent workflows, or even in multiple steps within the same " -"workflow." +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +#: ../../src/topics/workflows.md:341 358c612f175241f7bf148a04d75e00c9 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar " -"file at `tarball`, which we will prepare in the `create-tar` step. At this " -"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " -"specific input/output names, as those also appear in its usage as a tool." +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +#: ../../src/topics/workflows.md:347 c6297c120e004ae8b52d5b519fbc04d2 #, fuzzy msgid "" "It is also possible to do a less generic approach and avoid external " @@ -4135,572 +3940,693 @@ msgid "" "coded `Hello.java` file using the previously mentioned " "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -"また、あまり一般的でない方法で、ジョブファイルの外部依存を回避することも可能" -"です。そこで、このワークフローでは、先に述べた`InitialWorkDirRequirement` の" -"要件を使用して、ハードコードされた`Hello.java` ファイルを生成してから、それ" -"を tar ファイルに追加することができます。" +"また、あまり一般的でない方法で、ジョブファイルの外部依存を回避することも可能です。そこで、このワークフローでは、先に述べた`InitialWorkDirRequirement`" +" の要件を使用して、ハードコードされた`Hello.java` ファイルを生成してから、それを tar ファイルに追加することができます。" -#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +#: ../../src/topics/workflows.md:366 66f76677f4ce42baa8a8813410ea5aee #, fuzzy msgid "" -"In this case our step can assume `Hello.java` rather than be parameterized, " -"so we can use hardcoded values `hello.tar` and `Hello.java` in a " -"`baseCommand` and the resulting `outputs`:" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -"この場合、ステップではパラメータ化するのではなく、`Hello.java` を想定すること" -"ができるので、`baseCommand` で直接書かれた値`hello.tar` と`Hello.java` を使用" -"でき、結果として`outputs` が得られます：" +"この場合、ステップではパラメータ化するのではなく、`Hello.java` を想定することができるので、`baseCommand` " +"で直接書かれた値`hello.tar` と`Hello.java` を使用でき、結果として`outputs` が得られます：" -#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +#: ../../src/topics/workflows.md:383 a8ccb9f9ab4448e087ea8448d620d33c #, fuzzy msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This is " -"generally not best practice, as the tool then can't be reused. The reason " -"for doing it in this case is because the command line is hard-coded with " -"filenames that only make sense within this workflow." +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." msgstr "" -"`tar --create` ツールを別のファイルに分割せず、CWL Workflow 定義の中に埋め込" -"んだことにお気づきでしょうか。これは一般的にベストプラクティスではありませ" -"ん。なぜなら、そのツールを再利用できないからです。このケースでそれを行う理由" -"は、コマンドラインに、このワークフロー定義内でしか意味をなさないファイル名が" -"ハードコーディングされているためです。" +"`tar --create` ツールを別のファイルに分割せず、CWL Workflow " +"定義の中に埋め込んだことにお気づきでしょうか。これは一般的にベストプラクティスではありません。なぜなら、そのツールを再利用できないからです。このケースでそれを行う理由は、コマンドラインに、このワークフロー定義内でしか意味をなさないファイル名がハードコーディングされているためです。" -#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +#: ../../src/topics/workflows.md:389 afe43b9e92e949a589f493293eff2903 #, fuzzy msgid "" -"In this example we had to prepare a tar file outside, but only because our " -"inner workflow was designed to take that as an input. A better refactoring " -"of the inner workflow would be to take a list of Java files to compile, " -"which would simplify its usage as a tool step in other workflows." -msgstr "" -"この例では、外部にtarファイルを用意する必要がありましたが、これは内部のワーク" -"フローがそれを入力として受け取るように設計されているためです。内部ワークフ" -"ローのリファクタリングとしては、コンパイルするJavaファイルのリストを受け取る" -"ようにすれば、他のワークフローにおけるツールステップとしての使い方が簡単にな" -"ります。" +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." +msgstr "この例では、外部にtarファイルを用意する必要がありましたが、これは内部のワークフローがそれを入力として受け取るように設計されているためです。内部ワークフローのリファクタリングとしては、コンパイルするJavaファイルのリストを受け取るようにすれば、他のワークフローにおけるツールステップとしての使い方が簡単になります。" -#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +#: ../../src/topics/workflows.md:394 239eef3a740d42a69208a8f4e716d2b3 #, fuzzy msgid "" "Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL " -"Tool description, care must be taken to improve its usability in multiple " -"workflows." -msgstr "" -"ネストされたワークフローは、より高機能で再利用可能なワークフローユニットを生" -"成する強力な機能ですが、CWLツール定義の作成と同様に、複数のワークフローでの使" -"い勝手を向上させるための配慮が必要です。" +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." +msgstr "ネストされたワークフローは、より高機能で再利用可能なワークフローユニットを生成する強力な機能ですが、CWLツール定義の作成と同様に、複数のワークフローでの使い勝手を向上させるための配慮が必要です。" -#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +#: ../../src/topics/workflows.md:398 96d1ca78cc324f40b61c4b7330447db2 #, fuzzy msgid "Scattering Steps" msgstr "Scatter ステップ" -#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +#: ../../src/topics/workflows.md:400 eab4437bf9994b649954221375e3dd6d msgid "" "Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " -"run a tool or workflow multiple times over a list of inputs. The workflow " -"then takes the input(s) as an array and will run the specified step(s) on " -"each element of the array as if it were a single input. This allows you to " -"run the same workflow on multiple inputs without having to generate many " -"different commands or input yaml files." +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +#: ../../src/topics/workflows.md:411 c245ba0ae2074fa388ad6c35695033c8 msgid "" -"The most common reason a new user might want to use scatter is to perform " -"the same analysis on different samples. Let's start with a simple workflow " -"that calls our first example (`hello_world.cwl`) and takes an array of " -"strings as input to the workflow:" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" msgstr "" -"新規ユーザーがscatterを使いたいと思う最も一般的な理由は、異なるサンプルに対し" -"て同じ分析を実行することです。最初の例（`hello_world.cwl` ）を呼び出し、ワー" -"クフローへの入力として文字列の配列を受け取る、簡単なワークフローから始めま" -"しょう：" +"新規ユーザーがscatterを使いたいと思う最も一般的な理由は、異なるサンプルに対して同じ分析を実行することです。最初の例（`hello_world.cwl`" +" ）を呼び出し、ワークフローへの入力として文字列の配列を受け取る、簡単なワークフローから始めましょう：" -#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: ../../src/topics/workflows.md:415 83537938ce1244709f9b72269b048d63 msgid "`scatter-workflow.cwl`" msgstr "`scatter-workflow.cwl`" -#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +#: ../../src/topics/workflows.md:421 4f507925766e48ae8f713d56051a5e29 msgid "" -"Aside from the `requirements` section including `ScatterFeatureRequirement`, " -"what is going on here?" -msgstr "" -"`requirements` セクションの`ScatterFeatureRequirement` などを含めて、ここはど" -"うなっているのでしょうか？" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" +msgstr "`requirements` セクションの`ScatterFeatureRequirement` などを含めて、ここはどうなっているのでしょうか？" -#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +#: ../../src/topics/workflows.md:429 ccbbba3189404241a44736c970249b84 #, fuzzy msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." -msgstr "" -"まず、ここでのメインワークフローの入力には、文字列の配列が必要であることに注" -"目してください。" +msgstr "まず、ここでのメインワークフローの入力には、文字列の配列が必要であることに注目してください。" -#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +#: ../../src/topics/workflows.md:441 31eff13bb8334fc7b6d48ef6c5b1ce33 #, fuzzy msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This field " -"tells the runner that we'd like to scatter over this input for this " -"particular step. Note that the input name listed after scatter is the one of " -"the step's input, not a workflow level input." +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." msgstr "" -"ここでは、ステップ`echo` に、`scatter` という新しいフィールドを追加しました。" -"このフィールドは、CWLランナーに、この特定のステップのためにこの入力を分散した" -"いことを伝えます。scatterの後に記載されている入力名は、ワークフローレベルの入" -"力名ではなく、ステップの入力名であることに注意してください。" +"ここでは、ステップ`echo` に、`scatter` " +"という新しいフィールドを追加しました。このフィールドは、CWLランナーに、この特定のステップのためにこの入力を分散したいことを伝えます。scatterの後に記載されている入力名は、ワークフローレベルの入力名ではなく、ステップの入力名であることに注意してください。" -#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +#: ../../src/topics/workflows.md:445 0d5cf8b82dbd47f2abd1ed16b9b3eb61 #, fuzzy msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if you " -"expect that the final output of your workflow will now have multiple outputs " -"to collect, be sure to update that to an array type as well!" +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" msgstr "" -"最初のスキャッターでは、これと同じくらい簡単です！このツールは出力を回収しな" -"いので、`outputs: []` を使います。しかし、ワークフローの最終出力に収集する複" -"数の出力があることが予想される場合、それを配列型に更新するようにしてくださ" -"い！" +"最初のスキャッターでは、これと同じくらい簡単です！このツールは出力を回収しないので、`outputs: []` " +"を使います。しかし、ワークフローの最終出力に収集する複数の出力があることが予想される場合、それを配列型に更新するようにしてください！" -#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: ../../src/topics/workflows.md:450 38b7042a270043ba82c11cf2e758f0c8 msgid "Using the following input file:" msgstr "以下の入力ファイルを使用します：" -#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +#: ../../src/topics/workflows.md:452 b3fc75c262fe4a3a8e8bfba1abb07b3d msgid "`scatter-job.yml`" msgstr "`scatter-job.yml`" -#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +#: ../../src/topics/workflows.md:458 f9fa7046c89c417db51dc7c8a026fd5d #, fuzzy msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " -"calls the command `echo` on a message. If we invoke `cwltool scatter-" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -"注意点として、[`hello_world.cwl`](../introduction/quick-start.md) は単にメッ" -"セージに対して`echo` というコマンドを呼び出します。コマンドラインで `cwltool " -"scatter-workflow.cwl scatter-job.yml` を呼び出すとします：" +"注意点として、[`hello_world.cwl`](../introduction/quick-start.md) " +"は単にメッセージに対して`echo` というコマンドを呼び出します。コマンドラインで `cwltool scatter-workflow.cwl " +"scatter-job.yml` を呼び出すとします：" -#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +#: ../../src/topics/workflows.md:466 b6a33410ee9a45d7bf7b2ba56f786f8f msgid "" -"You can see that the workflow calls echo multiple times on each element of " -"our `message_array`. Ok, so how about if we want to scatter over two steps " -"in a workflow?" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" msgstr "" -"ワークフローは、`message_array` の各要素毎に、echo を呼び出していることがわか" -"ります。では、ワークフローの2つのステップに分散させたい場合はどうでしょうか？" +"ワークフローは、`message_array` の各要素毎に、echo " +"を呼び出していることがわかります。では、ワークフローの2つのステップに分散させたい場合はどうでしょうか？" -#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +#: ../../src/topics/workflows.md:469 99b5c8a845ab4beb8524a69c051e2d42 msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding the " -"following lines instead of `outputs: []`" -msgstr "" -"上記のような簡単なエコーを実行します、`outputs: []`の代わりに次の行を追加して" -"`stdout` をキャプチャしてみましょう" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" +msgstr "上記のような簡単なエコーを実行します、`outputs: []`の代わりに次の行を追加して`stdout` をキャプチャしてみましょう" -#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +#: ../../src/topics/workflows.md:472 97bf58937d3f4e98af702e3c1a418992 #, fuzzy msgid "`hello_world_to_stdout.cwl`" msgstr "`hello_world_to_stdout.cwl`" -#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +#: ../../src/topics/workflows.md:480 173bd28708834f11a2a1366b579b7ad7 msgid "" -"And add a second step that uses `wc` to count the characters in each file. " -"See the tool below:" -msgstr "" -"そして、`wc` を使って各ファイルの文字数をカウントする第2ステップを追加しま" -"す。以下のツールを見てください：" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" +msgstr "そして、`wc` を使って各ファイルの文字数をカウントする第2ステップを追加します。以下のツールを見てください：" -#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +#: ../../src/topics/workflows.md:483 4afccfe982ff4be2be96cbe5889e5014 #, fuzzy msgid "`wc-tool.cwl`" msgstr "`wc-tool.cwl`" -#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +#: ../../src/topics/workflows.md:489 63595d35dded4911aab0be3a165eec0c #, fuzzy msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under each " -"step:" -msgstr "" -"さて、スキャッターはどのように取り入れるのでしょうか？スキャッターフィールド" -"は各ステップの下にあることを思い出してください：" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" +msgstr "さて、スキャッターはどのように取り入れるのでしょうか？スキャッターフィールドは各ステップの下にあることを思い出してください：" -#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +#: ../../src/topics/workflows.md:491 a7f96ec6e4f24c62ac0f5b6edcc9734b #, fuzzy msgid "`scatter-two-steps.cwl`" msgstr "`scatter-two-steps.cwl`" -#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +#: ../../src/topics/workflows.md:497 122452b7d7114c3fa53cbea286703023 msgid "" -"Here we have placed the scatter field under each step. This is fine for this " -"example since it runs quickly, but if you're running many samples for a more " -"complex workflow, you may wish to consider an alternative. Here we are " -"running scatter on each step independently, but since the second step is not " -"dependent on the first step completing all languages, we aren't using the " -"scatter functionality efficiently. The second step expects an array as input " -"from the first step, so it will wait until everything in step one is " -"finished before doing anything. Pretend that `echo Hello World!` takes 1 " -"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " -"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " -"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " -"actually finish in 8 minutes because the first step must wait on `echo Hallo " -"welt!`. You can see how this might not scale well." +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +#: ../../src/topics/workflows.md:509 85dd63daf04546b78bdcb68c1d985fa9 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can " -"make an entire workflow a single step in another workflow! Convert our two-" -"step workflow to a single step subworkflow:" +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" msgstr "" -"では、他のサンプルと独立して進行できるステップを分散させるにはどうすればいい" -"のでしょうか？[Nested Workflows](#nested-workflows)で、ワークフロー全体を別の" -"ワークフローの1ステップにすることができることを思い出しましょう！2ステップの" -"ワークフローを1ステップのサブワークフローに変換してみましょう：" +"では、他のサンプルと独立して進行できるステップを分散させるにはどうすればいいのでしょうか？[Nested Workflows](#nested-" +"workflows)で、ワークフロー全体を別のワークフローの1ステップにすることができることを思い出しましょう！2ステップのワークフローを1ステップのサブワークフローに変換してみましょう：" -#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +#: ../../src/topics/workflows.md:513 fac138ba275745898b763a7d719a8235 #, fuzzy msgid "`scatter-nested-workflow.cwl`" msgstr "`scatter-nested-workflow.cwl`" -#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +#: ../../src/topics/workflows.md:519 508ef2240879445594b0f262ed11a01d #, fuzzy msgid "" -"Now the scatter acts on a single step, but that step consists of two steps " -"so each step is performed in parallel." -msgstr "" -"今、scatter は1つのステップに作用しますが、そのステップは2つのステップで構成" -"されているので、各ステップは並行して実行されます。" +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." +msgstr "今、scatter は1つのステップに作用しますが、そのステップは2つのステップで構成されているので、各ステップは並行して実行されます。" -#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +#: ../../src/topics/workflows.md:522 b0bf01dad1234a1db3c87b10953e42ef #, fuzzy msgid "Conditional Workflows" msgstr "条件分岐ワークフロー" -#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +#: ../../src/topics/workflows.md:524 8d933ed1ec6e408589f781e3a425b869 #, fuzzy msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." -msgstr "" -"このワークフローは、条件付きステップを含み、入力に基づき実行されます。これに" -"より、ワークフローは、プログラムの開始時に与えられた入力パラメータや以前のス" -"テップによって、追加のステップをスキップすることができます。" +msgstr "このワークフローは、条件付きステップを含み、入力に基づき実行されます。これにより、ワークフローは、プログラムの開始時に与えられた入力パラメータや以前のステップによって、追加のステップをスキップすることができます。" -#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +#: ../../src/topics/workflows.md:527 9ac7b4f71621411da9a4ca3bc277dcb0 msgid "`conditional-workflow.cwl`" msgstr "`conditional-workflow.cwl`" -#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +#: ../../src/topics/workflows.md:566 4a4a2b2b99b44d449adb246cebce0a26 #, fuzzy msgid "" -"The first thing you'll notice is that this workflow is only compatible for " -"version 1.2 or greater of the CWL standards." -msgstr "" -"まず、このワークフローはCWL仕様のバージョン1.2以降でしか対応していないことが" -"わかります。" +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." +msgstr "まず、このワークフローはCWL仕様のバージョン1.2以降でしか対応していないことがわかります。" -#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +#: ../../src/topics/workflows.md:573 4742fe09a4264fb8be6f092519de5d72 #, fuzzy msgid "" "The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when` is " -"where the condition validation takes place. In this case only when `in1` " -"from the workflow contains a value `< 1` this step will be executed." +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." msgstr "" -"ワークフローの最初のステップ（step1）には2つの入力プロパティがあり、条件を満" -"たしたときにfoo.cwlを実行します。新しいプロパティ`when` は、条件の検証が行わ" -"れる場所です。この場合、ワークフローから`in1` に値`< 1` が含まれるときの" -"み、このステップが実行されます。" +"ワークフローの最初のステップ（step1）には2つの入力プロパティがあり、条件を満たしたときにfoo.cwlを実行します。新しいプロパティ`when`" +" は、条件の検証が行われる場所です。この場合、ワークフローから`in1` に値`< 1` が含まれるときのみ、このステップが実行されます。" -#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +#: ../../src/topics/workflows.md:587 b33ecd2b8af042feb08687e32d4b6bbf #, fuzzy msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " -"will pass the first conditional step and will therefore be executed and is " -"shown in the log by `INFO [step step1] start` whereas the second step is " -"skipped as indicated by `INFO [step step2] will be skipped`." +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -"次のコマンドを実行します。`cwltool cond-wf-003.1.cwl --val 0` この値は最初の" -"条件ステップを通過するため実行され、ログには`INFO [step step1] start` で示さ" -"れています。一方、2番目のステップは`INFO [step step2] will be skipped` で示さ" -"れているようにスキップされ ます。" +"次のコマンドを実行します。`cwltool cond-wf-003.1.cwl --val 0` " +"この値は最初の条件ステップを通過するため実行され、ログには`INFO [step step1] start` " +"で示されています。一方、2番目のステップは`INFO [step step2] will be skipped` で示されているようにスキップされ" +" ます。" -#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +#: ../../src/topics/workflows.md:607 7cd80b31a94543358ece7a2d413adce9 #, fuzzy msgid "" -"When a value of 3 is given the first conditional step will not be executed " -"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -"値3が与えられた場合、最初の条件ステップは実行されませんが、2番目の条件ステッ" -"プは実行されます`cwltool cond-wf-003.1.cwl --val 3`." +"値3が与えられた場合、最初の条件ステップは実行されませんが、2番目の条件ステップは実行されます`cwltool cond-wf-003.1.cwl" +" --val 3`." -#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +#: ../../src/topics/workflows.md:627 9679e32f65e0482a8b083387e4a18c1f #, fuzzy msgid "" -"If no conditions are met for example when using `--val 2` the workflow will " -"raise a permanentFail." -msgstr "" -"`--val 2` を使用した場合など、条件を満たさない場合は、ワークフローは" -"permanentFailを発生させ、失敗となります。" +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." +msgstr "`--val 2` を使用した場合など、条件を満たさない場合は、ワークフローはpermanentFailを発生させ、失敗となります。" -#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +#: ../../src/topics/yaml-guide.md:1 4fa76441f95d45fab76ab7eef8d7d4d2 msgid "YAML Guide" msgstr "YAMLガイド" -#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +#: ../../src/topics/yaml-guide.md:6 705765787eb84ecaae004194225924cb #, fuzzy msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers and " -"humans. This guide introduces the features of YAML that are relevant when " -"writing CWL descriptions and input parameter files." -msgstr "" -"[YAML][yaml]は、コンピュータと人間の両方が読むことができるように設計された" -"ファイル形式です。本ガイドでは、CWL定義や入力パラメータファイルを書く際に関連" -"するYAMLの機能を紹介します。" +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." +msgstr "[YAML][yaml]は、コンピュータと人間の両方が読むことができるように設計されたファイル形式です。本ガイドでは、CWL定義や入力パラメータファイルを書く際に関連するYAMLの機能を紹介します。" -#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +#: ../../src/topics/yaml-guide.md:13 cb243f6ab11f48ffb5c91945c4e0d101 msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" -"すでにYAMLに慣れている方は、このセクションを読み飛ばしてもかまいません。" +msgstr "すでにYAMLに慣れている方は、このセクションを読み飛ばしてもかまいません。" -#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +#: ../../src/topics/yaml-guide.md:16 cfc95d15e33a492f842649f92ced941d msgid "Contents" msgstr "目次" -#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +#: ../../src/topics/yaml-guide.md:18 f618d44d202f4c2ea6ff72a1dca2c659 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "[キーバリューペア](#key-value-pairs)" -#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +#: ../../src/topics/yaml-guide.md:19 36bfa6ed40c54bd99826bedff12c759d msgid "[Comments](#comments)" msgstr "[コメント](#comments)" -#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +#: ../../src/topics/yaml-guide.md:20 61913753eb0c4c728889b47f1110be24 msgid "[Maps](#maps)" msgstr "[マップ](#maps)" -#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: ../../src/topics/yaml-guide.md:21 0de824a05eea46209aafa6f9e2e8623c msgid "[Arrays](#arrays)" msgstr "[配列](#arrays)" -#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: ../../src/topics/yaml-guide.md:22 95627bc476b3415ca4d77246125137d2 msgid "[JSON Style](#json-style)" msgstr "[JSON 形式](#json-style)" -#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +#: ../../src/topics/yaml-guide.md:24 3f64a6d33d9a4c22a8a839a8def82686 msgid "Key-Value Pairs" msgstr "キーバリューペア" -#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +#: ../../src/topics/yaml-guide.md:26 2f74f6eaa8d84dc9b4d0a166844dedbe msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " -"is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have special " -"meaning in the CWL specification and underscored key names otherwise. For " -"example:" +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" msgstr "" -"基本的に、YAML で書かれたファイルは_キーと値のペア_ のセットで構成されていま" -"す。各ペアは`key: value` として記述され、`:` の後に空白が必要です。CWLファイ" -"ルのキー名には、空白を含めるべきではありません。[_camelCase_][camelCase] は、" -"CWL仕様で特別な意味を持つ複数語のキー名、それ以外はアンダースコアのキー名とし" -"て使用します。例えば：" +"基本的に、YAML で書かれたファイルは_キーと値のペア_ のセットで構成されています。各ペアは`key: value` として記述され、`:` " +"の後に空白が必要です。CWLファイルのキー名には、空白を含めるべきではありません。[_camelCase_][camelCase] " +"は、CWL仕様で特別な意味を持つ複数語のキー名、それ以外はアンダースコアのキー名として使用します。例えば：" -#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b +#: ../../src/topics/yaml-guide.md:42 514365e59d9648deb896e2068d967a64 #, fuzzy msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " -"and `home` - with their four respective values. Values can be character " -"strings, numeric (integer, floating point, or scientific representation), " -"Boolean (`true` or `false`), or more complex nested types (see below)." +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." msgstr "" -"上記のYAMLは4つのキー -`first_name`,`last_name`,`age_years`, `home` - と4つの" -"それぞれの値を定義しています。値は、文字列、数値（整数、浮動小数点、科学的表" -"現）、ブール値（`true` または`false` ）、またはより複雑な入れ子型（下記参照）" -"にすることができます。" +"上記のYAMLは4つのキー -`first_name`,`last_name`,`age_years`, `home` - " +"と4つのそれぞれの値を定義しています。値は、文字列、数値（整数、浮動小数点、科学的表現）、ブール値（`true` または`false` " +"）、またはより複雑な入れ子型（下記参照）にすることができます。" -#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 +#: ../../src/topics/yaml-guide.md:51 6939eb7e783744d7bcf75ea0a7cae129 #, fuzzy msgid "" -"Values may be wrapped in quotation marks, but be aware that this may change " -"the way that they are interpreted i.e. `\"1234\"` will be treated as a " -"character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a " -"command: in CWL all parts of `baseCommand` must be strings so, if you want " -"to specify a fixed numeric value to a command, make sure that you wrap that " -"numeric value in quotes: `baseCommand: [echo, \"42\"]`." +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -"値は引用符で括ることができますが、意味が変わってきます。例えば、`\"1234\"` は" -"文字列として扱われ、`1234` は整数値として扱われます。CWLでは、`baseCommand` " -"のすべての部分が文字列でなければならないので、コマンドに固定した数値を指定す" -"る場合は、その数値を引用符で囲むようにしてください：[echo, \"42\"]`." +"値は引用符で括ることができますが、意味が変わってきます。例えば、`\"1234\"` は文字列として扱われ、`1234` " +"は整数値として扱われます。CWLでは、`baseCommand` " +"のすべての部分が文字列でなければならないので、コマンドに固定した数値を指定する場合は、その数値を引用符で囲むようにしてください：[echo, " +"\"42\"]`." -#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: ../../src/topics/yaml-guide.md:61 96e1776b09e840ebbc9b4b7e01da0e43 msgid "Comments" msgstr "コメント" -#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +#: ../../src/topics/yaml-guide.md:63 8b17f7557c3540b2b0d0beca0fe4ebc7 #, fuzzy msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program interpreting " -"the YAML. For example:" +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" msgstr "" -"`#` を使って、CWL定義と入力パラメータファイルにコメントを追加することができま" -"す。` #` の右側にある文字は、YAML を解釈するプログラムによって無視されます。" -"たとえば、次のようになります：" +"`#` を使って、CWL定義と入力パラメータファイルにコメントを追加することができます。` #` の右側にある文字は、YAML " +"を解釈するプログラムによって無視されます。たとえば、次のようになります：" -#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +#: ../../src/topics/yaml-guide.md:76 13da997c82c04023a4b7bb36b76e969d #, fuzzy msgid "" -"If there is anything on the line before the comment, be sure to add at least " -"one space before the `#`!" -msgstr "" -"同じ行内のコメントの前に何かある場合は、必ず`#` の前に少なくとも1つのスペース" -"を追加してください！" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" +msgstr "同じ行内のコメントの前に何かある場合は、必ず`#` の前に少なくとも1つのスペースを追加してください！" -#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +#: ../../src/topics/yaml-guide.md:79 b9fc191166a64450b64a8182adabad75 #, fuzzy msgid "Maps" msgstr "マップ" -#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +#: ../../src/topics/yaml-guide.md:81 aedf8c4f615845ad91a7947217005d6e msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, these " -"hierarchical structures are described in YAML by providing additional key-" -"value pairs as the value of any key. These pairs (sometimes referred to as " -"\"children\") are written on new lines under the key to which they belong " -"(the \"parent\"), and should be indented with two spaces (⇥tab characters " -"are not allowed). For example:" +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +#: ../../src/topics/yaml-guide.md:104 f0f1f414f74342a89065ba5ded8668e5 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " -"while one of these children, `inputBinding`, contains a further two key-" -"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " -"below for more information about providing multiple values/key-value pairs " -"for a single key. For comparison with the example YAML above, here is a " -"graphical representation of the `inputs` object it describes." +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +#: ../../src/topics/yaml-guide.md:127 965405e2a45a4cbb8f227bc8ceeb05df #, fuzzy msgid "Arrays" msgstr "配列" -#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +#: ../../src/topics/yaml-guide.md:129 5aca9a90fb6149529ed717992746a2f3 msgid "" "In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) section " -"above, more than one key-value pair can be mapped to a single key. However, " -"it is also possible to define multiple values for a key without having to " -"provide a unique key for each value. We can achieve this with an _array_, " -"where each value is defined on its own line and preceded by `-`. For example:" +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +#: ../../src/topics/yaml-guide.md:146 d1c9e72e004b4fb4a6efb7748a15ab6f #, fuzzy msgid "and a more complex example combining maps and arrays:" msgstr "と、マップと配列を組み合わせたより複雑な例です：" -#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +#: ../../src/topics/yaml-guide.md:167 9a3d6879404745a48cd394bf86865dbc msgid "JSON Style" msgstr "JSON形式" -#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +#: ../../src/topics/yaml-guide.md:169 6a7cca0339794e679329b00d89e29d2b msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " -"can also be defined in YAML using the native JSON syntax. For example:" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" msgstr "" -"YAMLは[JavaScript Object Notation (JSON)][json]に基づいています。マップと配列" -"は、JSON構文を使ってYAMLで定義することもできます。例えば:" +"YAMLは[JavaScript Object Notation " +"(JSON)][json]に基づいています。マップと配列は、JSON構文を使ってYAMLで定義することもできます。例えば:" -#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +#: ../../src/topics/yaml-guide.md:177 d8feed2d36d04fe283b9de9784d91941 #, fuzzy msgid "and:" msgstr "と：" -#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +#: ../../src/topics/yaml-guide.md:184 5156ad32791048f8ace51475d7689575 #, fuzzy msgid "" -"Native JSON can be useful in indicating where a field is intentionally left " -"empty (such as `[]` for an empty array), as well as where it makes more " -"sense for the values to be located on the same line (For example, when " -"providing option flags and their values in a shell command). However, as the " -"second example above shows, it can severely affect the readability of a YAML " -"file, and should be used sparingly." +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." msgstr "" -"ネイティブ JSON は、フィールドが意図的に空のままになっている場所 (空の配列を" -"表す`[]` など) や、値が同じ行にあることがより理にかなっている場所 (たとえば、" -"シェルコマンドでオプションフラグとその値を提供する場合) を示すのに便利なこと" -"があります。しかし、上の2番目の例が示すように、YAMLファイルの可読性に深刻な影" -"響を与える可能性があるので、控えめに使用する必要があります。" +"ネイティブ JSON は、フィールドが意図的に空のままになっている場所 (空の配列を表す`[]` など) " +"や、値が同じ行にあることがより理にかなっている場所 (たとえば、シェルコマンドでオプションフラグとその値を提供する場合) " +"を示すのに便利なことがあります。しかし、上の2番目の例が示すように、YAMLファイルの可読性に深刻な影響を与える可能性があるので、控えめに使用する必要があります。" -#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +#: ../../src/topics/yaml-guide.md:194 ce49f80e6fc0498b8ad298fb1f0268f3 msgid "Reference" msgstr "リファレンス" -#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +#: ../../src/topics/yaml-guide.md:196 180d261392a644fcb8ff47d7a4a160c0 #, fuzzy msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " -"while we wrote this guide, though it also covers features that are not valid " -"in CWL." +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." msgstr "" -"[Learn YAML in Y Minutes][yaml-y-mins] リファレンスは、CWLでは有効でない機能" -"もカバーしていますが、このガイドを書く間、私たちにとって非常に役に立ちまし" -"た。" +"[Learn YAML in Y Minutes][yaml-y-mins] " +"リファレンスは、CWLでは有効でない機能もカバーしていますが、このガイドを書く間、私たちにとって非常に役に立ちました。" -#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +#: ../../src/tutorials.md:1 d682035afebf4c128755bd4e58780dd2 msgid "Tutorials" msgstr "チュートリアル" -#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +#: ../../src/tutorials.md:5 d9adeab63ec54084bc41fb90f264d3ae msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to the " -"list." +"this page` link in the menu if you would like to add another tutorial to " +"the list." msgstr "" -"これは、CWL コミュニティによって提供されたチュートリアルのリストです。リスト" -"に他のチュートリアルを追加したい場合は、メニューの`Edit this page` リンクを使" -"用してください。" +"これは、CWL コミュニティによって提供されたチュートリアルのリストです。リストに他のチュートリアルを追加したい場合は、メニューの`Edit " +"this page` リンクを使用してください。" -#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +#: ../../src/tutorials.md:7 23c81edb650b4f86a60c5e0bcedeac1d msgid "Beginner Tutorials" msgstr "初心者向けチュートリアル" -#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +#: ../../src/tutorials.md:9 87ddaa1e5f57445c8f13803722aa146e msgid "" -"[Introduction to Workflows with Common Workflow Language: For Contributors.]" -"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" msgstr "" -"[Common Workflow Languageによるワークフロー入門：コントリビューターのために]" -"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +"[Common Workflow Languageによるワークフロー入門：コントリビューターのために](https://carpentries-" +"incubator.github.io/cwl-novice-tutorial/)" -#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +#: ../../src/tutorials.md:11 b8ee193ba533498db6263e0f5f4ec45f msgid "Advanced Tutorials" msgstr "上級者向けチュートリアル" -#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +#: ../../src/tutorials.md:13 67c4b3923fce46fdab025495125c91d4 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "[CWLでのTypeScript](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +#: ../../src/tutorials.md:15 e640316669104239970794191b6da38b msgid "Bioinformatics Tutorials" msgstr "バイオインフォマティクス・チュートリアル" -#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +#: ../../src/tutorials.md:17 efe94af44b874f9b81b245fbdee43f7f msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "[CWLでrnaseq](https://arvados.github.io/rnaseq-cwl-training/)" + +#~ msgid "In CWL, everything must be directly stated." +#~ msgstr "CWLでは、すべてを直接的に記述する必要があります。。" + +#~ msgid "Optional Inputs 💯" +#~ msgstr "オプション入力 💯" + +#~ msgid "Enum Inputs ⚜️" +#~ msgstr "列挙型入力 ⚜️" + +#~ msgid "Record Inputs 📀" +#~ msgstr "レコード入力 📀" + +#~ msgid "Debug JavaScript Expressions" +#~ msgstr "JavaScriptの式をデバッグする" + +#~ msgid "" +#~ "The FAIR principles have laid a " +#~ "foundation for sharing and publishing " +#~ "digital assets, and in particular, data." +#~ " The FAIR principles emphasize machine " +#~ "accessibility and that all digital " +#~ "assets should be Findable, Accessible, " +#~ "Interoperable, and Reusable. Workflows encode" +#~ " the methods by which the scientific" +#~ " process is conducted and via which" +#~ " data are created. It is thus " +#~ "important that workflows support the " +#~ "creation of FAIR data and adhere " +#~ "to the FAIR principles. — [FAIR " +#~ "Computational " +#~ "Workflows](https://workflows.community/groups/fair/), Workflows" +#~ " Community Initiative." +#~ msgstr "" + +#~ msgid "" +#~ "If you are using Windows, you will" +#~ " have to install the [Windows " +#~ "Subsystem for Linux 2](https://learn.microsoft.com" +#~ "/en-us/windows/wsl/install) (WSL2). Visit the " +#~ "`cwltool` [documentation](https://github.com/common-" +#~ "workflow-language/cwltool/blob/main/README.rst#ms-windows-" +#~ "users) for details on installing WSL2." +#~ " Your operating system also needs " +#~ "internet access and a recent version " +#~ "of Python (3.6+)." +#~ msgstr "" + +#~ msgid "" +#~ "`cwltool` can be installed with `pip`." +#~ " We recommend using a virtual " +#~ "environment like `venv` or `conda`. The" +#~ " following commands will create and " +#~ "activate a Python virtual environment " +#~ "using the `venv` module, and install " +#~ "`cwltool` in that environment:" +#~ msgstr "" +#~ "`cwltool` は、`pip` でインストールすることができます。`venv` または`conda`" +#~ " のような仮想環境を使用することをお勧めします。以下のコマンドは、`venv` モジュールを使用して " +#~ "Python 仮想環境を作成およびアクティブ化し、その環境内に`cwltool` をインストールします：" + +#~ msgid "Installing `cwltool` with `pip` and `venv`." +#~ msgstr "`pip` と `venv` での `cwltool` のインストール。" + +#~ msgid "Cwl-runner Python Module" +#~ msgstr "Cwl-runner Pythonモジュール" + +#~ msgid "" +#~ "This indicates whether a process " +#~ "requires outgoing IPv4/IPv6 network access." +#~ " If a command-line tool is " +#~ "written manually in CWL v1.1+, there " +#~ "is a need to specify when network" +#~ " access is required." +#~ msgstr "" +#~ "これは、プロセスが発信IPv4/IPv6ネットワークアクセスを必要とするかどうかを示します。CWL " +#~ "v1.1+でCommandLineToolを手動で記述する場合、ネットワークアクセスが必要なタイミングを指定する必要があります。" + +#~ msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +#~ msgstr "このようなファイルを生成するために、`InitialWorkDirRequirement` を利用することができます。" + +#~ msgid "" +#~ "Note also that the author of this" +#~ " CWL description has also included " +#~ "`ResourceRequirement`s, specifying the minimum " +#~ "amount of RAM and number of cores" +#~ " required for the tool to run " +#~ "successfully, as well as details of " +#~ "the version of the software that " +#~ "the description was written for and " +#~ "other useful metadata. These features " +#~ "are discussed further in other chapters" +#~ " of this user guide." +#~ msgstr "" + +#~ msgid "From `Workflow`" +#~ msgstr "`Workflow`から" + +#~ msgid "" +#~ "The field `inputBinding` is optional and" +#~ " indicates whether and how the input" +#~ " parameter should appear on the " +#~ "tool's command line. If `inputBinding` " +#~ "is missing, the parameter does not " +#~ "appear on the command line. Let's " +#~ "look at each example in detail." +#~ msgstr "" + +#~ msgid "" +#~ "If you try running it with " +#~ "`cwltool`, the command will fail since" +#~ " `cwltool` does not have enough " +#~ "information to know how to execute " +#~ "it:" +#~ msgstr "`cwltool` だけで実行しようとすると、`cwltool` は実行するのに必要な情報がないため、コマンドは失敗します：" + +#~ msgid "" +#~ "Often, tool descriptions will be written" +#~ " for a specific version of a " +#~ "software. To make it easier for " +#~ "others to use your descriptions, you " +#~ "can include a `SoftwareRequirement` field " +#~ "in the `hints` section. This may " +#~ "also help to avoid confusion about " +#~ "which version of a tool the " +#~ "description was written for." +#~ msgstr "" + +#~ msgid "" +#~ "As well as a version number, a " +#~ "unique resource identifier (URI) for the" +#~ " tool is given in the form of" +#~ " an [RRID][rrid]. Resources with RRIDs " +#~ "can be looked up in the " +#~ "[SciCrunch][scicrunch] registry, which provides " +#~ "a portal for finding, tracking, and " +#~ "referring to scientific resources " +#~ "consistently. If you want to specify " +#~ "a tool as a `SoftwareRequirement`, " +#~ "search for the tool on SciCrunch " +#~ "and use the RRID that it has " +#~ "been assigned in the registry. (Follow" +#~ " this [Adding a Resource Tutorial" +#~ "][scicrunch-add-tool] to add a tool" +#~ " to SciCrunch). You can use this " +#~ "RRID to refer to the tool (via " +#~ "[identifiers.org][identifiers]) in the `specs` " +#~ "field of your requirement description. " +#~ "Other good choices, in order of " +#~ "preference, are to include the DOI " +#~ "for the main tool citation and the" +#~ " URL to the tool." +#~ msgstr "" + +#~ msgid "" +#~ "Normally, input files are located in " +#~ "a read-only directory separate from " +#~ "the output directory. This causes " +#~ "problems if the underlying tool expects" +#~ " to write its output files alongside" +#~ " the input file in the same " +#~ "directory. You use `InitialWorkDirRequirement` " +#~ "to stage input files into the " +#~ "output directory. In this example, we" +#~ " use a JavaScript expression to " +#~ "extract the base name of the input" +#~ " file from its leading directory " +#~ "path." +#~ msgstr "" + diff --git a/locales/pt_BR/LC_MESSAGES/user_guide.po b/locales/pt_BR/LC_MESSAGES/user_guide.po index c81087b9..30ebfbda 100644 --- a/locales/pt_BR/LC_MESSAGES/user_guide.po +++ b/locales/pt_BR/LC_MESSAGES/user_guide.po @@ -8,346 +8,369 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-27 16:02+0100\n" +"POT-Creation-Date: 2023-12-16 11:48+0100\n" "PO-Revision-Date: 2023-04-29 16:47+0000\n" "Last-Translator: Michael Crusoe \n" -"Language-Team: Portuguese (Brazil) \n" "Language: pt_BR\n" +"Language-Team: Portuguese (Brazil) " +"\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=2; plural=n > 1;\n" -"X-Generator: Weblate 4.18-dev\n" -"Generated-By: Babel 2.10.3\n" +"Generated-By: Babel 2.12.1\n" -#: ../../LICENSE.md:2 3eb955b4f3dd4c3188924b97ea6ab592 +#: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.md:4 bf4480e7fff4460a87e8f43c11599f07 +#: ../../LICENSE.md:4 9dd9705700664b31a3f296d263b4028b msgid "Instructional Material" msgstr "Material Instrucional" -#: ../../LICENSE.md:6 9e9eab12205d4e82b4fedca520370f4c +#: ../../LICENSE.md:6 e54324bd39cd431d91b32e338217b8c7 msgid "" -"All Common Workflow Language project instructional material and changes to " -"the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable summary " -"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" -"[cc-by-legal]." +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." msgstr "" "Todo o material instrucional do projeto Common Workflow Language e " -"alterações na estrutura também são disponibilizados sob a [licença Creative " -"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " -"humanos de (e não um substituto para) o [texto legal completo da licença CC " -"BY 4.0][cc-by-legal]." +"alterações na estrutura também são disponibilizados sob a [licença " +"Creative Commons Attribution][cc-by-human]. O seguinte é um resumo " +"legível por humanos de (e não um substituto para) o [texto legal completo" +" da licença CC BY 4.0][cc-by-legal]." -#: ../../LICENSE.md:12 a8e98ad541c642e58e201afa625ec791 +#: ../../LICENSE.md:12 754f3f54aa4142ef9dac27f508dd0bca msgid "You are free:" msgstr "Tem o direito de:" -#: ../../LICENSE.md:14 b4cb4bc4261347fcb0d2c8a93995ab76 -msgid "" -"to **Share**---copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 d2b1d5e965ef4e71b64c359549919975 +msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" -"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " -"formato" +"**Compartilhar**---copiar e redistribuir o material em qualquer suporte " +"ou formato" -#: ../../LICENSE.md:15 d66dcbf95ccc41aaa53be523487ec913 +#: ../../LICENSE.md:15 fe9551ffef8149bf8da50e70318e8de8 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" -#: ../../LICENSE.md:17 ca1c299a1b834b868bcdd4ca9f244696 +#: ../../LICENSE.md:17 247db3bcc7024c44a044886a29ef1414 msgid "for any purpose, even commercially." msgstr "para qualquer fim, mesmo que comercial." -#: ../../LICENSE.md:19 6133f79f93be4991a6f5290f72d1a63d +#: ../../LICENSE.md:19 c04d906124854afc917707b7b4e45bb2 msgid "" -"The licensor cannot revoke these freedoms as long as you follow the license " -"terms:" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" msgstr "" "O licenciante não pode revogar estes direitos desde que você respeite os " "termos da licença:" -#: ../../LICENSE.md:24 2d6ce81add1043629b676187f890288c +#: ../../LICENSE.md:24 551cb5ab59dd4737b1042a4ef79ffab7 msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow Language " -"project, and, where practical, linking to https://www.commonwl.org/ ), " -"provide a [link to the license][cc-by-human], and indicate if changes were " -"made. You may do so in any reasonable manner, but not in any way that " -"suggests the licensor endorses you or your use." -msgstr "" -"**Atribuição**---Você deve atribuir o devido crédito (mencionando que o seu " -"trabalho deriva de um trabalho que é «Copyright © The Common Workflow " -"Language project», e, quando prático, criar uma ligação para https://www." -"commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " -"se foram feitas alterações. Você pode fazê-lo de qualquer forma razoável, " -"mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " -"uso." - -#: ../../LICENSE.md:32 f3f22597b6f845208a0cce3b3b2c8f5d +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." +msgstr "" +"**Atribuição**---Você deve atribuir o devido crédito (mencionando que o " +"seu trabalho deriva de um trabalho que é «Copyright © The Common Workflow" +" Language project», e, quando prático, criar uma ligação para " +"https://www.commonwl.org/%20),%20fornecer%20um%20[link%20para%20a%20licen%C3%A7a][cc-by-" +"human], e indicar se foram feitas alterações. Você pode fazê-lo de " +"qualquer forma razoável, mas não de uma forma que sugira que o " +"licenciante o apoia ou aprova o seu uso." + +#: ../../LICENSE.md:32 f6c3b2ccad494ed6811a35537fc1fb0d msgid "" "**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything the " -"license permits. With the understanding that:" +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" msgstr "" -"**Sem restrições adicionais**---Não pode aplicar termos jurídicos ou medidas " -"de caráter tecnológico que restrinjam legalmente outros de fazerem algo que " -"a licença permita. Com o entendimento de que:" +"**Sem restrições adicionais**---Não pode aplicar termos jurídicos ou " +"medidas de caráter tecnológico que restrinjam legalmente outros de " +"fazerem algo que a licença permita. Com o entendimento de que:" -#: ../../LICENSE.md:36 3cfedee64d4e46098a159cb2acdba4ef +#: ../../LICENSE.md:36 91c95248cd7f435c909ee263a9a8bf3f msgid "" -"You do not have to comply with the license for elements of the material in " -"the public domain or where your use is permitted by an applicable exception " -"or limitation." +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." msgstr "" "Não tem de cumprir com os termos da licença relativamente a elementos do " -"material que estejam no domínio público ou cuja utilização seja permitida " -"por uma exceção ou limitação que seja aplicável." +"material que estejam no domínio público ou cuja utilização seja permitida" +" por uma exceção ou limitação que seja aplicável." -#: ../../LICENSE.md:39 c836a570faaf449d9716da5f75556627 +#: ../../LICENSE.md:39 27f79b0b648b4de4b0eb3172b2dc4ae8 msgid "" -"No warranties are given. The license may not give you all of the permissions " -"necessary for your intended use. For example, other rights such as " -"publicity, privacy, or moral rights may limit how you use the material." +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." msgstr "" "Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " "autorizações necessárias para o uso pretendido. Por exemplo, outros " -"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " -"podem limitar o uso do material." +"direitos, tais como direitos de imagem, de privacidade ou direitos " +"morais, podem limitar o uso do material." -#: ../../LICENSE.md:44 896f9966e5014e8a88b060be3063fe09 +#: ../../LICENSE.md:44 1e367d07720d4f9fb7ebc3149052e823 msgid "Software" msgstr "Software" -#: ../../LICENSE.md:46 007f8613dc234c3fa8d5d92b18af0eb1 +#: ../../LICENSE.md:46 cf8b58d02b6943a48cb70aa78a27bea4 msgid "" "Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the " -"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Salvo indicação em contrário, os programas de exemplo e outro software " -"fornecido pelo projecto Common Workflow Language são disponibilizados sob a " -"[licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." +"fornecido pelo projecto Common Workflow Language são disponibilizados sob" +" a [licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." -#: ../../LICENSE.md:51 227bc635a06f49dbb771fd9b62157d00 +#: ../../LICENSE.md:51 96f1e5be3e1e48db8d9a4c7693008715 msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." msgstr "" -"A menos que exigido pela lei aplicável ou acordado por escrito, o software " -"distribuído sob a Licença é distribuído \"COMO ESTÁ\", SEM GARANTIAS OU " -"CONDIÇÕES DE QUALQUER TIPO, expressas ou implícitas. Consulte a Licença para " -"obter o texto específico sobre as permissões e limitações sob a Licença." +"A menos que exigido pela lei aplicável ou acordado por escrito, o " +"software distribuído sob a Licença é distribuído \"COMO ESTÁ\", SEM " +"GARANTIAS OU CONDIÇÕES DE QUALQUER TIPO, expressas ou implícitas. " +"Consulte a Licença para obter o texto específico sobre as permissões e " +"limitações sob a Licença." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 1861131d3df648ae9e74ce1c87f0be7b a2ffa927deb2451d95ec63528e8078dd -#: d6055d3f15604ce6940770c7b561d4c5 +#: 08aa9181d5304e0fa96b28db15718559 d37fc100eb6948bba8b5e757574b2aaf +#: ecdd0f28d5b048d69dd1ffae2fa1f6c0 msgid "" "CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece of " -"software, tools and workflows described using CWL are portable across a " -"variety of platforms that support the CWL standard." +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." msgstr "" -"CWL é uma maneira de descrever ferramentas de linha de comando e de conectá-" -"las formando workflows. Como a CWL é uma especificação e não um software, " -"ferramentas e workflows descritos com a CWL são portáveis entre uma " -"variedade de plataformas que suportam o padrão CWL." +"CWL é uma maneira de descrever ferramentas de linha de comando e de " +"conectá-las formando workflows. Como a CWL é uma especificação e não um " +"software, ferramentas e workflows descritos com a CWL são portáveis entre" +" uma variedade de plataformas que suportam o padrão CWL." #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 38b062f219b34e08a46bd8f6525353ec 89e7e1dd05474344a1d929cb492e9caf +#: 1361ff6bf4924efc9ce9a85785a6b381 eb254514301c491e81f72ae19c407261 msgid "This page has moved" msgstr "Esta página foi movida" -#: ../../src/episodes.md:9 d3357ff3c8874e368aea0d6062ef6190 +#: ../../src/episodes.md:9 f03d7cbe6670451db0896f1b674d56c7 msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. Please use the new [Table of Contents](index.md#table-of-" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -"O conteúdo desta página está desatualizado e foi mantido para preservar os " -"links do antigo Guia do Utilizador. Por favor, use o novo [Índice](index.md" -"#table-of-contents) para navegar o Guia do Utilizador." +"O conteúdo desta página está desatualizado e foi mantido para preservar " +"os links do antigo Guia do Utilizador. Por favor, use o novo " +"[Índice](index.md#table-of-contents) para navegar o Guia do Utilizador." -#: ../../src/faq.md:1 f2c4882e0e164c2b869e3eb969241061 +#: ../../src/faq.md:1 d65ad48ac6314bf0a74c34a6766561fc msgid "FAQ" msgstr "Perguntas Frequentes (FAQ)" -#: ../../src/faq.md:11 41099ab64e0544d894bd9e3af2718bda -msgid "Non \"`File`\" Types Using `evalFrom`" +#: ../../src/faq.md:11 370a9659c7904ef6b5e1ae7480f82ef6 +#, fuzzy +msgid "How do I create non \"`File`\" types using `evalFrom`?" msgstr "Usando `evalFrom` para Tipos Diferentes de \"`File`\"" -#: ../../src/faq.md:41 bb6aff70534148fa8a4b01140f7be150 -msgid "Rename an Input File" +#: ../../src/faq.md:41 8333f51e3f5945fe8963adfc6685bcb1 +#, fuzzy +msgid "How do I rename an input file?" msgstr "Renomear um Arquivo de Entrada" -#: ../../src/faq.md:43 70ebc653b0d54d60a866edc0dbf56b57 +#: ../../src/faq.md:43 f6b88d9154d049d7807afa9bb0f1ac98 msgid "" -"This example demonstrates how to change the name of an input file as part of " -"a tool description. This could be useful when you are taking files produced " -"from another step in a workflow, and don't want to work with the default " -"names that these files were given when they were created." +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." msgstr "" -"Este exemplo demonstra como mudar o nome de um arquivo de entrada como parte " -"da descrição da ferramenta. Isso pode ser útil quando você tem arquivos " -"produzidos em outro passo de um workflow, mas prefere não utilizar os nomes " -"dados por padrão quando estes arquivos foram criados." +"Este exemplo demonstra como mudar o nome de um arquivo de entrada como " +"parte da descrição da ferramenta. Isso pode ser útil quando você tem " +"arquivos produzidos em outro passo de um workflow, mas prefere não " +"utilizar os nomes dados por padrão quando estes arquivos foram criados." -#: ../../src/faq.md:59 38b687f707d2438b85df08a445ab816f -msgid "Rename an Output File" +#: ../../src/faq.md:59 833510f5896b4a6eb5875d25eca5b047 +#, fuzzy +msgid "How do I rename an output file?" msgstr "Renomear um Arquivo de Saída" -#: ../../src/faq.md:61 d48422c020004ef084ca11e6229b5450 +#: ../../src/faq.md:61 207e2f97d1c44233ae3f109c5a6ec944 msgid "" -"This example demonstrates how to change the name of an output file from the " -"default name given to it by a tool:" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" msgstr "" "Este exemplo demonstra como escolher o nome para um arquivo de saída " "diferente do nome padrão criado por uma ferramenta:" -#: ../../src/faq.md:82 48765409ab9d48ccbcecceb46ddf2e91 -msgid "Referencing a Local Script" +#: ../../src/faq.md:83 d66acc583da24273980a52be03e79e91 +msgid "" +"By modifying the `basename` field in the `outputEval` field, CWL workflow" +" engines will rename the file using the new name for subsequent steps or " +"as a workflow-level output." +msgstr "" + +#: ../../src/faq.md:86 8641f105131b4ac1bca7e0a46756ef79 +#, fuzzy +msgid "How do I reference a local script?" msgstr "Como Fazer Referência a um Script Local" -#: ../../src/faq.md:84 a59b8acd72124e2c95d1905ae494d928 +#: ../../src/faq.md:88 d3e43b40d6994b32bc37067ee116418e msgid "There are two ways to reference a local script:" msgstr "Há duas maneiras de fazer uma referência a um script local:" -#: ../../src/faq.md:86 f36088ba90d24f9f9c7c1bd59deb6f49 +#: ../../src/faq.md:90 64b140a321ca4087945339c523cc24dd +#, fuzzy msgid "" -"The first method involves adding the folder containing your scripts to the " -"`PATH` environment variable. This allows you to run the shell script " -"directly without using `sh` or `bash` commands." +"The first method involves adding the path to a folder containing your " +"scripts to the `PATH` environment variable. This allows you to execute " +"the shell script directly (without explicitly using the `sh` or `bash` " +"commands)." msgstr "" -"A primeira maneira é adicionando o arquivo que contém os seus scripts para a " -"variável de ambiente `PATH`. Desta maneira você pode executar o shell script " -"diretamente sem utilizar comandos via `sh` ou `bash`." +"A primeira maneira é adicionando o arquivo que contém os seus scripts " +"para a variável de ambiente `PATH`. Desta maneira você pode executar o " +"shell script diretamente sem utilizar comandos via `sh` ou `bash`." -#: ../../src/faq.md:89 45ee965ee4a7494a8354b82208e2ab45 +#: ../../src/faq.md:93 34ebca4487a54ceab5d087105820e945 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "Comece adicionando a _shebang_ no topo do seu arquivo:" -#: ../../src/faq.md:95 734cc1abe1c841ffac8d0895463d91fc +#: ../../src/faq.md:99 6b04a4dcdada4515b28d74aacff3537a msgid "" -"After that, make the script executable with the command `chmod +x scriptname." -"sh`" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" msgstr "" -"Em seguida faça o seu script executável com o comando `chmod +x scriptname." -"sh`" +"Em seguida faça o seu script executável com o comando `chmod +x " +"scriptname.sh`" -#: ../../src/faq.md:97 f01bc8c4d6134f0ea27dc7f5b39def24 +#: ../../src/faq.md:101 756ab4f7edcf42d3872bb86818e088c3 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -"E finalmente, modifique o seu `PATH` para adicionar o diretório que contém o " -"seu script. (É boa prática usar `$HOME/bin` para scripts do utilizador " -"local)." +"E finalmente, modifique o seu `PATH` para adicionar o diretório que " +"contém o seu script. (É boa prática usar `$HOME/bin` para scripts do " +"utilizador local)." -#: ../../src/faq.md:104 dd6fc2a04e3b476892f05bc5b746d0fa -msgid "" -"Now you can use `baseCommand: scriptname.sh` to run the script directly." +#: ../../src/faq.md:108 efb46b3a2d7c4c51b65998602bfa6f18 +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -"Agora você pode utilizar `baseCommand: scriptname.sh` para rodar o script " -"diretamente." +"Agora você pode utilizar `baseCommand: scriptname.sh` para rodar o script" +" diretamente." -#: ../../src/faq.md:113 e309eaad55144052866ce131eb80fd14 +#: ../../src/faq.md:117 844938d5d2304c6cb03184b4b4b0b024 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -"Depois quando você quiser compartilhar o seu trabalho, é possível utilizar " -"um container de software com ferramentas como Docker." +"Depois quando você quiser compartilhar o seu trabalho, é possível " +"utilizar um container de software com ferramentas como Docker." -#: ../../src/faq.md:115 f0d649a60a13404ebecd540789202b87 +#: ../../src/faq.md:119 796ce8155e32486d9651f8f13bfa3148 msgid "" -"The second method involves including an input of `type: File` in the script " -"itself:" +"The second method involves including an input of `type: File` in the " +"script itself:" msgstr "O segundo método utiliza um input `type: File` diretamente no script:" -#: ../../src/faq.md:135 e2b782f88d494de398af0c9002a3ccdc -msgid "In CWL, everything must be directly stated." -msgstr "Em CWL tudo deve ser declarado diretamente." - -#: ../../src/faq.md:138 b4a033731fcd4322bd2bb71c609a4cb7 -msgid "Setting `self`-based Input Bindings for Optional Inputs" +#: ../../src/faq.md:138 ba246320fdd94a1aab4736f83718d793 +#, fuzzy +msgid "How can I set `self`-based input bindings for optional inputs?" msgstr "Definindo Bindings de Inputs utilizando `self` para Inputs Opcionais" -#: ../../src/faq.md:140 43a64810b12b4c7d82a5803c3b910fe5 +#: ../../src/faq.md:140 6169b7be9af7448abcb57eaf91e1cc91 msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their input " -"binding makes use of `self`. Below is an example workaround for this, " -"pending a more sophisticated fix." +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." msgstr "" "No momento `cwltool` não funciona quando inputs opcionais não estão " "presentes se o binding de input deles utilizar `self`. O exemplo abaixo " -"contém uma solução alternativa para este problema, até que haja uma solução " -"mais elegante para este problema." +"contém uma solução alternativa para este problema, até que haja uma " +"solução mais elegante para este problema." -#: ../../src/faq.md:165 60f009e3714c405695da069204b196ea -msgid "Model a \"one-or-the-other\" Parameter" +#: ../../src/faq.md:165 6c98b7948059411b8e09cf03a552c5ab +#, fuzzy +msgid "How can I model a \"one-or-the-other\" parameter?" msgstr "Modelar um Parâmetro do tipo \"um-ou-o-outro\"" -#: ../../src/faq.md:167 98916ed9355842e49bef073430e10675 +#: ../../src/faq.md:167 d1424da3f43c4519a4c4735f4a720341 msgid "" -"Below is an example showing how to specify different strings to be added to " -"a command line, based on the value given to a Boolean parameter." +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." msgstr "" "O exemplo abaixo demonstra como especificar diferentes strings que serão " -"adicionadas à linha de comando, dependendo do valor de um parâmetro Boolean." +"adicionadas à linha de comando, dependendo do valor de um parâmetro " +"Boolean." -#: ../../src/faq.md:188 9b8f2d0b33db4bbc82aaf5836b6f7ed8 -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +#: ../../src/faq.md:188 5c9980839f404ba6aef92ef23034500f +#, fuzzy +msgid "" +"How do I connect a solo value to an input that expects an array of that " +"type?" msgstr "Conectar um Único valor a um Input que Espera uma Lista daquele Tipo" -#: ../../src/faq.md:190 a251693354d24bf0bda4938c8890090a +#: ../../src/faq.md:190 2525baf16c1f4725b096f33fd99009cf +#, fuzzy msgid "" -"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" -"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +"Add a " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput):" msgstr "" +"De " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" e " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -#: ../../src/faq.md:194 f46740ac0acb473583facb9f7528d03c +#: ../../src/faq.md:194 a00d5d96b15048a79ae099d22d63bb42 msgid "merge_nested" msgstr "merge_nested" -#: ../../src/faq.md:196 7de1f9e3175b4c2ab156192f28fd3535 +#: ../../src/faq.md:196 3a92c6cc5c2b40ffa0d692d03bad5c87 msgid "" -"The input must be an array consisting of exactly one entry for each input " -"link. If \"merge_nested\" is specified with a single link, the value from " -"the link must be wrapped in a single-item list." +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 225c6f08068e41f58eb62f99dc06210f -msgid "Which means \"create a list with exactly these sources as elements\"" +#: ../../src/faq.md:199 3af16c07e3f148ddb8849c94a3864158 +#, fuzzy +msgid "Which means \"create a list with exactly these sources as elements\"." msgstr "" -"Que significa \"criar uma lista com exatamente estes sources como elementos\"" +"Que significa \"criar uma lista com exatamente estes sources como " +"elementos\"" -#: ../../src/faq.md:201 4e741f4e3bc74e10bd9568826e81c478 +#: ../../src/faq.md:201 0ea3de393d2f42aeb82658c85a19ec45 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " -"add `linkMerge: merge_nested` under the appropriate `in` entry of the " -"destination step." +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." msgstr "" "Ou em outras palavras: se o parâmetro destino for do tipo `File[]` (uma " "lista de `File`s) e a fonte é um único `File`, adicione então " -"`MultipleInputFeatureRequirement` ao `requirements` no nível do Workflow e " -"adicione `linkMerge: merge_nested` sob a entrada apropriada `in` ao step que " -"receberá o parâmetro (target)." +"`MultipleInputFeatureRequirement` ao `requirements` no nível do Workflow " +"e adicione `linkMerge: merge_nested` sob a entrada apropriada `in` ao " +"step que receberá o parâmetro (target)." -#: ../../src/faq.md:229 bfdb011cb81c4ef9b9e56b24f1e9ccd5 -msgid "Optional Inputs 💯" -msgstr "Inputs Opcionais 💯" +#: ../../src/faq.md:229 2f1bbb611c9c4f80b7ae0566432f2f35 +msgid "How do make an input optional? 💯" +msgstr "" -#: ../../src/faq.md:231 09f385e325f942afaa3dd195c16a18d2 +#: ../../src/faq.md:231 08a226efe5d141e68215ac77725033db msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." @@ -355,864 +378,895 @@ msgstr "" "Para fazer um parâmetro de entrada opcional, adicione um ponto de " "interrogação à declaração do tipo." -#: ../../src/faq.md:247 c5d087082bb2468483e7ccda3ca45a07 +#: ../../src/faq.md:247 06e70a855a8f455ca0536eead77073c2 msgid "" msgstr "" -#: ../../src/faq.md:248 41e30b0224a0492f9047b4f320f39a23 -msgid "Enum Inputs ⚜️" -msgstr "Inputs Enum ⚜️" +#: ../../src/faq.md:248 7fda8eeb6a7f4689993ed0118c77f023 +msgid "" +"How do I specify an input that must come from a list of predefined values" +" (i.e. How do I use enum inputs) ?" +msgstr "" -#: ../../src/faq.md:250 f06d073014a44f33a60d947a8c5b0e59 +#: ../../src/faq.md:250 b1934a82553b4da3b7f981e576245dd8 msgid "" -"For command line flags that require a specific input as the argument an enum " -"type can be declared in CWL. **Specifying null here is known as long form " -"style. It does the same thing as the question mark on the other inputs.**" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" msgstr "" "O tipo enum por ser utilizado em CWL para flags de linha de comando que " -"requerem um tipo de input específico como argumento. **Especificar null aqui " -"é tido como forma estendida. O resultado é o mesmo que o uso do ponto de " -"interrogação nos outros inputs.**" +"requerem um tipo de input específico como argumento. **Especificar null " +"aqui é tido como forma estendida. O resultado é o mesmo que o uso do " +"ponto de interrogação nos outros inputs.**" -#: ../../src/faq.md:267 2fb74cd1b41e4fdb81a8f9b3b6c84373 +#: ../../src/faq.md:267 17fc34fad2094f5ea60e963dabd632b8 msgid "" msgstr "" -#: ../../src/faq.md:268 09e19f34d0fd4e388d4939cbc2be3436 -msgid "Record Inputs 📀" -msgstr "Inputs do tipo Record" +#: ../../src/faq.md:268 4d7acfbeba5b4e9cb31f08ef4b280447 +msgid "" +"How do I describe dependent or exclusive input parameters(e.g. How do I " +"use record inputs)?" +msgstr "" -#: ../../src/faq.md:270 1ecae448dfcf45a4ae0dd39bd011e449 +#: ../../src/faq.md:270 949ce95c082f4a05891a55fee25d4873 msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 6df3d4e918cc4bccb823859ce07b197a -msgid "Setting Mutually Exclusive Parameters" +#: ../../src/faq.md:322 6fd3c469d11d4d52b9fbb7a3d443a8db +#, fuzzy +msgid "How do I set mutually exclusive parameters?" msgstr "Definindo Parâmetros Mutualmente Exclusivos" -#: ../../src/faq.md:324 086db1a093e64caa88d958150accc19c +#: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f msgid "" -"To properly set fields in a record input type, you need to pass a dictionary " -"to the input to properly set the parameters. This is done by using inline " -"JavaScript and returning the dictionary with the key of the field you want " -"to set. The source field is set to indicate the input from the workflow to " -"be used as the value." +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 da77c818d8694ab99fb2eccf73083047 -msgid "Setting Booleans" +#: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 +#, fuzzy +msgid "How can I set Booleans?" msgstr "Utilizando Booleans" -#: ../../src/faq.md:344 254259509ed6462d8ebc296b5f811f44 +#: ../../src/faq.md:344 8dcb88744e5840029de0e1bbf1c4b967 msgid "These can be set by using the default field" msgstr "Estes são definidos através do campo padrão" -#: ../../src/faq.md:349 f7a44f76579d4709a61d2d61bc352b76 -msgid "Concatenating Strings in Inputs" +#: ../../src/faq.md:349 972b7a5551bb43e6b9fa30e0cb713ff7 +#, fuzzy +msgid "What should I do when concatenating strings in inputs?" msgstr "Concatenando Strings em Inputs" -#: ../../src/faq.md:351 d67278e99c684f488f1e3418e1c8c207 +#: ../../src/faq.md:351 68f74afc21d846dd9070d45dec0cc1d8 msgid "The valueFrom field must be used instead of default." msgstr "O campo valueFrom deve ser utilizado ao invés do valor padrão." -#: ../../src/faq.md:359 f5e35ee06cd24edf831589ebaa6193d2 -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +#: ../../src/faq.md:359 53b633c6f8644106beb95ae567eb0708 +#, fuzzy +msgid "" +"I get `cwltool` errors due to filenames with space characters inside. " +"What should I do?" msgstr "Erros do `cwltool` devido a Nomes de Arquivos com Espaços" -#: ../../src/faq.md:361 2ffb67e547c446499625a8db9a102da6 +#: ../../src/faq.md:361 7101bb5cb69e4faca4e60eabb4eb258e msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "" -"O `cwltool` não permite alguns caracteres em nomes de arquivos por padrão." +msgstr "O `cwltool` não permite alguns caracteres em nomes de arquivos por padrão." -#: ../../src/faq.md:363 ee653ff9fefe4771b35e2e76199b536a +#: ../../src/faq.md:363 0eaf834b0ca847cca6736794895f5f81 msgid "" -"For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "" -"Por exemplo, o nome de arquivo `um espaco vai aqui.txt` inclui 3 espaços.." +"For example, the filename `a space is here.txt` includes 3 space " +"characters." +msgstr "Por exemplo, o nome de arquivo `um espaco vai aqui.txt` inclui 3 espaços.." -#: ../../src/faq.md:371 02b1eb159e934fd692929f7c30319ddd +#: ../../src/faq.md:371 7dabd8aab7a5423b842433616640bac0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -"Se você não tem opção e precisa utilizar estes caracteres apesar do risco, " -"você deve então passar `--relax-path-verificks` ao chamar o `cwltool`." +"Se você não tem opção e precisa utilizar estes caracteres apesar do " +"risco, você deve então passar `--relax-path-verificks` ao chamar o " +"`cwltool`." -#: ../../src/faq.md:373 857024702f624885be706c405b7a088e -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +#: ../../src/faq.md:373 b7ec33f38ce74ceb890f4379e4c41054 +#, fuzzy +msgid "" +"What should I do when I get CWL Parameter Reference error due to hyphen " +"in an input identifier?" msgstr "" "Erro de Referência em Parâmetro CWL devido a Hífen no Identificador de " "Entrada" -#: ../../src/faq.md:375 d664e30899bd463bb48d38adec318dd4 +#: ../../src/faq.md:375 e39b65947b294b20a444f18d780246f4 msgid "If `cwltool --validate` returns valid" msgstr "Se `cwltool --validate` valida com sucesso" -#: ../../src/faq.md:384 9f3957bbe205454e8bffc4b5caac5970 +#: ../../src/faq.md:384 dcd42c65681b438bb541fb38ddebb536 msgid "But executing it causes an error like:" msgstr "Mas ao executar o workflow um erro como o seguinte aparece:" -#: ../../src/faq.md:396 6ec3bbc6a1ca4e23b47f025f0732e609 +#: ../../src/faq.md:396 2b96665acac449758b852bbe7600e007 msgid "The file is here" msgstr "Este é o arquivo" -#: ../../src/faq.md:410 3e727d79e65e4c6cb157550e80261c53 +#: ../../src/faq.md:410 f59751d2f0014e59af7879a748062cec msgid "Problem caused by `-` (hyphen character)." msgstr "O problema é causado pelo `-` (hífen)." -#: ../../src/faq.md:423 6e0705f4ab4b4e9093794cb4fccb6be9 -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +#: ../../src/faq.md:423 7780f461ca4c478b92fca893c0b0894a +#, fuzzy +msgid "To fix this error, change `-` (hyphen) to `_` (underscore):" msgstr "Para corrigir este erro, substitua o `-` (hífen) por `_` (sublinhado)" -#: ../../src/faq.md:436 0047d039317349679fb6a66d18ec8487 +#: ../../src/faq.md:436 88df56dfff854fc68fb6ad3835a846e4 msgid "" -"If it is not possible to change the input identifier, then you can use an " -"alternative CWL Parameter Reference syntax:" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" msgstr "" "Se não for possível mudar o identificador do input, você pode reescrever " "utilizando uma sintaxe alternativa para Referências de Parâmetros CWL:" -#: ../../src/faq.md:442 8c39608ad0494bee9a4a422cbeb34387 -msgid "Use CWL and cwltool with Singularity" +#: ../../src/faq.md:442 fc407a9e8d8c4b699d9cd14b369343b5 +#, fuzzy +msgid "How do I use CWL and cwltool with Singularity?" msgstr "Utilizar CWL e cwltool com Singularity" -#: ../../src/faq.md:445 7dac53bca8c14a3f9af75cb162cba4f9 +#: ../../src/faq.md:445 239f5f81cef042b08fb8015c36b3ecad msgid "" -"The CWL standards are built around (optional) Docker format containers. The " -"reference runner and several other CWL implementations support running those " -"Docker format containers using the Singularity engine. Directly specifying a " -"Singularity format container is not part of the CWL standards." +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." msgstr "" -#: ../../src/faq.md:450 ffcc38ff98324d71bfeb8d66d4901da7 -msgid "Debug JavaScript Expressions" -msgstr "Depurar Expressões JavaScript" +#: ../../src/faq.md:450 61641314d82b43e982e54c64c73232c5 +msgid "How do I debug the JavaScript in my CWL tool?" +msgstr "" -#: ../../src/faq.md:452 0d7bf2cefe4a4e22b186bdf4d0ed793d +#: ../../src/faq.md:452 5556d3c323664edea55cfb777f4efb3b msgid "" -"You can use the --js-console option of cwltool, or " -"you can try creating a JavaScript or TypeScript project for your code, and " -"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" -"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 1506b4e7ee014a01bfdb067489501a9e +#: ../../src/index.md:1 1c9fb72b83c9467a9672943fb47ffe32 msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 0ce058b5210d46a0b78eb78dbca07a9f +#: ../../src/index.md:3 aaa44578e27345e682ab44686b4da159 msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 3404c064950d453d8af446e8b6554cb6 +#: ../../src/index.md:7 0adfc2adb0c74372b25d197dd3a73b8b msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 1e239cad669648e48694eaf91284766a +#: ../../src/index.md:9 96c8dca812f1415db7c5c006b0c0e022 msgid "" -"If you find that something is missing from this guide, or if you would like " -"to provide other feedback, file an Issue on the [project repository for this " -"guide][repo]. You can also suggest changes directly in a Pull Request by " -"clicking the \"Edit this page\" button at the right sidebar of each page." +"If you find that something is missing from this guide, or if you would " +"like to provide other feedback, file an Issue on the [project repository " +"for this guide][repo]. You can also suggest changes directly in a Pull " +"Request by clicking the \"Edit this page\" button at the right sidebar of" +" each page." msgstr "" -#: ../../src/index.md:16 9dba2e06f1be4a50b1fabaaf216d02b4 +#: ../../src/index.md:16 35c50bb5c3a345b4a4ae66b2df065376 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 ba4074bbb69e4096a808001afaf2e0dc +#: ../../src/index.md:18 9431edcf4e344fb89b6a251e627279d2 msgid "" -"If you are a beginner user get started with the [Introduction](/introduction/" -"index.md) section. For advanced users the subsections of the [Topics](/" -"topics/index.md) have detailed information about the most common topics for " -"CWL." +"If you are a beginner user get started with the " +"[Introduction](/introduction/index.md) section. For advanced users the " +"subsections of the [Topics](/topics/index.md) have detailed information " +"about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 ad34a37bf4ec488bb825a34456f4fe8d +#: ../../src/index.md:23 61cf57e61a9f46e5a1bff6368c5ad5e3 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " -"subsections. The right sidebar contains links to the sections of each page, " -"and the Search form is on the left sidebar." +"subsections. The right sidebar contains links to the sections of each " +"page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 2bd8eb5957ed40f4a72a6b7408044c78 +#: ../../src/index.md:28 94381840d8a848c4a02fa97bfe83566d msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 8bb0df5531474301a185f1ba375320df +#: ../../src/introduction/basic-concepts.md:1 c1271d88e203454688a22e61ee88f02a msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 653373e1f11e4f81ad561378854a71fc +#: ../../src/introduction/basic-concepts.md:3 dd462818cc9a4205b38866d0c5137ece msgid "" "This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are expected " -"to be familiar with workflow managers, YAML, and comfortable with following " -"instructions for the command-line. The other sections of the user guide " -"cover the same concepts, but in more detail. If you are already familiar " -"with CWL or you are looking for more advanced content, you may want to skip " -"this section." +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 7766227bf91b48b2b9752b625e5a9084 +#: ../../src/introduction/basic-concepts.md:10 7a56d394fb244431aefce7ebbb834ecf msgid "The CWL Specification" msgstr "A Especificação CWL" -#: ../../src/introduction/basic-concepts.md:21 032d414ac29740aa9041d89d0ebf70e6 +#: ../../src/introduction/basic-concepts.md:21 35800ed2c56d489190d3702d9ad20fd7 msgid "" "The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered in " -"this user guide is the {{ cwl_version }}." +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 74e92eb0a4e64098b5aaf08d043e0641 +#: ../../src/introduction/basic-concepts.md:25 3ab6dd6b2f694afeb08f3984a74f3efb msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" "incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes that " -"are backward-compatible. The last number is used for bug fixes, like typos " -"and other corrections to the specification." +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 baa40b445f3c409b9a3e10a85fa38bfd +#: ../../src/introduction/basic-concepts.md:33 72ae1fb763a34c41b1b06adcbe1522c3 msgid "" -"The model used for the specification version is called Semantic Versioning. " -"See the end of this section to [learn more](#learn-more) about it." +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 648e94a9d368450dbdac706445254c9f +#: ../../src/introduction/basic-concepts.md:37 5aa7d3ee6cb048d888f1e1f49d0e08be msgid "Implementations" msgstr "Implementações" -#: ../../src/introduction/basic-concepts.md:39 e9ae15124dcd408395fc67e16b50696a +#: ../../src/introduction/basic-concepts.md:39 c87e6daefda74579a39924777b2e6809 msgid "" -"An implementation of the CWL specification is any software written following " -"what is defined in a version of the specification document. However, " -"implementations may not implement every aspect of the specification. CWL " -"implementations are licensed under both Open Source and commercial licenses." +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 b1c864d6775048cab01eb3de641f6475 +#: ../../src/introduction/basic-concepts.md:44 c995e699ae2949219af252f9d802a43d msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud " -"and high performance computing environments where tasks are scheduled in " -"parallel across many nodes." +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 a05d24121e534d65947eb26e4dada5b7 +#: ../../src/introduction/basic-concepts.md:51 09171f48a3d841b2acb6d803b2340c8e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: ace0388fd04845e79d31ec99a48a8a3f +#: 1c1647a3496c4251a3193f94ee4e78c8 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 70ecd37237e14ae19539f2bf692882ed +#: 854633336f4d4fc394e62c53ce022c6b msgid "" -"A process is a computing unit that takes inputs and produces outputs. The " -"behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification " -"{{ cwl_version }}:" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 38121b4b00324bebb6499184b3dcb5c1 +#: 142a847f11d7462f8bf77bfe789410ca msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: e0c278f52e824673ac708885d985b7d2 +#: 7c7567fa690043f9b4b89bdf8ca60cad msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: 6b4d0f0651cc46f5abf195b281967913 +#: 7afcf087d3ea49dabf1a641a2bb71b35 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 88bdc9e046e4487cb0eee3f1d4819e57 +#: 6399939602334819a20b92b957352a8a msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 12eed3ef7d444585b150bbdab0665bc8 +#: 8c55b15cebf142899045f229ccc86b1e msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: dfc85226313d46f9868dc4de53546a69 +#: ec54c0e67e894bfba2d0fbb0f87ffdf4 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: f636b10c47734e589291de95443d8115 +#: c88ad26efa794cbeb6f0690aa0cad5ea msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be used " -"to simplify workflows and command-line tools, moving common parts of a " -"workflow execution into reusable JavaScript code that takes inputs and " -"produces outputs like a command-line tool." +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: bb51025d04444dd5b16000d5d6a3f41a +#: 946825a7ea2c450eb3e41b5548670fb7 msgid "" -"Operation is an abstract process that also takes inputs, produces outputs, " -"and can be used in a workflow. But it is a special operation not so commonly " -"used. It is discussed in the [Operations section](../topics/operations.md) " -"of this user guide." +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 93dbaa0aa2c6493ab22a937c6861fac4 +#: 44aac23f302c4178accf7e431cfbb96c msgid "" -"The workflow is a process that contains steps. Steps can be other workflows " -"(nested workflows), command-line tools, or expression tools. The inputs of a " -"workflow can be passed to any of its steps, while the outputs produced by " -"its steps can be used in the final output of the workflow." +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: fcde5ef65ebf45a3b4b67eec993a1729 +#: 5afdb7aaf0bf4c1abf4c22cdbdd58be9 msgid "" "The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through *requirements*. " -"There are many requirements defined in the CWL specification, for instance:" +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: c8ff34ff5d3b4a508e8c291196d08067 -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +#: 07c5789c59224ed78a3ecd03cfe872e9 +msgid "" +"[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement)" +" - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: fe25f15fc11c49ab827b884d081c3df0 -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +#: 6f9854ae1b884ad39f88d2f39d66cb98 +msgid "" +"[`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow.html#SubworkflowFeatureRequirement)" +" - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 2b93b6219142431ca748a404a56ced5d +#: 23fef6de073f4da18118e4d0512670fe msgid "" -"`InitialWorkDirRequirement` - controls staging files in the input directory." +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow.html#InitialWorkDirRequirement)" +" - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 0094b13b26014ba3be61769b422802f5 +#: fb3762f91177401ea624d1e716d67ae6 msgid "" -"Some CWL runners may provide requirements that are not in the specification. " -"For example, GPU requirements are supported in `cwltool` through the " -"`cwltool:CUDARequirement` requirement, but it is not part of the " -"{{ cwl_version }} specification and may not be supported by other CWL " -"runners." +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: 576a0778d3dd44f68cb241346f441660 +#: b6a5cd431c324078a9a4e1513a14ee28 msgid "" -"Hints are similar to requirements, but while requirements list features that " -"are required, hints list optional features. Requirements are explained in " -"detail in the [Requirements](../topics/requirements-and-hints.md) section." +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 7d98949fe97744158fad81f41d780de9 +#: 88d7bad84dd341d2abb33673b8b8f250 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: fc142b791aa1434aa75b0782248de988 +#: bcbf5d76cf5f47b2a9691b7d2d8ef891 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " "machine accessibility and that all digital assets should be Findable, " "Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created. It " -"is thus important that workflows support the creation of FAIR data and " -"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" -"workflows.community/groups/fair/), Workflows Community Initiative." +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows both support the creation of FAIR " +"data and themselves adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: c3fc91ae3bae4e3db60e8271e95135a2 +#: 4ea1d3bf04dc42f0bc6735a45b9e0dc0 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\", " -"CWL tasks are isolated, and you must be explicit about your inputs and " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " "outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 8f097ae5ff6a4be0b7428345362dc55e +#: c0f53138bf084939a54b0a576b44199f msgid "" -"The benefit of explicitness and isolation are flexibility, portability, and " -"scalability; tools and workflows described with CWL can transparently " -"leverage technologies such as Docker and be used with CWL implementations " -"from different vendors." +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 60c56fa6a67346d6966f0d841213e11b +#: 91d6eb4984a6410ba99616b6617ba9af msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 7377b155e8694798994bbc911a3f3152 -#: 7699685836064bd89db530a9c1918865 7d187a209ebd4e3ba6c6aeb05743041a +#: ../../src/introduction/prerequisites.md:183 +#: ../../src/introduction/quick-start.md:94 0d7e607b00b9485aa2e3c5fb0a931bc6 +#: 161697ed3e864155bb89d8be794fc139 b4a7563eabf547c3bf7eab2567a27b51 msgid "Learn More" msgstr "Saiba Mais" #: ../../src/introduction/basic-concepts.md:180 -#: 3fcbf810c86f4cf7b8499de88147aa95 +#: 7221a89559944627b4c3db37f468f72c msgid "Semantic Versioning - " msgstr "Versionamento Semântico - " #: ../../src/introduction/basic-concepts.md:181 -#: e242228b6b3d440cbca8418050220267 +#: bccf086fc9514f76b60dc161e3a09da3 msgid "" -"The CWL Specification page in the CWL website: " +"The CWL Specification page in the CWL website: " +"" msgstr "" -"A página web da Especificação CWL: " +"A página web da Especificação CWL: " +"" #: ../../src/introduction/basic-concepts.md:182 -#: 6e01963a01cb49e39692455256679bfc +#: a5b37924c7d04ab984ff2542847afc4a msgid "" -"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +"The Command Line Tool Description Standard: " +"<[https://www.commonwl.org/v1.2/CommandLineTool.html](https://w3id.org/cwl/CommandLineTool.html)>" msgstr "" -"A especificação CWL atual no GitHub: {{ ''.format(cwl_version_text) }}" #: ../../src/introduction/basic-concepts.md:183 -#: ed81ea2234b041c79449dcd20f886cb6 +#: 44af015fa36644b99f07338d241d29c1 msgid "" -"The list of Implementations in the CWL website: " +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" -"A lista de Implementações na página web da CWL: " +"A especificação CWL atual no GitHub: {{ ''.format(cwl_version_text) }}" #: ../../src/introduction/basic-concepts.md:184 -#: e8e3996f6a894b4f9cc266b46cb8d756 +#: bffca993172048a4b7ab7c62637662e2 +msgid "" +"The list of Implementations in the CWL website: " +"" +msgstr "" +"A lista de Implementações na página web da CWL: " +"" + +#: ../../src/introduction/basic-concepts.md:185 +#: 84c61946406347c8b138772909110d54 msgid "PROV-O: The PROV Ontology - " msgstr "PROV-O: A Ontologia PROV - " -#: ../../src/introduction/basic-concepts.md:185 -#: 085e4d1a7a9744d2884f3003c64ca174 +#: ../../src/introduction/basic-concepts.md:186 +#: eb0b6a62e06143eabc7b92acff9643ea msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 dcd96950854f47a6ad4169320c1dab34 +#: ../../src/introduction/index.md:1 48532f7701c54166859098e521a43db0 msgid "Introduction" msgstr "Introdução" -#: ../../src/introduction/index.md:3 c4d17eec31874bf1ae9b49d73537d86c +#: ../../src/introduction/index.md:3 08db628a949b4513b824ee334e70a7df msgid "" "This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that " -"are useful to know before reading the rest of the user guide." +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 98a8bdfc7c91436d9cb46abbb7c19c57 +#: ../../src/introduction/prerequisites.md:1 d3f5749a76c14fdf8052f5f683d11b9e msgid "Prerequisites" msgstr "Pré-requisitos" -#: ../../src/introduction/prerequisites.md:6 244a716e267540c782e627adaea3a413 +#: ../../src/introduction/prerequisites.md:6 ab9e21b3e99641d096ba70012b4eb035 msgid "" -"The software and configurations listed in this section are prerequisites for " -"following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements focuses " -"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " -"runner or workflow system, but the results and interface may look different " -"(though the exact workflow outputs should be identical)." +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 2cdf453d2c8b4e2ea50555ef0b7364e5 +#: ../../src/introduction/prerequisites.md:12 8ed426ebcb744839915e7c414d69b1e9 msgid "CWL Implementations" msgstr "Implementações da CWL" -#: ../../src/introduction/prerequisites.md:14 53643a4f190c412d9552d1908f408318 +#: ../../src/introduction/prerequisites.md:14 ff74d48407464c4b9d451fa419137144 msgid "" -"There are many implementations of the CWL standards. Some are complete CWL " -"runners, while others could be plug-ins or extensions to workflow engines. " -"We have a better explanation in the [Implementations](basic-concepts." -"md#implementations) section." +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 1df6c63de3914af68f758054fe6955f4 +#: ../../src/introduction/prerequisites.md:19 eb98aa9c71d746a69e9610996ffc5b47 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 ceaa3a6bebab45a0907ee0cad01429a2 +#: ../../src/introduction/prerequisites.md:21 209a0018e7da48f09b27dc507ba14d24 msgid "" -"We recommend using an up-to-date operating system. You can choose any of the " -"following options for your operating system:" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 1506ac904c6345c5806704a0ccf235aa +#: ../../src/introduction/prerequisites.md:24 8baf869537ea478791356320280df928 msgid "Linux" msgstr "Linux" -#: ../../src/introduction/prerequisites.md:25 a616213ed24e427bb91ee33cb21ec131 +#: ../../src/introduction/prerequisites.md:25 248e9760ce60442eb10ab7247d6af23b msgid "macOS" msgstr "macOS" -#: ../../src/introduction/prerequisites.md:26 a4e9ae38103843739f13c62befd21f3e +#: ../../src/introduction/prerequisites.md:26 d89306bbadf44b6bba8959f1f68cc2f0 msgid "Windows" msgstr "Windows" -#: ../../src/introduction/prerequisites.md:29 2cd231aac42c4a69a925cea369999a8b +#: ../../src/introduction/prerequisites.md:29 aeeb990abbbd42cca122c342054be29c msgid "" -"If you are using Windows, you will have to install the [Windows Subsystem " -"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " -"installing WSL2. Your operating system also needs internet access and a " -"recent version of Python (3.6+)." +"If you are using Windows, you will have to install the Windows Subsystem " +"for Linux 2 as documented in the [`cwltool` documentation for Microsoft " +"Windows users](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users). Your operating " +"system also needs internet access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 051d7cd7d3a94baa865d180afdd71688 +#: ../../src/introduction/prerequisites.md:34 21d1f29fb15745c480194eae6acdd031 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 1a93aaf5bd5e4862b15e0636b4478640 +#: ../../src/introduction/prerequisites.md:39 89f0bf6ff8544a6d87114085be8e0bb6 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL community. " -"It is also the CWL reference runner, which means it must support everything " -"in the current CWL specification, {{ cwl_version }}." +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 edd0613118a2493c876652bdcb9e0fbf +#: ../../src/introduction/prerequisites.md:44 068f09d4d66547448693f7b9dadef497 msgid "" -"`cwltool` can be installed with `pip`. We recommend using a virtual " -"environment like `venv` or `conda`. The following commands will create and " -"activate a Python virtual environment using the `venv` module, and install " -"`cwltool` in that environment:" +"`cwltool` can be installed with `pip`, `apt`, or `conda`. We recommend " +"using a virtual environment like `venv` or `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:51 3448d215c2434866b8a4b340872ba81e -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "Instalando `cwltool` com `pip` e `venv`." - -#: ../../src/introduction/prerequisites.md:62 4c24d05f65794735b816024c78b63f1c +#: ../../src/introduction/prerequisites.md:48 1edf8b8438334ae29dc406dbfd711228 +#, fuzzy msgid "" -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool#install) for other ways to install `cwltool` with `apt` and " -"`conda`." +"Visit the `cwltool` " +"[documentation](https://cwltool.readthedocs.io/en/latest/#install) for " +"details on installing `cwltool`." msgstr "" -"Visite a [documentação](https://github.com/common-workflow-language/" -"cwltool#install) do `cwltool` para outras opções para instalar `cwltool` com " -"`apt` e `conda`." +"Visite a [documentação](https://github.com/common-workflow-" +"language/cwltool#install) do `cwltool` para outras opções para instalar " +"`cwltool` com `apt` e `conda`." -#: ../../src/introduction/prerequisites.md:65 3167f4a2a8394feda1f848334be62022 +#: ../../src/introduction/prerequisites.md:52 5e300141ce43435f9437507374987213 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -"Vamos usar uma simples descrição de ferramenta CWL `true.cwl` com `cwltool`." +"Vamos usar uma simples descrição de ferramenta CWL `true.cwl` com " +"`cwltool`." -#: ../../src/introduction/prerequisites.md:67 3c4b67d62c9c4d658ccaafcd1977ec08 +#: ../../src/introduction/prerequisites.md:54 282ac7ba2a2346feac2456bcda0f214a msgid "`true.cwl`" msgstr "`true.cwl`" -#: ../../src/introduction/prerequisites.md:73 30792f78348942e0acdde411342e8830 +#: ../../src/introduction/prerequisites.md:60 0b36f94f479a4bce9bd9be9983894421 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the CWL " -"standards. However, these actions will be performed without running the " -"document. To validate CWL workflows (or even a standalone command line tool " -"description like the above) pass the `--validate` option to the `cwltool` " -"command:" +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 4473e41281fb4e738e4eb26c2d178934 +#: ../../src/introduction/prerequisites.md:66 5fce122794e34892b430ca4bdba5ba50 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 548393974d4d4acc91738f9bc13a3a48 -msgid "" -"You can run the CWL tool description by omitting the `--validate` option:" +#: ../../src/introduction/prerequisites.md:71 73f074f47d1449dcb40ff960a84851fd +msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 2ab3963cf9504ec097eda2b14f3448c4 +#: ../../src/introduction/prerequisites.md:73 2dd5a67870ca41b48e17c468ba15888b msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 690882dcc29c48acbeb215a8be52eb9e -msgid "Cwl-runner Python Module" -msgstr "Módulo Python cwl-runner" +#: ../../src/introduction/prerequisites.md:78 d2dc809318be49cc996d892e93ad84ac +msgid "Generic ``cwl-runner`` alias" +msgstr "" -#: ../../src/introduction/prerequisites.md:93 6c3ba51b1e9a4add9203d62cec6ebae9 +#: ../../src/introduction/prerequisites.md:80 9809c2e262924ef286b0bd62e0b00995 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be invoked " -"independently, and is not reliant on a particular CWL runner program name. " -"Users can invoke `cwl-runner` instead of invoking a CWL runner like " -"`cwltool` directly. The `cwl-runner` is installed by a system administrator " -"or user to point to the preferred CWL implementation. This is convenient for " -"environments with multiple CWL runners." +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 b2360ef646854422ad6c0f90fa49306f +#: ../../src/introduction/prerequisites.md:88 6dd6aa836099469381fb564d63b84f3d msgid "" -"The CWL community publishes a Python package with the name `cwlref-runner` " -"that installs an alias for `cwltool` under the name `cwl-runner`" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:104 c9fadfa85a2641378e99a462e8e8d940 +#: ../../src/introduction/prerequisites.md:91 cc1a9b95508e44a1bf08ae75d990c301 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 abb8993ede4d4e479d88d2e848546f68 +#: ../../src/introduction/prerequisites.md:98 8f8c80f705d94d4899b250bbf9c54562 msgid "" -"Now you can validate and run your workflow with the `cwl-runner` executable, " -"which will invoke `cwltool`. You should have the same results and output as " -"in the previous section." +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 ba0f7606e6174e53a8bf23c1ccd99250 +#: ../../src/introduction/prerequisites.md:102 176e4214d18149f3ba0bda692bcf760f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 dd2e10f43e8f498cb01de5faa4fccb70 +#: ../../src/introduction/prerequisites.md:107 4890bf20bc3842d3a7421b555bcda94a msgid "Running `true.cwl` with `cwl-runner`." msgstr "Executando `true.cwl` com `cwl-runner`." -#: ../../src/introduction/prerequisites.md:125 e500e9c71c7042169c25b31f21a09142 +#: ../../src/introduction/prerequisites.md:112 2475a83cf6ed4389bb680fa37e8fe69c msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For " -"that, the first thing you need to do is copy `true.cwl` workflow into a new " -"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 d989516c873f4446bba005f42796b8b9 +#: ../../src/introduction/prerequisites.md:116 24da787aa76c4480838a93ba0533898d msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 e9d8610478094a98b5b5a0f568a315de -msgid "" -"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +#: ../../src/introduction/prerequisites.md:122 4f3cb8d1f9ce4e3d852e81aa4e0f60be +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 d6d8131f91b740189e56ab9d90bee55a +#: ../../src/introduction/prerequisites.md:124 27693d62faa045d9b03143d9bd2afcdf msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 def7400a00e84070a4bd80c2367d3bde +#: ../../src/introduction/prerequisites.md:131 703531514abe4fd48015c472005dbffa msgid "" -"And finally, you can execute it directly in the command-line. On execution, " -"the program specified in the shebang (`cwl-runner`) will be used to execute " -"the rest of the file." +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 564e7be94d254e52a6c44b234d6ddc63 +#: ../../src/introduction/prerequisites.md:135 abba2e14c4e54252bb75983274663a7a msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 bb5fe42ddd814ad4ac1071c0b18f24c2 +#: ../../src/introduction/prerequisites.md:141 11fea992c00940d29eb29ccf4b9370e9 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute the " -"script using the executable specified after the shebang. It is considered a " -"good practice to use `/usr/bin/env ` rather than using a hard-" -"coded location, since `/usr/bin/env ` looks for the " -"`` program in the system `PATH`," +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env [executable]` rather than" +" using a hard-coded location, since `/usr/bin/env [executable]` looks for" +" the `[executable]` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 53bb712a68cd49fca4db11e9e507c9a4 +#: ../../src/introduction/prerequisites.md:148 854736eef2ac4b63b187a4cea9660ae4 msgid "Text Editor" msgstr "Editor de Texto" -#: ../../src/introduction/prerequisites.md:163 bdcf61cce5294e45a9f964628a8a66bd +#: ../../src/introduction/prerequisites.md:150 480fbb7a743046068c114fff5b396a9f msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 28d33daee6e246c8a6d1382208e19c39 +#: ../../src/introduction/prerequisites.md:154 28da3eea8fd245d1936013d021c25164 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting " -"and better auto-complete:" +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 b071d7c87b7a4817b871085a652cd580 +#: ../../src/introduction/prerequisites.md:158 73c08e11e90d4c7f952307a1cdaa360b msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " +"Visual Studio Code with the Benten (CWL) plugin - " +"" msgstr "" -#: ../../src/introduction/prerequisites.md:172 97658a1b16874ba8b0bb748242d0da64 +#: ../../src/introduction/prerequisites.md:159 a5b788252a924338963f0ed198fc22ca msgid "" -"cwl-plugin for IntelliJ - " +"cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 6198aa6769b74ef0a2a1ba539789f3ee +#: ../../src/introduction/prerequisites.md:161 ee705b919acd461a8d9622821da246b6 msgid "" -"The CWL community also maintains a list of editors and viewers: " +"The CWL community also maintains a list of editors and viewers: " +"" msgstr "" -#: ../../src/introduction/prerequisites.md:177 0c17235a374e40099be37b9b8ac8f1f0 +#: ../../src/introduction/prerequisites.md:164 7724b63db3cc45139379898d047c0f83 msgid "Docker" msgstr "Docker" -#: ../../src/introduction/prerequisites.md:181 e3690e656b5a4348845c654689935a88 +#: ../../src/introduction/prerequisites.md:168 eff13997c1ce43d1ad2d7a4d927394fe msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: ." +"documentation to install it for your operating system: " +"." msgstr "" -#: ../../src/introduction/prerequisites.md:185 2db34e925a81422986ccb868463a7a42 +#: ../../src/introduction/prerequisites.md:172 2872503638624b7e904ae407375ac165 msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models with " -"and without containers." +"examples, and to clarify the differences between the execution models " +"with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 d677fb155b0343ba8771398cca967fed +#: ../../src/introduction/prerequisites.md:178 52ddcc9bc1554d809371fc0a503c40bc msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for pulling " -"images." +"Singularity. You can also use alternative container registries for " +"pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 22ed0b55de38408393af4a8309a995ea +#: ../../src/introduction/prerequisites.md:185 f3bbfa17f31a459386461951de157dd2 msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the next " -"section, Basic Concepts." +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 5ded73cae5db40ad840c3022e7cd447f +#: ../../src/introduction/prerequisites.md:186 e22b9e7c56104e018e6d2f3d547c01ea msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 23e5613df7c94e5f938c85b14f5441e4 +#: ../../src/introduction/quick-start.md:1 9ca367e3ca754a0fa88dab64724b95b6 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 3b425afc63d841d4be57c92b25b4ed2d +#: ../../src/introduction/quick-start.md:3 733db5702c774f32b8c91d13f74f3720 msgid "" -"This section will show you a brief overview of what CWL is, and where you " -"can learn more about it. No previous knowledge of CWL is required, but you " -"must be comfortable following instructions for the command-line." +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 75a26c48d3e04e24abb96d81cb31c94e +#: ../../src/introduction/quick-start.md:7 0b164074dd0849c3b2c8d2f78ea99e95 msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 88b4ecd45ea44dd4befe3ce89b30f6c2 +#: ../../src/introduction/quick-start.md:12 6485f96f638548fbb7addc57f6cde92b msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " -"example below shows a simple CWL “Hello World” workflow annotated with " -"comments. Note that comments start with `#`:" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 e1789ef78bd64332a18d8601094a0f72 +#: ../../src/introduction/quick-start.md:16 5e06f9c4754347b8bac88d24c21e0f67 msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 196ceef96c27434eb4b0b7222c2fe73c +#: ../../src/introduction/quick-start.md:22 6a13fb9112ab41acb60dc65b3656f63e msgid "" "The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the " -"same result as the command-line `echo \"Hello World\"`." +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 e6a44130c6b44d5bb6451a147f28dd8c +#: ../../src/introduction/quick-start.md:27 7b2ae93353184faea0ae4f4acdfc3350 msgid "" -"In CWL, there is a distinction between a command-line tool and a workflow. " -"But for the sake of simplicity, we are using the term “workflow” here. You " -"will learn more about this in the [basic concepts](basic-concepts.md) " -"section." +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 340b46acc7a34b7b978f5a734f529553 +#: ../../src/introduction/quick-start.md:32 1ed30b04073d47a9893774746479fb5d msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 139e48dcf0474fea932ca07a0001d208 +#: ../../src/introduction/quick-start.md:34 73a42cd9e0e54296985088b7221a8a93 msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the CWL " -"*Reference Runner* for the specification, and it is compliant with the " -"latest version of the specification: {{ cwl_version }}. You can install " -"`cwltool` using `pip`:" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 d6f6e061c0f4434eb6d70f9d84759042 +#: ../../src/introduction/quick-start.md:39 57aea587ade24610be62f5d993b0b755 msgid "Installing `cwltool` with `pip`." msgstr "Instalando `cwltool` com `pip`." -#: ../../src/introduction/quick-start.md:47 cb2b548489df45ee9d49b36116440eea +#: ../../src/introduction/quick-start.md:47 51183fc986014edbb026a53f222e6c2e msgid "" -"If installing the cwltool using the pip command doesn't work for you, the " -"[prerequisites](prerequisites.md) section contains other ways to install " -"`cwltool` and a more detailed list of software and libraries used for " +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 aa751bda67ec44ba988642b061e2a094 +#: ../../src/introduction/quick-start.md:51 a7582c3ae37a462a8ae1e72b3f321534 msgid "Running \"Hello World\"" msgstr "Executando \"Hello World\"" -#: ../../src/introduction/quick-start.md:53 a7e0209af0544b0ab31012864a43886c +#: ../../src/introduction/quick-start.md:53 0595e96912dc40e5a09f2ced2d2b7bcd msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " -"workflow without specifying any option:" +"[OPTIONS] [CWL_DOCUMENT] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 d0f424f0041c4635a0559fa32a76c86f +#: ../../src/introduction/quick-start.md:57 5b393c69816549b084516dda4d4274f5 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "Executando `hello_world.cwl` com `cwltool`." -#: ../../src/introduction/quick-start.md:62 eeee96c4e59447aea6b239c63e4bb3e5 +#: ../../src/introduction/quick-start.md:62 4306d8ad802f45c18487d932d04492fa msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 961a385b340141e980aa4f8791fa2f12 +#: ../../src/introduction/quick-start.md:65 8339ec411ad04c70ab8d795eb154fc38 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 c48cd1be543d4ccbab964b28c2e08584 +#: ../../src/introduction/quick-start.md:70 3ecca6985e754951aee00c93effe9517 msgid "" -"Another way of passing values to your workflow input parameters is via an " -"*Inputs Object*. This is a file containing the input fields with their " +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " "corresponding values. The Inputs Objects file can be written in JSON or " "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 e5619164bdf242f0b09cac668adc0ef7 +#: ../../src/introduction/quick-start.md:74 d05e8e016b1d40c28c4b6091103fe920 msgid "`hello_world-job.json`" msgstr "`hello_world-job.json`" -#: ../../src/introduction/quick-start.md:80 9f80772a53154bbeb27895d35435de10 +#: ../../src/introduction/quick-start.md:80 c5983ba6c86f4b749522c11cb3843911 msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" @@ -1220,226 +1274,231 @@ msgstr "" "Pode utilizar este arquivo de Objetos de Inputs agora para executar o " "workflow “Hello World”:" -#: ../../src/introduction/quick-start.md:82 98b6d400cb274d08ad6489adbef08c4b +#: ../../src/introduction/quick-start.md:82 4065124edf3a4678a37c82e3070595cb msgid "Passing an Inputs Object file to `cwltool`." msgstr "Passando um arquivo de Objeto de Inputs para o `cwltool`." -#: ../../src/introduction/quick-start.md:88 4faabaab56f1444da290cf64cc389f37 +#: ../../src/introduction/quick-start.md:88 52b1602b5c8d48db88d0b16f788e7703 msgid "" "We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but it " -"is not a requirement. You can choose any name for your workflows and Inputs " -"Object files." +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 48beaccb16a24427bd015c63f9e06d37 +#: ../../src/introduction/quick-start.md:96 3b06faf5f3194bd8a96118d9f050f61e msgid "Continue reading the next sections of this User Guide!" msgstr "Continue lendo as secções seguintes deste Guia do Utilizador!" -#: ../../src/introduction/quick-start.md:97 68035ead1c6844128011ca32c04fd20f -msgid "" -"[List of CWL Implementations](https://www.commonwl.org/implementations)." +#: ../../src/introduction/quick-start.md:97 669b8ac154e74181830a430b1dc7684b +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -"[Lista das Implementações da CWL](https://www.commonwl.org/implementations)." +"[Lista das Implementações da " +"CWL](https://www.commonwl.org/implementations)." -#: ../../src/introduction/quick-start.md:98 8fc1ebf21a6f4894a4acfba74a80602b +#: ../../src/introduction/quick-start.md:98 1c888f1b771d49b3a257ed534b5afa0a msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -"A [organização`common-workflow-language`](https://github.com/common-workflow-" -"language) no GitHub." +"A [organização`common-workflow-language`](https://github.com/common-" +"workflow-language) no GitHub." -#: ../../src/introduction/quick-start.md:99 27fbad579d8b4ebeacc6fd3ef7e85a39 +#: ../../src/introduction/quick-start.md:99 dbce82b7a930493486a585ecb8891121 msgid "" -"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" -"Common_Workflow_Language)." +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -"[Common Workflow Language na Wikipedia](https://en.wikipedia.org/wiki/" -"Common_Workflow_Language)." +"[Common Workflow Language na " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -#: ../../src/introduction/quick-start.md:100 a8791b670848474da292a467f01f8c45 +#: ../../src/introduction/quick-start.md:100 dc714ffd4278421b9f2417f41627722c msgid "" -"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." -"org/wiki/YAML)." +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -"[YAML.org](http://yaml.org/) e [YAML at Wikipedia](https://en.wikipedia.org/" -"wiki/YAML)." +"[YAML.org](http://yaml.org/) e [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." -#: ../../src/introduction/quick-start.md:101 fc20fa4c04104417b541a67ada2ab9a9 +#: ../../src/introduction/quick-start.md:101 2bf7b924182f4f2bab88edef5ef85baa msgid "" -"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." -"replace('VERSION', cwl_version_text) }}." +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." msgstr "" -"A {{'[Especificação CWL VERSION](https://www.commonwl.org/VERSION)'.replace(" -"'VERSION', cwl_version_text) }}." +"A {{'[Especificação CWL " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." -#: ../../src/introduction/quick-start.md:102 a93a7797a12b48dfa5bc3a7c50ab88e7 +#: ../../src/introduction/quick-start.md:102 936a7dfab11a4f2c82c0b59964e3ea28 msgid "" -"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" -"Workflow_management_system)." +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -"[Workflow management system na Wikipedia](https://en.wikipedia.org/wiki/" -"Workflow_management_system)." +"[Workflow management system na " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -#: ../../src/setup.md:9 6f02fa47aca14c59a35b3ab750f5f236 +#: ../../src/setup.md:9 24ea9c5144664d9599d7aca767b4730a msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. The information on this page has been migrated to the [FAQ](/faq." -"md) section of the new user guide." +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." msgstr "" "O conteúdo desta página está desatualizado mas foi mantido aqui para " -"preservar os links do antigo Guia do Utilizador. A informação desta página " -"foi migrada para a secção [FAQ](/faq.md) do novo guia do utilizador." +"preservar os links do antigo Guia do Utilizador. A informação desta " +"página foi migrada para a secção [FAQ](/faq.md) do novo guia do " +"utilizador." #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 3821c2d16b254672a494522e47386cb0 +#: 3843684b039a40dea163de951ca56738 msgid "Additional Arguments and Parameters" msgstr "Argumentos e Parâmetros Adicionais" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: 412a05f3492349a7bd26ea0c30e9bd80 +#: a6fd1842b938435aa2a3c889019eec71 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 1232f6c81da141cb8482294eee5955dc +#: dfed0747ed544547afd364086d828c9b msgid "" "In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files in " -"the same directory as the source file. However, CWL input files (and the " -"directories in which they appear) may be read-only, so we need to instruct " -"\"javac\" to write the class file to the designated output directory instead." +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 485bb71673144e3f90f05b420b7079ac +#: e690b567eae34f3f8dbdd7760e51449a msgid "`arguments.cwl`" msgstr "`arguments.cwl`" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0beb10c3133643f6b62c7d4aeec33709 -#: 5d48d9a2e977431f9a3625abaa466f5f +#: ../../src/topics/staging-input-files.md:15 4cee519b108143be89a0e47a75d7d649 +#: 79585673fd654bab9ba7c1927d7e153b msgid "`arguments-job.yml`" msgstr "`arguments-job.yml`" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: fcc1151a2e8b4a84b8595c7f913781a1 +#: ef070ebe5f7245489b05660fb6d7c178 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" -"Em seguida, crie um arquivo Java de exemplo para usar com a ferramenta de " -"linha de comando." +"Em seguida, crie um arquivo Java de exemplo para usar com a ferramenta de" +" linha de comando." #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 4a291c7ac7c84257b7402567d8364a36 +#: 4ae43e3e841442039e4bb8c740096c56 msgid "" -"And now invoke `cwltool` providing the tool description and the input object " -"on the command line:" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" msgstr "" -"E agora execute `cwltool` utilizando a descrição de ferramenta e o objeto de " -"input na linha de comando:" +"E agora execute `cwltool` utilizando a descrição de ferramenta e o objeto" +" de input na linha de comando:" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 3b1ae26038fd498ca0ae23aa70a35d3f +#: 8497291577914eb3a172c1ffb736d95d msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: 40388ebefb6947089c4a0f6d5d6e92e8 +#: dc9fa5f2cbb147b1853c4042c54010f3 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include `$(runtime.tmpdir)`, " -"`$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and " -"`$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of " -"the CWL specification for details." +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 a417fdd330db47a3aac07f7006c83ca9 +#: ../../src/topics/best-practices.md:1 964bf8276dd04b65887448e1386e63fe msgid "Best Practices" msgstr "Melhores Práticas" -#: ../../src/topics/best-practices.md:3 99bad0fd9bee428a8d936d5a8e84d97d +#: ../../src/topics/best-practices.md:3 7b59377bd56c47b8a71c18acfba4d3bb msgid "" -"The following are a set of recommended good practices to keep in mind when " -"writing a Common Workflow Language description for a tool or workflow. These " -"guidelines are presented for consideration on a scale of usefulness: " -"although more is better, not all are required." +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 935500b0e6e249eba585644cddbd0253 +#: ../../src/topics/best-practices.md:8 2292670347cd4549bc6a51e972de0ef4 msgid "" -"No `type: string` parameters for names of input or reference files/" -"directories; use `type: File` or `type: Directory` as appropriate." +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 96f924d6e02f4005b35d463e49be2982 +#: ../../src/topics/best-practices.md:11 ae127b776eed4894af8cb680377703e0 msgid "" "A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that " -"the usual rules of software licensing apply to this document. For example, " -"if the workflow is shared publicly, licensing terms must be clear so that a " -"future user understands under what conditions they can run the workflow, " -"modify it and/or combine it with other workflows. For this reason, please " -"consider including a license field in the document. The authors of this " -"guide urge you to choose a pre-existing license rather than trying to write " -"your own (see the link below to learn more about choosing a license), and " -"our recommended practice is to choose a license that allows for re-use by " -"anyone, e.g. [Apache 2.0][apache-license]." +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." msgstr "" -#: ../../src/topics/best-practices.md:20 25e0a5c93ccc49bc8b6206c7c2e3de5c +#: ../../src/topics/best-practices.md:20 384eb620dc31468e8c3f5f33a3436200 msgid "" -"If possible, the license should be specified with its corresponding [SPDX " -"identifier][spdx]. Construct the metadata field for the license by providing " -"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " -"taken from the list of identifiers linked above. See the example snippet " -"below for guidance. For non-standard licenses without an SPDX identifier, " -"provide a URL to the license." +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 34ad53bc5a40446daa0dac4571600d1e +#: ../../src/topics/best-practices.md:26 e8259b43fa6944eda73eae381db6b97b msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 4c397ffd2e9148e39bdd614683a98a78 +#: ../../src/topics/best-practices.md:28 5b976a5aec7d44bda55b0a019e955416 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 1ed7f7e73afb4bd2ad2e29b65d020ff1 +#: ../../src/topics/best-practices.md:37 924b8df24deb4c82b32732f491c9a246 msgid "" -"For more examples of providing metadata within CWL descriptions, see [the " -"Metadata and Authorship section of this User Guide](../topics/metadata-and-" -"authorship.md)." +"For more examples of providing metadata within CWL descriptions, see [the" +" Metadata and Authorship section of this User Guide](../topics/metadata-" +"and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 13b058dfa3cd4bbea54ae7d5a56c4c50 +#: ../../src/topics/best-practices.md:40 9e64a9fc89cb45cfbff0e925cc91b1be msgid "" -"Include [attribution information][license-example] for the author(s) of the " -"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" -"[orcid]." +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 69369b917c1a45199343266650b1b220 +#: ../../src/topics/best-practices.md:44 87030aef02044b8283c76debab4772bf msgid "" "In tool descriptions, list dependencies using short name(s) under " -"`SoftwareRequirement`." +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "" -#: ../../src/topics/best-practices.md:47 0245a61fd2ef4fb69cbb8d732086fb8f +#: ../../src/topics/best-practices.md:47 6c9eaae099fa4ca4b0986b1c4146df50 msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" -"identifiers.org/rrid/RRID:SCR_NNNNNN` format." +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 e9a56e3634a042279cae1745b7820658 +#: ../../src/topics/best-practices.md:50 5ae8950fd31541399c2fe59096581dbc msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1447,216 +1506,224 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 8a180861a66c4aaa9e8fdefd929ed829 +#: ../../src/topics/best-practices.md:55 b0493895105e43849bff2026763e472a msgid "" "In tool descriptions, include a list of version(s) of the tool that are " -"known to work with this description under `SoftwareRequirement`." +"known to work with this description under " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "" -#: ../../src/topics/best-practices.md:58 00f333a383b64578b32c687b42924a77 +#: ../../src/topics/best-practices.md:58 88806cb0462f4359801c1fa0ff0ebcc0 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with " -"`$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " -"[Full IANA media type list][iana-types] (also known as MIME types). For non-" -"bioinformatics tools, use or build an appropriate ontology/controlled " -"vocabulary in the same way. Please edit this page to let us know about it." +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 6b960d362bb540299f0560c14c5f2d8c +#: ../../src/topics/best-practices.md:66 b178c7296ed5491782a4180c76883c14 msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 9cf9342bf0864e87b495913d8e06d021 +#: ../../src/topics/best-practices.md:69 886d15c1972243acadccff5760f842f1 msgid "" -"Each `CommandLineTool` description should focus on a single operation only, " -"even if the (sub)command is capable of more. Don't overcomplicate your tool " +"Each " +"[`CommandLineTool`](https://w3id.org/cwl/CommandLineTool.html#CommandLineTool)" +" description should focus on a single operation only, even if the " +"(sub)command is capable of more. Don't overcomplicate your tool " "descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 587b048324e447cb85844d8c64ae9a1e +#: ../../src/topics/best-practices.md:73 ef5a5f9b253c4ca3916802a695fb7c6d msgid "" -"Custom types should be defined with one external YAML per type definition " -"for re-use." +"Custom types should be defined with one external YAML per type definition" +" for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 d8df6bbd5d324f7c9f48edb33e113b75 +#: ../../src/topics/best-practices.md:76 ff59f40e84004523904e3094be07cc80 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 2235174088ad48a89d4fc21223e627b7 +#: ../../src/topics/best-practices.md:78 78d73fde24e24beeab541a623d9530b6 msgid "" -"If useful, include a top-level `doc` as well. This should provide a longer, " -"more detailed description than was provided in the top-level `label` (see " -"above)." +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 a0f0953a1a9f40cebd4dbe028784ff96 +#: ../../src/topics/best-practices.md:82 d92013d662b44dbf8875e06c9dfbfd79 msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list of " -"valid values." +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 0ec380c683534892b6b8b8fcea84f765 +#: ../../src/topics/best-practices.md:85 c100d5192a52497fb6a890b81a388fcf msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. One " -"common example: manipulating `File` names and paths? Consider whether one of " -"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " -"`nameext`, etc., could be used instead." +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 65f23741db4e4a6abda8e5f7e036753a +#: ../../src/topics/best-practices.md:90 e22fbacdb2fb4202b1bd69cfc24af5cd msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 34c2caee8eb84e01a37033b67eb4aaba +#: ../../src/topics/best-practices.md:93 0060a863362140f6bb3932cb5da1df04 msgid "" -"Complex workflows with individual components which can be abstracted should " -"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " -"workflow modular and allow sections of them to be easily reused." +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 d7c7484b2f1048aea9802400410f0858 +#: ../../src/topics/best-practices.md:97 93f6d6b544c24ce780184272f66bacab msgid "" "Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics " -"software\"][containers] (also useful to other disciplines)." +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 a905abc2eead4dbaa035235936025499 +#: ../../src/topics/command-line-tool.md:1 a378a2f7d268401abfbbbe6e5090a952 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 eb91b6dab34d4d5f9854ac580a6cbde2 +#: ../../src/topics/command-line-tool.md:3 cf0f1c00c0b34c94a8e2460a700c303e msgid "" -"A command-line tool is a type of Process object that can be run by itself or " -"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " -"etc. The command-line tool is defined in the `baseCommand` attribute of the " -"command-line tool CWL document." +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 7caeb91564634091a932f1270c4f5ef9 +#: ../../src/topics/command-line-tool.md:8 7a180ba1f2d746a78b79be7e899cbad6 msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The following " -"example contains a minimal example of a CWL command-line tool for the `echo` " -"Linux command, using inputs and outputs." +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 c6ac4a60d102407991f40b892fb60560 +#: ../../src/topics/command-line-tool.md:19 128bd8cd6788431da54fa07a8dc87f99 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 51d3ce421db345f5ab19e02fbbc51df2 +#: ../../src/topics/command-line-tool.md:50 d742e9e59ea44ca1a1df2de85059343f msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 8311d1430e624435b7b04bf2574a90c5 +#: ../../src/topics/command-line-tool.md:57 e3a06ebe51b64b0183673a8acc04969f msgid "" -"The example above uses a simplified form to define inputs and outputs. You " -"will learn more about in the [Inputs](../topics/inputs.md) and in the " -"[Outputs](../topics/outputs.md) sections." +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 d1c03e5f19d64ea89276d126de6e4bda +#: ../../src/topics/command-line-tool.md:68 2bab464d19d14562a6501373aff13905 msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 8494b43e98dd424db7d57aa1d731f7b4 +#: ../../src/topics/command-line-tool.md:69 201712f3ceee4d4ea56ab96d3fef97b0 msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network access. " -"If a command-line tool is written manually in CWL v1.1+, there is a need to " -"specify when network access is required." +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. Starting with CWL v1.1, programs are not granted network access " +"by default, so you must include the requirement for network access in the" +" specification of your tool." msgstr "" -#: ../../src/topics/command-line-tool.md:83 8c4573fb120149269a0fe3a1ba6c9ef8 +#: ../../src/topics/command-line-tool.md:84 3282a357799f4a72a6b8bace206144c4 msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " -"Access automatically." +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 or v1.2 " +"will have `networkAccess: true` set automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: e1c709ac0fb249928d14aeced6551ae0 +#: 17c5b4ee43cc4a979676ad27e473d046 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: c26c9c640e0747c8b2c2977c860c9d82 +#: cd0dff10471c4ad2b84e3a0e4d7767ea msgid "" -"Sometimes you need to create a file on the fly from input parameters, such " -"as tools that expect to read their input configuration from a file rather " -"than the command line parameters, or need a small wrapper shell script." +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: edbe918d7df14cafb440e171e46c6de3 -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +#: bf4aea0a22334a1ca75cc20e937e6581 +msgid "" +"To generate such files, we can use the " +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 6d457d9b4ae746d384e65d9a37ca3591 +#: 008f768d56b8465bb4e8f4fde15853a7 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 868394c1b8374ee6bbd43463e73d7edc +#: 252f8e897b0942a8be098481890005f3 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the value " -"at the input `message`." +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 08a9e08cba674db09c9bfbef37e9579f +#: aca24b72687c4d4d84bf9de8b71413f7 msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later " -"during command line tool invocation. That means that any genuine need for " -"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " -"above is expanded to `${PREFIX}` in the generated file to be evaluated by " -"the shell script instead of the CWL engine." +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 6f6f437753dd4eddae0b2ea62046fe39 +#: 750b3232e8754448bc2b5913539495b8 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 096b17907bc3452d9927ef2fb6f5c11f 78ed5d8fb9bd4e068023d2c717e20f62 -#: c3a2e9e6b4414597a17db6d55d98e9d1 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:81 +#: 687c8a84bade43269f3cd767d32f9f47 81da7a18fe8d4659abc883cf43009f1f +#: d5d67eae63304ebb9b242133feacb0d1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: ac783e6415a44cb59d4b425bac5087b7 +#: c4f964450d014734877fb3c968353a74 msgid "" -"Before we run this, let us look at each step in a little more detail. The " -"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " "command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: b9e6e15b541149c6a2d3922c11405267 +#: 9aeea5a6a4244bc7a1626e0cb7351068 msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " -"array, we need a `-` on the first line of each element of the array, in this " -"case we have just one element. `entryname:` can have any value, but it must " -"match what was specified in the `baseCommand`. The final part is `entry:`, " -"this is followed by `|-` which is YAML quoting syntax, and means that you " -"are using a multiline string (without it, we would need to write the whole " -"script on one line)." +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 87088899567a4402aeb34605d3c6b06b +#: 867239e9ad3d4187a2703662a0ca3976 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1666,222 +1733,228 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 304c1bfe5ecd4d26b5dfaf9ad2e2c7f8 3ef7f0e3099147d78fd2d30bfa73cc6b -#: 4fef79a30282456eb9b5dd34a5eec0b1 afe775762ed348e5982b99bcf1451606 -#: f0689cd0e5b34414b6693331186ee4a3 +#: 0d7151b9f0194197bd686fe6c9c47afd 78bb40eeeda24d7b923162daa45d51a7 +#: 7b341a317347482ca86fc56119c3686f 7c637fa62cab4d0dbe670a3b72737cc9 +#: cfb4605a01dd4475aabcc086a4e65957 msgid "" -"Now invoke `cwltool` with the tool description and the input object on the " -"command line:" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 9f1967411aa7497fa43a4851f0645d6e +#: ../../src/topics/custom-types.md:1 252a3a17b1ec4d5a9a82ebbf6c2f314c msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 90bd62e4ef8b41e398a5c9b31f132774 +#: ../../src/topics/custom-types.md:3 e0275ddda8f84207a58d10c17ca99a45 msgid "" -"Sometimes you may want to write your own custom types for use and reuse in " -"CWL descriptions. Use of such custom types can reduce redundancy between " -"multiple descriptions that all use the same type, and also allow for " -"additional customisation/configuration of a tool/analysis without the need " -"to fiddle with the CWL description directly." +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 3465527b8ff4407587f7c46fa9fa2a98 +#: ../../src/topics/custom-types.md:9 8367e38e5e7c4a298d1d87b9001aaddc msgid "" -"The example below is a CWL description of the [biom convert format][biom] " -"tool for converting a standard biom table file to hdf5 format." +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 c0cc869690804ada96a5c1813d17b895 +#: ../../src/topics/custom-types.md:12 18b802f45ce0454ab7aa2a21812863c6 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 01f369931c8142c08fe821a0ca31bf92 +#: ../../src/topics/custom-types.md:18 66d1953f5dd54d448bddd0f30c330402 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 0b3ff704cdea44e28aee3c704ca98e27 +#: ../../src/topics/custom-types.md:24 56b8912a1ea84f28adeb8beaf92ab563 msgid "" -"___Note:___ To follow the example below, you need to [download the example " -"input file](https://github.com/common-workflow-language/user_guide/blob/main/" -"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " -"*rich_sparse_otu_table.biom* e.g. via `wget`:" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 cb456bcae0dd41ffbc514eeea283e130 +#: ../../src/topics/custom-types.md:30 a48539920c4944898918bc90b2d4e3c9 msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to be " -"used in the table conversion are imported as a custom object:" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 c610173365d04c57900b22f4024b47b4 +#: ../../src/topics/custom-types.md:46 c791096f537141e8bd7cc941d711d108 msgid "" -"The reference to a custom type is a combination of the name of the file in " -"which the object is defined (`biom-convert-table.yaml`) and the name of the " -"object within that file (`table_type`) that defines the custom type. In this " -"case the `symbols` array from the imported `biom-convert-table.yaml` file " -"define the allowable table options. For example, in `custom-types.yml`, we " -"pass `OTU table` as an `input` that tells the tool to create an OTU table in " -"hdf5 format." +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 c2b2e18d55c94721812431583cfc4725 -msgid "" -"The contents of the YAML file describing the custom type are given below:" +#: ../../src/topics/custom-types.md:53 5f6bc6ed72334a74b9a4c46c29ddda46 +msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 3e61c3920a7a45db8917c348bd44384d +#: ../../src/topics/custom-types.md:55 3b55419088e8446994703220bd8e8480 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 cd87d210b03c4da2a7608b40a6bbcca0 +#: ../../src/topics/custom-types.md:61 fe6f4ce5e7344af0abea9d5c03e32ecd msgid "" -"In order for the custom type to be used in the CWL description, it must be " -"imported. Imports are described in `requirements:SchemaDefRequirement`, as " -"below in the example `custom-types.cwl` description:" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 7af9ba3219e44ed49b8da781db5d6fb5 +#: ../../src/topics/custom-types.md:76 dce43b138ba24b22bfa9fa5692a17009 msgid "" "Note also that the author of this CWL description has also included " -"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " -"cores required for the tool to run successfully, as well as details of the " -"version of the software that the description was written for and other " -"useful metadata. These features are discussed further in other chapters of " -"this user guide." +"[`ResourceRequirement`](https://w3id.org/cwl/CommandLineTool.html#ResourceRequirement)s," +" specifying the minimum amount of RAM and number of cores required for " +"the tool to run successfully, as well as details of the version of the " +"software that the description was written for and other useful metadata. " +"These features are discussed further in other chapters of this user " +"guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 eae1994f3a4d481b863b5125c7f4a383 +#: ../../src/topics/environment-variables.md:1 19737f89f2994815969fa4a88346f49a msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 8bd8c06d416740b69d126eb9f5f24ad3 +#: ../../src/topics/environment-variables.md:3 ad965f75aa0c41cda8b82c46af49774d msgid "" -"Tools run in a restricted environment and do not inherit most environment " -"variables from the parent process. You can set environment variables for " -"the tool using `EnvVarRequirement`." +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 11c6bffc620b4c789b29ab4034a8bfbd +#: ../../src/topics/environment-variables.md:7 38b276f9b0114a0bb87734f0a07a736f msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 89888b1b994546ce8a93f9630b4bb07e +#: ../../src/topics/expression-tool.md:1 9f33532119dc47ffb6ade20fb1d950bd msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 191d3010b9244b39bc3bc50246ac7ad7 +#: ../../src/topics/expression-tool.md:3 b267056eae704737af5aaada3ea7e6e2 msgid "" -"An expression tool is a type of Process that can be run by itself or as a " -"Workflow step. It executes a pure JavaScript expression. It is meant to be " -"used as a way to isolate complex JavaScript expressions that need to operate " -"on input data and produce some result as output." +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 3437ed6e184748e4af1ef62f32c8cef1 +#: ../../src/topics/expression-tool.md:8 7e930144163e4d6e9f0bcaa764497ccf msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " -"instead of `baseCommand`, it requires an `expression` attribute." +"instead of `baseCommand`, it requires an " +"[`expression`](https://w3id.org/cwl/CommandLineTool.html#Expressions_(Optional))" +" attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 c3ae1ef318bb4e0fada76c353dd5f6f1 +#: ../../src/topics/expression-tool.md:17 f172488c19a94d688036197117d30b38 msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 a7f5e04d242c48a7b3deffb5ff6528be +#: ../../src/topics/expression-tool.md:48 ef978c951f1a4b7d9280d31367e5bae7 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 32b6841faed044409bc618cba54a22f0 +#: ../../src/topics/expression-tool.md:67 0b63da31bc274b3cad798b07149592ab msgid "" -"We had to use an `InlineJavascriptRequirement` as our expression contains a " -"JavaScript call in `.toUpperCase()`. This means to tools using the " -"expression tool that JavaScript is a requirement." +"We had to use an " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" as our expression contains a JavaScript call in `.toUpperCase()`. This " +"means to tools using the expression tool that JavaScript is a " +"requirement." msgstr "" -#: ../../src/topics/expressions.md:1 6821ba7a84a44d309d245c429948ad09 +#: ../../src/topics/expressions.md:1 b0e567a985f748538552bdb486a47998 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 8167269bc3a64c72bd6c909362350a15 +#: ../../src/topics/expressions.md:3 24d05cbbab8e460e99f2edc97ab0dcec msgid "" "If you need to manipulate input parameters, include the requirement " -"`InlineJavascriptRequirement` and then anywhere a parameter reference is " -"legal you can provide a fragment of Javascript that will be evaluated by the " -"CWL runner." +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" and then anywhere a parameter reference is legal you can provide a " +"fragment of Javascript that will be evaluated by the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 c0f75603a6024063a6911f17c70908cc +#: ../../src/topics/expressions.md:9 3d48d1a8f7f74bc1886e41653cb53a22 msgid "" -"JavaScript expressions should only be used when absolutely necessary. When " -"manipulating file names, extensions, paths etc, consider whether one of the " -"[built in `File` properties][file-prop] like `basename`, `nameroot`, " -"`nameext`, etc, could be used instead. See the [list of best practices](best-" -"practices.md)." +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 7faec63b389a4c07b6929b7a78f0cc70 +#: ../../src/topics/expressions.md:16 7d444aacd418466bbe588fa964b45179 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 d7dca89942f949d58cb18cb94bb7de72 +#: ../../src/topics/expressions.md:22 72a0558a83964796a8c1a0eb55fd78e8 msgid "" -"As this tool does not require any `inputs` we can run it with an (almost) " -"empty job file:" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 1abc1a21c0764415b138099e0e21432b +#: ../../src/topics/expressions.md:25 d679fd1363b24c81979c68e7342159cf msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 b8b5a50a82e44e49a37c6396f1ff9464 +#: ../../src/topics/expressions.md:31 d2ee4fcece744b6681f29322b5305111 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object is " -"represented simply by a set of empty brackets." +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 b38d66c12ab74dfc9395e69d9c04bbf5 +#: ../../src/topics/expressions.md:35 624e4a270e374b1699b780df508b9184 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 8417aa7a9d034361a41def6b71e93413 +#: ../../src/topics/expressions.md:37 c252eac9a35e46aab08bd07bc1cdb57d msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 c1f672b377da4605b9c5098ebb6e1147 +#: ../../src/topics/expressions.md:47 f6f64d57a50742b19b801c14806ee18a msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 af52f5197e8545d2be22cc0f7f03648c +#: ../../src/topics/expressions.md:54 052e24e2ad044cc28f04d7f39be871d6 msgid "" "Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " -"describe the additional command line arguments." +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 5e12ce15018942bf9010ce6519c17b00 +#: ../../src/topics/expressions.md:62 84b31c076d4b4826aae35e8c23fe6a25 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 e2e9c5f7b681427a9589476649e5a9d8 +#: ../../src/topics/expressions.md:64 8c3b402c40f64880a4bd42c47b910254 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 8a74763ead0147bbaf3892e552fad546 +#: ../../src/topics/expressions.md:66 9bf5ca0e769147c6a9705bc40bd1febc msgid "" -"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 0aab7de8d69f49438d4eeed17316df68 -#: 75f90cb870d14d0dbb4c4ee80d32a65e +#: ../../src/topics/parameter-references.md:64 7ab0dbd54c1441539673fa12ef96b89e +#: e76c6ece0c594fefa86b190879c5acaa msgid "`arguments`" msgstr "" @@ -1889,35 +1962,35 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 0b9d8268c177489b86b8eaa638dfa063 -#: 204cd6d8375a4462a8247863a96df906 2b7e56ceb4ad49a8b29a58b10bad7c0a -#: 81f15c64379941d8ac2a681b3879761c f11ae7d801db45989b598864dc6291c9 -#: fc4534b475334f7281d1740c9a78f640 +#: ../../src/topics/parameter-references.md:86 0209558b1013471eb708698537edaf06 +#: 4458393fdb0e451f9806e91122ea2534 594a163e08f04aa5a04a44a303a1c643 +#: a6fddc160afc4ef09717f69de72c11ce a9ec99ddcb344bcbbe5c1f59af0bcff2 +#: af2cdb5f66ac4fd5b8f91258f005cc62 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 70e9085b21f640d6893309a3375c0511 -#: f529003dd7a64bc7be0ccef8dbfa84b3 +#: ../../src/topics/parameter-references.md:66 afb175f182354cb19e23b1cad241437e +#: f9a6718845e24f46b76fcc8ab26eec7a msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 3fceb522ba6245129b826c342eaf31b4 -#: a5f71add5b8345a4bfa02853ef8a6d35 +#: ../../src/topics/parameter-references.md:67 3bce21dcc2da439daca80c4fcdf4c343 +#: 7f5ce097ca0442a6a200599342a6e24b msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 018300196ea24550988a0156894b5e85 -#: 2c799286e8204ed9a83c3fc006988139 +#: ../../src/topics/parameter-references.md:68 3397e8816f6a4d4b9af728c175f04917 +#: 7b14686e16eb4f488659b22d67ec3bfa msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 25d91d6624bd42e7948e29c684e8e441 +#: ../../src/topics/expressions.md:72 7a2d74aa018f4cab8c68e8775d83dd01 msgid "" -"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter)" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" #: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 @@ -1925,11 +1998,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 0944d6525c3c460aa4b5a0e72552ca4d -#: 1187b0d330cb470fbea82a8b8c95aa28 265602307ccd42458ba47ac1b689242c -#: 2febce1b1ad74b18af3a9b3fa137c780 3215ee41f96541cbbda60a1167386c2f -#: 80efeab6ec0e447bbe158cbaa57f83d8 8d2bbd91b4ab4faa923fc1a14ec49dd5 -#: b4a6e640275b4fc7a18e3083e86b72a1 +#: ../../src/topics/parameter-references.md:90 24f27702d0684bc98e3232103510232e +#: 26a8dff7b80c4e059f1e20eef9da6203 476aa37af5214bcf963c7aab1f859273 +#: 4b0a0cd934bd41b4b55c034b91392bc7 5182e2165e44429287b4d924c2f896a4 +#: 7de500d3be6b4c3e8f274fd6a092109f 953d824a494947a3ab0ca2988717ee01 +#: b301751f90af4700bbada5e5b166be35 msgid "`format`" msgstr "" @@ -1938,1494 +2011,1552 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 480b2e4207574b27b8d33dfe5e9ab64e -#: 4b4149a3b97a4de5b2d7fd84bd547ffe 7af1a82df41e40d0a430babafe1bc5e2 -#: be01787b66e34074af32bb45dcce8657 be099ab533504a7596fd56ec1ce7ca5d -#: c8b96271665444608f601a460dd28fb3 cb6dfa7bc68b41929a5247d929c2f94a -#: f7f452e92f6d4a14ba3912c62699019a +#: ../../src/topics/parameter-references.md:91 2c2b8db396b04ace8aa396c0a5a4858f +#: 33a9b77ce15b4910962a7f08bd2f47a3 57cba0191de3470bbe112ed2a0d3f252 +#: 6efe998094b3469eae61cfff551b1eb1 776de1ecfafc41ada7e916addd7229fd +#: 8595d62eb0274b3a8a7f0adf058b51d3 988966a2d4844e73961b0358aff8f6e1 +#: faa7d521fec240748407d03ffdb93aa0 msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 4811c1b9867b44caa70dec4b91970484 +#: ../../src/topics/expressions.md:75 d737a9e9bf1c45d695bf584bc3241d9a msgid "" -"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding)" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 0b1f2a8986e0419a90e484d3a945a037 +#: ../../src/topics/expressions.md:77 0e2052e16f6a41b8983dc64b4b3a7586 msgid "" -"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 dbc02876870d49d2b9e39db4133a0f62 +#: ../../src/topics/expressions.md:80 dff31dd961d540e3b8cd1247e978d60e msgid "" -"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding)" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 97339a3fa43849f7b292f4643b5fe35c -#: da8b81b1e1884406a188fb04825ef90e +#: ../../src/topics/parameter-references.md:78 249aba7c38ce49379b9d35e7ad81a0bf +#: 5a354eb4883948e0a2b5c96b5ae12da7 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 077e7b0d2dde443699050af8c63ab912 -#: c8cbe3dfd0984221ae72012ea26edc6f +#: ../../src/topics/parameter-references.md:79 2325a310f2bc4d09b53b32c54efae2df +#: 9e477e2cfab24861b517fe2fb52962f4 msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 3f07f4a8594640c2b2da4da521872b59 -#: 573f7e4b72ec4c47ab2e54e2c4877d9c -msgid "From `Workflow`" +#: ../../src/topics/parameter-references.md:80 9448462d104b4be5904623c85a9e16b7 +#: bf11a7a72147445c9b8e44b541e09f36 +#, fuzzy +msgid "From [`Workflow`](https://w3id.org/cwl/Workflow.html)" msgstr "" +"De " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -#: ../../src/topics/expressions.md:84 f03011b3479b47c690604c508d95c263 +#: ../../src/topics/expressions.md:84 0d54a777a33d4f17a2f3390384a3c0c5 msgid "" -"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" -"v1.0/Workflow.html#WorkflowOutputParameter)" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 1ec3f913909b4e04bb602767d23bd85d -#: 2f7130500b8c450fa4af226b18e38407 +#: ../../src/topics/parameter-references.md:84 7918d0661be746faaddf25ad49172f30 +#: b8439dbaa949427097e25ccb48fe15ee msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 a5849a856a374cda807ecf48034af915 +#: ../../src/topics/expressions.md:88 7b37eb600c9b4847a58a7e5077bef4c3 msgid "" -"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 bd8bbd60aaff4e7aacec91bcbad500f4 -#: f0c99004211e4adf8c0b524d5bbcc12b +#: ../../src/topics/parameter-references.md:87 368ef005c2ca4b8599f76242f7178375 +#: ab1ba7626eae483a8b614ee4cd5bab6f msgid "" -"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." -"html#ExpressionTool)" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 96c544cf213245cfb3d1f5196223c6cc -#: c6a04d4f3ef24104b0a86f9093935c13 +#: ../../src/topics/parameter-references.md:88 595b9ddcee734d6595c1b4b2d169dcb8 +#: 80b55c77a4384644acfc9472c3cedee0 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 946e0437a48b4d5da2a29d489250cbaa +#: ../../src/topics/expressions.md:92 fd504478a6c641e0a72321fa80ad1c9c msgid "" -"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [ExpressionToolOutputParameter](https://www." -"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 1f287ebf87ae4e93bd1ac65cc1d01bf4 +#: ../../src/topics/expressions.md:95 32b1a39cca1a4402af9bdc0abc4d70c8 msgid "" -"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement)" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 0d0f4f0e12174d588c131afef70efc5f -#: a74e0e3499d644b4a9d999d3555f03de +#: ../../src/topics/parameter-references.md:93 2518d499801e4bcf82e9e4666280504d +#: 98a511d138e9497c923963c2ca5f0a0b msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 b2e31c38f7cb4ecabd6b9b89ef051c0e -#: ddc9d9ae72a64a76a2a8e2bba22584ee +#: ../../src/topics/parameter-references.md:94 57a055b125f742dc8842b798b034161b +#: e84bc5505a6549ae9aacde8cb9225403 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 12f86817dfc14f2bb39509886d56017f -#: 8a94f2c3b1674162a268f67935a3025b +#: ../../src/topics/parameter-references.md:95 98cd455e080f43749090270e7a61cb42 +#: e698ea756fe94e99837312fb30c9f9bf msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 a800acfefb3f433fae2cdda9ac4a795a -#: bcb58fc2447a4472b86913871b8c12ee +#: ../../src/topics/parameter-references.md:96 8dfae10004a641fdb95c456c90a48d94 +#: bef90c153d4f4397b1f69f9beb38f7e6 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 5be337d412ba4d48877e991d535e810c -#: e6cf2f8498db4f549193be20d87e16f9 +#: ../../src/topics/parameter-references.md:97 47fddc711ce44086a7811bdfbd9167dd +#: e2bdf4fe676346cbb4443ee54fb7419b msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 3bc61c8197664f12a98d1ac38b421b38 -#: 9973a87f747445ad89ce959420cac5fd +#: ../../src/topics/parameter-references.md:98 7d143ba98f1f4dfcbe08b70389d43092 +#: 8f1665baca2e4e3b96026b50d132709a msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 0f5dc4f5a4c64f818e2e22f20472ae84 -#: 2ec9d1f191f44686b1cb8622336d6b92 +#: ../../src/topics/parameter-references.md:99 79bea45c2a484eda92c8578130b0b982 +#: d169949866a24e31947dffcb94620c5f msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 5382ff97ad2f419dbe1bed266997aa84 74406f77013443f28d4d6306c54b0df1 +#: 8d2e01f2aa314f1cb1231f2e08f89ce5 d5417397b1e242ef9878ac77d2f65005 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 f594a20dc038457e815dc17bae6e031d +#: ../../src/topics/expressions.md:104 08a66b2ab271494d810ff5834ca5c1bc msgid "" -"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" -"CommandLineTool.html#InitialWorkDirRequirement)" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 5814f96ee4ec4822aecad33c8eda0473 c46c44268b2a4b96b1df13e53e82e54c +#: 21e9582891cf4b87a7ee4693663040fa 51bc6d1ccef14729a0d5e63b56d73d20 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 b9824103ef8745bab30b65887c82f62f +#: ../../src/topics/expressions.md:106 7d8755f05d6541439f72ec9d6806d3fc msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 28b23f84c64549e7a0fe444ccc3e1b05 fdd5d742a6764e5db2281ed844bf3475 +#: 29c2424fc7dc43e68c9bfee179167bb3 30f25141bcce4670882e4a5bbe4fc3e2 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: b6123c911c804f3c8cb596d2aa495b2b d81a7d8b7db444409b286e5f1d863968 +#: 02cfd4f1c3014e1eaa598a329dc5a95d d76fb015595e4194a7e15d714baaaf98 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: eb6255a0f8d748588d87e7ad38e507bd fffc5a80bd68495396d32b7a1821eb4e +#: 408f69a2df1343a78f93ff2ac0a994ea d37c78309e8b427f835af4fbd367e643 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 b00a8a2a572742e0929470550433e929 +#: ../../src/topics/expressions.md:110 53752bdff0974e39b2a86e8f2d96455f msgid "" -"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef)" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 9b34c95e483e47f3828e79bf929a23b4 c968eebaf0114b23b789e9ce68e7588d +#: 242a12ec757947db894195c9aefba818 7b26b9972f7141bf950b3bb024b0e369 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 7c8fb996d1af4cfdb0d49d8ed2696745 -msgid "" -"Using External Libraries and Inline JavaScript Code with `expressionLib`" +#: ../../src/topics/expressions.md:116 93d6c90b49d8424f9283c384062ce333 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 75a29e9ff2cf4b5bb6afa87a741a111b +#: ../../src/topics/expressions.md:118 ea6cbaa5dae647538c0bd9a4d5cad3f9 msgid "" -"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " -"attribute that allows users to load external JavaScript files, or to provide " -"inline JavaScript code." +"The requirement " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" supports an `expressionLib` attribute that allows users to load external" +" JavaScript files, or to provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 5233d8baa8b74391bf8fee5ae2324234 +#: ../../src/topics/expressions.md:122 484dc17440524cfda4dc486a7c5d5f63 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts of " -"the CWL document." +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 343e8b78a1f94b8cbafac05212e5a333 +#: ../../src/topics/expressions.md:128 5b2336cae1ef4cae8ed187d3f33cff25 msgid "" -"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." -"org/v1.0/CommandLineTool.html#Expressions) that the only version of " -"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" -"international.org/5.1/). This means that any code that you include or write " -"in your CWL Document must be compliant with ECMAScript 5.1." +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 0657ee8f03d8462ca6ca6fc538386b0d +#: ../../src/topics/expressions.md:135 32eca3a47efc4685bf7be706e123adbe msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " -"function inline in `expressionLib`. That function can then be used in other " -"parts of the CWL document:" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 e3c593cf50da426f8d9df215c7db0bc9 +#: ../../src/topics/expressions.md:139 6839a02fb82d45c29ae518f2b00cb9d5 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 b971e53c3ed847f1b7c7a6d50e344baf +#: ../../src/topics/expressions.md:146 5b5e59fa1688499ea4560ee6f8023227 msgid "" -"Running this CWL workflow will invoke the JavaScript function and result in " -"the `echo` command printing the input message with capital initial letters:" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" msgstr "" -#: ../../src/topics/expressions.md:149 d2315d46369f4e9d9c871d7f88f7006e +#: ../../src/topics/expressions.md:149 a1e57c6833c848d3974cf448493ab924 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 04fdaa45a7ed47d5830181611bda924e +#: ../../src/topics/expressions.md:155 1a4dfef06b5c4402bdb7e7dbd79eeb5d msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 8d7686f62f314d98aae8c262befd5283 +#: ../../src/topics/expressions.md:158 71ac99c65d15451cbbf58d1e81934010 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 e68ee17607be4a06a66f9fc67624aff5 +#: ../../src/topics/expressions.md:164 60918e53189243d3872e61c7a4de20fc msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 76b85d3729274fc08adfadcbf1172650 +#: ../../src/topics/expressions.md:171 ad2a74bd983b47869dc78b2eb7b6fce1 msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 29f334957fa940c289f385160cca6d63 +#: ../../src/topics/expressions.md:175 82c02dd2446b4de9a4c4b87736107b30 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 6d255ae6b92a48fa9b7b98443cc2f5bb +#: ../../src/topics/expressions.md:181 6fa7ebeffc7b44c6a12cd84897d186a1 msgid "" -"Finally, note that you can have both inline and external JavaScript code in " -"your CWL document. In this final example we have added another entry to the " -"`expressionLib` attribute with the new function `createHelloWorldMessage`, " -"that calls the `capitalizeWords` function from the external file `custom-" -"functions.js`." +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 89734e7855654b2e8bfddeea96241539 +#: ../../src/topics/expressions.md:186 d34f3e688d2d49b6bfcda4c962895d8c msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 1915f8e68f624027827d28f8e17d2dec +#: ../../src/topics/expressions.md:193 9e2774fc35b14832a0f92b7afaafd537 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 750f94edb4f84e45a276f6ab28fad95e +#: ../../src/topics/expressions.md:200 8b797cfb232f4e5da51f6c21e9a8e7e3 msgid "" -"The `$include` statement can be used to include a file from the local disk " -"or from a remote location. It works with both relative and absolute paths. " -"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." -"html#Include) from the CWL specification to learn more about it." +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 2e9e8cfaf48a43a88c31a855dac4f748 +#: ../../src/topics/file-formats.md:1 ac906f26116c45d882e1afa42ae38e34 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 c574b54d998243f28d2caa91434968a7 +#: ../../src/topics/file-formats.md:3 d99dab4f2f264c68b839b59b80d570e0 msgid "" -"Tools and workflows can take `File` types as input and produce them as " -"output. We also recommend indicating the format for `File` types. This helps " -"document for others how to use your tool while allowing you to do some " -"simple type-checking when creating parameter files." +"Tools and workflows can take " +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types as input " +"and produce them as output. We also recommend indicating the format for " +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 b0ec34507eea473c91d6ada09a1c5c09 +#: ../../src/topics/file-formats.md:8 23ba3dd26f5543119e2c152105b58e98 msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM in " -"our example), reference a local ontology for your institution, or do not add " -"a file format initially for quick development before sharing your tool with " -"others. You can browse existing [IANA file format listings][IANA] and [EDAM " -"file format listings][EDAM] on their websites." +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 a688e39859734a518c0fcc19f532a432 +#: ../../src/topics/file-formats.md:14 81c441846fc249c58607bacf97095eb8 msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` section " -"of the document in greater detail, so don't worry about these for now." +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." msgstr "" -#: ../../src/topics/file-formats.md:17 e068422ad9b84ca1b27008127928cc0f +#: ../../src/topics/file-formats.md:17 c04841dbf4be4cf8a22cceca8b08bd14 msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 8c3ef5e145b14299bf3671add0da56ac +#: ../../src/topics/file-formats.md:20 c5f6f6e4c23e4bf19dee69acb8ebed8e msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 0d92f1c0f1ce448fb698e9b390b45c15 fc4773204ebc4e3789bb076dff0d0393 +#: 20e97d58596a4a959ad76ec6128ac414 4e070ae9110d437bbf008b0c60a00cd5 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 900abc5aa6a940f48f9c93e79cd1c47f +#: ../../src/topics/file-formats.md:32 632e441919094610b97afc17e9c5e625 msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 0390555b96c84aadbd9325c152972087 +#: ../../src/topics/file-formats.md:34 afd8633db1904897aa3e499354b1c376 msgid "" -"Below is an example of a parameter file for the example above. We encourage " -"checking in working examples of parameter files for your tool. This allows " -"others to quickly work with your tool, starting from a \"known good\" " -"parameterization." +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 d5752ee5437b496ca10f4f12b76fc5dc +#: ../../src/topics/file-formats.md:39 bb69d6963c174191bf527335c3f665b7 msgid "`sample.yml`" msgstr "`sample.yml`" -#: ../../src/topics/file-formats.md:45 91dc76bb4565473ab948eecf628a405c +#: ../../src/topics/file-formats.md:45 ddb4f6f81c7d462b974e98c88dd3f558 msgid "" -"___Note:___ To follow the example below, you need to download the example " -"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 0b8b9b7f533543a49f876421ce6057d9 +#: ../../src/topics/index.md:1 2995cd4fb85c423dba021611dac4a137 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 1b6cfac3a92347d4b98bb54de1e26870 +#: ../../src/topics/inputs.md:1 3bac021fe7614d74ae701fb3c3765b93 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 53dd5f476f064cbf9b9826d1e80eb830 +#: ../../src/topics/inputs.md:3 8bb3ee0cd0fc4d85ba007431fc541973 msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 420b33d143fc44d1b237bc678f0af663 +#: ../../src/topics/inputs.md:5 17365707f58242369dd6aa73fc8d7242 msgid "" -"The `inputs` of a tool is a list of input parameters that control how to run " -"the tool. Each parameter has an `id` for the name of parameter, and `type` " -"describing what types of values are valid for that parameter." +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 55136332e3bb48f892cf6a74c67a4ac6 +#: ../../src/topics/inputs.md:9 521cb5dead5d4e9ab5ff037fb4b683cb msgid "" -"Available primitive types are *string*, *int*, *long*, *float*, *double*, " -"and *null*; complex types are *array* and *record*; in addition there are " -"special types *File*, *Directory* and *Any*." +"Available primitive types are *string*, *boolean*, *int*, *long*, " +"*float*, *double*, and *null*; complex types are *array* and *record*; in" +" addition there are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 cb2527899cc04b6d8060c4d57883beb5 +#: ../../src/topics/inputs.md:13 fbdf2c1bed3e41d7a41ec6b14d134a98 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 c79668b856b14243b4fad0f46dc5d6d7 +#: ../../src/topics/inputs.md:16 008f79cdf0074c73948bf50deb0a8a47 msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 ed6f3e5c7b3f403a9a94359983107645 +#: ../../src/topics/inputs.md:18 94cd3f10e94f4735bd3ae7dc168e5deb msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 034075eb09db4897a96d3332408427db +#: ../../src/topics/inputs.md:24 b339be370e8742b69400c8040ad7d15b msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 08181d391cc543a5a81d3257654df213 +#: ../../src/topics/inputs.md:26 78974fb2475947ccb8b8c55e34df5fa6 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 15215522e38242c4b17ec3aa089269d4 +#: ../../src/topics/inputs.md:33 9cc4a60d01f945aa9b4c43afcf20098b msgid "" -"You can use `cwltool` to create a template input object. That saves you from " -"having to type all the input parameters in a input object file:" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in an input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 64bd3382ec234ec8a50217b794b96916 +#: ../../src/topics/inputs.md:40 5ac6da11d56446de97c251a37d997671 msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " -"> inp-job.yml`, and then modify the default values with your desired input " -"values." +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 3611c1ca498a4197a4a6612c60f5f565 +#: ../../src/topics/inputs.md:44 6a3edb0d259d4d7c900dd9811f978d4e msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 da924e8142d34e86bcb5de1cd1da71ca +#: ../../src/topics/inputs.md:47 f1d76be7ba0b48f4b605581d0a9a5c72 msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " -"command line." +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." msgstr "" -"Em sequência, cria um arquivo chamado whale.txt utilizando [touch] digitando " -"`touch whale.txt` na linha de comando." +"Em sequência, cria um arquivo chamado whale.txt utilizando [touch] " +"digitando `touch whale.txt` na linha de comando." -#: ../../src/topics/inputs.md:53 13c97256a5ee49c99f4010edf9dbc9bf +#: ../../src/topics/inputs.md:53 8cabfa0cbcfd4a5aa30d1aabd412136d msgid "" -"Now invoke `cwltool` with the tool description and the input object on the " -"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " -"boxed text describes these two commands and the expected output from the " -"command line:" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 dcc3f2a47a6449efb857af63ed4b65d0 +#: ../../src/topics/inputs.md:64 5c78d7824ef34636ae2ed68d524d79e8 msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not explicitly " -"specified" +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 cf54a30ae24f4013bb19f379a7ca67be +#: ../../src/topics/inputs.md:70 5bdf77c45346445d8f93353c1e73f768 msgid "" -"The field `inputBinding` is optional and indicates whether and how the input " -"parameter should appear on the tool's command line. If `inputBinding` is " -"missing, the parameter does not appear on the command line. Let's look at " -"each example in detail." +"The field " +"[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)" +" is optional and indicates whether and how the input parameter should " +"appear on the tool's command line. If `inputBinding` is missing, the " +"parameter does not appear on the command line. Let's look at each " +"example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 ff75644bae9c46af8379d78360d4c696 +#: ../../src/topics/inputs.md:83 d783fe52e86f4feda33ea0eecb622603 msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 e90abe59a84e48d4b8d6caa737e087aa +#: ../../src/topics/inputs.md:95 f99fb9a6d0374ef78503815d4db9006d msgid "" -"String types appear on the command line as literal values. The `prefix` is " -"optional, if provided, it appears as a separate argument on the command line " -"before the parameter . In the example above, this is rendered as `--example-" -"string hello`." +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 9275236d87b646cab1058dd750e11a50 +#: ../../src/topics/inputs.md:109 b106eed01c1744a792368f91f547e553 msgid "" -"Integer (and floating point) types appear on the command line with decimal " -"text representation. When the option `separate` is false (the default value " -"is true), the prefix and value are combined into a single argument. In the " -"example above, this is rendered as `-i42`." +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 6a39929af73f4ba9b6455ed9fd287e08 +#: ../../src/topics/inputs.md:124 1c70336741a842a5b16b687642d1d9b4 msgid "" "File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the parameter " -"is optional. In the example above, this is rendered as `--file=/tmp/random/" -"path/whale.txt`. However, if the \"example_file\" parameter were not " -"provided in the input, nothing would appear on the command line." +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." msgstr "" -#: ../../src/topics/inputs.md:131 44ce716561cc4dff8fef1ca59f816c7c +#: ../../src/topics/inputs.md:131 9294c07c672b414f9c3895ed70b9b4ee msgid "" -"Input files are read-only. If you wish to update an input file, you must " -"[first copy it to the output directory](staging-input-files.md)." +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 9f1da592350f40ee88920465e2004148 +#: ../../src/topics/inputs.md:134 a07137c36e63495f836c483fd472904f msgid "" -"The value of `position` is used to determine where parameter should appear " -"on the command line. Positions are relative to one another, not absolute. " -"As a result, positions do not have to be sequential, three parameters with " -"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " -"than one parameter can have the same position (ties are broken using the " -"parameter name), and the position field itself is optional. The default " -"position is 0." +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 5116d91f247f44518eb21840415f6eaa +#: ../../src/topics/inputs.md:142 7513adabd3ae4701b17f578ac9f321d7 msgid "" -"The `baseCommand` field will always appear in the final command line before " -"the parameters." +"The `baseCommand` field will always appear in the final command line " +"before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 08b26d1688e3470288e73d587f052d88 +#: ../../src/topics/inputs.md:146 c3c82d25a75941b0b50a4a6bb826568f msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 f91994a4279a41bda3de41fe79008c62 +#: ../../src/topics/inputs.md:148 b11a5c7a13b345939e4ae15e1e2c0786 msgid "" "It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to provide " -"`type` field with `type: array` and `items` defining the valid data types " -"that may appear in the array. Alternatively, brackets `[]` may be added " -"after the type name to indicate that input parameter is array of that type." +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." msgstr "" -#: ../../src/topics/inputs.md:154 4b93a4f980634e88a8f34a38703fc906 +#: ../../src/topics/inputs.md:154 aa00bcfc6c0f4085ae52621a2f4ae8d9 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 de3e760ebb0e4ae099deddb978046a2c +#: ../../src/topics/inputs.md:160 e730b2b9bace4427bdd045556963634f msgid "`array-inputs-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 06ec811e8f0e43b8b929198533ac8082 -#: 797c06f0605d4e4ba306c2803a7834f9 d76d42c490a24b6daed944f45fe7a351 +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:86 +#: ../../src/topics/outputs.md:109 015a0f00c2b245e2b0e87735926da736 +#: 390384208d7b4771888f164b587c7b9a edb3ae59c48945f29c3086b16a5265d3 msgid "" -"Now invoke `cwltool` providing the tool description and the input object on " -"the command line:" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" msgstr "" "Agora chame o `cwltool` passando a descrição da ferramenta e o objeto de " "entrada na linha de comando:" -#: ../../src/topics/inputs.md:178 49406f30f62346968bb1250efc940f70 +#: ../../src/topics/inputs.md:178 13e59751d43b49f0ac366538a14f9c84 msgid "" -"The `inputBinding` can appear either on the outer array parameter definition " -"or the inner array element definition, and these produce different behavior " -"when constructing the command line, as shown above. In addition, the " -"`itemSeparator` field, if provided, specifies that array values should be " -"concatenated into a single argument separated by the item separator string." +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 3d8711f0135e4ab1b59fce94c83b97c0 +#: ../../src/topics/inputs.md:185 bb31c6784ea843ec88f185523cfa25df msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` in " -"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " -"where array values that are not defined with an associated key are marked by " -"a leading `-`. This will be demonstrated in the next lesson and is discussed " -"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " -"arrays of arrays, arrays of records, and other complex types." +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 6f146779d6a84888948751b8b1fd0515 +#: ../../src/topics/inputs.md:191 53817379078548b2aeb6195cae9cbab7 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 e5970a83876e4b5e9a02f2ab0030eb83 +#: ../../src/topics/inputs.md:193 e163c0cfe9694a85b2e42682f42970a5 msgid "" "Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be provided " -"together (they are exclusive). You can use records and type unions to group " -"parameters together to describe these two conditions." +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 0db71b22173846d7b8d4aeb66d2ed8ed +#: ../../src/topics/inputs.md:198 84e1ab25511c49d1baabb1f80f247b49 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 f90fd48656a7424aac304987adf1b068 +#: ../../src/topics/inputs.md:204 3d5dfc8ee47b458db638a9eed84b4938 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 3c8bd9134a1c4bda9461362df3257d6b +#: ../../src/topics/inputs.md:215 ecfb1d911a84400ba3db12fd0adf9279 msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 63bd06780bb949e5b1a1d10389c8c23f +#: ../../src/topics/inputs.md:217 24ba804374b4471d8e925d80670f9dff msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 0d448baa57f14e7783d3167611e8c659 +#: ../../src/topics/inputs.md:233 436707d9c7634732ad1e60d8294bd4ba msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the first " -"matching item (`itemC`) is added to the command line and remaining item " -"(`itemD`) is ignored." +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 202239a6e90044e39b676d641aa6d58a +#: ../../src/topics/inputs.md:236 01b168c5faf94ead8d836dfe39e4c592 msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 512ecb3349b0450cb741de4ed2d2e850 +#: ../../src/topics/inputs.md:252 e6d81d6549984689bae4533c6d01bd5b msgid "" -"In the third example, only `itemD` is provided, so it appears on the command " -"line." +"In the third example, only `itemD` is provided, so it appears on the " +"command line." msgstr "" -#: ../../src/topics/inputs.md:255 185ff0bb49e841c592b29112eb171bdc +#: ../../src/topics/inputs.md:255 ffddeeda8f04408ba73f7a59a4618da5 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 6cd5df09e4594d78a526f199ac577881 +#: ../../src/topics/inputs.md:257 cf22f21ec44c483986979316544a7c3b msgid "" -"If you use exclusive input parameters combined with expressions, you need to " -"be aware that the `inputs` JavaScript object will contain one of the " -"exclusive input values. This means that you might need to use an **or** " -"boolean operator to check which values are present." +"If you use exclusive input parameters and reference them in expressions, " +"you need to be aware that the `inputs` JavaScript object will contain one" +" of the possible, mutually-exclusive input values. Because the types of " +"these exclusive values may differ, you may need to check which type is in" +" use when you reference the properties of the `input` object." msgstr "" -#: ../../src/topics/inputs.md:262 9db9f784a5cd4ca5b90691d1e2e827ea +#: ../../src/topics/inputs.md:263 0fecb128b19b44d796b6c1b6de4f7166 msgid "" "Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from an " -"enum." +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." msgstr "" -#: ../../src/topics/inputs.md:265 09b1db3cc6c845058cf0ad4c24d71733 +#: ../../src/topics/inputs.md:266 7f1941698a6046e9b9e8a53736af949a msgid "`exclusive-parameter-expressions.cwl`" msgstr "`exclusive-parameter-expressions.cwl`" -#: ../../src/topics/inputs.md:271 84aa6e0c479f4528836691005129056e +#: ../../src/topics/inputs.md:272 60b585142f06489d9f48090b664b6d32 msgid "" "Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you provide a " -"valid value, such as “fasta” (one of the values of the enum), your command " -"should execute successfully:" +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as `fasta` (one of the possible values of the" +" enum), your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 76611ebb19764bdc8a1f6eacfb76138f +#: ../../src/topics/inputs.md:281 11fdeb057d674f118830f431ff019c15 msgid "" -"However, if you do not provide any input value, then `file_format` will be " -"evaluated to a `null` value, which does not match the expected type for the " -"output field (a `string`), resulting in failure when running your workflow." +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to `null`, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your " +"workflow." msgstr "" -#: ../../src/topics/inputs.md:289 bf9750d215be4294b1cf1e0490a0796a +#: ../../src/topics/inputs.md:290 8594cca9d93b4280b6cfee64c8a7c578 msgid "" -"To correct it, you must remember to use an or operator in your JavaScript " -"expression when using exclusive parameters, or any parameter that allows " -"`null`. For example, the expression could be changed to `$(inputs." -"file_format || 'auto')`, to have a default value if none was provided in the " -"command line or job input file." +"To correct it, you should explicitly handle the possibility of a `null` " +"value. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value `\"auto\"` if " +"none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/inputs.md:295 b5055c77f85e43609fe3e9b9839778e3 +msgid "" +"Here, the boolean “or” operator `||` in JavaScript is used for its " +"_short-circuiting_ property. If `inputs.file_format` is “true” in a " +"boolean context (e.g. a valid non-empty string from the enum), the " +"evaluation of the expression stops at the first operand of `||`; it " +"“short-circuits”. If however `inputs.file_format` is `null`, the whole " +"expression’s value becomes that of the second operand, which is why a " +"reasonable default can be provided there." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 612f9efa0ed04559a174c37958def6f7 +#: 723c2232310c4276aeac2bd6728d2912 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: 57eb990c11f044dfb60c012a92a30eb1 +#: 4d81aac1830045229e5c60c7959074d8 msgid "" -"Implementation extensions not required for correct execution (for example, " -"fields related to GUI presentation) and metadata about the tool or workflow " -"itself (for example, authorship for use in citations) may be provided as " -"additional fields on any object. Such extensions fields (e.g. `format: edam:" -"format_2572`) can use a namespace prefix listed in the `$namespaces` section " -"of the document (e.g. edam: http://edamontology.org/) as described in the " -"[Schema Salad specification][schema-salad]. Once you add the namespace " -"prefix, you can access it anywhere in the document as shown below. " -"Otherwise, one must use full URLs: `format: http://edamontology.org/" -"format_2572`." +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: a6e6155cb8ff40fb9d8b1fff3e94fb02 +#: 368f8993ae9d401488081d74ae5acd49 msgid "" "For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to cite " -"your tool." +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 063c28fc9e654dfd91c66da164ac1d3d +#: c80f2b180ca74afb8a1fc18f8686304b msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 8fcd2ae1ce8d4c7f951281ced81ab32d +#: 37b07ea9b7124842b8ba3040f70308e9 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: 639533652456427480fa311da7beb4f0 +#: 1cd5989ade6741aabe625c13bed3c8ed msgid "" -"For those that are highly motivated, it is also possible to annotate your " -"tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints at " -"hardware requirements in order to use the tool, and a few more metadata " -"fields." +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 266808daf2004bbd9830045fbc67a541 +#: ae7369ba14404d23b72d1ef30dcd4153 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 fd9b715bfa3243b19a919ad19843232d +#: ../../src/topics/operations.md:1 a79974b2f4534fcd8c7a04401e8a5556 msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 fb568063fa7a4cbe83c271772d3d62bc +#: ../../src/topics/operations.md:3 b6507c8e1625476b97708423acb4fd0e msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-line " -"tool, or an expression tool. It is a step of a workflow that specifies " -"inputs and outputs, but it does not provide enough information to be " -"executed." +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." msgstr "" -#: ../../src/topics/operations.md:7 981486166754435cbcd8152e93679405 +#: ../../src/topics/operations.md:7 047b09455db64524a71c47ab5192039f msgid "" -"You can create operations to visualize a workflow during development, before " -"you are ready to submit the workflow to a CWL runner:" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 7b165718ffeb42e793c97fad807f216f +#: ../../src/topics/operations.md:10 e9b2b97f3059460b867577a49934a338 msgid "`operations.cwl`" msgstr "`operations.cwl`" -#: ../../src/topics/operations.md:16 5e31cddd14414d31b7bd0a6c2745d272 +#: ../../src/topics/operations.md:16 d21e9444182d4e27bae934db4573ae99 msgid "" -"The `uppercase` step of the workflow is an operation. It can be used like a " -"command line tool or an expression. You can also plot it with the CWL Viewer " -"or `cwltool`:" +"The `uppercase` step of the workflow is an operation. It can appear where" +" a command line tool or an expression is expected. You can also plot it " +"with the CWL Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 02c372245dc9453ea0841026335e405b +#: ../../src/topics/operations.md:24 61e4ae6ed18e41708270eb358cd55277 msgid "" -"The output of the command above can be rendered with a Graphviz renderer. " -"The following image is rendered with the Sphinx Graphviz directive (this " -"user guide is built with Sphinx):" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx `{graphviz}` directive " +"(this user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 d331327285d1434e8c17187737345919 +#: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd msgid "" -"If you try running it with `cwltool`, the command will fail since `cwltool` " -"does not have enough information to know how to execute it:" +"The operation file will fail to run with `cwltool` because `cwltool` " +"lacks the necessary information to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 72705f8940bb4194bc5554fcc29eed49 +#: ../../src/topics/operations.md:59 e184470550e645f6b9ce658af7e65ecf msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 76b7c63107e94323859904415d07d31c +#: ../../src/topics/operations.md:67 3b90445d3428444cafd7d5c0e5884980 msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A " -"CWL runner could, for instance, use abstract operations with ID's that " +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 ebf56d267612461799bf801136e61b69 +#: ../../src/topics/outputs.md:1 35e7bad6fdc04bcf9bbfbb2d8d42cfa5 msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 f9cff6b272a24ef6ada90e263c1b1784 +#: ../../src/topics/outputs.md:3 6d912d40359c4d33a4f08abca83c00be msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 e482821911004cdd8c3ff1539c69368a +#: ../../src/topics/outputs.md:5 a6bd3f9e23de488394958fe7b59a61e0 msgid "" "The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name of " -"parameter, and `type` describing what types of values are valid for that " -"parameter." +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 e11fcfe1e84b476ea879810b76ff2cb8 +#: ../../src/topics/outputs.md:10 a229d8d983344e51a231edb5f667d84b msgid "" -"When a tool runs under CWL, the starting working directory is the designated " -"output directory. The underlying tool or script must record its results in " -"the form of files created in the output directory. The output parameters " -"returned by the CWL tool are either the output files themselves, or come " -"from examining the content of those files." +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or the result of examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 65c73a37f06a4782bf43f4acf4f1c77e +#: ../../src/topics/outputs.md:16 9845e517f7d848e5b59a97880ca6999f msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 e172dde545164fefac826d910ddd399e +#: ../../src/topics/outputs.md:19 0bf1ad2c43174e57a3ba8dd86f7c96b2 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 225f4d04c28149898f06bd771f741358 +#: ../../src/topics/outputs.md:21 553d535b023e4d69a888fe5b24bb8c5b msgid "" "In previous examples, the `baseCommand` was just a string, with any " -"arguments passed as CWL inputs. Instead of a single string we can use an " -"_array of strings_. The first element is the command to run, and any " -"subsequent elements are mandatory command line arguments" +"arguments passed as CWL inputs. Instead of a single string, we can use an" +" _array of strings_ as the value of `baseCommand`. The first element of " +"the array is the command to run, and any subsequent elements are " +"mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 14e9e446768a454ea786b3256b49632e +#: ../../src/topics/outputs.md:28 9b65071222c94951bed12ac53e964ee3 msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 4bd659cee1904868a7c33345f94f1300 +#: ../../src/topics/outputs.md:34 759ab0847b97479fb4a15e4b7d4e6565 msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 8803a28ccff846eea7d06f4bd908c763 +#: ../../src/topics/outputs.md:40 f9752ec303ab419c8db8adef3fa2466f msgid "Next, create a tar file for the example." msgstr "Agora, crie um arquivo tar para o exemplo." -#: ../../src/topics/outputs.md:45 661b62e554d64e449c69e475e5188f99 +#: ../../src/topics/outputs.md:47 4f96576528684f28a72b805f777769e6 msgid "" -"And now invoke `cwltool` with the tool description and the input object on " -"the command line:" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 44cdca5b777441baa246c87940df7264 +#: ../../src/topics/outputs.md:53 707803bec0cb42919905c7c321bd9d30 msgid "" -"The field `outputBinding` describes how to set the value of each output " -"parameter." +"The field " +"[`outputBinding`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding)" +" describes how to set the value of each output parameter." msgstr "" -#: ../../src/topics/outputs.md:62 edb34af3b22d418d9a6178c0ecbb8b80 +#: ../../src/topics/outputs.md:64 cbaec50871e04718883c8c91ff475d20 msgid "" -"The `glob` field consists of the name of a file in the output directory. If " -"you don't know name of the file in advance, you can use a wildcard pattern " -"like `glob: '*.txt'`." +"The " +"[`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) " +"field consists of the pattern to match file names in the output " +"directory. This can simply be the file's exact name. But if you don't " +"know the name of the file in advance, you can use a wildcard pattern like" +" `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 10e68fad866f4187981f0b365b957b03 +#: ../../src/topics/outputs.md:69 8a6e9173198241429effd911c3a7c4d7 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 77e1261484964ba9ac67d9fc9139a1d6 +#: ../../src/topics/outputs.md:71 a7c4fdaeda3e411fbeb802c5fa529ce9 msgid "" -"To capture a tool's standard output stream, add the `stdout` field with the " -"name of the file where the output stream should go. Then add `type: stdout` " -"on the corresponding output parameter." +"To capture a tool's standard output stream, add the " +"[`stdout`](https://w3id.org/cwl/CommandLineTool.html#stdout) field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 c66bd08354d54ccb9e3e1da89634a816 +#: ../../src/topics/outputs.md:75 cf2ef8dc7fda49308c09efe4f4ef5d7b msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 7d4056355da1451dbed6733fba8c3c38 +#: ../../src/topics/outputs.md:93 cbe236266dd148aaa96355e490a87cbe msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 8fed80f9633a4e87a67c651dc3160ce6 +#: ../../src/topics/outputs.md:95 77f86a7b94924a08b6ea2660218fe3c5 msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 6cba36e037d54f93add05fb16d2359bd +#: ../../src/topics/outputs.md:97 b34e30481fbd489d95fb7f8d5b5ab50c msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 08862892ecf849a1ba2f25ecc9e98227 +#: ../../src/topics/outputs.md:103 3aab0e0c9a78430f9caaa29a93303b56 msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 c5dcc68bb28041b3b96ac1af716b0db8 +#: ../../src/topics/outputs.md:116 9a14271c3180429988aaa14869f783a0 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions to " -"mark entries in arrays, as demonstrated in several of the upcoming sections." +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 53b95fd10d61462daf153d45e5517dad +#: ../../src/topics/parameter-references.md:1 c8a6ea340e6a43398e97b68e03a8bb3b msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 0702e71de81e493dac08a91d667569e3 +#: ../../src/topics/parameter-references.md:3 f5c0592ca28c46c2a89943f4f6f69a27 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file we " -"were interested in was called \"hello.txt\", and this was written into the `." -"cwl` file. This is not the best way to do this, as the \"hello.txt\" " -"filename may vary or be dependent on the input file(s) used. To avoid this " -"we can specify the name of the file we want in the job parameters file (`." -"yml`). In this example, you will see how to reference the value of input " -"parameters dynamically from other fields, which will allow us to then " -"specify the name of the file to extract." +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 a1703da32ad64fd2b8bdd423605b50bd +#: ../../src/topics/parameter-references.md:13 50db8add9b1942d986e581b8d21c2ee4 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 2f32531e47b4465594d41ddd218fb2fd +#: ../../src/topics/parameter-references.md:19 d01ad5fd9fea462cab0d4d776824b4e1 msgid "`tar-param-job.yml`" msgstr "`tar-param-job.yml`" -#: ../../src/topics/parameter-references.md:25 501dd6f9dbb1438f9a59f6a025639f35 +#: ../../src/topics/parameter-references.md:25 9b1e2f1a23ea4fe2af97ef5108f33376 msgid "" -"Create your input files and invoke `cwltool` with the tool description and " -"the input object on the command line:" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 1bcdd99111bd4bc5b75a8297bb61d9bb +#: ../../src/topics/parameter-references.md:36 06926a516ae6432d96e3eaa62202cd86 msgid "" -"Certain fields permit parameter references which are enclosed in `$(...)`. " -"These are evaluated and replaced with value being referenced." +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 32eae36c593e43a9a6b4e103a0c2028a +#: ../../src/topics/parameter-references.md:47 384fe8188f414eafbbb8d6b81bdfd779 msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 1d785e8a450140a982142aa0fa906257 +#: ../../src/topics/parameter-references.md:51 56ead1c8d45c43bdbcbc6f7cbb8e1e92 msgid "" -"The value of the \"inputs\" variable is the input object provided when the " -"CWL tool was invoked." +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 e862bb8bc3e84e24a2aa5ec34298cfd5 +#: ../../src/topics/parameter-references.md:54 56bca89e314c4223b33d7fe63c9b771d msgid "" -"Note that because `File` parameters are objects, to get the path to an input " -"file you must reference the path field on a file object; to reference the " -"path to the tar file in the above example you would write `$(inputs.tarfile." -"path)`." +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 46ffaab11be040cea96a294d9a814738 +#: ../../src/topics/parameter-references.md:59 1c1ab240c4114572bb4e42955baad361 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 890d619c415741179c83ffcd56833fbe +#: ../../src/topics/parameter-references.md:61 055d3268859c46c4b7db5005608bae05 msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 373e1847d9f745d7a749928642c8e0e3 +#: ../../src/topics/parameter-references.md:63 2ed66835bd9044adbfdd0b5097787f22 msgid "" -"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 90d3624e062c41c7a6d1a9824515d0df +#: ../../src/topics/parameter-references.md:69 f592619e4b2c497e80cd75da0548cf07 msgid "" -"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter)" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 76d09490bd464b708c28991dbff0104e +#: ../../src/topics/parameter-references.md:72 81ea71a35020421187dc18ddd151c62f msgid "" -"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding)" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 f33c76e590dd4feaac1e3cf568069d33 +#: ../../src/topics/parameter-references.md:74 ea0117748adc4324901024f21eed04ac msgid "" -"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 74ed4a06c1984c58826ddceb1a45a4ea +#: ../../src/topics/parameter-references.md:77 3a30e73176cf4e4eb9f26770a176b9c9 msgid "" -"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding)" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 eba3362d34354daa89dc516722c6fbd0 +#: ../../src/topics/parameter-references.md:81 551c199c9a6344fca9bfacfb69fc4e53 msgid "" -"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" -"v1.0/Workflow.html#WorkflowOutputParameter)" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 e924874af32d4be19c5e8446768226dd +#: ../../src/topics/parameter-references.md:85 7008a1ff1af54fda827637e787e5c7dd #, fuzzy msgid "" -"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -"De [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" +"De " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -#: ../../src/topics/parameter-references.md:89 b162113f364445af9ff1bfc8a6610e13 +#: ../../src/topics/parameter-references.md:89 45743e1b261c4195856de0c2e30ea72e msgid "" -"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." -"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -"De [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) e [ExpressionToolOutputParameter](http://www.commonwl." -"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"De " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" e " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -#: ../../src/topics/parameter-references.md:92 aa721077e16948c3a5bb8ef5bd7aff04 +#: ../../src/topics/parameter-references.md:92 0ae32d1db5f9452bbfcbbc4719b0b9f1 msgid "" -"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement)" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 2fad0c2bc2834350826b22c454d33cf0 +#: 7e1907ff15c74f488187531de336eccf msgid "" -"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" -"CommandLineTool.html#InitialWorkDirRequirement)" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 9e303aa89a9b4447b0dbdc5ac0a0eb9e +#: 678874668fed4f4d80a1b0990e183e2f msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 7a4eb47c25a54d11a00eb73e9333ad1c +#: e2882880886046ac88ae1c0d414366d1 msgid "" -"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef)" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: 8a957bc8e577476bb59647661b3c0990 +#: 05324169d8ae48d4a1abe3a0ac07c891 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: 2b31f1dec3f5498e9e363a4f1f50dc8d +#: 1f5b72d7ec82442ba29baa14a03f061b msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 5a5f84ecc2f449bf9f037dc9da0ac670 +#: e708866921ea49d69d3c2a32d63ea468 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " -"include a `SoftwareRequirement` field in the `hints` section. This may also " -"help to avoid confusion about which version of a tool the description was " -"written for." +"include a " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)" +" field in the `hints` section. This may also help to avoid confusion " +"about which version of a tool the description was written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: ee89f1526c1f4452b4e36ba67bb59747 +#: 6f722d6fd54f485fa964076c8d08938b msgid "" -"In this example, the software requirement being described is InterProScan " -"version 5.21-60." +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: c76cec44f5424f6087df28aa33c521a2 +#: 5c1236ec57c64079bfb7c779524b12ad msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the [dependency " -"resolvers configuration][dependencies]." +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 072d7b3ce3284ed994ff0736b43bbb86 -msgid "" -"As well as a version number, a unique resource identifier (URI) for the tool " -"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " -"up in the [SciCrunch][scicrunch] registry, which provides a portal for " -"finding, tracking, and referring to scientific resources consistently. If " -"you want to specify a tool as a `SoftwareRequirement`, search for the tool " -"on SciCrunch and use the RRID that it has been assigned in the registry. " -"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " -"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." -"org][identifiers]) in the `specs` field of your requirement description. " -"Other good choices, in order of preference, are to include the DOI for the " -"main tool citation and the URL to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 395d611104604a28b78e11b112a95027 +#: 1a8b8aadf1c64e87b8b670e288bc14bc +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)," +" search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 d10c792550e8498c8ee384d3093da306 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 811b4db0b1794fa89dc870f6cb59a3cd +#: ../../src/topics/staging-input-files.md:3 ac2ef1fced5f4044861761a11c35e78a msgid "" -"Normally, input files are located in a read-only directory separate from the " -"output directory. This causes problems if the underlying tool expects to " -"write its output files alongside the input file in the same directory. You " -"use `InitialWorkDirRequirement` to stage input files into the output " -"directory. In this example, we use a JavaScript expression to extract the " -"base name of the input file from its leading directory path." +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use " +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)" +" to stage input files into the output directory. In this example, we use " +"a JavaScript expression to extract the base name of the input file from " +"its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 7159b5c5023c47128057c4116cce69f4 +#: ../../src/topics/staging-input-files.md:9 d8ca16f5321e486ebe8ea9f9752b3737 msgid "`linkfile.cwl`" msgstr "`linkfile.cwl`" -#: ../../src/topics/troubleshooting.md:1 3bfa6791d78f43629de90345f4441ebb +#: ../../src/topics/troubleshooting.md:1 aa3eddcaa0684f86ba67aafcd57872e7 msgid "Troubleshooting" msgstr "Solucionando Problemas" -#: ../../src/topics/troubleshooting.md:3 9a6bd5b684a740ed9e8993d9f8607774 +#: ../../src/topics/troubleshooting.md:3 3207f476afa04158bd26db39a16a2df5 msgid "" -"In this section you will find ways to troubleshoot when you have problems " -"executing CWL. We focus on `cwltool` here but some of these techniques may " -"apply to other CWL Runners." +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 6db8a02139644598894220d538c590b9 +#: ../../src/topics/troubleshooting.md:6 1d47f4ce04554cabb1ccf40a13ee42ec msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 f0da0f6283d44bcc95224eb9fe2d1764 +#: ../../src/topics/troubleshooting.md:8 0c25602a83e441b48b536eb49568f2b6 msgid "" "You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor output " -"files, but created while your workflow is running). By default, these files " -"are created in a temporary directory but writing them to a separate " -"directory makes accessing them easier." +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 e2fc28b44ffe4254892a7c7973dc80c4 +#: ../../src/topics/troubleshooting.md:14 36ec60b80c714357a4274217274136ff msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " -"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " -"olleH\". However, the second step, `step_b`, **has a typo**, where instead " -"of executing the `rev` command it tries to execute `revv`, which fails." +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 505c7cf9ee9c4af1aeed29002eed1b33 +#: ../../src/topics/troubleshooting.md:20 6f34038054ac4f4fa0b0ad9cbc3ecdc7 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 4c31fd11a28943538690d04baa2b5dd0 +#: ../../src/topics/troubleshooting.md:27 b777877c88024c9fb06a6614029ef8d6 msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " -"(`cwltool` will create the directory for you if it does not exist already):" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 a8532ac700014db4bd8ef690a27fb844 +#: ../../src/topics/troubleshooting.md:35 8654b7f2f4464d13be4b47729e1f07e5 msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. You " -"can inspect the intermediate files created:" +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 94a6148512b24b90b87fd1312a926d75 +#: ../../src/topics/troubleshooting.md:44 04e80f7ce14d4d73bc5d290dcf01bcdb msgid "" -"Each workflow step has received a unique ID (the long value that looks like " -"a hash). The `${HASH}.status` files display the status of each step executed " -"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " -"output of the command above." +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 ec4165b7c25c449db6a8804161805e80 +#: ../../src/topics/troubleshooting.md:48 719917cb0fd849f5a328671df8726189 msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " -"the `step_b`). After fixing the typo, when you execute `cwltool` with the " -"same arguments as the previous time, note that now `cwltool` output contains " -"information about pre-cached outputs for `step_a`, and about a new cache " -"entry for the output of `step_b`. Also note that the status of `step_b` is " -"now of success." +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 5c0b71a6376848d4aa491854ea2d185d +#: ../../src/topics/troubleshooting.md:59 2a9dbb3ad7564f5aa103349c45ee7925 msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had " -"been cached, and there was no change in its execution or output. " +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " "Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for " -"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " -"re-evaluate steps unnecessarily." +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 95b832552e8443ea9c652f8c95afc01e +#: ../../src/topics/using-containers.md:1 7439fe097aa4459ba1e4c0e28fc59b9a msgid "Using Containers" msgstr "Utilizando Containers" -#: ../../src/topics/using-containers.md:3 561fc9c561bc492ea82c17784dfd439c +#: ../../src/topics/using-containers.md:3 eff5c6ac1cad44f9862585daf0a91298 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 2420b16855cf4b25af5bcb87413f6dd9 +#: ../../src/topics/using-containers.md:5 50d1a644bc8c49f78c453e4e0f3c07c8 msgid "" -"[Docker][docker] containers simplify software installation by providing a " -"complete known-good runtime for software and its dependencies. However, " -"containers are also purposefully isolated from the host system, so in order " -"to run a tool inside a Docker container there is additional work to ensure " -"that input files are available inside the container and output files can be " -"recovered from the container. A CWL runner can perform this work " -"automatically, allowing you to use Docker to simplify your software " -"management while avoiding the complexity of invoking and managing Docker " -"containers." +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." msgstr "" -#: ../../src/topics/using-containers.md:15 f5266ee2c2b34170bc89cb501b869893 +#: ../../src/topics/using-containers.md:15 4b0f6cfc8a774c77bfbc99e568af2ece msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the container." +"input files to reflect the location where they appear inside the " +"container." msgstr "" -#: ../../src/topics/using-containers.md:18 728166bf41504e1d89b755400742a1b4 +#: ../../src/topics/using-containers.md:18 27c02a5d479a420eab7d14888d9fb288 msgid "" -"This example runs a simple Node.js script inside a Docker container which " -"will then print \"Hello World\" to the standard output." +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 104351ac29d247cb8e017228e2c9b3d8 +#: ../../src/topics/using-containers.md:21 1a62a93ab20b4f2ca1e13ded3a767dc5 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 e11a38bfb30b404c99d223647960cb16 +#: ../../src/topics/using-containers.md:27 ccc2874840c3476bb714ddf4bdbf0f3e msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 7ed0bd21e998417cb02fdcb8e44734b6 +#: ../../src/topics/using-containers.md:33 d766b66de4714a5da0cd87ed886cc32f msgid "" "Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that is " -"really new is the `dockerRequirement` section." +"Most of this has been explained in previous sections, the only part that " +"is really new is the " +"[`dockerRequirement`](https://w3id.org/cwl/CommandLineTool.html#DockerRequirement)" +" section." msgstr "" -#: ../../src/topics/using-containers.md:44 9dcddf6812ba4bc2a7d6c5fcdb978a68 +#: ../../src/topics/using-containers.md:44 1f02618ab6254459ae71f72844e3cc18 msgid "" -"`baseCommand: node` tells CWL that we will be running this command using the " -"Node Js runtime that is meant for Javascript files. We then need to specify " -"some `hints` for how to find the container we want. In this case we list " -"just our requirements for the docker container in `DockerRequirements`. The " -"`dockerPull:` parameter takes the same value that you would pass to a " -"`docker pull` command. That is, the name of the container image (you can " -"even specify the tag, which is good idea for best practices when using " -"containers for reproducible research). In this case we have used a container " -"called `node:slim`." +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 bc1a09475f154562a4db445bf81ac92f +#: ../../src/topics/using-containers.md:52 54cade4978ec463bbb5c0d8c08e27adb msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " -"the tool description and the input object on the command line:" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 2e117019ace84604a8ed5a31214c2587 +#: ../../src/topics/using-containers.md:55 6541d0cd9f6c4c43b8601715cc35e585 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 d0d5b2a1a008411e92859a72101088c1 +#: ../../src/topics/using-containers.md:69 6abf220b7fa4479394ed33447cdd070e msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 591d1cd0282b4095a267b44da7d59804 +#: ../../src/topics/using-containers.md:72 d2dd89a5edde4f2eab4c2baf0cc78745 msgid "" -"In this example, the path to the script `hello.js` is `/home/me/cwl/" -"user_guide/hello.js` outside the container but `/var/lib/cwl/" -"job369354770_examples/hello.js` inside the container, as reflected in the " -"invocation of the `node` command." +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 9f989fff165448ecbcaad6adc0f58d6b +#: ../../src/topics/workflows.md:1 06281a10592d42509566c8fc51f8d4da msgid "Workflows" msgstr "Workflows" -#: ../../src/topics/workflows.md:3 212c82dca23645e89d8b5bb7599f2d25 +#: ../../src/topics/workflows.md:3 325a656f9b8e4c1fa6f699cd8c447d00 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 7530029ec04746f2a888dcbc10aa5ce4 +#: ../../src/topics/workflows.md:13 b92275181c9e480da64e660b7aca0745 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 c1f1d644b37b4f018b87e15249d8758d +#: ../../src/topics/workflows.md:41 be2540315f854b8e9a1d257bcabd78db msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier examples." +"command-line tool, and the expression tool showed in the earlier " +"examples." msgstr "" -#: ../../src/topics/workflows.md:51 2d07232b7d9c415b8ad971e8cbcd9577 +#: ../../src/topics/workflows.md:51 3be900594bb743399854b95baa9ae2f9 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 fa1f770ffeba4b74bcb200cd3949e070 +#: ../../src/topics/workflows.md:81 5133c4e062bc4e479ce1dc8abbb08107 msgid "" -"A command-line tool or expression tool can also be written directly in the " -"same CWL document as the workflow. For example, we can rewrite the `echo-" -"uppercase.cwl` workflow as a single file:" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 570020792e824c2ba732bcc2c0134aa1 +#: ../../src/topics/workflows.md:91 83bc2796889f4dccb713764ac1b3c3ad msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 8a50c511004941d0917a8f0d471467f0 +#: ../../src/topics/workflows.md:150 5a9a1dd6ed1f4ca6803f1d235c4fd392 msgid "" -"Having separate files helps with modularity and code organization. But it " -"can be helpful writing everything in a single file for development. There " -"are other ways to combine multiple files into a single file (e.g. `cwltool --" -"pack`) discussed further in other sections of this user guide." +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 4d2bf0341836405d9729c47d8020faea +#: ../../src/topics/workflows.md:160 277ed30d4b3a4156a4523e8d10e6ce60 msgid "" "For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this " -"user guide in more detail." +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 dd6fc85f74984517b284853a0d46c122 +#: ../../src/topics/workflows.md:165 82818ab17aa4403eb982fd81a14a5865 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 f857d80cd5d84622a560c895ab260a92 +#: ../../src/topics/workflows.md:167 3d8b98e8d03548699fadb22198de9b20 msgid "" -"This workflow extracts a java source file from a tar file and then compiles " -"it." +"This workflow extracts a java source file from a tar file and then " +"compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 02e7e81cdf7e4226973f910cd57b8ccf +#: ../../src/topics/workflows.md:170 c61097c695424f7195e8205a23b6ecff msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 3a88d92f41aa4daaad4f4cc6829184b3 646367f222ea41e5987561941d17c4f9 +#: 6660c48f51d94d4fbcc05656e154059e bd2bab6c11614fa983ca8dab1408e1d8 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 aaba75eb272245db82d072fed97b311c +#: ../../src/topics/workflows.md:180 f0831481a43548039fbc4fd17555af57 msgid "" -"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" -"github.com/common-workflow-language/user_guide/blob/" -"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" "workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" -"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 f8a6e1af5f0349a5a384be0629c37ac8 +#: ../../src/topics/workflows.md:183 5ff059fc8ae6471c8ea86dab7e5a93f5 msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a " -"run:" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" msgstr "" -#: ../../src/topics/workflows.md:185 c4f854c7a279404da3688bdf424c7c5e +#: ../../src/topics/workflows.md:185 822e5d0a097b4109960d621a72a3c009 msgid "`1st-workflow-job.yml`" msgstr "`1st-workflow-job.yml`" -#: ../../src/topics/workflows.md:191 d383ce45139944cb85768627965d9467 +#: ../../src/topics/workflows.md:191 4a4db7da861547639524083bf35ccfc0 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 84293afa7a6c40f2af0b980c89581fc7 +#: ../../src/topics/workflows.md:205 ed16b30eaa4747f79b6dd10a19188d8c msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 e66daf8af53849109936c36ca7d2b2c9 +#: ../../src/topics/workflows.md:212 6428bd7bd3be4393bfe5675f8e45ff94 msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a workflow." +"document. The `class` field indicates this document describes a " +"workflow." msgstr "" -#: ../../src/topics/workflows.md:221 8fbfbb587b264dcf98a3cea16dd36ef3 +#: ../../src/topics/workflows.md:221 d6abec8805f649fca668292412263f78 msgid "" -"The `inputs` section describes the inputs of the workflow. This is a list " -"of input parameters where each parameter consists of an identifier and a " -"data type. These parameters can be used as sources for input to specific " -"workflows steps." +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 5cdbc4771ea841b4960362b930de2af6 +#: ../../src/topics/workflows.md:233 22bf3e4910ef4f86a2e8f6d5a6cf0d42 msgid "" -"The `outputs` section describes the outputs of the workflow. This is a list " -"of output parameters where each parameter consists of an identifier and a " -"data type. The `outputSource` connects the output parameter `classfile` of " -"the `compile` step to the workflow output parameter `compiled_class`." +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 2e8a41fe43984dc6b4cf430e1ff66b28 +#: ../../src/topics/workflows.md:248 e0429688fce445da8083e69323e5b020 msgid "" "The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second step " -"compiles the file from the first step using the java compiler. Workflow " -"steps are not necessarily run in the order they are listed, instead the " -"order is determined by the dependencies between steps (using `source`). In " -"addition, workflow steps which do not depend on one another may run in " -"parallel." +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 78c20aa5a5724da6a4c908849c571334 +#: ../../src/topics/workflows.md:256 980f5eada57c4fadbb783838ded1fa0b msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input " -"parameters, `tarfile` and `extractfile` and one output parameter " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 1606a2f059eb4b0c9e90f2f0cbbe779b +#: ../../src/topics/workflows.md:261 3532e165842f4ebb8db0c78208071555 msgid "" -"The ``in`` section of the workflow step connects these two input parameters " -"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " -"`source`. This means that when the workflow step is executed, the values " -"assigned to `tarball` and `name_of_file_to_extract` will be used for the " -"parameters `tarfile` and `extractfile` in order to run the tool." +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 b456b11e2760479bbf81a773a3e1f8ee +#: ../../src/topics/workflows.md:267 04a4db2f3da94ce29e7999039ee13fde msgid "" -"The `out` section of the workflow step lists the output parameters that are " -"expected from the tool." +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 0fa01fcec32049c989ad1d68841c74de +#: ../../src/topics/workflows.md:278 2651ee113a3d4b79b138854ebe729f48 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " -"in [Additional Arguments and Parameters](additional-arguments-and-parameters." -"md)). The output of this step `classfile` is connected to the `outputs` " -"section for the Workflow, described above." +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 2bc9829f95584a269eb577c610b2a80c +#: ../../src/topics/workflows.md:285 177040bf9c0045f2878f42bcdd8cbd2d msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 0e5e6445bfcb42a4bd03612316dd7225 +#: ../../src/topics/workflows.md:287 e8adc2f7c5ac4464b0711712617b8bbe msgid "" -"Workflows are ways to combine multiple tools to perform a larger operations. " -"We can also think of a workflow as being a tool itself; a CWL workflow can " -"be used as a step in another CWL workflow, if the workflow engine supports " -"the `SubworkflowFeatureRequirement`:" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 0b83c1028b0e43ba972609e4302bc8a2 +#: ../../src/topics/workflows.md:297 44d281d99cd944478db98446a984c001 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 cbe1ef068b0c417b953655e132333447 +#: ../../src/topics/workflows.md:300 d7b60ce81ea741ffa08f2c2d9d7cca69 msgid "`nestedworkflows.cwl`" msgstr "`nestedworkflows.cwl`" -#: ../../src/topics/workflows.md:309 a691c36a15044b11a6d037d16f818a6d +#: ../../src/topics/workflows.md:309 a5b7a1ab16e34bda8744ffadacdda3e8 msgid "" -"This two-step workflow starts with the `create-tar` step which is connected " -"to the `compile` step in orange; `compile` is another workflow, diagrammed " -"on the right. In purple we see the fixed string `\"Hello.java\"` being " -"supplied as the `name_of_file_to_extract`." +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 2e9797fcd4f04f56b5d2b2f1a3e306d5 +#: ../../src/topics/workflows.md:314 8654f2d86b644609aaa5b9b73db30bda msgid "" "\"Visualization \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/1st-" +"workflow.cwl\">\"Visualization" msgstr "" -#: ../../src/topics/workflows.md:322 28f4139911b44eeeb7afd31e9f7cae7b +#: ../../src/topics/workflows.md:322 7ce847ab54224452b6425de2a55ec893 msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " -"CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " -"to become the step's input/outputs." +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 4a6cb397a20241beab24d956920a8379 +#: ../../src/topics/workflows.md:336 d621821d2c1b403cb7415b381dd883f6 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and `*.java` " -"filename. This is generally best-practice, as it means it can be reused in " -"multiple parent workflows, or even in multiple steps within the same " -"workflow." +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 dccb5472a5dc42b7946dd9245a71ecf0 +#: ../../src/topics/workflows.md:341 358c612f175241f7bf148a04d75e00c9 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar " -"file at `tarball`, which we will prepare in the `create-tar` step. At this " -"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " -"specific input/output names, as those also appear in its usage as a tool." +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 de1e18b69f654cabb75e52b47058030a +#: ../../src/topics/workflows.md:347 c6297c120e004ae8b52d5b519fbc04d2 msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3433,443 +3564,879 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 b947e62f4b3b4c10b95737f1839bcc5a +#: ../../src/topics/workflows.md:366 66f76677f4ce42baa8a8813410ea5aee msgid "" -"In this case our step can assume `Hello.java` rather than be parameterized, " -"so we can use hardcoded values `hello.tar` and `Hello.java` in a " -"`baseCommand` and the resulting `outputs`:" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 2ed0258a3a104ed5ba3b6b95ad998839 +#: ../../src/topics/workflows.md:383 a8ccb9f9ab4448e087ea8448d620d33c msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This is " -"generally not best practice, as the tool then can't be reused. The reason " -"for doing it in this case is because the command line is hard-coded with " -"filenames that only make sense within this workflow." +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 6584c0995288450b8a01c35fa231afb6 +#: ../../src/topics/workflows.md:389 afe43b9e92e949a589f493293eff2903 msgid "" -"In this example we had to prepare a tar file outside, but only because our " -"inner workflow was designed to take that as an input. A better refactoring " -"of the inner workflow would be to take a list of Java files to compile, " -"which would simplify its usage as a tool step in other workflows." +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." msgstr "" -#: ../../src/topics/workflows.md:394 19237513fd134c33801a7af08f74e70c +#: ../../src/topics/workflows.md:394 239eef3a740d42a69208a8f4e716d2b3 msgid "" "Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL " -"Tool description, care must be taken to improve its usability in multiple " -"workflows." +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 b66e0d0a36994b3182a3784bda8ffc19 +#: ../../src/topics/workflows.md:398 96d1ca78cc324f40b61c4b7330447db2 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 3bfb9851302248568bb4535ddc87a27f +#: ../../src/topics/workflows.md:400 eab4437bf9994b649954221375e3dd6d msgid "" "Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " -"run a tool or workflow multiple times over a list of inputs. The workflow " -"then takes the input(s) as an array and will run the specified step(s) on " -"each element of the array as if it were a single input. This allows you to " -"run the same workflow on multiple inputs without having to generate many " -"different commands or input yaml files." +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 78a5a600f8cc49ce8055c77a596ad833 +#: ../../src/topics/workflows.md:411 c245ba0ae2074fa388ad6c35695033c8 msgid "" -"The most common reason a new user might want to use scatter is to perform " -"the same analysis on different samples. Let's start with a simple workflow " -"that calls our first example (`hello_world.cwl`) and takes an array of " -"strings as input to the workflow:" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 f9618882e0a14a0b84ff9751346dc291 +#: ../../src/topics/workflows.md:415 83537938ce1244709f9b72269b048d63 msgid "`scatter-workflow.cwl`" msgstr "`scatter-workflow.cwl`" -#: ../../src/topics/workflows.md:421 4fe03daddd304a9b828fdd1c29f0d072 +#: ../../src/topics/workflows.md:421 4f507925766e48ae8f713d56051a5e29 msgid "" -"Aside from the `requirements` section including `ScatterFeatureRequirement`, " -"what is going on here?" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 7ab022708a9642ab8aa2e79ea7810381 +#: ../../src/topics/workflows.md:429 ccbbba3189404241a44736c970249b84 msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 fe144641fc8040b283f15b2b99ecb5a2 +#: ../../src/topics/workflows.md:441 31eff13bb8334fc7b6d48ef6c5b1ce33 msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This field " -"tells the runner that we'd like to scatter over this input for this " -"particular step. Note that the input name listed after scatter is the one of " -"the step's input, not a workflow level input." +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 f13d1b071a7f4a75a4cdee40ecef14fa +#: ../../src/topics/workflows.md:445 0d5cf8b82dbd47f2abd1ed16b9b3eb61 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if you " -"expect that the final output of your workflow will now have multiple outputs " -"to collect, be sure to update that to an array type as well!" +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 b0b2e63d2b8a4fd0983e976c16440da4 +#: ../../src/topics/workflows.md:450 38b7042a270043ba82c11cf2e758f0c8 msgid "Using the following input file:" msgstr "Usando o seguinte arquivo de entrada:" -#: ../../src/topics/workflows.md:452 47ac993a90fe46ca92e97d6b67b3276b +#: ../../src/topics/workflows.md:452 b3fc75c262fe4a3a8e8bfba1abb07b3d msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 f5b8681b3c3b4890a86d7b9fb812d958 +#: ../../src/topics/workflows.md:458 f9fa7046c89c417db51dc7c8a026fd5d msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " -"calls the command `echo` on a message. If we invoke `cwltool scatter-" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 74e70fec6d2447bbbd2a5bc8af1fa58c +#: ../../src/topics/workflows.md:466 b6a33410ee9a45d7bf7b2ba56f786f8f msgid "" -"You can see that the workflow calls echo multiple times on each element of " -"our `message_array`. Ok, so how about if we want to scatter over two steps " -"in a workflow?" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 76fed9e7ad1d4792b7bb364bb684eeb2 +#: ../../src/topics/workflows.md:469 99b5c8a845ab4beb8524a69c051e2d42 msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding the " -"following lines instead of `outputs: []`" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 bef387d9be1f4ca19a97023cfdd1c910 +#: ../../src/topics/workflows.md:472 97bf58937d3f4e98af702e3c1a418992 msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 eea1be83da574f39914566d835701b4a +#: ../../src/topics/workflows.md:480 173bd28708834f11a2a1366b579b7ad7 msgid "" -"And add a second step that uses `wc` to count the characters in each file. " -"See the tool below:" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 2043f12eb2ce4424b133e0dc0b62aafc +#: ../../src/topics/workflows.md:483 4afccfe982ff4be2be96cbe5889e5014 msgid "`wc-tool.cwl`" msgstr "`wc-tool.cwl`" -#: ../../src/topics/workflows.md:489 87ba95507fc44dbca4cb6c5283ce50f9 +#: ../../src/topics/workflows.md:489 63595d35dded4911aab0be3a165eec0c msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under each " -"step:" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" msgstr "" -#: ../../src/topics/workflows.md:491 e6e1a79638d74547b00c64e3c8b05710 +#: ../../src/topics/workflows.md:491 a7f96ec6e4f24c62ac0f5b6edcc9734b msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 03fb16e74bf14c49b43e35ef6cb45030 +#: ../../src/topics/workflows.md:497 122452b7d7114c3fa53cbea286703023 msgid "" -"Here we have placed the scatter field under each step. This is fine for this " -"example since it runs quickly, but if you're running many samples for a more " -"complex workflow, you may wish to consider an alternative. Here we are " -"running scatter on each step independently, but since the second step is not " -"dependent on the first step completing all languages, we aren't using the " -"scatter functionality efficiently. The second step expects an array as input " -"from the first step, so it will wait until everything in step one is " -"finished before doing anything. Pretend that `echo Hello World!` takes 1 " -"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " -"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " -"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " -"actually finish in 8 minutes because the first step must wait on `echo Hallo " -"welt!`. You can see how this might not scale well." +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 eca3380c60094df2b91b44b5f7718fae +#: ../../src/topics/workflows.md:509 85dd63daf04546b78bdcb68c1d985fa9 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can " -"make an entire workflow a single step in another workflow! Convert our two-" -"step workflow to a single step subworkflow:" +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 6c61733fe4284f51a6b46e89cafe78c4 +#: ../../src/topics/workflows.md:513 fac138ba275745898b763a7d719a8235 msgid "`scatter-nested-workflow.cwl`" msgstr "`scatter-nested-workflow.cwl`" -#: ../../src/topics/workflows.md:519 0585f83162c349969391c9456a884f28 +#: ../../src/topics/workflows.md:519 508ef2240879445594b0f262ed11a01d msgid "" -"Now the scatter acts on a single step, but that step consists of two steps " -"so each step is performed in parallel." +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 f209343966db4d46b4611d3620c3b496 +#: ../../src/topics/workflows.md:522 b0bf01dad1234a1db3c87b10953e42ef msgid "Conditional Workflows" msgstr "Workflows Condicionais" -#: ../../src/topics/workflows.md:524 5a2661ce35dc4d79a15da1e17c0a95ec +#: ../../src/topics/workflows.md:524 8d933ed1ec6e408589f781e3a425b869 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 8f7ee09c9d6b491195e2d80315dae398 +#: ../../src/topics/workflows.md:527 9ac7b4f71621411da9a4ca3bc277dcb0 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 966acff0d3d24104ae9673df8a790fb1 +#: ../../src/topics/workflows.md:566 4a4a2b2b99b44d449adb246cebce0a26 msgid "" -"The first thing you'll notice is that this workflow is only compatible for " -"version 1.2 or greater of the CWL standards." +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 d60e1df759654f1b873276cf0296f234 +#: ../../src/topics/workflows.md:573 4742fe09a4264fb8be6f092519de5d72 msgid "" "The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when` is " -"where the condition validation takes place. In this case only when `in1` " -"from the workflow contains a value `< 1` this step will be executed." +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." msgstr "" -#: ../../src/topics/workflows.md:587 69aa8d3c9d9a4fe4a62875827648d95f +#: ../../src/topics/workflows.md:587 b33ecd2b8af042feb08687e32d4b6bbf msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " -"will pass the first conditional step and will therefore be executed and is " -"shown in the log by `INFO [step step1] start` whereas the second step is " -"skipped as indicated by `INFO [step step2] will be skipped`." +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 fee34c880e964e08b040adf2d3831803 +#: ../../src/topics/workflows.md:607 7cd80b31a94543358ece7a2d413adce9 msgid "" -"When a value of 3 is given the first conditional step will not be executed " -"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 cb9e82cf4b484ca7be19612b14fbdf33 +#: ../../src/topics/workflows.md:627 9679e32f65e0482a8b083387e4a18c1f msgid "" -"If no conditions are met for example when using `--val 2` the workflow will " -"raise a permanentFail." +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 8e7c3365f0f94038930f71666f05170f +#: ../../src/topics/yaml-guide.md:1 4fa76441f95d45fab76ab7eef8d7d4d2 msgid "YAML Guide" msgstr "Guia de YAML" -#: ../../src/topics/yaml-guide.md:6 cbe6f35c21044054a010767f2f0cae46 +#: ../../src/topics/yaml-guide.md:6 705765787eb84ecaae004194225924cb msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers and " -"humans. This guide introduces the features of YAML that are relevant when " -"writing CWL descriptions and input parameter files." +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 2cc21093311548cd837aa7b3f0939093 +#: ../../src/topics/yaml-guide.md:13 cb243f6ab11f48ffb5c91945c4e0d101 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 6e7ea76e8aeb477cbb8197efed33e53d +#: ../../src/topics/yaml-guide.md:16 cfc95d15e33a492f842649f92ced941d msgid "Contents" msgstr "Conteúdo" -#: ../../src/topics/yaml-guide.md:18 482e121a6e74428dbe6ad1f772f14684 +#: ../../src/topics/yaml-guide.md:18 f618d44d202f4c2ea6ff72a1dca2c659 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 179290eee12343dd9aa4d49207cf7c68 +#: ../../src/topics/yaml-guide.md:19 36bfa6ed40c54bd99826bedff12c759d msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 7880db40e98e4aaabdc96def3d9f515d +#: ../../src/topics/yaml-guide.md:20 61913753eb0c4c728889b47f1110be24 msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 75f3b499494b445f9f9a532d178cbc10 +#: ../../src/topics/yaml-guide.md:21 0de824a05eea46209aafa6f9e2e8623c msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 2b900b2779c84de5bbd3c933c56e5922 +#: ../../src/topics/yaml-guide.md:22 95627bc476b3415ca4d77246125137d2 msgid "[JSON Style](#json-style)" msgstr "[Estilo JSON](#json-style)" -#: ../../src/topics/yaml-guide.md:24 189db6d0e54a400eb5615e259354827e +#: ../../src/topics/yaml-guide.md:24 3f64a6d33d9a4c22a8a839a8def82686 msgid "Key-Value Pairs" msgstr "Pares de Chave-Valor" -#: ../../src/topics/yaml-guide.md:26 e689c0e1dcd645348ceed51e91eb9ad0 +#: ../../src/topics/yaml-guide.md:26 2f74f6eaa8d84dc9b4d0a166844dedbe msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " -"is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have special " -"meaning in the CWL specification and underscored key names otherwise. For " -"example:" -msgstr "" -"Em princípio, um arquivo escrito em YAML consiste de uma série de _pares de " -"chave-valor`. Cada par é escrito como `chave: valor`, onde o espaço em " -"branco entre o `:` é um requisito. Os nomes das chaves em arquivos CWL não " -"devem conter espaços em branco - [_camelCase_][camelCase] é usado para " -"valores de chaves que contém múltiplas palavras e possuem um valor especial " -"na especificação CWL, caso contrário os valores dos nomes de chaves aparecem " -"sublinhados. For exemplo:" - -#: ../../src/topics/yaml-guide.md:42 9532ac8e1dda479e890bf970323a0a32 -msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " -"and `home` - with their four respective values. Values can be character " -"strings, numeric (integer, floating point, or scientific representation), " -"Boolean (`true` or `false`), or more complex nested types (see below)." -msgstr "" -"O YAML acima define quatro chaves - `first_name`, `last_name`, `age_years`, " -"e `home` - com quatro valores respectivos. Os valores podem ser strings de " -"caracteres, númericos (integer, floating point, ou representação científica)" -", Boolean (`true` ou `false`), ou valores mais complexos com tipos aninhados " -"(veja abaixo)." - -#: ../../src/topics/yaml-guide.md:51 91a057a7d10f438fad10338dd44c013c -msgid "" -"Values may be wrapped in quotation marks, but be aware that this may change " -"the way that they are interpreted i.e. `\"1234\"` will be treated as a " -"character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a " -"command: in CWL all parts of `baseCommand` must be strings so, if you want " -"to specify a fixed numeric value to a command, make sure that you wrap that " -"numeric value in quotes: `baseCommand: [echo, \"42\"]`." -msgstr "" - -#: ../../src/topics/yaml-guide.md:61 d18c1f5ef55d4bb6b8334438fcbc96b8 +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" +msgstr "" +"Em princípio, um arquivo escrito em YAML consiste de uma série de _pares " +"de chave-valor`. Cada par é escrito como `chave: valor`, onde o espaço em" +" branco entre o `:` é um requisito. Os nomes das chaves em arquivos CWL " +"não devem conter espaços em branco - [_camelCase_][camelCase] é usado " +"para valores de chaves que contém múltiplas palavras e possuem um valor " +"especial na especificação CWL, caso contrário os valores dos nomes de " +"chaves aparecem sublinhados. For exemplo:" + +#: ../../src/topics/yaml-guide.md:42 514365e59d9648deb896e2068d967a64 +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." +msgstr "" +"O YAML acima define quatro chaves - `first_name`, `last_name`, " +"`age_years`, e `home` - com quatro valores respectivos. Os valores podem " +"ser strings de caracteres, númericos (integer, floating point, ou " +"representação científica), Boolean (`true` ou `false`), ou valores mais " +"complexos com tipos aninhados (veja abaixo)." + +#: ../../src/topics/yaml-guide.md:51 6939eb7e783744d7bcf75ea0a7cae129 +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 96e1776b09e840ebbc9b4b7e01da0e43 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 dc6869049fc143b4af91d172a419a125 +#: ../../src/topics/yaml-guide.md:63 8b17f7557c3540b2b0d0beca0fe4ebc7 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program interpreting " -"the YAML. For example:" +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 c3c7f5ecfedb4884ad5e91bb79ba2a7c +#: ../../src/topics/yaml-guide.md:76 13da997c82c04023a4b7bb36b76e969d msgid "" -"If there is anything on the line before the comment, be sure to add at least " -"one space before the `#`!" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 84f16419237a4789ac0f3c682b3a11ee +#: ../../src/topics/yaml-guide.md:79 b9fc191166a64450b64a8182adabad75 msgid "Maps" msgstr "Dicionários" -#: ../../src/topics/yaml-guide.md:81 269ca8e05ce14e899fc8b2a00b1e458e +#: ../../src/topics/yaml-guide.md:81 aedf8c4f615845ad91a7947217005d6e msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, these " -"hierarchical structures are described in YAML by providing additional key-" -"value pairs as the value of any key. These pairs (sometimes referred to as " -"\"children\") are written on new lines under the key to which they belong " -"(the \"parent\"), and should be indented with two spaces (⇥tab characters " -"are not allowed). For example:" +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 ce790af50da540eb9108ad89eae037cf +#: ../../src/topics/yaml-guide.md:104 f0f1f414f74342a89065ba5ded8668e5 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " -"while one of these children, `inputBinding`, contains a further two key-" -"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " -"below for more information about providing multiple values/key-value pairs " -"for a single key. For comparison with the example YAML above, here is a " -"graphical representation of the `inputs` object it describes." +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 c3c9ef616b5d472a894ad6330267bcd2 +#: ../../src/topics/yaml-guide.md:127 965405e2a45a4cbb8f227bc8ceeb05df msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 b8a7360f6e0640aa9a2c4907c1ba3fe8 +#: ../../src/topics/yaml-guide.md:129 5aca9a90fb6149529ed717992746a2f3 msgid "" "In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) section " -"above, more than one key-value pair can be mapped to a single key. However, " -"it is also possible to define multiple values for a key without having to " -"provide a unique key for each value. We can achieve this with an _array_, " -"where each value is defined on its own line and preceded by `-`. For example:" +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 363da878600a4d229efe0ba79835d73c +#: ../../src/topics/yaml-guide.md:146 d1c9e72e004b4fb4a6efb7748a15ab6f msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 209dfb0d0a1148ed962dbb33890a3160 +#: ../../src/topics/yaml-guide.md:167 9a3d6879404745a48cd394bf86865dbc msgid "JSON Style" msgstr "Estilo JSON" -#: ../../src/topics/yaml-guide.md:169 cd3a174dae334d0d977a3234e258bd25 +#: ../../src/topics/yaml-guide.md:169 6a7cca0339794e679329b00d89e29d2b msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " -"can also be defined in YAML using the native JSON syntax. For example:" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 b0f0b10de8f54e1e951e480f696976f1 +#: ../../src/topics/yaml-guide.md:177 d8feed2d36d04fe283b9de9784d91941 msgid "and:" msgstr "e:" -#: ../../src/topics/yaml-guide.md:184 b5597e8984ad4e0bad33433c1dab89bd +#: ../../src/topics/yaml-guide.md:184 5156ad32791048f8ace51475d7689575 msgid "" -"Native JSON can be useful in indicating where a field is intentionally left " -"empty (such as `[]` for an empty array), as well as where it makes more " -"sense for the values to be located on the same line (For example, when " -"providing option flags and their values in a shell command). However, as the " -"second example above shows, it can severely affect the readability of a YAML " -"file, and should be used sparingly." +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 5ad7d551d3d347a097508a8488f9d15c +#: ../../src/topics/yaml-guide.md:194 ce49f80e6fc0498b8ad298fb1f0268f3 msgid "Reference" msgstr "Referencia" -#: ../../src/topics/yaml-guide.md:196 58f80e6944f9402a810b9b02ba3ad917 +#: ../../src/topics/yaml-guide.md:196 180d261392a644fcb8ff47d7a4a160c0 msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " -"while we wrote this guide, though it also covers features that are not valid " -"in CWL." +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 8fdcc745f4684fa7816c62782507438e +#: ../../src/tutorials.md:1 d682035afebf4c128755bd4e58780dd2 msgid "Tutorials" msgstr "Tutoriais" -#: ../../src/tutorials.md:5 3c933ac074ee4d94b7aeacb7abeaf388 +#: ../../src/tutorials.md:5 d9adeab63ec54084bc41fb90f264d3ae msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to the " -"list." +"this page` link in the menu if you would like to add another tutorial to " +"the list." msgstr "" -#: ../../src/tutorials.md:7 1d6cdf13aa834cb4a682553227d9f725 +#: ../../src/tutorials.md:7 23c81edb650b4f86a60c5e0bcedeac1d msgid "Beginner Tutorials" msgstr "Tutoriais para Iniciantes" -#: ../../src/tutorials.md:9 606cc939c5014e2abdab163e4d726f1b +#: ../../src/tutorials.md:9 87ddaa1e5f57445c8f13803722aa146e msgid "" -"[Introduction to Workflows with Common Workflow Language: For Contributors.]" -"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 3505468d39c34a20bc55f431a3c697f7 +#: ../../src/tutorials.md:11 b8ee193ba533498db6263e0f5f4ec45f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 e5731a11b89e492d8d751100a46c5226 +#: ../../src/tutorials.md:13 67c4b3923fce46fdab025495125c91d4 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 cdfeabb88f6245d9a687197d242ed3f9 +#: ../../src/tutorials.md:15 e640316669104239970794191b6da38b msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 997679b781a84add9b6d8b1900deec35 +#: ../../src/tutorials.md:17 efe94af44b874f9b81b245fbdee43f7f msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" + +#~ msgid "In CWL, everything must be directly stated." +#~ msgstr "Em CWL tudo deve ser declarado diretamente." + +#~ msgid "" +#~ "Using " +#~ "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +#~ " along with [`linkMerge: " +#~ "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#~ msgstr "" + +#~ msgid "Optional Inputs 💯" +#~ msgstr "Inputs Opcionais 💯" + +#~ msgid "Enum Inputs ⚜️" +#~ msgstr "Inputs Enum ⚜️" + +#~ msgid "Record Inputs 📀" +#~ msgstr "Inputs do tipo Record" + +#~ msgid "Debug JavaScript Expressions" +#~ msgstr "Depurar Expressões JavaScript" + +#~ msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +#~ msgstr "" + +#~ msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +#~ msgstr "" + +#~ msgid "" +#~ "`InitialWorkDirRequirement` - controls staging " +#~ "files in the input directory." +#~ msgstr "" + +#~ msgid "" +#~ "The FAIR principles have laid a " +#~ "foundation for sharing and publishing " +#~ "digital assets, and in particular, data." +#~ " The FAIR principles emphasize machine " +#~ "accessibility and that all digital " +#~ "assets should be Findable, Accessible, " +#~ "Interoperable, and Reusable. Workflows encode" +#~ " the methods by which the scientific" +#~ " process is conducted and via which" +#~ " data are created. It is thus " +#~ "important that workflows support the " +#~ "creation of FAIR data and adhere " +#~ "to the FAIR principles. — [FAIR " +#~ "Computational " +#~ "Workflows](https://workflows.community/groups/fair/), Workflows" +#~ " Community Initiative." +#~ msgstr "" + +#~ msgid "" +#~ "If you are using Windows, you will" +#~ " have to install the [Windows " +#~ "Subsystem for Linux 2](https://learn.microsoft.com" +#~ "/en-us/windows/wsl/install) (WSL2). Visit the " +#~ "`cwltool` [documentation](https://github.com/common-" +#~ "workflow-language/cwltool/blob/main/README.rst#ms-windows-" +#~ "users) for details on installing WSL2." +#~ " Your operating system also needs " +#~ "internet access and a recent version " +#~ "of Python (3.6+)." +#~ msgstr "" + +#~ msgid "" +#~ "`cwltool` can be installed with `pip`." +#~ " We recommend using a virtual " +#~ "environment like `venv` or `conda`. The" +#~ " following commands will create and " +#~ "activate a Python virtual environment " +#~ "using the `venv` module, and install " +#~ "`cwltool` in that environment:" +#~ msgstr "" + +#~ msgid "Installing `cwltool` with `pip` and `venv`." +#~ msgstr "Instalando `cwltool` com `pip` e `venv`." + +#~ msgid "Cwl-runner Python Module" +#~ msgstr "Módulo Python cwl-runner" + +#~ msgid "" +#~ "The CWL community publishes a Python " +#~ "package with the name `cwlref-runner`" +#~ " that installs an alias for `cwltool`" +#~ " under the name `cwl-runner`" +#~ msgstr "" + +#~ msgid "" +#~ "The *shebang* is the two-character " +#~ "sequence `#!` at the beginning of " +#~ "a script. When the script is " +#~ "executable, the operating system will " +#~ "execute the script using the executable" +#~ " specified after the shebang. It is" +#~ " considered a good practice to use" +#~ " `/usr/bin/env ` rather than " +#~ "using a hard-coded location, since " +#~ "`/usr/bin/env ` looks for the " +#~ "`` program in the system " +#~ "`PATH`," +#~ msgstr "" + +#~ msgid "" +#~ "The usage of the `cwltool` command-" +#~ "line executable is basically `cwltool " +#~ "[OPTIONS] [INPUTS_OBJECT]`. You " +#~ "can run the `hello_world.cwl` workflow " +#~ "without specifying any option:" +#~ msgstr "" + +#~ msgid "" +#~ "For more examples of providing metadata" +#~ " within CWL descriptions, see [the " +#~ "Metadata and Authorship section of this" +#~ " User Guide](../topics/metadata-and-" +#~ "authorship.md)." +#~ msgstr "" + +#~ msgid "" +#~ "In tool descriptions, list dependencies " +#~ "using short name(s) under " +#~ "`SoftwareRequirement`." +#~ msgstr "" + +#~ msgid "" +#~ "In tool descriptions, include a list " +#~ "of version(s) of the tool that are" +#~ " known to work with this description" +#~ " under `SoftwareRequirement`." +#~ msgstr "" + +#~ msgid "" +#~ "Each `CommandLineTool` description should " +#~ "focus on a single operation only, " +#~ "even if the (sub)command is capable " +#~ "of more. Don't overcomplicate your tool" +#~ " descriptions with options that you " +#~ "don't need or use." +#~ msgstr "" + +#~ msgid "" +#~ "This indicates whether a process " +#~ "requires outgoing IPv4/IPv6 network access." +#~ " If a command-line tool is " +#~ "written manually in CWL v1.1+, there " +#~ "is a need to specify when network" +#~ " access is required." +#~ msgstr "" + +#~ msgid "" +#~ "CWL v1.0 command-line tools that " +#~ "are upgraded to v1.1 or v1.2 get" +#~ " Network Access automatically." +#~ msgstr "" + +#~ msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +#~ msgstr "" + +#~ msgid "" +#~ "Note also that the author of this" +#~ " CWL description has also included " +#~ "`ResourceRequirement`s, specifying the minimum " +#~ "amount of RAM and number of cores" +#~ " required for the tool to run " +#~ "successfully, as well as details of " +#~ "the version of the software that " +#~ "the description was written for and " +#~ "other useful metadata. These features " +#~ "are discussed further in other chapters" +#~ " of this user guide." +#~ msgstr "" + +#~ msgid "" +#~ "Similar to the command-line tool " +#~ "it requires `inputs` and `outputs`. But" +#~ " instead of `baseCommand`, it requires " +#~ "an `expression` attribute." +#~ msgstr "" + +#~ msgid "" +#~ "We had to use an " +#~ "`InlineJavascriptRequirement` as our expression " +#~ "contains a JavaScript call in " +#~ "`.toUpperCase()`. This means to tools " +#~ "using the expression tool that " +#~ "JavaScript is a requirement." +#~ msgstr "" + +#~ msgid "" +#~ "If you need to manipulate input " +#~ "parameters, include the requirement " +#~ "`InlineJavascriptRequirement` and then anywhere " +#~ "a parameter reference is legal you " +#~ "can provide a fragment of Javascript " +#~ "that will be evaluated by the CWL" +#~ " runner." +#~ msgstr "" + +#~ msgid "From `Workflow`" +#~ msgstr "" + +#~ msgid "" +#~ "The requirement `InlineJavascriptRequirement` " +#~ "supports an `expressionLib` attribute that " +#~ "allows users to load external JavaScript" +#~ " files, or to provide inline " +#~ "JavaScript code." +#~ msgstr "" + +#~ msgid "" +#~ "Tools and workflows can take `File` " +#~ "types as input and produce them as" +#~ " output. We also recommend indicating " +#~ "the format for `File` types. This " +#~ "helps document for others how to " +#~ "use your tool while allowing you " +#~ "to do some simple type-checking " +#~ "when creating parameter files." +#~ msgstr "" + +#~ msgid "" +#~ "Available primitive types are *string*, " +#~ "*int*, *long*, *float*, *double*, and " +#~ "*null*; complex types are *array* and" +#~ " *record*; in addition there are " +#~ "special types *File*, *Directory* and " +#~ "*Any*." +#~ msgstr "" + +#~ msgid "" +#~ "You can use `cwltool` to create a" +#~ " template input object. That saves " +#~ "you from having to type all the" +#~ " input parameters in a input object" +#~ " file:" +#~ msgstr "" + +#~ msgid "" +#~ "The field `inputBinding` is optional and" +#~ " indicates whether and how the input" +#~ " parameter should appear on the " +#~ "tool's command line. If `inputBinding` " +#~ "is missing, the parameter does not " +#~ "appear on the command line. Let's " +#~ "look at each example in detail." +#~ msgstr "" + +#~ msgid "" +#~ "If you use exclusive input parameters" +#~ " combined with expressions, you need " +#~ "to be aware that the `inputs` " +#~ "JavaScript object will contain one of" +#~ " the exclusive input values. This " +#~ "means that you might need to use" +#~ " an **or** boolean operator to check" +#~ " which values are present." +#~ msgstr "" + +#~ msgid "" +#~ "Note how the JavaScript expression uses" +#~ " the value of the exclusive input " +#~ "parameter without taking into consideration" +#~ " a `null` value. If you provide " +#~ "a valid value, such as “fasta” " +#~ "(one of the values of the enum)," +#~ " your command should execute successfully:" +#~ msgstr "" + +#~ msgid "" +#~ "However, if you do not provide any" +#~ " input value, then `file_format` will " +#~ "be evaluated to a `null` value, " +#~ "which does not match the expected " +#~ "type for the output field (a " +#~ "`string`), resulting in failure when " +#~ "running your workflow." +#~ msgstr "" + +#~ msgid "" +#~ "To correct it, you must remember " +#~ "to use an or operator in your " +#~ "JavaScript expression when using exclusive " +#~ "parameters, or any parameter that allows" +#~ " `null`. For example, the expression " +#~ "could be changed to `$(inputs.file_format " +#~ "|| 'auto')`, to have a default " +#~ "value if none was provided in the" +#~ " command line or job input file." +#~ msgstr "" + +#~ msgid "" +#~ "The `uppercase` step of the workflow " +#~ "is an operation. It can be used" +#~ " like a command line tool or an" +#~ " expression. You can also plot it " +#~ "with the CWL Viewer or `cwltool`:" +#~ msgstr "" + +#~ msgid "" +#~ "The output of the command above " +#~ "can be rendered with a Graphviz " +#~ "renderer. The following image is " +#~ "rendered with the Sphinx Graphviz " +#~ "directive (this user guide is built " +#~ "with Sphinx):" +#~ msgstr "" + +#~ msgid "" +#~ "If you try running it with " +#~ "`cwltool`, the command will fail since" +#~ " `cwltool` does not have enough " +#~ "information to know how to execute " +#~ "it:" +#~ msgstr "" + +#~ msgid "" +#~ "When a tool runs under CWL, the" +#~ " starting working directory is the " +#~ "designated output directory. The underlying" +#~ " tool or script must record its " +#~ "results in the form of files " +#~ "created in the output directory. The" +#~ " output parameters returned by the " +#~ "CWL tool are either the output " +#~ "files themselves, or come from examining" +#~ " the content of those files." +#~ msgstr "" + +#~ msgid "" +#~ "In previous examples, the `baseCommand` " +#~ "was just a string, with any " +#~ "arguments passed as CWL inputs. Instead" +#~ " of a single string we can use" +#~ " an _array of strings_. The first" +#~ " element is the command to run, " +#~ "and any subsequent elements are " +#~ "mandatory command line arguments" +#~ msgstr "" + +#~ msgid "" +#~ "The field `outputBinding` describes how " +#~ "to set the value of each output" +#~ " parameter." +#~ msgstr "" + +#~ msgid "" +#~ "The `glob` field consists of the " +#~ "name of a file in the output " +#~ "directory. If you don't know name " +#~ "of the file in advance, you can" +#~ " use a wildcard pattern like `glob:" +#~ " '*.txt'`." +#~ msgstr "" + +#~ msgid "" +#~ "To capture a tool's standard output " +#~ "stream, add the `stdout` field with " +#~ "the name of the file where the " +#~ "output stream should go. Then add " +#~ "`type: stdout` on the corresponding " +#~ "output parameter." +#~ msgstr "" + +#~ msgid "" +#~ "Often, tool descriptions will be written" +#~ " for a specific version of a " +#~ "software. To make it easier for " +#~ "others to use your descriptions, you " +#~ "can include a `SoftwareRequirement` field " +#~ "in the `hints` section. This may " +#~ "also help to avoid confusion about " +#~ "which version of a tool the " +#~ "description was written for." +#~ msgstr "" + +#~ msgid "" +#~ "As well as a version number, a " +#~ "unique resource identifier (URI) for the" +#~ " tool is given in the form of" +#~ " an [RRID][rrid]. Resources with RRIDs " +#~ "can be looked up in the " +#~ "[SciCrunch][scicrunch] registry, which provides " +#~ "a portal for finding, tracking, and " +#~ "referring to scientific resources " +#~ "consistently. If you want to specify " +#~ "a tool as a `SoftwareRequirement`, " +#~ "search for the tool on SciCrunch " +#~ "and use the RRID that it has " +#~ "been assigned in the registry. (Follow" +#~ " this [Adding a Resource Tutorial" +#~ "][scicrunch-add-tool] to add a tool" +#~ " to SciCrunch). You can use this " +#~ "RRID to refer to the tool (via " +#~ "[identifiers.org][identifiers]) in the `specs` " +#~ "field of your requirement description. " +#~ "Other good choices, in order of " +#~ "preference, are to include the DOI " +#~ "for the main tool citation and the" +#~ " URL to the tool." +#~ msgstr "" + +#~ msgid "" +#~ "Normally, input files are located in " +#~ "a read-only directory separate from " +#~ "the output directory. This causes " +#~ "problems if the underlying tool expects" +#~ " to write its output files alongside" +#~ " the input file in the same " +#~ "directory. You use `InitialWorkDirRequirement` " +#~ "to stage input files into the " +#~ "output directory. In this example, we" +#~ " use a JavaScript expression to " +#~ "extract the base name of the input" +#~ " file from its leading directory " +#~ "path." +#~ msgstr "" + +#~ msgid "" +#~ "Before we run this, let's just " +#~ "break it down and see what some" +#~ " bits do. Most of this has " +#~ "been explained in previous sections, the" +#~ " only part that is really new " +#~ "is the `dockerRequirement` section." +#~ msgstr "" + diff --git a/locales/pt_PT/LC_MESSAGES/user_guide.po b/locales/pt_PT/LC_MESSAGES/user_guide.po index 3f68a232..82b90eda 100644 --- a/locales/pt_PT/LC_MESSAGES/user_guide.po +++ b/locales/pt_PT/LC_MESSAGES/user_guide.po @@ -1,344 +1,369 @@ # SOME DESCRIPTIVE TITLE. # Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. # msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"POT-Creation-Date: 2023-12-16 11:48+0100\n" "PO-Revision-Date: 2023-04-03 19:41+0000\n" "Last-Translator: ssantos \n" -"Language-Team: Portuguese (Portugal) \n" "Language: pt_PT\n" +"Language-Team: Portuguese (Portugal) " +"\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" +"Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=2; plural=n > 1;\n" -"X-Generator: Weblate 4.17-dev\n" +"Generated-By: Babel 2.12.1\n" -#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.md:4 9dd9705700664b31a3f296d263b4028b msgid "Instructional Material" msgstr "Material Instrucional" -#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +#: ../../LICENSE.md:6 e54324bd39cd431d91b32e338217b8c7 msgid "" -"All Common Workflow Language project instructional material and changes to " -"the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable summary " -"of (and not a substitute for) the [full legal text of the CC BY 4.0 license]" -"[cc-by-legal]." +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." msgstr "" "Todo o material instrucional do projeto Common Workflow Language e " -"alterações na estrutura também são disponibilizados sob a [licença Creative " -"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " -"humanos de (e não um substituto para) o [texto legal completo da licença CC " -"BY 4.0][cc-by-legal]." +"alterações na estrutura também são disponibilizados sob a [licença " +"Creative Commons Attribution][cc-by-human]. O seguinte é um resumo " +"legível por humanos de (e não um substituto para) o [texto legal completo" +" da licença CC BY 4.0][cc-by-legal]." -#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.md:12 754f3f54aa4142ef9dac27f508dd0bca msgid "You are free:" msgstr "Tem o direito de:" -#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb -msgid "" -"to **Share**---copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 d2b1d5e965ef4e71b64c359549919975 +msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" -"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " -"formato" +"**Compartilhar**---copiar e redistribuir o material em qualquer suporte " +"ou formato" -#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +#: ../../LICENSE.md:15 fe9551ffef8149bf8da50e70318e8de8 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" -#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.md:17 247db3bcc7024c44a044886a29ef1414 msgid "for any purpose, even commercially." msgstr "para qualquer fim, mesmo que comercial." -#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +#: ../../LICENSE.md:19 c04d906124854afc917707b7b4e45bb2 msgid "" -"The licensor cannot revoke these freedoms as long as you follow the license " -"terms:" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" msgstr "" "O licenciante não pode revogar estes direitos desde que você respeite os " "termos da licença:" -#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +#: ../../LICENSE.md:24 551cb5ab59dd4737b1042a4ef79ffab7 msgid "" "**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow Language " -"project, and, where practical, linking to https://www.commonwl.org/ ), " -"provide a [link to the license][cc-by-human], and indicate if changes were " -"made. You may do so in any reasonable manner, but not in any way that " -"suggests the licensor endorses you or your use." +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." msgstr "" -#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +#: ../../LICENSE.md:32 f6c3b2ccad494ed6811a35537fc1fb0d msgid "" "**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything the " -"license permits. With the understanding that:" +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" msgstr "" -"**Sem restrições adicionais**---Não pode aplicar termos jurídicos ou medidas " -"de caráter tecnológico que restrinjam legalmente outros de fazerem algo que " -"a licença permita. Com o entendimento de que:" +"**Sem restrições adicionais**---Não pode aplicar termos jurídicos ou " +"medidas de caráter tecnológico que restrinjam legalmente outros de " +"fazerem algo que a licença permita. Com o entendimento de que:" -#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +#: ../../LICENSE.md:36 91c95248cd7f435c909ee263a9a8bf3f msgid "" -"You do not have to comply with the license for elements of the material in " -"the public domain or where your use is permitted by an applicable exception " -"or limitation." +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." msgstr "" "Não tem de cumprir com os termos da licença relativamente a elementos do " -"material que estejam no domínio público ou cuja utilização seja permitida " -"por uma exceção ou limitação que seja aplicável." +"material que estejam no domínio público ou cuja utilização seja permitida" +" por uma exceção ou limitação que seja aplicável." -#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +#: ../../LICENSE.md:39 27f79b0b648b4de4b0eb3172b2dc4ae8 msgid "" -"No warranties are given. The license may not give you all of the permissions " -"necessary for your intended use. For example, other rights such as " -"publicity, privacy, or moral rights may limit how you use the material." +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." msgstr "" "Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " "autorizações necessárias para o uso pretendido. Por exemplo, outros " -"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " -"podem limitar o uso do material." +"direitos, tais como direitos de imagem, de privacidade ou direitos " +"morais, podem limitar o uso do material." -#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.md:44 1e367d07720d4f9fb7ebc3149052e823 msgid "Software" msgstr "Software" -#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +#: ../../LICENSE.md:46 cf8b58d02b6943a48cb70aa78a27bea4 msgid "" "Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the " -"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Salvo indicação em contrário, os programas de exemplo e outro software " -"fornecido pelo projecto Common Workflow Language são disponibilizados sob a " -"[licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." +"fornecido pelo projecto Common Workflow Language são disponibilizados sob" +" a [licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." -#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 +#: ../../LICENSE.md:51 96f1e5be3e1e48db8d9a4c7693008715 msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " -"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " -"License for the specific language governing permissions and limitations " -"under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." msgstr "" -"A menos que exigido pela lei aplicável ou acordado por escrito, o software " -"distribuído sob a Licença é distribuído \"COMO ESTÁ\", SEM GARANTIAS OU " -"CONDIÇÕES DE QUALQUER TIPO, expressas ou implícitas. Consulte a Licença para " -"obter o texto específico sobre as permissões e limitações sob a Licença." +"A menos que exigido pela lei aplicável ou acordado por escrito, o " +"software distribuído sob a Licença é distribuído \"COMO ESTÁ\", SEM " +"GARANTIAS OU CONDIÇÕES DE QUALQUER TIPO, expressas ou implícitas. " +"Consulte a Licença para obter o texto específico sobre as permissões e " +"limitações sob a Licença." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: eab02dc13915490bb3c9ba744d78b6a7 d4f35995b0f6494d9771a4be0a82538f -#: d6ccd4b546254f56a597d67dd4fdc5d6 +#: 08aa9181d5304e0fa96b28db15718559 d37fc100eb6948bba8b5e757574b2aaf +#: ecdd0f28d5b048d69dd1ffae2fa1f6c0 msgid "" "CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece of " -"software, tools and workflows described using CWL are portable across a " -"variety of platforms that support the CWL standard." +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." msgstr "" -"CWL é uma maneira de descrever ferramentas de linha de comando e de conectá-" -"las formando workflows. Como a CWL é uma especificação e não um software, " -"ferramentas e workflows descritos com a CWL são portáveis entre uma " -"variedade de plataformas que suportam o padrão CWL." +"CWL é uma maneira de descrever ferramentas de linha de comando e de " +"conectá-las formando workflows. Como a CWL é uma especificação e não um " +"software, ferramentas e workflows descritos com a CWL são portáveis entre" +" uma variedade de plataformas que suportam o padrão CWL." #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f +#: 1361ff6bf4924efc9ce9a85785a6b381 eb254514301c491e81f72ae19c407261 msgid "This page has moved" msgstr "Esta página foi movida" -#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 +#: ../../src/episodes.md:9 f03d7cbe6670451db0896f1b674d56c7 msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. Please use the new [Table of Contents](index.md#table-of-" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -"O conteúdo desta página está desatualizado e foi mantido para preservar os " -"links do antigo Guia do Utilizador. Por favor, use o novo [Índice](index." -"md#table-of-contents) para navegar o Guia do Utilizador." +"O conteúdo desta página está desatualizado e foi mantido para preservar " +"os links do antigo Guia do Utilizador. Por favor, use o novo " +"[Índice](index.md#table-of-contents) para navegar o Guia do Utilizador." -#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 +#: ../../src/faq.md:1 d65ad48ac6314bf0a74c34a6766561fc msgid "FAQ" msgstr "Perguntas Frequentes (FAQ)" -#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 -msgid "Non \"`File`\" Types Using `evalFrom`" +#: ../../src/faq.md:11 370a9659c7904ef6b5e1ae7480f82ef6 +#, fuzzy +msgid "How do I create non \"`File`\" types using `evalFrom`?" msgstr "Usando `evalFrom` para Tipos Diferentes de \"`File`\"" -#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 -msgid "Rename an Input File" +#: ../../src/faq.md:41 8333f51e3f5945fe8963adfc6685bcb1 +#, fuzzy +msgid "How do I rename an input file?" msgstr "Renomear um Arquivo de Entrada" -#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 +#: ../../src/faq.md:43 f6b88d9154d049d7807afa9bb0f1ac98 msgid "" -"This example demonstrates how to change the name of an input file as part of " -"a tool description. This could be useful when you are taking files produced " -"from another step in a workflow, and don't want to work with the default " -"names that these files were given when they were created." +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." msgstr "" -"Este exemplo demonstra como mudar o nome de um arquivo de entrada como parte " -"da descrição da ferramenta. Isso pode ser útil quando você tem arquivos " -"produzidos em outro passo de um workflow, mas prefere não utilizar os nomes " -"dados por padrão quando estes arquivos foram criados." +"Este exemplo demonstra como mudar o nome de um arquivo de entrada como " +"parte da descrição da ferramenta. Isso pode ser útil quando você tem " +"arquivos produzidos em outro passo de um workflow, mas prefere não " +"utilizar os nomes dados por padrão quando estes arquivos foram criados." -#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f -msgid "Rename an Output File" +#: ../../src/faq.md:59 833510f5896b4a6eb5875d25eca5b047 +#, fuzzy +msgid "How do I rename an output file?" msgstr "Renomear um Arquivo de Saída" -#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 +#: ../../src/faq.md:61 207e2f97d1c44233ae3f109c5a6ec944 msgid "" -"This example demonstrates how to change the name of an output file from the " -"default name given to it by a tool:" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" msgstr "" "Este exemplo demonstra como escolher o nome para um arquivo de saída " "diferente do nome padrão criado por uma ferramenta:" -#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 -msgid "Referencing a Local Script" +#: ../../src/faq.md:83 d66acc583da24273980a52be03e79e91 +msgid "" +"By modifying the `basename` field in the `outputEval` field, CWL workflow" +" engines will rename the file using the new name for subsequent steps or " +"as a workflow-level output." +msgstr "" + +#: ../../src/faq.md:86 8641f105131b4ac1bca7e0a46756ef79 +#, fuzzy +msgid "How do I reference a local script?" msgstr "Como Fazer Referência a um Script Local" -#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 +#: ../../src/faq.md:88 d3e43b40d6994b32bc37067ee116418e msgid "There are two ways to reference a local script:" msgstr "Há duas maneiras de fazer uma referência a um script local:" -#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb +#: ../../src/faq.md:90 64b140a321ca4087945339c523cc24dd +#, fuzzy msgid "" -"The first method involves adding the folder containing your scripts to the " -"`PATH` environment variable. This allows you to run the shell script " -"directly without using `sh` or `bash` commands." +"The first method involves adding the path to a folder containing your " +"scripts to the `PATH` environment variable. This allows you to execute " +"the shell script directly (without explicitly using the `sh` or `bash` " +"commands)." msgstr "" -"A primeira maneira é adicionando o arquivo que contém os seus scripts para a " -"variável de ambiente `PATH`. Desta maneira você pode executar o shell script " -"diretamente sem utilizar comandos via `sh` ou `bash`." +"A primeira maneira é adicionando o arquivo que contém os seus scripts " +"para a variável de ambiente `PATH`. Desta maneira você pode executar o " +"shell script diretamente sem utilizar comandos via `sh` ou `bash`." -#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 +#: ../../src/faq.md:93 34ebca4487a54ceab5d087105820e945 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "Comece adicionando a _shebang_ no topo do seu arquivo:" -#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 +#: ../../src/faq.md:99 6b04a4dcdada4515b28d74aacff3537a msgid "" -"After that, make the script executable with the command `chmod +x scriptname." -"sh`" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" msgstr "" -"Em seguida faça o seu script executável com o comando `chmod +x scriptname." -"sh`" +"Em seguida faça o seu script executável com o comando `chmod +x " +"scriptname.sh`" -#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 +#: ../../src/faq.md:101 756ab4f7edcf42d3872bb86818e088c3 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -"E finalmente, modifique o seu `PATH` para adicionar o diretório que contém o " -"seu script. (É boa prática usar `$HOME/bin` para scripts do utilizador " -"local)." +"E finalmente, modifique o seu `PATH` para adicionar o diretório que " +"contém o seu script. (É boa prática usar `$HOME/bin` para scripts do " +"utilizador local)." -#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be -msgid "" -"Now you can use `baseCommand: scriptname.sh` to run the script directly." +#: ../../src/faq.md:108 efb46b3a2d7c4c51b65998602bfa6f18 +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -"Agora você pode utilizar `baseCommand: scriptname.sh` para rodar o script " -"diretamente." +"Agora você pode utilizar `baseCommand: scriptname.sh` para rodar o script" +" diretamente." -#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 +#: ../../src/faq.md:117 844938d5d2304c6cb03184b4b4b0b024 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -"Depois quando você quiser compartilhar o seu trabalho, é possível utilizar " -"um container de software com ferramentas como Docker." +"Depois quando você quiser compartilhar o seu trabalho, é possível " +"utilizar um container de software com ferramentas como Docker." -#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 +#: ../../src/faq.md:119 796ce8155e32486d9651f8f13bfa3148 msgid "" -"The second method involves including an input of `type: File` in the script " -"itself:" +"The second method involves including an input of `type: File` in the " +"script itself:" msgstr "O segundo método utiliza um input `type: File` diretamente no script:" -#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 -msgid "In CWL, everything must be directly stated." -msgstr "Em CWL tudo deve ser declarado diretamente." - -#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 -msgid "Setting `self`-based Input Bindings for Optional Inputs" +#: ../../src/faq.md:138 ba246320fdd94a1aab4736f83718d793 +#, fuzzy +msgid "How can I set `self`-based input bindings for optional inputs?" msgstr "Definindo Bindings de Inputs utilizando `self` para Inputs Opcionais" -#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c +#: ../../src/faq.md:140 6169b7be9af7448abcb57eaf91e1cc91 msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their input " -"binding makes use of `self`. Below is an example workaround for this, " -"pending a more sophisticated fix." +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." msgstr "" "No momento `cwltool` não funciona quando inputs opcionais não estão " "presentes se o binding de input deles utilizar `self`. O exemplo abaixo " -"contém uma solução alternativa para este problema, até que haja uma solução " -"mais elegante para este problema." +"contém uma solução alternativa para este problema, até que haja uma " +"solução mais elegante para este problema." -#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 -msgid "Model a \"one-or-the-other\" Parameter" +#: ../../src/faq.md:165 6c98b7948059411b8e09cf03a552c5ab +#, fuzzy +msgid "How can I model a \"one-or-the-other\" parameter?" msgstr "Modelar um Parâmetro do tipo \"um-ou-o-outro\"" -#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 +#: ../../src/faq.md:167 d1424da3f43c4519a4c4735f4a720341 msgid "" -"Below is an example showing how to specify different strings to be added to " -"a command line, based on the value given to a Boolean parameter." +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." msgstr "" "O exemplo abaixo demonstra como especificar diferentes strings que serão " -"adicionadas à linha de comando, dependendo do valor de um parâmetro Boolean." +"adicionadas à linha de comando, dependendo do valor de um parâmetro " +"Boolean." -#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +#: ../../src/faq.md:188 5c9980839f404ba6aef92ef23034500f +#, fuzzy +msgid "" +"How do I connect a solo value to an input that expects an array of that " +"type?" msgstr "Conectar um Único valor a um Input que Espera uma Lista daquele Tipo" -#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d +#: ../../src/faq.md:190 2525baf16c1f4725b096f33fd99009cf +#, fuzzy msgid "" -"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" -"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +"Add a " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput):" msgstr "" +"De " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" e " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 +#: ../../src/faq.md:194 a00d5d96b15048a79ae099d22d63bb42 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 +#: ../../src/faq.md:196 3a92c6cc5c2b40ffa0d692d03bad5c87 msgid "" -"The input must be an array consisting of exactly one entry for each input " -"link. If \"merge_nested\" is specified with a single link, the value from " -"the link must be wrapped in a single-item list." +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 -msgid "Which means \"create a list with exactly these sources as elements\"" +#: ../../src/faq.md:199 3af16c07e3f148ddb8849c94a3864158 +#, fuzzy +msgid "Which means \"create a list with exactly these sources as elements\"." msgstr "" -"Que significa \"criar uma lista com exatamente estes sources como elementos\"" +"Que significa \"criar uma lista com exatamente estes sources como " +"elementos\"" -#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 +#: ../../src/faq.md:201 0ea3de393d2f42aeb82658c85a19ec45 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " -"add `linkMerge: merge_nested` under the appropriate `in` entry of the " -"destination step." +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." msgstr "" "Ou em outras palavras: se o parâmetro destino for do tipo `File[]` (uma " "lista de `File`s) e a fonte é um único `File`, adicione então " -"`MultipleInputFeatureRequirement` ao `requirements` no nível do Workflow e " -"adicione `linkMerge: merge_nested` sob a entrada apropriada `in` ao step que " -"receberá o parâmetro (target)." +"`MultipleInputFeatureRequirement` ao `requirements` no nível do Workflow " +"e adicione `linkMerge: merge_nested` sob a entrada apropriada `in` ao " +"step que receberá o parâmetro (target)." -#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd -msgid "Optional Inputs 💯" -msgstr "Inputs Opcionais 💯" +#: ../../src/faq.md:229 2f1bbb611c9c4f80b7ae0566432f2f35 +msgid "How do make an input optional? 💯" +msgstr "" -#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 +#: ../../src/faq.md:231 08a226efe5d141e68215ac77725033db msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." @@ -346,864 +371,895 @@ msgstr "" "Para fazer um parâmetro de entrada opcional, adicione um ponto de " "interrogação à declaração do tipo." -#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 +#: ../../src/faq.md:247 06e70a855a8f455ca0536eead77073c2 msgid "" msgstr "" -#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c -msgid "Enum Inputs ⚜️" -msgstr "Inputs Enum ⚜️" +#: ../../src/faq.md:248 7fda8eeb6a7f4689993ed0118c77f023 +msgid "" +"How do I specify an input that must come from a list of predefined values" +" (i.e. How do I use enum inputs) ?" +msgstr "" -#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 +#: ../../src/faq.md:250 b1934a82553b4da3b7f981e576245dd8 msgid "" -"For command line flags that require a specific input as the argument an enum " -"type can be declared in CWL. **Specifying null here is known as long form " -"style. It does the same thing as the question mark on the other inputs.**" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" msgstr "" "O tipo enum por ser utilizado em CWL para flags de linha de comando que " -"requerem um tipo de input específico como argumento. **Especificar null aqui " -"é tido como forma estendida. O resultado é o mesmo que o uso do ponto de " -"interrogação nos outros inputs.**" +"requerem um tipo de input específico como argumento. **Especificar null " +"aqui é tido como forma estendida. O resultado é o mesmo que o uso do " +"ponto de interrogação nos outros inputs.**" -#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd +#: ../../src/faq.md:267 17fc34fad2094f5ea60e963dabd632b8 msgid "" msgstr "" -#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 -msgid "Record Inputs 📀" -msgstr "Inputs do tipo Record" +#: ../../src/faq.md:268 4d7acfbeba5b4e9cb31f08ef4b280447 +msgid "" +"How do I describe dependent or exclusive input parameters(e.g. How do I " +"use record inputs)?" +msgstr "" -#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c +#: ../../src/faq.md:270 949ce95c082f4a05891a55fee25d4873 msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 -msgid "Setting Mutually Exclusive Parameters" +#: ../../src/faq.md:322 6fd3c469d11d4d52b9fbb7a3d443a8db +#, fuzzy +msgid "How do I set mutually exclusive parameters?" msgstr "Definindo Parâmetros Mutualmente Exclusivos" -#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 +#: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f msgid "" -"To properly set fields in a record input type, you need to pass a dictionary " -"to the input to properly set the parameters. This is done by using inline " -"JavaScript and returning the dictionary with the key of the field you want " -"to set. The source field is set to indicate the input from the workflow to " -"be used as the value." +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 -msgid "Setting Booleans" +#: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 +#, fuzzy +msgid "How can I set Booleans?" msgstr "Utilizando Booleans" -#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 +#: ../../src/faq.md:344 8dcb88744e5840029de0e1bbf1c4b967 msgid "These can be set by using the default field" msgstr "Estes são definidos através do campo padrão" -#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 -msgid "Concatenating Strings in Inputs" +#: ../../src/faq.md:349 972b7a5551bb43e6b9fa30e0cb713ff7 +#, fuzzy +msgid "What should I do when concatenating strings in inputs?" msgstr "Concatenando Strings em Inputs" -#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 +#: ../../src/faq.md:351 68f74afc21d846dd9070d45dec0cc1d8 msgid "The valueFrom field must be used instead of default." msgstr "O campo valueFrom deve ser utilizado ao invés do valor padrão." -#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +#: ../../src/faq.md:359 53b633c6f8644106beb95ae567eb0708 +#, fuzzy +msgid "" +"I get `cwltool` errors due to filenames with space characters inside. " +"What should I do?" msgstr "Erros do `cwltool` devido a Nomes de Arquivos com Espaços" -#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 +#: ../../src/faq.md:361 7101bb5cb69e4faca4e60eabb4eb258e msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "" -"O `cwltool` não permite alguns caracteres em nomes de arquivos por padrão." +msgstr "O `cwltool` não permite alguns caracteres em nomes de arquivos por padrão." -#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a +#: ../../src/faq.md:363 0eaf834b0ca847cca6736794895f5f81 msgid "" -"For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "" -"Por exemplo, o nome de arquivo `um espaco vai aqui.txt` inclui 3 espaços.." +"For example, the filename `a space is here.txt` includes 3 space " +"characters." +msgstr "Por exemplo, o nome de arquivo `um espaco vai aqui.txt` inclui 3 espaços.." -#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde +#: ../../src/faq.md:371 7dabd8aab7a5423b842433616640bac0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -"Se você não tem opção e precisa utilizar estes caracteres apesar do risco, " -"você deve então passar `--relax-path-verificks` ao chamar o `cwltool`." +"Se você não tem opção e precisa utilizar estes caracteres apesar do " +"risco, você deve então passar `--relax-path-verificks` ao chamar o " +"`cwltool`." -#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +#: ../../src/faq.md:373 b7ec33f38ce74ceb890f4379e4c41054 +#, fuzzy +msgid "" +"What should I do when I get CWL Parameter Reference error due to hyphen " +"in an input identifier?" msgstr "" "Erro de Referência em Parâmetro CWL devido a Hífen no Identificador de " "Entrada" -#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 +#: ../../src/faq.md:375 e39b65947b294b20a444f18d780246f4 msgid "If `cwltool --validate` returns valid" msgstr "Se `cwltool --validate` valida com sucesso" -#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 +#: ../../src/faq.md:384 dcd42c65681b438bb541fb38ddebb536 msgid "But executing it causes an error like:" msgstr "Mas ao executar o workflow um erro como o seguinte aparece:" -#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 +#: ../../src/faq.md:396 2b96665acac449758b852bbe7600e007 msgid "The file is here" msgstr "Este é o arquivo" -#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 +#: ../../src/faq.md:410 f59751d2f0014e59af7879a748062cec msgid "Problem caused by `-` (hyphen character)." msgstr "O problema é causado pelo `-` (hífen)." -#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +#: ../../src/faq.md:423 7780f461ca4c478b92fca893c0b0894a +#, fuzzy +msgid "To fix this error, change `-` (hyphen) to `_` (underscore):" msgstr "Para corrigir este erro, substitua o `-` (hífen) por `_` (sublinhado)" -#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d +#: ../../src/faq.md:436 88df56dfff854fc68fb6ad3835a846e4 msgid "" -"If it is not possible to change the input identifier, then you can use an " -"alternative CWL Parameter Reference syntax:" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" msgstr "" "Se não for possível mudar o identificador do input, você pode reescrever " "utilizando uma sintaxe alternativa para Referências de Parâmetros CWL:" -#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 -msgid "Use CWL and cwltool with Singularity" +#: ../../src/faq.md:442 fc407a9e8d8c4b699d9cd14b369343b5 +#, fuzzy +msgid "How do I use CWL and cwltool with Singularity?" msgstr "Utilizar CWL e cwltool com Singularity" -#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e +#: ../../src/faq.md:445 239f5f81cef042b08fb8015c36b3ecad msgid "" -"The CWL standards are built around (optional) Docker format containers. The " -"reference runner and several other CWL implementations support running those " -"Docker format containers using the Singularity engine. Directly specifying a " -"Singularity format container is not part of the CWL standards." +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." msgstr "" -#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 -msgid "Debug JavaScript Expressions" -msgstr "Depurar Expressões JavaScript" +#: ../../src/faq.md:450 61641314d82b43e982e54c64c73232c5 +msgid "How do I debug the JavaScript in my CWL tool?" +msgstr "" -#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 +#: ../../src/faq.md:452 5556d3c323664edea55cfb777f4efb3b msgid "" -"You can use the --js-console option of cwltool, or " -"you can try creating a JavaScript or TypeScript project for your code, and " -"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" -"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e +#: ../../src/index.md:1 1c9fb72b83c9467a9672943fb47ffe32 msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab +#: ../../src/index.md:3 aaa44578e27345e682ab44686b4da159 msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 +#: ../../src/index.md:7 0adfc2adb0c74372b25d197dd3a73b8b msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 +#: ../../src/index.md:9 96c8dca812f1415db7c5c006b0c0e022 msgid "" -"If you find that something is missing from this guide, or if you would like " -"to provide other feedback, file an Issue on the [project repository for this " -"guide][repo]. You can also suggest changes directly in a Pull Request by " -"clicking the \"Edit this page\" button at the right sidebar of each page." +"If you find that something is missing from this guide, or if you would " +"like to provide other feedback, file an Issue on the [project repository " +"for this guide][repo]. You can also suggest changes directly in a Pull " +"Request by clicking the \"Edit this page\" button at the right sidebar of" +" each page." msgstr "" -#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f +#: ../../src/index.md:16 35c50bb5c3a345b4a4ae66b2df065376 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 +#: ../../src/index.md:18 9431edcf4e344fb89b6a251e627279d2 msgid "" -"If you are a beginner user get started with the [Introduction](/introduction/" -"index.md) section. For advanced users the subsections of the [Topics](/" -"topics/index.md) have detailed information about the most common topics for " -"CWL." +"If you are a beginner user get started with the " +"[Introduction](/introduction/index.md) section. For advanced users the " +"subsections of the [Topics](/topics/index.md) have detailed information " +"about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 +#: ../../src/index.md:23 61cf57e61a9f46e5a1bff6368c5ad5e3 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " -"subsections. The right sidebar contains links to the sections of each page, " -"and the Search form is on the left sidebar." +"subsections. The right sidebar contains links to the sections of each " +"page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c +#: ../../src/index.md:28 94381840d8a848c4a02fa97bfe83566d msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 +#: ../../src/introduction/basic-concepts.md:1 c1271d88e203454688a22e61ee88f02a msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 +#: ../../src/introduction/basic-concepts.md:3 dd462818cc9a4205b38866d0c5137ece msgid "" "This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are expected " -"to be familiar with workflow managers, YAML, and comfortable with following " -"instructions for the command-line. The other sections of the user guide " -"cover the same concepts, but in more detail. If you are already familiar " -"with CWL or you are looking for more advanced content, you may want to skip " -"this section." +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 +#: ../../src/introduction/basic-concepts.md:10 7a56d394fb244431aefce7ebbb834ecf msgid "The CWL Specification" msgstr "A Especificação CWL" -#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf +#: ../../src/introduction/basic-concepts.md:21 35800ed2c56d489190d3702d9ad20fd7 msgid "" "The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered in " -"this user guide is the {{ cwl_version }}." +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 +#: ../../src/introduction/basic-concepts.md:25 3ab6dd6b2f694afeb08f3984a74f3efb msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" "incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes that " -"are backward-compatible. The last number is used for bug fixes, like typos " -"and other corrections to the specification." +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d +#: ../../src/introduction/basic-concepts.md:33 72ae1fb763a34c41b1b06adcbe1522c3 msgid "" -"The model used for the specification version is called Semantic Versioning. " -"See the end of this section to [learn more](#learn-more) about it." +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d +#: ../../src/introduction/basic-concepts.md:37 5aa7d3ee6cb048d888f1e1f49d0e08be msgid "Implementations" msgstr "Implementações" -#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 +#: ../../src/introduction/basic-concepts.md:39 c87e6daefda74579a39924777b2e6809 msgid "" -"An implementation of the CWL specification is any software written following " -"what is defined in a version of the specification document. However, " -"implementations may not implement every aspect of the specification. CWL " -"implementations are licensed under both Open Source and commercial licenses." +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 +#: ../../src/introduction/basic-concepts.md:44 c995e699ae2949219af252f9d802a43d msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud " -"and high performance computing environments where tasks are scheduled in " -"parallel across many nodes." +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf +#: ../../src/introduction/basic-concepts.md:51 09171f48a3d841b2acb6d803b2340c8e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: 1c1647a3496c4251a3193f94ee4e78c8 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 +#: 854633336f4d4fc394e62c53ce022c6b msgid "" -"A process is a computing unit that takes inputs and produces outputs. The " -"behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification " -"{{ cwl_version }}:" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 142a847f11d7462f8bf77bfe789410ca msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 7c7567fa690043f9b4b89bdf8ca60cad msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: 7afcf087d3ea49dabf1a641a2bb71b35 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: 6399939602334819a20b92b957352a8a msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 8c55b15cebf142899045f229ccc86b1e msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a +#: ec54c0e67e894bfba2d0fbb0f87ffdf4 msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 +#: c88ad26efa794cbeb6f0690aa0cad5ea msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be used " -"to simplify workflows and command-line tools, moving common parts of a " -"workflow execution into reusable JavaScript code that takes inputs and " -"produces outputs like a command-line tool." +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef +#: 946825a7ea2c450eb3e41b5548670fb7 msgid "" -"Operation is an abstract process that also takes inputs, produces outputs, " -"and can be used in a workflow. But it is a special operation not so commonly " -"used. It is discussed in the [Operations section](../topics/operations.md) " -"of this user guide." +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +#: 44aac23f302c4178accf7e431cfbb96c msgid "" -"The workflow is a process that contains steps. Steps can be other workflows " -"(nested workflows), command-line tools, or expression tools. The inputs of a " -"workflow can be passed to any of its steps, while the outputs produced by " -"its steps can be used in the final output of the workflow." +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 +#: 5afdb7aaf0bf4c1abf4c22cdbdd58be9 msgid "" "The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through *requirements*. " -"There are many requirements defined in the CWL specification, for instance:" +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +#: 07c5789c59224ed78a3ecd03cfe872e9 +msgid "" +"[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement)" +" - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +#: 6f9854ae1b884ad39f88d2f39d66cb98 +msgid "" +"[`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow.html#SubworkflowFeatureRequirement)" +" - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 +#: 23fef6de073f4da18118e4d0512670fe msgid "" -"`InitialWorkDirRequirement` - controls staging files in the input directory." +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow.html#InitialWorkDirRequirement)" +" - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee +#: fb3762f91177401ea624d1e716d67ae6 msgid "" -"Some CWL runners may provide requirements that are not in the specification. " -"For example, GPU requirements are supported in `cwltool` through the " -"`cwltool:CUDARequirement` requirement, but it is not part of the " -"{{ cwl_version }} specification and may not be supported by other CWL " -"runners." +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e +#: b6a5cd431c324078a9a4e1513a14ee28 msgid "" -"Hints are similar to requirements, but while requirements list features that " -"are required, hints list optional features. Requirements are explained in " -"detail in the [Requirements](../topics/requirements-and-hints.md) section." +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: 88d7bad84dd341d2abb33673b8b8f250 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 +#: bcbf5d76cf5f47b2a9691b7d2d8ef891 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " "machine accessibility and that all digital assets should be Findable, " "Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created. It " -"is thus important that workflows support the creation of FAIR data and " -"adhere to the FAIR principles. — [FAIR Computational Workflows](https://" -"workflows.community/groups/fair/), Workflows Community Initiative." +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows both support the creation of FAIR " +"data and themselves adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a +#: 4ea1d3bf04dc42f0bc6735a45b9e0dc0 msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\", " -"CWL tasks are isolated, and you must be explicit about your inputs and " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " "outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee +#: c0f53138bf084939a54b0a576b44199f msgid "" -"The benefit of explicitness and isolation are flexibility, portability, and " -"scalability; tools and workflows described with CWL can transparently " -"leverage technologies such as Docker and be used with CWL implementations " -"from different vendors." +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: 91d6eb4984a6410ba99616b6617ba9af msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 65c24244713741e196da08cb9ba237b2 -#: f059896039524095b4deb65d693f8ddf 3439764fab0e49d2bcb7c9fbae556e65 +#: ../../src/introduction/prerequisites.md:183 +#: ../../src/introduction/quick-start.md:94 0d7e607b00b9485aa2e3c5fb0a931bc6 +#: 161697ed3e864155bb89d8be794fc139 b4a7563eabf547c3bf7eab2567a27b51 msgid "Learn More" msgstr "Saiba Mais" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 7221a89559944627b4c3db37f468f72c msgid "Semantic Versioning - " msgstr "Versionamento Semântico - " #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 +#: bccf086fc9514f76b60dc161e3a09da3 msgid "" -"The CWL Specification page in the CWL website: " +"The CWL Specification page in the CWL website: " +"" msgstr "" -"A página web da Especificação CWL: " +"A página web da Especificação CWL: " +"" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 +#: a5b37924c7d04ab984ff2542847afc4a msgid "" -"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +"The Command Line Tool Description Standard: " +"<[https://www.commonwl.org/v1.2/CommandLineTool.html](https://w3id.org/cwl/CommandLineTool.html)>" msgstr "" -"A especificação CWL atual no GitHub: {{ ''.format(cwl_version_text) }}" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 +#: 44af015fa36644b99f07338d241d29c1 msgid "" -"The list of Implementations in the CWL website: " +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" -"A lista de Implementações na página web da CWL: " +"A especificação CWL atual no GitHub: {{ ''.format(cwl_version_text) }}" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: bffca993172048a4b7ab7c62637662e2 +msgid "" +"The list of Implementations in the CWL website: " +"" +msgstr "" +"A lista de Implementações na página web da CWL: " +"" + +#: ../../src/introduction/basic-concepts.md:185 +#: 84c61946406347c8b138772909110d54 msgid "PROV-O: The PROV Ontology - " msgstr "PROV-O: A Ontologia PROV - " -#: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b +#: ../../src/introduction/basic-concepts.md:186 +#: eb0b6a62e06143eabc7b92acff9643ea msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 +#: ../../src/introduction/index.md:1 48532f7701c54166859098e521a43db0 msgid "Introduction" msgstr "Introdução" -#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 +#: ../../src/introduction/index.md:3 08db628a949b4513b824ee334e70a7df msgid "" "This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that " -"are useful to know before reading the rest of the user guide." +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 +#: ../../src/introduction/prerequisites.md:1 d3f5749a76c14fdf8052f5f683d11b9e msgid "Prerequisites" msgstr "Pré-requisitos" -#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 +#: ../../src/introduction/prerequisites.md:6 ab9e21b3e99641d096ba70012b4eb035 msgid "" -"The software and configurations listed in this section are prerequisites for " -"following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements focuses " -"on the CWL reference runner, `cwltool`. You can use another CWL-compatible " -"runner or workflow system, but the results and interface may look different " -"(though the exact workflow outputs should be identical)." +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 +#: ../../src/introduction/prerequisites.md:12 8ed426ebcb744839915e7c414d69b1e9 msgid "CWL Implementations" msgstr "Implementações da CWL" -#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf +#: ../../src/introduction/prerequisites.md:14 ff74d48407464c4b9d451fa419137144 msgid "" -"There are many implementations of the CWL standards. Some are complete CWL " -"runners, while others could be plug-ins or extensions to workflow engines. " -"We have a better explanation in the [Implementations](basic-concepts." -"md#implementations) section." +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 +#: ../../src/introduction/prerequisites.md:19 eb98aa9c71d746a69e9610996ffc5b47 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b +#: ../../src/introduction/prerequisites.md:21 209a0018e7da48f09b27dc507ba14d24 msgid "" -"We recommend using an up-to-date operating system. You can choose any of the " -"following options for your operating system:" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 +#: ../../src/introduction/prerequisites.md:24 8baf869537ea478791356320280df928 msgid "Linux" msgstr "Linux" -#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf +#: ../../src/introduction/prerequisites.md:25 248e9760ce60442eb10ab7247d6af23b msgid "macOS" msgstr "macOS" -#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 +#: ../../src/introduction/prerequisites.md:26 d89306bbadf44b6bba8959f1f68cc2f0 msgid "Windows" msgstr "Windows" -#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +#: ../../src/introduction/prerequisites.md:29 aeeb990abbbd42cca122c342054be29c msgid "" -"If you are using Windows, you will have to install the [Windows Subsystem " -"for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). " -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool/blob/main/README.rst#ms-windows-users) for details on " -"installing WSL2. Your operating system also needs internet access and a " -"recent version of Python (3.6+)." +"If you are using Windows, you will have to install the Windows Subsystem " +"for Linux 2 as documented in the [`cwltool` documentation for Microsoft " +"Windows users](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users). Your operating " +"system also needs internet access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 +#: ../../src/introduction/prerequisites.md:34 21d1f29fb15745c480194eae6acdd031 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 +#: ../../src/introduction/prerequisites.md:39 89f0bf6ff8544a6d87114085be8e0bb6 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL community. " -"It is also the CWL reference runner, which means it must support everything " -"in the current CWL specification, {{ cwl_version }}." +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 +#: ../../src/introduction/prerequisites.md:44 068f09d4d66547448693f7b9dadef497 msgid "" -"`cwltool` can be installed with `pip`. We recommend using a virtual " -"environment like `venv` or `conda`. The following commands will create and " -"activate a Python virtual environment using the `venv` module, and install " -"`cwltool` in that environment:" +"`cwltool` can be installed with `pip`, `apt`, or `conda`. We recommend " +"using a virtual environment like `venv` or `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "Instalando `cwltool` com `pip` e `venv`." - -#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 +#: ../../src/introduction/prerequisites.md:48 1edf8b8438334ae29dc406dbfd711228 +#, fuzzy msgid "" -"Visit the `cwltool` [documentation](https://github.com/common-workflow-" -"language/cwltool#install) for other ways to install `cwltool` with `apt` and " -"`conda`." +"Visit the `cwltool` " +"[documentation](https://cwltool.readthedocs.io/en/latest/#install) for " +"details on installing `cwltool`." msgstr "" -"Visite a [documentação](https://github.com/common-workflow-language/" -"cwltool#install) do `cwltool` para outras opções para instalar `cwltool` com " -"`apt` e `conda`." +"Visite a [documentação](https://github.com/common-workflow-" +"language/cwltool#install) do `cwltool` para outras opções para instalar " +"`cwltool` com `apt` e `conda`." -#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 +#: ../../src/introduction/prerequisites.md:52 5e300141ce43435f9437507374987213 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -"Vamos usar uma simples descrição de ferramenta CWL `true.cwl` com `cwltool`." +"Vamos usar uma simples descrição de ferramenta CWL `true.cwl` com " +"`cwltool`." -#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b +#: ../../src/introduction/prerequisites.md:54 282ac7ba2a2346feac2456bcda0f214a msgid "`true.cwl`" msgstr "`true.cwl`" -#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 +#: ../../src/introduction/prerequisites.md:60 0b36f94f479a4bce9bd9be9983894421 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the CWL " -"standards. However, these actions will be performed without running the " -"document. To validate CWL workflows (or even a standalone command line tool " -"description like the above) pass the `--validate` option to the `cwltool` " -"command:" +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 +#: ../../src/introduction/prerequisites.md:66 5fce122794e34892b430ca4bdba5ba50 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 -msgid "" -"You can run the CWL tool description by omitting the `--validate` option:" +#: ../../src/introduction/prerequisites.md:71 73f074f47d1449dcb40ff960a84851fd +msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 +#: ../../src/introduction/prerequisites.md:73 2dd5a67870ca41b48e17c468ba15888b msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 -msgid "Cwl-runner Python Module" -msgstr "Módulo Python cwl-runner" +#: ../../src/introduction/prerequisites.md:78 d2dc809318be49cc996d892e93ad84ac +msgid "Generic ``cwl-runner`` alias" +msgstr "" -#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 +#: ../../src/introduction/prerequisites.md:80 9809c2e262924ef286b0bd62e0b00995 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be invoked " -"independently, and is not reliant on a particular CWL runner program name. " -"Users can invoke `cwl-runner` instead of invoking a CWL runner like " -"`cwltool` directly. The `cwl-runner` is installed by a system administrator " -"or user to point to the preferred CWL implementation. This is convenient for " -"environments with multiple CWL runners." +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 +#: ../../src/introduction/prerequisites.md:88 6dd6aa836099469381fb564d63b84f3d msgid "" -"The CWL community publishes a Python package with the name `cwlref-runner` " -"that installs an alias for `cwltool` under the name `cwl-runner`" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 +#: ../../src/introduction/prerequisites.md:91 cc1a9b95508e44a1bf08ae75d990c301 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 +#: ../../src/introduction/prerequisites.md:98 8f8c80f705d94d4899b250bbf9c54562 msgid "" -"Now you can validate and run your workflow with the `cwl-runner` executable, " -"which will invoke `cwltool`. You should have the same results and output as " -"in the previous section." +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 +#: ../../src/introduction/prerequisites.md:102 176e4214d18149f3ba0bda692bcf760f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 +#: ../../src/introduction/prerequisites.md:107 4890bf20bc3842d3a7421b555bcda94a msgid "Running `true.cwl` with `cwl-runner`." msgstr "Executando `true.cwl` com `cwl-runner`." -#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 +#: ../../src/introduction/prerequisites.md:112 2475a83cf6ed4389bb680fa37e8fe69c msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For " -"that, the first thing you need to do is copy `true.cwl` workflow into a new " -"file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: ../../src/introduction/prerequisites.md:116 24da787aa76c4480838a93ba0533898d msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 -msgid "" -"Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +#: ../../src/introduction/prerequisites.md:122 4f3cb8d1f9ce4e3d852e81aa4e0f60be +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 +#: ../../src/introduction/prerequisites.md:124 27693d62faa045d9b03143d9bd2afcdf msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 +#: ../../src/introduction/prerequisites.md:131 703531514abe4fd48015c472005dbffa msgid "" -"And finally, you can execute it directly in the command-line. On execution, " -"the program specified in the shebang (`cwl-runner`) will be used to execute " -"the rest of the file." +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f +#: ../../src/introduction/prerequisites.md:135 abba2e14c4e54252bb75983274663a7a msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 +#: ../../src/introduction/prerequisites.md:141 11fea992c00940d29eb29ccf4b9370e9 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute the " -"script using the executable specified after the shebang. It is considered a " -"good practice to use `/usr/bin/env ` rather than using a hard-" -"coded location, since `/usr/bin/env ` looks for the " -"`` program in the system `PATH`," +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env [executable]` rather than" +" using a hard-coded location, since `/usr/bin/env [executable]` looks for" +" the `[executable]` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 +#: ../../src/introduction/prerequisites.md:148 854736eef2ac4b63b187a4cea9660ae4 msgid "Text Editor" msgstr "Editor de Texto" -#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed +#: ../../src/introduction/prerequisites.md:150 480fbb7a743046068c114fff5b396a9f msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 +#: ../../src/introduction/prerequisites.md:154 28da3eea8fd245d1936013d021c25164 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting " -"and better auto-complete:" +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 +#: ../../src/introduction/prerequisites.md:158 73c08e11e90d4c7f952307a1cdaa360b msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " +"Visual Studio Code with the Benten (CWL) plugin - " +"" msgstr "" -#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 +#: ../../src/introduction/prerequisites.md:159 a5b788252a924338963f0ed198fc22ca msgid "" -"cwl-plugin for IntelliJ - " +"cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 +#: ../../src/introduction/prerequisites.md:161 ee705b919acd461a8d9622821da246b6 msgid "" -"The CWL community also maintains a list of editors and viewers: " +"The CWL community also maintains a list of editors and viewers: " +"" msgstr "" -#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 +#: ../../src/introduction/prerequisites.md:164 7724b63db3cc45139379898d047c0f83 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c +#: ../../src/introduction/prerequisites.md:168 eff13997c1ce43d1ad2d7a4d927394fe msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: ." +"documentation to install it for your operating system: " +"." msgstr "" -#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c +#: ../../src/introduction/prerequisites.md:172 2872503638624b7e904ae407375ac165 msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models with " -"and without containers." +"examples, and to clarify the differences between the execution models " +"with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 +#: ../../src/introduction/prerequisites.md:178 52ddcc9bc1554d809371fc0a503c40bc msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for pulling " -"images." +"Singularity. You can also use alternative container registries for " +"pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 +#: ../../src/introduction/prerequisites.md:185 f3bbfa17f31a459386461951de157dd2 msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the next " -"section, Basic Concepts." +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 +#: ../../src/introduction/prerequisites.md:186 e22b9e7c56104e018e6d2f3d547c01ea msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 +#: ../../src/introduction/quick-start.md:1 9ca367e3ca754a0fa88dab64724b95b6 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a +#: ../../src/introduction/quick-start.md:3 733db5702c774f32b8c91d13f74f3720 msgid "" -"This section will show you a brief overview of what CWL is, and where you " -"can learn more about it. No previous knowledge of CWL is required, but you " -"must be comfortable following instructions for the command-line." +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee +#: ../../src/introduction/quick-start.md:7 0b164074dd0849c3b2c8d2f78ea99e95 msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 +#: ../../src/introduction/quick-start.md:12 6485f96f638548fbb7addc57f6cde92b msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The " -"example below shows a simple CWL “Hello World” workflow annotated with " -"comments. Note that comments start with `#`:" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb +#: ../../src/introduction/quick-start.md:16 5e06f9c4754347b8bac88d24c21e0f67 msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 +#: ../../src/introduction/quick-start.md:22 6a13fb9112ab41acb60dc65b3656f63e msgid "" "The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the " -"same result as the command-line `echo \"Hello World\"`." +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 +#: ../../src/introduction/quick-start.md:27 7b2ae93353184faea0ae4f4acdfc3350 msgid "" -"In CWL, there is a distinction between a command-line tool and a workflow. " -"But for the sake of simplicity, we are using the term “workflow” here. You " -"will learn more about this in the [basic concepts](basic-concepts.md) " -"section." +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 +#: ../../src/introduction/quick-start.md:32 1ed30b04073d47a9893774746479fb5d msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 +#: ../../src/introduction/quick-start.md:34 73a42cd9e0e54296985088b7221a8a93 msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the CWL " -"*Reference Runner* for the specification, and it is compliant with the " -"latest version of the specification: {{ cwl_version }}. You can install " -"`cwltool` using `pip`:" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 +#: ../../src/introduction/quick-start.md:39 57aea587ade24610be62f5d993b0b755 msgid "Installing `cwltool` with `pip`." msgstr "Instalando `cwltool` com `pip`." -#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 +#: ../../src/introduction/quick-start.md:47 51183fc986014edbb026a53f222e6c2e msgid "" -"If installing the cwltool using the pip command doesn't work for you, the " -"[prerequisites](prerequisites.md) section contains other ways to install " -"`cwltool` and a more detailed list of software and libraries used for " +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 +#: ../../src/introduction/quick-start.md:51 a7582c3ae37a462a8ae1e72b3f321534 msgid "Running \"Hello World\"" msgstr "Executando \"Hello World\"" -#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe +#: ../../src/introduction/quick-start.md:53 0595e96912dc40e5a09f2ced2d2b7bcd msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` " -"workflow without specifying any option:" +"[OPTIONS] [CWL_DOCUMENT] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 +#: ../../src/introduction/quick-start.md:57 5b393c69816549b084516dda4d4274f5 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "Executando `hello_world.cwl` com `cwltool`." -#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 +#: ../../src/introduction/quick-start.md:62 4306d8ad802f45c18487d932d04492fa msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 +#: ../../src/introduction/quick-start.md:65 8339ec411ad04c70ab8d795eb154fc38 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 +#: ../../src/introduction/quick-start.md:70 3ecca6985e754951aee00c93effe9517 msgid "" -"Another way of passing values to your workflow input parameters is via an " -"*Inputs Object*. This is a file containing the input fields with their " +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " "corresponding values. The Inputs Objects file can be written in JSON or " "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 +#: ../../src/introduction/quick-start.md:74 d05e8e016b1d40c28c4b6091103fe920 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c +#: ../../src/introduction/quick-start.md:80 c5983ba6c86f4b749522c11cb3843911 msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" @@ -1211,226 +1267,231 @@ msgstr "" "Pode utilizar este arquivo de Objetos de Inputs agora para executar o " "workflow “Hello World”:" -#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 +#: ../../src/introduction/quick-start.md:82 4065124edf3a4678a37c82e3070595cb msgid "Passing an Inputs Object file to `cwltool`." msgstr "Passando um arquivo de Objeto de Inputs para o `cwltool`." -#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 +#: ../../src/introduction/quick-start.md:88 52b1602b5c8d48db88d0b16f788e7703 msgid "" "We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but it " -"is not a requirement. You can choose any name for your workflows and Inputs " -"Object files." +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 +#: ../../src/introduction/quick-start.md:96 3b06faf5f3194bd8a96118d9f050f61e msgid "Continue reading the next sections of this User Guide!" msgstr "Continue lendo as secções seguintes deste Guia do Utilizador!" -#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 -msgid "" -"[List of CWL Implementations](https://www.commonwl.org/implementations)." +#: ../../src/introduction/quick-start.md:97 669b8ac154e74181830a430b1dc7684b +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -"[Lista das Implementações da CWL](https://www.commonwl.org/implementations)." +"[Lista das Implementações da " +"CWL](https://www.commonwl.org/implementations)." -#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 +#: ../../src/introduction/quick-start.md:98 1c888f1b771d49b3a257ed534b5afa0a msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -"A [organização`common-workflow-language`](https://github.com/common-workflow-" -"language) no GitHub." +"A [organização`common-workflow-language`](https://github.com/common-" +"workflow-language) no GitHub." -#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 +#: ../../src/introduction/quick-start.md:99 dbce82b7a930493486a585ecb8891121 msgid "" -"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" -"Common_Workflow_Language)." +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -"[Common Workflow Language na Wikipedia](https://en.wikipedia.org/wiki/" -"Common_Workflow_Language)." +"[Common Workflow Language na " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b +#: ../../src/introduction/quick-start.md:100 dc714ffd4278421b9f2417f41627722c msgid "" -"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." -"org/wiki/YAML)." +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -"[YAML.org](http://yaml.org/) e [YAML at Wikipedia](https://en.wikipedia.org/" -"wiki/YAML)." +"[YAML.org](http://yaml.org/) e [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." -#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff +#: ../../src/introduction/quick-start.md:101 2bf7b924182f4f2bab88edef5ef85baa msgid "" -"The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'." -"replace('VERSION', cwl_version_text) }}." +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." msgstr "" -"A {{'[Especificação CWL VERSION](https://www.commonwl.org/VERSION)'." -"replace('VERSION', cwl_version_text) }}." +"A {{'[Especificação CWL " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." -#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b +#: ../../src/introduction/quick-start.md:102 936a7dfab11a4f2c82c0b59964e3ea28 msgid "" -"[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/" -"Workflow_management_system)." +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -"[Workflow management system na Wikipedia](https://en.wikipedia.org/wiki/" -"Workflow_management_system)." +"[Workflow management system na " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d +#: ../../src/setup.md:9 24ea9c5144664d9599d7aca767b4730a msgid "" -"This page is out-of-date and was kept here to preserve the links of the old " -"User Guide. The information on this page has been migrated to the [FAQ](/faq." -"md) section of the new user guide." +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." msgstr "" "O conteúdo desta página está desatualizado mas foi mantido aqui para " -"preservar os links do antigo Guia do Utilizador. A informação desta página " -"foi migrada para a secção [FAQ](/faq.md) do novo guia do utilizador." +"preservar os links do antigo Guia do Utilizador. A informação desta " +"página foi migrada para a secção [FAQ](/faq.md) do novo guia do " +"utilizador." #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 3843684b039a40dea163de951ca56738 msgid "Additional Arguments and Parameters" msgstr "Argumentos e Parâmetros Adicionais" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 +#: a6fd1842b938435aa2a3c889019eec71 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf +#: dfed0747ed544547afd364086d828c9b msgid "" "In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files in " -"the same directory as the source file. However, CWL input files (and the " -"directories in which they appear) may be read-only, so we need to instruct " -"\"javac\" to write the class file to the designated output directory instead." +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: e690b567eae34f3f8dbdd7760e51449a msgid "`arguments.cwl`" msgstr "`arguments.cwl`" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: ../../src/topics/staging-input-files.md:15 4cee519b108143be89a0e47a75d7d649 +#: 79585673fd654bab9ba7c1927d7e153b msgid "`arguments-job.yml`" msgstr "`arguments-job.yml`" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: ef070ebe5f7245489b05660fb6d7c178 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" -"Em seguida, crie um arquivo Java de exemplo para usar com a ferramenta de " -"linha de comando." +"Em seguida, crie um arquivo Java de exemplo para usar com a ferramenta de" +" linha de comando." #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb +#: 4ae43e3e841442039e4bb8c740096c56 msgid "" -"And now invoke `cwltool` providing the tool description and the input object " -"on the command line:" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" msgstr "" -"E agora execute `cwltool` utilizando a descrição de ferramenta e o objeto de " -"input na linha de comando:" +"E agora execute `cwltool` utilizando a descrição de ferramenta e o objeto" +" de input na linha de comando:" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a +#: 8497291577914eb3a172c1ffb736d95d msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 +#: dc9fa5f2cbb147b1853c4042c54010f3 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " "actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include `$(runtime.tmpdir)`, `" -"$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime." -"tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL " -"specification for details." +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 +#: ../../src/topics/best-practices.md:1 964bf8276dd04b65887448e1386e63fe msgid "Best Practices" msgstr "Melhores Práticas" -#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 +#: ../../src/topics/best-practices.md:3 7b59377bd56c47b8a71c18acfba4d3bb msgid "" -"The following are a set of recommended good practices to keep in mind when " -"writing a Common Workflow Language description for a tool or workflow. These " -"guidelines are presented for consideration on a scale of usefulness: " -"although more is better, not all are required." +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 +#: ../../src/topics/best-practices.md:8 2292670347cd4549bc6a51e972de0ef4 msgid "" -"No `type: string` parameters for names of input or reference files/" -"directories; use `type: File` or `type: Directory` as appropriate." +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 +#: ../../src/topics/best-practices.md:11 ae127b776eed4894af8cb680377703e0 msgid "" "A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that " -"the usual rules of software licensing apply to this document. For example, " -"if the workflow is shared publicly, licensing terms must be clear so that a " -"future user understands under what conditions they can run the workflow, " -"modify it and/or combine it with other workflows. For this reason, please " -"consider including a license field in the document. The authors of this " -"guide urge you to choose a pre-existing license rather than trying to write " -"your own (see the link below to learn more about choosing a license), and " -"our recommended practice is to choose a license that allows for re-use by " -"anyone, e.g. [Apache 2.0][apache-license]." +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." msgstr "" -#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f +#: ../../src/topics/best-practices.md:20 384eb620dc31468e8c3f5f33a3436200 msgid "" -"If possible, the license should be specified with its corresponding [SPDX " -"identifier][spdx]. Construct the metadata field for the license by providing " -"a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is " -"taken from the list of identifiers linked above. See the example snippet " -"below for guidance. For non-standard licenses without an SPDX identifier, " -"provide a URL to the license." +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc +#: ../../src/topics/best-practices.md:26 e8259b43fa6944eda73eae381db6b97b msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 +#: ../../src/topics/best-practices.md:28 5b976a5aec7d44bda55b0a019e955416 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 +#: ../../src/topics/best-practices.md:37 924b8df24deb4c82b32732f491c9a246 msgid "" -"For more examples of providing metadata within CWL descriptions, see [the " -"Metadata and Authorship section of this User Guide](../topics/metadata-and-" -"authorship.md)." +"For more examples of providing metadata within CWL descriptions, see [the" +" Metadata and Authorship section of this User Guide](../topics/metadata-" +"and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 +#: ../../src/topics/best-practices.md:40 9e64a9fc89cb45cfbff0e925cc91b1be msgid "" -"Include [attribution information][license-example] for the author(s) of the " -"CWL tool or workflow description. Use unambiguous identifiers like [ORCID]" -"[orcid]." +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 +#: ../../src/topics/best-practices.md:44 87030aef02044b8283c76debab4772bf msgid "" "In tool descriptions, list dependencies using short name(s) under " -"`SoftwareRequirement`." +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "" -#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 +#: ../../src/topics/best-practices.md:47 6c9eaae099fa4ca4b0986b1c4146df50 msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in `https://" -"identifiers.org/rrid/RRID:SCR_NNNNNN` format." +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb +#: ../../src/topics/best-practices.md:50 5ae8950fd31541399c2fe59096581dbc msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1438,216 +1499,224 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 +#: ../../src/topics/best-practices.md:55 b0493895105e43849bff2026763e472a msgid "" "In tool descriptions, include a list of version(s) of the tool that are " -"known to work with this description under `SoftwareRequirement`." +"known to work with this description under " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "" -#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 +#: ../../src/topics/best-practices.md:58 88806cb0462f4359801c1fa0ff0ebcc0 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `" -"$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. " -"[Full IANA media type list][iana-types] (also known as MIME types). For non-" -"bioinformatics tools, use or build an appropriate ontology/controlled " -"vocabulary in the same way. Please edit this page to let us know about it." +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a +#: ../../src/topics/best-practices.md:66 b178c7296ed5491782a4180c76883c14 msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c +#: ../../src/topics/best-practices.md:69 886d15c1972243acadccff5760f842f1 msgid "" -"Each `CommandLineTool` description should focus on a single operation only, " -"even if the (sub)command is capable of more. Don't overcomplicate your tool " +"Each " +"[`CommandLineTool`](https://w3id.org/cwl/CommandLineTool.html#CommandLineTool)" +" description should focus on a single operation only, even if the " +"(sub)command is capable of more. Don't overcomplicate your tool " "descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 +#: ../../src/topics/best-practices.md:73 ef5a5f9b253c4ca3916802a695fb7c6d msgid "" -"Custom types should be defined with one external YAML per type definition " -"for re-use." +"Custom types should be defined with one external YAML per type definition" +" for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 +#: ../../src/topics/best-practices.md:76 ff59f40e84004523904e3094be07cc80 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae +#: ../../src/topics/best-practices.md:78 78d73fde24e24beeab541a623d9530b6 msgid "" -"If useful, include a top-level `doc` as well. This should provide a longer, " -"more detailed description than was provided in the top-level `label` (see " -"above)." +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 +#: ../../src/topics/best-practices.md:82 d92013d662b44dbf8875e06c9dfbfd79 msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list of " -"valid values." +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a +#: ../../src/topics/best-practices.md:85 c100d5192a52497fb6a890b81a388fcf msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. One " -"common example: manipulating `File` names and paths? Consider whether one of " -"the [built in `File` properties][file-prop] like `basename`, `nameroot`, " -"`nameext`, etc., could be used instead." +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 +#: ../../src/topics/best-practices.md:90 e22fbacdb2fb4202b1bd69cfc24af5cd msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 +#: ../../src/topics/best-practices.md:93 0060a863362140f6bb3932cb5da1df04 msgid "" -"Complex workflows with individual components which can be abstracted should " -"utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their " -"workflow modular and allow sections of them to be easily reused." +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 +#: ../../src/topics/best-practices.md:97 93f6d6b544c24ce780184272f66bacab msgid "" "Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics " -"software\"][containers] (also useful to other disciplines)." +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 +#: ../../src/topics/command-line-tool.md:1 a378a2f7d268401abfbbbe6e5090a952 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 +#: ../../src/topics/command-line-tool.md:3 cf0f1c00c0b34c94a8e2460a700c303e msgid "" -"A command-line tool is a type of Process object that can be run by itself or " -"as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, " -"etc. The command-line tool is defined in the `baseCommand` attribute of the " -"command-line tool CWL document." +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab +#: ../../src/topics/command-line-tool.md:8 7a180ba1f2d746a78b79be7e899cbad6 msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The following " -"example contains a minimal example of a CWL command-line tool for the `echo` " -"Linux command, using inputs and outputs." +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 +#: ../../src/topics/command-line-tool.md:19 128bd8cd6788431da54fa07a8dc87f99 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 +#: ../../src/topics/command-line-tool.md:50 d742e9e59ea44ca1a1df2de85059343f msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d +#: ../../src/topics/command-line-tool.md:57 e3a06ebe51b64b0183673a8acc04969f msgid "" -"The example above uses a simplified form to define inputs and outputs. You " -"will learn more about in the [Inputs](../topics/inputs.md) and in the " -"[Outputs](../topics/outputs.md) sections." +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e +#: ../../src/topics/command-line-tool.md:68 2bab464d19d14562a6501373aff13905 msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 +#: ../../src/topics/command-line-tool.md:69 201712f3ceee4d4ea56ab96d3fef97b0 msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network access. " -"If a command-line tool is written manually in CWL v1.1+, there is a need to " -"specify when network access is required." +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. Starting with CWL v1.1, programs are not granted network access " +"by default, so you must include the requirement for network access in the" +" specification of your tool." msgstr "" -#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e +#: ../../src/topics/command-line-tool.md:84 3282a357799f4a72a6b8bace206144c4 msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network " -"Access automatically." +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 or v1.2 " +"will have `networkAccess: true` set automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: 17c5b4ee43cc4a979676ad27e473d046 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d +#: cd0dff10471c4ad2b84e3a0e4d7767ea msgid "" -"Sometimes you need to create a file on the fly from input parameters, such " -"as tools that expect to read their input configuration from a file rather " -"than the command line parameters, or need a small wrapper shell script." +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +#: bf4aea0a22334a1ca75cc20e937e6581 +msgid "" +"To generate such files, we can use the " +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: 008f768d56b8465bb4e8f4fde15853a7 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df +#: 252f8e897b0942a8be098481890005f3 msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the value " -"at the input `message`." +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 +#: aca24b72687c4d4d84bf9de8b71413f7 msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later " -"during command line tool invocation. That means that any genuine need for " -"the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` " -"above is expanded to `${PREFIX}` in the generated file to be evaluated by " -"the shell script instead of the CWL engine." +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa +#: 750b3232e8754448bc2b5913539495b8 msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 2d2ef4769b2347e79db827655f1bcdeb 2699fbc4376148af91b7a5a6cdac467c -#: ca03defa3ad14cf698171cb09e3055c1 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:81 +#: 687c8a84bade43269f3cd767d32f9f47 81da7a18fe8d4659abc883cf43009f1f +#: d5d67eae63304ebb9b242133feacb0d1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d +#: c4f964450d014734877fb3c968353a74 msgid "" -"Before we run this, let us look at each step in a little more detail. The " -"base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " "command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c +#: 9aeea5a6a4244bc7a1626e0cb7351068 msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML " -"array, we need a `-` on the first line of each element of the array, in this " -"case we have just one element. `entryname:` can have any value, but it must " -"match what was specified in the `baseCommand`. The final part is `entry:`, " -"this is followed by `|-` which is YAML quoting syntax, and means that you " -"are using a multiline string (without it, we would need to write the whole " -"script on one line)." +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 +#: 867239e9ad3d4187a2703662a0ca3976 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1657,222 +1726,228 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: b372f33c65bb4707b2a462a960bb1373 293fb1d428b849aebccad598a932992d -#: f924d65fed0c4cb5b0a019b084a8b535 d6255506eebe44be94c5ce703c44a513 -#: 7bbd2d738fc54649aeb10f8d2bc38b6f +#: 0d7151b9f0194197bd686fe6c9c47afd 78bb40eeeda24d7b923162daa45d51a7 +#: 7b341a317347482ca86fc56119c3686f 7c637fa62cab4d0dbe670a3b72737cc9 +#: cfb4605a01dd4475aabcc086a4e65957 msgid "" -"Now invoke `cwltool` with the tool description and the input object on the " -"command line:" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 +#: ../../src/topics/custom-types.md:1 252a3a17b1ec4d5a9a82ebbf6c2f314c msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a +#: ../../src/topics/custom-types.md:3 e0275ddda8f84207a58d10c17ca99a45 msgid "" -"Sometimes you may want to write your own custom types for use and reuse in " -"CWL descriptions. Use of such custom types can reduce redundancy between " -"multiple descriptions that all use the same type, and also allow for " -"additional customisation/configuration of a tool/analysis without the need " -"to fiddle with the CWL description directly." +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc +#: ../../src/topics/custom-types.md:9 8367e38e5e7c4a298d1d87b9001aaddc msgid "" -"The example below is a CWL description of the [biom convert format][biom] " -"tool for converting a standard biom table file to hdf5 format." +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 +#: ../../src/topics/custom-types.md:12 18b802f45ce0454ab7aa2a21812863c6 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c +#: ../../src/topics/custom-types.md:18 66d1953f5dd54d448bddd0f30c330402 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 +#: ../../src/topics/custom-types.md:24 56b8912a1ea84f28adeb8beaf92ab563 msgid "" -"___Note:___ To follow the example below, you need to [download the example " -"input file](https://github.com/common-workflow-language/user_guide/blob/main/" -"src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), " -"*rich_sparse_otu_table.biom* e.g. via `wget`:" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea +#: ../../src/topics/custom-types.md:30 a48539920c4944898918bc90b2d4e3c9 msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to be " -"used in the table conversion are imported as a custom object:" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e +#: ../../src/topics/custom-types.md:46 c791096f537141e8bd7cc941d711d108 msgid "" -"The reference to a custom type is a combination of the name of the file in " -"which the object is defined (`biom-convert-table.yaml`) and the name of the " -"object within that file (`table_type`) that defines the custom type. In this " -"case the `symbols` array from the imported `biom-convert-table.yaml` file " -"define the allowable table options. For example, in `custom-types.yml`, we " -"pass `OTU table` as an `input` that tells the tool to create an OTU table in " -"hdf5 format." +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e -msgid "" -"The contents of the YAML file describing the custom type are given below:" +#: ../../src/topics/custom-types.md:53 5f6bc6ed72334a74b9a4c46c29ddda46 +msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 +#: ../../src/topics/custom-types.md:55 3b55419088e8446994703220bd8e8480 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 +#: ../../src/topics/custom-types.md:61 fe6f4ce5e7344af0abea9d5c03e32ecd msgid "" -"In order for the custom type to be used in the CWL description, it must be " -"imported. Imports are described in `requirements:SchemaDefRequirement`, as " -"below in the example `custom-types.cwl` description:" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c +#: ../../src/topics/custom-types.md:76 dce43b138ba24b22bfa9fa5692a17009 msgid "" "Note also that the author of this CWL description has also included " -"`ResourceRequirement`s, specifying the minimum amount of RAM and number of " -"cores required for the tool to run successfully, as well as details of the " -"version of the software that the description was written for and other " -"useful metadata. These features are discussed further in other chapters of " -"this user guide." +"[`ResourceRequirement`](https://w3id.org/cwl/CommandLineTool.html#ResourceRequirement)s," +" specifying the minimum amount of RAM and number of cores required for " +"the tool to run successfully, as well as details of the version of the " +"software that the description was written for and other useful metadata. " +"These features are discussed further in other chapters of this user " +"guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 +#: ../../src/topics/environment-variables.md:1 19737f89f2994815969fa4a88346f49a msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 +#: ../../src/topics/environment-variables.md:3 ad965f75aa0c41cda8b82c46af49774d msgid "" -"Tools run in a restricted environment and do not inherit most environment " -"variables from the parent process. You can set environment variables for " -"the tool using `EnvVarRequirement`." +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 +#: ../../src/topics/environment-variables.md:7 38b276f9b0114a0bb87734f0a07a736f msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 +#: ../../src/topics/expression-tool.md:1 9f33532119dc47ffb6ade20fb1d950bd msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 +#: ../../src/topics/expression-tool.md:3 b267056eae704737af5aaada3ea7e6e2 msgid "" -"An expression tool is a type of Process that can be run by itself or as a " -"Workflow step. It executes a pure JavaScript expression. It is meant to be " -"used as a way to isolate complex JavaScript expressions that need to operate " -"on input data and produce some result as output." +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 +#: ../../src/topics/expression-tool.md:8 7e930144163e4d6e9f0bcaa764497ccf msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " -"instead of `baseCommand`, it requires an `expression` attribute." +"instead of `baseCommand`, it requires an " +"[`expression`](https://w3id.org/cwl/CommandLineTool.html#Expressions_(Optional))" +" attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe +#: ../../src/topics/expression-tool.md:17 f172488c19a94d688036197117d30b38 msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 +#: ../../src/topics/expression-tool.md:48 ef978c951f1a4b7d9280d31367e5bae7 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a +#: ../../src/topics/expression-tool.md:67 0b63da31bc274b3cad798b07149592ab msgid "" -"We had to use an `InlineJavascriptRequirement` as our expression contains a " -"JavaScript call in `.toUpperCase()`. This means to tools using the " -"expression tool that JavaScript is a requirement." +"We had to use an " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" as our expression contains a JavaScript call in `.toUpperCase()`. This " +"means to tools using the expression tool that JavaScript is a " +"requirement." msgstr "" -#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 +#: ../../src/topics/expressions.md:1 b0e567a985f748538552bdb486a47998 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 +#: ../../src/topics/expressions.md:3 24d05cbbab8e460e99f2edc97ab0dcec msgid "" "If you need to manipulate input parameters, include the requirement " -"`InlineJavascriptRequirement` and then anywhere a parameter reference is " -"legal you can provide a fragment of Javascript that will be evaluated by the " -"CWL runner." +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" and then anywhere a parameter reference is legal you can provide a " +"fragment of Javascript that will be evaluated by the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 +#: ../../src/topics/expressions.md:9 3d48d1a8f7f74bc1886e41653cb53a22 msgid "" -"JavaScript expressions should only be used when absolutely necessary. When " -"manipulating file names, extensions, paths etc, consider whether one of the " -"[built in `File` properties][file-prop] like `basename`, `nameroot`, " -"`nameext`, etc, could be used instead. See the [list of best practices](best-" -"practices.md)." +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: ../../src/topics/expressions.md:16 7d444aacd418466bbe588fa964b45179 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 +#: ../../src/topics/expressions.md:22 72a0558a83964796a8c1a0eb55fd78e8 msgid "" -"As this tool does not require any `inputs` we can run it with an (almost) " -"empty job file:" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 +#: ../../src/topics/expressions.md:25 d679fd1363b24c81979c68e7342159cf msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 +#: ../../src/topics/expressions.md:31 d2ee4fcece744b6681f29322b5305111 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object is " -"represented simply by a set of empty brackets." +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d +#: ../../src/topics/expressions.md:35 624e4a270e374b1699b780df508b9184 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc +#: ../../src/topics/expressions.md:37 c252eac9a35e46aab08bd07bc1cdb57d msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 +#: ../../src/topics/expressions.md:47 f6f64d57a50742b19b801c14806ee18a msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 +#: ../../src/topics/expressions.md:54 052e24e2ad044cc28f04d7f39be871d6 msgid "" "Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to " -"describe the additional command line arguments." +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 +#: ../../src/topics/expressions.md:62 84b31c076d4b4826aae35e8c23fe6a25 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 +#: ../../src/topics/expressions.md:64 8c3b402c40f64880a4bd42c47b910254 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c +#: ../../src/topics/expressions.md:66 9bf5ca0e769147c6a9705bc40bd1febc msgid "" -"From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 1acb064f7a4a482aa0174bdc847c6382 -#: 0222780b98ac48e89b1b4f57c9df8590 +#: ../../src/topics/parameter-references.md:64 7ab0dbd54c1441539673fa12ef96b89e +#: e76c6ece0c594fefa86b190879c5acaa msgid "`arguments`" msgstr "" @@ -1880,35 +1955,35 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 ef2b8433778a40408f179c3e6f0cf99e -#: 224732683a9c41f3ba1b778851e745a8 17b10d1e91b24dc582df98fcd2ac850e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 e4e68011dc5f42e4918c747afa7d764b -#: d44e3cfa661840eb851782e24caf1b68 +#: ../../src/topics/parameter-references.md:86 0209558b1013471eb708698537edaf06 +#: 4458393fdb0e451f9806e91122ea2534 594a163e08f04aa5a04a44a303a1c643 +#: a6fddc160afc4ef09717f69de72c11ce a9ec99ddcb344bcbbe5c1f59af0bcff2 +#: af2cdb5f66ac4fd5b8f91258f005cc62 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: ../../src/topics/parameter-references.md:66 afb175f182354cb19e23b1cad241437e +#: f9a6718845e24f46b76fcc8ab26eec7a msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: ../../src/topics/parameter-references.md:67 3bce21dcc2da439daca80c4fcdf4c343 +#: 7f5ce097ca0442a6a200599342a6e24b msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: ../../src/topics/parameter-references.md:68 3397e8816f6a4d4b9af728c175f04917 +#: 7b14686e16eb4f488659b22d67ec3bfa msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e +#: ../../src/topics/expressions.md:72 7a2d74aa018f4cab8c68e8775d83dd01 msgid "" -"From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter)" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" #: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 @@ -1916,11 +1991,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 d0a92a3792b549e9b5ddce4667d168d2 -#: 801729c7c71b4109824b035437e69bf9 1bc510d525f0414e88692e356e67fbbc -#: d2e246ae56a24e4abdd6b7d9812a86e2 b1446bab2732412e91f721a08067b0bd -#: e89dbeb22f41430ca39c923d9fdf68cb bd61499b71e64164878dea08d6d7141e -#: ed875a006df64f9e8a55fa5e9fa87404 +#: ../../src/topics/parameter-references.md:90 24f27702d0684bc98e3232103510232e +#: 26a8dff7b80c4e059f1e20eef9da6203 476aa37af5214bcf963c7aab1f859273 +#: 4b0a0cd934bd41b4b55c034b91392bc7 5182e2165e44429287b4d924c2f896a4 +#: 7de500d3be6b4c3e8f274fd6a092109f 953d824a494947a3ab0ca2988717ee01 +#: b301751f90af4700bbada5e5b166be35 msgid "`format`" msgstr "" @@ -1929,1491 +2004,1546 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 8a1748579de14f0888d5ee9023e37c2d -#: f760465a49d64d4c8468ad9c4fea62b1 28b6b5ffa7524374aaa9525ebfafb762 -#: d11f6a19ddf34cf19ec856bacf998e29 bcb7cd10cb5947bb9d85c040f57f954f -#: da5188d3bedc4997a35bdf417f2f643c cd7a0190511d4613b09600a3b1e9d55f -#: 47def3b078e2402182039be0227090ae +#: ../../src/topics/parameter-references.md:91 2c2b8db396b04ace8aa396c0a5a4858f +#: 33a9b77ce15b4910962a7f08bd2f47a3 57cba0191de3470bbe112ed2a0d3f252 +#: 6efe998094b3469eae61cfff551b1eb1 776de1ecfafc41ada7e916addd7229fd +#: 8595d62eb0274b3a8a7f0adf058b51d3 988966a2d4844e73961b0358aff8f6e1 +#: faa7d521fec240748407d03ffdb93aa0 msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac +#: ../../src/topics/expressions.md:75 d737a9e9bf1c45d695bf584bc3241d9a msgid "" -"From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding)" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 +#: ../../src/topics/expressions.md:77 0e2052e16f6a41b8983dc64b4b3a7586 msgid "" -"From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 +#: ../../src/topics/expressions.md:80 dff31dd961d540e3b8cd1247e978d60e msgid "" -"From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding)" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: ../../src/topics/parameter-references.md:78 249aba7c38ce49379b9d35e7ad81a0bf +#: 5a354eb4883948e0a2b5c96b5ae12da7 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 d555a3d991e344a5a8e1289168d7c6d1 -#: 44b3f123c9b04a308c1161b742a7b34b +#: ../../src/topics/parameter-references.md:79 2325a310f2bc4d09b53b32c54efae2df +#: 9e477e2cfab24861b517fe2fb52962f4 msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 e9fa9430535c424fa3e8be5d460d2ba4 -#: 0e306cc923974d1db83fdfb45105a11c -msgid "From `Workflow`" +#: ../../src/topics/parameter-references.md:80 9448462d104b4be5904623c85a9e16b7 +#: bf11a7a72147445c9b8e44b541e09f36 +msgid "From [`Workflow`](https://w3id.org/cwl/Workflow.html)" msgstr "" -#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 +#: ../../src/topics/expressions.md:84 0d54a777a33d4f17a2f3390384a3c0c5 msgid "" -"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" -"v1.0/Workflow.html#WorkflowOutputParameter)" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 b0290d1a477b48119e17cf1fed9d6dff -#: 446f1190af7a40a0913ff04ce7aa938c +#: ../../src/topics/parameter-references.md:84 7918d0661be746faaddf25ad49172f30 +#: b8439dbaa949427097e25ccb48fe15ee msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 +#: ../../src/topics/expressions.md:88 7b37eb600c9b4847a58a7e5077bef4c3 msgid "" -"From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 e1cde4aa32c041238ed2596173c6d824 -#: 557694f82e314baa9ccafba14d6ff2c9 +#: ../../src/topics/parameter-references.md:87 368ef005c2ca4b8599f76242f7178375 +#: ab1ba7626eae483a8b614ee4cd5bab6f msgid "" -"From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." -"html#ExpressionTool)" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 c2a92d3eca7f4ee39cec649170eeea53 -#: 3c939769ede94602a67fc50c435741cf +#: ../../src/topics/parameter-references.md:88 595b9ddcee734d6595c1b4b2d169dcb8 +#: 80b55c77a4384644acfc9472c3cedee0 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 +#: ../../src/topics/expressions.md:92 fd504478a6c641e0a72321fa80ad1c9c msgid "" -"From [InputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [ExpressionToolOutputParameter](https://www." -"commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f +#: ../../src/topics/expressions.md:95 32b1a39cca1a4402af9bdc0abc4d70c8 msgid "" -"From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement)" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: ../../src/topics/parameter-references.md:93 2518d499801e4bcf82e9e4666280504d +#: 98a511d138e9497c923963c2ca5f0a0b msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 718ceee9973240ec9c100977bbcc8921 -#: 2b25152f6df5494a8632f3ce631c20d8 +#: ../../src/topics/parameter-references.md:94 57a055b125f742dc8842b798b034161b +#: e84bc5505a6549ae9aacde8cb9225403 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 c07ab08eb75d4528949c56a3d7c12b28 -#: 846cd427ae25410eae7c920b237edcb0 +#: ../../src/topics/parameter-references.md:95 98cd455e080f43749090270e7a61cb42 +#: e698ea756fe94e99837312fb30c9f9bf msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: ../../src/topics/parameter-references.md:96 8dfae10004a641fdb95c456c90a48d94 +#: bef90c153d4f4397b1f69f9beb38f7e6 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: ../../src/topics/parameter-references.md:97 47fddc711ce44086a7811bdfbd9167dd +#: e2bdf4fe676346cbb4443ee54fb7419b msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: ../../src/topics/parameter-references.md:98 7d143ba98f1f4dfcbe08b70389d43092 +#: 8f1665baca2e4e3b96026b50d132709a msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: ../../src/topics/parameter-references.md:99 79bea45c2a484eda92c8578130b0b982 +#: d169949866a24e31947dffcb94620c5f msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 +#: 8d2e01f2aa314f1cb1231f2e08f89ce5 d5417397b1e242ef9878ac77d2f65005 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 +#: ../../src/topics/expressions.md:104 08a66b2ab271494d810ff5834ca5c1bc msgid "" -"From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" -"CommandLineTool.html#InitialWorkDirRequirement)" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 +#: 21e9582891cf4b87a7ee4693663040fa 51bc6d1ccef14729a0d5e63b56d73d20 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce +#: ../../src/topics/expressions.md:106 7d8755f05d6541439f72ec9d6806d3fc msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: effc0208cf4f4551958db6e526c0528b 9d4889c8cec24351a7a9e3c547e331b6 +#: 29c2424fc7dc43e68c9bfee179167bb3 30f25141bcce4670882e4a5bbe4fc3e2 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: be6c1e85c7b6495d8086c262daad20e7 af4f7f232a9d42388c0ba1cfc7c2cdf7 +#: 02cfd4f1c3014e1eaa598a329dc5a95d d76fb015595e4194a7e15d714baaaf98 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 +#: 408f69a2df1343a78f93ff2ac0a994ea d37c78309e8b427f835af4fbd367e643 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 +#: ../../src/topics/expressions.md:110 53752bdff0974e39b2a86e8f2d96455f msgid "" -"From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef)" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 +#: 242a12ec757947db894195c9aefba818 7b26b9972f7141bf950b3bb024b0e369 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 -msgid "" -"Using External Libraries and Inline JavaScript Code with `expressionLib`" +#: ../../src/topics/expressions.md:116 93d6c90b49d8424f9283c384062ce333 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 +#: ../../src/topics/expressions.md:118 ea6cbaa5dae647538c0bd9a4d5cad3f9 msgid "" -"The requirement `InlineJavascriptRequirement` supports an `expressionLib` " -"attribute that allows users to load external JavaScript files, or to provide " -"inline JavaScript code." +"The requirement " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" supports an `expressionLib` attribute that allows users to load external" +" JavaScript files, or to provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d +#: ../../src/topics/expressions.md:122 484dc17440524cfda4dc486a7c5d5f63 msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts of " -"the CWL document." +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b +#: ../../src/topics/expressions.md:128 5b2336cae1ef4cae8ed187d3f33cff25 msgid "" -"The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl." -"org/v1.0/CommandLineTool.html#Expressions) that the only version of " -"JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-" -"international.org/5.1/). This means that any code that you include or write " -"in your CWL Document must be compliant with ECMAScript 5.1." +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c +#: ../../src/topics/expressions.md:135 32eca3a47efc4685bf7be706e123adbe msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a JavaScript " -"function inline in `expressionLib`. That function can then be used in other " -"parts of the CWL document:" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e +#: ../../src/topics/expressions.md:139 6839a02fb82d45c29ae518f2b00cb9d5 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 +#: ../../src/topics/expressions.md:146 5b5e59fa1688499ea4560ee6f8023227 msgid "" -"Running this CWL workflow will invoke the JavaScript function and result in " -"the `echo` command printing the input message with capital initial letters:" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" msgstr "" -#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 +#: ../../src/topics/expressions.md:149 a1e57c6833c848d3974cf448493ab924 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 +#: ../../src/topics/expressions.md:155 1a4dfef06b5c4402bdb7e7dbd79eeb5d msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db +#: ../../src/topics/expressions.md:158 71ac99c65d15451cbbf58d1e81934010 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 +#: ../../src/topics/expressions.md:164 60918e53189243d3872e61c7a4de20fc msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac +#: ../../src/topics/expressions.md:171 ad2a74bd983b47869dc78b2eb7b6fce1 msgid "" -"The `custom-functions.js` file is included in the CWL document with the `" -"$include: custom-functions.js` statement. That makes the functions and " +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 +#: ../../src/topics/expressions.md:175 82c02dd2446b4de9a4c4b87736107b30 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 +#: ../../src/topics/expressions.md:181 6fa7ebeffc7b44c6a12cd84897d186a1 msgid "" -"Finally, note that you can have both inline and external JavaScript code in " -"your CWL document. In this final example we have added another entry to the " -"`expressionLib` attribute with the new function `createHelloWorldMessage`, " -"that calls the `capitalizeWords` function from the external file `custom-" -"functions.js`." +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b +#: ../../src/topics/expressions.md:186 d34f3e688d2d49b6bfcda4c962895d8c msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f +#: ../../src/topics/expressions.md:193 9e2774fc35b14832a0f92b7afaafd537 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 +#: ../../src/topics/expressions.md:200 8b797cfb232f4e5da51f6c21e9a8e7e3 msgid "" -"The `$include` statement can be used to include a file from the local disk " -"or from a remote location. It works with both relative and absolute paths. " -"Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad." -"html#Include) from the CWL specification to learn more about it." +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 +#: ../../src/topics/file-formats.md:1 ac906f26116c45d882e1afa42ae38e34 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a +#: ../../src/topics/file-formats.md:3 d99dab4f2f264c68b839b59b80d570e0 msgid "" -"Tools and workflows can take `File` types as input and produce them as " -"output. We also recommend indicating the format for `File` types. This helps " -"document for others how to use your tool while allowing you to do some " -"simple type-checking when creating parameter files." +"Tools and workflows can take " +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types as input " +"and produce them as output. We also recommend indicating the format for " +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 +#: ../../src/topics/file-formats.md:8 23ba3dd26f5543119e2c152105b58e98 msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM in " -"our example), reference a local ontology for your institution, or do not add " -"a file format initially for quick development before sharing your tool with " -"others. You can browse existing [IANA file format listings][IANA] and [EDAM " -"file format listings][EDAM] on their websites." +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a +#: ../../src/topics/file-formats.md:14 81c441846fc249c58607bacf97095eb8 msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` section " -"of the document in greater detail, so don't worry about these for now." +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." msgstr "" -#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f +#: ../../src/topics/file-formats.md:17 c04841dbf4be4cf8a22cceca8b08bd14 msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 +#: ../../src/topics/file-formats.md:20 c5f6f6e4c23e4bf19dee69acb8ebed8e msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 +#: 20e97d58596a4a959ad76ec6128ac414 4e070ae9110d437bbf008b0c60a00cd5 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e +#: ../../src/topics/file-formats.md:32 632e441919094610b97afc17e9c5e625 msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b +#: ../../src/topics/file-formats.md:34 afd8633db1904897aa3e499354b1c376 msgid "" -"Below is an example of a parameter file for the example above. We encourage " -"checking in working examples of parameter files for your tool. This allows " -"others to quickly work with your tool, starting from a \"known good\" " -"parameterization." +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc +#: ../../src/topics/file-formats.md:39 bb69d6963c174191bf527335c3f665b7 msgid "`sample.yml`" msgstr "`sample.yml`" -#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d +#: ../../src/topics/file-formats.md:45 ddb4f6f81c7d462b974e98c88dd3f558 msgid "" -"___Note:___ To follow the example below, you need to download the example " -"input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff +#: ../../src/topics/index.md:1 2995cd4fb85c423dba021611dac4a137 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 +#: ../../src/topics/inputs.md:1 3bac021fe7614d74ae701fb3c3765b93 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea +#: ../../src/topics/inputs.md:3 8bb3ee0cd0fc4d85ba007431fc541973 msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e +#: ../../src/topics/inputs.md:5 17365707f58242369dd6aa73fc8d7242 msgid "" -"The `inputs` of a tool is a list of input parameters that control how to run " -"the tool. Each parameter has an `id` for the name of parameter, and `type` " -"describing what types of values are valid for that parameter." +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a +#: ../../src/topics/inputs.md:9 521cb5dead5d4e9ab5ff037fb4b683cb msgid "" -"Available primitive types are *string*, *int*, *long*, *float*, *double*, " -"and *null*; complex types are *array* and *record*; in addition there are " -"special types *File*, *Directory* and *Any*." +"Available primitive types are *string*, *boolean*, *int*, *long*, " +"*float*, *double*, and *null*; complex types are *array* and *record*; in" +" addition there are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 +#: ../../src/topics/inputs.md:13 fbdf2c1bed3e41d7a41ec6b14d134a98 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed +#: ../../src/topics/inputs.md:16 008f79cdf0074c73948bf50deb0a8a47 msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d +#: ../../src/topics/inputs.md:18 94cd3f10e94f4735bd3ae7dc168e5deb msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e +#: ../../src/topics/inputs.md:24 b339be370e8742b69400c8040ad7d15b msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 +#: ../../src/topics/inputs.md:26 78974fb2475947ccb8b8c55e34df5fa6 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 +#: ../../src/topics/inputs.md:33 9cc4a60d01f945aa9b4c43afcf20098b msgid "" -"You can use `cwltool` to create a template input object. That saves you from " -"having to type all the input parameters in a input object file:" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in an input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b +#: ../../src/topics/inputs.md:40 5ac6da11d56446de97c251a37d997671 msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl " -"> inp-job.yml`, and then modify the default values with your desired input " -"values." +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 +#: ../../src/topics/inputs.md:44 6a3edb0d259d4d7c900dd9811f978d4e msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b +#: ../../src/topics/inputs.md:47 f1d76be7ba0b48f4b605581d0a9a5c72 msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the " -"command line." +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." msgstr "" -"Em sequência, cria um arquivo chamado whale.txt utilizando [touch] digitando " -"`touch whale.txt` na linha de comando." +"Em sequência, cria um arquivo chamado whale.txt utilizando [touch] " +"digitando `touch whale.txt` na linha de comando." -#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da +#: ../../src/topics/inputs.md:53 8cabfa0cbcfd4a5aa30d1aabd412136d msgid "" -"Now invoke `cwltool` with the tool description and the input object on the " -"command line, using the command `cwltool inp.cwl inp-job.yml`. The following " -"boxed text describes these two commands and the expected output from the " -"command line:" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c +#: ../../src/topics/inputs.md:64 5c78d7824ef34636ae2ed68d524d79e8 msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not explicitly " -"specified" +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 +#: ../../src/topics/inputs.md:70 5bdf77c45346445d8f93353c1e73f768 msgid "" -"The field `inputBinding` is optional and indicates whether and how the input " -"parameter should appear on the tool's command line. If `inputBinding` is " -"missing, the parameter does not appear on the command line. Let's look at " -"each example in detail." +"The field " +"[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)" +" is optional and indicates whether and how the input parameter should " +"appear on the tool's command line. If `inputBinding` is missing, the " +"parameter does not appear on the command line. Let's look at each " +"example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c +#: ../../src/topics/inputs.md:83 d783fe52e86f4feda33ea0eecb622603 msgid "" -"Boolean types are treated as a flag. If the input parameter \"example_flag" -"\" is \"true\", then `prefix` will be added to the command line. If false, " -"no flag is added." +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 +#: ../../src/topics/inputs.md:95 f99fb9a6d0374ef78503815d4db9006d msgid "" -"String types appear on the command line as literal values. The `prefix` is " -"optional, if provided, it appears as a separate argument on the command line " -"before the parameter . In the example above, this is rendered as `--example-" -"string hello`." +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e +#: ../../src/topics/inputs.md:109 b106eed01c1744a792368f91f547e553 msgid "" -"Integer (and floating point) types appear on the command line with decimal " -"text representation. When the option `separate` is false (the default value " -"is true), the prefix and value are combined into a single argument. In the " -"example above, this is rendered as `-i42`." +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 +#: ../../src/topics/inputs.md:124 1c70336741a842a5b16b687642d1d9b4 msgid "" "File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the parameter " -"is optional. In the example above, this is rendered as `--file=/tmp/random/" -"path/whale.txt`. However, if the \"example_file\" parameter were not " -"provided in the input, nothing would appear on the command line." +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." msgstr "" -#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 +#: ../../src/topics/inputs.md:131 9294c07c672b414f9c3895ed70b9b4ee msgid "" -"Input files are read-only. If you wish to update an input file, you must " -"[first copy it to the output directory](staging-input-files.md)." +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 +#: ../../src/topics/inputs.md:134 a07137c36e63495f836c483fd472904f msgid "" -"The value of `position` is used to determine where parameter should appear " -"on the command line. Positions are relative to one another, not absolute. " -"As a result, positions do not have to be sequential, three parameters with " -"positions 1, 3, 5 will result in the same command line as 1, 2, 3. More " -"than one parameter can have the same position (ties are broken using the " -"parameter name), and the position field itself is optional. The default " -"position is 0." +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 +#: ../../src/topics/inputs.md:142 7513adabd3ae4701b17f578ac9f321d7 msgid "" -"The `baseCommand` field will always appear in the final command line before " -"the parameters." +"The `baseCommand` field will always appear in the final command line " +"before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 +#: ../../src/topics/inputs.md:146 c3c82d25a75941b0b50a4a6bb826568f msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d +#: ../../src/topics/inputs.md:148 b11a5c7a13b345939e4ae15e1e2c0786 msgid "" "It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to provide " -"`type` field with `type: array` and `items` defining the valid data types " -"that may appear in the array. Alternatively, brackets `[]` may be added " -"after the type name to indicate that input parameter is array of that type." +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." msgstr "" -#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 +#: ../../src/topics/inputs.md:154 aa00bcfc6c0f4085ae52621a2f4ae8d9 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 +#: ../../src/topics/inputs.md:160 e730b2b9bace4427bdd045556963634f msgid "`array-inputs-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 588f0f7f967f4d69af27c9729d6d3119 -#: 02adef8ee8204842b5b4a0408f3bac33 9db68837918a4a349f32f15f12697a1d +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:86 +#: ../../src/topics/outputs.md:109 015a0f00c2b245e2b0e87735926da736 +#: 390384208d7b4771888f164b587c7b9a edb3ae59c48945f29c3086b16a5265d3 msgid "" -"Now invoke `cwltool` providing the tool description and the input object on " -"the command line:" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" msgstr "" "Agora chame o `cwltool` passando a descrição da ferramenta e o objeto de " "entrada na linha de comando:" -#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 +#: ../../src/topics/inputs.md:178 13e59751d43b49f0ac366538a14f9c84 msgid "" -"The `inputBinding` can appear either on the outer array parameter definition " -"or the inner array element definition, and these produce different behavior " -"when constructing the command line, as shown above. In addition, the " -"`itemSeparator` field, if provided, specifies that array values should be " -"concatenated into a single argument separated by the item separator string." +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d +#: ../../src/topics/inputs.md:185 bb31c6784ea843ec88f185523cfa25df msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` in " -"`array-inputs-job.yml`. Arrays can also be expressed over multiple lines, " -"where array values that are not defined with an associated key are marked by " -"a leading `-`. This will be demonstrated in the next lesson and is discussed " -"in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify " -"arrays of arrays, arrays of records, and other complex types." +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 +#: ../../src/topics/inputs.md:191 53817379078548b2aeb6195cae9cbab7 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d +#: ../../src/topics/inputs.md:193 e163c0cfe9694a85b2e42682f42970a5 msgid "" "Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be provided " -"together (they are exclusive). You can use records and type unions to group " -"parameters together to describe these two conditions." +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 +#: ../../src/topics/inputs.md:198 84e1ab25511c49d1baabb1f80f247b49 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 +#: ../../src/topics/inputs.md:204 3d5dfc8ee47b458db638a9eed84b4938 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f +#: ../../src/topics/inputs.md:215 ecfb1d911a84400ba3db12fd0adf9279 msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: ../../src/topics/inputs.md:217 24ba804374b4471d8e925d80670f9dff msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add +#: ../../src/topics/inputs.md:233 436707d9c7634732ad1e60d8294bd4ba msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the first " -"matching item (`itemC`) is added to the command line and remaining item " -"(`itemD`) is ignored." +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea +#: ../../src/topics/inputs.md:236 01b168c5faf94ead8d836dfe39e4c592 msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c +#: ../../src/topics/inputs.md:252 e6d81d6549984689bae4533c6d01bd5b msgid "" -"In the third example, only `itemD` is provided, so it appears on the command " -"line." +"In the third example, only `itemD` is provided, so it appears on the " +"command line." msgstr "" -#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 +#: ../../src/topics/inputs.md:255 ffddeeda8f04408ba73f7a59a4618da5 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d +#: ../../src/topics/inputs.md:257 cf22f21ec44c483986979316544a7c3b msgid "" -"If you use exclusive input parameters combined with expressions, you need to " -"be aware that the `inputs` JavaScript object will contain one of the " -"exclusive input values. This means that you might need to use an **or** " -"boolean operator to check which values are present." +"If you use exclusive input parameters and reference them in expressions, " +"you need to be aware that the `inputs` JavaScript object will contain one" +" of the possible, mutually-exclusive input values. Because the types of " +"these exclusive values may differ, you may need to check which type is in" +" use when you reference the properties of the `input` object." msgstr "" -#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb +#: ../../src/topics/inputs.md:263 0fecb128b19b44d796b6c1b6de4f7166 msgid "" "Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from an " -"enum." +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." msgstr "" -#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 +#: ../../src/topics/inputs.md:266 7f1941698a6046e9b9e8a53736af949a msgid "`exclusive-parameter-expressions.cwl`" msgstr "`exclusive-parameter-expressions.cwl`" -#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 +#: ../../src/topics/inputs.md:272 60b585142f06489d9f48090b664b6d32 msgid "" "Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you provide a " -"valid value, such as “fasta” (one of the values of the enum), your command " -"should execute successfully:" +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as `fasta` (one of the possible values of the" +" enum), your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 +#: ../../src/topics/inputs.md:281 11fdeb057d674f118830f431ff019c15 msgid "" -"However, if you do not provide any input value, then `file_format` will be " -"evaluated to a `null` value, which does not match the expected type for the " -"output field (a `string`), resulting in failure when running your workflow." +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to `null`, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your " +"workflow." msgstr "" -#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 +#: ../../src/topics/inputs.md:290 8594cca9d93b4280b6cfee64c8a7c578 msgid "" -"To correct it, you must remember to use an or operator in your JavaScript " -"expression when using exclusive parameters, or any parameter that allows " -"`null`. For example, the expression could be changed to `$(inputs." -"file_format || 'auto')`, to have a default value if none was provided in the " -"command line or job input file." +"To correct it, you should explicitly handle the possibility of a `null` " +"value. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value `\"auto\"` if " +"none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/inputs.md:295 b5055c77f85e43609fe3e9b9839778e3 +msgid "" +"Here, the boolean “or” operator `||` in JavaScript is used for its " +"_short-circuiting_ property. If `inputs.file_format` is “true” in a " +"boolean context (e.g. a valid non-empty string from the enum), the " +"evaluation of the expression stops at the first operand of `||`; it " +"“short-circuits”. If however `inputs.file_format` is `null`, the whole " +"expression’s value becomes that of the second operand, which is why a " +"reasonable default can be provided there." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: 723c2232310c4276aeac2bd6728d2912 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 +#: 4d81aac1830045229e5c60c7959074d8 msgid "" -"Implementation extensions not required for correct execution (for example, " -"fields related to GUI presentation) and metadata about the tool or workflow " -"itself (for example, authorship for use in citations) may be provided as " -"additional fields on any object. Such extensions fields (e.g. `format: edam:" -"format_2572`) can use a namespace prefix listed in the `$namespaces` section " -"of the document (e.g. edam: http://edamontology.org/) as described in the " -"[Schema Salad specification][schema-salad]. Once you add the namespace " -"prefix, you can access it anywhere in the document as shown below. " -"Otherwise, one must use full URLs: `format: http://edamontology.org/" -"format_2572`." +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b +#: 368f8993ae9d401488081d74ae5acd49 msgid "" "For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to cite " -"your tool." +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: c80f2b180ca74afb8a1fc18f8686304b msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: 37b07ea9b7124842b8ba3040f70308e9 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 +#: 1cd5989ade6741aabe625c13bed3c8ed msgid "" -"For those that are highly motivated, it is also possible to annotate your " -"tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints at " -"hardware requirements in order to use the tool, and a few more metadata " -"fields." +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: ae7369ba14404d23b72d1ef30dcd4153 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f +#: ../../src/topics/operations.md:1 a79974b2f4534fcd8c7a04401e8a5556 msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 +#: ../../src/topics/operations.md:3 b6507c8e1625476b97708423acb4fd0e msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-line " -"tool, or an expression tool. It is a step of a workflow that specifies " -"inputs and outputs, but it does not provide enough information to be " -"executed." +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." msgstr "" -#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d +#: ../../src/topics/operations.md:7 047b09455db64524a71c47ab5192039f msgid "" -"You can create operations to visualize a workflow during development, before " -"you are ready to submit the workflow to a CWL runner:" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf +#: ../../src/topics/operations.md:10 e9b2b97f3059460b867577a49934a338 msgid "`operations.cwl`" msgstr "`operations.cwl`" -#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 +#: ../../src/topics/operations.md:16 d21e9444182d4e27bae934db4573ae99 msgid "" -"The `uppercase` step of the workflow is an operation. It can be used like a " -"command line tool or an expression. You can also plot it with the CWL Viewer " -"or `cwltool`:" +"The `uppercase` step of the workflow is an operation. It can appear where" +" a command line tool or an expression is expected. You can also plot it " +"with the CWL Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 +#: ../../src/topics/operations.md:24 61e4ae6ed18e41708270eb358cd55277 msgid "" -"The output of the command above can be rendered with a Graphviz renderer. " -"The following image is rendered with the Sphinx Graphviz directive (this " -"user guide is built with Sphinx):" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx `{graphviz}` directive " +"(this user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 +#: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd msgid "" -"If you try running it with `cwltool`, the command will fail since `cwltool` " -"does not have enough information to know how to execute it:" +"The operation file will fail to run with `cwltool` because `cwltool` " +"lacks the necessary information to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb +#: ../../src/topics/operations.md:59 e184470550e645f6b9ce658af7e65ecf msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f +#: ../../src/topics/operations.md:67 3b90445d3428444cafd7d5c0e5884980 msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A " -"CWL runner could, for instance, use abstract operations with ID's that " +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de +#: ../../src/topics/outputs.md:1 35e7bad6fdc04bcf9bbfbb2d8d42cfa5 msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d +#: ../../src/topics/outputs.md:3 6d912d40359c4d33a4f08abca83c00be msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 +#: ../../src/topics/outputs.md:5 a6bd3f9e23de488394958fe7b59a61e0 msgid "" "The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name of " -"parameter, and `type` describing what types of values are valid for that " -"parameter." +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 +#: ../../src/topics/outputs.md:10 a229d8d983344e51a231edb5f667d84b msgid "" -"When a tool runs under CWL, the starting working directory is the designated " -"output directory. The underlying tool or script must record its results in " -"the form of files created in the output directory. The output parameters " -"returned by the CWL tool are either the output files themselves, or come " -"from examining the content of those files." +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or the result of examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 +#: ../../src/topics/outputs.md:16 9845e517f7d848e5b59a97880ca6999f msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 +#: ../../src/topics/outputs.md:19 0bf1ad2c43174e57a3ba8dd86f7c96b2 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c +#: ../../src/topics/outputs.md:21 553d535b023e4d69a888fe5b24bb8c5b msgid "" "In previous examples, the `baseCommand` was just a string, with any " -"arguments passed as CWL inputs. Instead of a single string we can use an " -"_array of strings_. The first element is the command to run, and any " -"subsequent elements are mandatory command line arguments" +"arguments passed as CWL inputs. Instead of a single string, we can use an" +" _array of strings_ as the value of `baseCommand`. The first element of " +"the array is the command to run, and any subsequent elements are " +"mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f +#: ../../src/topics/outputs.md:28 9b65071222c94951bed12ac53e964ee3 msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a +#: ../../src/topics/outputs.md:34 759ab0847b97479fb4a15e4b7d4e6565 msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 +#: ../../src/topics/outputs.md:40 f9752ec303ab419c8db8adef3fa2466f msgid "Next, create a tar file for the example." msgstr "Agora, crie um arquivo tar para o exemplo." -#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb +#: ../../src/topics/outputs.md:47 4f96576528684f28a72b805f777769e6 msgid "" -"And now invoke `cwltool` with the tool description and the input object on " -"the command line:" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d +#: ../../src/topics/outputs.md:53 707803bec0cb42919905c7c321bd9d30 msgid "" -"The field `outputBinding` describes how to set the value of each output " -"parameter." +"The field " +"[`outputBinding`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding)" +" describes how to set the value of each output parameter." msgstr "" -#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 +#: ../../src/topics/outputs.md:64 cbaec50871e04718883c8c91ff475d20 msgid "" -"The `glob` field consists of the name of a file in the output directory. If " -"you don't know name of the file in advance, you can use a wildcard pattern " -"like `glob: '*.txt'`." +"The " +"[`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) " +"field consists of the pattern to match file names in the output " +"directory. This can simply be the file's exact name. But if you don't " +"know the name of the file in advance, you can use a wildcard pattern like" +" `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 +#: ../../src/topics/outputs.md:69 8a6e9173198241429effd911c3a7c4d7 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 +#: ../../src/topics/outputs.md:71 a7c4fdaeda3e411fbeb802c5fa529ce9 msgid "" -"To capture a tool's standard output stream, add the `stdout` field with the " -"name of the file where the output stream should go. Then add `type: stdout` " -"on the corresponding output parameter." +"To capture a tool's standard output stream, add the " +"[`stdout`](https://w3id.org/cwl/CommandLineTool.html#stdout) field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 +#: ../../src/topics/outputs.md:75 cf2ef8dc7fda49308c09efe4f4ef5d7b msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 +#: ../../src/topics/outputs.md:93 cbe236266dd148aaa96355e490a87cbe msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d +#: ../../src/topics/outputs.md:95 77f86a7b94924a08b6ea2660218fe3c5 msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 +#: ../../src/topics/outputs.md:97 b34e30481fbd489d95fb7f8d5b5ab50c msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae +#: ../../src/topics/outputs.md:103 3aab0e0c9a78430f9caaa29a93303b56 msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 +#: ../../src/topics/outputs.md:116 9a14271c3180429988aaa14869f783a0 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions to " -"mark entries in arrays, as demonstrated in several of the upcoming sections." +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 +#: ../../src/topics/parameter-references.md:1 c8a6ea340e6a43398e97b68e03a8bb3b msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 +#: ../../src/topics/parameter-references.md:3 f5c0592ca28c46c2a89943f4f6f69a27 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file we " -"were interested in was called \"hello.txt\", and this was written into the `." -"cwl` file. This is not the best way to do this, as the \"hello.txt\" " -"filename may vary or be dependent on the input file(s) used. To avoid this " -"we can specify the name of the file we want in the job parameters file (`." -"yml`). In this example, you will see how to reference the value of input " -"parameters dynamically from other fields, which will allow us to then " -"specify the name of the file to extract." +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 +#: ../../src/topics/parameter-references.md:13 50db8add9b1942d986e581b8d21c2ee4 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 +#: ../../src/topics/parameter-references.md:19 d01ad5fd9fea462cab0d4d776824b4e1 msgid "`tar-param-job.yml`" msgstr "`tar-param-job.yml`" -#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 +#: ../../src/topics/parameter-references.md:25 9b1e2f1a23ea4fe2af97ef5108f33376 msgid "" -"Create your input files and invoke `cwltool` with the tool description and " -"the input object on the command line:" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 +#: ../../src/topics/parameter-references.md:36 06926a516ae6432d96e3eaa62202cd86 msgid "" -"Certain fields permit parameter references which are enclosed in `$(...)`. " -"These are evaluated and replaced with value being referenced." +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 +#: ../../src/topics/parameter-references.md:47 384fe8188f414eafbbb8d6b81bdfd779 msgid "" "References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `" -"$(inputs['extractfile'])` are equivalent." +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 +#: ../../src/topics/parameter-references.md:51 56ead1c8d45c43bdbcbc6f7cbb8e1e92 msgid "" -"The value of the \"inputs\" variable is the input object provided when the " -"CWL tool was invoked." +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 +#: ../../src/topics/parameter-references.md:54 56bca89e314c4223b33d7fe63c9b771d msgid "" -"Note that because `File` parameters are objects, to get the path to an input " -"file you must reference the path field on a file object; to reference the " -"path to the tar file in the above example you would write `$(inputs.tarfile." -"path)`." +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 +#: ../../src/topics/parameter-references.md:59 1c1ab240c4114572bb4e42955baad361 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad +#: ../../src/topics/parameter-references.md:61 055d3268859c46c4b7db5005608bae05 msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 +#: ../../src/topics/parameter-references.md:63 2ed66835bd9044adbfdd0b5097787f22 msgid "" -"From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 +#: ../../src/topics/parameter-references.md:69 f592619e4b2c497e80cd75da0548cf07 msgid "" -"From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter)" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 +#: ../../src/topics/parameter-references.md:72 81ea71a35020421187dc18ddd151c62f msgid "" -"From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding)" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f +#: ../../src/topics/parameter-references.md:74 ea0117748adc4324901024f21eed04ac msgid "" -"From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 +#: ../../src/topics/parameter-references.md:77 3a30e73176cf4e4eb9f26770a176b9c9 msgid "" -"From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding)" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 +#: ../../src/topics/parameter-references.md:81 551c199c9a6344fca9bfacfb69fc4e53 msgid "" -"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/" -"v1.0/Workflow.html#WorkflowOutputParameter)" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 +#: ../../src/topics/parameter-references.md:85 7008a1ff1af54fda827637e787e5c7dd msgid "" -"From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 +#: ../../src/topics/parameter-references.md:89 45743e1b261c4195856de0c2e30ea72e msgid "" -"From [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." -"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -"De [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) e [ExpressionToolOutputParameter](http://www.commonwl." -"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"De " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" e " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c +#: ../../src/topics/parameter-references.md:92 0ae32d1db5f9452bbfcbbc4719b0b9f1 msgid "" -"From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement)" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 +#: 7e1907ff15c74f488187531de336eccf msgid "" -"From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" -"CommandLineTool.html#InitialWorkDirRequirement)" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: 678874668fed4f4d80a1b0990e183e2f msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 +#: e2882880886046ac88ae1c0d414366d1 msgid "" -"From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef)" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: 05324169d8ae48d4a1abe3a0ac07c891 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: 1f5b72d7ec82442ba29baa14a03f061b msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb +#: e708866921ea49d69d3c2a32d63ea468 msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " -"include a `SoftwareRequirement` field in the `hints` section. This may also " -"help to avoid confusion about which version of a tool the description was " -"written for." +"include a " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)" +" field in the `hints` section. This may also help to avoid confusion " +"about which version of a tool the description was written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 +#: 6f722d6fd54f485fa964076c8d08938b msgid "" -"In this example, the software requirement being described is InterProScan " -"version 5.21-60." +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 +#: 5c1236ec57c64079bfb7c779524b12ad msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the [dependency " -"resolvers configuration][dependencies]." +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 -msgid "" -"As well as a version number, a unique resource identifier (URI) for the tool " -"is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked " -"up in the [SciCrunch][scicrunch] registry, which provides a portal for " -"finding, tracking, and referring to scientific resources consistently. If " -"you want to specify a tool as a `SoftwareRequirement`, search for the tool " -"on SciCrunch and use the RRID that it has been assigned in the registry. " -"(Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool " -"to SciCrunch). You can use this RRID to refer to the tool (via [identifiers." -"org][identifiers]) in the `specs` field of your requirement description. " -"Other good choices, in order of preference, are to include the DOI for the " -"main tool citation and the URL to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 +#: 1a8b8aadf1c64e87b8b670e288bc14bc +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)," +" search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 d10c792550e8498c8ee384d3093da306 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 +#: ../../src/topics/staging-input-files.md:3 ac2ef1fced5f4044861761a11c35e78a msgid "" -"Normally, input files are located in a read-only directory separate from the " -"output directory. This causes problems if the underlying tool expects to " -"write its output files alongside the input file in the same directory. You " -"use `InitialWorkDirRequirement` to stage input files into the output " -"directory. In this example, we use a JavaScript expression to extract the " -"base name of the input file from its leading directory path." +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use " +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)" +" to stage input files into the output directory. In this example, we use " +"a JavaScript expression to extract the base name of the input file from " +"its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: ../../src/topics/staging-input-files.md:9 d8ca16f5321e486ebe8ea9f9752b3737 msgid "`linkfile.cwl`" msgstr "`linkfile.cwl`" -#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 +#: ../../src/topics/troubleshooting.md:1 aa3eddcaa0684f86ba67aafcd57872e7 msgid "Troubleshooting" msgstr "Solucionando Problemas" -#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 +#: ../../src/topics/troubleshooting.md:3 3207f476afa04158bd26db39a16a2df5 msgid "" -"In this section you will find ways to troubleshoot when you have problems " -"executing CWL. We focus on `cwltool` here but some of these techniques may " -"apply to other CWL Runners." +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da +#: ../../src/topics/troubleshooting.md:6 1d47f4ce04554cabb1ccf40a13ee42ec msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 +#: ../../src/topics/troubleshooting.md:8 0c25602a83e441b48b536eb49568f2b6 msgid "" "You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor output " -"files, but created while your workflow is running). By default, these files " -"are created in a temporary directory but writing them to a separate " -"directory makes accessing them easier." +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b +#: ../../src/topics/troubleshooting.md:14 36ec60b80c714357a4274217274136ff msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | " -"rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW " -"olleH\". However, the second step, `step_b`, **has a typo**, where instead " -"of executing the `rev` command it tries to execute `revv`, which fails." +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b +#: ../../src/topics/troubleshooting.md:20 6f34038054ac4f4fa0b0ad9cbc3ecdc7 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f +#: ../../src/topics/troubleshooting.md:27 b777877c88024c9fb06a6614029ef8d6 msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value " -"(`cwltool` will create the directory for you if it does not exist already):" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac +#: ../../src/topics/troubleshooting.md:35 8654b7f2f4464d13be4b47729e1f07e5 msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. You " -"can inspect the intermediate files created:" +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 +#: ../../src/topics/troubleshooting.md:44 04e80f7ce14d4d73bc5d290dcf01bcdb msgid "" -"Each workflow step has received a unique ID (the long value that looks like " -"a hash). The `${HASH}.status` files display the status of each step executed " -"by the workflow. And the `step_a` output file `stdout.txt` is visible in the " -"output of the command above." +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 +#: ../../src/topics/troubleshooting.md:48 719917cb0fd849f5a328671df8726189 msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in " -"the `step_b`). After fixing the typo, when you execute `cwltool` with the " -"same arguments as the previous time, note that now `cwltool` output contains " -"information about pre-cached outputs for `step_a`, and about a new cache " -"entry for the output of `step_b`. Also note that the status of `step_b` is " -"now of success." +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 +#: ../../src/topics/troubleshooting.md:59 2a9dbb3ad7564f5aa103349c45ee7925 msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had " -"been cached, and there was no change in its execution or output. " +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " "Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for " -"troubleshooting your CWL documents and also as a way to prevent `cwltool` to " -"re-evaluate steps unnecessarily." +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 +#: ../../src/topics/using-containers.md:1 7439fe097aa4459ba1e4c0e28fc59b9a msgid "Using Containers" msgstr "Utilizando Containers" -#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 +#: ../../src/topics/using-containers.md:3 eff5c6ac1cad44f9862585daf0a91298 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 +#: ../../src/topics/using-containers.md:5 50d1a644bc8c49f78c453e4e0f3c07c8 msgid "" -"[Docker][docker] containers simplify software installation by providing a " -"complete known-good runtime for software and its dependencies. However, " -"containers are also purposefully isolated from the host system, so in order " -"to run a tool inside a Docker container there is additional work to ensure " -"that input files are available inside the container and output files can be " -"recovered from the container. A CWL runner can perform this work " -"automatically, allowing you to use Docker to simplify your software " -"management while avoiding the complexity of invoking and managing Docker " -"containers." +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." msgstr "" -#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 +#: ../../src/topics/using-containers.md:15 4b0f6cfc8a774c77bfbc99e568af2ece msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the container." +"input files to reflect the location where they appear inside the " +"container." msgstr "" -#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a +#: ../../src/topics/using-containers.md:18 27c02a5d479a420eab7d14888d9fb288 msgid "" -"This example runs a simple Node.js script inside a Docker container which " -"will then print \"Hello World\" to the standard output." +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 +#: ../../src/topics/using-containers.md:21 1a62a93ab20b4f2ca1e13ded3a767dc5 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 +#: ../../src/topics/using-containers.md:27 ccc2874840c3476bb714ddf4bdbf0f3e msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed +#: ../../src/topics/using-containers.md:33 d766b66de4714a5da0cd87ed886cc32f msgid "" "Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that is " -"really new is the `dockerRequirement` section." +"Most of this has been explained in previous sections, the only part that " +"is really new is the " +"[`dockerRequirement`](https://w3id.org/cwl/CommandLineTool.html#DockerRequirement)" +" section." msgstr "" -#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 +#: ../../src/topics/using-containers.md:44 1f02618ab6254459ae71f72844e3cc18 msgid "" -"`baseCommand: node` tells CWL that we will be running this command using the " -"Node Js runtime that is meant for Javascript files. We then need to specify " -"some `hints` for how to find the container we want. In this case we list " -"just our requirements for the docker container in `DockerRequirements`. The " -"`dockerPull:` parameter takes the same value that you would pass to a " -"`docker pull` command. That is, the name of the container image (you can " -"even specify the tag, which is good idea for best practices when using " -"containers for reproducible research). In this case we have used a container " -"called `node:slim`." +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 +#: ../../src/topics/using-containers.md:52 54cade4978ec463bbb5c0d8c08e27adb msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` providing " -"the tool description and the input object on the command line:" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 +#: ../../src/topics/using-containers.md:55 6541d0cd9f6c4c43b8601715cc35e585 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 +#: ../../src/topics/using-containers.md:69 6abf220b7fa4479394ed33447cdd070e msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 +#: ../../src/topics/using-containers.md:72 d2dd89a5edde4f2eab4c2baf0cc78745 msgid "" -"In this example, the path to the script `hello.js` is `/home/me/cwl/" -"user_guide/hello.js` outside the container but `/var/lib/cwl/" -"job369354770_examples/hello.js` inside the container, as reflected in the " -"invocation of the `node` command." +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 +#: ../../src/topics/workflows.md:1 06281a10592d42509566c8fc51f8d4da msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 +#: ../../src/topics/workflows.md:3 325a656f9b8e4c1fa6f699cd8c447d00 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 +#: ../../src/topics/workflows.md:13 b92275181c9e480da64e660b7aca0745 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 +#: ../../src/topics/workflows.md:41 be2540315f854b8e9a1d257bcabd78db msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier examples." +"command-line tool, and the expression tool showed in the earlier " +"examples." msgstr "" -#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 +#: ../../src/topics/workflows.md:51 3be900594bb743399854b95baa9ae2f9 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb +#: ../../src/topics/workflows.md:81 5133c4e062bc4e479ce1dc8abbb08107 msgid "" -"A command-line tool or expression tool can also be written directly in the " -"same CWL document as the workflow. For example, we can rewrite the `echo-" -"uppercase.cwl` workflow as a single file:" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa +#: ../../src/topics/workflows.md:91 83bc2796889f4dccb713764ac1b3c3ad msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a +#: ../../src/topics/workflows.md:150 5a9a1dd6ed1f4ca6803f1d235c4fd392 msgid "" -"Having separate files helps with modularity and code organization. But it " -"can be helpful writing everything in a single file for development. There " -"are other ways to combine multiple files into a single file (e.g. `cwltool --" -"pack`) discussed further in other sections of this user guide." +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe +#: ../../src/topics/workflows.md:160 277ed30d4b3a4156a4523e8d10e6ce60 msgid "" "For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this " -"user guide in more detail." +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 +#: ../../src/topics/workflows.md:165 82818ab17aa4403eb982fd81a14a5865 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c +#: ../../src/topics/workflows.md:167 3d8b98e8d03548699fadb22198de9b20 msgid "" -"This workflow extracts a java source file from a tar file and then compiles " -"it." +"This workflow extracts a java source file from a tar file and then " +"compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 +#: ../../src/topics/workflows.md:170 c61097c695424f7195e8205a23b6ecff msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 +#: 6660c48f51d94d4fbcc05656e154059e bd2bab6c11614fa983ca8dab1408e1d8 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 +#: ../../src/topics/workflows.md:180 f0831481a43548039fbc4fd17555af57 msgid "" -"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" -"github.com/common-workflow-language/user_guide/blob/" -"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" "workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/" -"_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 +#: ../../src/topics/workflows.md:183 5ff059fc8ae6471c8ea86dab7e5a93f5 msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a " -"run:" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" msgstr "" -#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda +#: ../../src/topics/workflows.md:185 822e5d0a097b4109960d621a72a3c009 msgid "`1st-workflow-job.yml`" msgstr "`1st-workflow-job.yml`" -#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 +#: ../../src/topics/workflows.md:191 4a4db7da861547639524083bf35ccfc0 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 +#: ../../src/topics/workflows.md:205 ed16b30eaa4747f79b6dd10a19188d8c msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde +#: ../../src/topics/workflows.md:212 6428bd7bd3be4393bfe5675f8e45ff94 msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a workflow." +"document. The `class` field indicates this document describes a " +"workflow." msgstr "" -#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 +#: ../../src/topics/workflows.md:221 d6abec8805f649fca668292412263f78 msgid "" -"The `inputs` section describes the inputs of the workflow. This is a list " -"of input parameters where each parameter consists of an identifier and a " -"data type. These parameters can be used as sources for input to specific " -"workflows steps." +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 +#: ../../src/topics/workflows.md:233 22bf3e4910ef4f86a2e8f6d5a6cf0d42 msgid "" -"The `outputs` section describes the outputs of the workflow. This is a list " -"of output parameters where each parameter consists of an identifier and a " -"data type. The `outputSource` connects the output parameter `classfile` of " -"the `compile` step to the workflow output parameter `compiled_class`." +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 +#: ../../src/topics/workflows.md:248 e0429688fce445da8083e69323e5b020 msgid "" "The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second step " -"compiles the file from the first step using the java compiler. Workflow " -"steps are not necessarily run in the order they are listed, instead the " -"order is determined by the dependencies between steps (using `source`). In " -"addition, workflow steps which do not depend on one another may run in " -"parallel." +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 +#: ../../src/topics/workflows.md:256 980f5eada57c4fadbb783838ded1fa0b msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input " -"parameters, `tarfile` and `extractfile` and one output parameter " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 +#: ../../src/topics/workflows.md:261 3532e165842f4ebb8db0c78208071555 msgid "" -"The ``in`` section of the workflow step connects these two input parameters " -"to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using " -"`source`. This means that when the workflow step is executed, the values " -"assigned to `tarball` and `name_of_file_to_extract` will be used for the " -"parameters `tarfile` and `extractfile` in order to run the tool." +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea +#: ../../src/topics/workflows.md:267 04a4db2f3da94ce29e7999039ee13fde msgid "" -"The `out` section of the workflow step lists the output parameters that are " -"expected from the tool." +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed +#: ../../src/topics/workflows.md:278 2651ee113a3d4b79b138854ebe729f48 msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described previously " -"in [Additional Arguments and Parameters](additional-arguments-and-parameters." -"md)). The output of this step `classfile` is connected to the `outputs` " -"section for the Workflow, described above." +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 +#: ../../src/topics/workflows.md:285 177040bf9c0045f2878f42bcdd8cbd2d msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e +#: ../../src/topics/workflows.md:287 e8adc2f7c5ac4464b0711712617b8bbe msgid "" -"Workflows are ways to combine multiple tools to perform a larger operations. " -"We can also think of a workflow as being a tool itself; a CWL workflow can " -"be used as a step in another CWL workflow, if the workflow engine supports " -"the `SubworkflowFeatureRequirement`:" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 +#: ../../src/topics/workflows.md:297 44d281d99cd944478db98446a984c001 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 +#: ../../src/topics/workflows.md:300 d7b60ce81ea741ffa08f2c2d9d7cca69 msgid "`nestedworkflows.cwl`" msgstr "`nestedworkflows.cwl`" -#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 +#: ../../src/topics/workflows.md:309 a5b7a1ab16e34bda8744ffadacdda3e8 msgid "" -"This two-step workflow starts with the `create-tar` step which is connected " -"to the `compile` step in orange; `compile` is another workflow, diagrammed " -"on the right. In purple we see the fixed string `\"Hello.java\"` being " -"supplied as the `name_of_file_to_extract`." +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a +#: ../../src/topics/workflows.md:314 8654f2d86b644609aaa5b9b73db30bda msgid "" " \"Visualization" +"language/user_guide/blob/main/_includes/cwl/workflows/nestedworkflows.cwl\"> \"Visualization" msgstr "" -#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 +#: ../../src/topics/workflows.md:322 7ce847ab54224452b6425de2a55ec893 msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its " -"CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped " -"to become the step's input/outputs." +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 +#: ../../src/topics/workflows.md:336 d621821d2c1b403cb7415b381dd883f6 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and `*.java` " -"filename. This is generally best-practice, as it means it can be reused in " -"multiple parent workflows, or even in multiple steps within the same " -"workflow." +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be +#: ../../src/topics/workflows.md:341 358c612f175241f7bf148a04d75e00c9 msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar " -"file at `tarball`, which we will prepare in the `create-tar` step. At this " -"point it is probably a good idea to refactor `1st-workflow.cwl` to have more " -"specific input/output names, as those also appear in its usage as a tool." +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 +#: ../../src/topics/workflows.md:347 c6297c120e004ae8b52d5b519fbc04d2 msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3421,443 +3551,879 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 +#: ../../src/topics/workflows.md:366 66f76677f4ce42baa8a8813410ea5aee msgid "" -"In this case our step can assume `Hello.java` rather than be parameterized, " -"so we can use hardcoded values `hello.tar` and `Hello.java` in a " -"`baseCommand` and the resulting `outputs`:" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 +#: ../../src/topics/workflows.md:383 a8ccb9f9ab4448e087ea8448d620d33c msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This is " -"generally not best practice, as the tool then can't be reused. The reason " -"for doing it in this case is because the command line is hard-coded with " -"filenames that only make sense within this workflow." +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 +#: ../../src/topics/workflows.md:389 afe43b9e92e949a589f493293eff2903 msgid "" -"In this example we had to prepare a tar file outside, but only because our " -"inner workflow was designed to take that as an input. A better refactoring " -"of the inner workflow would be to take a list of Java files to compile, " -"which would simplify its usage as a tool step in other workflows." +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." msgstr "" -#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 +#: ../../src/topics/workflows.md:394 239eef3a740d42a69208a8f4e716d2b3 msgid "" "Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL " -"Tool description, care must be taken to improve its usability in multiple " -"workflows." +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 +#: ../../src/topics/workflows.md:398 96d1ca78cc324f40b61c4b7330447db2 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 +#: ../../src/topics/workflows.md:400 eab4437bf9994b649954221375e3dd6d msgid "" "Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish to " -"run a tool or workflow multiple times over a list of inputs. The workflow " -"then takes the input(s) as an array and will run the specified step(s) on " -"each element of the array as if it were a single input. This allows you to " -"run the same workflow on multiple inputs without having to generate many " -"different commands or input yaml files." +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 +#: ../../src/topics/workflows.md:411 c245ba0ae2074fa388ad6c35695033c8 msgid "" -"The most common reason a new user might want to use scatter is to perform " -"the same analysis on different samples. Let's start with a simple workflow " -"that calls our first example (`hello_world.cwl`) and takes an array of " -"strings as input to the workflow:" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: ../../src/topics/workflows.md:415 83537938ce1244709f9b72269b048d63 msgid "`scatter-workflow.cwl`" msgstr "`scatter-workflow.cwl`" -#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 +#: ../../src/topics/workflows.md:421 4f507925766e48ae8f713d56051a5e29 msgid "" -"Aside from the `requirements` section including `ScatterFeatureRequirement`, " -"what is going on here?" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c +#: ../../src/topics/workflows.md:429 ccbbba3189404241a44736c970249b84 msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f +#: ../../src/topics/workflows.md:441 31eff13bb8334fc7b6d48ef6c5b1ce33 msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This field " -"tells the runner that we'd like to scatter over this input for this " -"particular step. Note that the input name listed after scatter is the one of " -"the step's input, not a workflow level input." +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d +#: ../../src/topics/workflows.md:445 0d5cf8b82dbd47f2abd1ed16b9b3eb61 msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if you " -"expect that the final output of your workflow will now have multiple outputs " -"to collect, be sure to update that to an array type as well!" +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: ../../src/topics/workflows.md:450 38b7042a270043ba82c11cf2e758f0c8 msgid "Using the following input file:" msgstr "Usando o seguinte arquivo de entrada:" -#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be +#: ../../src/topics/workflows.md:452 b3fc75c262fe4a3a8e8bfba1abb07b3d msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 +#: ../../src/topics/workflows.md:458 f9fa7046c89c417db51dc7c8a026fd5d msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply " -"calls the command `echo` on a message. If we invoke `cwltool scatter-" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f +#: ../../src/topics/workflows.md:466 b6a33410ee9a45d7bf7b2ba56f786f8f msgid "" -"You can see that the workflow calls echo multiple times on each element of " -"our `message_array`. Ok, so how about if we want to scatter over two steps " -"in a workflow?" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 +#: ../../src/topics/workflows.md:469 99b5c8a845ab4beb8524a69c051e2d42 msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding the " -"following lines instead of `outputs: []`" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de +#: ../../src/topics/workflows.md:472 97bf58937d3f4e98af702e3c1a418992 msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 +#: ../../src/topics/workflows.md:480 173bd28708834f11a2a1366b579b7ad7 msgid "" -"And add a second step that uses `wc` to count the characters in each file. " -"See the tool below:" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a +#: ../../src/topics/workflows.md:483 4afccfe982ff4be2be96cbe5889e5014 msgid "`wc-tool.cwl`" msgstr "`wc-tool.cwl`" -#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b +#: ../../src/topics/workflows.md:489 63595d35dded4911aab0be3a165eec0c msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under each " -"step:" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" msgstr "" -#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d +#: ../../src/topics/workflows.md:491 a7f96ec6e4f24c62ac0f5b6edcc9734b msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 +#: ../../src/topics/workflows.md:497 122452b7d7114c3fa53cbea286703023 msgid "" -"Here we have placed the scatter field under each step. This is fine for this " -"example since it runs quickly, but if you're running many samples for a more " -"complex workflow, you may wish to consider an alternative. Here we are " -"running scatter on each step independently, but since the second step is not " -"dependent on the first step completing all languages, we aren't using the " -"scatter functionality efficiently. The second step expects an array as input " -"from the first step, so it will wait until everything in step one is " -"finished before doing anything. Pretend that `echo Hello World!` takes 1 " -"minute to perform, `wc -c` on the output takes 3 minutes and that `echo " -"Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 " -"minutes. Even though `echo Hello World!` could finish in 4 minutes, it will " -"actually finish in 8 minutes because the first step must wait on `echo Hallo " -"welt!`. You can see how this might not scale well." +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df +#: ../../src/topics/workflows.md:509 85dd63daf04546b78bdcb68c1d985fa9 msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can " -"make an entire workflow a single step in another workflow! Convert our two-" -"step workflow to a single step subworkflow:" +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b +#: ../../src/topics/workflows.md:513 fac138ba275745898b763a7d719a8235 msgid "`scatter-nested-workflow.cwl`" msgstr "`scatter-nested-workflow.cwl`" -#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb +#: ../../src/topics/workflows.md:519 508ef2240879445594b0f262ed11a01d msgid "" -"Now the scatter acts on a single step, but that step consists of two steps " -"so each step is performed in parallel." +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 +#: ../../src/topics/workflows.md:522 b0bf01dad1234a1db3c87b10953e42ef msgid "Conditional Workflows" msgstr "Workflows Condicionais" -#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 +#: ../../src/topics/workflows.md:524 8d933ed1ec6e408589f781e3a425b869 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 +#: ../../src/topics/workflows.md:527 9ac7b4f71621411da9a4ca3bc277dcb0 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 +#: ../../src/topics/workflows.md:566 4a4a2b2b99b44d449adb246cebce0a26 msgid "" -"The first thing you'll notice is that this workflow is only compatible for " -"version 1.2 or greater of the CWL standards." +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 +#: ../../src/topics/workflows.md:573 4742fe09a4264fb8be6f092519de5d72 msgid "" "The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when` is " -"where the condition validation takes place. In this case only when `in1` " -"from the workflow contains a value `< 1` this step will be executed." +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." msgstr "" -#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 +#: ../../src/topics/workflows.md:587 b33ecd2b8af042feb08687e32d4b6bbf msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value " -"will pass the first conditional step and will therefore be executed and is " -"shown in the log by `INFO [step step1] start` whereas the second step is " -"skipped as indicated by `INFO [step step2] will be skipped`." +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec +#: ../../src/topics/workflows.md:607 7cd80b31a94543358ece7a2d413adce9 msgid "" -"When a value of 3 is given the first conditional step will not be executed " -"but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 +#: ../../src/topics/workflows.md:627 9679e32f65e0482a8b083387e4a18c1f msgid "" -"If no conditions are met for example when using `--val 2` the workflow will " -"raise a permanentFail." +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e +#: ../../src/topics/yaml-guide.md:1 4fa76441f95d45fab76ab7eef8d7d4d2 msgid "YAML Guide" msgstr "Guia de YAML" -#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c +#: ../../src/topics/yaml-guide.md:6 705765787eb84ecaae004194225924cb msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers and " -"humans. This guide introduces the features of YAML that are relevant when " -"writing CWL descriptions and input parameter files." +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 +#: ../../src/topics/yaml-guide.md:13 cb243f6ab11f48ffb5c91945c4e0d101 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea +#: ../../src/topics/yaml-guide.md:16 cfc95d15e33a492f842649f92ced941d msgid "Contents" msgstr "Conteúdo" -#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee +#: ../../src/topics/yaml-guide.md:18 f618d44d202f4c2ea6ff72a1dca2c659 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a +#: ../../src/topics/yaml-guide.md:19 36bfa6ed40c54bd99826bedff12c759d msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c +#: ../../src/topics/yaml-guide.md:20 61913753eb0c4c728889b47f1110be24 msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: ../../src/topics/yaml-guide.md:21 0de824a05eea46209aafa6f9e2e8623c msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: ../../src/topics/yaml-guide.md:22 95627bc476b3415ca4d77246125137d2 msgid "[JSON Style](#json-style)" msgstr "[Estilo JSON](#json-style)" -#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 +#: ../../src/topics/yaml-guide.md:24 3f64a6d33d9a4c22a8a839a8def82686 msgid "Key-Value Pairs" msgstr "Pares de Chave-Valor" -#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 +#: ../../src/topics/yaml-guide.md:26 2f74f6eaa8d84dc9b4d0a166844dedbe msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the `:` " -"is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have special " -"meaning in the CWL specification and underscored key names otherwise. For " -"example:" -msgstr "" -"Em princípio, um arquivo escrito em YAML consiste de uma série de _pares de " -"chave-valor`. Cada par é escrito como `chave: valor`, onde o espaço em " -"branco entre o `:` é um requisito. Os nomes das chaves em arquivos CWL não " -"devem conter espaços em branco - [_camelCase_][camelCase] é usado para " -"valores de chaves que contém múltiplas palavras e possuem um valor especial " -"na especificação CWL, caso contrário os valores dos nomes de chaves aparecem " -"sublinhados. For exemplo:" - -#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b -msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, `age_years`, " -"and `home` - with their four respective values. Values can be character " -"strings, numeric (integer, floating point, or scientific representation), " -"Boolean (`true` or `false`), or more complex nested types (see below)." -msgstr "" -"O YAML acima define quatro chaves - `first_name`, `last_name`, `age_years`, " -"e `home` - com quatro valores respectivos. Os valores podem ser strings de " -"caracteres, númericos (integer, floating point, ou representação " -"científica), Boolean (`true` ou `false`), ou valores mais complexos com " -"tipos aninhados (veja abaixo)." - -#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 -msgid "" -"Values may be wrapped in quotation marks, but be aware that this may change " -"the way that they are interpreted i.e. `\"1234\"` will be treated as a " -"character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a " -"command: in CWL all parts of `baseCommand` must be strings so, if you want " -"to specify a fixed numeric value to a command, make sure that you wrap that " -"numeric value in quotes: `baseCommand: [echo, \"42\"]`." -msgstr "" - -#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" +msgstr "" +"Em princípio, um arquivo escrito em YAML consiste de uma série de _pares " +"de chave-valor`. Cada par é escrito como `chave: valor`, onde o espaço em" +" branco entre o `:` é um requisito. Os nomes das chaves em arquivos CWL " +"não devem conter espaços em branco - [_camelCase_][camelCase] é usado " +"para valores de chaves que contém múltiplas palavras e possuem um valor " +"especial na especificação CWL, caso contrário os valores dos nomes de " +"chaves aparecem sublinhados. For exemplo:" + +#: ../../src/topics/yaml-guide.md:42 514365e59d9648deb896e2068d967a64 +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." +msgstr "" +"O YAML acima define quatro chaves - `first_name`, `last_name`, " +"`age_years`, e `home` - com quatro valores respectivos. Os valores podem " +"ser strings de caracteres, númericos (integer, floating point, ou " +"representação científica), Boolean (`true` ou `false`), ou valores mais " +"complexos com tipos aninhados (veja abaixo)." + +#: ../../src/topics/yaml-guide.md:51 6939eb7e783744d7bcf75ea0a7cae129 +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 96e1776b09e840ebbc9b4b7e01da0e43 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 +#: ../../src/topics/yaml-guide.md:63 8b17f7557c3540b2b0d0beca0fe4ebc7 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program interpreting " -"the YAML. For example:" +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d +#: ../../src/topics/yaml-guide.md:76 13da997c82c04023a4b7bb36b76e969d msgid "" -"If there is anything on the line before the comment, be sure to add at least " -"one space before the `#`!" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf +#: ../../src/topics/yaml-guide.md:79 b9fc191166a64450b64a8182adabad75 msgid "Maps" msgstr "Dicionários" -#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 +#: ../../src/topics/yaml-guide.md:81 aedf8c4f615845ad91a7947217005d6e msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, these " -"hierarchical structures are described in YAML by providing additional key-" -"value pairs as the value of any key. These pairs (sometimes referred to as " -"\"children\") are written on new lines under the key to which they belong " -"(the \"parent\"), and should be indented with two spaces (⇥tab characters " -"are not allowed). For example:" +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 +#: ../../src/topics/yaml-guide.md:104 f0f1f414f74342a89065ba5ded8668e5 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and `inputBinding`, " -"while one of these children, `inputBinding`, contains a further two key-" -"value pairs (`position` and `prefix`). See the [Arrays](#arrays) section " -"below for more information about providing multiple values/key-value pairs " -"for a single key. For comparison with the example YAML above, here is a " -"graphical representation of the `inputs` object it describes." +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 +#: ../../src/topics/yaml-guide.md:127 965405e2a45a4cbb8f227bc8ceeb05df msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 +#: ../../src/topics/yaml-guide.md:129 5aca9a90fb6149529ed717992746a2f3 msgid "" "In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) section " -"above, more than one key-value pair can be mapped to a single key. However, " -"it is also possible to define multiple values for a key without having to " -"provide a unique key for each value. We can achieve this with an _array_, " -"where each value is defined on its own line and preceded by `-`. For example:" +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 +#: ../../src/topics/yaml-guide.md:146 d1c9e72e004b4fb4a6efb7748a15ab6f msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d +#: ../../src/topics/yaml-guide.md:167 9a3d6879404745a48cd394bf86865dbc msgid "JSON Style" msgstr "Estilo JSON" -#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d +#: ../../src/topics/yaml-guide.md:169 6a7cca0339794e679329b00d89e29d2b msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays " -"can also be defined in YAML using the native JSON syntax. For example:" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc +#: ../../src/topics/yaml-guide.md:177 d8feed2d36d04fe283b9de9784d91941 msgid "and:" msgstr "e:" -#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 +#: ../../src/topics/yaml-guide.md:184 5156ad32791048f8ace51475d7689575 msgid "" -"Native JSON can be useful in indicating where a field is intentionally left " -"empty (such as `[]` for an empty array), as well as where it makes more " -"sense for the values to be located on the same line (For example, when " -"providing option flags and their values in a shell command). However, as the " -"second example above shows, it can severely affect the readability of a YAML " -"file, and should be used sparingly." +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d +#: ../../src/topics/yaml-guide.md:194 ce49f80e6fc0498b8ad298fb1f0268f3 msgid "Reference" msgstr "Referencia" -#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 +#: ../../src/topics/yaml-guide.md:196 180d261392a644fcb8ff47d7a4a160c0 msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us " -"while we wrote this guide, though it also covers features that are not valid " -"in CWL." +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 +#: ../../src/tutorials.md:1 d682035afebf4c128755bd4e58780dd2 msgid "Tutorials" msgstr "Tutoriais" -#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 +#: ../../src/tutorials.md:5 d9adeab63ec54084bc41fb90f264d3ae msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to the " -"list." +"this page` link in the menu if you would like to add another tutorial to " +"the list." msgstr "" -#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c +#: ../../src/tutorials.md:7 23c81edb650b4f86a60c5e0bcedeac1d msgid "Beginner Tutorials" msgstr "Tutoriais para Iniciantes" -#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 +#: ../../src/tutorials.md:9 87ddaa1e5f57445c8f13803722aa146e msgid "" -"[Introduction to Workflows with Common Workflow Language: For Contributors.]" -"(https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f +#: ../../src/tutorials.md:11 b8ee193ba533498db6263e0f5f4ec45f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f +#: ../../src/tutorials.md:13 67c4b3923fce46fdab025495125c91d4 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f +#: ../../src/tutorials.md:15 e640316669104239970794191b6da38b msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 +#: ../../src/tutorials.md:17 efe94af44b874f9b81b245fbdee43f7f msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" + +#~ msgid "In CWL, everything must be directly stated." +#~ msgstr "Em CWL tudo deve ser declarado diretamente." + +#~ msgid "" +#~ "Using " +#~ "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +#~ " along with [`linkMerge: " +#~ "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#~ msgstr "" + +#~ msgid "Optional Inputs 💯" +#~ msgstr "Inputs Opcionais 💯" + +#~ msgid "Enum Inputs ⚜️" +#~ msgstr "Inputs Enum ⚜️" + +#~ msgid "Record Inputs 📀" +#~ msgstr "Inputs do tipo Record" + +#~ msgid "Debug JavaScript Expressions" +#~ msgstr "Depurar Expressões JavaScript" + +#~ msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +#~ msgstr "" + +#~ msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +#~ msgstr "" + +#~ msgid "" +#~ "`InitialWorkDirRequirement` - controls staging " +#~ "files in the input directory." +#~ msgstr "" + +#~ msgid "" +#~ "The FAIR principles have laid a " +#~ "foundation for sharing and publishing " +#~ "digital assets, and in particular, data." +#~ " The FAIR principles emphasize machine " +#~ "accessibility and that all digital " +#~ "assets should be Findable, Accessible, " +#~ "Interoperable, and Reusable. Workflows encode" +#~ " the methods by which the scientific" +#~ " process is conducted and via which" +#~ " data are created. It is thus " +#~ "important that workflows support the " +#~ "creation of FAIR data and adhere " +#~ "to the FAIR principles. — [FAIR " +#~ "Computational " +#~ "Workflows](https://workflows.community/groups/fair/), Workflows" +#~ " Community Initiative." +#~ msgstr "" + +#~ msgid "" +#~ "If you are using Windows, you will" +#~ " have to install the [Windows " +#~ "Subsystem for Linux 2](https://learn.microsoft.com" +#~ "/en-us/windows/wsl/install) (WSL2). Visit the " +#~ "`cwltool` [documentation](https://github.com/common-" +#~ "workflow-language/cwltool/blob/main/README.rst#ms-windows-" +#~ "users) for details on installing WSL2." +#~ " Your operating system also needs " +#~ "internet access and a recent version " +#~ "of Python (3.6+)." +#~ msgstr "" + +#~ msgid "" +#~ "`cwltool` can be installed with `pip`." +#~ " We recommend using a virtual " +#~ "environment like `venv` or `conda`. The" +#~ " following commands will create and " +#~ "activate a Python virtual environment " +#~ "using the `venv` module, and install " +#~ "`cwltool` in that environment:" +#~ msgstr "" + +#~ msgid "Installing `cwltool` with `pip` and `venv`." +#~ msgstr "Instalando `cwltool` com `pip` e `venv`." + +#~ msgid "Cwl-runner Python Module" +#~ msgstr "Módulo Python cwl-runner" + +#~ msgid "" +#~ "The CWL community publishes a Python " +#~ "package with the name `cwlref-runner`" +#~ " that installs an alias for `cwltool`" +#~ " under the name `cwl-runner`" +#~ msgstr "" + +#~ msgid "" +#~ "The *shebang* is the two-character " +#~ "sequence `#!` at the beginning of " +#~ "a script. When the script is " +#~ "executable, the operating system will " +#~ "execute the script using the executable" +#~ " specified after the shebang. It is" +#~ " considered a good practice to use" +#~ " `/usr/bin/env ` rather than " +#~ "using a hard-coded location, since " +#~ "`/usr/bin/env ` looks for the " +#~ "`` program in the system " +#~ "`PATH`," +#~ msgstr "" + +#~ msgid "" +#~ "The usage of the `cwltool` command-" +#~ "line executable is basically `cwltool " +#~ "[OPTIONS] [INPUTS_OBJECT]`. You " +#~ "can run the `hello_world.cwl` workflow " +#~ "without specifying any option:" +#~ msgstr "" + +#~ msgid "" +#~ "For more examples of providing metadata" +#~ " within CWL descriptions, see [the " +#~ "Metadata and Authorship section of this" +#~ " User Guide](../topics/metadata-and-" +#~ "authorship.md)." +#~ msgstr "" + +#~ msgid "" +#~ "In tool descriptions, list dependencies " +#~ "using short name(s) under " +#~ "`SoftwareRequirement`." +#~ msgstr "" + +#~ msgid "" +#~ "In tool descriptions, include a list " +#~ "of version(s) of the tool that are" +#~ " known to work with this description" +#~ " under `SoftwareRequirement`." +#~ msgstr "" + +#~ msgid "" +#~ "Each `CommandLineTool` description should " +#~ "focus on a single operation only, " +#~ "even if the (sub)command is capable " +#~ "of more. Don't overcomplicate your tool" +#~ " descriptions with options that you " +#~ "don't need or use." +#~ msgstr "" + +#~ msgid "" +#~ "This indicates whether a process " +#~ "requires outgoing IPv4/IPv6 network access." +#~ " If a command-line tool is " +#~ "written manually in CWL v1.1+, there " +#~ "is a need to specify when network" +#~ " access is required." +#~ msgstr "" + +#~ msgid "" +#~ "CWL v1.0 command-line tools that " +#~ "are upgraded to v1.1 or v1.2 get" +#~ " Network Access automatically." +#~ msgstr "" + +#~ msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +#~ msgstr "" + +#~ msgid "" +#~ "Note also that the author of this" +#~ " CWL description has also included " +#~ "`ResourceRequirement`s, specifying the minimum " +#~ "amount of RAM and number of cores" +#~ " required for the tool to run " +#~ "successfully, as well as details of " +#~ "the version of the software that " +#~ "the description was written for and " +#~ "other useful metadata. These features " +#~ "are discussed further in other chapters" +#~ " of this user guide." +#~ msgstr "" + +#~ msgid "" +#~ "Similar to the command-line tool " +#~ "it requires `inputs` and `outputs`. But" +#~ " instead of `baseCommand`, it requires " +#~ "an `expression` attribute." +#~ msgstr "" + +#~ msgid "" +#~ "We had to use an " +#~ "`InlineJavascriptRequirement` as our expression " +#~ "contains a JavaScript call in " +#~ "`.toUpperCase()`. This means to tools " +#~ "using the expression tool that " +#~ "JavaScript is a requirement." +#~ msgstr "" + +#~ msgid "" +#~ "If you need to manipulate input " +#~ "parameters, include the requirement " +#~ "`InlineJavascriptRequirement` and then anywhere " +#~ "a parameter reference is legal you " +#~ "can provide a fragment of Javascript " +#~ "that will be evaluated by the CWL" +#~ " runner." +#~ msgstr "" + +#~ msgid "From `Workflow`" +#~ msgstr "" + +#~ msgid "" +#~ "The requirement `InlineJavascriptRequirement` " +#~ "supports an `expressionLib` attribute that " +#~ "allows users to load external JavaScript" +#~ " files, or to provide inline " +#~ "JavaScript code." +#~ msgstr "" + +#~ msgid "" +#~ "Tools and workflows can take `File` " +#~ "types as input and produce them as" +#~ " output. We also recommend indicating " +#~ "the format for `File` types. This " +#~ "helps document for others how to " +#~ "use your tool while allowing you " +#~ "to do some simple type-checking " +#~ "when creating parameter files." +#~ msgstr "" + +#~ msgid "" +#~ "Available primitive types are *string*, " +#~ "*int*, *long*, *float*, *double*, and " +#~ "*null*; complex types are *array* and" +#~ " *record*; in addition there are " +#~ "special types *File*, *Directory* and " +#~ "*Any*." +#~ msgstr "" + +#~ msgid "" +#~ "You can use `cwltool` to create a" +#~ " template input object. That saves " +#~ "you from having to type all the" +#~ " input parameters in a input object" +#~ " file:" +#~ msgstr "" + +#~ msgid "" +#~ "The field `inputBinding` is optional and" +#~ " indicates whether and how the input" +#~ " parameter should appear on the " +#~ "tool's command line. If `inputBinding` " +#~ "is missing, the parameter does not " +#~ "appear on the command line. Let's " +#~ "look at each example in detail." +#~ msgstr "" + +#~ msgid "" +#~ "If you use exclusive input parameters" +#~ " combined with expressions, you need " +#~ "to be aware that the `inputs` " +#~ "JavaScript object will contain one of" +#~ " the exclusive input values. This " +#~ "means that you might need to use" +#~ " an **or** boolean operator to check" +#~ " which values are present." +#~ msgstr "" + +#~ msgid "" +#~ "Note how the JavaScript expression uses" +#~ " the value of the exclusive input " +#~ "parameter without taking into consideration" +#~ " a `null` value. If you provide " +#~ "a valid value, such as “fasta” " +#~ "(one of the values of the enum)," +#~ " your command should execute successfully:" +#~ msgstr "" + +#~ msgid "" +#~ "However, if you do not provide any" +#~ " input value, then `file_format` will " +#~ "be evaluated to a `null` value, " +#~ "which does not match the expected " +#~ "type for the output field (a " +#~ "`string`), resulting in failure when " +#~ "running your workflow." +#~ msgstr "" + +#~ msgid "" +#~ "To correct it, you must remember " +#~ "to use an or operator in your " +#~ "JavaScript expression when using exclusive " +#~ "parameters, or any parameter that allows" +#~ " `null`. For example, the expression " +#~ "could be changed to `$(inputs.file_format " +#~ "|| 'auto')`, to have a default " +#~ "value if none was provided in the" +#~ " command line or job input file." +#~ msgstr "" + +#~ msgid "" +#~ "The `uppercase` step of the workflow " +#~ "is an operation. It can be used" +#~ " like a command line tool or an" +#~ " expression. You can also plot it " +#~ "with the CWL Viewer or `cwltool`:" +#~ msgstr "" + +#~ msgid "" +#~ "The output of the command above " +#~ "can be rendered with a Graphviz " +#~ "renderer. The following image is " +#~ "rendered with the Sphinx Graphviz " +#~ "directive (this user guide is built " +#~ "with Sphinx):" +#~ msgstr "" + +#~ msgid "" +#~ "If you try running it with " +#~ "`cwltool`, the command will fail since" +#~ " `cwltool` does not have enough " +#~ "information to know how to execute " +#~ "it:" +#~ msgstr "" + +#~ msgid "" +#~ "When a tool runs under CWL, the" +#~ " starting working directory is the " +#~ "designated output directory. The underlying" +#~ " tool or script must record its " +#~ "results in the form of files " +#~ "created in the output directory. The" +#~ " output parameters returned by the " +#~ "CWL tool are either the output " +#~ "files themselves, or come from examining" +#~ " the content of those files." +#~ msgstr "" + +#~ msgid "" +#~ "In previous examples, the `baseCommand` " +#~ "was just a string, with any " +#~ "arguments passed as CWL inputs. Instead" +#~ " of a single string we can use" +#~ " an _array of strings_. The first" +#~ " element is the command to run, " +#~ "and any subsequent elements are " +#~ "mandatory command line arguments" +#~ msgstr "" + +#~ msgid "" +#~ "The field `outputBinding` describes how " +#~ "to set the value of each output" +#~ " parameter." +#~ msgstr "" + +#~ msgid "" +#~ "The `glob` field consists of the " +#~ "name of a file in the output " +#~ "directory. If you don't know name " +#~ "of the file in advance, you can" +#~ " use a wildcard pattern like `glob:" +#~ " '*.txt'`." +#~ msgstr "" + +#~ msgid "" +#~ "To capture a tool's standard output " +#~ "stream, add the `stdout` field with " +#~ "the name of the file where the " +#~ "output stream should go. Then add " +#~ "`type: stdout` on the corresponding " +#~ "output parameter." +#~ msgstr "" + +#~ msgid "" +#~ "Often, tool descriptions will be written" +#~ " for a specific version of a " +#~ "software. To make it easier for " +#~ "others to use your descriptions, you " +#~ "can include a `SoftwareRequirement` field " +#~ "in the `hints` section. This may " +#~ "also help to avoid confusion about " +#~ "which version of a tool the " +#~ "description was written for." +#~ msgstr "" + +#~ msgid "" +#~ "As well as a version number, a " +#~ "unique resource identifier (URI) for the" +#~ " tool is given in the form of" +#~ " an [RRID][rrid]. Resources with RRIDs " +#~ "can be looked up in the " +#~ "[SciCrunch][scicrunch] registry, which provides " +#~ "a portal for finding, tracking, and " +#~ "referring to scientific resources " +#~ "consistently. If you want to specify " +#~ "a tool as a `SoftwareRequirement`, " +#~ "search for the tool on SciCrunch " +#~ "and use the RRID that it has " +#~ "been assigned in the registry. (Follow" +#~ " this [Adding a Resource Tutorial" +#~ "][scicrunch-add-tool] to add a tool" +#~ " to SciCrunch). You can use this " +#~ "RRID to refer to the tool (via " +#~ "[identifiers.org][identifiers]) in the `specs` " +#~ "field of your requirement description. " +#~ "Other good choices, in order of " +#~ "preference, are to include the DOI " +#~ "for the main tool citation and the" +#~ " URL to the tool." +#~ msgstr "" + +#~ msgid "" +#~ "Normally, input files are located in " +#~ "a read-only directory separate from " +#~ "the output directory. This causes " +#~ "problems if the underlying tool expects" +#~ " to write its output files alongside" +#~ " the input file in the same " +#~ "directory. You use `InitialWorkDirRequirement` " +#~ "to stage input files into the " +#~ "output directory. In this example, we" +#~ " use a JavaScript expression to " +#~ "extract the base name of the input" +#~ " file from its leading directory " +#~ "path." +#~ msgstr "" + +#~ msgid "" +#~ "Before we run this, let's just " +#~ "break it down and see what some" +#~ " bits do. Most of this has " +#~ "been explained in previous sections, the" +#~ " only part that is really new " +#~ "is the `dockerRequirement` section." +#~ msgstr "" + diff --git a/locales/ru/LC_MESSAGES/user_guide.po b/locales/ru/LC_MESSAGES/user_guide.po index c6f3ca0c..2ccbe00b 100644 --- a/locales/ru/LC_MESSAGES/user_guide.po +++ b/locales/ru/LC_MESSAGES/user_guide.po @@ -1,3122 +1,4336 @@ # SOME DESCRIPTIVE TITLE. # Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. # msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"POT-Creation-Date: 2023-12-16 11:48+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: Automatically generated\n" -"Language-Team: none\n" "Language: ru\n" +"Language-Team: none\n" +"Plural-Forms: nplurals=3; plural=(n%10==1 && n%100!=11 ? 0 : n%10>=2 && " +"n%10<=4 && (n%100<10 || n%100>=20) ? 1 : 2);\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" +"Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 2.12.1\n" -#: ../../LICENSE.md:2 -#: 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac msgid "Licenses" msgstr "" -#: ../../LICENSE.md:4 -#: 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.md:4 9dd9705700664b31a3f296d263b4028b msgid "Instructional Material" msgstr "" -#: ../../LICENSE.md:6 -#: 747f9dd48bc54f44adcd8b18c57f4d9d -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +#: ../../LICENSE.md:6 e54324bd39cd431d91b32e338217b8c7 +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." msgstr "" -#: ../../LICENSE.md:12 -#: 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.md:12 754f3f54aa4142ef9dac27f508dd0bca msgid "You are free:" msgstr "" -#: ../../LICENSE.md:14 -#: 466be810dd8d4a838e0edb5869f2c4eb +#: ../../LICENSE.md:14 d2b1d5e965ef4e71b64c359549919975 msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" -#: ../../LICENSE.md:15 -#: 18a3a0aec35743848c97bc178f9c94ff +#: ../../LICENSE.md:15 fe9551ffef8149bf8da50e70318e8de8 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "" -#: ../../LICENSE.md:17 -#: b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.md:17 247db3bcc7024c44a044886a29ef1414 msgid "for any purpose, even commercially." msgstr "" -#: ../../LICENSE.md:19 -#: 6021e65292a149d5b15e14491f3eb05e -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +#: ../../LICENSE.md:19 c04d906124854afc917707b7b4e45bb2 +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" msgstr "" -#: ../../LICENSE.md:24 -#: 8fb7a2946c384364814c6ec3910997d3 -msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.md:24 551cb5ab59dd4737b1042a4ef79ffab7 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." msgstr "" -#: ../../LICENSE.md:32 -#: 8161753b7526445db319210044566200 -msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.md:32 f6c3b2ccad494ed6811a35537fc1fb0d +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" msgstr "" -#: ../../LICENSE.md:36 -#: 15314ba527864eaa834cf1185cfcc4e3 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +#: ../../LICENSE.md:36 91c95248cd7f435c909ee263a9a8bf3f +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." msgstr "" -#: ../../LICENSE.md:39 -#: b351ddf9847d48b1a2a87fc78eaba4d2 -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +#: ../../LICENSE.md:39 27f79b0b648b4de4b0eb3172b2dc4ae8 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." msgstr "" -#: ../../LICENSE.md:44 -#: a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.md:44 1e367d07720d4f9fb7ebc3149052e823 msgid "Software" msgstr "" -#: ../../LICENSE.md:46 -#: 84b2c685bbab48449fdc72d2a1e42bf4 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +#: ../../LICENSE.md:46 cf8b58d02b6943a48cb70aa78a27bea4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" -#: ../../LICENSE.md:51 -#: 0f68eafafaef4b54accba7e13bfaa702 -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +#: ../../LICENSE.md:51 96f1e5be3e1e48db8d9a4c7693008715 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." msgstr "" -#: ../../src/_includes/what-is-cwl.md:1 -#: ../../src/_includes/what-is-cwl.md:2 -#: eab02dc13915490bb3c9ba744d78b6a7 -#: d4f35995b0f6494d9771a4be0a82538f -#: d6ccd4b546254f56a597d67dd4fdc5d6 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +#: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 +#: 08aa9181d5304e0fa96b28db15718559 d37fc100eb6948bba8b5e757574b2aaf +#: ecdd0f28d5b048d69dd1ffae2fa1f6c0 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." msgstr "" -#: ../../src/episodes.md:5 -#: ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc -#: 436cfca6f857469bbff7c652df32160f +#: ../../src/episodes.md:5 ../../src/setup.md:5 +#: 1361ff6bf4924efc9ce9a85785a6b381 eb254514301c491e81f72ae19c407261 msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 -#: cc11f5d29206492d9f2f0922882b6159 -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +#: ../../src/episodes.md:9 f03d7cbe6670451db0896f1b674d56c7 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 -#: e2ed894d325a4f50a5e2dc69da5531a1 +#: ../../src/faq.md:1 d65ad48ac6314bf0a74c34a6766561fc msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 -#: 61edb787dab04ca2ad3ed07616d878a0 -msgid "Non \"`File`\" Types Using `evalFrom`" +#: ../../src/faq.md:11 370a9659c7904ef6b5e1ae7480f82ef6 +msgid "How do I create non \"`File`\" types using `evalFrom`?" msgstr "" -#: ../../src/faq.md:41 -#: d5321589e7ed4f0db3c630cc39800791 -msgid "Rename an Input File" +#: ../../src/faq.md:41 8333f51e3f5945fe8963adfc6685bcb1 +msgid "How do I rename an input file?" msgstr "" -#: ../../src/faq.md:43 -#: fc62427c0a004810b055dee90ec5e2d9 -msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +#: ../../src/faq.md:43 f6b88d9154d049d7807afa9bb0f1ac98 +msgid "" +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 833510f5896b4a6eb5875d25eca5b047 +msgid "How do I rename an output file?" msgstr "" -#: ../../src/faq.md:59 -#: 1c6b8a4194a14611b4061b1540c3807f -msgid "Rename an Output File" +#: ../../src/faq.md:61 207e2f97d1c44233ae3f109c5a6ec944 +msgid "" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:61 -#: bc7ad10c929848a3a9a240a3c501d299 -msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +#: ../../src/faq.md:83 d66acc583da24273980a52be03e79e91 +msgid "" +"By modifying the `basename` field in the `outputEval` field, CWL workflow" +" engines will rename the file using the new name for subsequent steps or " +"as a workflow-level output." msgstr "" -#: ../../src/faq.md:82 -#: 7225a993d281421b95c8e3df2846a0e3 -msgid "Referencing a Local Script" +#: ../../src/faq.md:86 8641f105131b4ac1bca7e0a46756ef79 +msgid "How do I reference a local script?" msgstr "" -#: ../../src/faq.md:84 -#: 7ef1dbb81993473f948d9c6f3c64b381 +#: ../../src/faq.md:88 d3e43b40d6994b32bc37067ee116418e msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 -#: 450edf800a18423195bea4fe8793a2cb -msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +#: ../../src/faq.md:90 64b140a321ca4087945339c523cc24dd +msgid "" +"The first method involves adding the path to a folder containing your " +"scripts to the `PATH` environment variable. This allows you to execute " +"the shell script directly (without explicitly using the `sh` or `bash` " +"commands)." msgstr "" -#: ../../src/faq.md:89 -#: 1a8cc75ea6174b9297871b2e58971077 +#: ../../src/faq.md:93 34ebca4487a54ceab5d087105820e945 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 -#: a7d84f740a714ec588503ee084fbbc34 -msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +#: ../../src/faq.md:99 6b04a4dcdada4515b28d74aacff3537a +msgid "" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 -#: 569d553abe85450c9d1c37456bf412f4 -msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +#: ../../src/faq.md:101 756ab4f7edcf42d3872bb86818e088c3 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." msgstr "" -#: ../../src/faq.md:104 -#: 95f5dbbd21084a318413b9528fb867be +#: ../../src/faq.md:108 efb46b3a2d7c4c51b65998602bfa6f18 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 -#: 1b3cae80fa9a40ffb2259b8c1cd2b468 -msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." -msgstr "" - -#: ../../src/faq.md:115 -#: 8d86baa239364f799d4f9d5ea2b0e314 -msgid "The second method involves including an input of `type: File` in the script itself:" +#: ../../src/faq.md:117 844938d5d2304c6cb03184b4b4b0b024 +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." msgstr "" -#: ../../src/faq.md:135 -#: f2c109998c76434893ff16b17fdb2bd0 -msgid "In CWL, everything must be directly stated." +#: ../../src/faq.md:119 796ce8155e32486d9651f8f13bfa3148 +msgid "" +"The second method involves including an input of `type: File` in the " +"script itself:" msgstr "" -#: ../../src/faq.md:138 -#: c2c752b86bf94d6fb3751f4dd81bc7a7 -msgid "Setting `self`-based Input Bindings for Optional Inputs" +#: ../../src/faq.md:138 ba246320fdd94a1aab4736f83718d793 +msgid "How can I set `self`-based input bindings for optional inputs?" msgstr "" -#: ../../src/faq.md:140 -#: 2c38cc58cbb340bc935a5f00e96ba95c -msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +#: ../../src/faq.md:140 6169b7be9af7448abcb57eaf91e1cc91 +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 -#: ce6db54bd0f54839a5beb948530a21f0 -msgid "Model a \"one-or-the-other\" Parameter" +#: ../../src/faq.md:165 6c98b7948059411b8e09cf03a552c5ab +msgid "How can I model a \"one-or-the-other\" parameter?" msgstr "" -#: ../../src/faq.md:167 -#: d06cbf89028b4638ad54c2529bcbfa25 -msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +#: ../../src/faq.md:167 d1424da3f43c4519a4c4735f4a720341 +msgid "" +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 -#: d53fb28dcad04e7788cba9e280a2343c -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +#: ../../src/faq.md:188 5c9980839f404ba6aef92ef23034500f +msgid "" +"How do I connect a solo value to an input that expects an array of that " +"type?" msgstr "" -#: ../../src/faq.md:190 -#: d9e30e11533b4d53a144f5df7041268d -msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/faq.md:190 2525baf16c1f4725b096f33fd99009cf +msgid "" +"Add a " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput):" msgstr "" -#: ../../src/faq.md:194 -#: 941077158ec54ae19bfa2e2ad6662da1 +#: ../../src/faq.md:194 a00d5d96b15048a79ae099d22d63bb42 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 -#: 937cb94a370640c788fbc3fe0b19f2e5 -msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +#: ../../src/faq.md:196 3a92c6cc5c2b40ffa0d692d03bad5c87 +msgid "" +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 -#: a1d57e15656548128a76a8b975c564c9 -msgid "Which means \"create a list with exactly these sources as elements\"" +#: ../../src/faq.md:199 3af16c07e3f148ddb8849c94a3864158 +msgid "Which means \"create a list with exactly these sources as elements\"." msgstr "" -#: ../../src/faq.md:201 -#: c8c235a9bf6240628f0b5493ffebf7e0 -msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +#: ../../src/faq.md:201 0ea3de393d2f42aeb82658c85a19ec45 +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." msgstr "" -#: ../../src/faq.md:229 -#: 3da4dcb043eb4423a53a14182949d9cd -msgid "Optional Inputs 💯" +#: ../../src/faq.md:229 2f1bbb611c9c4f80b7ae0566432f2f35 +msgid "How do make an input optional? 💯" msgstr "" -#: ../../src/faq.md:231 -#: 89b90d3bf1ea4ebd88482d435241fac5 -msgid "To make an input parameter optional, add a question mark to the type declaration." +#: ../../src/faq.md:231 08a226efe5d141e68215ac77725033db +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." msgstr "" -#: ../../src/faq.md:247 -#: a854006054ce4ffe94bbfa73bdbecbf2 +#: ../../src/faq.md:247 06e70a855a8f455ca0536eead77073c2 msgid "" msgstr "" -#: ../../src/faq.md:248 -#: f80eb714e9df417fbba555b5dd5f4d8c -msgid "Enum Inputs ⚜️" +#: ../../src/faq.md:248 7fda8eeb6a7f4689993ed0118c77f023 +msgid "" +"How do I specify an input that must come from a list of predefined values" +" (i.e. How do I use enum inputs) ?" msgstr "" -#: ../../src/faq.md:250 -#: 10af80fa13af4158aec7060550485350 -msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +#: ../../src/faq.md:250 b1934a82553b4da3b7f981e576245dd8 +msgid "" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" msgstr "" -#: ../../src/faq.md:267 -#: ad1c26711ccd4efd8fdb25f9293d33fd +#: ../../src/faq.md:267 17fc34fad2094f5ea60e963dabd632b8 msgid "" msgstr "" -#: ../../src/faq.md:268 -#: 49e2095b51f84f609f5d4bc088ad9745 -msgid "Record Inputs 📀" +#: ../../src/faq.md:268 4d7acfbeba5b4e9cb31f08ef4b280447 +msgid "" +"How do I describe dependent or exclusive input parameters(e.g. How do I " +"use record inputs)?" msgstr "" -#: ../../src/faq.md:270 -#: 52b8538177c64090af51f5f6a696c28c -msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +#: ../../src/faq.md:270 949ce95c082f4a05891a55fee25d4873 +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 -#: f96c9257e3734b8aa0cc5e065f74f944 -msgid "Setting Mutually Exclusive Parameters" +#: ../../src/faq.md:322 6fd3c469d11d4d52b9fbb7a3d443a8db +msgid "How do I set mutually exclusive parameters?" msgstr "" -#: ../../src/faq.md:324 -#: 7dc0540508084a3495ff3b2ac90fd323 -msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +#: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f +msgid "" +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 -#: b53dc77466b24a67b52b8aadf4fab724 -msgid "Setting Booleans" +#: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 +msgid "How can I set Booleans?" msgstr "" -#: ../../src/faq.md:344 -#: cf4e7f3977ae4f9b877072c2b1c4b533 +#: ../../src/faq.md:344 8dcb88744e5840029de0e1bbf1c4b967 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 -#: 99b37739ef18443ca7c0e715a131e0c7 -msgid "Concatenating Strings in Inputs" +#: ../../src/faq.md:349 972b7a5551bb43e6b9fa30e0cb713ff7 +msgid "What should I do when concatenating strings in inputs?" msgstr "" -#: ../../src/faq.md:351 -#: 9b00b5a55ee941e1adbfe89e133791e3 +#: ../../src/faq.md:351 68f74afc21d846dd9070d45dec0cc1d8 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 -#: 07922147f7ab487ba2a1e7c43c9f410c -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +#: ../../src/faq.md:359 53b633c6f8644106beb95ae567eb0708 +msgid "" +"I get `cwltool` errors due to filenames with space characters inside. " +"What should I do?" msgstr "" -#: ../../src/faq.md:361 -#: 7a11806f0c7045b48fe58a271f814797 +#: ../../src/faq.md:361 7101bb5cb69e4faca4e60eabb4eb258e msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 -#: fdaec25650ab4b0fb1c527610e24ae5a -msgid "For example, the filename `a space is here.txt` includes 3 space characters." +#: ../../src/faq.md:363 0eaf834b0ca847cca6736794895f5f81 +msgid "" +"For example, the filename `a space is here.txt` includes 3 space " +"characters." msgstr "" -#: ../../src/faq.md:371 -#: 182959fc9f4746d082994e07d05c8cde -msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +#: ../../src/faq.md:371 7dabd8aab7a5423b842433616640bac0 +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 -#: cc7752e9989e4a6d957682f479d6fc60 -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +#: ../../src/faq.md:373 b7ec33f38ce74ceb890f4379e4c41054 +msgid "" +"What should I do when I get CWL Parameter Reference error due to hyphen " +"in an input identifier?" msgstr "" -#: ../../src/faq.md:375 -#: 6db1ebd2d6c74ceca889662cd7df5cd5 +#: ../../src/faq.md:375 e39b65947b294b20a444f18d780246f4 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 -#: 3de2513c7d7b4569ba63f7e6d29137b7 +#: ../../src/faq.md:384 dcd42c65681b438bb541fb38ddebb536 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 -#: ae3a9188706649e28f97bc4ec34c0821 +#: ../../src/faq.md:396 2b96665acac449758b852bbe7600e007 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 -#: e1ac97ab6ad3449b8c54933d25257f73 +#: ../../src/faq.md:410 f59751d2f0014e59af7879a748062cec msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 -#: f6c402f7f6974edbbb5582c8e22f3869 -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +#: ../../src/faq.md:423 7780f461ca4c478b92fca893c0b0894a +msgid "To fix this error, change `-` (hyphen) to `_` (underscore):" msgstr "" -#: ../../src/faq.md:436 -#: 190099a242a645c9b9f8bc3ce89d920d -msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +#: ../../src/faq.md:436 88df56dfff854fc68fb6ad3835a846e4 +msgid "" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 -#: 06a4f6ffc2da4d43b453d4784b42efd3 -msgid "Use CWL and cwltool with Singularity" +#: ../../src/faq.md:442 fc407a9e8d8c4b699d9cd14b369343b5 +msgid "How do I use CWL and cwltool with Singularity?" msgstr "" -#: ../../src/faq.md:445 -#: 1901c34201054a9cae199b0dbb8b945e -msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +#: ../../src/faq.md:445 239f5f81cef042b08fb8015c36b3ecad +msgid "" +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." msgstr "" -#: ../../src/faq.md:450 -#: 2d498470524d47f18f9936ace6acebb0 -msgid "Debug JavaScript Expressions" +#: ../../src/faq.md:450 61641314d82b43e982e54c64c73232c5 +msgid "How do I debug the JavaScript in my CWL tool?" msgstr "" -#: ../../src/faq.md:452 -#: d7b044f5224a48eda09bc949cf645193 -msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +#: ../../src/faq.md:452 5556d3c323664edea55cfb777f4efb3b +msgid "" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 -#: 2754519265eb426b940bbbd2b8d64e1e +#: ../../src/index.md:1 1c9fb72b83c9467a9672943fb47ffe32 msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 -#: f8d6e4cd54cb42c88182a43171d97bab -msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +#: ../../src/index.md:3 aaa44578e27345e682ab44686b4da159 +msgid "" +"This guide will introduce you to writing workflows using the [Common " +"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " +"guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 -#: 132d40fee3b84469afa80d5ff613bf77 +#: ../../src/index.md:7 0adfc2adb0c74372b25d197dd3a73b8b msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 -#: 0f47157605a34ea58770ea898deebae4 -msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +#: ../../src/index.md:9 96c8dca812f1415db7c5c006b0c0e022 +msgid "" +"If you find that something is missing from this guide, or if you would " +"like to provide other feedback, file an Issue on the [project repository " +"for this guide][repo]. You can also suggest changes directly in a Pull " +"Request by clicking the \"Edit this page\" button at the right sidebar of" +" each page." msgstr "" -#: ../../src/index.md:16 -#: 6d269e8d70184034bcb56385a6ca198f +#: ../../src/index.md:16 35c50bb5c3a345b4a4ae66b2df065376 msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 -#: ed74c9a4b623464480e2c184668fcec0 -msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +#: ../../src/index.md:18 9431edcf4e344fb89b6a251e627279d2 +msgid "" +"If you are a beginner user get started with the " +"[Introduction](/introduction/index.md) section. For advanced users the " +"subsections of the [Topics](/topics/index.md) have detailed information " +"about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 -#: cfa67cf5521b414da6f7d34cbed283f7 -msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +#: ../../src/index.md:23 61cf57e61a9f46e5a1bff6368c5ad5e3 +msgid "" +"The Table of Contents is displayed at the top menu and also on the left " +"sidebar. It also appears further down this page but with links to " +"subsections. The right sidebar contains links to the sections of each " +"page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 -#: ee6b82bd86264e4bb1e8e4065b1e6b9c +#: ../../src/index.md:28 94381840d8a848c4a02fa97bfe83566d msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 -#: e208c8a7506e41dcac9a403c5d2850c1 +#: ../../src/introduction/basic-concepts.md:1 c1271d88e203454688a22e61ee88f02a msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 -#: ac62d326a68145b695e46b714d4e8156 -msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +#: ../../src/introduction/basic-concepts.md:3 dd462818cc9a4205b38866d0c5137ece +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 -#: 984e6676b9d04c7092bc492f195dfb91 +#: ../../src/introduction/basic-concepts.md:10 7a56d394fb244431aefce7ebbb834ecf msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 -#: cbe1d761da5b403d9605fa1fb8e62fdf -msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +#: ../../src/introduction/basic-concepts.md:21 35800ed2c56d489190d3702d9ad20fd7 +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 -#: 3a71b269bd3c49eb913cf69b60373c24 -msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +#: ../../src/introduction/basic-concepts.md:25 3ab6dd6b2f694afeb08f3984a74f3efb +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 -#: b171b72c48d44050a3416a7a42c4021d -msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +#: ../../src/introduction/basic-concepts.md:33 72ae1fb763a34c41b1b06adcbe1522c3 +msgid "" +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 -#: b3df1607e9d242d78b22dc44335fbe2d +#: ../../src/introduction/basic-concepts.md:37 5aa7d3ee6cb048d888f1e1f49d0e08be msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 -#: 078b58ffc1cc4d25a7c4eea3bb76e025 -msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +#: ../../src/introduction/basic-concepts.md:39 c87e6daefda74579a39924777b2e6809 +msgid "" +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 -#: c3869b4ec5ff47d99e8da79770722e04 -msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +#: ../../src/introduction/basic-concepts.md:44 c995e699ae2949219af252f9d802a43d +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 -#: 2482c84831fc4dfab629e7bfcfb41cbf +#: ../../src/introduction/basic-concepts.md:51 09171f48a3d841b2acb6d803b2340c8e msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: 1c1647a3496c4251a3193f94ee4e78c8 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 -msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +#: 854633336f4d4fc394e62c53ce022c6b +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 142a847f11d7462f8bf77bfe789410ca msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 7c7567fa690043f9b4b89bdf8ca60cad msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: 7afcf087d3ea49dabf1a641a2bb71b35 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: 6399939602334819a20b92b957352a8a msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 8c55b15cebf142899045f229ccc86b1e msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a -msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +#: ec54c0e67e894bfba2d0fbb0f87ffdf4 +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 -msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +#: c88ad26efa794cbeb6f0690aa0cad5ea +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef -msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +#: 946825a7ea2c450eb3e41b5548670fb7 +msgid "" +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 -msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +#: 44aac23f302c4178accf7e431cfbb96c +msgid "" +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 -msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +#: 5afdb7aaf0bf4c1abf4c22cdbdd58be9 +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +#: 07c5789c59224ed78a3ecd03cfe872e9 +msgid "" +"[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement)" +" - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +#: 6f9854ae1b884ad39f88d2f39d66cb98 +msgid "" +"[`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow.html#SubworkflowFeatureRequirement)" +" - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 -msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +#: 23fef6de073f4da18118e4d0512670fe +msgid "" +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow.html#InitialWorkDirRequirement)" +" - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee -msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +#: fb3762f91177401ea624d1e716d67ae6 +msgid "" +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e -msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +#: b6a5cd431c324078a9a4e1513a14ee28 +msgid "" +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: 88d7bad84dd341d2abb33673b8b8f250 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 -msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +#: bcbf5d76cf5f47b2a9691b7d2d8ef891 +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows both support the creation of FAIR " +"data and themselves adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a -msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +#: 4ea1d3bf04dc42f0bc6735a45b9e0dc0 +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee -msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +#: c0f53138bf084939a54b0a576b44199f +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: 91d6eb4984a6410ba99616b6617ba9af msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 -#: 65c24244713741e196da08cb9ba237b2 -#: f059896039524095b4deb65d693f8ddf -#: 3439764fab0e49d2bcb7c9fbae556e65 +#: ../../src/introduction/prerequisites.md:183 +#: ../../src/introduction/quick-start.md:94 0d7e607b00b9485aa2e3c5fb0a931bc6 +#: 161697ed3e864155bb89d8be794fc139 b4a7563eabf547c3bf7eab2567a27b51 msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 7221a89559944627b4c3db37f468f72c msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 -msgid "The CWL Specification page in the CWL website: " +#: bccf086fc9514f76b60dc161e3a09da3 +msgid "" +"The CWL Specification page in the CWL website: " +"" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 -msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +#: a5b37924c7d04ab984ff2542847afc4a +msgid "" +"The Command Line Tool Description Standard: " +"<[https://www.commonwl.org/v1.2/CommandLineTool.html](https://w3id.org/cwl/CommandLineTool.html)>" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 -msgid "The list of Implementations in the CWL website: " +#: 44af015fa36644b99f07338d241d29c1 +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 -msgid "PROV-O: The PROV Ontology - " +#: bffca993172048a4b7ab7c62637662e2 +msgid "" +"The list of Implementations in the CWL website: " +"" msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b -msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +#: 84c61946406347c8b138772909110d54 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:186 +#: eb0b6a62e06143eabc7b92acff9643ea +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 -#: 1769a0cbf4de4d77879c1f202cd11af9 +#: ../../src/introduction/index.md:1 48532f7701c54166859098e521a43db0 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 -#: 950370f0a36048b38e1bde9b78f80816 -msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +#: ../../src/introduction/index.md:3 08db628a949b4513b824ee334e70a7df +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 -#: f01faaf1b253407cbbc2f353c24774f3 +#: ../../src/introduction/prerequisites.md:1 d3f5749a76c14fdf8052f5f683d11b9e msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 -#: 353b14f06ee845d0a06a829643e31534 -msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +#: ../../src/introduction/prerequisites.md:6 ab9e21b3e99641d096ba70012b4eb035 +msgid "" +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 -#: b5a0607096814c0aa577f977c3b57c54 +#: ../../src/introduction/prerequisites.md:12 8ed426ebcb744839915e7c414d69b1e9 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 -#: ff2bb4c6504b456bac7ca9c514414dbf -msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +#: ../../src/introduction/prerequisites.md:14 ff74d48407464c4b9d451fa419137144 +msgid "" +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 -#: cbbcce4c2a96471b8b0ae3593ad59de4 +#: ../../src/introduction/prerequisites.md:19 eb98aa9c71d746a69e9610996ffc5b47 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 -#: 5089fdba8aed4113983fa86e698df98b -msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +#: ../../src/introduction/prerequisites.md:21 209a0018e7da48f09b27dc507ba14d24 +msgid "" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 -#: dbaa4bae22fe4d05b18d7351967ddbc3 +#: ../../src/introduction/prerequisites.md:24 8baf869537ea478791356320280df928 msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 -#: c05187af85be41b782678b79627f8fbf +#: ../../src/introduction/prerequisites.md:25 248e9760ce60442eb10ab7247d6af23b msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 -#: beb6cf4d7c154eb9b6d7fe024a318ed7 +#: ../../src/introduction/prerequisites.md:26 d89306bbadf44b6bba8959f1f68cc2f0 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 -#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 -msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +#: ../../src/introduction/prerequisites.md:29 aeeb990abbbd42cca122c342054be29c +msgid "" +"If you are using Windows, you will have to install the Windows Subsystem " +"for Linux 2 as documented in the [`cwltool` documentation for Microsoft " +"Windows users](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users). Your operating " +"system also needs internet access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 -#: 56d78c95daa54135b6aa9b2bfdc34d01 +#: ../../src/introduction/prerequisites.md:34 21d1f29fb15745c480194eae6acdd031 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 -#: 0f2704bf1f7148be95e999e312899f11 -msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/prerequisites.md:46 -#: 86264c9e56104ecea9146407c379aae2 -msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +#: ../../src/introduction/prerequisites.md:39 89f0bf6ff8544a6d87114085be8e0bb6 +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:51 -#: 0a0f0e5151ab4c498b4f8a12c016f28d -msgid "Installing `cwltool` with `pip` and `venv`." +#: ../../src/introduction/prerequisites.md:44 068f09d4d66547448693f7b9dadef497 +msgid "" +"`cwltool` can be installed with `pip`, `apt`, or `conda`. We recommend " +"using a virtual environment like `venv` or `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 -#: f7aaafeee230400da056464c853582c2 -msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +#: ../../src/introduction/prerequisites.md:48 1edf8b8438334ae29dc406dbfd711228 +msgid "" +"Visit the `cwltool` " +"[documentation](https://cwltool.readthedocs.io/en/latest/#install) for " +"details on installing `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 -#: 5eced7e4cd084e8a806b1d3b12d0c000 +#: ../../src/introduction/prerequisites.md:52 5e300141ce43435f9437507374987213 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 -#: 040c019b6e844eda8c8c2b210852516b +#: ../../src/introduction/prerequisites.md:54 282ac7ba2a2346feac2456bcda0f214a msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 -#: 6391e08e0bde49f4b21286d8fdb97433 -msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +#: ../../src/introduction/prerequisites.md:60 0b36f94f479a4bce9bd9be9983894421 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 -#: cdef47fca304479c9a9df75afc0afb35 +#: ../../src/introduction/prerequisites.md:66 5fce122794e34892b430ca4bdba5ba50 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 -#: d41c4bc740aa474ea09a7cbd267c8840 +#: ../../src/introduction/prerequisites.md:71 73f074f47d1449dcb40ff960a84851fd msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 -#: 24d7be55d3994f0b82c38da47918e0c9 +#: ../../src/introduction/prerequisites.md:73 2dd5a67870ca41b48e17c468ba15888b msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 -#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 -msgid "Cwl-runner Python Module" +#: ../../src/introduction/prerequisites.md:78 d2dc809318be49cc996d892e93ad84ac +msgid "Generic ``cwl-runner`` alias" msgstr "" -#: ../../src/introduction/prerequisites.md:93 -#: 096d0a50f69e48bd9915238d1b4264c1 -msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +#: ../../src/introduction/prerequisites.md:80 9809c2e262924ef286b0bd62e0b00995 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 -#: f9df974a8e2645a6918e67466bd1fdc2 -msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +#: ../../src/introduction/prerequisites.md:88 6dd6aa836099469381fb564d63b84f3d +msgid "" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:104 -#: 71ebe91d4bda473abe87578929433212 +#: ../../src/introduction/prerequisites.md:91 cc1a9b95508e44a1bf08ae75d990c301 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 -#: 746c6fc9c29d466494458a08d4c96672 -msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +#: ../../src/introduction/prerequisites.md:98 8f8c80f705d94d4899b250bbf9c54562 +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 -#: b9cc5a843a0f49daad56e9303657bdd5 +#: ../../src/introduction/prerequisites.md:102 176e4214d18149f3ba0bda692bcf760f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 -#: 34ab40437ab646488ba3ee86cd7fe071 +#: ../../src/introduction/prerequisites.md:107 4890bf20bc3842d3a7421b555bcda94a msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 -#: 705807fae182425dbf4244dbf2be1226 -msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +#: ../../src/introduction/prerequisites.md:112 2475a83cf6ed4389bb680fa37e8fe69c +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 -#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: ../../src/introduction/prerequisites.md:116 24da787aa76c4480838a93ba0533898d msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 -#: 164c438baab54ec19bbb4584a10dd411 +#: ../../src/introduction/prerequisites.md:122 4f3cb8d1f9ce4e3d852e81aa4e0f60be msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 -#: bf8be77af6154326b28442c5d2e2b852 +#: ../../src/introduction/prerequisites.md:124 27693d62faa045d9b03143d9bd2afcdf msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 -#: 695184d1b45a42f393e2da99c3721773 -msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +#: ../../src/introduction/prerequisites.md:131 703531514abe4fd48015c472005dbffa +msgid "" +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 -#: 7c4f45b3e7b549e186126693aa4a3d4f +#: ../../src/introduction/prerequisites.md:135 abba2e14c4e54252bb75983274663a7a msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 -#: 3ba23b4ea01c46848e4e43bbeff5f5a1 -msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +#: ../../src/introduction/prerequisites.md:141 11fea992c00940d29eb29ccf4b9370e9 +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env [executable]` rather than" +" using a hard-coded location, since `/usr/bin/env [executable]` looks for" +" the `[executable]` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 -#: eec6c07455384630809ff1c532bfe7d4 +#: ../../src/introduction/prerequisites.md:148 854736eef2ac4b63b187a4cea9660ae4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 -#: f6b39b12bd5c495cb53e2795bf9200ed -msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +#: ../../src/introduction/prerequisites.md:150 480fbb7a743046068c114fff5b396a9f +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 -#: 2fdb62a13f9447bc89183426260ce781 -msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +#: ../../src/introduction/prerequisites.md:154 28da3eea8fd245d1936013d021c25164 +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 -#: 1f07135156254f74a6b043bf33d00cc3 -msgid "Visual Studio Code with the Benten (CWL) plugin - " +#: ../../src/introduction/prerequisites.md:158 73c08e11e90d4c7f952307a1cdaa360b +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " +"" msgstr "" -#: ../../src/introduction/prerequisites.md:172 -#: de344f356b1c466d9131cdbd4d7353a3 -msgid "cwl-plugin for IntelliJ - " +#: ../../src/introduction/prerequisites.md:159 a5b788252a924338963f0ed198fc22ca +msgid "" +"cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 -#: 3f9324ede11441f58d93875867034cf0 -msgid "The CWL community also maintains a list of editors and viewers: " +#: ../../src/introduction/prerequisites.md:161 ee705b919acd461a8d9622821da246b6 +msgid "" +"The CWL community also maintains a list of editors and viewers: " +"" msgstr "" -#: ../../src/introduction/prerequisites.md:177 -#: 6ce8b81560e341c580d316d69202b268 +#: ../../src/introduction/prerequisites.md:164 7724b63db3cc45139379898d047c0f83 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 -#: 40cfd559d6a848d1aae354d3bdaa8e9c -msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +#: ../../src/introduction/prerequisites.md:168 eff13997c1ce43d1ad2d7a4d927394fe +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: " +"." msgstr "" -#: ../../src/introduction/prerequisites.md:185 -#: 8a9a50b0ebe847ce90593881ffe0d69c -msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +#: ../../src/introduction/prerequisites.md:172 2872503638624b7e904ae407375ac165 +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models " +"with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 -#: 923cf9dd6d6c417aabe42f9fa62ffa35 -msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +#: ../../src/introduction/prerequisites.md:178 52ddcc9bc1554d809371fc0a503c40bc +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for " +"pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 -#: 9390b03889de44638141d705e0ef8322 -msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +#: ../../src/introduction/prerequisites.md:185 f3bbfa17f31a459386461951de157dd2 +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 -#: 12042e411482458f8c35a2491f9433e0 +#: ../../src/introduction/prerequisites.md:186 e22b9e7c56104e018e6d2f3d547c01ea msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 -#: cdd4196f9aa34beba115901ec97913b6 +#: ../../src/introduction/quick-start.md:1 9ca367e3ca754a0fa88dab64724b95b6 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 -#: c43d9675ed134b78b02acb5a102a764a -msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +#: ../../src/introduction/quick-start.md:3 733db5702c774f32b8c91d13f74f3720 +msgid "" +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 -#: 280936bb2a22469799b2c9e9ba22adee +#: ../../src/introduction/quick-start.md:7 0b164074dd0849c3b2c8d2f78ea99e95 msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 -#: cb203354977d42a58112d09357f62565 -msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +#: ../../src/introduction/quick-start.md:12 6485f96f638548fbb7addc57f6cde92b +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 -#: 9e51962a7e5c47248f3e20703ae101eb +#: ../../src/introduction/quick-start.md:16 5e06f9c4754347b8bac88d24c21e0f67 msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 -#: 7e475e3f3c4a4404bb0236124c0f7ce7 -msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +#: ../../src/introduction/quick-start.md:22 6a13fb9112ab41acb60dc65b3656f63e +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 -#: 82613ca4e32b4ccab1b7735f5ba2d5a1 -msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +#: ../../src/introduction/quick-start.md:27 7b2ae93353184faea0ae4f4acdfc3350 +msgid "" +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 -#: 498a43362a4749f3b8b433709d34a1d5 +#: ../../src/introduction/quick-start.md:32 1ed30b04073d47a9893774746479fb5d msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 -#: f3e56aedd56b4b93bdc3894273e8c144 -msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +#: ../../src/introduction/quick-start.md:34 73a42cd9e0e54296985088b7221a8a93 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 -#: 81481f5b82e4488398f87f0a169bd359 +#: ../../src/introduction/quick-start.md:39 57aea587ade24610be62f5d993b0b755 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 -#: a81342e756d24c40acc15835d0a768f2 -msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +#: ../../src/introduction/quick-start.md:47 51183fc986014edbb026a53f222e6c2e +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 -#: c12cf89f8b9a421ebd05330326e219b3 +#: ../../src/introduction/quick-start.md:51 a7582c3ae37a462a8ae1e72b3f321534 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 -#: 9b68bcb1a41849dc9601ab47c5bbb0fe -msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +#: ../../src/introduction/quick-start.md:53 0595e96912dc40e5a09f2ced2d2b7bcd +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [CWL_DOCUMENT] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 -#: ce04027dfcfe4b7b91ea3c2136b18b23 +#: ../../src/introduction/quick-start.md:57 5b393c69816549b084516dda4d4274f5 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 -#: 0d8a788402914ebd8f09a5ca80650011 -msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +#: ../../src/introduction/quick-start.md:62 4306d8ad802f45c18487d932d04492fa +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 -#: 6d0b679efab24813a7a3b709ade940d1 +#: ../../src/introduction/quick-start.md:65 8339ec411ad04c70ab8d795eb154fc38 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 -#: 2ea056ab04b6419a9faf350de22a17f2 -msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +#: ../../src/introduction/quick-start.md:70 3ecca6985e754951aee00c93effe9517 +msgid "" +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 -#: 1a44a545434b448aa956005deeed90a8 +#: ../../src/introduction/quick-start.md:74 d05e8e016b1d40c28c4b6091103fe920 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 -#: e76bfcc0c9f84bcdb3f6d5277869a88c -msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +#: ../../src/introduction/quick-start.md:80 c5983ba6c86f4b749522c11cb3843911 +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 -#: d4cdbe870a6f4a68b542ca719d989062 +#: ../../src/introduction/quick-start.md:82 4065124edf3a4678a37c82e3070595cb msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 -#: b6d59e4b9c854abab1b3f7a0fa26f504 -msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +#: ../../src/introduction/quick-start.md:88 52b1602b5c8d48db88d0b16f788e7703 +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 -#: 5535b98e8b1342f09f003ec6db2b44b1 +#: ../../src/introduction/quick-start.md:96 3b06faf5f3194bd8a96118d9f050f61e msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 -#: 77e43c7117fd4c52b140f0dd52cc3963 +#: ../../src/introduction/quick-start.md:97 669b8ac154e74181830a430b1dc7684b msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 -#: 7282abfa7155497ca47c30f9abfb6474 -msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +#: ../../src/introduction/quick-start.md:98 1c888f1b771d49b3a257ed534b5afa0a +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 -#: 176d8d47830f4031bb95dc231ebf1303 -msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +#: ../../src/introduction/quick-start.md:99 dbce82b7a930493486a585ecb8891121 +msgid "" +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 -#: 82a7ca3703bc4f0daa18942a1ac8943b -msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +#: ../../src/introduction/quick-start.md:100 dc714ffd4278421b9f2417f41627722c +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 -#: d039a9d6461c44628d4660c00d9ce6ff -msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +#: ../../src/introduction/quick-start.md:101 2bf7b924182f4f2bab88edef5ef85baa +msgid "" +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 -#: fbc3383d9e1c4eaca7931c3cc4f1752b -msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +#: ../../src/introduction/quick-start.md:102 936a7dfab11a4f2c82c0b59964e3ea28 +msgid "" +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 -#: 1330bd38c4b5495f890b98c669f81a9d -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +#: ../../src/setup.md:9 24ea9c5144664d9599d7aca767b4730a +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 3843684b039a40dea163de951ca56738 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 -msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +#: a6fd1842b938435aa2a3c889019eec71 +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf -msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +#: dfed0747ed544547afd364086d828c9b +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: e690b567eae34f3f8dbdd7760e51449a msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 -#: 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: ../../src/topics/staging-input-files.md:15 4cee519b108143be89a0e47a75d7d649 +#: 79585673fd654bab9ba7c1927d7e153b msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: ef070ebe5f7245489b05660fb6d7c178 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb -msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +#: 4ae43e3e841442039e4bb8c740096c56 +msgid "" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a -msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +#: 8497291577914eb3a172c1ffb736d95d +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 -msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +#: dc9fa5f2cbb147b1853c4042c54010f3 +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 -#: 612c4a66c36a43d4ac5d74c1757d6845 +#: ../../src/topics/best-practices.md:1 964bf8276dd04b65887448e1386e63fe msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 -#: 939cd9e9eaff4e3ab74fe707a5d4eb21 -msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." -msgstr "" - -#: ../../src/topics/best-practices.md:8 -#: 4bcb84707acb40a0bfe2ea0853cb10b7 -msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +#: ../../src/topics/best-practices.md:3 7b59377bd56c47b8a71c18acfba4d3bb +msgid "" +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:11 -#: 4dee8504a8e5496081dadc386ab45540 -msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +#: ../../src/topics/best-practices.md:8 2292670347cd4549bc6a51e972de0ef4 +msgid "" +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:20 -#: 674c238b25e240eda05e22e399f2f78f -msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +#: ../../src/topics/best-practices.md:11 ae127b776eed4894af8cb680377703e0 +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 384eb620dc31468e8c3f5f33a3436200 +msgid "" +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 -#: b651f80f47b4442fbf29454a233697fc -msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +#: ../../src/topics/best-practices.md:26 e8259b43fa6944eda73eae381db6b97b +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 -#: 263a127a77cf4c41af76854f22f1f260 +#: ../../src/topics/best-practices.md:28 5b976a5aec7d44bda55b0a019e955416 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 -#: 3a87a0fb2a364e3da5aaa4017e430b19 -msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +#: ../../src/topics/best-practices.md:37 924b8df24deb4c82b32732f491c9a246 +msgid "" +"For more examples of providing metadata within CWL descriptions, see [the" +" Metadata and Authorship section of this User Guide](../topics/metadata-" +"and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 -#: ecf2b9c0b1664afe9c4e180610610021 -msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +#: ../../src/topics/best-practices.md:40 9e64a9fc89cb45cfbff0e925cc91b1be +msgid "" +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 -#: e24cb13d98014e558b6a6946758359e0 -msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +#: ../../src/topics/best-practices.md:44 87030aef02044b8283c76debab4772bf +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "" -#: ../../src/topics/best-practices.md:47 -#: f2b14a92374e449d9fb1e8c86ae0dd61 -msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +#: ../../src/topics/best-practices.md:47 6c9eaae099fa4ca4b0986b1c4146df50 +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 -#: 928e3df7ca3e479ca6474a8e72cf36eb -msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +#: ../../src/topics/best-practices.md:50 5ae8950fd31541399c2fe59096581dbc +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 -#: d355f035676446c88b028f327aeb4829 -msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +#: ../../src/topics/best-practices.md:55 b0493895105e43849bff2026763e472a +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "" -#: ../../src/topics/best-practices.md:58 -#: 339b852df24242189d6efcd2898a3396 -msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +#: ../../src/topics/best-practices.md:58 88806cb0462f4359801c1fa0ff0ebcc0 +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 -#: 3ef57e6862f240bebcf193a52397af0a -msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +#: ../../src/topics/best-practices.md:66 b178c7296ed5491782a4180c76883c14 +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." msgstr "" -#: ../../src/topics/best-practices.md:69 -#: f1a7c4f896a04a80b0c5f6a1db61ff8c -msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +#: ../../src/topics/best-practices.md:69 886d15c1972243acadccff5760f842f1 +msgid "" +"Each " +"[`CommandLineTool`](https://w3id.org/cwl/CommandLineTool.html#CommandLineTool)" +" description should focus on a single operation only, even if the " +"(sub)command is capable of more. Don't overcomplicate your tool " +"descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 -#: 1ac4c3d8c3e44bd1af3fc5df70051926 -msgid "Custom types should be defined with one external YAML per type definition for re-use." +#: ../../src/topics/best-practices.md:73 ef5a5f9b253c4ca3916802a695fb7c6d +msgid "" +"Custom types should be defined with one external YAML per type definition" +" for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 -#: c858f64e66f048a5b0032ef3e4d83694 +#: ../../src/topics/best-practices.md:76 ff59f40e84004523904e3094be07cc80 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 -#: fae385da16aa443da996fa23ac03d6ae -msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +#: ../../src/topics/best-practices.md:78 78d73fde24e24beeab541a623d9530b6 +msgid "" +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 -#: 92430be71ecc40e18bbbb80d5576c613 -msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +#: ../../src/topics/best-practices.md:82 d92013d662b44dbf8875e06c9dfbfd79 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 -#: 387d83db81024f65aa9a890c2d07874a -msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +#: ../../src/topics/best-practices.md:85 c100d5192a52497fb6a890b81a388fcf +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 -#: d8e2280a75a74916a1630afaa2fe2ae3 -msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +#: ../../src/topics/best-practices.md:90 e22fbacdb2fb4202b1bd69cfc24af5cd +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 -#: f1c1340f9745458980e0fbd641738687 -msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +#: ../../src/topics/best-practices.md:93 0060a863362140f6bb3932cb5da1df04 +msgid "" +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 -#: 5424e5472c3d466fa2a3d2022c6cb475 -msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +#: ../../src/topics/best-practices.md:97 93f6d6b544c24ce780184272f66bacab +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 -#: 3f4e98f6bfa141feba8c4b120e3d03e8 +#: ../../src/topics/command-line-tool.md:1 a378a2f7d268401abfbbbe6e5090a952 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 -#: 12f57b2ba76b492abe1816e06bfb1417 -msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +#: ../../src/topics/command-line-tool.md:3 cf0f1c00c0b34c94a8e2460a700c303e +msgid "" +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 -#: e1f657a46ce94a0d83671540e2cc2dab -msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +#: ../../src/topics/command-line-tool.md:8 7a180ba1f2d746a78b79be7e899cbad6 +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 -#: abb83f0097654a43bd78639d3dbb2bc8 +#: ../../src/topics/command-line-tool.md:19 128bd8cd6788431da54fa07a8dc87f99 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 -#: 3b1a9ae3412f4d6e96a39b9a16934232 +#: ../../src/topics/command-line-tool.md:50 d742e9e59ea44ca1a1df2de85059343f msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 -#: a5eacdbc9aa142c890b177869da4143d -msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +#: ../../src/topics/command-line-tool.md:57 e3a06ebe51b64b0183673a8acc04969f +msgid "" +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 -#: 1849b8f3ae1c4a84ae59a78ffd6b371e +#: ../../src/topics/command-line-tool.md:68 2bab464d19d14562a6501373aff13905 msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 -#: e3bdaceae8784ab0807b2cf356a98580 -msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +#: ../../src/topics/command-line-tool.md:69 201712f3ceee4d4ea56ab96d3fef97b0 +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. Starting with CWL v1.1, programs are not granted network access " +"by default, so you must include the requirement for network access in the" +" specification of your tool." msgstr "" -#: ../../src/topics/command-line-tool.md:83 -#: ed521ac365db4a6ba5a1051fbaa2932e -msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +#: ../../src/topics/command-line-tool.md:84 3282a357799f4a72a6b8bace206144c4 +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 or v1.2 " +"will have `networkAccess: true` set automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: 17c5b4ee43cc4a979676ad27e473d046 msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d -msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +#: cd0dff10471c4ad2b84e3a0e4d7767ea +msgid "" +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +#: bf4aea0a22334a1ca75cc20e937e6581 +msgid "" +"To generate such files, we can use the " +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: 008f768d56b8465bb4e8f4fde15853a7 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df -msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +#: 252f8e897b0942a8be098481890005f3 +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 -msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +#: aca24b72687c4d4d84bf9de8b71413f7 +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa -msgid "To test the above CWL tool, use this job to provide the input value `message`:" +#: 750b3232e8754448bc2b5913539495b8 +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 -#: ../../src/topics/outputs.md:77 -#: 2d2ef4769b2347e79db827655f1bcdeb -#: 2699fbc4376148af91b7a5a6cdac467c -#: ca03defa3ad14cf698171cb09e3055c1 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:81 +#: 687c8a84bade43269f3cd767d32f9f47 81da7a18fe8d4659abc883cf43009f1f +#: d5d67eae63304ebb9b242133feacb0d1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d -msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +#: c4f964450d014734877fb3c968353a74 +msgid "" +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c -msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +#: 9aeea5a6a4244bc7a1626e0cb7351068 +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 -msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +#: 867239e9ad3d4187a2703662a0ca3976 +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:54 #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 -#: ../../src/topics/staging-input-files.md:20 -#: ../../src/topics/workflows.md:198 -#: b372f33c65bb4707b2a462a960bb1373 -#: 293fb1d428b849aebccad598a932992d -#: f924d65fed0c4cb5b0a019b084a8b535 -#: d6255506eebe44be94c5ce703c44a513 -#: 7bbd2d738fc54649aeb10f8d2bc38b6f -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/custom-types.md:1 -#: cb34fd4c8cb04053ada491a227651048 +#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 +#: 0d7151b9f0194197bd686fe6c9c47afd 78bb40eeeda24d7b923162daa45d51a7 +#: 7b341a317347482ca86fc56119c3686f 7c637fa62cab4d0dbe670a3b72737cc9 +#: cfb4605a01dd4475aabcc086a4e65957 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 252a3a17b1ec4d5a9a82ebbf6c2f314c msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 -#: 67573252cc064b27ab13eebc468ac58a -msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +#: ../../src/topics/custom-types.md:3 e0275ddda8f84207a58d10c17ca99a45 +msgid "" +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 -#: 73e68b3af9cf41338d843c0c40e50cdc -msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +#: ../../src/topics/custom-types.md:9 8367e38e5e7c4a298d1d87b9001aaddc +msgid "" +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 -#: ef5f35acb97f4ddfad7b688712f53484 +#: ../../src/topics/custom-types.md:12 18b802f45ce0454ab7aa2a21812863c6 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 -#: 7015dfa99a6f4cfb87ebf0ed61e8043c +#: ../../src/topics/custom-types.md:18 66d1953f5dd54d448bddd0f30c330402 msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 -#: a999b1acda2641598086648c64aa3831 -msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +#: ../../src/topics/custom-types.md:24 56b8912a1ea84f28adeb8beaf92ab563 +msgid "" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 -#: f8c12a58cb0b46a488823c6ae95f25ea -msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +#: ../../src/topics/custom-types.md:30 a48539920c4944898918bc90b2d4e3c9 +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 -#: f25a63e0926d4932bbe64b2e4bdabf9e -msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +#: ../../src/topics/custom-types.md:46 c791096f537141e8bd7cc941d711d108 +msgid "" +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 -#: b0a4df0fd3ca42338cff4689235dcf4e +#: ../../src/topics/custom-types.md:53 5f6bc6ed72334a74b9a4c46c29ddda46 msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 -#: fecfbb44456640d8ba05e519bf2ff564 +#: ../../src/topics/custom-types.md:55 3b55419088e8446994703220bd8e8480 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 -#: d718630a296545f3a989c8c71e9ddc77 -msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +#: ../../src/topics/custom-types.md:61 fe6f4ce5e7344af0abea9d5c03e32ecd +msgid "" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 -#: 9a97acd430064710bcdf76edbd9f711c -msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +#: ../../src/topics/custom-types.md:76 dce43b138ba24b22bfa9fa5692a17009 +msgid "" +"Note also that the author of this CWL description has also included " +"[`ResourceRequirement`](https://w3id.org/cwl/CommandLineTool.html#ResourceRequirement)s," +" specifying the minimum amount of RAM and number of cores required for " +"the tool to run successfully, as well as details of the version of the " +"software that the description was written for and other useful metadata. " +"These features are discussed further in other chapters of this user " +"guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 -#: 59014808cbef4c02aaef03129d8a29b0 +#: ../../src/topics/environment-variables.md:1 19737f89f2994815969fa4a88346f49a msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 -#: 3c821c9c46d841ec89b8a5b1018f3af8 -msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +#: ../../src/topics/environment-variables.md:3 ad965f75aa0c41cda8b82c46af49774d +msgid "" +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 -#: bfdebb32440a4034beb42135e38884e8 +#: ../../src/topics/environment-variables.md:7 38b276f9b0114a0bb87734f0a07a736f msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 -#: 777d4a52f7554eff84db2df6d4d0f729 +#: ../../src/topics/expression-tool.md:1 9f33532119dc47ffb6ade20fb1d950bd msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 -#: 48deb71f361a43e48a56ed483075bca8 -msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +#: ../../src/topics/expression-tool.md:3 b267056eae704737af5aaada3ea7e6e2 +msgid "" +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 -#: 716b56506ca7470299899c5d820a9ea2 -msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +#: ../../src/topics/expression-tool.md:8 7e930144163e4d6e9f0bcaa764497ccf +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an " +"[`expression`](https://w3id.org/cwl/CommandLineTool.html#Expressions_(Optional))" +" attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 -#: b63e6f5a2e89431c8fc7d04f47fd69fe +#: ../../src/topics/expression-tool.md:17 f172488c19a94d688036197117d30b38 msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 -#: 39727e9058f24b62b8746a46d3f812c2 +#: ../../src/topics/expression-tool.md:48 ef978c951f1a4b7d9280d31367e5bae7 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 -#: e3ecac0a8e604f2b98a2a12b0579990a -msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +#: ../../src/topics/expression-tool.md:67 0b63da31bc274b3cad798b07149592ab +msgid "" +"We had to use an " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" as our expression contains a JavaScript call in `.toUpperCase()`. This " +"means to tools using the expression tool that JavaScript is a " +"requirement." msgstr "" -#: ../../src/topics/expressions.md:1 -#: c8d648b765ec499a8e9c464590838492 +#: ../../src/topics/expressions.md:1 b0e567a985f748538552bdb486a47998 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 -#: 007a345b4bad49cf996c4301b8386473 -msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +#: ../../src/topics/expressions.md:3 24d05cbbab8e460e99f2edc97ab0dcec +msgid "" +"If you need to manipulate input parameters, include the requirement " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" and then anywhere a parameter reference is legal you can provide a " +"fragment of Javascript that will be evaluated by the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 -#: 2edbd398eadb458b8eacd5fa5496f0a2 -msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +#: ../../src/topics/expressions.md:9 3d48d1a8f7f74bc1886e41653cb53a22 +msgid "" +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 -#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: ../../src/topics/expressions.md:16 7d444aacd418466bbe588fa964b45179 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 -#: efb5fd14988c4e2a8f834ee5369d4102 -msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +#: ../../src/topics/expressions.md:22 72a0558a83964796a8c1a0eb55fd78e8 +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 -#: e833649b951841c49397796f996d29f3 +#: ../../src/topics/expressions.md:25 d679fd1363b24c81979c68e7342159cf msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 -#: 276f688ba7cc471a842f085ca852b1d9 -msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +#: ../../src/topics/expressions.md:31 d2ee4fcece744b6681f29322b5305111 +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 -#: ebf399ea4d5f47b9be03e24f04c69f2d +#: ../../src/topics/expressions.md:35 624e4a270e374b1699b780df508b9184 msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 -#: 65e0cdd505b944caa40f65e612cdddfc +#: ../../src/topics/expressions.md:37 c252eac9a35e46aab08bd07bc1cdb57d msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 -#: 8b70a1ad70514039b97164fa630c12e4 -msgid "Note that requirements can be provided with the map syntax, as in the example above:" +#: ../../src/topics/expressions.md:47 f6f64d57a50742b19b801c14806ee18a +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" msgstr "" -#: ../../src/topics/expressions.md:54 -#: 2f28ab412d2843ffa5f14acdc01fc732 -msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +#: ../../src/topics/expressions.md:54 052e24e2ad044cc28f04d7f39be871d6 +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 -#: d957f55a6377422c9834f85d45e35009 +#: ../../src/topics/expressions.md:62 84b31c076d4b4826aae35e8c23fe6a25 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 -#: cbec9277b5004e50af2728cbda0df740 -msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +#: ../../src/topics/expressions.md:64 8c3b402c40f64880a4bd42c47b910254 +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 -#: e259f55f8000479bbd8009e25cf0ca6c -msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +#: ../../src/topics/expressions.md:66 9bf5ca0e769147c6a9705bc40bd1febc +msgid "" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 -#: 1acb064f7a4a482aa0174bdc847c6382 -#: 0222780b98ac48e89b1b4f57c9df8590 +#: ../../src/topics/parameter-references.md:64 7ab0dbd54c1441539673fa12ef96b89e +#: e76c6ece0c594fefa86b190879c5acaa msgid "`arguments`" msgstr "" -#: ../../src/topics/expressions.md:68 -#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 -#: ef2b8433778a40408f179c3e6f0cf99e -#: 224732683a9c41f3ba1b778851e745a8 -#: 17b10d1e91b24dc582df98fcd2ac850e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 -#: e4e68011dc5f42e4918c747afa7d764b -#: d44e3cfa661840eb851782e24caf1b68 +#: ../../src/topics/parameter-references.md:86 0209558b1013471eb708698537edaf06 +#: 4458393fdb0e451f9806e91122ea2534 594a163e08f04aa5a04a44a303a1c643 +#: a6fddc160afc4ef09717f69de72c11ce a9ec99ddcb344bcbbe5c1f59af0bcff2 +#: af2cdb5f66ac4fd5b8f91258f005cc62 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 -#: 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: ../../src/topics/parameter-references.md:66 afb175f182354cb19e23b1cad241437e +#: f9a6718845e24f46b76fcc8ab26eec7a msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 -#: 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: ../../src/topics/parameter-references.md:67 3bce21dcc2da439daca80c4fcdf4c343 +#: 7f5ce097ca0442a6a200599342a6e24b msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 -#: 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: ../../src/topics/parameter-references.md:68 3397e8816f6a4d4b9af728c175f04917 +#: 7b14686e16eb4f488659b22d67ec3bfa msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 -#: 8210b36347a749889450529ecdf4ff0e -msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +#: ../../src/topics/expressions.md:72 7a2d74aa018f4cab8c68e8775d83dd01 +msgid "" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/expressions.md:73 -#: ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 -#: ../../src/topics/expressions.md:93 +#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 -#: d0a92a3792b549e9b5ddce4667d168d2 -#: 801729c7c71b4109824b035437e69bf9 -#: 1bc510d525f0414e88692e356e67fbbc -#: d2e246ae56a24e4abdd6b7d9812a86e2 -#: b1446bab2732412e91f721a08067b0bd -#: e89dbeb22f41430ca39c923d9fdf68cb -#: bd61499b71e64164878dea08d6d7141e -#: ed875a006df64f9e8a55fa5e9fa87404 +#: ../../src/topics/parameter-references.md:90 24f27702d0684bc98e3232103510232e +#: 26a8dff7b80c4e059f1e20eef9da6203 476aa37af5214bcf963c7aab1f859273 +#: 4b0a0cd934bd41b4b55c034b91392bc7 5182e2165e44429287b4d924c2f896a4 +#: 7de500d3be6b4c3e8f274fd6a092109f 953d824a494947a3ab0ca2988717ee01 +#: b301751f90af4700bbada5e5b166be35 msgid "`format`" msgstr "" -#: ../../src/topics/expressions.md:74 -#: ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 -#: ../../src/topics/expressions.md:94 +#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 -#: 8a1748579de14f0888d5ee9023e37c2d -#: f760465a49d64d4c8468ad9c4fea62b1 -#: 28b6b5ffa7524374aaa9525ebfafb762 -#: d11f6a19ddf34cf19ec856bacf998e29 -#: bcb7cd10cb5947bb9d85c040f57f954f -#: da5188d3bedc4997a35bdf417f2f643c -#: cd7a0190511d4613b09600a3b1e9d55f -#: 47def3b078e2402182039be0227090ae +#: ../../src/topics/parameter-references.md:91 2c2b8db396b04ace8aa396c0a5a4858f +#: 33a9b77ce15b4910962a7f08bd2f47a3 57cba0191de3470bbe112ed2a0d3f252 +#: 6efe998094b3469eae61cfff551b1eb1 776de1ecfafc41ada7e916addd7229fd +#: 8595d62eb0274b3a8a7f0adf058b51d3 988966a2d4844e73961b0358aff8f6e1 +#: faa7d521fec240748407d03ffdb93aa0 msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 -#: 23088850ad02459696f6bbd385109aac -msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +#: ../../src/topics/expressions.md:75 d737a9e9bf1c45d695bf584bc3241d9a +msgid "" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 -#: f02257a822ad46ac93c5981531cc85d5 -msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +#: ../../src/topics/expressions.md:77 0e2052e16f6a41b8983dc64b4b3a7586 +msgid "" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 -#: 989a1c4aaa1143be9f53b90cd8b6d500 -msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +#: ../../src/topics/expressions.md:80 dff31dd961d540e3b8cd1247e978d60e +msgid "" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 -#: 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: ../../src/topics/parameter-references.md:78 249aba7c38ce49379b9d35e7ad81a0bf +#: 5a354eb4883948e0a2b5c96b5ae12da7 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 -#: d555a3d991e344a5a8e1289168d7c6d1 -#: 44b3f123c9b04a308c1161b742a7b34b +#: ../../src/topics/parameter-references.md:79 2325a310f2bc4d09b53b32c54efae2df +#: 9e477e2cfab24861b517fe2fb52962f4 msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 -#: e9fa9430535c424fa3e8be5d460d2ba4 -#: 0e306cc923974d1db83fdfb45105a11c -msgid "From `Workflow`" +#: ../../src/topics/parameter-references.md:80 9448462d104b4be5904623c85a9e16b7 +#: bf11a7a72147445c9b8e44b541e09f36 +msgid "From [`Workflow`](https://w3id.org/cwl/Workflow.html)" msgstr "" -#: ../../src/topics/expressions.md:84 -#: d289541e460147aa933f7878996f8649 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +#: ../../src/topics/expressions.md:84 0d54a777a33d4f17a2f3390384a3c0c5 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 -#: b0290d1a477b48119e17cf1fed9d6dff -#: 446f1190af7a40a0913ff04ce7aa938c +#: ../../src/topics/parameter-references.md:84 7918d0661be746faaddf25ad49172f30 +#: b8439dbaa949427097e25ccb48fe15ee msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 -#: 81b4d1f23a3642bfa9bb395b94260cd1 -msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/topics/expressions.md:88 7b37eb600c9b4847a58a7e5077bef4c3 +msgid "" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 -#: e1cde4aa32c041238ed2596173c6d824 -#: 557694f82e314baa9ccafba14d6ff2c9 -msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +#: ../../src/topics/parameter-references.md:87 368ef005c2ca4b8599f76242f7178375 +#: ab1ba7626eae483a8b614ee4cd5bab6f +msgid "" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 -#: c2a92d3eca7f4ee39cec649170eeea53 -#: 3c939769ede94602a67fc50c435741cf +#: ../../src/topics/parameter-references.md:88 595b9ddcee734d6595c1b4b2d169dcb8 +#: 80b55c77a4384644acfc9472c3cedee0 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 -#: f495da32f05a4a5ba9539be0a54c1a59 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +#: ../../src/topics/expressions.md:92 fd504478a6c641e0a72321fa80ad1c9c +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 -#: bdb4c68a175047ddbe141ca24960127f -msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +#: ../../src/topics/expressions.md:95 32b1a39cca1a4402af9bdc0abc4d70c8 +msgid "" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 -#: 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: ../../src/topics/parameter-references.md:93 2518d499801e4bcf82e9e4666280504d +#: 98a511d138e9497c923963c2ca5f0a0b msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 -#: 718ceee9973240ec9c100977bbcc8921 -#: 2b25152f6df5494a8632f3ce631c20d8 +#: ../../src/topics/parameter-references.md:94 57a055b125f742dc8842b798b034161b +#: e84bc5505a6549ae9aacde8cb9225403 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 -#: c07ab08eb75d4528949c56a3d7c12b28 -#: 846cd427ae25410eae7c920b237edcb0 +#: ../../src/topics/parameter-references.md:95 98cd455e080f43749090270e7a61cb42 +#: e698ea756fe94e99837312fb30c9f9bf msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 -#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: ../../src/topics/parameter-references.md:96 8dfae10004a641fdb95c456c90a48d94 +#: bef90c153d4f4397b1f69f9beb38f7e6 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 -#: 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: ../../src/topics/parameter-references.md:97 47fddc711ce44086a7811bdfbd9167dd +#: e2bdf4fe676346cbb4443ee54fb7419b msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 -#: 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: ../../src/topics/parameter-references.md:98 7d143ba98f1f4dfcbe08b70389d43092 +#: 8f1665baca2e4e3b96026b50d132709a msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 -#: 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: ../../src/topics/parameter-references.md:99 79bea45c2a484eda92c8578130b0b982 +#: d169949866a24e31947dffcb94620c5f msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b -#: e3b76f42c924489f9a0bcf5a7b636d23 +#: 8d2e01f2aa314f1cb1231f2e08f89ce5 d5417397b1e242ef9878ac77d2f65005 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 -#: 97b61352363f47cb890e8937c5613fa3 -msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +#: ../../src/topics/expressions.md:104 08a66b2ab271494d810ff5834ca5c1bc +msgid "" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e -#: a258554d462f4f5f83ece28d5b2fc584 +#: 21e9582891cf4b87a7ee4693663040fa 51bc6d1ccef14729a0d5e63b56d73d20 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 -#: 8d0b142bb7ed4e61b8fb03de197240ce +#: ../../src/topics/expressions.md:106 7d8755f05d6541439f72ec9d6806d3fc msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: effc0208cf4f4551958db6e526c0528b -#: 9d4889c8cec24351a7a9e3c547e331b6 +#: 29c2424fc7dc43e68c9bfee179167bb3 30f25141bcce4670882e4a5bbe4fc3e2 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: be6c1e85c7b6495d8086c262daad20e7 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +#: 02cfd4f1c3014e1eaa598a329dc5a95d d76fb015595e4194a7e15d714baaaf98 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 -#: 6abeba392b0444b19f92a19f178a4682 +#: 408f69a2df1343a78f93ff2ac0a994ea d37c78309e8b427f835af4fbd367e643 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 -#: 0bc424ef2ca346099f29b937379908a0 -msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +#: ../../src/topics/expressions.md:110 53752bdff0974e39b2a86e8f2d96455f +msgid "" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd -#: 949c376120d8441796ec9c89364f8851 +#: 242a12ec757947db894195c9aefba818 7b26b9972f7141bf950b3bb024b0e369 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 -#: 10d36a1adfd04144b401c993b12b4094 +#: ../../src/topics/expressions.md:116 93d6c90b49d8424f9283c384062ce333 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 -#: 29b73e1dd72744f68377f0a38c10f062 -msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +#: ../../src/topics/expressions.md:118 ea6cbaa5dae647538c0bd9a4d5cad3f9 +msgid "" +"The requirement " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" supports an `expressionLib` attribute that allows users to load external" +" JavaScript files, or to provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 -#: 38a2afaf4a6c4d04909af22c93f2808d -msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +#: ../../src/topics/expressions.md:122 484dc17440524cfda4dc486a7c5d5f63 +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 -#: cd74f34b21af4de9be96fd897efc469b -msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +#: ../../src/topics/expressions.md:128 5b2336cae1ef4cae8ed187d3f33cff25 +msgid "" +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 -#: f12e371f3f1a4b0cb2cff9800352d48c -msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +#: ../../src/topics/expressions.md:135 32eca3a47efc4685bf7be706e123adbe +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 -#: 49d0fda2fc144e0b8b7c92afc1d8945e +#: ../../src/topics/expressions.md:139 6839a02fb82d45c29ae518f2b00cb9d5 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 -#: 8f0e8f050e334ac08334e9215e1dcf61 -msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +#: ../../src/topics/expressions.md:146 5b5e59fa1688499ea4560ee6f8023227 +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" msgstr "" -#: ../../src/topics/expressions.md:149 -#: 26c74b11bb1849cea0763bb74ec43e42 +#: ../../src/topics/expressions.md:149 a1e57c6833c848d3974cf448493ab924 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 -#: 7a6be0005a6441feb67f036d005d7885 -msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +#: ../../src/topics/expressions.md:155 1a4dfef06b5c4402bdb7e7dbd79eeb5d +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 -#: ed590f9e6f4f425da886b110295c45db +#: ../../src/topics/expressions.md:158 71ac99c65d15451cbbf58d1e81934010 msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 -#: 093235307d6f47d4858e559b780ef5e5 +#: ../../src/topics/expressions.md:164 60918e53189243d3872e61c7a4de20fc msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 -#: 06635145b441418aaae84dc804f3d6ac -msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +#: ../../src/topics/expressions.md:171 ad2a74bd983b47869dc78b2eb7b6fce1 +msgid "" +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 -#: 973a9b257b1a4f0dbd4444d4f11dadd7 +#: ../../src/topics/expressions.md:175 82c02dd2446b4de9a4c4b87736107b30 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 -#: 04eaf1f7c630450db318dcd8b7626e15 -msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +#: ../../src/topics/expressions.md:181 6fa7ebeffc7b44c6a12cd84897d186a1 +msgid "" +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 -#: c4098489fbb049789f022cd3e5c3d49b +#: ../../src/topics/expressions.md:186 d34f3e688d2d49b6bfcda4c962895d8c msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 -#: 5979e4ae5c424276bdbc47f69b379d0f +#: ../../src/topics/expressions.md:193 9e2774fc35b14832a0f92b7afaafd537 msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 -#: fd4579a3c9844492b314b5c3c1775fc7 -msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +#: ../../src/topics/expressions.md:200 8b797cfb232f4e5da51f6c21e9a8e7e3 +msgid "" +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 -#: 3f038e7371f84ed9b4547358dfb55a11 +#: ../../src/topics/file-formats.md:1 ac906f26116c45d882e1afa42ae38e34 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 -#: e024bcb70e04412e90e1838426d1b69a -msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +#: ../../src/topics/file-formats.md:3 d99dab4f2f264c68b839b59b80d570e0 +msgid "" +"Tools and workflows can take " +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types as input " +"and produce them as output. We also recommend indicating the format for " +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 -#: a3db21c0b3114802a8a5b610e252ef13 -msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +#: ../../src/topics/file-formats.md:8 23ba3dd26f5543119e2c152105b58e98 +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 -#: 0f5bc8520d6a4dafa37c65343da9702a -msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +#: ../../src/topics/file-formats.md:14 81c441846fc249c58607bacf97095eb8 +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." msgstr "" -#: ../../src/topics/file-formats.md:17 -#: 5cb830da47464a8b9c3950983fa4d56f -msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +#: ../../src/topics/file-formats.md:17 c04841dbf4be4cf8a22cceca8b08bd14 +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 -#: 0535d5de416b4ea3b2f5996583deecc1 +#: ../../src/topics/file-formats.md:20 c5f6f6e4c23e4bf19dee69acb8ebed8e msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 -#: fb47f73c38cf4ec59bd3021866a631f8 +#: 20e97d58596a4a959ad76ec6128ac414 4e070ae9110d437bbf008b0c60a00cd5 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 -#: 74b28c1b09c6429b82e462e4ec61808e +#: ../../src/topics/file-formats.md:32 632e441919094610b97afc17e9c5e625 msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 -#: a2ce43b391864e8bbde16328cc19b32b -msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +#: ../../src/topics/file-formats.md:34 afd8633db1904897aa3e499354b1c376 +msgid "" +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 -#: aebee48b742c4145a600fd2daf8c75dc +#: ../../src/topics/file-formats.md:39 bb69d6963c174191bf527335c3f665b7 msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 -#: 56ee4dcfff6141d5bef80eb96559876d -msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +#: ../../src/topics/file-formats.md:45 ddb4f6f81c7d462b974e98c88dd3f558 +msgid "" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 -#: 8d3a6d83e2e54c56995893c41590b7ff +#: ../../src/topics/index.md:1 2995cd4fb85c423dba021611dac4a137 msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 -#: 5abcdebfa1cb401bb8892553be285fd3 +#: ../../src/topics/inputs.md:1 3bac021fe7614d74ae701fb3c3765b93 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 -#: d3a55f71dc244026a97902de9ed819ea +#: ../../src/topics/inputs.md:3 8bb3ee0cd0fc4d85ba007431fc541973 msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 -#: 96671c56523c4ea9992fb5dfcfa6490e -msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +#: ../../src/topics/inputs.md:5 17365707f58242369dd6aa73fc8d7242 +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 -#: bcc6246742cb46bfb185e415c4a3431a -msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +#: ../../src/topics/inputs.md:9 521cb5dead5d4e9ab5ff037fb4b683cb +msgid "" +"Available primitive types are *string*, *boolean*, *int*, *long*, " +"*float*, *double*, and *null*; complex types are *array* and *record*; in" +" addition there are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 -#: 86dce36de687449c88fb5eb9d64eb045 -msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +#: ../../src/topics/inputs.md:13 fbdf2c1bed3e41d7a41ec6b14d134a98 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 -#: cd9cea15f57b492ba4098237cd7c5bed +#: ../../src/topics/inputs.md:16 008f79cdf0074c73948bf50deb0a8a47 msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 -#: 8bdb875b63104f699efe28ea0abb1e3d +#: ../../src/topics/inputs.md:18 94cd3f10e94f4735bd3ae7dc168e5deb msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 -#: c6a0151a68494c0cb0176781e65e252e +#: ../../src/topics/inputs.md:24 b339be370e8742b69400c8040ad7d15b msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 -#: dc5e6b5e01d64226bd5dbbf3175fe010 +#: ../../src/topics/inputs.md:26 78974fb2475947ccb8b8c55e34df5fa6 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 -#: 36ab1d9edafc4831bb1bca5f123b04b0 -msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +#: ../../src/topics/inputs.md:33 9cc4a60d01f945aa9b4c43afcf20098b +msgid "" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in an input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 -#: 7dc630ea86464b1dba3a4e5079260b3b -msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +#: ../../src/topics/inputs.md:40 5ac6da11d56446de97c251a37d997671 +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 -#: ae37901a8dbe48a59e27ab4e2e6e2d30 -msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +#: ../../src/topics/inputs.md:44 6a3edb0d259d4d7c900dd9811f978d4e +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 -#: 651e032007ea4a119d20c820bb61f86b -msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +#: ../../src/topics/inputs.md:47 f1d76be7ba0b48f4b605581d0a9a5c72 +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." msgstr "" -#: ../../src/topics/inputs.md:53 -#: 0b056dde9e87428996e47870b12119da -msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +#: ../../src/topics/inputs.md:53 8cabfa0cbcfd4a5aa30d1aabd412136d +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 -#: 628124a1670b4b058bb0fb6e495a099c -msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +#: ../../src/topics/inputs.md:64 5c78d7824ef34636ae2ed68d524d79e8 +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 -#: 10ca6321ce3e4b08ab6a5bb380b19c11 -msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +#: ../../src/topics/inputs.md:70 5bdf77c45346445d8f93353c1e73f768 +msgid "" +"The field " +"[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)" +" is optional and indicates whether and how the input parameter should " +"appear on the tool's command line. If `inputBinding` is missing, the " +"parameter does not appear on the command line. Let's look at each " +"example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 -#: ec2adb3912bc46e28891229e9e0d9a1c -msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +#: ../../src/topics/inputs.md:83 d783fe52e86f4feda33ea0eecb622603 +msgid "" +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 -#: a519be60726a44af9941fdce04735353 -msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +#: ../../src/topics/inputs.md:95 f99fb9a6d0374ef78503815d4db9006d +msgid "" +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 -#: cb8fc8c4c79e467eac5fab4ca685201e -msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +#: ../../src/topics/inputs.md:109 b106eed01c1744a792368f91f547e553 +msgid "" +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 -#: a26cc105716f47cb807174c9003153b0 -msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +#: ../../src/topics/inputs.md:124 1c70336741a842a5b16b687642d1d9b4 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." msgstr "" -#: ../../src/topics/inputs.md:131 -#: cc159dd5fe5748caac838862f5b8c4d1 -msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +#: ../../src/topics/inputs.md:131 9294c07c672b414f9c3895ed70b9b4ee +msgid "" +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 -#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 -msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +#: ../../src/topics/inputs.md:134 a07137c36e63495f836c483fd472904f +msgid "" +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 -#: 6812698e9ad84d3385de5e88e9dde0b3 -msgid "The `baseCommand` field will always appear in the final command line before the parameters." +#: ../../src/topics/inputs.md:142 7513adabd3ae4701b17f578ac9f321d7 +msgid "" +"The `baseCommand` field will always appear in the final command line " +"before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 -#: 9654e65b1c0642dbb5d4f34edb211989 +#: ../../src/topics/inputs.md:146 c3c82d25a75941b0b50a4a6bb826568f msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 -#: d1f02be278754267893dfce5a940997d -msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +#: ../../src/topics/inputs.md:148 b11a5c7a13b345939e4ae15e1e2c0786 +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." msgstr "" -#: ../../src/topics/inputs.md:154 -#: 01f30e38dfdd452dba3a996073936e16 +#: ../../src/topics/inputs.md:154 aa00bcfc6c0f4085ae52621a2f4ae8d9 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 -#: 787d4bfb093c4ad287b902084706b751 +#: ../../src/topics/inputs.md:160 e730b2b9bace4427bdd045556963634f msgid "`array-inputs-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:166 -#: ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 -#: 588f0f7f967f4d69af27c9729d6d3119 -#: 02adef8ee8204842b5b4a0408f3bac33 -#: 9db68837918a4a349f32f15f12697a1d -msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:86 +#: ../../src/topics/outputs.md:109 015a0f00c2b245e2b0e87735926da736 +#: 390384208d7b4771888f164b587c7b9a edb3ae59c48945f29c3086b16a5265d3 +msgid "" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 -#: 75d59e395c66416cae9b352db5081516 -msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +#: ../../src/topics/inputs.md:178 13e59751d43b49f0ac366538a14f9c84 +msgid "" +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 -#: 874c6f19abbf45d7ab7d30a378c4048d -msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +#: ../../src/topics/inputs.md:185 bb31c6784ea843ec88f185523cfa25df +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 -#: 5d7d7a28cc5d4862803032aec78174d9 +#: ../../src/topics/inputs.md:191 53817379078548b2aeb6195cae9cbab7 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 -#: dea0d4b681f94e73b13965dcfe75cf7d -msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +#: ../../src/topics/inputs.md:193 e163c0cfe9694a85b2e42682f42970a5 +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 -#: ddf598abf4f34aca9fffa045860fbf96 +#: ../../src/topics/inputs.md:198 84e1ab25511c49d1baabb1f80f247b49 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 -#: d52a8089920e45bd89d582533b50e3a1 +#: ../../src/topics/inputs.md:204 3d5dfc8ee47b458db638a9eed84b4938 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 -#: 750474486a84482292eeba45f118287f -msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +#: ../../src/topics/inputs.md:215 ecfb1d911a84400ba3db12fd0adf9279 +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 -#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: ../../src/topics/inputs.md:217 24ba804374b4471d8e925d80670f9dff msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 -#: 1eb0e39bb6d04b8cab300f44a79f3add -msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +#: ../../src/topics/inputs.md:233 436707d9c7634732ad1e60d8294bd4ba +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 -#: bc21ee10bff843689cc98ac6630edcea +#: ../../src/topics/inputs.md:236 01b168c5faf94ead8d836dfe39e4c592 msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 -#: 4b2ab812f62c4f949dd25c8527f2411c -msgid "In the third example, only `itemD` is provided, so it appears on the command line." +#: ../../src/topics/inputs.md:252 e6d81d6549984689bae4533c6d01bd5b +msgid "" +"In the third example, only `itemD` is provided, so it appears on the " +"command line." msgstr "" -#: ../../src/topics/inputs.md:255 -#: b771302d1bec4050a9417b080eef76c9 +#: ../../src/topics/inputs.md:255 ffddeeda8f04408ba73f7a59a4618da5 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 -#: 2c3b884cb1c54521900cc90782e8a58d -msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +#: ../../src/topics/inputs.md:257 cf22f21ec44c483986979316544a7c3b +msgid "" +"If you use exclusive input parameters and reference them in expressions, " +"you need to be aware that the `inputs` JavaScript object will contain one" +" of the possible, mutually-exclusive input values. Because the types of " +"these exclusive values may differ, you may need to check which type is in" +" use when you reference the properties of the `input` object." msgstr "" -#: ../../src/topics/inputs.md:262 -#: a1073b6306044dffb414319ae01f68bb -msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +#: ../../src/topics/inputs.md:263 0fecb128b19b44d796b6c1b6de4f7166 +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." msgstr "" -#: ../../src/topics/inputs.md:265 -#: 4a31c733092142b1af834eab1747c224 +#: ../../src/topics/inputs.md:266 7f1941698a6046e9b9e8a53736af949a msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 -#: 9a1d92334685449386dfa3b3a899ed48 -msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +#: ../../src/topics/inputs.md:272 60b585142f06489d9f48090b664b6d32 +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as `fasta` (one of the possible values of the" +" enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:281 11fdeb057d674f118830f431ff019c15 +msgid "" +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to `null`, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your " +"workflow." msgstr "" -#: ../../src/topics/inputs.md:280 -#: fb623af4c480411b8fde28d01c981411 -msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +#: ../../src/topics/inputs.md:290 8594cca9d93b4280b6cfee64c8a7c578 +msgid "" +"To correct it, you should explicitly handle the possibility of a `null` " +"value. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value `\"auto\"` if " +"none was provided in the command line or job input file." msgstr "" -#: ../../src/topics/inputs.md:289 -#: e98e165f6bba40809c90473d72f9d592 -msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +#: ../../src/topics/inputs.md:295 b5055c77f85e43609fe3e9b9839778e3 +msgid "" +"Here, the boolean “or” operator `||` in JavaScript is used for its " +"_short-circuiting_ property. If `inputs.file_format` is “true” in a " +"boolean context (e.g. a valid non-empty string from the enum), the " +"evaluation of the expression stops at the first operand of `||`; it " +"“short-circuits”. If however `inputs.file_format` is `null`, the whole " +"expression’s value becomes that of the second operand, which is why a " +"reasonable default can be provided there." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: 723c2232310c4276aeac2bd6728d2912 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 -msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +#: 4d81aac1830045229e5c60c7959074d8 +msgid "" +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b -msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +#: 368f8993ae9d401488081d74ae5acd49 +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: c80f2b180ca74afb8a1fc18f8686304b msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: 37b07ea9b7124842b8ba3040f70308e9 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 -msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +#: 1cd5989ade6741aabe625c13bed3c8ed +msgid "" +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: ae7369ba14404d23b72d1ef30dcd4153 msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 -#: 8acf361cf77c4d45ba3f2e344146259f +#: ../../src/topics/operations.md:1 a79974b2f4534fcd8c7a04401e8a5556 msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 -#: 83d3b9a0ed3148fda9ce72cd108cb9e1 -msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +#: ../../src/topics/operations.md:3 b6507c8e1625476b97708423acb4fd0e +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." msgstr "" -#: ../../src/topics/operations.md:7 -#: 5565c1b2d8a349169a305a9b26b4574d -msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +#: ../../src/topics/operations.md:7 047b09455db64524a71c47ab5192039f +msgid "" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 -#: 49cf614893d8438299b3bca384eb40cf +#: ../../src/topics/operations.md:10 e9b2b97f3059460b867577a49934a338 msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 -#: 88160cef4cfa4add9020aa89511a5749 -msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +#: ../../src/topics/operations.md:16 d21e9444182d4e27bae934db4573ae99 +msgid "" +"The `uppercase` step of the workflow is an operation. It can appear where" +" a command line tool or an expression is expected. You can also plot it " +"with the CWL Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 -#: 2f73a786b5d94dc0b23ed0cdd185afc8 -msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +#: ../../src/topics/operations.md:24 61e4ae6ed18e41708270eb358cd55277 +msgid "" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx `{graphviz}` directive " +"(this user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 -#: 730ba1434a1445ae847ec6153b6a3b72 -msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +#: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd +msgid "" +"The operation file will fail to run with `cwltool` because `cwltool` " +"lacks the necessary information to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 -#: 98d9b8d867594543890af99e77e24edb +#: ../../src/topics/operations.md:59 e184470550e645f6b9ce658af7e65ecf msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 -#: a25d0b1e13324b40a6b8fcd227948c4f -msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +#: ../../src/topics/operations.md:67 3b90445d3428444cafd7d5c0e5884980 +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 -#: da077da5eb8a4ffebfde041fc16300de +#: ../../src/topics/outputs.md:1 35e7bad6fdc04bcf9bbfbb2d8d42cfa5 msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 -#: 1b3016f0462f42deb42ddaa33f28bf3d +#: ../../src/topics/outputs.md:3 6d912d40359c4d33a4f08abca83c00be msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 -#: d661df070e3040869da412d07a71f716 -msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +#: ../../src/topics/outputs.md:5 a6bd3f9e23de488394958fe7b59a61e0 +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 -#: a11585474d3849cca5467512ed964743 -msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +#: ../../src/topics/outputs.md:10 a229d8d983344e51a231edb5f667d84b +msgid "" +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or the result of examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 -#: 2682f9ca8e604a0c9986f7746fdec960 -msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +#: ../../src/topics/outputs.md:16 9845e517f7d848e5b59a97880ca6999f +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 -#: 7e3fa7baf0f549ec89457e7004ac9545 +#: ../../src/topics/outputs.md:19 0bf1ad2c43174e57a3ba8dd86f7c96b2 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 -#: 22447a560f6f4317bf67bd7c4336126c -msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +#: ../../src/topics/outputs.md:21 553d535b023e4d69a888fe5b24bb8c5b +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string, we can use an" +" _array of strings_ as the value of `baseCommand`. The first element of " +"the array is the command to run, and any subsequent elements are " +"mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 -#: f1ee2e00b0cc4112b51c9df3a919b73f +#: ../../src/topics/outputs.md:28 9b65071222c94951bed12ac53e964ee3 msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 -#: ad8e1acb251246d2a47c39b20d4e483a +#: ../../src/topics/outputs.md:34 759ab0847b97479fb4a15e4b7d4e6565 msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 -#: dc200c6960ae4476a772645d021f14b8 +#: ../../src/topics/outputs.md:40 f9752ec303ab419c8db8adef3fa2466f msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 -#: 52703d6b7f914097934bfad13663abeb -msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +#: ../../src/topics/outputs.md:47 4f96576528684f28a72b805f777769e6 +msgid "" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 -#: 5e1c79df657d4a6e84e055dd6b300a5d -msgid "The field `outputBinding` describes how to set the value of each output parameter." +#: ../../src/topics/outputs.md:53 707803bec0cb42919905c7c321bd9d30 +msgid "" +"The field " +"[`outputBinding`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding)" +" describes how to set the value of each output parameter." msgstr "" -#: ../../src/topics/outputs.md:62 -#: 329d2809dfae4f90bc638f5f03a47ee3 -msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +#: ../../src/topics/outputs.md:64 cbaec50871e04718883c8c91ff475d20 +msgid "" +"The " +"[`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) " +"field consists of the pattern to match file names in the output " +"directory. This can simply be the file's exact name. But if you don't " +"know the name of the file in advance, you can use a wildcard pattern like" +" `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 -#: 96df2d45e42441d49ce193ccbfab78a3 +#: ../../src/topics/outputs.md:69 8a6e9173198241429effd911c3a7c4d7 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 -#: c6bcf7c6a8774dd6be41cc775848c3b8 -msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +#: ../../src/topics/outputs.md:71 a7c4fdaeda3e411fbeb802c5fa529ce9 +msgid "" +"To capture a tool's standard output stream, add the " +"[`stdout`](https://w3id.org/cwl/CommandLineTool.html#stdout) field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 -#: 9d86c03ab44841c785b924cc44727e31 +#: ../../src/topics/outputs.md:75 cf2ef8dc7fda49308c09efe4f4ef5d7b msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 -#: 2fb58c2feaa84970bb5274c49f4b5b64 +#: ../../src/topics/outputs.md:93 cbe236266dd148aaa96355e490a87cbe msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 -#: 9647019d8c37466886e7aab6f176634d -msgid "You can also capture multiple output files into an array of files using `glob`." +#: ../../src/topics/outputs.md:95 77f86a7b94924a08b6ea2660218fe3c5 +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 -#: b9eaf21f5e014eefaae301c47dafd144 +#: ../../src/topics/outputs.md:97 b34e30481fbd489d95fb7f8d5b5ab50c msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 -#: cffff6c43b4945daa3b2a49763bc50ae +#: ../../src/topics/outputs.md:103 3aab0e0c9a78430f9caaa29a93303b56 msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 -#: cc067051f22f433bbece08f60933e002 -msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +#: ../../src/topics/outputs.md:116 9a14271c3180429988aaa14869f783a0 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 -#: a190a6440ec34898990cdac05d809f22 +#: ../../src/topics/parameter-references.md:1 c8a6ea340e6a43398e97b68e03a8bb3b msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 -#: dbfe2c1123144316aa026374b0f353d3 -msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../src/topics/parameter-references.md:13 -#: 280f1a07d0ae41d7a4674504f832fcf0 +#: ../../src/topics/parameter-references.md:3 f5c0592ca28c46c2a89943f4f6f69a27 +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 50db8add9b1942d986e581b8d21c2ee4 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 -#: 5c64d938862747cb9fb52515a656ce27 +#: ../../src/topics/parameter-references.md:19 d01ad5fd9fea462cab0d4d776824b4e1 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 -#: 074cf5d912854d8c864607cc24b15302 -msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +#: ../../src/topics/parameter-references.md:25 9b1e2f1a23ea4fe2af97ef5108f33376 +msgid "" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 -#: 0290af3e3cbb4b32b0450c8771f3bf95 -msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +#: ../../src/topics/parameter-references.md:36 06926a516ae6432d96e3eaa62202cd86 +msgid "" +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 -#: b54240bb94f746bba7511633aa969db0 -msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +#: ../../src/topics/parameter-references.md:47 384fe8188f414eafbbb8d6b81bdfd779 +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 -#: 8b70a072aa87414c88e89a3e19af0a51 -msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +#: ../../src/topics/parameter-references.md:51 56ead1c8d45c43bdbcbc6f7cbb8e1e92 +msgid "" +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 -#: eea20f89c45f424a888178df53713b28 -msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +#: ../../src/topics/parameter-references.md:54 56bca89e314c4223b33d7fe63c9b771d +msgid "" +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 -#: cb4ea13f5db84c0da43df3f7f2478d78 +#: ../../src/topics/parameter-references.md:59 1c1ab240c4114572bb4e42955baad361 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 -#: 6d3fb423e6c4434697cd113fb27e28ad +#: ../../src/topics/parameter-references.md:61 055d3268859c46c4b7db5005608bae05 msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 -#: 7647e0229a924f988cf02b7812a55c06 -msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +#: ../../src/topics/parameter-references.md:63 2ed66835bd9044adbfdd0b5097787f22 +msgid "" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 -#: 9d663249666045618a0d3acddb85a9a9 -msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +#: ../../src/topics/parameter-references.md:69 f592619e4b2c497e80cd75da0548cf07 +msgid "" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 -#: 5fed4984f6784347b4cbe0630b1dd2c2 -msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +#: ../../src/topics/parameter-references.md:72 81ea71a35020421187dc18ddd151c62f +msgid "" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 -#: dbf6153cd02542a6a01c172803122b7f -msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +#: ../../src/topics/parameter-references.md:74 ea0117748adc4324901024f21eed04ac +msgid "" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 -#: b6250cf6fa8a4a0c94b33302e0decca5 -msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +#: ../../src/topics/parameter-references.md:77 3a30e73176cf4e4eb9f26770a176b9c9 +msgid "" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 -#: fa6ca3bbc6784380a03a950a6f49a180 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +#: ../../src/topics/parameter-references.md:81 551c199c9a6344fca9bfacfb69fc4e53 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 -#: b92b516e537a4773ad67b4af586e7a25 -msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/topics/parameter-references.md:85 7008a1ff1af54fda827637e787e5c7dd +msgid "" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 -#: 467a701228504d06b971b79a59c69064 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +#: ../../src/topics/parameter-references.md:89 45743e1b261c4195856de0c2e30ea72e +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 -#: 2634f989eb304009a8568d70ed42786c -msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +#: ../../src/topics/parameter-references.md:92 0ae32d1db5f9452bbfcbbc4719b0b9f1 +msgid "" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 -msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +#: 7e1907ff15c74f488187531de336eccf +msgid "" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: 678874668fed4f4d80a1b0990e183e2f msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 -msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +#: e2882880886046ac88ae1c0d414366d1 +msgid "" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: 05324169d8ae48d4a1abe3a0ac07c891 msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: 1f5b72d7ec82442ba29baa14a03f061b msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb -msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +#: e708866921ea49d69d3c2a32d63ea468 +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)" +" field in the `hints` section. This may also help to avoid confusion " +"about which version of a tool the description was written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 -msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +#: 6f722d6fd54f485fa964076c8d08938b +msgid "" +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 -msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +#: 5c1236ec57c64079bfb7c779524b12ad +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 -msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 -#: b85eb83e05e845d7a179f1b1d74db444 +#: 1a8b8aadf1c64e87b8b670e288bc14bc +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)," +" search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 d10c792550e8498c8ee384d3093da306 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 -#: 35f97d37492b4c7ca3ad6cfc1e6fa366 -msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +#: ../../src/topics/staging-input-files.md:3 ac2ef1fced5f4044861761a11c35e78a +msgid "" +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use " +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)" +" to stage input files into the output directory. In this example, we use " +"a JavaScript expression to extract the base name of the input file from " +"its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 -#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: ../../src/topics/staging-input-files.md:9 d8ca16f5321e486ebe8ea9f9752b3737 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 -#: 0f7508ce59754a7eb230dea6042244c6 +#: ../../src/topics/troubleshooting.md:1 aa3eddcaa0684f86ba67aafcd57872e7 msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 -#: fbe0c65b444441f785d0054176d036a6 -msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +#: ../../src/topics/troubleshooting.md:3 3207f476afa04158bd26db39a16a2df5 +msgid "" +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 -#: 1b6b7a75cc754775bf9dd80c0941e8da +#: ../../src/topics/troubleshooting.md:6 1d47f4ce04554cabb1ccf40a13ee42ec msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 -#: 9a710602e00c4934ae3a3b471aa68458 -msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +#: ../../src/topics/troubleshooting.md:8 0c25602a83e441b48b536eb49568f2b6 +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 -#: 21b5be7270a14f0987240c81d1ec879b -msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +#: ../../src/topics/troubleshooting.md:14 36ec60b80c714357a4274217274136ff +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 -#: 0490b1fab86749e49b473949c52bbe8b +#: ../../src/topics/troubleshooting.md:20 6f34038054ac4f4fa0b0ad9cbc3ecdc7 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 -#: cfe9d8241fe84bd5b74042a5625d933f -msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +#: ../../src/topics/troubleshooting.md:27 b777877c88024c9fb06a6614029ef8d6 +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 -#: 764d933cc4da446abd8dd8f913f05dac -msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +#: ../../src/topics/troubleshooting.md:35 8654b7f2f4464d13be4b47729e1f07e5 +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 -#: c93efc6d4e004859981ee7f5fa28ed03 -msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +#: ../../src/topics/troubleshooting.md:44 04e80f7ce14d4d73bc5d290dcf01bcdb +msgid "" +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 -#: 546601da44cb49bd9611b1c85807fd90 -msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +#: ../../src/topics/troubleshooting.md:48 719917cb0fd849f5a328671df8726189 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 -#: 7e0bf00f8ce542b9b009cdcf1945a9e5 -msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +#: ../../src/topics/troubleshooting.md:59 2a9dbb3ad7564f5aa103349c45ee7925 +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 -#: eff5f28ca83c458a9b07faf7a81f7e91 +#: ../../src/topics/using-containers.md:1 7439fe097aa4459ba1e4c0e28fc59b9a msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 -#: 2e634f3737d04d279ae78ceee4b0a664 +#: ../../src/topics/using-containers.md:3 eff5c6ac1cad44f9862585daf0a91298 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 -#: e07f33d01b804663a25ffb08aad74821 -msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 -#: 7a644506619a4f08958ec7d4540cd557 -msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +#: ../../src/topics/using-containers.md:5 50d1a644bc8c49f78c453e4e0f3c07c8 +msgid "" +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 4b0f6cfc8a774c77bfbc99e568af2ece +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the " +"container." msgstr "" -#: ../../src/topics/using-containers.md:18 -#: b5195b7d8eaa419fb2b90cb33a57783a -msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +#: ../../src/topics/using-containers.md:18 27c02a5d479a420eab7d14888d9fb288 +msgid "" +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 -#: 7921a837ee744c5aa9a5bda04b0c8db1 +#: ../../src/topics/using-containers.md:21 1a62a93ab20b4f2ca1e13ded3a767dc5 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 -#: 387e9bc9381a4450af54aff77e4df6a2 +#: ../../src/topics/using-containers.md:27 ccc2874840c3476bb714ddf4bdbf0f3e msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 -#: 2713594c937d4c528fc8d04d9e9819ed -msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 -#: cf94c1424fc2413c85647fd1ee73d951 -msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +#: ../../src/topics/using-containers.md:33 d766b66de4714a5da0cd87ed886cc32f +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that " +"is really new is the " +"[`dockerRequirement`](https://w3id.org/cwl/CommandLineTool.html#DockerRequirement)" +" section." msgstr "" -#: ../../src/topics/using-containers.md:52 -#: dc0452107c604e29bdf32bb289fe5db8 -msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +#: ../../src/topics/using-containers.md:44 1f02618ab6254459ae71f72844e3cc18 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 54cade4978ec463bbb5c0d8c08e27adb +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 -#: 1a5596243cec4c948d9b6bf0bb12fad0 +#: ../../src/topics/using-containers.md:55 6541d0cd9f6c4c43b8601715cc35e585 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 -#: 483181f498fc4d968b5fe6ef427709f7 -msgid "Notice the CWL runner has constructed a Docker command line to run the script." +#: ../../src/topics/using-containers.md:69 6abf220b7fa4479394ed33447cdd070e +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." msgstr "" -#: ../../src/topics/using-containers.md:72 -#: 7487485d6aa4458089a4b4bdf107ea64 -msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +#: ../../src/topics/using-containers.md:72 d2dd89a5edde4f2eab4c2baf0cc78745 +msgid "" +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 -#: 7394e7690f934043af617436b40845f0 +#: ../../src/topics/workflows.md:1 06281a10592d42509566c8fc51f8d4da msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 -#: b9ae9e9a896048caad7e6c38a5bc1bd1 -msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +#: ../../src/topics/workflows.md:3 325a656f9b8e4c1fa6f699cd8c447d00 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 -#: f228fb7953ea48ed99d89880205f4620 +#: ../../src/topics/workflows.md:13 b92275181c9e480da64e660b7aca0745 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 -#: 5870ac44e4c24b8daf5f06c49f95ce04 -msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +#: ../../src/topics/workflows.md:41 be2540315f854b8e9a1d257bcabd78db +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier " +"examples." msgstr "" -#: ../../src/topics/workflows.md:51 -#: a913c76d06164fa18718a8a6a7dcf0d6 +#: ../../src/topics/workflows.md:51 3be900594bb743399854b95baa9ae2f9 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 -#: 93188ed43ee949cc98b3ea679ce14feb -msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +#: ../../src/topics/workflows.md:81 5133c4e062bc4e479ce1dc8abbb08107 +msgid "" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 -#: 36618126a4df4326b236ebe2ea42cffa +#: ../../src/topics/workflows.md:91 83bc2796889f4dccb713764ac1b3c3ad msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 -#: 1cc17ad26e9c474b895ba5cd20c8b66a -msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +#: ../../src/topics/workflows.md:150 5a9a1dd6ed1f4ca6803f1d235c4fd392 +msgid "" +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 -#: 24aca0bea4d94e3593b844cf0586cffe -msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +#: ../../src/topics/workflows.md:160 277ed30d4b3a4156a4523e8d10e6ce60 +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 -#: 46cc4859856e4367a9e5e68eecd48b73 +#: ../../src/topics/workflows.md:165 82818ab17aa4403eb982fd81a14a5865 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 -#: 9c56528acd5f49deb139e034dfbfac7c -msgid "This workflow extracts a java source file from a tar file and then compiles it." +#: ../../src/topics/workflows.md:167 3d8b98e8d03548699fadb22198de9b20 +msgid "" +"This workflow extracts a java source file from a tar file and then " +"compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 -#: 55ab007d472f43388e4c77aae8f165e7 +#: ../../src/topics/workflows.md:170 c61097c695424f7195e8205a23b6ecff msgid "`1st-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:179 -#: ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa -#: 307b6618a92948fca4203ccb497c77e6 +#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 +#: 6660c48f51d94d4fbcc05656e154059e bd2bab6c11614fa983ca8dab1408e1d8 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 -#: a2dd833fdca4443181648e41051a5232 -msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" -msgstr "" - -#: ../../src/topics/workflows.md:183 -#: 7e40cc9f9e1341c195e843c009575b94 -msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +#: ../../src/topics/workflows.md:180 f0831481a43548039fbc4fd17555af57 +msgid "" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 5ff059fc8ae6471c8ea86dab7e5a93f5 +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" msgstr "" -#: ../../src/topics/workflows.md:185 -#: 26c51dcb76364ed780376aecb7cbacda +#: ../../src/topics/workflows.md:185 822e5d0a097b4109960d621a72a3c009 msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 -#: 6fcf8ad3d1bd49afa4a105622437bd59 -msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +#: ../../src/topics/workflows.md:191 4a4db7da861547639524083bf35ccfc0 +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 -#: 71cb81fa4511495b80422244849979e4 +#: ../../src/topics/workflows.md:205 ed16b30eaa4747f79b6dd10a19188d8c msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 -#: def35d6021394def80a53ae49a2cdbde -msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +#: ../../src/topics/workflows.md:212 6428bd7bd3be4393bfe5675f8e45ff94 +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a " +"workflow." msgstr "" -#: ../../src/topics/workflows.md:221 -#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 -msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +#: ../../src/topics/workflows.md:221 d6abec8805f649fca668292412263f78 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 -#: c84d4450bc6a475dbf34e0b22cea9130 -msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +#: ../../src/topics/workflows.md:233 22bf3e4910ef4f86a2e8f6d5a6cf0d42 +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 -#: cca9665f6daa44b49233baf34ab9fcc7 -msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +#: ../../src/topics/workflows.md:248 e0429688fce445da8083e69323e5b020 +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 -#: 547edbf5fa424b8286cc21674ff159b0 -msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +#: ../../src/topics/workflows.md:256 980f5eada57c4fadbb783838ded1fa0b +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 -#: 7ca248888b9d484cb544cd76ba538662 -msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +#: ../../src/topics/workflows.md:261 3532e165842f4ebb8db0c78208071555 +msgid "" +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 -#: ae6b240718104380b08db5552d7355ea -msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +#: ../../src/topics/workflows.md:267 04a4db2f3da94ce29e7999039ee13fde +msgid "" +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 -#: e5a8b7f84be64020b191099f3fad30ed -msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +#: ../../src/topics/workflows.md:278 2651ee113a3d4b79b138854ebe729f48 +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 -#: f0b04849253c4693904512ddd7f9ce84 +#: ../../src/topics/workflows.md:285 177040bf9c0045f2878f42bcdd8cbd2d msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 -#: 12a06d8358534102b202965d4258c18e -msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +#: ../../src/topics/workflows.md:287 e8adc2f7c5ac4464b0711712617b8bbe +msgid "" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 -#: 1658cac0de1b47e9b60f6d4a4ad9bb19 -msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +#: ../../src/topics/workflows.md:297 44d281d99cd944478db98446a984c001 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 -#: 49ed137fe996452a8534c68d100db941 +#: ../../src/topics/workflows.md:300 d7b60ce81ea741ffa08f2c2d9d7cca69 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 -#: b7f93705e5b8416696be01850072e8c0 -msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 -#: e87045829b344089ab59dc27063ddd7a -msgid "\"Visualization \"Visualization" +#: ../../src/topics/workflows.md:309 a5b7a1ab16e34bda8744ffadacdda3e8 +msgid "" +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:322 -#: 42ef2f145b824d69b63abc1da175c216 -msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +#: ../../src/topics/workflows.md:314 8654f2d86b644609aaa5b9b73db30bda +msgid "" +" \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 7ce847ab54224452b6425de2a55ec893 +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 -#: c61cedf543664d388183e04b3939cc39 -msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +#: ../../src/topics/workflows.md:336 d621821d2c1b403cb7415b381dd883f6 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 -#: 9e39e3f1501c4fcaab3e8962e090f6be -msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +#: ../../src/topics/workflows.md:341 358c612f175241f7bf148a04d75e00c9 +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 -#: 03e2f767c4da461982fc3c0f3ba94762 -msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +#: ../../src/topics/workflows.md:347 c6297c120e004ae8b52d5b519fbc04d2 +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 -#: 3bea5822b8694e2aa32c446e1c54a045 -msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +#: ../../src/topics/workflows.md:366 66f76677f4ce42baa8a8813410ea5aee +msgid "" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 -#: 426023bd6e3a471cbb30dbda3d6f9e57 -msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +#: ../../src/topics/workflows.md:383 a8ccb9f9ab4448e087ea8448d620d33c +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 -#: 0d498cd4caf54c15891ca1afe58e2727 -msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +#: ../../src/topics/workflows.md:389 afe43b9e92e949a589f493293eff2903 +msgid "" +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." msgstr "" -#: ../../src/topics/workflows.md:394 -#: b2d75045e02741b4850f5ff1243f7858 -msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +#: ../../src/topics/workflows.md:394 239eef3a740d42a69208a8f4e716d2b3 +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 -#: cfa765264a27411ab914de569aa3dac4 +#: ../../src/topics/workflows.md:398 96d1ca78cc324f40b61c4b7330447db2 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 -#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 -msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +#: ../../src/topics/workflows.md:400 eab4437bf9994b649954221375e3dd6d +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 -#: 5fa79c62049a447c8328ebf9db54ebf4 -msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +#: ../../src/topics/workflows.md:411 c245ba0ae2074fa388ad6c35695033c8 +msgid "" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 -#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: ../../src/topics/workflows.md:415 83537938ce1244709f9b72269b048d63 msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 -#: 3a67d77a2e7b4c0bb61cc3585ceae942 -msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +#: ../../src/topics/workflows.md:421 4f507925766e48ae8f713d56051a5e29 +msgid "" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 -#: f1cb55fc59824cc18a95fd6dcb32cf4c -msgid "First of all, notice that the main workflow level input here requires an array of strings." +#: ../../src/topics/workflows.md:429 ccbbba3189404241a44736c970249b84 +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 -#: d947c54933d64aad90df392a1cedd63f -msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +#: ../../src/topics/workflows.md:441 31eff13bb8334fc7b6d48ef6c5b1ce33 +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 -#: 651d35997332404186aa6d5711da4a3d -msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +#: ../../src/topics/workflows.md:445 0d5cf8b82dbd47f2abd1ed16b9b3eb61 +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 -#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: ../../src/topics/workflows.md:450 38b7042a270043ba82c11cf2e758f0c8 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 -#: 842b926ae34542cb9023021f137b08be +#: ../../src/topics/workflows.md:452 b3fc75c262fe4a3a8e8bfba1abb07b3d msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 -#: b662c1a5a4424c8d8350a806356acc61 -msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +#: ../../src/topics/workflows.md:458 f9fa7046c89c417db51dc7c8a026fd5d +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 -#: 04d6babfd87343d7a5f13867ea02b65f -msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +#: ../../src/topics/workflows.md:466 b6a33410ee9a45d7bf7b2ba56f786f8f +msgid "" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 -#: 2eaacf1a90204a2b9bd621344560f2a1 -msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +#: ../../src/topics/workflows.md:469 99b5c8a845ab4beb8524a69c051e2d42 +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 -#: 242993d42b164ee5abe7ca10d45856de +#: ../../src/topics/workflows.md:472 97bf58937d3f4e98af702e3c1a418992 msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 -#: 4a94e5f7e1bc4d628702140e4e51d6d3 -msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +#: ../../src/topics/workflows.md:480 173bd28708834f11a2a1366b579b7ad7 +msgid "" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 -#: e61d93b848184c8e8e573928427b4d0a +#: ../../src/topics/workflows.md:483 4afccfe982ff4be2be96cbe5889e5014 msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 -#: e3a7182f00f440b8b5461da91194a64b -msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +#: ../../src/topics/workflows.md:489 63595d35dded4911aab0be3a165eec0c +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" msgstr "" -#: ../../src/topics/workflows.md:491 -#: 99fa96caacaa45cb97aded9a24fcac6d +#: ../../src/topics/workflows.md:491 a7f96ec6e4f24c62ac0f5b6edcc9734b msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 -#: b5338f39e8c74ff28e139da68089a742 -msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 -#: f6d92156d67c4a339bcfd194cff897df -msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +#: ../../src/topics/workflows.md:497 122452b7d7114c3fa53cbea286703023 +msgid "" +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 85dd63daf04546b78bdcb68c1d985fa9 +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 -#: 1c9e386922324ec8a59306572c19fb8b +#: ../../src/topics/workflows.md:513 fac138ba275745898b763a7d719a8235 msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 -#: d80ab383eec9402faba997b548fe42eb -msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +#: ../../src/topics/workflows.md:519 508ef2240879445594b0f262ed11a01d +msgid "" +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 -#: f7d2827d97db4bf4ab84b5d6621c3b48 +#: ../../src/topics/workflows.md:522 b0bf01dad1234a1db3c87b10953e42ef msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 -#: 49217c02f58c43ff9ec00f10da8d4e84 -msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +#: ../../src/topics/workflows.md:524 8d933ed1ec6e408589f781e3a425b869 +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 -#: 20b9f181420c401d8615c17a10027517 +#: ../../src/topics/workflows.md:527 9ac7b4f71621411da9a4ca3bc277dcb0 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 -#: 8dbd56473f8c40c0bb12a48be06117e3 -msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +#: ../../src/topics/workflows.md:566 4a4a2b2b99b44d449adb246cebce0a26 +msgid "" +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 -#: 78d7f3ede2c746d482042adef050b2c4 -msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +#: ../../src/topics/workflows.md:573 4742fe09a4264fb8be6f092519de5d72 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." msgstr "" -#: ../../src/topics/workflows.md:587 -#: cbbf93c70fe04ba7932ba25758ddc611 -msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +#: ../../src/topics/workflows.md:587 b33ecd2b8af042feb08687e32d4b6bbf +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 -#: cfa1c1fde4454df283f87cc54a9c59ec -msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +#: ../../src/topics/workflows.md:607 7cd80b31a94543358ece7a2d413adce9 +msgid "" +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 -#: 1a8be2950cbb475bbb2617e005f0fac9 -msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +#: ../../src/topics/workflows.md:627 9679e32f65e0482a8b083387e4a18c1f +msgid "" +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 -#: 5f09d4d897cf457d80b9a11b8c01747e +#: ../../src/topics/yaml-guide.md:1 4fa76441f95d45fab76ab7eef8d7d4d2 msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 -#: 5d83c56102e141cc978500f678dd0c1c -msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +#: ../../src/topics/yaml-guide.md:6 705765787eb84ecaae004194225924cb +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 -#: c38438fbf9a04e729ec2e3c962435289 +#: ../../src/topics/yaml-guide.md:13 cb243f6ab11f48ffb5c91945c4e0d101 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 -#: fdb9cc750cec43ee962517e637dc5fea +#: ../../src/topics/yaml-guide.md:16 cfc95d15e33a492f842649f92ced941d msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 -#: 08da9cd8056b4ddd8f5150cc85ba72ee +#: ../../src/topics/yaml-guide.md:18 f618d44d202f4c2ea6ff72a1dca2c659 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 -#: b027fc234ed943bbb00d4c6bc03c040a +#: ../../src/topics/yaml-guide.md:19 36bfa6ed40c54bd99826bedff12c759d msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 -#: b8befec0d8684638aaa616a659e0100c +#: ../../src/topics/yaml-guide.md:20 61913753eb0c4c728889b47f1110be24 msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 -#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: ../../src/topics/yaml-guide.md:21 0de824a05eea46209aafa6f9e2e8623c msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 -#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: ../../src/topics/yaml-guide.md:22 95627bc476b3415ca4d77246125137d2 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 -#: 98056c5cfd5640ad9de0679360797cc7 +#: ../../src/topics/yaml-guide.md:24 3f64a6d33d9a4c22a8a839a8def82686 msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 -#: cda73485875d4c8e9464679a20558616 -msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +#: ../../src/topics/yaml-guide.md:26 2f74f6eaa8d84dc9b4d0a166844dedbe +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 -#: 98cae24919b74c088a5d89706aec581b -msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +#: ../../src/topics/yaml-guide.md:42 514365e59d9648deb896e2068d967a64 +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 -#: b4b0940b4b5743c09637b36b964202d0 -msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +#: ../../src/topics/yaml-guide.md:51 6939eb7e783744d7bcf75ea0a7cae129 +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 -#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: ../../src/topics/yaml-guide.md:61 96e1776b09e840ebbc9b4b7e01da0e43 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 -#: 9ca3554d771d45998e88aaede525b227 -msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +#: ../../src/topics/yaml-guide.md:63 8b17f7557c3540b2b0d0beca0fe4ebc7 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 -#: 3fca839cede94cfd8e4f605c73ba699d -msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +#: ../../src/topics/yaml-guide.md:76 13da997c82c04023a4b7bb36b76e969d +msgid "" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 -#: da34c635707345b2a5e85a2fcd30bbaf +#: ../../src/topics/yaml-guide.md:79 b9fc191166a64450b64a8182adabad75 msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 -#: 3ded0f125249485c921994b6e6b93ac9 -msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:104 -#: 53ece35d309a4c8d99f1efb2122a7092 -msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +#: ../../src/topics/yaml-guide.md:81 aedf8c4f615845ad91a7947217005d6e +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:127 -#: d74321b111d84ae7a515f2f17dd39e23 +#: ../../src/topics/yaml-guide.md:104 f0f1f414f74342a89065ba5ded8668e5 +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 965405e2a45a4cbb8f227bc8ceeb05df msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 -#: 7fc0bdf2489a44f2a29e71b86f7c0055 -msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +#: ../../src/topics/yaml-guide.md:129 5aca9a90fb6149529ed717992746a2f3 +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 -#: fd64dd818ec64bb6aa9a11586a5747f6 +#: ../../src/topics/yaml-guide.md:146 d1c9e72e004b4fb4a6efb7748a15ab6f msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 -#: 8c06e542dd4144fa83388d8142552c8d +#: ../../src/topics/yaml-guide.md:167 9a3d6879404745a48cd394bf86865dbc msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 -#: 87bafb845c714b109874f6137b84462d -msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +#: ../../src/topics/yaml-guide.md:169 6a7cca0339794e679329b00d89e29d2b +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 -#: 5ab9ddf613a540a2b8228e37600cc5dc +#: ../../src/topics/yaml-guide.md:177 d8feed2d36d04fe283b9de9784d91941 msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 -#: fcd05b1ef31a4046946a2399c7fc5575 -msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +#: ../../src/topics/yaml-guide.md:184 5156ad32791048f8ace51475d7689575 +msgid "" +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 -#: f4b8fc8236044fada420def13a02813d +#: ../../src/topics/yaml-guide.md:194 ce49f80e6fc0498b8ad298fb1f0268f3 msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 -#: 859368c1f25c4a4aad57abfd046c63f5 -msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +#: ../../src/topics/yaml-guide.md:196 180d261392a644fcb8ff47d7a4a160c0 +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 -#: 2203c93f02ac4514a43508ecb98dfcc5 +#: ../../src/tutorials.md:1 d682035afebf4c128755bd4e58780dd2 msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 -#: 5d92464923c245818c070fbef102be89 -msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +#: ../../src/tutorials.md:5 d9adeab63ec54084bc41fb90f264d3ae +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to " +"the list." msgstr "" -#: ../../src/tutorials.md:7 -#: 8a5cd557dab5456bb41cdc24af73b50c +#: ../../src/tutorials.md:7 23c81edb650b4f86a60c5e0bcedeac1d msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 -#: 13d7e2e92e96432787c712cf6a595424 -msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +#: ../../src/tutorials.md:9 87ddaa1e5f57445c8f13803722aa146e +msgid "" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 -#: 0abdd85c9b964a4e89ba3d80a6c78d6f +#: ../../src/tutorials.md:11 b8ee193ba533498db6263e0f5f4ec45f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 -#: 3cbf1f69a5514fd3bee90e68b201190f +#: ../../src/tutorials.md:13 67c4b3923fce46fdab025495125c91d4 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 -#: 68c97a7065634d02956f3f5c1d4eeb9f +#: ../../src/tutorials.md:15 e640316669104239970794191b6da38b msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 -#: a67c7e0eaf4e4d27b3e5db303333a088 +#: ../../src/tutorials.md:17 efe94af44b874f9b81b245fbdee43f7f msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" + +#~ msgid "Non \"`File`\" Types Using `evalFrom`" +#~ msgstr "" + +#~ msgid "Rename an Input File" +#~ msgstr "" + +#~ msgid "Rename an Output File" +#~ msgstr "" + +#~ msgid "Referencing a Local Script" +#~ msgstr "" + +#~ msgid "" +#~ "The first method involves adding the " +#~ "folder containing your scripts to the" +#~ " `PATH` environment variable. This allows" +#~ " you to run the shell script " +#~ "directly without using `sh` or `bash`" +#~ " commands." +#~ msgstr "" + +#~ msgid "In CWL, everything must be directly stated." +#~ msgstr "" + +#~ msgid "Setting `self`-based Input Bindings for Optional Inputs" +#~ msgstr "" + +#~ msgid "Model a \"one-or-the-other\" Parameter" +#~ msgstr "" + +#~ msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +#~ msgstr "" + +#~ msgid "" +#~ "Using " +#~ "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +#~ " along with [`linkMerge: " +#~ "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#~ msgstr "" + +#~ msgid "Which means \"create a list with exactly these sources as elements\"" +#~ msgstr "" + +#~ msgid "Optional Inputs 💯" +#~ msgstr "" + +#~ msgid "Enum Inputs ⚜️" +#~ msgstr "" + +#~ msgid "Record Inputs 📀" +#~ msgstr "" + +#~ msgid "Setting Mutually Exclusive Parameters" +#~ msgstr "" + +#~ msgid "Setting Booleans" +#~ msgstr "" + +#~ msgid "Concatenating Strings in Inputs" +#~ msgstr "" + +#~ msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +#~ msgstr "" + +#~ msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +#~ msgstr "" + +#~ msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +#~ msgstr "" + +#~ msgid "Use CWL and cwltool with Singularity" +#~ msgstr "" + +#~ msgid "Debug JavaScript Expressions" +#~ msgstr "" + +#~ msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +#~ msgstr "" + +#~ msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +#~ msgstr "" + +#~ msgid "" +#~ "`InitialWorkDirRequirement` - controls staging " +#~ "files in the input directory." +#~ msgstr "" + +#~ msgid "" +#~ "The FAIR principles have laid a " +#~ "foundation for sharing and publishing " +#~ "digital assets, and in particular, data." +#~ " The FAIR principles emphasize machine " +#~ "accessibility and that all digital " +#~ "assets should be Findable, Accessible, " +#~ "Interoperable, and Reusable. Workflows encode" +#~ " the methods by which the scientific" +#~ " process is conducted and via which" +#~ " data are created. It is thus " +#~ "important that workflows support the " +#~ "creation of FAIR data and adhere " +#~ "to the FAIR principles. — [FAIR " +#~ "Computational " +#~ "Workflows](https://workflows.community/groups/fair/), Workflows" +#~ " Community Initiative." +#~ msgstr "" + +#~ msgid "" +#~ "If you are using Windows, you will" +#~ " have to install the [Windows " +#~ "Subsystem for Linux 2](https://learn.microsoft.com" +#~ "/en-us/windows/wsl/install) (WSL2). Visit the " +#~ "`cwltool` [documentation](https://github.com/common-" +#~ "workflow-language/cwltool/blob/main/README.rst#ms-windows-" +#~ "users) for details on installing WSL2." +#~ " Your operating system also needs " +#~ "internet access and a recent version " +#~ "of Python (3.6+)." +#~ msgstr "" + +#~ msgid "" +#~ "`cwltool` can be installed with `pip`." +#~ " We recommend using a virtual " +#~ "environment like `venv` or `conda`. The" +#~ " following commands will create and " +#~ "activate a Python virtual environment " +#~ "using the `venv` module, and install " +#~ "`cwltool` in that environment:" +#~ msgstr "" + +#~ msgid "Installing `cwltool` with `pip` and `venv`." +#~ msgstr "" + +#~ msgid "" +#~ "Visit the `cwltool` " +#~ "[documentation](https://github.com/common-workflow-" +#~ "language/cwltool#install) for other ways to" +#~ " install `cwltool` with `apt` and " +#~ "`conda`." +#~ msgstr "" + +#~ msgid "Cwl-runner Python Module" +#~ msgstr "" + +#~ msgid "" +#~ "The CWL community publishes a Python " +#~ "package with the name `cwlref-runner`" +#~ " that installs an alias for `cwltool`" +#~ " under the name `cwl-runner`" +#~ msgstr "" + +#~ msgid "" +#~ "The *shebang* is the two-character " +#~ "sequence `#!` at the beginning of " +#~ "a script. When the script is " +#~ "executable, the operating system will " +#~ "execute the script using the executable" +#~ " specified after the shebang. It is" +#~ " considered a good practice to use" +#~ " `/usr/bin/env ` rather than " +#~ "using a hard-coded location, since " +#~ "`/usr/bin/env ` looks for the " +#~ "`` program in the system " +#~ "`PATH`," +#~ msgstr "" + +#~ msgid "" +#~ "The usage of the `cwltool` command-" +#~ "line executable is basically `cwltool " +#~ "[OPTIONS] [INPUTS_OBJECT]`. You " +#~ "can run the `hello_world.cwl` workflow " +#~ "without specifying any option:" +#~ msgstr "" + +#~ msgid "" +#~ "For more examples of providing metadata" +#~ " within CWL descriptions, see [the " +#~ "Metadata and Authorship section of this" +#~ " User Guide](../topics/metadata-and-" +#~ "authorship.md)." +#~ msgstr "" + +#~ msgid "" +#~ "In tool descriptions, list dependencies " +#~ "using short name(s) under " +#~ "`SoftwareRequirement`." +#~ msgstr "" + +#~ msgid "" +#~ "In tool descriptions, include a list " +#~ "of version(s) of the tool that are" +#~ " known to work with this description" +#~ " under `SoftwareRequirement`." +#~ msgstr "" + +#~ msgid "" +#~ "Each `CommandLineTool` description should " +#~ "focus on a single operation only, " +#~ "even if the (sub)command is capable " +#~ "of more. Don't overcomplicate your tool" +#~ " descriptions with options that you " +#~ "don't need or use." +#~ msgstr "" + +#~ msgid "" +#~ "This indicates whether a process " +#~ "requires outgoing IPv4/IPv6 network access." +#~ " If a command-line tool is " +#~ "written manually in CWL v1.1+, there " +#~ "is a need to specify when network" +#~ " access is required." +#~ msgstr "" + +#~ msgid "" +#~ "CWL v1.0 command-line tools that " +#~ "are upgraded to v1.1 or v1.2 get" +#~ " Network Access automatically." +#~ msgstr "" + +#~ msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +#~ msgstr "" + +#~ msgid "" +#~ "Note also that the author of this" +#~ " CWL description has also included " +#~ "`ResourceRequirement`s, specifying the minimum " +#~ "amount of RAM and number of cores" +#~ " required for the tool to run " +#~ "successfully, as well as details of " +#~ "the version of the software that " +#~ "the description was written for and " +#~ "other useful metadata. These features " +#~ "are discussed further in other chapters" +#~ " of this user guide." +#~ msgstr "" + +#~ msgid "" +#~ "Similar to the command-line tool " +#~ "it requires `inputs` and `outputs`. But" +#~ " instead of `baseCommand`, it requires " +#~ "an `expression` attribute." +#~ msgstr "" + +#~ msgid "" +#~ "We had to use an " +#~ "`InlineJavascriptRequirement` as our expression " +#~ "contains a JavaScript call in " +#~ "`.toUpperCase()`. This means to tools " +#~ "using the expression tool that " +#~ "JavaScript is a requirement." +#~ msgstr "" + +#~ msgid "" +#~ "If you need to manipulate input " +#~ "parameters, include the requirement " +#~ "`InlineJavascriptRequirement` and then anywhere " +#~ "a parameter reference is legal you " +#~ "can provide a fragment of Javascript " +#~ "that will be evaluated by the CWL" +#~ " runner." +#~ msgstr "" + +#~ msgid "From `Workflow`" +#~ msgstr "" + +#~ msgid "" +#~ "The requirement `InlineJavascriptRequirement` " +#~ "supports an `expressionLib` attribute that " +#~ "allows users to load external JavaScript" +#~ " files, or to provide inline " +#~ "JavaScript code." +#~ msgstr "" + +#~ msgid "" +#~ "Tools and workflows can take `File` " +#~ "types as input and produce them as" +#~ " output. We also recommend indicating " +#~ "the format for `File` types. This " +#~ "helps document for others how to " +#~ "use your tool while allowing you " +#~ "to do some simple type-checking " +#~ "when creating parameter files." +#~ msgstr "" + +#~ msgid "" +#~ "Available primitive types are *string*, " +#~ "*int*, *long*, *float*, *double*, and " +#~ "*null*; complex types are *array* and" +#~ " *record*; in addition there are " +#~ "special types *File*, *Directory* and " +#~ "*Any*." +#~ msgstr "" + +#~ msgid "" +#~ "You can use `cwltool` to create a" +#~ " template input object. That saves " +#~ "you from having to type all the" +#~ " input parameters in a input object" +#~ " file:" +#~ msgstr "" + +#~ msgid "" +#~ "The field `inputBinding` is optional and" +#~ " indicates whether and how the input" +#~ " parameter should appear on the " +#~ "tool's command line. If `inputBinding` " +#~ "is missing, the parameter does not " +#~ "appear on the command line. Let's " +#~ "look at each example in detail." +#~ msgstr "" + +#~ msgid "" +#~ "If you use exclusive input parameters" +#~ " combined with expressions, you need " +#~ "to be aware that the `inputs` " +#~ "JavaScript object will contain one of" +#~ " the exclusive input values. This " +#~ "means that you might need to use" +#~ " an **or** boolean operator to check" +#~ " which values are present." +#~ msgstr "" + +#~ msgid "" +#~ "Note how the JavaScript expression uses" +#~ " the value of the exclusive input " +#~ "parameter without taking into consideration" +#~ " a `null` value. If you provide " +#~ "a valid value, such as “fasta” " +#~ "(one of the values of the enum)," +#~ " your command should execute successfully:" +#~ msgstr "" + +#~ msgid "" +#~ "However, if you do not provide any" +#~ " input value, then `file_format` will " +#~ "be evaluated to a `null` value, " +#~ "which does not match the expected " +#~ "type for the output field (a " +#~ "`string`), resulting in failure when " +#~ "running your workflow." +#~ msgstr "" + +#~ msgid "" +#~ "To correct it, you must remember " +#~ "to use an or operator in your " +#~ "JavaScript expression when using exclusive " +#~ "parameters, or any parameter that allows" +#~ " `null`. For example, the expression " +#~ "could be changed to `$(inputs.file_format " +#~ "|| 'auto')`, to have a default " +#~ "value if none was provided in the" +#~ " command line or job input file." +#~ msgstr "" + +#~ msgid "" +#~ "The `uppercase` step of the workflow " +#~ "is an operation. It can be used" +#~ " like a command line tool or an" +#~ " expression. You can also plot it " +#~ "with the CWL Viewer or `cwltool`:" +#~ msgstr "" + +#~ msgid "" +#~ "The output of the command above " +#~ "can be rendered with a Graphviz " +#~ "renderer. The following image is " +#~ "rendered with the Sphinx Graphviz " +#~ "directive (this user guide is built " +#~ "with Sphinx):" +#~ msgstr "" + +#~ msgid "" +#~ "If you try running it with " +#~ "`cwltool`, the command will fail since" +#~ " `cwltool` does not have enough " +#~ "information to know how to execute " +#~ "it:" +#~ msgstr "" + +#~ msgid "" +#~ "When a tool runs under CWL, the" +#~ " starting working directory is the " +#~ "designated output directory. The underlying" +#~ " tool or script must record its " +#~ "results in the form of files " +#~ "created in the output directory. The" +#~ " output parameters returned by the " +#~ "CWL tool are either the output " +#~ "files themselves, or come from examining" +#~ " the content of those files." +#~ msgstr "" + +#~ msgid "" +#~ "In previous examples, the `baseCommand` " +#~ "was just a string, with any " +#~ "arguments passed as CWL inputs. Instead" +#~ " of a single string we can use" +#~ " an _array of strings_. The first" +#~ " element is the command to run, " +#~ "and any subsequent elements are " +#~ "mandatory command line arguments" +#~ msgstr "" + +#~ msgid "" +#~ "The field `outputBinding` describes how " +#~ "to set the value of each output" +#~ " parameter." +#~ msgstr "" + +#~ msgid "" +#~ "The `glob` field consists of the " +#~ "name of a file in the output " +#~ "directory. If you don't know name " +#~ "of the file in advance, you can" +#~ " use a wildcard pattern like `glob:" +#~ " '*.txt'`." +#~ msgstr "" + +#~ msgid "" +#~ "To capture a tool's standard output " +#~ "stream, add the `stdout` field with " +#~ "the name of the file where the " +#~ "output stream should go. Then add " +#~ "`type: stdout` on the corresponding " +#~ "output parameter." +#~ msgstr "" + +#~ msgid "" +#~ "Often, tool descriptions will be written" +#~ " for a specific version of a " +#~ "software. To make it easier for " +#~ "others to use your descriptions, you " +#~ "can include a `SoftwareRequirement` field " +#~ "in the `hints` section. This may " +#~ "also help to avoid confusion about " +#~ "which version of a tool the " +#~ "description was written for." +#~ msgstr "" + +#~ msgid "" +#~ "As well as a version number, a " +#~ "unique resource identifier (URI) for the" +#~ " tool is given in the form of" +#~ " an [RRID][rrid]. Resources with RRIDs " +#~ "can be looked up in the " +#~ "[SciCrunch][scicrunch] registry, which provides " +#~ "a portal for finding, tracking, and " +#~ "referring to scientific resources " +#~ "consistently. If you want to specify " +#~ "a tool as a `SoftwareRequirement`, " +#~ "search for the tool on SciCrunch " +#~ "and use the RRID that it has " +#~ "been assigned in the registry. (Follow" +#~ " this [Adding a Resource Tutorial" +#~ "][scicrunch-add-tool] to add a tool" +#~ " to SciCrunch). You can use this " +#~ "RRID to refer to the tool (via " +#~ "[identifiers.org][identifiers]) in the `specs` " +#~ "field of your requirement description. " +#~ "Other good choices, in order of " +#~ "preference, are to include the DOI " +#~ "for the main tool citation and the" +#~ " URL to the tool." +#~ msgstr "" + +#~ msgid "" +#~ "Normally, input files are located in " +#~ "a read-only directory separate from " +#~ "the output directory. This causes " +#~ "problems if the underlying tool expects" +#~ " to write its output files alongside" +#~ " the input file in the same " +#~ "directory. You use `InitialWorkDirRequirement` " +#~ "to stage input files into the " +#~ "output directory. In this example, we" +#~ " use a JavaScript expression to " +#~ "extract the base name of the input" +#~ " file from its leading directory " +#~ "path." +#~ msgstr "" + +#~ msgid "" +#~ "Before we run this, let's just " +#~ "break it down and see what some" +#~ " bits do. Most of this has " +#~ "been explained in previous sections, the" +#~ " only part that is really new " +#~ "is the `dockerRequirement` section." +#~ msgstr "" + diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 41a1d23f..e55e61c3 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -1,3673 +1,4377 @@ # SOME DESCRIPTIVE TITLE. # Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. +# This file is distributed under the same license as the Common Workflow +# Language User Guide package. +# FIRST AUTHOR , 2023. # msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"POT-Creation-Date: 2023-12-16 11:48+0100\n" "PO-Revision-Date: 2023-07-05 09:51+0000\n" "Last-Translator: Michael Crusoe \n" -"Language-Team: Chinese (Simplified) \n" "Language: zh_Hans\n" +"Language-Team: Chinese (Simplified) " +"\n" +"Plural-Forms: nplurals=1; plural=0;\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" +"Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.0-dev\n" +"Generated-By: Babel 2.12.1\n" -#: ../../LICENSE.md:2 -#: 4e203044f0464fd5a3256430391dde12 +#: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac msgid "Licenses" msgstr "许可协议" -#: ../../LICENSE.md:4 -#: 79a9837f877147fa8e3931968aae7fb5 +#: ../../LICENSE.md:4 9dd9705700664b31a3f296d263b4028b msgid "Instructional Material" msgstr "指南资料" -#: ../../LICENSE.md:6 -#: 747f9dd48bc54f44adcd8b18c57f4d9d -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +#: ../../LICENSE.md:6 e54324bd39cd431d91b32e338217b8c7 +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." msgstr "" -"通用工作流语言项目的所有指南资料，以及对其结构的修改，均可在遵照[" -"知识共享署名公共许可协议 (Creative Commons Attribution license)][cc-by-" -"human]的前提下获得授权使用。以下是[CC BY 4.0许可完整法律条文][cc-by-" -"legal]的可读摘要（不能替代原条文）。" +"通用工作流语言项目的所有指南资料，以及对其结构的修改，均可在遵照[知识共享署名公共许可协议 (Creative Commons " +"Attribution license)][cc-by-human]的前提下获得授权使用。以下是[CC BY 4.0许可完整法律条文][cc-" +"by-legal]的可读摘要（不能替代原条文）。" -#: ../../LICENSE.md:12 -#: 98f18f72afa043f9a79aa9b5fc8bdf22 +#: ../../LICENSE.md:12 754f3f54aa4142ef9dac27f508dd0bca msgid "You are free:" msgstr "您可以自由地：" -#: ../../LICENSE.md:14 -#: 466be810dd8d4a838e0edb5869f2c4eb +#: ../../LICENSE.md:14 d2b1d5e965ef4e71b64c359549919975 msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "**共享**——通过任何媒介、以任意格式复制和重新分发本作品" -#: ../../LICENSE.md:15 -#: 18a3a0aec35743848c97bc178f9c94ff +#: ../../LICENSE.md:15 fe9551ffef8149bf8da50e70318e8de8 msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "**演绎**——修改、转换或以本作品为基础进行创作" -#: ../../LICENSE.md:17 -#: b746b1e4dca14de1a8e18036b7602a73 +#: ../../LICENSE.md:17 247db3bcc7024c44a044886a29ef1414 msgid "for any purpose, even commercially." msgstr "在任何用途下，甚至商业目的。" -#: ../../LICENSE.md:19 -#: 6021e65292a149d5b15e14491f3eb05e -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +#: ../../LICENSE.md:19 c04d906124854afc917707b7b4e45bb2 +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" msgstr "只要你遵守许可协议条款，许可人就无法收回你的这些权利：" -#: ../../LICENSE.md:24 -#: 8fb7a2946c384364814c6ec3910997d3 -msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." -msgstr "" -"**署名**——您必须给出适当的署名，即声明您作品之原始版本的版权为 Common " -"Workflow Language Project 所有 (\"Copyright © the Common Workflow Language " -"project\")。如条件允许，您应提供 https://www.commonwl.org/ 和[许可协议][cc-" -"by-human]的链接，同时标明是否对原始作品作了修改。您可以用任何合理的方式来署名" -"，但是不得以任何方式暗示许可人为您或您的使用背书。" - -#: ../../LICENSE.md:32 -#: 8161753b7526445db319210044566200 -msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" -msgstr "**没有附加限制**——您不得适用法律术语或者技术措施从而限制其他人做许可协议允许" -"的事情。并且您理解：" - -#: ../../LICENSE.md:36 -#: 15314ba527864eaa834cf1185cfcc4e3 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." -msgstr "您不必因为公共领域的作品要素而遵守许可协议，或者您的使用被可适用的例外或限制" -"所允许。" - -#: ../../LICENSE.md:39 -#: b351ddf9847d48b1a2a87fc78eaba4d2 -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." -msgstr "不提供担保。许可协议可能不会给与您意图使用的所必须的所有许可。例如，其他权利" -"比如形象权、隐私权或人格权可能限制您如何使用作品。" - -#: ../../LICENSE.md:44 -#: a091addc2dea4830a06bb72ead56c5ea +#: ../../LICENSE.md:24 551cb5ab59dd4737b1042a4ef79ffab7 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." +msgstr "" +"**署名**——您必须给出适当的署名，即声明您作品之原始版本的版权为 Common Workflow Language Project 所有 " +"(\"Copyright © the Common Workflow Language project\")。如条件允许，您应提供 " +"https://www.commonwl.org/%20%E5%92%8C[%E8%AE%B8%E5%8F%AF%E5%8D%8F%E8%AE%AE][cc-by-" +"human]的链接，同时标明是否对原始作品作了修改。您可以用任何合理的方式来署名，但是不得以任何方式暗示许可人为您或您的使用背书。" + +#: ../../LICENSE.md:32 f6c3b2ccad494ed6811a35537fc1fb0d +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" +msgstr "**没有附加限制**——您不得适用法律术语或者技术措施从而限制其他人做许可协议允许的事情。并且您理解：" + +#: ../../LICENSE.md:36 91c95248cd7f435c909ee263a9a8bf3f +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." +msgstr "您不必因为公共领域的作品要素而遵守许可协议，或者您的使用被可适用的例外或限制所允许。" + +#: ../../LICENSE.md:39 27f79b0b648b4de4b0eb3172b2dc4ae8 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." +msgstr "不提供担保。许可协议可能不会给与您意图使用的所必须的所有许可。例如，其他权利比如形象权、隐私权或人格权可能限制您如何使用作品。" + +#: ../../LICENSE.md:44 1e367d07720d4f9fb7ebc3149052e823 msgid "Software" msgstr "软件" -#: ../../LICENSE.md:46 -#: 84b2c685bbab48449fdc72d2a1e42bf4 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +#: ../../LICENSE.md:46 cf8b58d02b6943a48cb70aa78a27bea4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "除非另有注明，Common Workflow Language project " "提供的示例程序及其他软件均可在遵照[OSI][osi]所批准的[Apache 2.0 " "许可协议][apache-2.0-license]之前提下获取并使用。" -#: ../../LICENSE.md:51 -#: 0f68eafafaef4b54accba7e13bfaa702 -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." -msgstr "" -"除非受适用法律要求或者经书面许可，据本许可协议发行的软件均为“依照其原样”发行" -"，不存在任何种类的、无论是明文还是隐含的担保或合约要件。请查阅许可协议中关于" -"本协议下授权许可行为和责任免除的具体条文。" - -#: ../../src/_includes/what-is-cwl.md:1 -#: ../../src/_includes/what-is-cwl.md:2 -#: eab02dc13915490bb3c9ba744d78b6a7 -#: d4f35995b0f6494d9771a4be0a82538f -#: d6ccd4b546254f56a597d67dd4fdc5d6 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" -"CWL 的作用在于描述各种命令行工具，并且将它们连接起来，以创建工作流 " -"(workflow)。CWL 是一种规范，而非某种特定的软件。因此，由 CWL " -"描述的工具和工作流能够移植到支持 CWL 标准的多种平台。" - -#: ../../src/episodes.md:5 -#: ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc -#: 436cfca6f857469bbff7c652df32160f +#: ../../LICENSE.md:51 96f1e5be3e1e48db8d9a4c7693008715 +msgid "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." +msgstr "除非受适用法律要求或者经书面许可，据本许可协议发行的软件均为“依照其原样”发行，不存在任何种类的、无论是明文还是隐含的担保或合约要件。请查阅许可协议中关于本协议下授权许可行为和责任免除的具体条文。" + +#: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 +#: 08aa9181d5304e0fa96b28db15718559 d37fc100eb6948bba8b5e757574b2aaf +#: ecdd0f28d5b048d69dd1ffae2fa1f6c0 +msgid "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece" +" of software, tools and workflows described using CWL are portable across" +" a variety of platforms that support the CWL standard." +msgstr "" +"CWL 的作用在于描述各种命令行工具，并且将它们连接起来，以创建工作流 (workflow)。CWL 是一种规范，而非某种特定的软件。因此，由 " +"CWL 描述的工具和工作流能够移植到支持 CWL 标准的多种平台。" + +#: ../../src/episodes.md:5 ../../src/setup.md:5 +#: 1361ff6bf4924efc9ce9a85785a6b381 eb254514301c491e81f72ae19c407261 msgid "This page has moved" msgstr "此页面已转移" -#: ../../src/episodes.md:9 -#: cc11f5d29206492d9f2f0922882b6159 -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." -msgstr "" -"此页面已过时，保留在此仅用于留存旧版《用户指南》的链接。请使用[新版目录](inde" -"x.md#table-of-contents)浏览《用户指南》。" +#: ../../src/episodes.md:9 f03d7cbe6670451db0896f1b674d56c7 +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. Please use the new [Table of Contents](index.md#table-of-" +"contents) to browse the User Guide." +msgstr "此页面已过时，保留在此仅用于留存旧版《用户指南》的链接。请使用[新版目录](index.md#table-of-contents)浏览《用户指南》。" -#: ../../src/faq.md:1 -#: e2ed894d325a4f50a5e2dc69da5531a1 +#: ../../src/faq.md:1 d65ad48ac6314bf0a74c34a6766561fc msgid "FAQ" msgstr "常见问题" -#: ../../src/faq.md:11 -#: 61edb787dab04ca2ad3ed07616d878a0 -msgid "Non \"`File`\" Types Using `evalFrom`" +#: ../../src/faq.md:11 370a9659c7904ef6b5e1ae7480f82ef6 +#, fuzzy +msgid "How do I create non \"`File`\" types using `evalFrom`?" msgstr "使用 `evalFrom` 的非“`File`”类型" -#: ../../src/faq.md:41 -#: d5321589e7ed4f0db3c630cc39800791 -msgid "Rename an Input File" +#: ../../src/faq.md:41 8333f51e3f5945fe8963adfc6685bcb1 +#, fuzzy +msgid "How do I rename an input file?" msgstr "重命名输入文件" -#: ../../src/faq.md:43 -#: fc62427c0a004810b055dee90ec5e2d9 -msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +#: ../../src/faq.md:43 f6b88d9154d049d7807afa9bb0f1ac98 +msgid "" +"This example demonstrates how to change the name of an input file as part" +" of a tool description. This could be useful when you are taking files " +"produced from another step in a workflow, and don't want to work with the" +" default names that these files were given when they were created." msgstr "" -"本示例演示如何在工具描述 (tool description) 中更改输入文件名称。如果要使用工" -"作流中其它步骤产生的文件，但又不想使用这些文件创建时的默认名称，这时候更名操" -"作可以派上用场。" +"本示例演示如何在工具描述 (tool description) " +"中更改输入文件名称。如果要使用工作流中其它步骤产生的文件，但又不想使用这些文件创建时的默认名称，这时候更名操作可以派上用场。" -#: ../../src/faq.md:59 -#: 1c6b8a4194a14611b4061b1540c3807f -msgid "Rename an Output File" +#: ../../src/faq.md:59 833510f5896b4a6eb5875d25eca5b047 +#, fuzzy +msgid "How do I rename an output file?" msgstr "重命名输出文件" -#: ../../src/faq.md:61 -#: bc7ad10c929848a3a9a240a3c501d299 -msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +#: ../../src/faq.md:61 207e2f97d1c44233ae3f109c5a6ec944 +msgid "" +"This example demonstrates how to change the name of an output file from " +"the default name given to it by a tool:" msgstr "本示例演示更改输出文件名，不再使用某个工具赋予它的默认名称：" -#: ../../src/faq.md:82 -#: 7225a993d281421b95c8e3df2846a0e3 -msgid "Referencing a Local Script" +#: ../../src/faq.md:83 d66acc583da24273980a52be03e79e91 +msgid "" +"By modifying the `basename` field in the `outputEval` field, CWL workflow" +" engines will rename the file using the new name for subsequent steps or " +"as a workflow-level output." +msgstr "" + +#: ../../src/faq.md:86 8641f105131b4ac1bca7e0a46756ef79 +#, fuzzy +msgid "How do I reference a local script?" msgstr "引用本地脚本" -#: ../../src/faq.md:84 -#: 7ef1dbb81993473f948d9c6f3c64b381 +#: ../../src/faq.md:88 d3e43b40d6994b32bc37067ee116418e msgid "There are two ways to reference a local script:" msgstr "引用本地脚本有两种方法：" -#: ../../src/faq.md:86 -#: 450edf800a18423195bea4fe8793a2cb -msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +#: ../../src/faq.md:90 64b140a321ca4087945339c523cc24dd +#, fuzzy +msgid "" +"The first method involves adding the path to a folder containing your " +"scripts to the `PATH` environment variable. This allows you to execute " +"the shell script directly (without explicitly using the `sh` or `bash` " +"commands)." msgstr "" -"第一种方法是将包含相关脚本的文件夹添加至`PATH`（路径）环境变量。" -"这样可以直接运行 shell 脚本，无需使用 `sh` 或 `bash` 命令。" +"第一种方法是将包含相关脚本的文件夹添加至`PATH`（路径）环境变量。这样可以直接运行 shell 脚本，无需使用 `sh` 或 `bash` " +"命令。" -#: ../../src/faq.md:89 -#: 1a8cc75ea6174b9297871b2e58971077 +#: ../../src/faq.md:93 34ebca4487a54ceab5d087105820e945 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "首先，将 _\"shebang\"_ 添加为文件首行：" -#: ../../src/faq.md:95 -#: a7d84f740a714ec588503ee084fbbc34 -msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +#: ../../src/faq.md:99 6b04a4dcdada4515b28d74aacff3537a +msgid "" +"After that, make the script executable with the command `chmod +x " +"scriptname.sh`" msgstr "然后，用 `chmod +x scriptname.sh` 命令将脚本设为可执行。" -#: ../../src/faq.md:97 -#: 569d553abe85450c9d1c37456bf412f4 -msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." -msgstr "最后，修改 `PATH`, 添加该脚本所在的目录。（把你自己的脚本保存在 `$HOME/bin` " -"目录下是较好的做法）。" +#: ../../src/faq.md:101 756ab4f7edcf42d3872bb86818e088c3 +msgid "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." +msgstr "最后，修改 `PATH`, 添加该脚本所在的目录。（把你自己的脚本保存在 `$HOME/bin` 目录下是较好的做法）。" -#: ../../src/faq.md:104 -#: 95f5dbbd21084a318413b9528fb867be +#: ../../src/faq.md:108 efb46b3a2d7c4c51b65998602bfa6f18 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "这样，您就能用 `baseCommand: scriptname.sh` 直接运行脚本了。" -#: ../../src/faq.md:113 -#: 1b3cae80fa9a40ffb2259b8c1cd2b468 -msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +#: ../../src/faq.md:117 844938d5d2304c6cb03184b4b4b0b024 +msgid "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." msgstr "接下来若想共享您的工作，可将脚本存放在 Docker 格式的容器 (container) 中。" -#: ../../src/faq.md:115 -#: 8d86baa239364f799d4f9d5ea2b0e314 -msgid "The second method involves including an input of `type: File` in the script itself:" +#: ../../src/faq.md:119 796ce8155e32486d9651f8f13bfa3148 +msgid "" +"The second method involves including an input of `type: File` in the " +"script itself:" msgstr "第二种方法是将 `type: File` 输入内容编写进脚本：" -#: ../../src/faq.md:135 -#: f2c109998c76434893ff16b17fdb2bd0 -msgid "In CWL, everything must be directly stated." -msgstr "在CWL中，一切都必须直接说明。" - -#: ../../src/faq.md:138 -#: c2c752b86bf94d6fb3751f4dd81bc7a7 -msgid "Setting `self`-based Input Bindings for Optional Inputs" +#: ../../src/faq.md:138 ba246320fdd94a1aab4736f83718d793 +#, fuzzy +msgid "How can I set `self`-based input bindings for optional inputs?" msgstr "为可选输入项设置用到 `self` 变量的输入绑定" -#: ../../src/faq.md:140 -#: 2c38cc58cbb340bc935a5f00e96ba95c -msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." -msgstr "目前，如果缺失的可选输入项用到了 `self`, `cwltool` " -"将无法处理。在更高明的解决办法出现前，下面的例子可作为临时变通一用。" - -#: ../../src/faq.md:165 -#: ce6db54bd0f54839a5beb948530a21f0 -msgid "Model a \"one-or-the-other\" Parameter" +#: ../../src/faq.md:140 6169b7be9af7448abcb57eaf91e1cc91 +msgid "" +"Currently, `cwltool` can't cope with missing optional inputs if their " +"input binding makes use of `self`. Below is an example workaround for " +"this, pending a more sophisticated fix." +msgstr "目前，如果缺失的可选输入项用到了 `self`, `cwltool` 将无法处理。在更高明的解决办法出现前，下面的例子可作为临时变通一用。" + +#: ../../src/faq.md:165 6c98b7948059411b8e09cf03a552c5ab +#, fuzzy +msgid "How can I model a \"one-or-the-other\" parameter?" msgstr "构建“非此即彼”参数的模型" -#: ../../src/faq.md:167 -#: d06cbf89028b4638ad54c2529bcbfa25 -msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +#: ../../src/faq.md:167 d1424da3f43c4519a4c4735f4a720341 +msgid "" +"Below is an example showing how to specify different strings to be added " +"to a command line, based on the value given to a Boolean parameter." msgstr "以下示例演示的，是根据某个布尔参数的取值，来指定添加到命令行的字符串。" -#: ../../src/faq.md:188 -#: d53fb28dcad04e7788cba9e280a2343c -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +#: ../../src/faq.md:188 5c9980839f404ba6aef92ef23034500f +#, fuzzy +msgid "" +"How do I connect a solo value to an input that expects an array of that " +"type?" msgstr "将某个元素值与期待该值类型的数组关联起来" -#: ../../src/faq.md:190 -#: d9e30e11533b4d53a144f5df7041268d -msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" -"将 [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow" -".html#MultipleInputFeatureRequirement) 与 [`linkMerge: " +#: ../../src/faq.md:190 2525baf16c1f4725b096f33fd99009cf +#, fuzzy +msgid "" +"Add a " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput):" +msgstr "" +"将 " +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" +" 与 [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" " 联合使用" -#: ../../src/faq.md:194 -#: 941077158ec54ae19bfa2e2ad6662da1 +#: ../../src/faq.md:194 a00d5d96b15048a79ae099d22d63bb42 msgid "merge_nested" msgstr "merge_nested" -#: ../../src/faq.md:196 -#: 937cb94a370640c788fbc3fe0b19f2e5 -msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." -msgstr "输入必须是一个数组，每个输入链接只包含一个条目。如果使用单个链接指定“merge_ne" -"sted”，则链接中的值必须包含在单项列表中。" - -#: ../../src/faq.md:199 -#: a1d57e15656548128a76a8b975c564c9 -msgid "Which means \"create a list with exactly these sources as elements\"" +#: ../../src/faq.md:196 3a92c6cc5c2b40ffa0d692d03bad5c87 +msgid "" +"The input must be an array consisting of exactly one entry for each input" +" link. If \"merge_nested\" is specified with a single link, the value " +"from the link must be wrapped in a single-item list." +msgstr "输入必须是一个数组，每个输入链接只包含一个条目。如果使用单个链接指定“merge_nested”，则链接中的值必须包含在单项列表中。" + +#: ../../src/faq.md:199 3af16c07e3f148ddb8849c94a3864158 +#, fuzzy +msgid "Which means \"create a list with exactly these sources as elements\"." msgstr "这段话意思是，“创建一个列表，其中的元素正是这些源”" -#: ../../src/faq.md:201 -#: c8c235a9bf6240628f0b5493ffebf7e0 -msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +#: ../../src/faq.md:201 0ea3de393d2f42aeb82658c85a19ec45 +msgid "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " +"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" +" destination step." msgstr "" -"换言之：如果目标的类型是 `File[]`（元素类型为 `File ` 的数组），" -"而源是单独一个 `File`，那么将 `MultipleInputFeatureRequirements` " -"添加到工作流级别的 `requirements`，并在目标步骤相应的 `in` 条目下添加 " -"`linkMerge： merge_nested`。" +"换言之：如果目标的类型是 `File[]`（元素类型为 `File ` 的数组），而源是单独一个 `File`，那么将 " +"`MultipleInputFeatureRequirements` 添加到工作流级别的 `requirements`，并在目标步骤相应的 " +"`in` 条目下添加 `linkMerge： merge_nested`。" -#: ../../src/faq.md:229 -#: 3da4dcb043eb4423a53a14182949d9cd -msgid "Optional Inputs 💯" -msgstr "可选输入💯" +#: ../../src/faq.md:229 2f1bbb611c9c4f80b7ae0566432f2f35 +msgid "How do make an input optional? 💯" +msgstr "" -#: ../../src/faq.md:231 -#: 89b90d3bf1ea4ebd88482d435241fac5 -msgid "To make an input parameter optional, add a question mark to the type declaration." +#: ../../src/faq.md:231 08a226efe5d141e68215ac77725033db +msgid "" +"To make an input parameter optional, add a question mark to the type " +"declaration." msgstr "若要令某个输入参数为可选，请在其类型声明中添加问号。" -#: ../../src/faq.md:247 -#: a854006054ce4ffe94bbfa73bdbecbf2 +#: ../../src/faq.md:247 06e70a855a8f455ca0536eead77073c2 msgid "" msgstr "" -#: ../../src/faq.md:248 -#: f80eb714e9df417fbba555b5dd5f4d8c -msgid "Enum Inputs ⚜️" -msgstr "枚举输入 ⚜️" +#: ../../src/faq.md:248 7fda8eeb6a7f4689993ed0118c77f023 +msgid "" +"How do I specify an input that must come from a list of predefined values" +" (i.e. How do I use enum inputs) ?" +msgstr "" -#: ../../src/faq.md:250 -#: 10af80fa13af4158aec7060550485350 -msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +#: ../../src/faq.md:250 b1934a82553b4da3b7f981e576245dd8 +msgid "" +"For command line flags that require a specific input as the argument an " +"enum type can be declared in CWL. **Specifying null here is known as long" +" form style. It does the same thing as the question mark on the other " +"inputs.**" msgstr "" -"某些命令行标志需要特定的参数值；对此，可以在 CWL 中声明枚举类型。**此处指定 " -"null, 这样的编程风格称为“长格式” (long " +"某些命令行标志需要特定的参数值；对此，可以在 CWL 中声明枚举类型。**此处指定 null, 这样的编程风格称为“长格式” (long " "form)。它的作用与其他输入上的问号相同。**" -#: ../../src/faq.md:267 -#: ad1c26711ccd4efd8fdb25f9293d33fd +#: ../../src/faq.md:267 17fc34fad2094f5ea60e963dabd632b8 msgid "" msgstr "" -#: ../../src/faq.md:268 -#: 49e2095b51f84f609f5d4bc088ad9745 -msgid "Record Inputs 📀" -msgstr "记录输入 📀" +#: ../../src/faq.md:268 4d7acfbeba5b4e9cb31f08ef4b280447 +msgid "" +"How do I describe dependent or exclusive input parameters(e.g. How do I " +"use record inputs)?" +msgstr "" -#: ../../src/faq.md:270 -#: 52b8538177c64090af51f5f6a696c28c -msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +#: ../../src/faq.md:270 949ce95c082f4a05891a55fee25d4873 +msgid "" +"For commandline flags that are either **mutually exclusive** or " +"**dependent** a special record type can be defined. You can also specify " +"null here to create optional inputs." msgstr "" -"如果部分命令行标志之间存在 **互斥** 或 **依赖** 的关系，" -"可以为其定义专门的记录类型 (record type)。此处也可以指定 null 创建可选输入。" +"如果部分命令行标志之间存在 **互斥** 或 **依赖** 的关系，可以为其定义专门的记录类型 (record type)。此处也可以指定 " +"null 创建可选输入。" -#: ../../src/faq.md:322 -#: f96c9257e3734b8aa0cc5e065f74f944 -msgid "Setting Mutually Exclusive Parameters" +#: ../../src/faq.md:322 6fd3c469d11d4d52b9fbb7a3d443a8db +#, fuzzy +msgid "How do I set mutually exclusive parameters?" msgstr "设定互斥参数" -#: ../../src/faq.md:324 -#: 7dc0540508084a3495ff3b2ac90fd323 -msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." -msgstr "" -"为了正确地设置记录输入类型的字段，您需要将字典传递给输入，以正确设置参数。" -"具体方法是使用内联 JavaScript 返回以待设置字段为主键的字典。此处设定了 " -"source （源）字段，以指示工作流中要充当其键值的输入。" - -#: ../../src/faq.md:342 -#: b53dc77466b24a67b52b8aadf4fab724 -msgid "Setting Booleans" +#: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f +msgid "" +"To properly set fields in a record input type, you need to pass a " +"dictionary to the input to properly set the parameters. This is done by " +"using inline JavaScript and returning the dictionary with the key of the " +"field you want to set. The source field is set to indicate the input from" +" the workflow to be used as the value." +msgstr "" +"为了正确地设置记录输入类型的字段，您需要将字典传递给输入，以正确设置参数。具体方法是使用内联 JavaScript " +"返回以待设置字段为主键的字典。此处设定了 source （源）字段，以指示工作流中要充当其键值的输入。" + +#: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 +#, fuzzy +msgid "How can I set Booleans?" msgstr "设置布尔参数" -#: ../../src/faq.md:344 -#: cf4e7f3977ae4f9b877072c2b1c4b533 +#: ../../src/faq.md:344 8dcb88744e5840029de0e1bbf1c4b967 msgid "These can be set by using the default field" msgstr "可使用 default（默认）字段设置" -#: ../../src/faq.md:349 -#: 99b37739ef18443ca7c0e715a131e0c7 -msgid "Concatenating Strings in Inputs" +#: ../../src/faq.md:349 972b7a5551bb43e6b9fa30e0cb713ff7 +#, fuzzy +msgid "What should I do when concatenating strings in inputs?" msgstr "在输入中串联字符串" -#: ../../src/faq.md:351 -#: 9b00b5a55ee941e1adbfe89e133791e3 +#: ../../src/faq.md:351 68f74afc21d846dd9070d45dec0cc1d8 msgid "The valueFrom field must be used instead of default." msgstr "为此必须使用 valueFrom 而非 default 字段。" -#: ../../src/faq.md:359 -#: 07922147f7ab487ba2a1e7c43c9f410c -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +#: ../../src/faq.md:359 53b633c6f8644106beb95ae567eb0708 +#, fuzzy +msgid "" +"I get `cwltool` errors due to filenames with space characters inside. " +"What should I do?" msgstr "因文件名含有空格字符，`cwltool`报错" -#: ../../src/faq.md:361 -#: 7a11806f0c7045b48fe58a271f814797 +#: ../../src/faq.md:361 7101bb5cb69e4faca4e60eabb4eb258e msgid "`cwltool` does not allow some characters in filenames by default." msgstr "默认情况下，`cwltool`不允许某些字符出现在文件名中。" -#: ../../src/faq.md:363 -#: fdaec25650ab4b0fb1c527610e24ae5a -msgid "For example, the filename `a space is here.txt` includes 3 space characters." +#: ../../src/faq.md:363 0eaf834b0ca847cca6736794895f5f81 +msgid "" +"For example, the filename `a space is here.txt` includes 3 space " +"characters." msgstr "例如，文件名 `a space is here.txt`包含三个空格字符。" -#: ../../src/faq.md:371 -#: 182959fc9f4746d082994e07d05c8cde -msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." -msgstr "如果不能避开这些危险的字符，您可以为 `cwltool` 传递 `--relax-path-checks` " -"选项。" +#: ../../src/faq.md:371 7dabd8aab7a5423b842433616640bac0 +msgid "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." +msgstr "如果不能避开这些危险的字符，您可以为 `cwltool` 传递 `--relax-path-checks` 选项。" -#: ../../src/faq.md:373 -#: cc7752e9989e4a6d957682f479d6fc60 -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +#: ../../src/faq.md:373 b7ec33f38ce74ceb890f4379e4c41054 +#, fuzzy +msgid "" +"What should I do when I get CWL Parameter Reference error due to hyphen " +"in an input identifier?" msgstr "输入标识符中包含连字符导致 CWL 参数引用错误" -#: ../../src/faq.md:375 -#: 6db1ebd2d6c74ceca889662cd7df5cd5 +#: ../../src/faq.md:375 e39b65947b294b20a444f18d780246f4 msgid "If `cwltool --validate` returns valid" msgstr "如 `cwltool --validate` 返回 valid（验证通过）" -#: ../../src/faq.md:384 -#: 3de2513c7d7b4569ba63f7e6d29137b7 +#: ../../src/faq.md:384 dcd42c65681b438bb541fb38ddebb536 msgid "But executing it causes an error like:" msgstr "但执行时导致如下错误：" -#: ../../src/faq.md:396 -#: ae3a9188706649e28f97bc4ec34c0821 +#: ../../src/faq.md:396 2b96665acac449758b852bbe7600e007 msgid "The file is here" msgstr "该文件如下" -#: ../../src/faq.md:410 -#: e1ac97ab6ad3449b8c54933d25257f73 +#: ../../src/faq.md:410 f59751d2f0014e59af7879a748062cec msgid "Problem caused by `-` (hyphen character)." msgstr "问题由 `-`（连字符）引发。" -#: ../../src/faq.md:423 -#: f6c402f7f6974edbbb5582c8e22f3869 -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +#: ../../src/faq.md:423 7780f461ca4c478b92fca893c0b0894a +#, fuzzy +msgid "To fix this error, change `-` (hyphen) to `_` (underscore):" msgstr "修复方法是将 `-`（连字符）更改为 `_`（下划线）" -#: ../../src/faq.md:436 -#: 190099a242a645c9b9f8bc3ce89d920d -msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +#: ../../src/faq.md:436 88df56dfff854fc68fb6ad3835a846e4 +msgid "" +"If it is not possible to change the input identifier, then you can use an" +" alternative CWL Parameter Reference syntax:" msgstr "如果不能改动输入标识符，您可使用另一种 CWL 参数引用句法：" -#: ../../src/faq.md:442 -#: 06a4f6ffc2da4d43b453d4784b42efd3 -msgid "Use CWL and cwltool with Singularity" +#: ../../src/faq.md:442 fc407a9e8d8c4b699d9cd14b369343b5 +#, fuzzy +msgid "How do I use CWL and cwltool with Singularity?" msgstr "在 Singularity 下使用 CWL 和 cwltool" -#: ../../src/faq.md:445 -#: 1901c34201054a9cae199b0dbb8b945e -msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +#: ../../src/faq.md:445 239f5f81cef042b08fb8015c36b3ecad +msgid "" +"The CWL standards are built around (optional) Docker format containers. " +"The reference runner and several other CWL implementations support " +"running those Docker format containers using the Singularity engine. " +"Directly specifying a Singularity format container is not part of the CWL" +" standards." msgstr "" -"CWL 标准是依照 Docker 容器格式建立的，其参考运行程序和另外几种 CWL " -"实现均支持适应 Singularity 引擎运行 Docker 格式容器。不过，直接指定 " -"Singularity 格式容器不在 CWL 标准之内。" +"CWL 标准是依照 Docker 容器格式建立的，其参考运行程序和另外几种 CWL 实现均支持适应 Singularity 引擎运行 Docker" +" 格式容器。不过，直接指定 Singularity 格式容器不在 CWL 标准之内。" -#: ../../src/faq.md:450 -#: 2d498470524d47f18f9936ace6acebb0 -msgid "Debug JavaScript Expressions" -msgstr "调试 JavaScript 表达式" - -#: ../../src/faq.md:452 -#: d7b044f5224a48eda09bc949cf645193 -msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +#: ../../src/faq.md:450 61641314d82b43e982e54c64c73232c5 +msgid "How do I debug the JavaScript in my CWL tool?" msgstr "" -"您可使用 cwltool 的 --js-console 选项，" -"也可以考虑为您的代码创建 JavaScript 或 TypeScript 项目后使用 " -"expressionLib 加载， 比如： https://github.com/common-workflow-language/" -"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" -#: ../../src/index.md:1 -#: 2754519265eb426b940bbbd2b8d64e1e +#: ../../src/faq.md:452 5556d3c323664edea55cfb777f4efb3b +msgid "" +"You can use the --js-console option of cwltool," +" or you can try creating a JavaScript or TypeScript project for your " +"code, and load it using expressionLib, e.g.: " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" +"您可使用 cwltool 的 --js-console 选项，也可以考虑为您的代码创建 " +"JavaScript 或 TypeScript 项目后使用 expressionLib 加载， 比如： " +"https://github.com/common-workflow-language/common-workflow-" +"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" + +#: ../../src/index.md:1 1c9fb72b83c9467a9672943fb47ffe32 msgid "Common Workflow Language User Guide" msgstr "通用工作流语言用户指南" -#: ../../src/index.md:3 -#: f8d6e4cd54cb42c88182a43171d97bab -msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +#: ../../src/index.md:3 aaa44578e27345e682ab44686b4da159 +msgid "" +"This guide will introduce you to writing workflows using the [Common " +"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " +"guide describes the latest specification {{ cwl_version }}." msgstr "" -"这本指南将向您介绍使用 [Common Workflow Language](https://www.commonwl.org/) " -"(CWL) 开放标准编写工作流。本指南所描述的是 {{ cwl_version }} 版本最新规范。" +"这本指南将向您介绍使用 [Common Workflow Language](https://www.commonwl.org/) (CWL) " +"开放标准编写工作流。本指南所描述的是 {{ cwl_version }} 版本最新规范。" -#: ../../src/index.md:7 -#: 132d40fee3b84469afa80d5ff613bf77 +#: ../../src/index.md:7 0adfc2adb0c74372b25d197dd3a73b8b msgid "Contributions and Feedback are Welcome!" msgstr "欢迎您的来稿和意见！" -#: ../../src/index.md:9 -#: 0f47157605a34ea58770ea898deebae4 -msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +#: ../../src/index.md:9 96c8dca812f1415db7c5c006b0c0e022 +msgid "" +"If you find that something is missing from this guide, or if you would " +"like to provide other feedback, file an Issue on the [project repository " +"for this guide][repo]. You can also suggest changes directly in a Pull " +"Request by clicking the \"Edit this page\" button at the right sidebar of" +" each page." msgstr "" -"如您发现本指南的疏漏之处，或想提供其他反馈，请在[本指南项目源码库][repo]" -"上提交报告 (Issue). 您也可在任意页面点击右边栏的 “Edit this " -"page”（编辑本页）按钮，创建 Pull Request（拉取请求）直接提交修改建议。" +"如您发现本指南的疏漏之处，或想提供其他反馈，请在[本指南项目源码库][repo]上提交报告 (Issue). 您也可在任意页面点击右边栏的 " +"“Edit this page”（编辑本页）按钮，创建 Pull Request（拉取请求）直接提交修改建议。" -#: ../../src/index.md:16 -#: 6d269e8d70184034bcb56385a6ca198f +#: ../../src/index.md:16 35c50bb5c3a345b4a4ae66b2df065376 msgid "Navigating the User Guide" msgstr "浏览《用户指南》" -#: ../../src/index.md:18 -#: ed74c9a4b623464480e2c184668fcec0 -msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +#: ../../src/index.md:18 9431edcf4e344fb89b6a251e627279d2 +msgid "" +"If you are a beginner user get started with the " +"[Introduction](/introduction/index.md) section. For advanced users the " +"subsections of the [Topics](/topics/index.md) have detailed information " +"about the most common topics for CWL." msgstr "" -"如您是新用户，请从 [《入门》](/introduction/index.md) " -"章节出发。而对于进阶用户而言， [《主题》](/topics/index.md)" -"部分各小节涵盖了关于 CWL 最常见话题的详细信息。" +"如您是新用户，请从 [《入门》](/introduction/index.md) 章节出发。而对于进阶用户而言， " +"[《主题》](/topics/index.md)部分各小节涵盖了关于 CWL 最常见话题的详细信息。" -#: ../../src/index.md:23 -#: cfa67cf5521b414da6f7d34cbed283f7 -msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." -msgstr "目录显示在顶部菜单和左侧边栏，本页更下方也有带小节链接的目录。右侧边栏有当前" -"单页分节链接，搜索功能在左侧边栏。" +#: ../../src/index.md:23 61cf57e61a9f46e5a1bff6368c5ad5e3 +msgid "" +"The Table of Contents is displayed at the top menu and also on the left " +"sidebar. It also appears further down this page but with links to " +"subsections. The right sidebar contains links to the sections of each " +"page, and the Search form is on the left sidebar." +msgstr "目录显示在顶部菜单和左侧边栏，本页更下方也有带小节链接的目录。右侧边栏有当前单页分节链接，搜索功能在左侧边栏。" -#: ../../src/index.md:28 -#: ee6b82bd86264e4bb1e8e4065b1e6b9c +#: ../../src/index.md:28 94381840d8a848c4a02fa97bfe83566d msgid "Table of Contents" msgstr "目录" -#: ../../src/introduction/basic-concepts.md:1 -#: e208c8a7506e41dcac9a403c5d2850c1 +#: ../../src/introduction/basic-concepts.md:1 c1271d88e203454688a22e61ee88f02a msgid "Basic Concepts" msgstr "基本概念" -#: ../../src/introduction/basic-concepts.md:3 -#: ac62d326a68145b695e46b714d4e8156 -msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." -msgstr "" -"本章节介绍用户开始运用通用工作流语言（CWL）所需的基本概念。" -"读者应了解工作流管理工具和 YAML, 且能较为自如地按照文中指示操作命令行。这些概" -"念在《用户指南》其他部分有更详尽的说明。如果您已了解 CWL, " -"或想查阅进阶内容，可以考虑跳过本章节。" - -#: ../../src/introduction/basic-concepts.md:10 -#: 984e6676b9d04c7092bc492f195dfb91 +#: ../../src/introduction/basic-concepts.md:3 dd462818cc9a4205b38866d0c5137ece +msgid "" +"This section describes the basic concepts for users to get started on " +"working with Common Workflow Language (CWL) workflows. Readers are " +"expected to be familiar with workflow managers, YAML, and comfortable " +"with following instructions for the command-line. The other sections of " +"the user guide cover the same concepts, but in more detail. If you are " +"already familiar with CWL or you are looking for more advanced content, " +"you may want to skip this section." +msgstr "" +"本章节介绍用户开始运用通用工作流语言（CWL）所需的基本概念。读者应了解工作流管理工具和 YAML, " +"且能较为自如地按照文中指示操作命令行。这些概念在《用户指南》其他部分有更详尽的说明。如果您已了解 CWL, 或想查阅进阶内容，可以考虑跳过本章节。" + +#: ../../src/introduction/basic-concepts.md:10 7a56d394fb244431aefce7ebbb834ecf msgid "The CWL Specification" msgstr "CWL 规约" -#: ../../src/introduction/basic-concepts.md:21 -#: cbe1d761da5b403d9605fa1fb8e62fdf -msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." -msgstr "CWL 规约由 CWL 社群撰写并维护，此规约现有多个版本，本《用户指南》" -"所涵盖的是版本 {{ cwl_version }}." - -#: ../../src/introduction/basic-concepts.md:25 -#: 3a71b269bd3c49eb913cf69b60373c24 -msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." -msgstr "" -"规约的版本号码由至多三个数字构成，以 `.`（圆点）分隔。第一个数字为主发布版本" -"，用于向后不可兼容的更改，例如删除过时的功能。第二个数字是次级发布版本，用于" -"新增功能或向后兼容的小幅调整。最后一个数字用于错误修复，例如打字错误或其他更" -"正。" - -#: ../../src/introduction/basic-concepts.md:33 -#: b171b72c48d44050a3416a7a42c4021d -msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." -msgstr "规约所使用的版本标号模型称为“语义型版本”，请参阅本章结尾以[了解更多](#learn-" -"more)相关信息。" - -#: ../../src/introduction/basic-concepts.md:37 -#: b3df1607e9d242d78b22dc44335fbe2d +#: ../../src/introduction/basic-concepts.md:21 35800ed2c56d489190d3702d9ad20fd7 +msgid "" +"The CWL specification is a document written and maintained by the CWL " +"community. The specification has different versions. The version covered " +"in this user guide is the {{ cwl_version }}." +msgstr "CWL 规约由 CWL 社群撰写并维护，此规约现有多个版本，本《用户指南》所涵盖的是版本 {{ cwl_version }}." + +#: ../../src/introduction/basic-concepts.md:25 3ab6dd6b2f694afeb08f3984a74f3efb +msgid "" +"The specification version can have up to three numbers separated by `.`s " +"(dots). The first number is the major release, used for backward-" +"incompatible changes like the removal of deprecated features. The second " +"number is the minor release, used for new features or smaller changes " +"that are backward-compatible. The last number is used for bug fixes, like" +" typos and other corrections to the specification." +msgstr "" +"规约的版本号码由至多三个数字构成，以 " +"`.`（圆点）分隔。第一个数字为主发布版本，用于向后不可兼容的更改，例如删除过时的功能。第二个数字是次级发布版本，用于新增功能或向后兼容的小幅调整。最后一个数字用于错误修复，例如打字错误或其他更正。" + +#: ../../src/introduction/basic-concepts.md:33 72ae1fb763a34c41b1b06adcbe1522c3 +msgid "" +"The model used for the specification version is called Semantic " +"Versioning. See the end of this section to [learn more](#learn-more) " +"about it." +msgstr "规约所使用的版本标号模型称为“语义型版本”，请参阅本章结尾以[了解更多](#learn-more)相关信息。" + +#: ../../src/introduction/basic-concepts.md:37 5aa7d3ee6cb048d888f1e1f49d0e08be msgid "Implementations" msgstr "实现" -#: ../../src/introduction/basic-concepts.md:39 -#: 078b58ffc1cc4d25a7c4eea3bb76e025 -msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +#: ../../src/introduction/basic-concepts.md:39 c87e6daefda74579a39924777b2e6809 +msgid "" +"An implementation of the CWL specification is any software written " +"following what is defined in a version of the specification document. " +"However, implementations may not implement every aspect of the " +"specification. CWL implementations are licensed under both Open Source " +"and commercial licenses." msgstr "" -"所谓 CWL 规约的某种“实现” (implementation), 指的是任何一种依照某版本的规约内" -"容而编写的软件。然而，诸实现未必能将规约的每个方面都转化为软件实体。目前，" -"CWL 各种实现的许可协议包括开源和商业许可。" +"所谓 CWL 规约的某种“实现” (implementation), " +"指的是任何一种依照某版本的规约内容而编写的软件。然而，诸实现未必能将规约的每个方面都转化为软件实体。目前，CWL " +"各种实现的许可协议包括开源和商业许可。" -#: ../../src/introduction/basic-concepts.md:44 -#: c3869b4ec5ff47d99e8da79770722e04 -msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." -msgstr "CWL非常适用于描述集群、云计算和高性能计算 (HPC) " -"等多节点、任务并行调度环境中的大规模工作流。" +#: ../../src/introduction/basic-concepts.md:44 c995e699ae2949219af252f9d802a43d +msgid "" +"CWL is well suited for describing large-scale workflows in cluster, cloud" +" and high performance computing environments where tasks are scheduled in" +" parallel across many nodes." +msgstr "CWL非常适用于描述集群、云计算和高性能计算 (HPC) 等多节点、任务并行调度环境中的大规模工作流。" -#: ../../src/introduction/basic-concepts.md:51 -#: 2482c84831fc4dfab629e7bfcfb41cbf +#: ../../src/introduction/basic-concepts.md:51 09171f48a3d841b2acb6d803b2340c8e msgid "CWL specification, implementations, and other tools." msgstr "CWL 规约、实现及其他工具。" #: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 +#: 1c1647a3496c4251a3193f94ee4e78c8 msgid "Processes and Requirements" msgstr "流程和要求" #: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 -msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +#: 854633336f4d4fc394e62c53ce022c6b +msgid "" +"A process is a computing unit that takes inputs and produces outputs. The" +" behavior of a process can be affected by the inputs, requirements, and " +"hints. There are four types of processes defined in the CWL specification" +" {{ cwl_version }}:" msgstr "" -"流程 (process) 是指接收输入并生成输出的计算单元，影响其行为的包括输入 " -"(input)、要求 (requirement) 及提示 (hint)。CWL 规约 {{ cwl_version }} " -"版定义了如下四种流程：" +"流程 (process) 是指接收输入并生成输出的计算单元，影响其行为的包括输入 (input)、要求 (requirement) 及提示 " +"(hint)。CWL 规约 {{ cwl_version }} 版定义了如下四种流程：" #: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f +#: 142a847f11d7462f8bf77bfe789410ca msgid "A command-line tool." msgstr "命令行工具。" #: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b +#: 7c7567fa690043f9b4b89bdf8ca60cad msgid "An expression tool." msgstr "表达式工具。" #: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 +#: 7afcf087d3ea49dabf1a641a2bb71b35 msgid "An operation." msgstr "操作。" #: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f +#: 6399939602334819a20b92b957352a8a msgid "A workflow." msgstr "工作流。" #: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 +#: 8c55b15cebf142899045f229ccc86b1e msgid "The processing units available in the CWL objects model." msgstr "可用在 CWL 对象模型中的处理单元。" #: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a -msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "“命令行工具”指的是 `echo`、`ls` 及 `tar` 等命令行程序的包装器 " -"(wrapper)。从工作流中可以调用命令行工具。" +#: ec54c0e67e894bfba2d0fbb0f87ffdf4 +msgid "" +"A command-line tool is a wrapper for a command-line utility like `echo`, " +"`ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "“命令行工具”指的是 `echo`、`ls` 及 `tar` 等命令行程序的包装器 (wrapper)。从工作流中可以调用命令行工具。" #: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 -msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +#: c88ad26efa794cbeb6f0690aa0cad5ea +msgid "" +"An expression tool is a wrapper for a JavaScript expression. It can be " +"used to simplify workflows and command-line tools, moving common parts of" +" a workflow execution into reusable JavaScript code that takes inputs and" +" produces outputs like a command-line tool." msgstr "" -"“表达式工具”是 JavaScript 表达式的包装器。" -"通过将工作流执行过程中的相同部分整理为可重用的 JavaScript " +"“表达式工具”是 JavaScript 表达式的包装器。通过将工作流执行过程中的相同部分整理为可重用的 JavaScript " "代码，像命令行工具一样接受输入并生成输出，工作流和命令行工具可以得到简化。" #: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef -msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +#: 946825a7ea2c450eb3e41b5548670fb7 +msgid "" +"Operation is an abstract process that also takes inputs, produces " +"outputs, and can be used in a workflow. But it is a special operation not" +" so commonly used. It is discussed in the [Operations " +"section](../topics/operations.md) of this user guide." msgstr "" -"“操作”是一种抽象的过程，它同样可接受输入、生成输出，并用于工作流中。但是，这" -"一类特殊操作并不十分常用。用户指南的 [《操作》](../topics/operations." -"md)一节将进行讨论。" +"“操作”是一种抽象的过程，它同样可接受输入、生成输出，并用于工作流中。但是，这一类特殊操作并不十分常用。用户指南的 " +"[《操作》](../topics/operations.md)一节将进行讨论。" #: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 -msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." -msgstr "" -"“工作流”指的是可分为步骤的流程。“步骤”可以是其他工作流（嵌套工作流），也可以" -"是命令行工具或表达式工具。工作流的输入可以传递给它的任一步骤，而其步骤生成的" -"输出可用作工作流的最终输出。" +#: 44aac23f302c4178accf7e431cfbb96c +msgid "" +"The workflow is a process that contains steps. Steps can be other " +"workflows (nested workflows), command-line tools, or expression tools. " +"The inputs of a workflow can be passed to any of its steps, while the " +"outputs produced by its steps can be used in the final output of the " +"workflow." +msgstr "“工作流”指的是可分为步骤的流程。“步骤”可以是其他工作流（嵌套工作流），也可以是命令行工具或表达式工具。工作流的输入可以传递给它的任一步骤，而其步骤生成的输出可用作工作流的最终输出。" #: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 -msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" -msgstr "CWL 规约允许其实现提供额外功能，或通过 *requirements* " -"（要求）指定工作流的先决条件。CWL 规约定义了诸种要求，如：" +#: 5afdb7aaf0bf4c1abf4c22cdbdd58be9 +msgid "" +"The CWL specification allows for implementations to provide extra " +"functionality and specify prerequisites to workflows through " +"*requirements*. There are many requirements defined in the CWL " +"specification, for instance:" +msgstr "CWL 规约允许其实现提供额外功能，或通过 *requirements* （要求）指定工作流的先决条件。CWL 规约定义了诸种要求，如：" #: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +#: 07c5789c59224ed78a3ecd03cfe872e9 +#, fuzzy +msgid "" +"[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement)" +" - enables JavaScript in expressions." msgstr "`InlineJavascriptWorkflow` —— 在表达式中启用 JavaScript。" #: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +#: 6f9854ae1b884ad39f88d2f39d66cb98 +#, fuzzy +msgid "" +"[`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow.html#SubworkflowFeatureRequirement)" +" - enables nested workflows." msgstr "`SubworkflowFeatureRequirement` —— 启用嵌套工作流。" #: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 -msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +#: 23fef6de073f4da18118e4d0512670fe +#, fuzzy +msgid "" +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow.html#InitialWorkDirRequirement)" +" - controls staging files in the input directory." msgstr "`InitialWorkDirRequirement` —— 控制输入目录中的暂存文件。" #: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee -msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +#: fb3762f91177401ea624d1e716d67ae6 +msgid "" +"Some CWL runners may provide requirements that are not in the " +"specification. For example, GPU requirements are supported in `cwltool` " +"through the `cwltool:CUDARequirement` requirement, but it is not part of " +"the {{ cwl_version }} specification and may not be supported by other CWL" +" runners." msgstr "" -"某些 CWL 运行程序可能提供规约之外的需求。例如 `cwltool` 提供 " -"`cwltool:CUDARequirement` 以支持GPU需求，但这不在 {{ cwl_version }} " -"版本规约之内，可能不受其他 CWL 运行程序支持。" +"某些 CWL 运行程序可能提供规约之外的需求。例如 `cwltool` 提供 `cwltool:CUDARequirement` " +"以支持GPU需求，但这不在 {{ cwl_version }} 版本规约之内，可能不受其他 CWL 运行程序支持。" #: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e -msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +#: b6a5cd431c324078a9a4e1513a14ee28 +msgid "" +"Hints are similar to requirements, but while requirements list features " +"that are required, hints list optional features. Requirements are " +"explained in detail in the [Requirements](../topics/requirements-and-" +"hints.md) section." msgstr "" -"“提示”与需求类似。其区别是，列为“需求”的功能是不可缺少的，而提示仅列出可选功" -"能。更详细介绍请见 [《需求》](../topics/requirements-and-hints.md)一章。" +"“提示”与需求类似。其区别是，列为“需求”的功能是不可缺少的，而提示仅列出可选功能。更详细介绍请见 [《需求》](../topics" +"/requirements-and-hints.md)一章。" #: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 +#: 88d7bad84dd341d2abb33673b8b8f250 msgid "FAIR Workflows" msgstr "FAIR 工作流" #: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 -msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +#: bcbf5d76cf5f47b2a9691b7d2d8ef891 +#, fuzzy +msgid "" +"The FAIR principles have laid a foundation for sharing and publishing " +"digital assets, and in particular, data. The FAIR principles emphasize " +"machine accessibility and that all digital assets should be Findable, " +"Accessible, Interoperable, and Reusable. Workflows encode the methods by " +"which the scientific process is conducted and via which data are created." +" It is thus important that workflows both support the creation of FAIR " +"data and themselves adhere to the FAIR principles. — [FAIR Computational " +"Workflows](https://workflows.community/groups/fair/), Workflows Community" +" Initiative." msgstr "" "FAIR 为数字资源（尤其是数据）的共享和发布提供了一组基本原则。FAIR " -"四项原则强调了“机器可读”的重要性，进而提出应使所有数字资源可发现、可访问、" -"可互操作以及可重用 (Findable, Accessible, Interoperable, and Reusable)。工作" -"流通过代码所描述的，正是科学工作得以开展、数据得以创建的过程。因此，" -"应强调工作流须支持创建 FAIR 数据，遵从 FAIR 原则。—— 工作流社群行动之[FAIR " -"计算工作流](https://workflows.community/groups/fair/)。" +"四项原则强调了“机器可读”的重要性，进而提出应使所有数字资源可发现、可访问、可互操作以及可重用 (Findable, Accessible, " +"Interoperable, and " +"Reusable)。工作流通过代码所描述的，正是科学工作得以开展、数据得以创建的过程。因此，应强调工作流须支持创建 FAIR 数据，遵从 FAIR" +" 原则。—— 工作流社群行动之[FAIR 计算工作流](https://workflows.community/groups/fair/)。" #: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a -msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +#: 4ea1d3bf04dc42f0bc6735a45b9e0dc0 +msgid "" +"CWL has roots in \"make\" and many similar tools that determine order of " +"execution, based on dependencies between tasks. However, unlike \"make\"," +" CWL tasks are isolated, and you must be explicit about your inputs and " +"outputs." msgstr "" -"CWL 滥觞于“make”一类推定任务间依赖关系，并据此决定其执行次序的工具。但与“make" -"”的不同在于，CWL 任务是存在于独立环境中的，其输入和输出需要明确指定。" +"CWL 滥觞于“make”一类推定任务间依赖关系，并据此决定其执行次序的工具。但与“make”的不同在于，CWL " +"任务是存在于独立环境中的，其输入和输出需要明确指定。" #: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee -msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +#: c0f53138bf084939a54b0a576b44199f +msgid "" +"The benefit of explicitness and isolation are flexibility, portability, " +"and scalability; tools and workflows described with CWL can transparently" +" leverage technologies such as Docker and be used with CWL " +"implementations from different vendors." msgstr "" -"明确而独立，其益处在于灵活、可移植及可扩缩。CWL 所描述的工具和工作流，" -"既能无缝对接 Docker 等技术以发挥其优势，又能通用于不同供应方的 CWL " -"实现环境中。" +"明确而独立，其益处在于灵活、可移植及可扩缩。CWL 所描述的工具和工作流，既能无缝对接 Docker 等技术以发挥其优势，又能通用于不同供应方的 " +"CWL 实现环境中。" #: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 +#: 91d6eb4984a6410ba99616b6617ba9af msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "同时，`cwltool` 将 PROV-O 标准本体 (standard ontology) 运用于数据来源的保证。" #: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 -#: 65c24244713741e196da08cb9ba237b2 -#: f059896039524095b4deb65d693f8ddf -#: 3439764fab0e49d2bcb7c9fbae556e65 +#: ../../src/introduction/prerequisites.md:183 +#: ../../src/introduction/quick-start.md:94 0d7e607b00b9485aa2e3c5fb0a931bc6 +#: 161697ed3e864155bb89d8be794fc139 b4a7563eabf547c3bf7eab2567a27b51 msgid "Learn More" msgstr "了解更多信息" #: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de +#: 7221a89559944627b4c3db37f468f72c msgid "Semantic Versioning - " msgstr "语义型版本 —— " #: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 -msgid "The CWL Specification page in the CWL website: " +#: bccf086fc9514f76b60dc161e3a09da3 +msgid "" +"The CWL Specification page in the CWL website: " +"" msgstr "CWL网站上的规约页面： " #: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 -msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +#: a5b37924c7d04ab984ff2542847afc4a +#, fuzzy +msgid "" +"The Command Line Tool Description Standard: " +"<[https://www.commonwl.org/v1.2/CommandLineTool.html](https://w3id.org/cwl/CommandLineTool.html)>" msgstr "" -"GitHub 上的 CWL 规约当前版本： {{ ''.format(cwl_version_text) }}" +"来自 " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" #: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 -msgid "The list of Implementations in the CWL website: " -msgstr "CWL 网站所列的诸种实现：" +#: 44af015fa36644b99f07338d241d29c1 +msgid "" +"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" +"GitHub 上的 CWL 规约当前版本： {{ ''.format(cwl_version_text) }}" #: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 +#: bffca993172048a4b7ab7c62637662e2 +msgid "" +"The list of Implementations in the CWL website: " +"" +msgstr "CWL 网站所列的诸种实现：" + +#: ../../src/introduction/basic-concepts.md:185 +#: 84c61946406347c8b138772909110d54 msgid "PROV-O: The PROV Ontology - " msgstr "PROV-O：PROV 本体 —— " -#: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b -msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." -msgstr "CWL 操作 (operations) 见于本《用户指南》中[《操作》](../topics/operations." -"md)一章。" +#: ../../src/introduction/basic-concepts.md:186 +#: eb0b6a62e06143eabc7b92acff9643ea +msgid "" +"CWL Operations are covered in the [Operations](../topics/operations.md) " +"section of this user guide." +msgstr "CWL 操作 (operations) 见于本《用户指南》中[《操作》](../topics/operations.md)一章。" -#: ../../src/introduction/index.md:1 -#: 1769a0cbf4de4d77879c1f202cd11af9 +#: ../../src/introduction/index.md:1 48532f7701c54166859098e521a43db0 msgid "Introduction" msgstr "概述" -#: ../../src/introduction/index.md:3 -#: 950370f0a36048b38e1bde9b78f80816 -msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." -msgstr "本章节将引导您了解 CWL简介、学习本《用户指南》所需的准备，以及有利于您阅读理" -"解本《指南》的若干基本概念。" +#: ../../src/introduction/index.md:3 08db628a949b4513b824ee334e70a7df +msgid "" +"This section will guide you through a short introduction to CWL, the " +"prerequisites for following this user guide, and some basic concepts that" +" are useful to know before reading the rest of the user guide." +msgstr "本章节将引导您了解 CWL简介、学习本《用户指南》所需的准备，以及有利于您阅读理解本《指南》的若干基本概念。" -#: ../../src/introduction/prerequisites.md:1 -#: f01faaf1b253407cbbc2f353c24774f3 +#: ../../src/introduction/prerequisites.md:1 d3f5749a76c14fdf8052f5f683d11b9e msgid "Prerequisites" msgstr "学习前的准备" -#: ../../src/introduction/prerequisites.md:6 -#: 353b14f06ee845d0a06a829643e31534 -msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." -msgstr "" -"学习本《用户指南》前，首先需要准备好本节所述的软件及其配置。CWL " -"标准现有多种工作流运行器和平台实现。本节列出的要求主要着眼于 CWL " -"的参考运行程序即 `cwltool`。您也可以使用与之兼容的其他 CWL 运行程序或工作流系" -"统，但运行结果和界面可能有所出入（尽管严格意义上属于工作流的输出应该相同）。" - -#: ../../src/introduction/prerequisites.md:12 -#: b5a0607096814c0aa577f977c3b57c54 +#: ../../src/introduction/prerequisites.md:6 ab9e21b3e99641d096ba70012b4eb035 +msgid "" +"The software and configurations listed in this section are prerequisites " +"for following this user guide. The CWL standards are implemented by many " +"different workflow runners and platforms. This list of requirements " +"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" +"compatible runner or workflow system, but the results and interface may " +"look different (though the exact workflow outputs should be identical)." +msgstr "" +"学习本《用户指南》前，首先需要准备好本节所述的软件及其配置。CWL 标准现有多种工作流运行器和平台实现。本节列出的要求主要着眼于 CWL " +"的参考运行程序即 `cwltool`。您也可以使用与之兼容的其他 CWL " +"运行程序或工作流系统，但运行结果和界面可能有所出入（尽管严格意义上属于工作流的输出应该相同）。" + +#: ../../src/introduction/prerequisites.md:12 8ed426ebcb744839915e7c414d69b1e9 msgid "CWL Implementations" msgstr "CWL 实现" -#: ../../src/introduction/prerequisites.md:14 -#: ff2bb4c6504b456bac7ca9c514414dbf -msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +#: ../../src/introduction/prerequisites.md:14 ff74d48407464c4b9d451fa419137144 +msgid "" +"There are many implementations of the CWL standards. Some are complete " +"CWL runners, while others could be plug-ins or extensions to workflow " +"engines. We have a better explanation in the [Implementations](basic-" +"concepts.md#implementations) section." msgstr "" -"CWL 标准有多种实现，既包括完整的 CWL " -"运行程序，也有工作流引擎的插件或扩展程序。 详见[《实现》](basic-concepts." -"md#implementations)一章。" +"CWL 标准有多种实现，既包括完整的 CWL 运行程序，也有工作流引擎的插件或扩展程序。 详见[《实现》](basic-" +"concepts.md#implementations)一章。" -#: ../../src/introduction/prerequisites.md:19 -#: cbbcce4c2a96471b8b0ae3593ad59de4 +#: ../../src/introduction/prerequisites.md:19 eb98aa9c71d746a69e9610996ffc5b47 msgid "Operating System" msgstr "操作系统" -#: ../../src/introduction/prerequisites.md:21 -#: 5089fdba8aed4113983fa86e698df98b -msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +#: ../../src/introduction/prerequisites.md:21 209a0018e7da48f09b27dc507ba14d24 +msgid "" +"We recommend using an up-to-date operating system. You can choose any of " +"the following options for your operating system:" msgstr "建议使用以下任一可选系统的最新版本：" -#: ../../src/introduction/prerequisites.md:24 -#: dbaa4bae22fe4d05b18d7351967ddbc3 +#: ../../src/introduction/prerequisites.md:24 8baf869537ea478791356320280df928 msgid "Linux" msgstr "Linux" -#: ../../src/introduction/prerequisites.md:25 -#: c05187af85be41b782678b79627f8fbf +#: ../../src/introduction/prerequisites.md:25 248e9760ce60442eb10ab7247d6af23b msgid "macOS" msgstr "macOS" -#: ../../src/introduction/prerequisites.md:26 -#: beb6cf4d7c154eb9b6d7fe024a318ed7 +#: ../../src/introduction/prerequisites.md:26 d89306bbadf44b6bba8959f1f68cc2f0 msgid "Windows" msgstr "Windows" -#: ../../src/introduction/prerequisites.md:29 -#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 -msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +#: ../../src/introduction/prerequisites.md:29 aeeb990abbbd42cca122c342054be29c +#, fuzzy +msgid "" +"If you are using Windows, you will have to install the Windows Subsystem " +"for Linux 2 as documented in the [`cwltool` documentation for Microsoft " +"Windows users](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users). Your operating " +"system also needs internet access and a recent version of Python (3.6+)." msgstr "" "如使用 Windows 操作系统，须首先安装[适用于 Linux 的 Windows 子系统 " "2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2)。请参阅 " -"`cwltool` [说明文件](https://github.com/common-workflow-language/cwltool/" -"blob/main/README.rst#ms-windows-users) ，了解关于安装 WSL2 " -"的细节。同时，您的操作系统还需能接入互联网，以及运行较新版本（3.6 以上）的 " -"Python." +"`cwltool` [说明文件](https://github.com/common-workflow-" +"language/cwltool/blob/main/README.rst#ms-windows-users) ，了解关于安装 WSL2 " +"的细节。同时，您的操作系统还需能接入互联网，以及运行较新版本（3.6 以上）的 Python." -#: ../../src/introduction/prerequisites.md:35 -#: 56d78c95daa54135b6aa9b2bfdc34d01 +#: ../../src/introduction/prerequisites.md:34 21d1f29fb15745c480194eae6acdd031 msgid "CWL Runner" msgstr "CWL 运行程序" -#: ../../src/introduction/prerequisites.md:41 -#: 0f2704bf1f7148be95e999e312899f11 -msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +#: ../../src/introduction/prerequisites.md:39 89f0bf6ff8544a6d87114085be8e0bb6 +msgid "" +"The first thing you will need for running CWL workflows is a CWL runner. " +"`cwltool` is a Python Open Source project maintained by the CWL " +"community. It is also the CWL reference runner, which means it must " +"support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -"要运行CWL工作流，首先要用到的就是 CWL 运行程序 (runner). `cwltool`作为 CWL " -"社群共同维护开发的 Python 开源项目，正是 CWL 运行程序的参考实现，也就是说，" -"它必须完整支持当前 {{ cwl_version }} 版本 CWL 规约。" +"要运行CWL工作流，首先要用到的就是 CWL 运行程序 (runner). `cwltool`作为 CWL 社群共同维护开发的 Python " +"开源项目，正是 CWL 运行程序的参考实现，也就是说，它必须完整支持当前 {{ cwl_version }} 版本 CWL 规约。" -#: ../../src/introduction/prerequisites.md:46 -#: 86264c9e56104ecea9146407c379aae2 -msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +#: ../../src/introduction/prerequisites.md:44 068f09d4d66547448693f7b9dadef497 +msgid "" +"`cwltool` can be installed with `pip`, `apt`, or `conda`. We recommend " +"using a virtual environment like `venv` or `conda`." msgstr "" -"`cwltool` 可以用 `pip` 命令安装，而且我们推荐使用 `venv` 或 `conda` " -"等虚拟环境。以下命令将使用 `venv` 模块创建并激活一个 Python 虚拟环境，" -"并在该环境中安装 `cwltool`:" - -#: ../../src/introduction/prerequisites.md:51 -#: 0a0f0e5151ab4c498b4f8a12c016f28d -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "使用 `pip` 和 `venv` 安装 `cwltool`." -#: ../../src/introduction/prerequisites.md:62 -#: f7aaafeee230400da056464c853582c2 -msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +#: ../../src/introduction/prerequisites.md:48 1edf8b8438334ae29dc406dbfd711228 +#, fuzzy +msgid "" +"Visit the `cwltool` " +"[documentation](https://cwltool.readthedocs.io/en/latest/#install) for " +"details on installing `cwltool`." msgstr "" -"请参阅 `cwltool` [说明文件](https://github.com/common-workflow-language/" -"cwltool#install)查看其他安装方法，包括用 `apt` 或 `conda`." +"请参阅 `cwltool` [说明文件](https://github.com/common-workflow-" +"language/cwltool#install)查看其他安装方法，包括用 `apt` 或 `conda`." -#: ../../src/introduction/prerequisites.md:65 -#: 5eced7e4cd084e8a806b1d3b12d0c000 +#: ../../src/introduction/prerequisites.md:52 5e300141ce43435f9437507374987213 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "我们来用`cwltool` 处理名为 `true.cwl` 的一个简单 CWL 工具描述。" -#: ../../src/introduction/prerequisites.md:67 -#: 040c019b6e844eda8c8c2b210852516b +#: ../../src/introduction/prerequisites.md:54 282ac7ba2a2346feac2456bcda0f214a msgid "`true.cwl`" msgstr "`true.cwl`" -#: ../../src/introduction/prerequisites.md:73 -#: 6391e08e0bde49f4b21286d8fdb97433 -msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" -msgstr "" -"`cwltool` 命令有一个选项可用于“确认” (validate) 也就是检验 CWL " -"工具和工作流描述。使用该选项可以进行 CWL 文件语法分析，查找语法错误，并以 " -"CWL 标准验证工作流描述的规范性。然而，进行这一系列操作并不会运行 CWL 文件。" -"要确认 CWL 工作流（包括类似前例的独立命令行工具描述），请将 `--validate` " -"选项传递给 `cwltool` 命令：" - -#: ../../src/introduction/prerequisites.md:79 -#: cdef47fca304479c9a9df75afc0afb35 +#: ../../src/introduction/prerequisites.md:60 0b36f94f479a4bce9bd9be9983894421 +msgid "" +"The `cwltool` command has an option to validate CWL tool and workflow " +"descriptions. This option will parse the CWL document, look for syntax " +"errors, and verify that the workflow descriptions are compliant with the " +"CWL standards. However, these actions will be performed without running " +"the document. To validate CWL workflows (or even a standalone command " +"line tool description like the above) pass the `--validate` option to the" +" `cwltool` command:" +msgstr "" +"`cwltool` 命令有一个选项可用于“确认” (validate) 也就是检验 CWL 工具和工作流描述。使用该选项可以进行 CWL " +"文件语法分析，查找语法错误，并以 CWL 标准验证工作流描述的规范性。然而，进行这一系列操作并不会运行 CWL 文件。要确认 CWL " +"工作流（包括类似前例的独立命令行工具描述），请将 `--validate` 选项传递给 `cwltool` 命令：" + +#: ../../src/introduction/prerequisites.md:66 5fce122794e34892b430ca4bdba5ba50 msgid "Validating `true.cwl` with `cwltool`." msgstr "用 `cwltool` 确认（即检验）`true.cwl`." -#: ../../src/introduction/prerequisites.md:84 -#: d41c4bc740aa474ea09a7cbd267c8840 +#: ../../src/introduction/prerequisites.md:71 73f074f47d1449dcb40ff960a84851fd msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "去掉 `--validate` 选项，才能运行 CWL 工具描述：" -#: ../../src/introduction/prerequisites.md:86 -#: 24d7be55d3994f0b82c38da47918e0c9 +#: ../../src/introduction/prerequisites.md:73 2dd5a67870ca41b48e17c468ba15888b msgid "Running `true.cwl` with `cwltool`." msgstr "用 `cwltool` 运行 `true.cwl`." -#: ../../src/introduction/prerequisites.md:91 -#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 -msgid "Cwl-runner Python Module" -msgstr "Python 模块 cwl-runner" - -#: ../../src/introduction/prerequisites.md:93 -#: 096d0a50f69e48bd9915238d1b4264c1 -msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +#: ../../src/introduction/prerequisites.md:78 d2dc809318be49cc996d892e93ad84ac +msgid "Generic ``cwl-runner`` alias" msgstr "" -"`cwl-runner` 是任何符合标准的 CWL 运行程序“不分实现”的别名 (alias). 简言之" -"，`cwl-runner` 这个别名命令可独立地启用，不依赖于 CWL 运行程序的具体名称。" -"用户只需调用 `cwl-runner`, 而无需直接调用诸如 `cwltool` 这样的某个 CWL " -"运行程序。经系统管理员或用户安装后，`cwl-runner` 命令用来代指其首选的 CWL " -"实现。这样的安排更便利于多个 CWL 运行程序共存的环境。" -#: ../../src/introduction/prerequisites.md:101 -#: f9df974a8e2645a6918e67466bd1fdc2 -msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" -msgstr "" -"CWL 社群发布有名为 `cwlref-runner` 的 Python 包，以安装 `cwl-runner` 作为 " -"`cwltool` 的别名" +#: ../../src/introduction/prerequisites.md:80 9809c2e262924ef286b0bd62e0b00995 +msgid "" +"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " +"runner. This simply means that the `cwl-runner` alias command can be " +"invoked independently, and is not reliant on a particular CWL runner " +"program name. Users can invoke `cwl-runner` instead of invoking a CWL " +"runner like `cwltool` directly. The `cwl-runner` is installed by a system" +" administrator or user to point to the preferred CWL implementation. This" +" is convenient for environments with multiple CWL runners." +msgstr "" +"`cwl-runner` 是任何符合标准的 CWL 运行程序“不分实现”的别名 (alias). 简言之，`cwl-runner` " +"这个别名命令可独立地启用，不依赖于 CWL 运行程序的具体名称。用户只需调用 `cwl-runner`, 而无需直接调用诸如 `cwltool` " +"这样的某个 CWL 运行程序。经系统管理员或用户安装后，`cwl-runner` 命令用来代指其首选的 CWL 实现。这样的安排更便利于多个 " +"CWL 运行程序共存的环境。" + +#: ../../src/introduction/prerequisites.md:88 6dd6aa836099469381fb564d63b84f3d +#, fuzzy +msgid "" +"The CWL community publishes a Python package with the name `cwlref-" +"runner` that installs an alias for `cwltool` under the name `cwl-runner`." +msgstr "CWL 社群发布有名为 `cwlref-runner` 的 Python 包，以安装 `cwl-runner` 作为 `cwltool` 的别名" -#: ../../src/introduction/prerequisites.md:104 -#: 71ebe91d4bda473abe87578929433212 +#: ../../src/introduction/prerequisites.md:91 cc1a9b95508e44a1bf08ae75d990c301 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "用 `pip` 为 cwltool 安装别名 `cwl-runner`." -#: ../../src/introduction/prerequisites.md:111 -#: 746c6fc9c29d466494458a08d4c96672 -msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." -msgstr "现在要检验或运行工作流就可以用 `cwl-runner` 这个命令了，它将为你调用 " -"`cwltool`. 其运行结果和输出应当与上一节中相同。" +#: ../../src/introduction/prerequisites.md:98 8f8c80f705d94d4899b250bbf9c54562 +msgid "" +"Now you can validate and run your workflow with the `cwl-runner` " +"executable, which will invoke `cwltool`. You should have the same results" +" and output as in the previous section." +msgstr "现在要检验或运行工作流就可以用 `cwl-runner` 这个命令了，它将为你调用 `cwltool`. 其运行结果和输出应当与上一节中相同。" -#: ../../src/introduction/prerequisites.md:115 -#: b9cc5a843a0f49daad56e9303657bdd5 +#: ../../src/introduction/prerequisites.md:102 176e4214d18149f3ba0bda692bcf760f msgid "Validating `true.cwl` with `cwl-runner`." msgstr "用 `cwl-runner` 检验 `true.cwl`." -#: ../../src/introduction/prerequisites.md:120 -#: 34ab40437ab646488ba3ee86cd7fe071 +#: ../../src/introduction/prerequisites.md:107 4890bf20bc3842d3a7421b555bcda94a msgid "Running `true.cwl` with `cwl-runner`." msgstr "用 `cwl-runner` 运行 `true.cwl`." -#: ../../src/introduction/prerequisites.md:125 -#: 705807fae182425dbf4244dbf2be1226 -msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +#: ../../src/introduction/prerequisites.md:112 2475a83cf6ed4389bb680fa37e8fe69c +msgid "" +"Another way to execute `cwl-runner` is by invoking the file directly. For" +" that, the first thing you need to do is copy `true.cwl` workflow into a " +"new file: `true_shebang.cwl`, and include a special first line, a " +"*shebang*:" msgstr "" -"执行 `cwl-runner` 还有一种方法，即直接调用 CWL 文件。为此，首先将 `true.cwl` " -"工作流复制为新文件 `true_shebang.cwl`, 然后加入特定的 *shebang* (即 \"hash-" -"bang\") 作为首行：" +"执行 `cwl-runner` 还有一种方法，即直接调用 CWL 文件。为此，首先将 `true.cwl` 工作流复制为新文件 " +"`true_shebang.cwl`, 然后加入特定的 *shebang* (即 \"hash-bang\") 作为首行：" -#: ../../src/introduction/prerequisites.md:129 -#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#: ../../src/introduction/prerequisites.md:116 24da787aa76c4480838a93ba0533898d msgid "`true_shebang.cwl`" msgstr "`true_shebang.cwl`" -#: ../../src/introduction/prerequisites.md:135 -#: 164c438baab54ec19bbb4584a10dd411 +#: ../../src/introduction/prerequisites.md:122 4f3cb8d1f9ce4e3d852e81aa4e0f60be msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "现在，用 `chmod u+x` 命令将 `true_shebang.cwl` 设为可执行。" -#: ../../src/introduction/prerequisites.md:137 -#: bf8be77af6154326b28442c5d2e2b852 +#: ../../src/introduction/prerequisites.md:124 27693d62faa045d9b03143d9bd2afcdf msgid "Making `true.cwl` executable." msgstr "令 `true.cwl` 可执行。" -#: ../../src/introduction/prerequisites.md:144 -#: 695184d1b45a42f393e2da99c3721773 -msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +#: ../../src/introduction/prerequisites.md:131 703531514abe4fd48015c472005dbffa +msgid "" +"And finally, you can execute it directly in the command-line. On " +"execution, the program specified in the shebang (`cwl-runner`) will be " +"used to execute the rest of the file." msgstr "" -"到此，此 CWL 文件即可在命令行直接执行了。一旦下令执行这个文件，“shebang”" -"所指定的程序 (即 `cwl-runner`) 将实际执行其余部分。" +"到此，此 CWL 文件即可在命令行直接执行了。一旦下令执行这个文件，“shebang”所指定的程序 (即 `cwl-runner`) " +"将实际执行其余部分。" -#: ../../src/introduction/prerequisites.md:148 -#: 7c4f45b3e7b549e186126693aa4a3d4f +#: ../../src/introduction/prerequisites.md:135 abba2e14c4e54252bb75983274663a7a msgid "Running `true_shebang.cwl` with a shebang." msgstr "使用 shebang 运行 `true_shebang.cwl`." -#: ../../src/introduction/prerequisites.md:154 -#: 3ba23b4ea01c46848e4e43bbeff5f5a1 -msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," -msgstr "" -"所谓 *shebang* 是指脚本起始处的 `#!` 两个连续字符。如果脚本可执行，" -"操作系统将用紧跟在 shebang 之后写明的可执行程序来执行此脚本。一个好习惯是用 " -"`/usr/bin/env <可执行程序名>`， 而不是硬性编码其所在路径，理由是 `/usr/" -"bin/env <可执行程序名>` 进行的，是在系统 `PATH`（命令路径环境变量）" -"中查找 `<可执行程序名>` 的实际路径" - -#: ../../src/introduction/prerequisites.md:161 -#: eec6c07455384630809ff1c532bfe7d4 +#: ../../src/introduction/prerequisites.md:141 11fea992c00940d29eb29ccf4b9370e9 +#, fuzzy +msgid "" +"The *shebang* is the two-character sequence `#!` at the beginning of a " +"script. When the script is executable, the operating system will execute " +"the script using the executable specified after the shebang. It is " +"considered a good practice to use `/usr/bin/env [executable]` rather than" +" using a hard-coded location, since `/usr/bin/env [executable]` looks for" +" the `[executable]` program in the system `PATH`," +msgstr "" +"所谓 *shebang* 是指脚本起始处的 `#!` 两个连续字符。如果脚本可执行，操作系统将用紧跟在 shebang " +"之后写明的可执行程序来执行此脚本。一个好习惯是用 `/usr/bin/env <可执行程序名>`， 而不是硬性编码其所在路径，理由是 " +"`/usr/bin/env <可执行程序名>` 进行的，是在系统 `PATH`（命令路径环境变量）中查找 " +"`<可执行程序名>` 的实际路径" + +#: ../../src/introduction/prerequisites.md:148 854736eef2ac4b63b187a4cea9660ae4 msgid "Text Editor" msgstr "文本编辑器" -#: ../../src/introduction/prerequisites.md:163 -#: f6b39b12bd5c495cb53e2795bf9200ed -msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +#: ../../src/introduction/prerequisites.md:150 480fbb7a743046068c114fff5b396a9f +msgid "" +"You can use any text editor with CWL, but for syntax highlighting we " +"recommend an editor with YAML support. Popular editors are Visual Studio " +"Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -"任何文本编辑器都可以用于 CWL 编程。不过，我们建议使用支持显示 YAML " -"语法的编辑器。常用的编辑器包括 Visual Studio Code、Sublime、WebStorm、vim/" -"neovim 以及 Emacs 等。" +"任何文本编辑器都可以用于 CWL 编程。不过，我们建议使用支持显示 YAML 语法的编辑器。常用的编辑器包括 Visual Studio " +"Code、Sublime、WebStorm、vim/neovim 以及 Emacs 等。" -#: ../../src/introduction/prerequisites.md:167 -#: 2fdb62a13f9447bc89183426260ce781 -msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" -msgstr "以下 Visual Studio Code 和 WebStorm 的扩展程序支持 CWL " -"集成，提供自定义语法显示、改进的自动补全等功能：" +#: ../../src/introduction/prerequisites.md:154 28da3eea8fd245d1936013d021c25164 +msgid "" +"There are extensions for Visual Studio Code and WebStorm that provide " +"integration with CWL, and features such as customized syntax highlighting" +" and better auto-complete:" +msgstr "以下 Visual Studio Code 和 WebStorm 的扩展程序支持 CWL 集成，提供自定义语法显示、改进的自动补全等功能：" -#: ../../src/introduction/prerequisites.md:171 -#: 1f07135156254f74a6b043bf33d00cc3 -msgid "Visual Studio Code with the Benten (CWL) plugin - " +#: ../../src/introduction/prerequisites.md:158 73c08e11e90d4c7f952307a1cdaa360b +msgid "" +"Visual Studio Code with the Benten (CWL) plugin - " +"" msgstr "" "带 Benten (CWL) 插件的 Visual Studio Code —— " -#: ../../src/introduction/prerequisites.md:172 -#: de344f356b1c466d9131cdbd4d7353a3 -msgid "cwl-plugin for IntelliJ - " +#: ../../src/introduction/prerequisites.md:159 a5b788252a924338963f0ed198fc22ca +msgid "" +"cwl-plugin for IntelliJ - " msgstr "" "IntelliJ 的 cwl-plugin 插件 —— " -#: ../../src/introduction/prerequisites.md:174 -#: 3f9324ede11441f58d93875867034cf0 -msgid "The CWL community also maintains a list of editors and viewers: " +#: ../../src/introduction/prerequisites.md:161 ee705b919acd461a8d9622821da246b6 +msgid "" +"The CWL community also maintains a list of editors and viewers: " +"" msgstr "CWL 社群维护的编辑器和阅览器列表：" -#: ../../src/introduction/prerequisites.md:177 -#: 6ce8b81560e341c580d316d69202b268 +#: ../../src/introduction/prerequisites.md:164 7724b63db3cc45139379898d047c0f83 msgid "Docker" msgstr "Docker" -#: ../../src/introduction/prerequisites.md:181 -#: 40cfd559d6a848d1aae354d3bdaa8e9c -msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +#: ../../src/introduction/prerequisites.md:168 eff13997c1ce43d1ad2d7a4d927394fe +msgid "" +"`cwltool` uses Docker to run tools, workflows, and workflow steps that " +"specify a software container. Follow the instructions in the Docker " +"documentation to install it for your operating system: " +"." msgstr "" -"`cwltool` 使用 Docker 运行指定了软件容器的工具、工作流及工作流步骤。请按照 " -"Docker 文档在您的操作系统中安装 Docker: 。" +"`cwltool` 使用 Docker 运行指定了软件容器的工具、工作流及工作流步骤。请按照 Docker 文档在您的操作系统中安装 " +"Docker: 。" -#: ../../src/introduction/prerequisites.md:185 -#: 8a9a50b0ebe847ce90593881ffe0d69c -msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." -msgstr "" -"您无需掌握如何编写和构建 Docker 容器。在接下来的部分里，我们将用现成的 " -"Docker 映像来运行范例，并阐明有无容器的执行模型之间有何不同。" +#: ../../src/introduction/prerequisites.md:172 2872503638624b7e904ae407375ac165 +msgid "" +"You do not need to know how to write and build Docker containers. In the " +"rest of the user guide, we will use existing Docker images for running " +"examples, and to clarify the differences between the execution models " +"with and without containers." +msgstr "您无需掌握如何编写和构建 Docker 容器。在接下来的部分里，我们将用现成的 Docker 映像来运行范例，并阐明有无容器的执行模型之间有何不同。" -#: ../../src/introduction/prerequisites.md:191 -#: 923cf9dd6d6c417aabe42f9fa62ffa35 -msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." -msgstr "" -"`cwltool` 支持使用 Docker、Podman、udocker 和 Singularity " -"运行容器，并支持从非官方容器仓库拉取映像。" +#: ../../src/introduction/prerequisites.md:178 52ddcc9bc1554d809371fc0a503c40bc +msgid "" +"`cwltool` supports running containers with Docker, Podman, udocker, and " +"Singularity. You can also use alternative container registries for " +"pulling images." +msgstr "`cwltool` 支持使用 Docker、Podman、udocker 和 Singularity 运行容器，并支持从非官方容器仓库拉取映像。" -#: ../../src/introduction/prerequisites.md:198 -#: 9390b03889de44638141d705e0ef8322 -msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +#: ../../src/introduction/prerequisites.md:185 f3bbfa17f31a459386461951de157dd2 +msgid "" +"The [Implementations](basic-concepts.md#implementations) topic in the " +"next section, Basic Concepts." msgstr "下一节《基本概念》之[“实现”](basic-concepts.md#implementations)主题。" -#: ../../src/introduction/prerequisites.md:199 -#: 12042e411482458f8c35a2491f9433e0 +#: ../../src/introduction/prerequisites.md:186 e22b9e7c56104e018e6d2f3d547c01ea msgid "The Python `venv` module: " msgstr "Python `venv` 模块：" -#: ../../src/introduction/quick-start.md:1 -#: cdd4196f9aa34beba115901ec97913b6 +#: ../../src/introduction/quick-start.md:1 9ca367e3ca754a0fa88dab64724b95b6 msgid "Quick Start" msgstr "快速入门" -#: ../../src/introduction/quick-start.md:3 -#: c43d9675ed134b78b02acb5a102a764a -msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." -msgstr "本节将为您概述 CWL 是什么，以及在何处可以进一步学习。您不需要有 CWL " -"知识储备，但要能较为自如地按照文中指示操作命令行。" +#: ../../src/introduction/quick-start.md:3 733db5702c774f32b8c91d13f74f3720 +msgid "" +"This section will show you a brief overview of what CWL is, and where you" +" can learn more about it. No previous knowledge of CWL is required, but " +"you must be comfortable following instructions for the command-line." +msgstr "本节将为您概述 CWL 是什么，以及在何处可以进一步学习。您不需要有 CWL 知识储备，但要能较为自如地按照文中指示操作命令行。" -#: ../../src/introduction/quick-start.md:7 -#: 280936bb2a22469799b2c9e9ba22adee +#: ../../src/introduction/quick-start.md:7 0b164074dd0849c3b2c8d2f78ea99e95 msgid "“Hello World”" msgstr "“Hello World”（“世界您好”程序）" -#: ../../src/introduction/quick-start.md:12 -#: cb203354977d42a58112d09357f62565 -msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +#: ../../src/introduction/quick-start.md:12 6485f96f638548fbb7addc57f6cde92b +msgid "" +"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " +"The example below shows a simple CWL “Hello World” workflow annotated " +"with comments. Note that comments start with `#`:" msgstr "" -"CWL 文件按照 [YAML](../topics/index.md) 或者 JSON 格式编写的。" -"下例演示了一个简单的 CWL 工作流“Hello World”，并且标有注释，即 `#` " -"符号后面的文字：" +"CWL 文件按照 [YAML](../topics/index.md) 或者 JSON 格式编写的。下例演示了一个简单的 CWL " +"工作流“Hello World”，并且标有注释，即 `#` 符号后面的文字：" -#: ../../src/introduction/quick-start.md:16 -#: 9e51962a7e5c47248f3e20703ae101eb +#: ../../src/introduction/quick-start.md:16 5e06f9c4754347b8bac88d24c21e0f67 msgid "`hello_world.cwl`" msgstr "`hello_world.cwl`" -#: ../../src/introduction/quick-start.md:22 -#: 7e475e3f3c4a4404bb0236124c0f7ce7 -msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +#: ../../src/introduction/quick-start.md:22 6a13fb9112ab41acb60dc65b3656f63e +msgid "" +"The example above is just a wrapper for the `echo` command-line tool. " +"Running the workflow above with the default input values will produce the" +" same result as the command-line `echo \"Hello World\"`." msgstr "" -"上面的示例不过是 `echo` 命令行工具的包装器 (wrapper). " -"使用默认输入值运行上述工作流，产生的结果会和命令 `echo \"Hello World\"` " -"别无二致。" +"上面的示例不过是 `echo` 命令行工具的包装器 (wrapper). 使用默认输入值运行上述工作流，产生的结果会和命令 `echo " +"\"Hello World\"` 别无二致。" -#: ../../src/introduction/quick-start.md:27 -#: 82613ca4e32b4ccab1b7735f5ba2d5a1 -msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +#: ../../src/introduction/quick-start.md:27 7b2ae93353184faea0ae4f4acdfc3350 +msgid "" +"In CWL, there is a distinction between a command-line tool and a " +"workflow. But for the sake of simplicity, we are using the term " +"“workflow” here. You will learn more about this in the [basic concepts" +"](basic-concepts.md) section." msgstr "" -"CWL 中“命令行工具”和“工作流”是有所区别的。但为了简单起见，这里我们仍然用了“工" -"作流”一次。更多有关信息可在[《基本概念》](basic-concepts.md)一节中学到。" +"CWL 中“命令行工具”和“工作流”是有所区别的。但为了简单起见，这里我们仍然用了“工作流”一次。更多有关信息可在[《基本概念》](basic-" +"concepts.md)一节中学到。" -#: ../../src/introduction/quick-start.md:32 -#: 498a43362a4749f3b8b433709d34a1d5 +#: ../../src/introduction/quick-start.md:32 1ed30b04073d47a9893774746479fb5d msgid "Installing a CWL Runner" msgstr "安装 CWL 运行程序" -#: ../../src/introduction/quick-start.md:34 -#: f3e56aedd56b4b93bdc3894273e8c144 -msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +#: ../../src/introduction/quick-start.md:34 73a42cd9e0e54296985088b7221a8a93 +msgid "" +"`cwltool` is an implementation of the CWL specification. It is also the " +"CWL *Reference Runner* for the specification, and it is compliant with " +"the latest version of the specification: {{ cwl_version }}. You can " +"install `cwltool` using `pip`:" msgstr "" -"`cwltool` 是 CWL 规约的一种实现，也为该规约编写的 CWL *参考运行程序*。" -"它符合规约的最新版本 {{ cwl_version }} 版。您可用 `pip` 安装 `cwltool`:" +"`cwltool` 是 CWL 规约的一种实现，也为该规约编写的 CWL *参考运行程序*。它符合规约的最新版本 {{ cwl_version " +"}} 版。您可用 `pip` 安装 `cwltool`:" -#: ../../src/introduction/quick-start.md:39 -#: 81481f5b82e4488398f87f0a169bd359 +#: ../../src/introduction/quick-start.md:39 57aea587ade24610be62f5d993b0b755 msgid "Installing `cwltool` with `pip`." msgstr "使用 `pip` 安装 `cwltool`." -#: ../../src/introduction/quick-start.md:47 -#: a81342e756d24c40acc15835d0a768f2 -msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +#: ../../src/introduction/quick-start.md:47 51183fc986014edbb026a53f222e6c2e +msgid "" +"If installing the cwltool using the pip command doesn't work for you, the" +" [prerequisites](prerequisites.md) section contains other ways to install" +" `cwltool` and a more detailed list of software and libraries used for " +"following the rest of this user guide." msgstr "" -"如果您无法用 pip 命令安装 cwltool，请参阅[《学习前的准备》](prerequisites.md)" -" 一节，了解安装 `cwltool` " -"的其他方法，以及继续学习《用户指南》所需软件和库的详细列表。" +"如果您无法用 pip 命令安装 cwltool，请参阅[《学习前的准备》](prerequisites.md) 一节，了解安装 `cwltool`" +" 的其他方法，以及继续学习《用户指南》所需软件和库的详细列表。" -#: ../../src/introduction/quick-start.md:51 -#: c12cf89f8b9a421ebd05330326e219b3 +#: ../../src/introduction/quick-start.md:51 a7582c3ae37a462a8ae1e72b3f321534 msgid "Running \"Hello World\"" msgstr "运行“Hello World”" -#: ../../src/introduction/quick-start.md:53 -#: 9b68bcb1a41849dc9601ab47c5bbb0fe -msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +#: ../../src/introduction/quick-start.md:53 0595e96912dc40e5a09f2ced2d2b7bcd +#, fuzzy +msgid "" +"The usage of the `cwltool` command-line executable is basically `cwltool " +"[OPTIONS] [CWL_DOCUMENT] [INPUTS_OBJECT]`. You can run the " +"`hello_world.cwl` workflow without specifying any option:" msgstr "" -"`cwltool` 命令行程序的基本用法是 `cwltool [选项] <CWL 文件名> " -"[输入对象]`. 您可以不指定任何选项，直接运行 `hello_world.cwl` 工作流：" +"`cwltool` 命令行程序的基本用法是 `cwltool [选项] <CWL 文件名> [输入对象]`. " +"您可以不指定任何选项，直接运行 `hello_world.cwl` 工作流：" -#: ../../src/introduction/quick-start.md:57 -#: ce04027dfcfe4b7b91ea3c2136b18b23 +#: ../../src/introduction/quick-start.md:57 5b393c69816549b084516dda4d4274f5 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "使用 `cwltool` 运行 `hello_world.cwl`." -#: ../../src/introduction/quick-start.md:62 -#: 0d8a788402914ebd8f09a5ca80650011 -msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +#: ../../src/introduction/quick-start.md:62 4306d8ad802f45c18487d932d04492fa +msgid "" +"Or you can override the default value of the input parameter `message`, " +"similar to how you would change the argument of the `echo` base command:" msgstr "您还可以撤销输入参数 `message` 的默认值，有如更改 `echo` 基本命令的参数：" -#: ../../src/introduction/quick-start.md:65 -#: 6d0b679efab24813a7a3b709ade940d1 +#: ../../src/introduction/quick-start.md:65 8339ec411ad04c70ab8d795eb154fc38 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "向 `cwltool` 传递输入参数值运行 `hello_world.cwl`." -#: ../../src/introduction/quick-start.md:70 -#: 2ea056ab04b6419a9faf350de22a17f2 -msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +#: ../../src/introduction/quick-start.md:70 3ecca6985e754951aee00c93effe9517 +msgid "" +"Another way of passing values to your workflow input parameters is via an" +" *Inputs Object*. This is a file containing the input fields with their " +"corresponding values. The Inputs Objects file can be written in JSON or " +"YAML. For example:" msgstr "" -"将值传递给工作流输入参数的另一种方法是利用*输入对象* (Inputs " -"Object)。它是由输入字段及其相应值构成的文件，可使用 JSON 或 YAML " -"格式编写。例如：" +"将值传递给工作流输入参数的另一种方法是利用*输入对象* (Inputs Object)。它是由输入字段及其相应值构成的文件，可使用 JSON 或 " +"YAML 格式编写。例如：" -#: ../../src/introduction/quick-start.md:74 -#: 1a44a545434b448aa956005deeed90a8 +#: ../../src/introduction/quick-start.md:74 d05e8e016b1d40c28c4b6091103fe920 msgid "`hello_world-job.json`" msgstr "`hello_world-job.json`" -#: ../../src/introduction/quick-start.md:80 -#: e76bfcc0c9f84bcdb3f6d5277869a88c -msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +#: ../../src/introduction/quick-start.md:80 c5983ba6c86f4b749522c11cb3843911 +msgid "" +"You can use this Inputs Object file now to execute the “Hello World” " +"workflow:" msgstr "这样就可以在执行“Hello World”工作流时使用此输入对象文件：" -#: ../../src/introduction/quick-start.md:82 -#: d4cdbe870a6f4a68b542ca719d989062 +#: ../../src/introduction/quick-start.md:82 4065124edf3a4678a37c82e3070595cb msgid "Passing an Inputs Object file to `cwltool`." msgstr "将输入对象文件传递给 `cwltool`." -#: ../../src/introduction/quick-start.md:88 -#: b6d59e4b9c854abab1b3f7a0fa26f504 -msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +#: ../../src/introduction/quick-start.md:88 52b1602b5c8d48db88d0b16f788e7703 +msgid "" +"We used a similar file name for the workflow and for the Inputs Object " +"files. The *-job.json* suffix is very common in Inputs Object files, but " +"it is not a requirement. You can choose any name for your workflows and " +"Inputs Object files." msgstr "" "我们为工作流和输入对象文件起了类似的文件名。输入对象文件名中的 *-job.json* " "后缀是很常见的，但并非规定。工作流和输入对象文件的命名方式可由您任意选择。" -#: ../../src/introduction/quick-start.md:96 -#: 5535b98e8b1342f09f003ec6db2b44b1 +#: ../../src/introduction/quick-start.md:96 3b06faf5f3194bd8a96118d9f050f61e msgid "Continue reading the next sections of this User Guide!" msgstr "请继续阅读《用户指南》后续部分！" -#: ../../src/introduction/quick-start.md:97 -#: 77e43c7117fd4c52b140f0dd52cc3963 +#: ../../src/introduction/quick-start.md:97 669b8ac154e74181830a430b1dc7684b msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "[ 各种 CWL 实现汇总](https://www.commonwl.org/implementations)。" -#: ../../src/introduction/quick-start.md:98 -#: 7282abfa7155497ca47c30f9abfb6474 -msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +#: ../../src/introduction/quick-start.md:98 1c888f1b771d49b3a257ed534b5afa0a +msgid "" +"The [`common-workflow-language` organization](https://github.com/common-" +"workflow-language) at GitHub." msgstr "" "GitHub上的 [`common-workflow-language` 组织](https://github.com/common-" "workflow-language)。" -#: ../../src/introduction/quick-start.md:99 -#: 176d8d47830f4031bb95dc231ebf1303 -msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +#: ../../src/introduction/quick-start.md:99 dbce82b7a930493486a585ecb8891121 +msgid "" +"[Common Workflow Language at " +"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -"[英文维基百科中的 Common Workflow Language 条目](https://en.wikipedia.org/" -"wiki/Common_Workflow_Language)。" +"[英文维基百科中的 Common Workflow Language " +"条目](https://en.wikipedia.org/wiki/Common_Workflow_Language)。" -#: ../../src/introduction/quick-start.md:100 -#: 82a7ca3703bc4f0daa18942a1ac8943b -msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +#: ../../src/introduction/quick-start.md:100 dc714ffd4278421b9f2417f41627722c +msgid "" +"[YAML.org](http://yaml.org/) and [YAML at " +"Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -"[YAML.org](http://yaml.org/) 网站，以及[维基百科中的 YAML 条目](https://en." -"wikipedia.org/wiki/YAML)。" +"[YAML.org](http://yaml.org/) 网站，以及[维基百科中的 YAML " +"条目](https://en.wikipedia.org/wiki/YAML)。" -#: ../../src/introduction/quick-start.md:101 -#: d039a9d6461c44628d4660c00d9ce6ff -msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +#: ../../src/introduction/quick-start.md:101 2bf7b924182f4f2bab88edef5ef85baa +msgid "" +"The {{'[CWL Specification " +"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." msgstr "" -"{{'[CWL 规约 VERSION 版](https://www.commonwl.org/VERSION)'.replace(" -"'VERSION', cwl_version_text) }}." +"{{'[CWL 规约 VERSION " +"版](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }}." -#: ../../src/introduction/quick-start.md:102 -#: fbc3383d9e1c4eaca7931c3cc4f1752b -msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +#: ../../src/introduction/quick-start.md:102 936a7dfab11a4f2c82c0b59964e3ea28 +msgid "" +"[Workflow management system at " +"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -"[Wikipedia 条目 Workflow Management System ](https://en.wikipedia.org/wiki/" -"Workflow_management_system)." +"[Wikipedia 条目 Workflow Management System " +"](https://en.wikipedia.org/wiki/Workflow_management_system)." -#: ../../src/setup.md:9 -#: 1330bd38c4b5495f890b98c669f81a9d -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." -msgstr "此页面已过时，存留在此仅用于保留旧《用户指南》链接。此页面上的内容已迁移到新" -"《用户指南》的[《常见问题》](/faq.md)一节。" +#: ../../src/setup.md:9 24ea9c5144664d9599d7aca767b4730a +msgid "" +"This page is out-of-date and was kept here to preserve the links of the " +"old User Guide. The information on this page has been migrated to the " +"[FAQ](/faq.md) section of the new user guide." +msgstr "此页面已过时，存留在此仅用于保留旧《用户指南》链接。此页面上的内容已迁移到新《用户指南》的[《常见问题》](/faq.md)一节。" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 +#: 3843684b039a40dea163de951ca56738 msgid "Additional Arguments and Parameters" msgstr "附加参数" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 -msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." -msgstr "有时，一些工具需要额外的命令行选项，但我们无法让它们与 (CWL) " -"输入参数一一对应。" +#: a6fd1842b938435aa2a3c889019eec71 +msgid "" +"Sometimes tools require additional command line options that don't " +"correspond exactly to input parameters." +msgstr "有时，一些工具需要额外的命令行选项，但我们无法让它们与 (CWL) 输入参数一一对应。" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf -msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +#: dfed0747ed544547afd364086d828c9b +msgid "" +"In this example, we will wrap the Java compiler to compile a java source " +"file to a class file. By default, \"javac\" will create the class files " +"in the same directory as the source file. However, CWL input files (and " +"the directories in which they appear) may be read-only, so we need to " +"instruct \"javac\" to write the class file to the designated output " +"directory instead." msgstr "" -"本例中，我们将包装 Java 编译器，将 java 源文件编译为类 (class) 文件。 " -"默认情况下，“javac” 将在源文件所在目录中创建类文件。 然而，CWL " -"输入文件（及其所在目录）可能是只读的，因此我们需要令 “javac” " -"将类文件写入指定的输出目录。" +"本例中，我们将包装 Java 编译器，将 java 源文件编译为类 (class) 文件。 默认情况下，“javac” " +"将在源文件所在目录中创建类文件。 然而，CWL 输入文件（及其所在目录）可能是只读的，因此我们需要令 “javac” 将类文件写入指定的输出目录。" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c +#: e690b567eae34f3f8dbdd7760e51449a msgid "`arguments.cwl`" msgstr "`arguments.cwl`" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 -#: 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 +#: ../../src/topics/staging-input-files.md:15 4cee519b108143be89a0e47a75d7d649 +#: 79585673fd654bab9ba7c1927d7e153b msgid "`arguments-job.yml`" msgstr "`arguments-job.yml`" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 +#: ef070ebe5f7245489b05660fb6d7c178 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "接下来，创建一个示例 Java 文件，用来让命令行工具处理它。" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb -msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +#: 4ae43e3e841442039e4bb8c740096c56 +msgid "" +"And now invoke `cwltool` providing the tool description and the input " +"object on the command line:" msgstr "现在，将刚才创建的工具描述和输入对象通过命令行传递给 `cwltool` ：" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a -msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." -msgstr "此处我们使用 `arguments` " -"字段，给命令行添加一个与任何具体输入参数都无关的附加参数。" +#: 8497291577914eb3a172c1ffb736d95d +msgid "" +"Here we use the `arguments` field to add an additional argument to the " +"command line that isn't tied to a specific input parameter." +msgstr "此处我们使用 `arguments` 字段，给命令行添加一个与任何具体输入参数都无关的附加参数。" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 -msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." -msgstr "" -"此示例用到了运行时 (runtime) " -"参数，它们提供的是工具实际执行时的硬件或软件环境信息。 `$(runtime.outdir)` " -"参数是指定输出目录的路径。其他运行时参数还有 `$(runtime.tmpdir)`、`$(runtime." -"ram)`、`$(runtime.cores)`、`$(runtime.outdirSize)`, 以及 `$(runtime." -"tmpdirSize)` 等，详见 CWL 规约的 [Runtime " +#: dc9fa5f2cbb147b1853c4042c54010f3 +msgid "" +"This example references a runtime parameter. Runtime parameters provide " +"information about the hardware or software environment when the tool is " +"actually executed. The `$(runtime.outdir)` parameter is the path to the " +"designated output directory. Other parameters include " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " +"Environment][runtime] section of the CWL specification for details." +msgstr "" +"此示例用到了运行时 (runtime) 参数，它们提供的是工具实际执行时的硬件或软件环境信息。 `$(runtime.outdir)` " +"参数是指定输出目录的路径。其他运行时参数还有 " +"`$(runtime.tmpdir)`、`$(runtime.ram)`、`$(runtime.cores)`、`$(runtime.outdirSize)`," +" 以及 `$(runtime.tmpdirSize)` 等，详见 CWL 规约的 [Runtime " "Environment][runtime]（运行环境）部分。" -#: ../../src/topics/best-practices.md:1 -#: 612c4a66c36a43d4ac5d74c1757d6845 +#: ../../src/topics/best-practices.md:1 964bf8276dd04b65887448e1386e63fe msgid "Best Practices" msgstr "优良习惯" -#: ../../src/topics/best-practices.md:3 -#: 939cd9e9eaff4e3ab74fe707a5d4eb21 -msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." -msgstr "本节列举一组值得留心的好习惯，推荐您在用 CWL " -"编写工具或工作流描述时参考。您只需结合实际尽量做到，无需求全。" - -#: ../../src/topics/best-practices.md:8 -#: 4bcb84707acb40a0bfe2ea0853cb10b7 -msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." -msgstr "" -"不要将 `type: string` 参数用于输入或引用文件、目录的名称；请根据实际情况选用 " -"`type: File` 或 `type: Directory`." - -#: ../../src/topics/best-practices.md:11 -#: 4dee8504a8e5496081dadc386ab45540 -msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." -msgstr "" -"CWL 文件（连同 `Dockerfile` " -"等外部组件）是一种软件代码。工作流开发人员应明白的是，" -"关于软件许可的通用规则也同样适用于您编写的 CWL 文件。例如，如果您的工作流是公" -"开共享的，则许可条款一定要明确，以便将来的用户了解在什么条件下可以将它运行、" -"修改、或并入其他工作流。因此，请考虑在 CWL 文件中加入 license（许可协议）字段" -"。笔者敦促您选用现成的许可协议，不要独辟蹊径（关于挑选许可协议请参见下文链接" -"）。同时，建议您选取允许任何人重复使用的许可证，如 [Apache 2.0][apache-" -"license]." +#: ../../src/topics/best-practices.md:3 7b59377bd56c47b8a71c18acfba4d3bb +msgid "" +"The following are a set of recommended good practices to keep in mind " +"when writing a Common Workflow Language description for a tool or " +"workflow. These guidelines are presented for consideration on a scale of " +"usefulness: although more is better, not all are required." +msgstr "本节列举一组值得留心的好习惯，推荐您在用 CWL 编写工具或工作流描述时参考。您只需结合实际尽量做到，无需求全。" -#: ../../src/topics/best-practices.md:20 -#: 674c238b25e240eda05e22e399f2f78f -msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +#: ../../src/topics/best-practices.md:8 2292670347cd4549bc6a51e972de0ef4 +msgid "" +"No `type: string` parameters for names of input or reference " +"files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" +"不要将 `type: string` 参数用于输入或引用文件、目录的名称；请根据实际情况选用 `type: File` 或 `type: " +"Directory`." + +#: ../../src/topics/best-practices.md:11 ae127b776eed4894af8cb680377703e0 +msgid "" +"A CWL document (in conjunction with any external components like " +"`Dockerfile`s) is software code. Workflow developers should be aware that" +" the usual rules of software licensing apply to this document. For " +"example, if the workflow is shared publicly, licensing terms must be " +"clear so that a future user understands under what conditions they can " +"run the workflow, modify it and/or combine it with other workflows. For " +"this reason, please consider including a license field in the document. " +"The authors of this guide urge you to choose a pre-existing license " +"rather than trying to write your own (see the link below to learn more " +"about choosing a license), and our recommended practice is to choose a " +"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" +"license]." msgstr "" -"请尽可能使用 [SPDX 标识符][spdx] 指定许可协议。许可协议的元数据字段由形如 " -"`https://spdx.org/licenses/[SPDX-ID]` 的 URL 构成，其中 `SPDX-ID` " -"取自前面链接提到的标识符列表，参见下例这段代码。对于没有 SPDX " +"CWL 文件（连同 `Dockerfile` 等外部组件）是一种软件代码。工作流开发人员应明白的是，关于软件许可的通用规则也同样适用于您编写的 " +"CWL " +"文件。例如，如果您的工作流是公开共享的，则许可条款一定要明确，以便将来的用户了解在什么条件下可以将它运行、修改、或并入其他工作流。因此，请考虑在 " +"CWL 文件中加入 " +"license（许可协议）字段。笔者敦促您选用现成的许可协议，不要独辟蹊径（关于挑选许可协议请参见下文链接）。同时，建议您选取允许任何人重复使用的许可证，如" +" [Apache 2.0][apache-license]." + +#: ../../src/topics/best-practices.md:20 384eb620dc31468e8c3f5f33a3436200 +msgid "" +"If possible, the license should be specified with its corresponding [SPDX" +" identifier][spdx]. Construct the metadata field for the license by " +"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " +"`SPDX-ID` is taken from the list of identifiers linked above. See the " +"example snippet below for guidance. For non-standard licenses without an " +"SPDX identifier, provide a URL to the license." +msgstr "" +"请尽可能使用 [SPDX 标识符][spdx] 指定许可协议。许可协议的元数据字段由形如 `https://spdx.org/licenses" +"/[SPDX-ID]` 的 URL 构成，其中 `SPDX-ID` 取自前面链接提到的标识符列表，参见下例这段代码。对于没有 SPDX " "标识符的非标准许可协议，请提供许可协议的 URL。" -#: ../../src/topics/best-practices.md:26 -#: b651f80f47b4442fbf29454a233697fc -msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +#: ../../src/topics/best-practices.md:26 e8259b43fa6944eda73eae381db6b97b +msgid "" +"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" +"Programmer][sci-license]\"" msgstr "相关阅读：《[给科学界程序员的软件许可简明指南][sci-license]》" -#: ../../src/topics/best-practices.md:28 -#: 263a127a77cf4c41af76854f22f1f260 +#: ../../src/topics/best-practices.md:28 5b976a5aec7d44bda55b0a019e955416 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "_用 SPDX 标识符指定许可协议的元数据字段示例：_" -#: ../../src/topics/best-practices.md:37 -#: 3a87a0fb2a364e3da5aaa4017e430b19 -msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +#: ../../src/topics/best-practices.md:37 924b8df24deb4c82b32732f491c9a246 +#, fuzzy +msgid "" +"For more examples of providing metadata within CWL descriptions, see [the" +" Metadata and Authorship section of this User Guide](../topics/metadata-" +"and-authorship.md)." msgstr "" -"关于在 CWL " -"描述中提供元数据的更多示例，请参见[《用户指南》的“元数据和著作权”一节](../" -"topics/metadata-and-authorship.md)。" +"关于在 CWL 描述中提供元数据的更多示例，请参见[《用户指南》的“元数据和著作权”一节](../topics/metadata-and-" +"authorship.md)。" -#: ../../src/topics/best-practices.md:40 -#: ecf2b9c0b1664afe9c4e180610610021 -msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." -msgstr "" -"为 CWL 工具或工作流描述的作者添加[署名信息][license-" -"example]。请使用明确、独一无二的标识符，如[ORCID][orcid]." +#: ../../src/topics/best-practices.md:40 9e64a9fc89cb45cfbff0e925cc91b1be +msgid "" +"Include [attribution information][license-example] for the author(s) of " +"the CWL tool or workflow description. Use unambiguous identifiers like " +"[ORCID][orcid]." +msgstr "为 CWL 工具或工作流描述的作者添加[署名信息][license-example]。请使用明确、独一无二的标识符，如[ORCID][orcid]." -#: ../../src/topics/best-practices.md:44 -#: e24cb13d98014e558b6a6946758359e0 -msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +#: ../../src/topics/best-practices.md:44 87030aef02044b8283c76debab4772bf +#, fuzzy +msgid "" +"In tool descriptions, list dependencies using short name(s) under " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "在工具描述中，将所依赖的软件在 `SoftwareRequirement` 下以简短的名称列出。" -#: ../../src/topics/best-practices.md:47 -#: f2b14a92374e449d9fb1e8c86ae0dd61 -msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +#: ../../src/topics/best-practices.md:47 6c9eaae099fa4ca4b0986b1c4146df50 +msgid "" +"Include [SciCrunch][scicrunch] identifiers for dependencies in " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -"为依赖关系添加 [SciCrunch][scicrunch] 标识符。其格式形如 `https://identifiers" -".org/rrid/RRID:SCR_NNNNNN`." +"为依赖关系添加 [SciCrunch][scicrunch] 标识符。其格式形如 " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN`." -#: ../../src/topics/best-practices.md:50 -#: 928e3df7ca3e479ca6474a8e72cf36eb -msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +#: ../../src/topics/best-practices.md:50 5ae8950fd31541399c2fe59096581dbc +msgid "" +"All `input` and `output` identifiers should reflect their conceptual " +"identity. Use informative names like `unaligned_sequences`, " +"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " +"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -"一切 `input`（输入）和 `output`（输出）标识符均应体现其概念上的特质。" -"请使用类似 `unaligned_sequences`、`reference_genome`、 `phylogeny`、或 " +"一切 `input`（输入）和 `output`（输出）标识符均应体现其概念上的特质。请使用类似 " +"`unaligned_sequences`、`reference_genome`、 `phylogeny`、或 " "`aligned_sequences` 这样望文知义的变量名，而非 " "`foo_input`、`foo_file`、`result`、`input`、`output` 等缺乏明确内涵的名称。" -#: ../../src/topics/best-practices.md:55 -#: d355f035676446c88b028f327aeb4829 -msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +#: ../../src/topics/best-practices.md:55 b0493895105e43849bff2026763e472a +#, fuzzy +msgid "" +"In tool descriptions, include a list of version(s) of the tool that are " +"known to work with this description under " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "在工具描述中 `SoftwareRequirement` 下，请列出已知能与该描述兼容的工具版本。" -#: ../../src/topics/best-practices.md:58 -#: 339b852df24242189d6efcd2898a3396 -msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." -msgstr "" -"所有输入和输出 `File`（文件）都需要指明 `format`（格式）。" -"生物信息学工具应使用来自 [EDAM][edam-example] 的格式标识符。另请参考 `iana:" -"text/plain`、`iana:text/tab-separated-values` 等在 `$namespaces: { iana: " -"\"https://www.iana.org/assignments/media-types//" } 下使用的格式名，以及[" -"IANA 媒体类型][iana-types]（又称 MIME " -"类型）的完整列表。对于非生物信息学工具，请同样运用或创建合适的本体或受控词表 " -"(controlled vocabulary). 如果您对此有经验，请编辑此页面，以告知我们。" - -#: ../../src/topics/best-practices.md:66 -#: 3ef57e6862f240bebcf193a52397af0a -msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." -msgstr "将所有能作为流读写（即单次、非随机访问）的输入和输出 `File`（文件）标记为 " -"`streamable: true`." - -#: ../../src/topics/best-practices.md:69 -#: f1a7c4f896a04a80b0c5f6a1db61ff8c -msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." -msgstr "" -"即使某个命令或其子命令能够执行更多操作，每个 `CommandLineTool`（命令行工具）" -"描述也应侧重于单个操作。请勿添加非必需或用不到的选项，以免工作描述过于复杂。" - -#: ../../src/topics/best-practices.md:73 -#: 1ac4c3d8c3e44bd1af3fc5df70051926 -msgid "Custom types should be defined with one external YAML per type definition for re-use." +#: ../../src/topics/best-practices.md:58 88806cb0462f4359801c1fa0ff0ebcc0 +msgid "" +"`format` should be specified for all input and output `File`s. " +"Bioinformatics tools should use format identifiers from [EDAM][edam-" +"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " +"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" +"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " +"types). For non-bioinformatics tools, use or build an appropriate " +"ontology/controlled vocabulary in the same way. Please edit this page to " +"let us know about it." +msgstr "" +"所有输入和输出 `File`（文件）都需要指明 `format`（格式）。生物信息学工具应使用来自 [EDAM][edam-example] " +"的格式标识符。另请参考 `iana:text/plain`、`iana:text/tab-separated-values` 等在 " +"`$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }" +" 下使用的格式名，以及[IANA 媒体类型][iana-types]（又称 MIME " +"类型）的完整列表。对于非生物信息学工具，请同样运用或创建合适的本体或受控词表 (controlled vocabulary). " +"如果您对此有经验，请编辑此页面，以告知我们。" + +#: ../../src/topics/best-practices.md:66 b178c7296ed5491782a4180c76883c14 +msgid "" +"Mark all input and output `File`s that are read from or written to in a " +"streaming compatible way (only once, no random-access), as `streamable: " +"true`." +msgstr "将所有能作为流读写（即单次、非随机访问）的输入和输出 `File`（文件）标记为 `streamable: true`." + +#: ../../src/topics/best-practices.md:69 886d15c1972243acadccff5760f842f1 +#, fuzzy +msgid "" +"Each " +"[`CommandLineTool`](https://w3id.org/cwl/CommandLineTool.html#CommandLineTool)" +" description should focus on a single operation only, even if the " +"(sub)command is capable of more. Don't overcomplicate your tool " +"descriptions with options that you don't need or use." +msgstr "" +"即使某个命令或其子命令能够执行更多操作，每个 " +"`CommandLineTool`（命令行工具）描述也应侧重于单个操作。请勿添加非必需或用不到的选项，以免工作描述过于复杂。" + +#: ../../src/topics/best-practices.md:73 ef5a5f9b253c4ca3916802a695fb7c6d +msgid "" +"Custom types should be defined with one external YAML per type definition" +" for re-use." msgstr "关于自定义类型，每个外部 YAML 文件应与单个类型定义一一对应，以便重复使用。" -#: ../../src/topics/best-practices.md:76 -#: c858f64e66f048a5b0032ef3e4d83694 +#: ../../src/topics/best-practices.md:76 ff59f40e84004523904e3094be07cc80 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "请使用位于顶级的简短 `label`（标签）对工具或工作流加以概括。" -#: ../../src/topics/best-practices.md:78 -#: fae385da16aa443da996fa23ac03d6ae -msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." -msgstr "在用得到的时候，还应添加顶级 `doc`. 相比上述顶级 `label`, " -"此处应提供更长、更详细的描述。" +#: ../../src/topics/best-practices.md:78 78d73fde24e24beeab541a623d9530b6 +msgid "" +"If useful, include a top-level `doc` as well. This should provide a " +"longer, more detailed description than was provided in the top-level " +"`label` (see above)." +msgstr "在用得到的时候，还应添加顶级 `doc`. 相比上述顶级 `label`, 此处应提供更长、更详细的描述。" -#: ../../src/topics/best-practices.md:82 -#: 92430be71ecc40e18bbbb80d5576c613 -msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +#: ../../src/topics/best-practices.md:82 d92013d662b44dbf8875e06c9dfbfd79 +msgid "" +"Use `type: enum` instead of `type: string` for elements with a fixed list" +" of valid values." msgstr "对于有效取值为若干固定值的元素，应使用 `type: enum` 而非 `type: string`." -#: ../../src/topics/best-practices.md:85 -#: 387d83db81024f65aa9a890c2d07874a -msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +#: ../../src/topics/best-practices.md:85 c100d5192a52497fb6a890b81a388fcf +msgid "" +"Evaluate all use of JavaScript for possible elimination or replacement. " +"One common example: manipulating `File` names and paths? Consider whether" +" one of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc., could be used instead." msgstr "" -"所有用到 JavaScript " -"之处都应进行评估，考虑是否能将它去除或替代。经常遇到的一例，是处理 `File` " -"（文件）名称和路径。这时应考虑是否能用 [`File` 的内置属性][file-" -"prop]（如`basename`、`nameroot` 和 `nameext` 等）取代 JavaScript." +"所有用到 JavaScript 之处都应进行评估，考虑是否能将它去除或替代。经常遇到的一例，是处理 `File` " +"（文件）名称和路径。这时应考虑是否能用 [`File` 的内置属性][file-prop]（如`basename`、`nameroot` 和 " +"`nameext` 等）取代 JavaScript." -#: ../../src/topics/best-practices.md:90 -#: d8e2280a75a74916a1630afaa2fe2ae3 -msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +#: ../../src/topics/best-practices.md:90 e22fbacdb2fb4202b1bd69cfc24af5cd +msgid "" +"Give the tool description to a colleague (preferably at a different " +"institution) to test and provide feedback." msgstr "写好工具描述后， 把它交给同行（最好来自其他机构）进行测试并获取反馈。" -#: ../../src/topics/best-practices.md:93 -#: f1c1340f9745458980e0fbd641738687 -msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +#: ../../src/topics/best-practices.md:93 0060a863362140f6bb3932cb5da1df04 +msgid "" +"Complex workflows with individual components which can be abstracted " +"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" +" their workflow modular and allow sections of them to be easily reused." msgstr "" -"若复杂的工作流中包含可以抽象出来的单独组件，应利用 " -"[`SubworkflowFeatureRequirement`][subworkflow] " +"若复杂的工作流中包含可以抽象出来的单独组件，应利用 [`SubworkflowFeatureRequirement`][subworkflow] " "将工作流模块化，以便重复使用其组成部分。" -#: ../../src/topics/best-practices.md:97 -#: 5424e5472c3d466fa2a3d2022c6cb475 -msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +#: ../../src/topics/best-practices.md:97 93f6d6b544c24ce780184272f66bacab +msgid "" +"Software containers should be made to be conformant to the " +"[\"Recommendations for the packaging and containerizing of bioinformatics" +" software\"][containers] (also useful to other disciplines)." msgstr "" "应使软件容器 (container) 符合 [Recommendations for the packaging and " -"containerizing of bioinformatics software][containers]（《生物信息学软件封装" -"与容器化建议》）一文提出的标准。该文对其他学科也有参考价值。" +"containerizing of bioinformatics " +"software][containers]（《生物信息学软件封装与容器化建议》）一文提出的标准。该文对其他学科也有参考价值。" -#: ../../src/topics/command-line-tool.md:1 -#: 3f4e98f6bfa141feba8c4b120e3d03e8 +#: ../../src/topics/command-line-tool.md:1 a378a2f7d268401abfbbbe6e5090a952 msgid "Command Line Tool" msgstr "命令行工具" -#: ../../src/topics/command-line-tool.md:3 -#: 12f57b2ba76b492abe1816e06bfb1417 -msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +#: ../../src/topics/command-line-tool.md:3 cf0f1c00c0b34c94a8e2460a700c303e +msgid "" +"A command-line tool is a type of Process object that can be run by itself" +" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " +"`tar`, etc. The command-line tool is defined in the `baseCommand` " +"attribute of the command-line tool CWL document." msgstr "" -"命令行工具是可以单独运行或作为工作流步骤运行的一类流程 (process) 对象。" -"它是诸如 `ls`、`echo`、`tar` 等命令的包装器，由相应的 CWL 文件中 " -"`baseCommand` 这一属性定义。" +"命令行工具是可以单独运行或作为工作流步骤运行的一类流程 (process) 对象。它是诸如 `ls`、`echo`、`tar` " +"等命令的包装器，由相应的 CWL 文件中 `baseCommand` 这一属性定义。" -#: ../../src/topics/command-line-tool.md:8 -#: e1f657a46ce94a0d83671540e2cc2dab -msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +#: ../../src/topics/command-line-tool.md:8 7a180ba1f2d746a78b79be7e899cbad6 +msgid "" +"A CWL command-line tool must also have `inputs` and `outputs`. The " +"following example contains a minimal example of a CWL command-line tool " +"for the `echo` Linux command, using inputs and outputs." msgstr "" -"CWL 命令行工具还必具有 `inputs`（输入）和 `outputs`（输出）。以下是一个 CWL " -"命令行工具的极简示例，用 Linux 下的 `echo` 命令演示输入和输出。" +"CWL 命令行工具还必具有 `inputs`（输入）和 `outputs`（输出）。以下是一个 CWL 命令行工具的极简示例，用 Linux 下的" +" `echo` 命令演示输入和输出。" -#: ../../src/topics/command-line-tool.md:19 -#: abb83f0097654a43bd78639d3dbb2bc8 +#: ../../src/topics/command-line-tool.md:19 128bd8cd6788431da54fa07a8dc87f99 msgid "CWL command-line tool." msgstr "CWL 命令行工具。" -#: ../../src/topics/command-line-tool.md:50 -#: 3b1a9ae3412f4d6e96a39b9a16934232 +#: ../../src/topics/command-line-tool.md:50 d742e9e59ea44ca1a1df2de85059343f msgid "`echo.cwl`" msgstr "`echo.cwl`" -#: ../../src/topics/command-line-tool.md:57 -#: a5eacdbc9aa142c890b177869da4143d -msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +#: ../../src/topics/command-line-tool.md:57 e3a06ebe51b64b0183673a8acc04969f +msgid "" +"The example above uses a simplified form to define inputs and outputs. " +"You will learn more about in the [Inputs](../topics/inputs.md) and in the" +" [Outputs](../topics/outputs.md) sections." msgstr "" -"上例以简化的形式定义了输入和输出。在[《输入》](../topics/inputs." -"md)和[《输出》](../topics/outputs.md) 章节中，您将进一步学习。" +"上例以简化的形式定义了输入和输出。在[《输入》](../topics/inputs.md)和[《输出》](../topics/outputs.md)" +" 章节中，您将进一步学习。" -#: ../../src/topics/command-line-tool.md:68 -#: 1849b8f3ae1c4a84ae59a78ffd6b371e +#: ../../src/topics/command-line-tool.md:68 2bab464d19d14562a6501373aff13905 msgid "Network Access" msgstr "网络访问 (Network Access)" -#: ../../src/topics/command-line-tool.md:69 -#: e3bdaceae8784ab0807b2cf356a98580 -msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +#: ../../src/topics/command-line-tool.md:69 201712f3ceee4d4ea56ab96d3fef97b0 +msgid "" +"This indicates whether a process requires outgoing IPv4/IPv6 network " +"access. Starting with CWL v1.1, programs are not granted network access " +"by default, so you must include the requirement for network access in the" +" specification of your tool." msgstr "" -"这指的是流程是否需要发起 IPv4/IPv6 网络访问。如果命令行工具是基于 CWL v1.1+ " -"版本新编写的，则有必要明文指定何时需要访问网络。" -#: ../../src/topics/command-line-tool.md:83 -#: ed521ac365db4a6ba5a1051fbaa2932e -msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +#: ../../src/topics/command-line-tool.md:84 3282a357799f4a72a6b8bace206144c4 +#, fuzzy +msgid "" +"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 or v1.2 " +"will have `networkAccess: true` set automatically." msgstr "从 CWL v1.0 版本升级到 1.1 或 1.2 版的命令行工具将自动获取网络访问权限。" #: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +#: 17c5b4ee43cc4a979676ad27e473d046 msgid "Creating Files at Runtime" msgstr "在运行时创建文件" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d -msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +#: cd0dff10471c4ad2b84e3a0e4d7767ea +msgid "" +"Sometimes you need to create a file on the fly from input parameters, " +"such as tools that expect to read their input configuration from a file " +"rather than the command line parameters, or need a small wrapper shell " +"script." msgstr "" -"有些情况下，您需要根据输入参数动态创建文件。例如有的工具需要通过文件（而非命" -"令行参数）读取输入配置，还有的需要小型 shell 脚本作为包装器 (wrapper)." +"有些情况下，您需要根据输入参数动态创建文件。例如有的工具需要通过文件（而非命令行参数）读取输入配置，还有的需要小型 shell 脚本作为包装器 " +"(wrapper)." #: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "要生成此类文件，我们可以使用 `InitialWorkDirRequirements`." +#: bf4aea0a22334a1ca75cc20e937e6581 +#, fuzzy +msgid "" +"To generate such files, we can use the " +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)." +msgstr "" +"来自 " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" #: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 +#: 008f768d56b8465bb4e8f4fde15853a7 msgid "`createfile.cwl`" msgstr "`createfile.cwl`" #: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df -msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +#: 252f8e897b0942a8be098481890005f3 +msgid "" +"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " +"expanded by the CWL engine before creating the file. Here, insert the " +"value at the input `message`." msgstr "" -"在创建文件之前，CWL引擎将扩展所有形如 `$(inputs.message)` 的[表达式](../" -"topics/expressions.md)。此处将插入输入项`message` 实际的值。" +"在创建文件之前，CWL引擎将扩展所有形如 `$(inputs.message)` " +"的[表达式](../topics/expressions.md)。此处将插入输入项`message` 实际的值。" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 -msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +#: aca24b72687c4d4d84bf9de8b71413f7 +msgid "" +"The _CWL expressions_ are independent of any _shell variables_ used later" +" during command line tool invocation. That means that any genuine need " +"for the character `$` must be **escaped** with `\\`. For instance, " +"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " +"be evaluated by the shell script instead of the CWL engine." msgstr "" -"_CWL 表达式 _ 与后期在命令行工具调用时用到的任何 _shell 变量 _ " -"是相互独立的。这意味着，所有（后期）实际用到字符 `$` 的地方必须由 `\\` " -"（斜线）字符加以** 转义 **。例如，上例中的 `\\${PREFIX}` " -"在生成的文件中扩展为 `${PREFIX}`，以供 shell 脚本（而非 CWL 引擎）计算其值。" +"_CWL 表达式 _ 与后期在命令行工具调用时用到的任何 _shell 变量 _ 是相互独立的。这意味着，所有（后期）实际用到字符 `$` " +"的地方必须由 `\\` （斜线）字符加以** 转义 **。例如，上例中的 `\\${PREFIX}` 在生成的文件中扩展为 " +"`${PREFIX}`，以供 shell 脚本（而非 CWL 引擎）计算其值。" #: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa -msgid "To test the above CWL tool, use this job to provide the input value `message`:" +#: 750b3232e8754448bc2b5913539495b8 +msgid "" +"To test the above CWL tool, use this job to provide the input value " +"`message`:" msgstr "测试上述 CWL 工具时，请使用此作业提供输入项 `message` 的值：" #: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 -#: ../../src/topics/outputs.md:77 -#: 2d2ef4769b2347e79db827655f1bcdeb -#: 2699fbc4376148af91b7a5a6cdac467c -#: ca03defa3ad14cf698171cb09e3055c1 +#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:81 +#: 687c8a84bade43269f3cd767d32f9f47 81da7a18fe8d4659abc883cf43009f1f +#: d5d67eae63304ebb9b242133feacb0d1 msgid "`echo-job.yml`" msgstr "`echo-job.yml`" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d -msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +#: c4f964450d014734877fb3c968353a74 +msgid "" +"Before we run this, let us look at each step in a little more detail. The" +" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " +"command `sh example.sh`. This will run the file we create in the shell." msgstr "" -"运行前，我们来细看一下每个步骤。基础命令 `baseCommand: [\"sh\", \"example." -"sh\"]` 将执行的命令是 `sh example.sh`. 这将在 shell 中运行我们创建的文件。" +"运行前，我们来细看一下每个步骤。基础命令 `baseCommand: [\"sh\", \"example.sh\"]` 将执行的命令是 `sh " +"example.sh`. 这将在 shell 中运行我们创建的文件。" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c -msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +#: 9aeea5a6a4244bc7a1626e0cb7351068 +msgid "" +"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " +"YAML array, we need a `-` on the first line of each element of the array," +" in this case we have just one element. `entryname:` can have any value, " +"but it must match what was specified in the `baseCommand`. The final part" +" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " +"means that you are using a multiline string (without it, we would need to" +" write the whole script on one line)." msgstr "" "`InitialWorkDirRequirements` 需要一个 `listing`。由于 `listing` 是个 YAML " -"数组，我们需要在数组每个元素的首行添加一个 `-` " -"字符，不过本示例中只有一个元素。`entryname:` 可以取任何值，但它必须与 " -"`baseCommand` 中指定的值相匹配。最后的部分是 `entry:`，后面跟着 `|-`，这是 " -"YAML 中表示引用的语法，意味着此处使用的是多行字符串（要是没有它，我们就得将整" -"个脚本写在同一行之内）。" +"数组，我们需要在数组每个元素的首行添加一个 `-` 字符，不过本示例中只有一个元素。`entryname:` 可以取任何值，但它必须与 " +"`baseCommand` 中指定的值相匹配。最后的部分是 `entry:`，后面跟着 `|-`，这是 YAML " +"中表示引用的语法，意味着此处使用的是多行字符串（要是没有它，我们就得将整个脚本写在同一行之内）。" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 -msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +#: 867239e9ad3d4187a2703662a0ca3976 +msgid "" +"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " +"formatting." msgstr "请参阅[《YAML 指南》 ](../topics/yaml-guide.md#maps) ，进一步了解代码格式。" #: ../../src/topics/creating-files-at-runtime.md:54 #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 -#: ../../src/topics/staging-input-files.md:20 -#: ../../src/topics/workflows.md:198 -#: b372f33c65bb4707b2a462a960bb1373 -#: 293fb1d428b849aebccad598a932992d -#: f924d65fed0c4cb5b0a019b084a8b535 -#: d6255506eebe44be94c5ce703c44a513 -#: 7bbd2d738fc54649aeb10f8d2bc38b6f -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 +#: 0d7151b9f0194197bd686fe6c9c47afd 78bb40eeeda24d7b923162daa45d51a7 +#: 7b341a317347482ca86fc56119c3686f 7c637fa62cab4d0dbe670a3b72737cc9 +#: cfb4605a01dd4475aabcc086a4e65957 +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line:" msgstr "现在，在命令行上以工具描述和输入对象为参数调用 `cwltool`:" -#: ../../src/topics/custom-types.md:1 -#: cb34fd4c8cb04053ada491a227651048 +#: ../../src/topics/custom-types.md:1 252a3a17b1ec4d5a9a82ebbf6c2f314c msgid "Custom Types" msgstr "自定义类型" -#: ../../src/topics/custom-types.md:3 -#: 67573252cc064b27ab13eebc468ac58a -msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +#: ../../src/topics/custom-types.md:3 e0275ddda8f84207a58d10c17ca99a45 +msgid "" +"Sometimes you may want to write your own custom types for use and reuse " +"in CWL descriptions. Use of such custom types can reduce redundancy " +"between multiple descriptions that all use the same type, and also allow " +"for additional customisation/configuration of a tool/analysis without the" +" need to fiddle with the CWL description directly." msgstr "" -"有时您可能希望自己编写自定义的类型，以便用于 CWL 描述中并重复利用。在多个描述" -"用到相同类型的情况下，使用这样的自定义类型可以删繁就简，还可以让我们对工具或" -"分析进行额外的自定义和配置，而无需直接在 CWL 描述上做手脚。" +"有时您可能希望自己编写自定义的类型，以便用于 CWL " +"描述中并重复利用。在多个描述用到相同类型的情况下，使用这样的自定义类型可以删繁就简，还可以让我们对工具或分析进行额外的自定义和配置，而无需直接在 " +"CWL 描述上做手脚。" -#: ../../src/topics/custom-types.md:9 -#: 73e68b3af9cf41338d843c0c40e50cdc -msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." -msgstr "下例用 CWL 描述了一个 [biom 转换格式][biom]工具，用于将标准 biom " -"表文件转换为 hdf5 格式。" +#: ../../src/topics/custom-types.md:9 8367e38e5e7c4a298d1d87b9001aaddc +msgid "" +"The example below is a CWL description of the [biom convert format][biom]" +" tool for converting a standard biom table file to hdf5 format." +msgstr "下例用 CWL 描述了一个 [biom 转换格式][biom]工具，用于将标准 biom 表文件转换为 hdf5 格式。" -#: ../../src/topics/custom-types.md:12 -#: ef5f35acb97f4ddfad7b688712f53484 +#: ../../src/topics/custom-types.md:12 18b802f45ce0454ab7aa2a21812863c6 msgid "`custom-types.cwl`" msgstr "`custom-types.cwl`" -#: ../../src/topics/custom-types.md:18 -#: 7015dfa99a6f4cfb87ebf0ed61e8043c +#: ../../src/topics/custom-types.md:18 66d1953f5dd54d448bddd0f30c330402 msgid "`custom-types.yml`" msgstr "`custom-types.yml`" -#: ../../src/topics/custom-types.md:24 -#: a999b1acda2641598086648c64aa3831 -msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" -msgstr "" -"___注意：___ 按照下例演练前，您需要先[下载示例输入文件](https://github.com/" -"common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/" -"rich_sparse_otu_table.biom) *rich_sparse_otu_table.biom*. 例如，使用 `wget`:" - -#: ../../src/topics/custom-types.md:30 -#: f8c12a58cb0b46a488823c6ae95f25ea -msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" -msgstr "在文件第 29 行，`inputs:table_type` " -"项目中，允许用于数据表转换的选项列表以自定义对象的形式导入：" - -#: ../../src/topics/custom-types.md:46 -#: f25a63e0926d4932bbe64b2e4bdabf9e -msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." -msgstr "" -"对自定义类型的引用由两部分构成：对象定义所在的文件名（`biom-convert-table." -"yaml` ），和该文件中定义该类型的对象名（`table_type` ）。这里，导入的 `biom-" -"convert-table.yaml` 文件中的 `symbols` 数组定义了允许的表选项。例如，在 " -"`custom-types.yml` 中，我们把 `OTU table` 作为一个 `input`（输入）传入，" -"令工具创建一个 hdf5 格式的 OTU 表。" +#: ../../src/topics/custom-types.md:24 56b8912a1ea84f28adeb8beaf92ab563 +msgid "" +"___Note:___ To follow the example below, you need to [download the " +"example input file](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " +"`wget`:" +msgstr "" +"___注意：___ 按照下例演练前，您需要先[下载示例输入文件](https://github.com/common-workflow-" +"language/user_guide/blob/main/src/_includes/cwl/custom-" +"types/rich_sparse_otu_table.biom) *rich_sparse_otu_table.biom*. 例如，使用 " +"`wget`:" + +#: ../../src/topics/custom-types.md:30 a48539920c4944898918bc90b2d4e3c9 +msgid "" +"On line 29, in `inputs:table_type`, a list of allowable table options to " +"be used in the table conversion are imported as a custom object:" +msgstr "在文件第 29 行，`inputs:table_type` 项目中，允许用于数据表转换的选项列表以自定义对象的形式导入：" -#: ../../src/topics/custom-types.md:53 -#: b0a4df0fd3ca42338cff4689235dcf4e +#: ../../src/topics/custom-types.md:46 c791096f537141e8bd7cc941d711d108 +msgid "" +"The reference to a custom type is a combination of the name of the file " +"in which the object is defined (`biom-convert-table.yaml`) and the name " +"of the object within that file (`table_type`) that defines the custom " +"type. In this case the `symbols` array from the imported `biom-convert-" +"table.yaml` file define the allowable table options. For example, in " +"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" +" to create an OTU table in hdf5 format." +msgstr "" +"对自定义类型的引用由两部分构成：对象定义所在的文件名（`biom-convert-table.yaml` " +"），和该文件中定义该类型的对象名（`table_type` ）。这里，导入的 `biom-convert-table.yaml` 文件中的 " +"`symbols` 数组定义了允许的表选项。例如，在 `custom-types.yml` 中，我们把 `OTU table` 作为一个 " +"`input`（输入）传入，令工具创建一个 hdf5 格式的 OTU 表。" + +#: ../../src/topics/custom-types.md:53 5f6bc6ed72334a74b9a4c46c29ddda46 msgid "The contents of the YAML file describing the custom type are given below:" msgstr "描述自定义类型的 YAML 文件内容如下：" -#: ../../src/topics/custom-types.md:55 -#: fecfbb44456640d8ba05e519bf2ff564 +#: ../../src/topics/custom-types.md:55 3b55419088e8446994703220bd8e8480 msgid "`biom-convert-table.yaml`" msgstr "`biom-convert-table.yaml`" -#: ../../src/topics/custom-types.md:61 -#: d718630a296545f3a989c8c71e9ddc77 -msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" -msgstr "" -"为了在 CWL 描述中使用自定义类型，必须首先导入。 关于导入的描述位于 " -"`requirements:SchemaDefRequirement` 项，如下例 `custom-types.cwl` 所示：" - -#: ../../src/topics/custom-types.md:76 -#: 9a97acd430064710bcdf76edbd9f711c -msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +#: ../../src/topics/custom-types.md:61 fe6f4ce5e7344af0abea9d5c03e32ecd +msgid "" +"In order for the custom type to be used in the CWL description, it must " +"be imported. Imports are described in " +"`requirements:SchemaDefRequirement`, as below in the example `custom-" +"types.cwl` description:" msgstr "" -"另请注意，作者还在此 CWL 描述中加入了 `ResourceRequirement`, 指定了工具正常运" -"行所需的最低内存容量和内核数、该描述针对的软件具体版本、以及其他有用的元数据" -"。这些功能将在《用户指南》其他章节中进一步讨论。" +"为了在 CWL 描述中使用自定义类型，必须首先导入。 关于导入的描述位于 `requirements:SchemaDefRequirement` " +"项，如下例 `custom-types.cwl` 所示：" -#: ../../src/topics/environment-variables.md:1 -#: 59014808cbef4c02aaef03129d8a29b0 +#: ../../src/topics/custom-types.md:76 dce43b138ba24b22bfa9fa5692a17009 +#, fuzzy +msgid "" +"Note also that the author of this CWL description has also included " +"[`ResourceRequirement`](https://w3id.org/cwl/CommandLineTool.html#ResourceRequirement)s," +" specifying the minimum amount of RAM and number of cores required for " +"the tool to run successfully, as well as details of the version of the " +"software that the description was written for and other useful metadata. " +"These features are discussed further in other chapters of this user " +"guide." +msgstr "" +"另请注意，作者还在此 CWL 描述中加入了 `ResourceRequirement`, " +"指定了工具正常运行所需的最低内存容量和内核数、该描述针对的软件具体版本、以及其他有用的元数据。这些功能将在《用户指南》其他章节中进一步讨论。" + +#: ../../src/topics/environment-variables.md:1 19737f89f2994815969fa4a88346f49a msgid "Environment Variables" msgstr "环境变量" -#: ../../src/topics/environment-variables.md:3 -#: 3c821c9c46d841ec89b8a5b1018f3af8 -msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." -msgstr "CWL 工具运行于受限环境中，大多数环境变量都不会从父进程继承。 您可以使用 " -"`EnvVarRequirements` 为该工具设置环境变量。" +#: ../../src/topics/environment-variables.md:3 ad965f75aa0c41cda8b82c46af49774d +msgid "" +"Tools run in a restricted environment and do not inherit most environment" +" variables from the parent process. You can set environment variables " +"for the tool using `EnvVarRequirement`." +msgstr "CWL 工具运行于受限环境中，大多数环境变量都不会从父进程继承。 您可以使用 `EnvVarRequirements` 为该工具设置环境变量。" -#: ../../src/topics/environment-variables.md:7 -#: bfdebb32440a4034beb42135e38884e8 +#: ../../src/topics/environment-variables.md:7 38b276f9b0114a0bb87734f0a07a736f msgid "`env.cwl`" msgstr "`env.cwl`" -#: ../../src/topics/expression-tool.md:1 -#: 777d4a52f7554eff84db2df6d4d0f729 +#: ../../src/topics/expression-tool.md:1 9f33532119dc47ffb6ade20fb1d950bd msgid "Expression Tool" msgstr "表达式工具" -#: ../../src/topics/expression-tool.md:3 -#: 48deb71f361a43e48a56ed483075bca8 -msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +#: ../../src/topics/expression-tool.md:3 b267056eae704737af5aaada3ea7e6e2 +msgid "" +"An expression tool is a type of Process that can be run by itself or as a" +" Workflow step. It executes a pure JavaScript expression. It is meant to " +"be used as a way to isolate complex JavaScript expressions that need to " +"operate on input data and produce some result as output." msgstr "" -"表达式工具是一种类型的流程 (process), " -"可单独运行，或作为工作流的一个步骤运行。它执行纯 JavaScript 表达式，" -"意在隔离复杂的 JavaScript 表达式，以对输入数据进行运算，并生成结果作为输出。" +"表达式工具是一种类型的流程 (process), 可单独运行，或作为工作流的一个步骤运行。它执行纯 JavaScript 表达式，意在隔离复杂的 " +"JavaScript 表达式，以对输入数据进行运算，并生成结果作为输出。" -#: ../../src/topics/expression-tool.md:8 -#: 716b56506ca7470299899c5d820a9ea2 -msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +#: ../../src/topics/expression-tool.md:8 7e930144163e4d6e9f0bcaa764497ccf +#, fuzzy +msgid "" +"Similar to the command-line tool it requires `inputs` and `outputs`. But " +"instead of `baseCommand`, it requires an " +"[`expression`](https://w3id.org/cwl/CommandLineTool.html#Expressions_(Optional))" +" attribute." msgstr "" -"与命令行工具一样，它需要 `inputs`（输入）和 " -"`outputs`（输出），但与之不同的是，它需要的是 `expression` 属性，而非 " -"`baseCommand`." +"与命令行工具一样，它需要 `inputs`（输入）和 `outputs`（输出），但与之不同的是，它需要的是 `expression` 属性，而非" +" `baseCommand`." -#: ../../src/topics/expression-tool.md:17 -#: b63e6f5a2e89431c8fc7d04f47fd69fe +#: ../../src/topics/expression-tool.md:17 f172488c19a94d688036197117d30b38 msgid "CWL expression tool." msgstr "CWL 表达式工具。" -#: ../../src/topics/expression-tool.md:48 -#: 39727e9058f24b62b8746a46d3f812c2 +#: ../../src/topics/expression-tool.md:48 ef978c951f1a4b7d9280d31367e5bae7 msgid "`uppercase.cwl`" msgstr "`uppercase.cwl`" -#: ../../src/topics/expression-tool.md:67 -#: e3ecac0a8e604f2b98a2a12b0579990a -msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +#: ../../src/topics/expression-tool.md:67 0b63da31bc274b3cad798b07149592ab +#, fuzzy +msgid "" +"We had to use an " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" as our expression contains a JavaScript call in `.toUpperCase()`. This " +"means to tools using the expression tool that JavaScript is a " +"requirement." msgstr "" "因为我们的表达式在 `.toUpperCase()` 处含有一个 JavaScript 调用，所以必须使用 " -"`InlineJavascriptRequirements`. 这向使用表达式工具的其他工具表明 JavaScript " -"是必备条件。" +"`InlineJavascriptRequirements`. 这向使用表达式工具的其他工具表明 JavaScript 是必备条件。" -#: ../../src/topics/expressions.md:1 -#: c8d648b765ec499a8e9c464590838492 +#: ../../src/topics/expressions.md:1 b0e567a985f748538552bdb486a47998 msgid "Expressions" msgstr "表达式" -#: ../../src/topics/expressions.md:3 -#: 007a345b4bad49cf996c4301b8386473 -msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +#: ../../src/topics/expressions.md:3 24d05cbbab8e460e99f2edc97ab0dcec +#, fuzzy +msgid "" +"If you need to manipulate input parameters, include the requirement " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" and then anywhere a parameter reference is legal you can provide a " +"fragment of Javascript that will be evaluated by the CWL runner." msgstr "" "如果需要对输入参数进行处理，请添加需求 `InlineJavascriptRequirement`. " -"然后，在可以合法引用参数的任何地方，您都可以提供一 JavaScript 片段，让 CWL " -"运行程序计算其值。" +"然后，在可以合法引用参数的任何地方，您都可以提供一 JavaScript 片段，让 CWL 运行程序计算其值。" -#: ../../src/topics/expressions.md:9 -#: 2edbd398eadb458b8eacd5fa5496f0a2 -msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +#: ../../src/topics/expressions.md:9 3d48d1a8f7f74bc1886e41653cb53a22 +msgid "" +"JavaScript expressions should only be used when absolutely necessary. " +"When manipulating file names, extensions, paths etc, consider whether one" +" of the [built in `File` properties][file-prop] like `basename`, " +"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " +"practices](best-practices.md)." msgstr "" -"JavaScript 表达式应当仅在绝对必要时使用。要处理文件名、扩展名、路径等，" -"请优先考虑能否使用 `basename`、`nameroot`、`nameext` 等 [`File` 内置属性" -"][file-prop]。对此，请参阅[优良习惯一览](best-practice.md)。" +"JavaScript 表达式应当仅在绝对必要时使用。要处理文件名、扩展名、路径等，请优先考虑能否使用 " +"`basename`、`nameroot`、`nameext` 等 [`File` 内置属性][file-prop]。对此，请参阅[优良习惯一览" +"](best-practice.md)。" -#: ../../src/topics/expressions.md:16 -#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +#: ../../src/topics/expressions.md:16 7d444aacd418466bbe588fa964b45179 msgid "`expression.cwl`" msgstr "`expression.cwl`" -#: ../../src/topics/expressions.md:22 -#: efb5fd14988c4e2a8f834ee5369d4102 -msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" -msgstr "由于此工具不需要任何 " -"`inputs`（输入），因此运行的时候可以使用一个几乎为空的作业文件：" +#: ../../src/topics/expressions.md:22 72a0558a83964796a8c1a0eb55fd78e8 +msgid "" +"As this tool does not require any `inputs` we can run it with an (almost)" +" empty job file:" +msgstr "由于此工具不需要任何 `inputs`（输入），因此运行的时候可以使用一个几乎为空的作业文件：" -#: ../../src/topics/expressions.md:25 -#: e833649b951841c49397796f996d29f3 +#: ../../src/topics/expressions.md:25 d679fd1363b24c81979c68e7342159cf msgid "`empty.yml`" msgstr "`empty.yml`" -#: ../../src/topics/expressions.md:31 -#: 276f688ba7cc471a842f085ca852b1d9 -msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +#: ../../src/topics/expressions.md:31 d2ee4fcece744b6681f29322b5305111 +msgid "" +"`empty.yml` contains a description of an empty JSON object. JSON objects " +"descriptions are contained inside curly brackets `{}`, so an empty object" +" is represented simply by a set of empty brackets." msgstr "" "`empty.yml` 的内容是一个空 JSON 对象的描述。JSON 对象描述是用大括号 `{}` " "围起来的，因此，表示空对象仅需一对空括号就够了。" -#: ../../src/topics/expressions.md:35 -#: ebf399ea4d5f47b9be03e24f04c69f2d +#: ../../src/topics/expressions.md:35 624e4a270e374b1699b780df508b9184 msgid "We can then run `expression.cwl`:" msgstr "然后我们可以运行 `expression.cwl`:" -#: ../../src/topics/expressions.md:37 -#: 65e0cdd505b944caa40f65e612cdddfc +#: ../../src/topics/expressions.md:37 c252eac9a35e46aab08bd07bc1cdb57d msgid "Running `expression.cwl`" msgstr "运行 `expression.cwl`" -#: ../../src/topics/expressions.md:47 -#: 8b70a1ad70514039b97164fa630c12e4 -msgid "Note that requirements can be provided with the map syntax, as in the example above:" +#: ../../src/topics/expressions.md:47 f6f64d57a50742b19b801c14806ee18a +msgid "" +"Note that requirements can be provided with the map syntax, as in the " +"example above:" msgstr "请注意，如上例所示，requirements（要求）可通过映射语法来提供：" -#: ../../src/topics/expressions.md:54 -#: 2f28ab412d2843ffa5f14acdc01fc732 -msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +#: ../../src/topics/expressions.md:54 052e24e2ad044cc28f04d7f39be871d6 +msgid "" +"Or as an array, with each entry (in this case, only `class: " +"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" +" describe the additional command line arguments." msgstr "" -"也可以作为一个数组，每个元素均用 `-` 标记（本例中只有一个 `class: " -"InlineJavascriptRequirement` ），就和描述额外命令行参数的语法一样。" +"也可以作为一个数组，每个元素均用 `-` 标记（本例中只有一个 `class: InlineJavascriptRequirement` " +"），就和描述额外命令行参数的语法一样。" -#: ../../src/topics/expressions.md:62 -#: d957f55a6377422c9834f85d45e35009 +#: ../../src/topics/expressions.md:62 84b31c076d4b4826aae35e8c23fe6a25 msgid "Where are JavaScript expressions allowed?" msgstr "哪里可以使用 JavaScript 表达式？" -#: ../../src/topics/expressions.md:64 -#: cbec9277b5004e50af2728cbda0df740 -msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" -msgstr "JavaScript 表达式如同[参数引用](parameter-references." -"md)一样，只能用于某些特定字段，即：" +#: ../../src/topics/expressions.md:64 8c3b402c40f64880a4bd42c47b910254 +msgid "" +"Just like [parameter references](parameter-references.md), you can use " +"JavaScript Expressions only in certain fields. These are:" +msgstr "JavaScript 表达式如同[参数引用](parameter-references.md)一样，只能用于某些特定字段，即：" -#: ../../src/topics/expressions.md:66 -#: e259f55f8000479bbd8009e25cf0ca6c -msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +#: ../../src/topics/expressions.md:66 9bf5ca0e769147c6a9705bc40bd1febc +msgid "" +"From " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -"来自 [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)" +"来自 " +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 -#: 1acb064f7a4a482aa0174bdc847c6382 -#: 0222780b98ac48e89b1b4f57c9df8590 +#: ../../src/topics/parameter-references.md:64 7ab0dbd54c1441539673fa12ef96b89e +#: e76c6ece0c594fefa86b190879c5acaa msgid "`arguments`" msgstr "`arguments`" -#: ../../src/topics/expressions.md:68 -#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 -#: ef2b8433778a40408f179c3e6f0cf99e -#: 224732683a9c41f3ba1b778851e745a8 -#: 17b10d1e91b24dc582df98fcd2ac850e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 -#: e4e68011dc5f42e4918c747afa7d764b -#: d44e3cfa661840eb851782e24caf1b68 +#: ../../src/topics/parameter-references.md:86 0209558b1013471eb708698537edaf06 +#: 4458393fdb0e451f9806e91122ea2534 594a163e08f04aa5a04a44a303a1c643 +#: a6fddc160afc4ef09717f69de72c11ce a9ec99ddcb344bcbbe5c1f59af0bcff2 +#: af2cdb5f66ac4fd5b8f91258f005cc62 msgid "`valueFrom`" msgstr "`valueFrom`" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 -#: 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff +#: ../../src/topics/parameter-references.md:66 afb175f182354cb19e23b1cad241437e +#: f9a6718845e24f46b76fcc8ab26eec7a msgid "`stdin`" msgstr "`stdin`" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 -#: 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#: ../../src/topics/parameter-references.md:67 3bce21dcc2da439daca80c4fcdf4c343 +#: 7f5ce097ca0442a6a200599342a6e24b msgid "`stdout`" msgstr "`stdout`" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 -#: 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 +#: ../../src/topics/parameter-references.md:68 3397e8816f6a4d4b9af728c175f04917 +#: 7b14686e16eb4f488659b22d67ec3bfa msgid "`stderr`" msgstr "`stderr`" -#: ../../src/topics/expressions.md:72 -#: 8210b36347a749889450529ecdf4ff0e -msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +#: ../../src/topics/expressions.md:72 7a2d74aa018f4cab8c68e8775d83dd01 +msgid "" +"From " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -"来自 [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter)" +"来自 " +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -#: ../../src/topics/expressions.md:73 -#: ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 -#: ../../src/topics/expressions.md:93 +#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 -#: d0a92a3792b549e9b5ddce4667d168d2 -#: 801729c7c71b4109824b035437e69bf9 -#: 1bc510d525f0414e88692e356e67fbbc -#: d2e246ae56a24e4abdd6b7d9812a86e2 -#: b1446bab2732412e91f721a08067b0bd -#: e89dbeb22f41430ca39c923d9fdf68cb -#: bd61499b71e64164878dea08d6d7141e -#: ed875a006df64f9e8a55fa5e9fa87404 +#: ../../src/topics/parameter-references.md:90 24f27702d0684bc98e3232103510232e +#: 26a8dff7b80c4e059f1e20eef9da6203 476aa37af5214bcf963c7aab1f859273 +#: 4b0a0cd934bd41b4b55c034b91392bc7 5182e2165e44429287b4d924c2f896a4 +#: 7de500d3be6b4c3e8f274fd6a092109f 953d824a494947a3ab0ca2988717ee01 +#: b301751f90af4700bbada5e5b166be35 msgid "`format`" msgstr "`format`" -#: ../../src/topics/expressions.md:74 -#: ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 -#: ../../src/topics/expressions.md:94 +#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 -#: 8a1748579de14f0888d5ee9023e37c2d -#: f760465a49d64d4c8468ad9c4fea62b1 -#: 28b6b5ffa7524374aaa9525ebfafb762 -#: d11f6a19ddf34cf19ec856bacf998e29 -#: bcb7cd10cb5947bb9d85c040f57f954f -#: da5188d3bedc4997a35bdf417f2f643c -#: cd7a0190511d4613b09600a3b1e9d55f -#: 47def3b078e2402182039be0227090ae +#: ../../src/topics/parameter-references.md:91 2c2b8db396b04ace8aa396c0a5a4858f +#: 33a9b77ce15b4910962a7f08bd2f47a3 57cba0191de3470bbe112ed2a0d3f252 +#: 6efe998094b3469eae61cfff551b1eb1 776de1ecfafc41ada7e916addd7229fd +#: 8595d62eb0274b3a8a7f0adf058b51d3 988966a2d4844e73961b0358aff8f6e1 +#: faa7d521fec240748407d03ffdb93aa0 msgid "`secondaryFiles`" msgstr "`secondaryFiles`" -#: ../../src/topics/expressions.md:75 -#: 23088850ad02459696f6bbd385109aac -msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +#: ../../src/topics/expressions.md:75 d737a9e9bf1c45d695bf584bc3241d9a +msgid "" +"From " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -"来自 [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding)" +"来自 " +"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -#: ../../src/topics/expressions.md:77 -#: f02257a822ad46ac93c5981531cc85d5 -msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +#: ../../src/topics/expressions.md:77 0e2052e16f6a41b8983dc64b4b3a7586 +msgid "" +"From " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -"来自 [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)" +"来自 " +"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -#: ../../src/topics/expressions.md:80 -#: 989a1c4aaa1143be9f53b90cd8b6d500 -msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +#: ../../src/topics/expressions.md:80 dff31dd961d540e3b8cd1247e978d60e +msgid "" +"From " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -"来自 [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding)" +"来自 " +"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 -#: 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 +#: ../../src/topics/parameter-references.md:78 249aba7c38ce49379b9d35e7ad81a0bf +#: 5a354eb4883948e0a2b5c96b5ae12da7 msgid "`glob`" msgstr "`glob`" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 -#: d555a3d991e344a5a8e1289168d7c6d1 -#: 44b3f123c9b04a308c1161b742a7b34b +#: ../../src/topics/parameter-references.md:79 2325a310f2bc4d09b53b32c54efae2df +#: 9e477e2cfab24861b517fe2fb52962f4 msgid "`outputEval`" msgstr "`outputEval`" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 -#: e9fa9430535c424fa3e8be5d460d2ba4 -#: 0e306cc923974d1db83fdfb45105a11c -msgid "From `Workflow`" -msgstr "来自 `Workflow`" +#: ../../src/topics/parameter-references.md:80 9448462d104b4be5904623c85a9e16b7 +#: bf11a7a72147445c9b8e44b541e09f36 +#, fuzzy +msgid "From [`Workflow`](https://w3id.org/cwl/Workflow.html)" +msgstr "" +"来自 " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -#: ../../src/topics/expressions.md:84 -#: d289541e460147aa933f7878996f8649 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +#: ../../src/topics/expressions.md:84 0d54a777a33d4f17a2f3390384a3c0c5 +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -"来自 [InputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) 和 [WorkflowOutputParameter](https://www.commonwl.org/v1" -".0/Workflow.html#WorkflowOutputParameter)" +"来自 " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" 和 " +"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 -#: b0290d1a477b48119e17cf1fed9d6dff -#: 446f1190af7a40a0913ff04ce7aa938c +#: ../../src/topics/parameter-references.md:84 7918d0661be746faaddf25ad49172f30 +#: b8439dbaa949427097e25ccb48fe15ee msgid "From `steps`" msgstr "来自 `steps`" -#: ../../src/topics/expressions.md:88 -#: 81b4d1f23a3642bfa9bb395b94260cd1 -msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/topics/expressions.md:88 7b37eb600c9b4847a58a7e5077bef4c3 +msgid "" +"From " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -"来自 [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" +"来自 " +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 -#: e1cde4aa32c041238ed2596173c6d824 -#: 557694f82e314baa9ccafba14d6ff2c9 -msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +#: ../../src/topics/parameter-references.md:87 368ef005c2ca4b8599f76242f7178375 +#: ab1ba7626eae483a8b614ee4cd5bab6f +msgid "" +"From " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" -"来自 [ExpressionTool](https://www.commonwl.org/v1.0/Workflow." -"html#ExpressionTool)" +"来自 " +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 -#: c2a92d3eca7f4ee39cec649170eeea53 -#: 3c939769ede94602a67fc50c435741cf +#: ../../src/topics/parameter-references.md:88 595b9ddcee734d6595c1b4b2d169dcb8 +#: 80b55c77a4384644acfc9472c3cedee0 msgid "`expression`" msgstr "`expression`" -#: ../../src/topics/expressions.md:92 -#: f495da32f05a4a5ba9539be0a54c1a59 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +#: ../../src/topics/expressions.md:92 fd504478a6c641e0a72321fa80ad1c9c +msgid "" +"From " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -"来自 [InputParameter](https://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) 和 [ExpressionToolOutputParameter](https://www.commonwl." -"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"来自 " +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" 和 " +"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -#: ../../src/topics/expressions.md:95 -#: bdb4c68a175047ddbe141ca24960127f -msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +#: ../../src/topics/expressions.md:95 32b1a39cca1a4402af9bdc0abc4d70c8 +msgid "" +"From " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" -"来自 [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement)" +"来自 " +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 -#: 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 +#: ../../src/topics/parameter-references.md:93 2518d499801e4bcf82e9e4666280504d +#: 98a511d138e9497c923963c2ca5f0a0b msgid "`coresMin`" msgstr "`coresMin`" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 -#: 718ceee9973240ec9c100977bbcc8921 -#: 2b25152f6df5494a8632f3ce631c20d8 +#: ../../src/topics/parameter-references.md:94 57a055b125f742dc8842b798b034161b +#: e84bc5505a6549ae9aacde8cb9225403 msgid "`coresMax`" msgstr "`coresMax`" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 -#: c07ab08eb75d4528949c56a3d7c12b28 -#: 846cd427ae25410eae7c920b237edcb0 +#: ../../src/topics/parameter-references.md:95 98cd455e080f43749090270e7a61cb42 +#: e698ea756fe94e99837312fb30c9f9bf msgid "`ramMin`" msgstr "`ramMin`" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 -#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 +#: ../../src/topics/parameter-references.md:96 8dfae10004a641fdb95c456c90a48d94 +#: bef90c153d4f4397b1f69f9beb38f7e6 msgid "`ramMax`" msgstr "`ramMax`" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 -#: 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 +#: ../../src/topics/parameter-references.md:97 47fddc711ce44086a7811bdfbd9167dd +#: e2bdf4fe676346cbb4443ee54fb7419b msgid "`tmpdirMin`" msgstr "`tmpdirMin`" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 -#: 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 +#: ../../src/topics/parameter-references.md:98 7d143ba98f1f4dfcbe08b70389d43092 +#: 8f1665baca2e4e3b96026b50d132709a msgid "`tmpdirMax`" msgstr "`tmpdirMax`" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 -#: 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 +#: ../../src/topics/parameter-references.md:99 79bea45c2a484eda92c8578130b0b982 +#: d169949866a24e31947dffcb94620c5f msgid "`outdirMin`" msgstr "`outdirMin`" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b -#: e3b76f42c924489f9a0bcf5a7b636d23 +#: 8d2e01f2aa314f1cb1231f2e08f89ce5 d5417397b1e242ef9878ac77d2f65005 msgid "`outdirMax`" msgstr "`outdirMax`" -#: ../../src/topics/expressions.md:104 -#: 97b61352363f47cb890e8937c5613fa3 -msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +#: ../../src/topics/expressions.md:104 08a66b2ab271494d810ff5834ca5c1bc +msgid "" +"From " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" -"来自 [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" -"CommandLineTool.html#InitialWorkDirRequirement)" +"来自 " +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e -#: a258554d462f4f5f83ece28d5b2fc584 +#: 21e9582891cf4b87a7ee4693663040fa 51bc6d1ccef14729a0d5e63b56d73d20 msgid "`listing`" msgstr "`listing`" -#: ../../src/topics/expressions.md:106 -#: 8d0b142bb7ed4e61b8fb03de197240ce +#: ../../src/topics/expressions.md:106 7d8755f05d6541439f72ec9d6806d3fc msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "来自 [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: effc0208cf4f4551958db6e526c0528b -#: 9d4889c8cec24351a7a9e3c547e331b6 +#: 29c2424fc7dc43e68c9bfee179167bb3 30f25141bcce4670882e4a5bbe4fc3e2 msgid "`entry`" msgstr "`entry`" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: be6c1e85c7b6495d8086c262daad20e7 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +#: 02cfd4f1c3014e1eaa598a329dc5a95d d76fb015595e4194a7e15d714baaaf98 msgid "`entryname`" msgstr "`entryname`" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 -#: 6abeba392b0444b19f92a19f178a4682 +#: 408f69a2df1343a78f93ff2ac0a994ea d37c78309e8b427f835af4fbd367e643 msgid "From `EnvVarRequirement`" msgstr "来自 `EnvVarRequirement`" -#: ../../src/topics/expressions.md:110 -#: 0bc424ef2ca346099f29b937379908a0 -msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +#: ../../src/topics/expressions.md:110 53752bdff0974e39b2a86e8f2d96455f +msgid "" +"From " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" -"来自 [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef)" +"来自 " +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd -#: 949c376120d8441796ec9c89364f8851 +#: 242a12ec757947db894195c9aefba818 7b26b9972f7141bf950b3bb024b0e369 msgid "`envValue`" msgstr "`envValue`" -#: ../../src/topics/expressions.md:116 -#: 10d36a1adfd04144b401c993b12b4094 +#: ../../src/topics/expressions.md:116 93d6c90b49d8424f9283c384062ce333 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "通过 `expressionLib` 使用外部库和内联 JavaScript 代码" -#: ../../src/topics/expressions.md:118 -#: 29b73e1dd72744f68377f0a38c10f062 -msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +#: ../../src/topics/expressions.md:118 ea6cbaa5dae647538c0bd9a4d5cad3f9 +#, fuzzy +msgid "" +"The requirement " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" +" supports an `expressionLib` attribute that allows users to load external" +" JavaScript files, or to provide inline JavaScript code." msgstr "" -"`InlineJavascriptRequirements` 这一需求支持 `expressionLib` 属性，" -"可以让用户加载外部 JavaScript 文件或提供内联 JavaScript 代码。" +"`InlineJavascriptRequirements` 这一需求支持 `expressionLib` 属性，可以让用户加载外部 " +"JavaScript 文件或提供内联 JavaScript 代码。" -#: ../../src/topics/expressions.md:122 -#: 38a2afaf4a6c4d04909af22c93f2808d -msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +#: ../../src/topics/expressions.md:122 484dc17440524cfda4dc486a7c5d5f63 +msgid "" +"Entries added to the `expressionLib` attribute are parsed with the " +"JavaScript engine of a CWL runner. This can be used to include external " +"files or to create JavaScript functions that can be called in other parts" +" of the CWL document." msgstr "" "添加到 `expressionLib` 属性的条目将由 CWL 运行程序的 JavaScript " -"引擎进行语法分析。这可以用来纳入外部文件中的代码，或创建可在 CWL " -"文件其他部分调用的 JavaScript 函数。" +"引擎进行语法分析。这可以用来纳入外部文件中的代码，或创建可在 CWL 文件其他部分调用的 JavaScript 函数。" -#: ../../src/topics/expressions.md:128 -#: cd74f34b21af4de9be96fd897efc469b -msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." -msgstr "" -"版本 1.0 到 1.2 的 CWL 标准中[写道](https://www.commonwl.org/v1.0/" -"CommandLineTool.html#Expressions)，在 CWL 表达式中唯一有效的 JavaScript " -"版本是 [ECMAScript 5.1](https://262.ecma-international.org/5.1/) . 也就是说，" -"在 CWL 文件中纳入或写入的所有 JS 代码都必须符合该版本。" - -#: ../../src/topics/expressions.md:135 -#: f12e371f3f1a4b0cb2cff9800352d48c -msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +#: ../../src/topics/expressions.md:128 5b2336cae1ef4cae8ed187d3f33cff25 +msgid "" +"The CWL standards (versions 1.0 through 1.2) " +"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" +" that the only version of JavaScript valid in CWL expressions is " +"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " +"that any code that you include or write in your CWL Document must be " +"compliant with ECMAScript 5.1." +msgstr "" +"版本 1.0 到 1.2 的 CWL " +"标准中[写道](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)，在" +" CWL 表达式中唯一有效的 JavaScript 版本是 [ECMAScript 5.1](https://262.ecma-" +"international.org/5.1/) . 也就是说，在 CWL 文件中纳入或写入的所有 JS 代码都必须符合该版本。" + +#: ../../src/topics/expressions.md:135 32eca3a47efc4685bf7be706e123adbe +msgid "" +"For example, we can use `InlineJavascriptRequirement` and write a " +"JavaScript function inline in `expressionLib`. That function can then be " +"used in other parts of the CWL document:" msgstr "" -"例如，我们可以使用 `InlineJavascriptRequirements`, 在 `expressionLib` " -"下编写内联 JavaScript 函数，让它能在 CWL 文件其他部分调用：" +"例如，我们可以使用 `InlineJavascriptRequirements`, 在 `expressionLib` 下编写内联 " +"JavaScript 函数，让它能在 CWL 文件其他部分调用：" -#: ../../src/topics/expressions.md:139 -#: 49d0fda2fc144e0b8b7c92afc1d8945e +#: ../../src/topics/expressions.md:139 6839a02fb82d45c29ae518f2b00cb9d5 msgid "`hello-world-expressionlib-inline.cwl`" msgstr "`hello-world-expressionlib-inline.cwl`" -#: ../../src/topics/expressions.md:146 -#: 8f0e8f050e334ac08334e9215e1dcf61 -msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" -msgstr "运行此 CWL 工作流将调用这个 JavaScript 函数，使得 `echo` " -"命令以大写首字母排印输入的“报文”：" +#: ../../src/topics/expressions.md:146 5b5e59fa1688499ea4560ee6f8023227 +msgid "" +"Running this CWL workflow will invoke the JavaScript function and result " +"in the `echo` command printing the input message with capital initial " +"letters:" +msgstr "运行此 CWL 工作流将调用这个 JavaScript 函数，使得 `echo` 命令以大写首字母排印输入的“报文”：" -#: ../../src/topics/expressions.md:149 -#: 26c74b11bb1849cea0763bb74ec43e42 +#: ../../src/topics/expressions.md:149 a1e57c6833c848d3974cf448493ab924 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "运行 `hello-world-expressionlib-inline.cwl`." -#: ../../src/topics/expressions.md:155 -#: 7a6be0005a6441feb67f036d005d7885 -msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" -msgstr "" -"我们来将 `capitalizeWords` 函数移动到外部文件 `custom-functions.js`, " -"并将它导入我们的 CWL 文件：" +#: ../../src/topics/expressions.md:155 1a4dfef06b5c4402bdb7e7dbd79eeb5d +msgid "" +"Let's move the `capitalizeWords` function to an external file, `custom-" +"functions.js`, and import it in our CWL document:" +msgstr "我们来将 `capitalizeWords` 函数移动到外部文件 `custom-functions.js`, 并将它导入我们的 CWL 文件：" -#: ../../src/topics/expressions.md:158 -#: ed590f9e6f4f425da886b110295c45db +#: ../../src/topics/expressions.md:158 71ac99c65d15451cbbf58d1e81934010 msgid "`custom-functions.js`" msgstr "`custom-functions.js`" -#: ../../src/topics/expressions.md:164 -#: 093235307d6f47d4858e559b780ef5e5 +#: ../../src/topics/expressions.md:164 60918e53189243d3872e61c7a4de20fc msgid "`hello-world-expressionlib-external.cwl`" msgstr "`hello-world-expressionlib-external.cwl`" -#: ../../src/topics/expressions.md:171 -#: 06635145b441418aaae84dc804f3d6ac -msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +#: ../../src/topics/expressions.md:171 ad2a74bd983b47869dc78b2eb7b6fce1 +msgid "" +"The `custom-functions.js` file is included in the CWL document with the " +"`$include: custom-functions.js` statement. That makes the functions and " +"variables available to be used in other parts of the CWL document." msgstr "" -"文件 `custom-functions.js` 通过 `$include: custom-functions.js` " -"语句纳入到这个 CWL 文件里，使这个 JavaScript 文件中定义的函数和变量可在 CWL " -"文件其他部分使用。" +"文件 `custom-functions.js` 通过 `$include: custom-functions.js` 语句纳入到这个 CWL " +"文件里，使这个 JavaScript 文件中定义的函数和变量可在 CWL 文件其他部分使用。" -#: ../../src/topics/expressions.md:175 -#: 973a9b257b1a4f0dbd4444d4f11dadd7 +#: ../../src/topics/expressions.md:175 82c02dd2446b4de9a4c4b87736107b30 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "运行 `hello-world-expressionlib-external.cwl`." -#: ../../src/topics/expressions.md:181 -#: 04eaf1f7c630450db318dcd8b7626e15 -msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." -msgstr "" -"最后请注意，CWL 文件中可以同时运用内联和外部 JavaScript " -"代码。下面是最后一个例子，这里我们向 `expressionLib` 属性中加入新函数 " -"`createHelloWorldMessage`, 调用外部文件 `custom-functions.js` 中的 " +#: ../../src/topics/expressions.md:181 6fa7ebeffc7b44c6a12cd84897d186a1 +msgid "" +"Finally, note that you can have both inline and external JavaScript code " +"in your CWL document. In this final example we have added another entry " +"to the `expressionLib` attribute with the new function " +"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" +" the external file `custom-functions.js`." +msgstr "" +"最后请注意，CWL 文件中可以同时运用内联和外部 JavaScript 代码。下面是最后一个例子，这里我们向 `expressionLib` " +"属性中加入新函数 `createHelloWorldMessage`, 调用外部文件 `custom-functions.js` 中的 " "`capitalizeWords` 函数。" -#: ../../src/topics/expressions.md:186 -#: c4098489fbb049789f022cd3e5c3d49b +#: ../../src/topics/expressions.md:186 d34f3e688d2d49b6bfcda4c962895d8c msgid "`hello-world-expressionlib.cwl`" msgstr "`hello-world-expressionlib.cwl`" -#: ../../src/topics/expressions.md:193 -#: 5979e4ae5c424276bdbc47f69b379d0f +#: ../../src/topics/expressions.md:193 9e2774fc35b14832a0f92b7afaafd537 msgid "Running `hello-world-expressionlib.cwl`." msgstr "运行 `hello-world-expressionlib.cwl`." -#: ../../src/topics/expressions.md:200 -#: fd4579a3c9844492b314b5c3c1775fc7 -msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +#: ../../src/topics/expressions.md:200 8b797cfb232f4e5da51f6c21e9a8e7e3 +msgid "" +"The `$include` statement can be used to include a file from the local " +"disk or from a remote location. It works with both relative and absolute " +"paths. Read the [text about " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " +"the CWL specification to learn more about it." msgstr "" -"`$include` 语句可以用来添加位于本地或远程的文件，并且接受相对路径和绝对路径。" -"详情请参见 CWL 规约中[关于 `$include`](https://www.commonwl.org/v1.0/" -"SchemaSalad.html#Include) 的内容。" +"`$include` 语句可以用来添加位于本地或远程的文件，并且接受相对路径和绝对路径。详情请参见 CWL 规约中[关于 " +"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) 的内容。" -#: ../../src/topics/file-formats.md:1 -#: 3f038e7371f84ed9b4547358dfb55a11 +#: ../../src/topics/file-formats.md:1 ac906f26116c45d882e1afa42ae38e34 msgid "File Formats" msgstr "文件格式" -#: ../../src/topics/file-formats.md:3 -#: e024bcb70e04412e90e1838426d1b69a -msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +#: ../../src/topics/file-formats.md:3 d99dab4f2f264c68b839b59b80d570e0 +#, fuzzy +msgid "" +"Tools and workflows can take " +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types as input " +"and produce them as output. We also recommend indicating the format for " +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types. This " +"helps document for others how to use your tool while allowing you to do " +"some simple type-checking when creating parameter files." msgstr "" -"`File` 类型既可作为工具和工作流的输入，也可以成为它们生成的输出。另外，" -"我们建议指明 `File` 类型的格式，以便向他人说明您的工具如何使用，同时还能让您" -"在创建参数文件时进行简单的类型检验。" +"`File` 类型既可作为工具和工作流的输入，也可以成为它们生成的输出。另外，我们建议指明 `File` " +"类型的格式，以便向他人说明您的工具如何使用，同时还能让您在创建参数文件时进行简单的类型检验。" -#: ../../src/topics/file-formats.md:8 -#: a3db21c0b3114802a8a5b610e252ef13 -msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +#: ../../src/topics/file-formats.md:8 23ba3dd26f5543119e2c152105b58e98 +msgid "" +"For file formats, we recommend referencing existing ontologies (like EDAM" +" in our example), reference a local ontology for your institution, or do " +"not add a file format initially for quick development before sharing your" +" tool with others. You can browse existing [IANA file format " +"listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -"对于文件格式，我们建议参考现有本体（如示例中的 EDAM）或您所在机构内部使用的本" -"体，不然，则在与他人共享工具之前不要先添加文件格式，以便快速开发。" -"您可以通过网站浏览现有的 [IANA][IANA] 和 [EDAM 文件格式列表][EDAM]。" +"对于文件格式，我们建议参考现有本体（如示例中的 " +"EDAM）或您所在机构内部使用的本体，不然，则在与他人共享工具之前不要先添加文件格式，以便快速开发。您可以通过网站浏览现有的 " +"[IANA][IANA] 和 [EDAM 文件格式列表][EDAM]。" -#: ../../src/topics/file-formats.md:14 -#: 0f5bc8520d6a4dafa37c65343da9702a -msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." -msgstr "我们将在下一篇教程中更详细地解释文件中的 `$namespaces` 和 `$schemas` " -"部分，眼下无需为此分心。" +#: ../../src/topics/file-formats.md:14 81c441846fc249c58607bacf97095eb8 +msgid "" +"In the next tutorial, we explain the `$namespaces` and `$schemas` " +"section of the document in greater detail, so don't worry about these for" +" now." +msgstr "我们将在下一篇教程中更详细地解释文件中的 `$namespaces` 和 `$schemas` 部分，眼下无需为此分心。" -#: ../../src/topics/file-formats.md:17 -#: 5cb830da47464a8b9c3950983fa4d56f -msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." -msgstr "请注意， `cwltool` 有一项附加功能，即依据文件格式做一些初步推断，一旦出现较明" -"显的不匹配则发出警告。" +#: ../../src/topics/file-formats.md:17 c04841dbf4be4cf8a22cceca8b08bd14 +msgid "" +"Note that for added value `cwltool` can do some basic reasoning based on " +"file formats and warn you if there seem to be some obvious mismatches." +msgstr "请注意， `cwltool` 有一项附加功能，即依据文件格式做一些初步推断，一旦出现较明显的不匹配则发出警告。" -#: ../../src/topics/file-formats.md:20 -#: 0535d5de416b4ea3b2f5996583deecc1 +#: ../../src/topics/file-formats.md:20 c5f6f6e4c23e4bf19dee69acb8ebed8e msgid "`metadata_example.cwl`" msgstr "`metadata_example.cwl`" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 -#: fb47f73c38cf4ec59bd3021866a631f8 +#: 20e97d58596a4a959ad76ec6128ac414 4e070ae9110d437bbf008b0c60a00cd5 msgid "The equivalent of this CWL description in command line format is:" msgstr "这一 CWL 描述的等效命令行形式为：" -#: ../../src/topics/file-formats.md:32 -#: 74b28c1b09c6429b82e462e4ec61808e +#: ../../src/topics/file-formats.md:32 632e441919094610b97afc17e9c5e625 msgid "Sample Parameter Files" msgstr "参数文件样本" -#: ../../src/topics/file-formats.md:34 -#: a2ce43b391864e8bbde16328cc19b32b -msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." -msgstr "" -"以上例子的样本参数文件见下。我们提倡为您的工具加入经您测试可用的参数文件样例" -"，这将帮助他人从做好的“合格品”参数文件入手，更快地上手操作您的工具。" +#: ../../src/topics/file-formats.md:34 afd8633db1904897aa3e499354b1c376 +msgid "" +"Below is an example of a parameter file for the example above. We " +"encourage checking in working examples of parameter files for your tool. " +"This allows others to quickly work with your tool, starting from a " +"\"known good\" parameterization." +msgstr "以上例子的样本参数文件见下。我们提倡为您的工具加入经您测试可用的参数文件样例，这将帮助他人从做好的“合格品”参数文件入手，更快地上手操作您的工具。" -#: ../../src/topics/file-formats.md:39 -#: aebee48b742c4145a600fd2daf8c75dc +#: ../../src/topics/file-formats.md:39 bb69d6963c174191bf527335c3f665b7 msgid "`sample.yml`" msgstr "`sample.yml`" -#: ../../src/topics/file-formats.md:45 -#: 56ee4dcfff6141d5bef80eb96559876d -msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" -msgstr "" -"___注意：___ 按照下例演练前，您需要先下载示例输入文件 *file-formats.bam*. " -"该文件位于 , 可以用 `wget` 等工具下载：" - -#: ../../src/topics/index.md:1 -#: 8d3a6d83e2e54c56995893c41590b7ff +#: ../../src/topics/file-formats.md:45 ddb4f6f81c7d462b974e98c88dd3f558 +msgid "" +"___Note:___ To follow the example below, you need to download the example" +" input file, *file-formats.bam*. The file is available from " +" and can be downloaded e.g. via `wget`:" +msgstr "" +"___注意：___ 按照下例演练前，您需要先下载示例输入文件 *file-formats.bam*. 该文件位于 " +", 可以用 `wget` 等工具下载：" + +#: ../../src/topics/index.md:1 2995cd4fb85c423dba021611dac4a137 msgid "Topics" msgstr "主题" -#: ../../src/topics/inputs.md:1 -#: 5abcdebfa1cb401bb8892553be285fd3 +#: ../../src/topics/inputs.md:1 3bac021fe7614d74ae701fb3c3765b93 msgid "Inputs" msgstr "输入 (inputs)" -#: ../../src/topics/inputs.md:3 -#: d3a55f71dc244026a97902de9ed819ea +#: ../../src/topics/inputs.md:3 8bb3ee0cd0fc4d85ba007431fc541973 msgid "Essential Input Parameters" msgstr "基本输入参数" -#: ../../src/topics/inputs.md:5 -#: 96671c56523c4ea9992fb5dfcfa6490e -msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +#: ../../src/topics/inputs.md:5 17365707f58242369dd6aa73fc8d7242 +msgid "" +"The `inputs` of a tool is a list of input parameters that control how to " +"run the tool. Each parameter has an `id` for the name of parameter, and " +"`type` describing what types of values are valid for that parameter." msgstr "" -"工具的 `inputs`（输入）用于列出控制工具运行方式的输入参数。每个参数都包含 " -"`id` 字段作为名称，以及 `type` 字段描述有效参数值的类型。" +"工具的 `inputs`（输入）用于列出控制工具运行方式的输入参数。每个参数都包含 `id` 字段作为名称，以及 `type` " +"字段描述有效参数值的类型。" -#: ../../src/topics/inputs.md:9 -#: bcc6246742cb46bfb185e415c4a3431a -msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +#: ../../src/topics/inputs.md:9 521cb5dead5d4e9ab5ff037fb4b683cb +#, fuzzy +msgid "" +"Available primitive types are *string*, *boolean*, *int*, *long*, " +"*float*, *double*, and *null*; complex types are *array* and *record*; in" +" addition there are special types *File*, *Directory* and *Any*." msgstr "" "可用的原始类型有 *string*（字符串）、 *int*（整型）、*long*（长整型）、 " -"*float*（浮点数）、*double*（双精度浮点数）以及 *null*（空）等；" -"复合类型指的是 *array*（数组）和 *record*（记录）；此外还有特殊类型 " -"*File*（文件）、*Directory*（目录）以及 *Any*（任意）等。" +"*float*（浮点数）、*double*（双精度浮点数）以及 *null*（空）等；复合类型指的是 *array*（数组）和 " +"*record*（记录）；此外还有特殊类型 *File*（文件）、*Directory*（目录）以及 *Any*（任意）等。" -#: ../../src/topics/inputs.md:13 -#: 86dce36de687449c88fb5eb9d64eb045 -msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +#: ../../src/topics/inputs.md:13 fbdf2c1bed3e41d7a41ec6b14d134a98 +msgid "" +"The following example demonstrates some input parameters with different " +"types and appearing on the command line in different ways." msgstr "下面的例子展示了一些类型各异、以不同方式出现在命令行上的输入参数。" -#: ../../src/topics/inputs.md:16 -#: cd9cea15f57b492ba4098237cd7c5bed +#: ../../src/topics/inputs.md:16 008f79cdf0074c73948bf50deb0a8a47 msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "首先，创建一个名为 `inp.cwl` 的文件，包含以下内容：" -#: ../../src/topics/inputs.md:18 -#: 8bdb875b63104f699efe28ea0abb1e3d +#: ../../src/topics/inputs.md:18 94cd3f10e94f4735bd3ae7dc168e5deb msgid "`inp.cwl`" msgstr "`inp.cwl`" -#: ../../src/topics/inputs.md:24 -#: c6a0151a68494c0cb0176781e65e252e +#: ../../src/topics/inputs.md:24 b339be370e8742b69400c8040ad7d15b msgid "Create a file called `inp-job.yml`:" msgstr "创建名为 `inp-job.yml` 的文件：" -#: ../../src/topics/inputs.md:26 -#: dc5e6b5e01d64226bd5dbbf3175fe010 +#: ../../src/topics/inputs.md:26 78974fb2475947ccb8b8c55e34df5fa6 msgid "`inp-job.yml`" msgstr "`inp-job.yml`" -#: ../../src/topics/inputs.md:33 -#: 36ab1d9edafc4831bb1bca5f123b04b0 -msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +#: ../../src/topics/inputs.md:33 9cc4a60d01f945aa9b4c43afcf20098b +#, fuzzy +msgid "" +"You can use `cwltool` to create a template input object. That saves you " +"from having to type all the input parameters in an input object file:" msgstr "您可以用 `cwltool` 创建模板输入对象，以省去在输入对象文件中一一键入输入参数：" -#: ../../src/topics/inputs.md:40 -#: 7dc630ea86464b1dba3a4e5079260b3b -msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +#: ../../src/topics/inputs.md:40 5ac6da11d56446de97c251a37d997671 +msgid "" +"You can redirect the output to a file, i.e. `cwltool --make-template " +"inp.cwl > inp-job.yml`, and then modify the default values with your " +"desired input values." msgstr "" -"您可将输出重定向到一个文件：`cwltool --make-template inp.cwl > inp-job." -"yml`，然后将生成的默认值改为您想要的输入值。" +"您可将输出重定向到一个文件：`cwltool --make-template inp.cwl > inp-" +"job.yml`，然后将生成的默认值改为您想要的输入值。" -#: ../../src/topics/inputs.md:44 -#: ae37901a8dbe48a59e27ab4e2e6e2d30 -msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." -msgstr "" -"注意，“example_file” 属于 `File`（文件）类型，因此必须作为含有 `class: File` " -"和 `path` 字段的对象出现。" +#: ../../src/topics/inputs.md:44 6a3edb0d259d4d7c900dd9811f978d4e +msgid "" +"Notice that \"example_file\", as a `File` type, must be provided as an " +"object with the fields `class: File` and `path`." +msgstr "注意，“example_file” 属于 `File`（文件）类型，因此必须作为含有 `class: File` 和 `path` 字段的对象出现。" -#: ../../src/topics/inputs.md:47 -#: 651e032007ea4a119d20c820bb61f86b -msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +#: ../../src/topics/inputs.md:47 f1d76be7ba0b48f4b605581d0a9a5c72 +msgid "" +"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" +" command line." msgstr "然后，在命令行键入 `touch whale.txt`, 用 [touch] 命令创建文件 whale.txt." -#: ../../src/topics/inputs.md:53 -#: 0b056dde9e87428996e47870b12119da -msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +#: ../../src/topics/inputs.md:53 8cabfa0cbcfd4a5aa30d1aabd412136d +msgid "" +"Now invoke `cwltool` with the tool description and the input object on " +"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " +"following boxed text describes these two commands and the expected output" +" from the command line:" msgstr "" -"现在，使用 `cwltool inp.cwl inp-job.yml` 命令，即指定工具描述和输入对象、" -"通过命令行调用 `cwltool`. 下方文本框描述了这两个命令及命令行的预期输出：" +"现在，使用 `cwltool inp.cwl inp-job.yml` 命令，即指定工具描述和输入对象、通过命令行调用 `cwltool`. " +"下方文本框描述了这两个命令及命令行的预期输出：" -#: ../../src/topics/inputs.md:64 -#: 628124a1670b4b058bb0fb6e495a099c -msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +#: ../../src/topics/inputs.md:64 5c78d7824ef34636ae2ed68d524d79e8 +msgid "" +"The CWL reference runner (cwltool) and other runners create temporary " +"directories with symbolic (\"soft\") links to your input files to ensure " +"that the tools aren't accidentally accessing files that were not " +"explicitly specified" msgstr "" -"CWL 参考运行程序 (cwltool) 和其他运行程序会建立临时目录，在其中创建指向您文件" -"的符号链接（又称“软”链接），以防工具意外访问未经明文指定的文件" +"CWL 参考运行程序 (cwltool) " +"和其他运行程序会建立临时目录，在其中创建指向您文件的符号链接（又称“软”链接），以防工具意外访问未经明文指定的文件" -#: ../../src/topics/inputs.md:70 -#: 10ca6321ce3e4b08ab6a5bb380b19c11 -msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +#: ../../src/topics/inputs.md:70 5bdf77c45346445d8f93353c1e73f768 +#, fuzzy +msgid "" +"The field " +"[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)" +" is optional and indicates whether and how the input parameter should " +"appear on the tool's command line. If `inputBinding` is missing, the " +"parameter does not appear on the command line. Let's look at each " +"example in detail." msgstr "" -"字段 `inputBinding` " -"为可选项，用来说明该输入参数是否应出现在工具的命令行上、以何种方式出现。 " -"如果没有 `inputBinding`, 则该参数不会出现在命令行上。 " -"我们来仔细看看每个示例。" +"字段 `inputBinding` 为可选项，用来说明该输入参数是否应出现在工具的命令行上、以何种方式出现。 如果没有 " +"`inputBinding`, 则该参数不会出现在命令行上。 我们来仔细看看每个示例。" -#: ../../src/topics/inputs.md:83 -#: ec2adb3912bc46e28891229e9e0d9a1c -msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +#: ../../src/topics/inputs.md:83 d783fe52e86f4feda33ea0eecb622603 +msgid "" +"Boolean types are treated as a flag. If the input parameter " +"\"example_flag\" is \"true\", then `prefix` will be added to the command " +"line. If false, no flag is added." msgstr "" -"布尔类型的处理相当于一种“旗标”。如果输入参数“example_flag”为“true”（真），则 " -"`prefix` 会被添加到命令行，否则将不添加旗标。" +"布尔类型的处理相当于一种“旗标”。如果输入参数“example_flag”为“true”（真），则 `prefix` " +"会被添加到命令行，否则将不添加旗标。" -#: ../../src/topics/inputs.md:95 -#: a519be60726a44af9941fdce04735353 -msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +#: ../../src/topics/inputs.md:95 f99fb9a6d0374ef78503815d4db9006d +msgid "" +"String types appear on the command line as literal values. The `prefix` " +"is optional, if provided, it appears as a separate argument on the " +"command line before the parameter . In the example above, this is " +"rendered as `--example-string hello`." msgstr "" "字符串类型以字面值 (literal value) 的方式出现在命令行上。 `prefix` " -"是可选的；如果提供，它将作为单独的参数，在命令行上出现在参数值之前。上例中，" -"相应的结果是 `--example-string hello`." +"是可选的；如果提供，它将作为单独的参数，在命令行上出现在参数值之前。上例中，相应的结果是 `--example-string hello`." -#: ../../src/topics/inputs.md:109 -#: cb8fc8c4c79e467eac5fab4ca685201e -msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +#: ../../src/topics/inputs.md:109 b106eed01c1744a792368f91f547e553 +msgid "" +"Integer (and floating point) types appear on the command line with " +"decimal text representation. When the option `separate` is false (the " +"default value is true), the prefix and value are combined into a single " +"argument. In the example above, this is rendered as `-i42`." msgstr "" -"整型和浮点型以其十进制表示，作为文本出现在命令行上。 若选项 `separate` 为 " -"false（伪，默认为 true 真），前缀将和它的值合并为一个参数。上例中，其产物为 " -"`-i42`." +"整型和浮点型以其十进制表示，作为文本出现在命令行上。 若选项 `separate` 为 false（伪，默认为 true " +"真），前缀将和它的值合并为一个参数。上例中，其产物为 `-i42`." -#: ../../src/topics/inputs.md:124 -#: a26cc105716f47cb807174c9003153b0 -msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." -msgstr "" -"文件类型在命令行上以文件路径的方式出现。参数类型末尾如有问号 `?` " -"意指该参数为可选。上例中，这一部分的命令行产物是 `--file=/tmp/random/path/" -"whale.txt`. " +#: ../../src/topics/inputs.md:124 1c70336741a842a5b16b687642d1d9b4 +msgid "" +"File types appear on the command line as the path to the file. When the " +"parameter type ends with a question mark `?` it indicates that the " +"parameter is optional. In the example above, this is rendered as " +"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " +"parameter were not provided in the input, nothing would appear on the " +"command line." +msgstr "" +"文件类型在命令行上以文件路径的方式出现。参数类型末尾如有问号 `?` 意指该参数为可选。上例中，这一部分的命令行产物是 " +"`--file=/tmp/random/path/whale.txt`. " "不过，如果输入中未提供“example_file”参数，则不会在命令行上加入任何内容。" -#: ../../src/topics/inputs.md:131 -#: cc159dd5fe5748caac838862f5b8c4d1 -msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." -msgstr "输入文件是只读的。 如果要更新输入文件，必须将它[事先复制到输出目录](staging-" -"input-files.md)。" +#: ../../src/topics/inputs.md:131 9294c07c672b414f9c3895ed70b9b4ee +msgid "" +"Input files are read-only. If you wish to update an input file, you must" +" [first copy it to the output directory](staging-input-files.md)." +msgstr "输入文件是只读的。 如果要更新输入文件，必须将它[事先复制到输出目录](staging-input-files.md)。" -#: ../../src/topics/inputs.md:134 -#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 -msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +#: ../../src/topics/inputs.md:134 a07137c36e63495f836c483fd472904f +msgid "" +"The value of `position` is used to determine where parameter should " +"appear on the command line. Positions are relative to one another, not " +"absolute. As a result, positions do not have to be sequential, three " +"parameters with positions 1, 3, 5 will result in the same command line as" +" 1, 2, 3. More than one parameter can have the same position (ties are " +"broken using the parameter name), and the position field itself is " +"optional. The default position is 0." msgstr "" "`position`（位置）的值用于指定参数在命令行上应出现的位置 — " -"并非绝对位置，而是彼此间的相对顺序。这意味着，位置值不一定要连续；`position` " -"值为 1、3、5 的三个参数生成的命令行将与其值分别为 1、2、3 时相同。 " -"多个参数可能有相同的 `position` 值（这种情况下由参数名进一步决定顺序），而且 " -"`position` 字段本身是可选的。 默认的位置是0." - -#: ../../src/topics/inputs.md:142 -#: 6812698e9ad84d3385de5e88e9dde0b3 -msgid "The `baseCommand` field will always appear in the final command line before the parameters." +"并非绝对位置，而是彼此间的相对顺序。这意味着，位置值不一定要连续；`position` 值为 1、3、5 的三个参数生成的命令行将与其值分别为 " +"1、2、3 时相同。 多个参数可能有相同的 `position` 值（这种情况下由参数名进一步决定顺序），而且 `position` " +"字段本身是可选的。 默认的位置是0." + +#: ../../src/topics/inputs.md:142 7513adabd3ae4701b17f578ac9f321d7 +msgid "" +"The `baseCommand` field will always appear in the final command line " +"before the parameters." msgstr "`baseCommand` 字段一定会出现在最终生成的命令行中，而且位于所有参数之前。" -#: ../../src/topics/inputs.md:146 -#: 9654e65b1c0642dbb5d4f34edb211989 +#: ../../src/topics/inputs.md:146 c3c82d25a75941b0b50a4a6bb826568f msgid "Array Inputs" msgstr "数组输入" -#: ../../src/topics/inputs.md:148 -#: d1f02be278754267893dfce5a940997d -msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +#: ../../src/topics/inputs.md:148 b11a5c7a13b345939e4ae15e1e2c0786 +msgid "" +"It is easy to add arrays of input parameters represented to the command " +"line. There are two ways to specify an array parameter. First is to " +"provide `type` field with `type: array` and `items` defining the valid " +"data types that may appear in the array. Alternatively, brackets `[]` may" +" be added after the type name to indicate that input parameter is array " +"of that type." msgstr "" -"将以数组形式出现的参数添加至命令行很简单。指定数组参数有两种办法。第一种是在 " -"`type` 字段下给出 `type: array`, 并且用 `items` " -"定义数组中允许出现的有效数据类型。另一种办法，是在类型的名称后添加方括号 " -"`[]`，以表明输入参数为此类型的数组。" +"将以数组形式出现的参数添加至命令行很简单。指定数组参数有两种办法。第一种是在 `type` 字段下给出 `type: array`, 并且用 " +"`items` 定义数组中允许出现的有效数据类型。另一种办法，是在类型的名称后添加方括号 `[]`，以表明输入参数为此类型的数组。" -#: ../../src/topics/inputs.md:154 -#: 01f30e38dfdd452dba3a996073936e16 +#: ../../src/topics/inputs.md:154 aa00bcfc6c0f4085ae52621a2f4ae8d9 msgid "`array-inputs.cwl`" msgstr "`array-inputs.cwl`" -#: ../../src/topics/inputs.md:160 -#: 787d4bfb093c4ad287b902084706b751 +#: ../../src/topics/inputs.md:160 e730b2b9bace4427bdd045556963634f msgid "`array-inputs-job.yml`" msgstr "`array-inputs-job.yml`" -#: ../../src/topics/inputs.md:166 -#: ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 -#: 588f0f7f967f4d69af27c9729d6d3119 -#: 02adef8ee8204842b5b4a0408f3bac33 -#: 9db68837918a4a349f32f15f12697a1d -msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:86 +#: ../../src/topics/outputs.md:109 015a0f00c2b245e2b0e87735926da736 +#: 390384208d7b4771888f164b587c7b9a edb3ae59c48945f29c3086b16a5265d3 +msgid "" +"Now invoke `cwltool` providing the tool description and the input object " +"on the command line:" msgstr "现在，调用命令 `cwltool` 并为它提供工具描述和输入对象：" -#: ../../src/topics/inputs.md:178 -#: 75d59e395c66416cae9b352db5081516 -msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." -msgstr "" -"`inputBinding` 既可以出现在外部，即数组参数本身的定义中，也可以出现在内部，即" -"数组元素的定义中。如上所示，这两种定义方式在构建命令行时所产生的行为是不一样" -"的。另外，`itemSeparator`（项目分隔符）字段如果出现，则指明数组各元素的值应并" -"入单独的一个参数，以指定的项目分隔符插入相邻的元素值之间。" - -#: ../../src/topics/inputs.md:185 -#: 874c6f19abbf45d7ab7d30a378c4048d -msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +#: ../../src/topics/inputs.md:178 13e59751d43b49f0ac366538a14f9c84 +msgid "" +"The `inputBinding` can appear either on the outer array parameter " +"definition or the inner array element definition, and these produce " +"different behavior when constructing the command line, as shown above. In" +" addition, the `itemSeparator` field, if provided, specifies that array " +"values should be concatenated into a single argument separated by the " +"item separator string." msgstr "" -"请注意，在 `array-inputs-job.yml` 中，数组输入由方括号 `[]` " -"指定。表达数组的另一种形式是多行句法，即用行首的 `-` " -"标明数组元素，示意它并非键值。下一课中将演示后一种用法，在[《YAML 指南" -"》](yaml-guide.md#arrays) 中也有详细讨论。可以指定的数组包括数组的数组、记录" -"的数组及其他复合类型的数组。" +"`inputBinding` " +"既可以出现在外部，即数组参数本身的定义中，也可以出现在内部，即数组元素的定义中。如上所示，这两种定义方式在构建命令行时所产生的行为是不一样的。另外，`itemSeparator`（项目分隔符）字段如果出现，则指明数组各元素的值应并入单独的一个参数，以指定的项目分隔符插入相邻的元素值之间。" -#: ../../src/topics/inputs.md:191 -#: 5d7d7a28cc5d4862803032aec78174d9 +#: ../../src/topics/inputs.md:185 bb31c6784ea843ec88f185523cfa25df +msgid "" +"Note that the arrays of inputs are specified inside square brackets `[]` " +"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " +"lines, where array values that are not defined with an associated key are" +" marked by a leading `-`. This will be demonstrated in the next lesson " +"and is discussed in more detail in the [YAML Guide](yaml-" +"guide.md#arrays). You can specify arrays of arrays, arrays of records, " +"and other complex types." +msgstr "" +"请注意，在 `array-inputs-job.yml` 中，数组输入由方括号 `[]` 指定。表达数组的另一种形式是多行句法，即用行首的 `-`" +" 标明数组元素，示意它并非键值。下一课中将演示后一种用法，在[《YAML 指南》](yaml-guide.md#arrays) " +"中也有详细讨论。可以指定的数组包括数组的数组、记录的数组及其他复合类型的数组。" + +#: ../../src/topics/inputs.md:191 53817379078548b2aeb6195cae9cbab7 msgid "Inclusive and Exclusive Inputs" msgstr "相容和互斥输入" -#: ../../src/topics/inputs.md:193 -#: dea0d4b681f94e73b13965dcfe75cf7d -msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +#: ../../src/topics/inputs.md:193 e163c0cfe9694a85b2e42682f42970a5 +msgid "" +"Sometimes an underlying tool has several arguments that must be provided " +"together (they are dependent) or several arguments that cannot be " +"provided together (they are exclusive). You can use records and type " +"unions to group parameters together to describe these two conditions." msgstr "" -"有时，基础工具具有多个必须一起提供的参数（它们是相互依赖的）或多个不能一起提" -"供的参数（它们是互斥的）。 您可以使用记录类型或共用体 (union) " -"类型将参数加以组合，以分别描述这两种情况。" +"有时，基础工具具有多个必须一起提供的参数（它们是相互依赖的）或多个不能一起提供的参数（它们是互斥的）。 您可以使用记录类型或共用体 (union)" +" 类型将参数加以组合，以分别描述这两种情况。" -#: ../../src/topics/inputs.md:198 -#: ddf598abf4f34aca9fffa045860fbf96 +#: ../../src/topics/inputs.md:198 84e1ab25511c49d1baabb1f80f247b49 msgid "`record.cwl`" msgstr "`record.cwl`" -#: ../../src/topics/inputs.md:204 -#: d52a8089920e45bd89d582533b50e3a1 +#: ../../src/topics/inputs.md:204 3d5dfc8ee47b458db638a9eed84b4938 msgid "`record-job1.yml`" msgstr "`record-job1.yml`" -#: ../../src/topics/inputs.md:215 -#: 750474486a84482292eeba45f118287f -msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +#: ../../src/topics/inputs.md:215 ecfb1d911a84400ba3db12fd0adf9279 +msgid "" +"In the first example, you can't provide `itemA` without also providing " +"`itemB`." msgstr "在第一个示例中，一旦提供 `itemA` 就必须同时提供 `itemB`." -#: ../../src/topics/inputs.md:217 -#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +#: ../../src/topics/inputs.md:217 24ba804374b4471d8e925d80670f9dff msgid "`record-job2.yml`" msgstr "`record-job2.yml`" -#: ../../src/topics/inputs.md:233 -#: 1eb0e39bb6d04b8cab300f44a79f3add -msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +#: ../../src/topics/inputs.md:233 436707d9c7634732ad1e60d8294bd4ba +msgid "" +"In the second example, `itemC` and `itemD` are exclusive, so only the " +"first matching item (`itemC`) is added to the command line and remaining " +"item (`itemD`) is ignored." msgstr "" -"在第二个示例中，`itemC` 和 `itemD` 是互斥的。因此，只有第一个匹配项 (`itemC`)" -" 会添加到命令行，而余下的 (`itemD`) 将被忽略。" +"在第二个示例中，`itemC` 和 `itemD` 是互斥的。因此，只有第一个匹配项 (`itemC`) 会添加到命令行，而余下的 " +"(`itemD`) 将被忽略。" -#: ../../src/topics/inputs.md:236 -#: bc21ee10bff843689cc98ac6630edcea +#: ../../src/topics/inputs.md:236 01b168c5faf94ead8d836dfe39e4c592 msgid "`record-job3.yml`" msgstr "`record-job3.yml`" -#: ../../src/topics/inputs.md:252 -#: 4b2ab812f62c4f949dd25c8527f2411c -msgid "In the third example, only `itemD` is provided, so it appears on the command line." +#: ../../src/topics/inputs.md:252 e6d81d6549984689bae4533c6d01bd5b +msgid "" +"In the third example, only `itemD` is provided, so it appears on the " +"command line." msgstr "在第三个示例中，仅提供了 `itemD`, 因此它出现在命令行上。" -#: ../../src/topics/inputs.md:255 -#: b771302d1bec4050a9417b080eef76c9 +#: ../../src/topics/inputs.md:255 ffddeeda8f04408ba73f7a59a4618da5 msgid "Exclusive Input Parameters with Expressions" msgstr "互斥输入参数与表达式" -#: ../../src/topics/inputs.md:257 -#: 2c3b884cb1c54521900cc90782e8a58d -msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +#: ../../src/topics/inputs.md:257 cf22f21ec44c483986979316544a7c3b +#, fuzzy +msgid "" +"If you use exclusive input parameters and reference them in expressions, " +"you need to be aware that the `inputs` JavaScript object will contain one" +" of the possible, mutually-exclusive input values. Because the types of " +"these exclusive values may differ, you may need to check which type is in" +" use when you reference the properties of the `input` object." msgstr "" -"将互斥的输入参数与表达式结合使用时，需要注意 `inputs` 这个 JavaScript 对象可" -"能包含互斥输入值中的任何一个。这意味着你可能需要用逻辑“**或**”运算符来检查哪" -"些值是存在的。" +"将互斥的输入参数与表达式结合使用时，需要注意 `inputs` 这个 JavaScript " +"对象可能包含互斥输入值中的任何一个。这意味着你可能需要用逻辑“**或**”运算符来检查哪些值是存在的。" -#: ../../src/topics/inputs.md:262 -#: a1073b6306044dffb414319ae01f68bb -msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +#: ../../src/topics/inputs.md:263 0fecb128b19b44d796b6c1b6de4f7166 +msgid "" +"Let's use an example that contains an exclusive `file_format` input " +"parameter that accepts `null` (i.e. no value provided), or any value from" +" an enum." msgstr "" "我们来看一个例子，其中 `file_format` 输入参数的取值是互斥的。该参数接受 " "`null`（即未提供任何值），或一个特定的枚举类型所包括的值。" -#: ../../src/topics/inputs.md:265 -#: 4a31c733092142b1af834eab1747c224 +#: ../../src/topics/inputs.md:266 7f1941698a6046e9b9e8a53736af949a msgid "`exclusive-parameter-expressions.cwl`" msgstr "`exclusive-parameter-expressions.cwl`" -#: ../../src/topics/inputs.md:271 -#: 9a1d92334685449386dfa3b3a899ed48 -msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +#: ../../src/topics/inputs.md:272 60b585142f06489d9f48090b664b6d32 +#, fuzzy +msgid "" +"Note how the JavaScript expression uses the value of the exclusive input " +"parameter without taking into consideration a `null` value. If you " +"provide a valid value, such as `fasta` (one of the possible values of the" +" enum), your command should execute successfully:" +msgstr "" +"请注意，这里的 JavaScript 表达式用到了互斥输入参数的值，但没有考虑到空值 `null` 的情况。如果提供的值有效，比如 “fasta”" +" （枚举中的一个值），命令将会成功执行：" + +#: ../../src/topics/inputs.md:281 11fdeb057d674f118830f431ff019c15 +#, fuzzy +msgid "" +"However, if you do not provide any input value, then `file_format` will " +"be evaluated to `null`, which does not match the expected type for the " +"output field (a `string`), resulting in failure when running your " +"workflow." msgstr "" -"请注意，这里的 JavaScript 表达式用到了互斥输入参数的值，但没有考虑到空值 " -"`null` 的情况。如果提供的值有效，比如 “fasta” " -"（枚举中的一个值），命令将会成功执行：" +"但是，如果未提供任何输入值，则 `file_format` 的值为 `null`, 从而不符合输出字段的预期类型（字符串 " +"`string`），导致工作流运行失败。" -#: ../../src/topics/inputs.md:280 -#: fb623af4c480411b8fde28d01c981411 -msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +#: ../../src/topics/inputs.md:290 8594cca9d93b4280b6cfee64c8a7c578 +#, fuzzy +msgid "" +"To correct it, you should explicitly handle the possibility of a `null` " +"value. For example, the expression could be changed to " +"`$(inputs.file_format || 'auto')`, to have a default value `\"auto\"` if " +"none was provided in the command line or job input file." msgstr "" -"但是，如果未提供任何输入值，则 `file_format` 的值为 `null`, " -"从而不符合输出字段的预期类型（字符串 `string`），导致工作流运行失败。" +"为了修正这个问题，需要记住的，是在 JavaScript 表达式中使用互斥参数或任何允许为空 (`null`) " +"的参数时，应使用逻辑“或”运算符。例如，表达式可以修改为 `$(inputs.file_format || 'auto')`, " +"从而在命令行或作业输入文件未提供值的情况下有默认值可用。" -#: ../../src/topics/inputs.md:289 -#: e98e165f6bba40809c90473d72f9d592 -msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +#: ../../src/topics/inputs.md:295 b5055c77f85e43609fe3e9b9839778e3 +msgid "" +"Here, the boolean “or” operator `||` in JavaScript is used for its " +"_short-circuiting_ property. If `inputs.file_format` is “true” in a " +"boolean context (e.g. a valid non-empty string from the enum), the " +"evaluation of the expression stops at the first operand of `||`; it " +"“short-circuits”. If however `inputs.file_format` is `null`, the whole " +"expression’s value becomes that of the second operand, which is why a " +"reasonable default can be provided there." msgstr "" -"为了修正这个问题，需要记住的，是在 JavaScript " -"表达式中使用互斥参数或任何允许为空 (`null`) " -"的参数时，应使用逻辑“或”运算符。例如，表达式可以修改为 `$(inputs.file_format " -"|| 'auto')`, 从而在命令行或作业输入文件未提供值的情况下有默认值可用。" #: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 +#: 723c2232310c4276aeac2bd6728d2912 msgid "Metadata and Authorship" msgstr "元数据和著作人信息" #: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 -msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." -msgstr "" -"由某个实现所提供的非必需、不影响正确执行的扩展（如关于图形界面中展示的字段）" -"，以及关于工具或工作流本身的元数据（如用于引文的作者信息），都可以作为任意对" -"象的附加字段提供。这种扩展字段（形如 `format: edam:format_2572`）" -"可以使用文件 `$namespaces`（命名空间）部分依照 [Schema Salad 规约][schema-" -"salad]的要求列举的命名空间前缀（例如 `edam：http://edamontology.org/" -"`）。如下所示，一旦添加了命名空间前缀，便可在文档的任何位置使用它。否则，" -"必须使用完整的 URL: `format: http://edamontology.org/format_2572`." +#: 4d81aac1830045229e5c60c7959074d8 +msgid "" +"Implementation extensions not required for correct execution (for " +"example, fields related to GUI presentation) and metadata about the tool " +"or workflow itself (for example, authorship for use in citations) may be " +"provided as additional fields on any object. Such extensions fields (e.g." +" `format: edam:format_2572`) can use a namespace prefix listed in the " +"`$namespaces` section of the document (e.g. edam: " +"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" +"][schema-salad]. Once you add the namespace prefix, you can access it " +"anywhere in the document as shown below. Otherwise, one must use full " +"URLs: `format: http://edamontology.org/format_2572`." +msgstr "" +"由某个实现所提供的非必需、不影响正确执行的扩展（如关于图形界面中展示的字段），以及关于工具或工作流本身的元数据（如用于引文的作者信息），都可以作为任意对象的附加字段提供。这种扩展字段（形如" +" `format: edam:format_2572`）可以使用文件 `$namespaces`（命名空间）部分依照 [Schema Salad " +"规约][schema-salad]的要求列举的命名空间前缀（例如 " +"`edam：http://edamontology.org/`）。如下所示，一旦添加了命名空间前缀，便可在文档的任何位置使用它。否则，必须使用完整的" +" URL: `format: http://edamontology.org/format_2572`." #: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b -msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." -msgstr "我们建议所有的开发者为自己编写的工具和工作流提供类似下面所示的精简版元数据。" -"此例中的元数据向他人说明如何在文献中引用你的工具。" +#: 368f8993ae9d401488081d74ae5acd49 +msgid "" +"For all developers, we recommend the following minimal metadata for your " +"tool and workflows. This example includes metadata allowing others to " +"cite your tool." +msgstr "我们建议所有的开发者为自己编写的工具和工作流提供类似下面所示的精简版元数据。此例中的元数据向他人说明如何在文献中引用你的工具。" #: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#: c80f2b180ca74afb8a1fc18f8686304b msgid "`metadata_example2.cwl`" msgstr "`metadata_example2.cwl`" #: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 +#: 37b07ea9b7124842b8ba3040f70308e9 msgid "Extended Example" msgstr "进一步扩展的例子" #: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 -msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +#: 1cd5989ade6741aabe625c13bed3c8ed +msgid "" +"For those that are highly motivated, it is also possible to annotate your" +" tool with a much larger amount of metadata. This example includes EDAM " +"ontology tags as keywords (allowing the grouping of related tools), hints" +" at hardware requirements in order to use the tool, and a few more " +"metadata fields." msgstr "" -"如果您积极性更高，也可以加入更多的元数据来注释工具。此例中加入了 EDAM 本体标" -"签作为关键字（以便将彼此关联的工具分组）、关于硬件要求的软性提示，以及其他元" -"数据字段。" +"如果您积极性更高，也可以加入更多的元数据来注释工具。此例中加入了 EDAM " +"本体标签作为关键字（以便将彼此关联的工具分组）、关于硬件要求的软性提示，以及其他元数据字段。" #: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e +#: ae7369ba14404d23b72d1ef30dcd4153 msgid "`metadata_example3.cwl`" msgstr "`metadata_example3.cwl`" -#: ../../src/topics/operations.md:1 -#: 8acf361cf77c4d45ba3f2e344146259f +#: ../../src/topics/operations.md:1 a79974b2f4534fcd8c7a04401e8a5556 msgid "Operations" msgstr "抽象操作" -#: ../../src/topics/operations.md:3 -#: 83d3b9a0ed3148fda9ce72cd108cb9e1 -msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +#: ../../src/topics/operations.md:3 b6507c8e1625476b97708423acb4fd0e +msgid "" +"An Operation is a type of CWL process, just like a workflow, a command-" +"line tool, or an expression tool. It is a step of a workflow that " +"specifies inputs and outputs, but it does not provide enough information " +"to be executed." msgstr "" -"抽象操作 (Operation) 与工作流、命令行工具或表达式工具类似，是一种 CWL 流程。" -"作为工作流中的一个步骤，它可以指定输入和输出，但不完全提供具体执行所需的信息" -"。" +"抽象操作 (Operation) 与工作流、命令行工具或表达式工具类似，是一种 CWL " +"流程。作为工作流中的一个步骤，它可以指定输入和输出，但不完全提供具体执行所需的信息。" -#: ../../src/topics/operations.md:7 -#: 5565c1b2d8a349169a305a9b26b4574d -msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" -msgstr "在开发周期中，工作流准备就绪、可以提交给 CWL " -"运行程序之前，您可以创建抽象操作，将工作流可视化：" +#: ../../src/topics/operations.md:7 047b09455db64524a71c47ab5192039f +msgid "" +"You can create operations to visualize a workflow during development, " +"before you are ready to submit the workflow to a CWL runner:" +msgstr "在开发周期中，工作流准备就绪、可以提交给 CWL 运行程序之前，您可以创建抽象操作，将工作流可视化：" -#: ../../src/topics/operations.md:10 -#: 49cf614893d8438299b3bca384eb40cf +#: ../../src/topics/operations.md:10 e9b2b97f3059460b867577a49934a338 msgid "`operations.cwl`" msgstr "`operations.cwl`" -#: ../../src/topics/operations.md:16 -#: 88160cef4cfa4add9020aa89511a5749 -msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +#: ../../src/topics/operations.md:16 d21e9444182d4e27bae934db4573ae99 +#, fuzzy +msgid "" +"The `uppercase` step of the workflow is an operation. It can appear where" +" a command line tool or an expression is expected. You can also plot it " +"with the CWL Viewer or `cwltool`:" msgstr "" -"工作流中的 `uppercase` 步骤是一个抽象操作，可以充当命令行工具或表达式使用。" -"您可以用 CWL Viewer 或 `cwltool` 将它绘制出来：" +"工作流中的 `uppercase` 步骤是一个抽象操作，可以充当命令行工具或表达式使用。您可以用 CWL Viewer 或 `cwltool` " +"将它绘制出来：" -#: ../../src/topics/operations.md:24 -#: 2f73a786b5d94dc0b23ed0cdd185afc8 -msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +#: ../../src/topics/operations.md:24 61e4ae6ed18e41708270eb358cd55277 +#, fuzzy +msgid "" +"The output of the command above can be rendered with a Graphviz renderer." +" The following image is rendered with the Sphinx `{graphviz}` directive " +"(this user guide is built with Sphinx):" msgstr "" -"以上命令的输出可用 Graphviz 渲染出来。下面的图片是使用 Sphinx Graphviz " -"指令来渲染的（本《用户指南》是以 Sphinx 编译）：" +"以上命令的输出可用 Graphviz 渲染出来。下面的图片是使用 Sphinx Graphviz 指令来渲染的（本《用户指南》是以 Sphinx " +"编译）：" -#: ../../src/topics/operations.md:55 -#: 730ba1434a1445ae847ec6153b6a3b72 -msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" -msgstr "如果您尝试用 `cwltool` 运行它，该命令会失败，因为 `cwltool` " -"缺少足够信息，无从知晓如何运行它：" +#: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd +msgid "" +"The operation file will fail to run with `cwltool` because `cwltool` " +"lacks the necessary information to execute it:" +msgstr "" -#: ../../src/topics/operations.md:58 -#: 98d9b8d867594543890af99e77e24edb +#: ../../src/topics/operations.md:59 e184470550e645f6b9ce658af7e65ecf msgid "`cwltool` does not know how to run operations" msgstr "`cwltool` 不知道如何运行抽象操作" -#: ../../src/topics/operations.md:66 -#: a25d0b1e13324b40a6b8fcd227948c4f -msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." -msgstr "CWL 运行程序可能安排一些将抽象操作绑定到具体步骤的方法。例如，带有 ID " -"的抽象操作有可能对映到其他工作流引擎中执行的步骤。" +#: ../../src/topics/operations.md:67 3b90445d3428444cafd7d5c0e5884980 +msgid "" +"CWL runners may come up with ways to bind operations to concrete steps. A" +" CWL runner could, for instance, use abstract operations with ID's that " +"correspond to steps executed by a different workflow engine." +msgstr "CWL 运行程序可能安排一些将抽象操作绑定到具体步骤的方法。例如，带有 ID 的抽象操作有可能对映到其他工作流引擎中执行的步骤。" -#: ../../src/topics/outputs.md:1 -#: da077da5eb8a4ffebfde041fc16300de +#: ../../src/topics/outputs.md:1 35e7bad6fdc04bcf9bbfbb2d8d42cfa5 msgid "Outputs" msgstr "输出" -#: ../../src/topics/outputs.md:3 -#: 1b3016f0462f42deb42ddaa33f28bf3d +#: ../../src/topics/outputs.md:3 6d912d40359c4d33a4f08abca83c00be msgid "Returning Output Files" msgstr "返回输出文件" -#: ../../src/topics/outputs.md:5 -#: d661df070e3040869da412d07a71f716 -msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +#: ../../src/topics/outputs.md:5 a6bd3f9e23de488394958fe7b59a61e0 +msgid "" +"The `outputs` of a tool is a list of output parameters that should be " +"returned after running the tool. Each parameter has an `id` for the name" +" of parameter, and `type` describing what types of values are valid for " +"that parameter." msgstr "" -"某个工具的 ` outputs `（输出）项是运行该工具后应返回的输出参数列表。 " -"每个参数都有一个代表其名称的 `id`字段，以及描述其有效值类型的 `type` 字段。" +"某个工具的 ` outputs `（输出）项是运行该工具后应返回的输出参数列表。 每个参数都有一个代表其名称的 " +"`id`字段，以及描述其有效值类型的 `type` 字段。" -#: ../../src/topics/outputs.md:10 -#: a11585474d3849cca5467512ed964743 -msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +#: ../../src/topics/outputs.md:10 a229d8d983344e51a231edb5f667d84b +#, fuzzy +msgid "" +"When a tool runs under CWL, the starting working directory is the " +"designated output directory. The underlying tool or script must record " +"its results in the form of files created in the output directory. The " +"output parameters returned by the CWL tool are either the output files " +"themselves, or the result of examining the content of those files." msgstr "" -"工具在 CWL 下运行时，起始工作目录即指定输出目录。 " -"基础工具或脚本记录运行结果，必须以输出目录下文件的形式实现。 CWL " +"工具在 CWL 下运行时，起始工作目录即指定输出目录。 基础工具或脚本记录运行结果，必须以输出目录下文件的形式实现。 CWL " "工具返回的输出参数要么是输出文件本身，要么是分析这些文件的内容而得出的信息。" -#: ../../src/topics/outputs.md:16 -#: 2682f9ca8e604a0c9986f7746fdec960 -msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +#: ../../src/topics/outputs.md:16 9845e517f7d848e5b59a97880ca6999f +msgid "" +"The following example demonstrates how to return a file that has been " +"extracted from a tar file." msgstr "下例演示怎样返回从 tar 文件中提取的文件。" -#: ../../src/topics/outputs.md:19 -#: 7e3fa7baf0f549ec89457e7004ac9545 +#: ../../src/topics/outputs.md:19 0bf1ad2c43174e57a3ba8dd86f7c96b2 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "将必要参数传递给 `baseCommand`" -#: ../../src/topics/outputs.md:21 -#: 22447a560f6f4317bf67bd7c4336126c -msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +#: ../../src/topics/outputs.md:21 553d535b023e4d69a888fe5b24bb8c5b +#, fuzzy +msgid "" +"In previous examples, the `baseCommand` was just a string, with any " +"arguments passed as CWL inputs. Instead of a single string, we can use an" +" _array of strings_ as the value of `baseCommand`. The first element of " +"the array is the command to run, and any subsequent elements are " +"mandatory command line arguments" msgstr "" -"在此前的例子里，`baseCommand` 命令不过是一个字符串，命令的参数都由 CWL 输入传" -"递而来。不过，我们也可以用字符串数组构建命令。为此，只需要让待运行的命令成为" -"数组的第一个元素，这样所有后续元素均成为命令行的必要参数" +"在此前的例子里，`baseCommand` 命令不过是一个字符串，命令的参数都由 CWL " +"输入传递而来。不过，我们也可以用字符串数组构建命令。为此，只需要让待运行的命令成为数组的第一个元素，这样所有后续元素均成为命令行的必要参数" -#: ../../src/topics/outputs.md:26 -#: f1ee2e00b0cc4112b51c9df3a919b73f +#: ../../src/topics/outputs.md:28 9b65071222c94951bed12ac53e964ee3 msgid "`tar.cwl`" msgstr "`tar.cwl`" -#: ../../src/topics/outputs.md:32 -#: ad8e1acb251246d2a47c39b20d4e483a +#: ../../src/topics/outputs.md:34 759ab0847b97479fb4a15e4b7d4e6565 msgid "`tar-job.yml`" msgstr "`tar-job.yml`" -#: ../../src/topics/outputs.md:38 -#: dc200c6960ae4476a772645d021f14b8 +#: ../../src/topics/outputs.md:40 f9752ec303ab419c8db8adef3fa2466f msgid "Next, create a tar file for the example." msgstr "接下来，新建一个 tar 文件供本示例使用。" -#: ../../src/topics/outputs.md:45 -#: 52703d6b7f914097934bfad13663abeb -msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +#: ../../src/topics/outputs.md:47 4f96576528684f28a72b805f777769e6 +msgid "" +"And now invoke `cwltool` with the tool description and the input object " +"on the command line:" msgstr "现在，在命令行上结合工具描述和输入对象运行 `cwltool`:" -#: ../../src/topics/outputs.md:51 -#: 5e1c79df657d4a6e84e055dd6b300a5d -msgid "The field `outputBinding` describes how to set the value of each output parameter." +#: ../../src/topics/outputs.md:53 707803bec0cb42919905c7c321bd9d30 +#, fuzzy +msgid "" +"The field " +"[`outputBinding`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding)" +" describes how to set the value of each output parameter." msgstr "`outputBinding` 字段描述如何设置每个输出参数的值。" -#: ../../src/topics/outputs.md:62 -#: 329d2809dfae4f90bc638f5f03a47ee3 -msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." -msgstr "`glob` 字段由输出目录中的文件名组成。如果事先不知道文件名，可以使用通配符，" -"例如 `glob: '*.txt'`." - -#: ../../src/topics/outputs.md:65 -#: 96df2d45e42441d49ce193ccbfab78a3 +#: ../../src/topics/outputs.md:64 cbaec50871e04718883c8c91ff475d20 +#, fuzzy +msgid "" +"The " +"[`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) " +"field consists of the pattern to match file names in the output " +"directory. This can simply be the file's exact name. But if you don't " +"know the name of the file in advance, you can use a wildcard pattern like" +" `glob: '*.txt'`." +msgstr "`glob` 字段由输出目录中的文件名组成。如果事先不知道文件名，可以使用通配符，例如 `glob: '*.txt'`." + +#: ../../src/topics/outputs.md:69 8a6e9173198241429effd911c3a7c4d7 msgid "Capturing Standard Output" msgstr "捕获标准输出" -#: ../../src/topics/outputs.md:67 -#: c6bcf7c6a8774dd6be41cc775848c3b8 -msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +#: ../../src/topics/outputs.md:71 a7c4fdaeda3e411fbeb802c5fa529ce9 +#, fuzzy +msgid "" +"To capture a tool's standard output stream, add the " +"[`stdout`](https://w3id.org/cwl/CommandLineTool.html#stdout) field with " +"the name of the file where the output stream should go. Then add `type: " +"stdout` on the corresponding output parameter." msgstr "" -"要捕获工具的标准输出流，请添加 `stdout` 字段，配上输出流应定向到的文件名。 " -"然后，给相应的输出参数添加 `type: stdout` 字段。" +"要捕获工具的标准输出流，请添加 `stdout` 字段，配上输出流应定向到的文件名。 然后，给相应的输出参数添加 `type: stdout` " +"字段。" -#: ../../src/topics/outputs.md:71 -#: 9d86c03ab44841c785b924cc44727e31 +#: ../../src/topics/outputs.md:75 cf2ef8dc7fda49308c09efe4f4ef5d7b msgid "`stdout.cwl`" msgstr "`stdout.cwl`" -#: ../../src/topics/outputs.md:89 -#: 2fb58c2feaa84970bb5274c49f4b5b64 +#: ../../src/topics/outputs.md:93 cbe236266dd148aaa96355e490a87cbe msgid "Array Outputs" msgstr "数组输出" -#: ../../src/topics/outputs.md:91 -#: 9647019d8c37466886e7aab6f176634d -msgid "You can also capture multiple output files into an array of files using `glob`." +#: ../../src/topics/outputs.md:95 77f86a7b94924a08b6ea2660218fe3c5 +msgid "" +"You can also capture multiple output files into an array of files using " +"`glob`." msgstr "您也可以用 `glob` 将多个输出文件捕获至一个文件数组。" -#: ../../src/topics/outputs.md:93 -#: b9eaf21f5e014eefaae301c47dafd144 +#: ../../src/topics/outputs.md:97 b34e30481fbd489d95fb7f8d5b5ab50c msgid "`array-outputs.cwl`" msgstr "`array-outputs.cwl`" -#: ../../src/topics/outputs.md:99 -#: cffff6c43b4945daa3b2a49763bc50ae +#: ../../src/topics/outputs.md:103 3aab0e0c9a78430f9caaa29a93303b56 msgid "`array-outputs-job.yml`" msgstr "`array-outputs-job.yml`" -#: ../../src/topics/outputs.md:112 -#: cc067051f22f433bbece08f60933e002 -msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +#: ../../src/topics/outputs.md:116 9a14271c3180429988aaa14869f783a0 +msgid "" +"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " +"expected outputs is specified in `array-outputs-job.yml` with each entry " +"marked by a leading `-`. This format can also be used in CWL descriptions" +" to mark entries in arrays, as demonstrated in several of the upcoming " +"sections." msgstr "" -"如[《YAML 指南》](yaml-guide.md#arrays)中所述，`array-outputs-job.yml` " -"文件中行首为 `-` 的成员代表数组元素，用以指明我们期待的各个输出。" -"这种格式还可以用在 CWL 描述中表示数组成员。接下来若干章节中会演示这一用法。" +"如[《YAML 指南》](yaml-guide.md#arrays)中所述，`array-outputs-job.yml` 文件中行首为 `-` " +"的成员代表数组元素，用以指明我们期待的各个输出。这种格式还可以用在 CWL 描述中表示数组成员。接下来若干章节中会演示这一用法。" -#: ../../src/topics/parameter-references.md:1 -#: a190a6440ec34898990cdac05d809f22 +#: ../../src/topics/parameter-references.md:1 c8a6ea340e6a43398e97b68e03a8bb3b msgid "Parameter References" msgstr "参数引用" -#: ../../src/topics/parameter-references.md:3 -#: dbfe2c1123144316aa026374b0f353d3 -msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." -msgstr "" -"在前面的例子中，我们使用 “tar” 程序提取了一个文件。但是，该示例局限性很强，" -"因为它假定了我们感兴趣的文件名就是 “hello.txt”, 而且这种假设直接写入了 `.cwl`" -" 代码文件里。这种做法有欠妥当，因为文件名 “hello.txt” " -"可能会改变，也可能依赖我们实际用到的输入文件。 为了避免这类情况，" -"我们可以在作业参数 (`.yml`) 文件中指定我们想要的文件名。本示例将演示如何从其" -"他字段动态引用输入参数值，以便指定待提取的文件名。" - -#: ../../src/topics/parameter-references.md:13 -#: 280f1a07d0ae41d7a4674504f832fcf0 +#: ../../src/topics/parameter-references.md:3 f5c0592ca28c46c2a89943f4f6f69a27 +msgid "" +"In a previous example, we extracted a file using the \"tar\" program. " +"However, that example was very limited because it assumed that the file " +"we were interested in was called \"hello.txt\", and this was written into" +" the `.cwl` file. This is not the best way to do this, as the " +"\"hello.txt\" filename may vary or be dependent on the input file(s) " +"used. To avoid this we can specify the name of the file we want in the " +"job parameters file (`.yml`). In this example, you will see how to " +"reference the value of input parameters dynamically from other fields, " +"which will allow us to then specify the name of the file to extract." +msgstr "" +"在前面的例子中，我们使用 “tar” 程序提取了一个文件。但是，该示例局限性很强，因为它假定了我们感兴趣的文件名就是 “hello.txt”, " +"而且这种假设直接写入了 `.cwl` 代码文件里。这种做法有欠妥当，因为文件名 “hello.txt” " +"可能会改变，也可能依赖我们实际用到的输入文件。 为了避免这类情况，我们可以在作业参数 (`.yml`) " +"文件中指定我们想要的文件名。本示例将演示如何从其他字段动态引用输入参数值，以便指定待提取的文件名。" + +#: ../../src/topics/parameter-references.md:13 50db8add9b1942d986e581b8d21c2ee4 msgid "`tar-param.cwl`" msgstr "`tar-param.cwl`" -#: ../../src/topics/parameter-references.md:19 -#: 5c64d938862747cb9fb52515a656ce27 +#: ../../src/topics/parameter-references.md:19 d01ad5fd9fea462cab0d4d776824b4e1 msgid "`tar-param-job.yml`" msgstr "`tar-param-job.yml`" -#: ../../src/topics/parameter-references.md:25 -#: 074cf5d912854d8c864607cc24b15302 -msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +#: ../../src/topics/parameter-references.md:25 9b1e2f1a23ea4fe2af97ef5108f33376 +msgid "" +"Create your input files and invoke `cwltool` with the tool description " +"and the input object on the command line:" msgstr "创建输入文件，然后以工具描述和输入对象为命令行参数调用 `cwltool`:" -#: ../../src/topics/parameter-references.md:36 -#: 0290af3e3cbb4b32b0450c8771f3bf95 -msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +#: ../../src/topics/parameter-references.md:36 06926a516ae6432d96e3eaa62202cd86 +msgid "" +"Certain fields permit parameter references which are enclosed in " +"`$(...)`. These are evaluated and replaced with value being referenced." msgstr "某些字段允许出现用 `$(...)` 符号括起来的参数引用，由求值的结果代入。" -#: ../../src/topics/parameter-references.md:47 -#: b54240bb94f746bba7511633aa969db0 -msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +#: ../../src/topics/parameter-references.md:47 384fe8188f414eafbbb8d6b81bdfd779 +msgid "" +"References are written using a subset of Javascript syntax. In this " +"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " +"`$(inputs['extractfile'])` are equivalent." msgstr "" -"引用的编写用的是 JavaScript 语法的一个子集。 本例中，`$(inputs." -"extractfile)`、`$(inputs[\"extractfile\"])` 和 `$(inputs['extractfile'])` " -"效果相同。" +"引用的编写用的是 JavaScript 语法的一个子集。 " +"本例中，`$(inputs.extractfile)`、`$(inputs[\"extractfile\"])` 和 " +"`$(inputs['extractfile'])` 效果相同。" -#: ../../src/topics/parameter-references.md:51 -#: 8b70a072aa87414c88e89a3e19af0a51 -msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +#: ../../src/topics/parameter-references.md:51 56ead1c8d45c43bdbcbc6f7cbb8e1e92 +msgid "" +"The value of the \"inputs\" variable is the input object provided when " +"the CWL tool was invoked." msgstr "“inputs” 变量的取值为 CWL 工具被调用时获得的输入对象。" -#: ../../src/topics/parameter-references.md:54 -#: eea20f89c45f424a888178df53713b28 -msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +#: ../../src/topics/parameter-references.md:54 56bca89e314c4223b33d7fe63c9b771d +msgid "" +"Note that because `File` parameters are objects, to get the path to an " +"input file you must reference the path field on a file object; to " +"reference the path to the tar file in the above example you would write " +"`$(inputs.tarfile.path)`." msgstr "" -"请注意，由于 `File`（文件）参数是对象。因此，要获取输入文件的路径，须引用文件" -"对象上的“path”（路径）字段。例如，要引用上面例子中 tar 文件的路径，" -"则需要写为 `$(inputs.tarfile.path)`." +"请注意，由于 `File`（文件）参数是对象。因此，要获取输入文件的路径，须引用文件对象上的“path”（路径）字段。例如，要引用上面例子中 " +"tar 文件的路径，则需要写为 `$(inputs.tarfile.path)`." -#: ../../src/topics/parameter-references.md:59 -#: cb4ea13f5db84c0da43df3f7f2478d78 +#: ../../src/topics/parameter-references.md:59 1c1ab240c4114572bb4e42955baad361 msgid "Where are parameter references allowed?" msgstr "参数引用可以出现在哪些地方？" -#: ../../src/topics/parameter-references.md:61 -#: 6d3fb423e6c4434697cd113fb27e28ad +#: ../../src/topics/parameter-references.md:61 055d3268859c46c4b7db5005608bae05 msgid "You can only use parameter references in certain fields. These are:" msgstr "参数引用只能出现在有限的字段中，即：" -#: ../../src/topics/parameter-references.md:63 -#: 7647e0229a924f988cf02b7812a55c06 -msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +#: ../../src/topics/parameter-references.md:63 2ed66835bd9044adbfdd0b5097787f22 +msgid "" +"From " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -"来自 [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)" +"来自 " +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -#: ../../src/topics/parameter-references.md:69 -#: 9d663249666045618a0d3acddb85a9a9 -msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +#: ../../src/topics/parameter-references.md:69 f592619e4b2c497e80cd75da0548cf07 +msgid "" +"From " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -"来自 [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandInputParameter)" +"来自 " +"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -#: ../../src/topics/parameter-references.md:72 -#: 5fed4984f6784347b4cbe0630b1dd2c2 -msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +#: ../../src/topics/parameter-references.md:72 81ea71a35020421187dc18ddd151c62f +msgid "" +"From " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -"来自 [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineBinding)" +"来自 " +"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -#: ../../src/topics/parameter-references.md:74 -#: dbf6153cd02542a6a01c172803122b7f -msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +#: ../../src/topics/parameter-references.md:74 ea0117748adc4324901024f21eed04ac +msgid "" +"From " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -"来自 [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputParameter)" +"来自 " +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -#: ../../src/topics/parameter-references.md:77 -#: b6250cf6fa8a4a0c94b33302e0decca5 -msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +#: ../../src/topics/parameter-references.md:77 3a30e73176cf4e4eb9f26770a176b9c9 +msgid "" +"From " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -"来自 [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandOutputBinding)" +"来自 " +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -#: ../../src/topics/parameter-references.md:81 -#: fa6ca3bbc6784380a03a950a6f49a180 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +#: ../../src/topics/parameter-references.md:81 551c199c9a6344fca9bfacfb69fc4e53 +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -"来自[InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) 和 [WorkflowOutputParameter](http://www.commonwl.org/v1." -"0/Workflow.html#WorkflowOutputParameter)" +"来自[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" 和 " +"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -#: ../../src/topics/parameter-references.md:85 -#: b92b516e537a4773ad67b4af586e7a25 -msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +#: ../../src/topics/parameter-references.md:85 7008a1ff1af54fda827637e787e5c7dd +msgid "" +"From " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -"来自 [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow." -"html#WorkflowStepInput)" +"来自 " +"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -#: ../../src/topics/parameter-references.md:89 -#: 467a701228504d06b971b79a59c69064 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +#: ../../src/topics/parameter-references.md:89 45743e1b261c4195856de0c2e30ea72e +msgid "" +"From " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" and " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -"来自 [InputParameter](http://www.commonwl.org/v1.0/Workflow." -"html#InputParameter) 和 [ExpressionToolOutputParameter](http://www.commonwl." -"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +"来自 " +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" +" 和 " +"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -#: ../../src/topics/parameter-references.md:92 -#: 2634f989eb304009a8568d70ed42786c -msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +#: ../../src/topics/parameter-references.md:92 0ae32d1db5f9452bbfcbbc4719b0b9f1 +msgid "" +"From " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" -"来自 [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." -"html#ResourceRequirement)" +"来自 " +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" #: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 -msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +#: 7e1907ff15c74f488187531de336eccf +msgid "" +"From " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" -"来自 [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" -"CommandLineTool.html#InitialWorkDirRequirement)" +"来自 " +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" #: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 +#: 678874668fed4f4d80a1b0990e183e2f msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "[Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent) 对象中" #: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 -msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +#: e2882880886046ac88ae1c0d414366d1 +msgid "" +"From " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" -"来自 [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." -"html#EnvironmentDef)" +"来自 " +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" #: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae +#: 05324169d8ae48d4a1abe3a0ac07c891 msgid "Requirements and Hints" msgstr "需求和提示" #: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 +#: 1f5b72d7ec82442ba29baa14a03f061b msgid "Specifying Software Requirements" msgstr "指定软件需求" #: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb -msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +#: e708866921ea49d69d3c2a32d63ea468 +#, fuzzy +msgid "" +"Often, tool descriptions will be written for a specific version of a " +"software. To make it easier for others to use your descriptions, you can " +"include a " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)" +" field in the `hints` section. This may also help to avoid confusion " +"about which version of a tool the description was written for." msgstr "" -"工具描述往往是针对特定版本的软件而编写。为了方便他人使用您的工具描述，" -"您可以在 `hints` 部分添加`SoftwareRequirement` " -"字段，用来指明该描述适用于哪些版本的工具。" +"工具描述往往是针对特定版本的软件而编写。为了方便他人使用您的工具描述，您可以在 `hints` 部分添加`SoftwareRequirement`" +" 字段，用来指明该描述适用于哪些版本的工具。" #: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 -msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +#: 6f722d6fd54f485fa964076c8d08938b +msgid "" +"In this example, the software requirement being described is InterProScan" +" version 5.21-60." msgstr "本例中描述的软件要求为 5.21-60 版本的 InterProScan." #: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 -msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +#: 5c1236ec57c64079bfb7c779524b12ad +msgid "" +"Depending on your CWL runner, these hints may be used to check that the " +"required software is installed and available before the job is run. To " +"enable these checks with the reference implementation, use the " +"[dependency resolvers configuration][dependencies]." msgstr "" -"您的 CWL 运行程序有可能支持在运行作业之前，根据提示检查所需软件是否已安装就绪" -"。如果要让参考实现启用这些检查，请使用[依赖项解析配置][dependencies]。" +"您的 CWL " +"运行程序有可能支持在运行作业之前，根据提示检查所需软件是否已安装就绪。如果要让参考实现启用这些检查，请使用[依赖项解析配置][dependencies]。" #: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 -msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." -msgstr "" -"除了版本号之外，该工具的唯一资源标识符 (URI) 以 [RRID][rrid] 的形式给出。" -"可以在 [SciCrunch][scicrunch] 注册表中查找具有 RRID " -"的资源，该注册表提供了一个用于查找、跟踪和一致引用科学资源的门户。" -"如果要将工具指定为 `SoftwareRequirement`，请在 SciCrunch " -"上搜索该工具并使用在注册表中分配的 RRID。 （按照 [添加资源教程][scicrunch-" -"add-tool] 将工具添加到 SciCrunch）。您可以使用此 RRID 在需求描述的 `specs` " -"字段中引用该工具（通过 [identifiers." -"org][identifiers]）。其他不错的选择（按优先顺序）包括主要工具引用的 DOI " +#: 1a8b8aadf1c64e87b8b670e288bc14bc +#, fuzzy +msgid "" +"As well as a version number, a unique resource identifier (URI) for the " +"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" +" looked up in the [SciCrunch][scicrunch] registry, which provides a " +"portal for finding, tracking, and referring to scientific resources " +"consistently. If you want to specify a tool as a " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)," +" search for the tool on SciCrunch and use the RRID that it has been " +"assigned in the registry. (Follow this [Adding a Resource Tutorial" +"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " +"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " +"field of your requirement description. Other good choices, in order of " +"preference, are to include the DOI for the main tool citation and the URL" +" to the tool." +msgstr "" +"除了版本号之外，该工具的唯一资源标识符 (URI) 以 [RRID][rrid] 的形式给出。可以在 [SciCrunch][scicrunch]" +" 注册表中查找具有 RRID 的资源，该注册表提供了一个用于查找、跟踪和一致引用科学资源的门户。如果要将工具指定为 " +"`SoftwareRequirement`，请在 SciCrunch 上搜索该工具并使用在注册表中分配的 RRID。 （按照 [添加资源教程" +"][scicrunch-add-tool] 将工具添加到 SciCrunch）。您可以使用此 RRID 在需求描述的 `specs` " +"字段中引用该工具（通过 [identifiers.org][identifiers]）。其他不错的选择（按优先顺序）包括主要工具引用的 DOI " "和工具的 URL。" -#: ../../src/topics/staging-input-files.md:1 -#: b85eb83e05e845d7a179f1b1d74db444 +#: ../../src/topics/staging-input-files.md:1 d10c792550e8498c8ee384d3093da306 msgid "Staging Input Files" msgstr "暂存输入文件" -#: ../../src/topics/staging-input-files.md:3 -#: 35f97d37492b4c7ca3ad6cfc1e6fa366 -msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." -msgstr "" -"通常，输入文件位于独立于输出目录的只读目录中。 " -"如果基础工具希望将其输出文件与输入文件一起写入同一目录中，则会导致问题。 " -"使用 `InitialWorkDirRequirement` 将输入文件暂存到输出目录中。在此示例中，" -"我们使用 JavaScript 表达式从输入文件的前导目录路径中提取该文件的基本名称。" - -#: ../../src/topics/staging-input-files.md:9 -#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +#: ../../src/topics/staging-input-files.md:3 ac2ef1fced5f4044861761a11c35e78a +#, fuzzy +msgid "" +"Normally, input files are located in a read-only directory separate from " +"the output directory. This causes problems if the underlying tool " +"expects to write its output files alongside the input file in the same " +"directory. You use " +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)" +" to stage input files into the output directory. In this example, we use " +"a JavaScript expression to extract the base name of the input file from " +"its leading directory path." +msgstr "" +"通常，输入文件位于独立于输出目录的只读目录中。 如果基础工具希望将其输出文件与输入文件一起写入同一目录中，则会导致问题。 使用 " +"`InitialWorkDirRequirement` 将输入文件暂存到输出目录中。在此示例中，我们使用 JavaScript " +"表达式从输入文件的前导目录路径中提取该文件的基本名称。" + +#: ../../src/topics/staging-input-files.md:9 d8ca16f5321e486ebe8ea9f9752b3737 msgid "`linkfile.cwl`" msgstr "`linkfile.cwl`" -#: ../../src/topics/troubleshooting.md:1 -#: 0f7508ce59754a7eb230dea6042244c6 +#: ../../src/topics/troubleshooting.md:1 aa3eddcaa0684f86ba67aafcd57872e7 msgid "Troubleshooting" msgstr "疑难解答" -#: ../../src/topics/troubleshooting.md:3 -#: fbe0c65b444441f785d0054176d036a6 -msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +#: ../../src/topics/troubleshooting.md:3 3207f476afa04158bd26db39a16a2df5 +msgid "" +"In this section you will find ways to troubleshoot when you have problems" +" executing CWL. We focus on `cwltool` here but some of these techniques " +"may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 -#: 1b6b7a75cc754775bf9dd80c0941e8da +#: ../../src/topics/troubleshooting.md:6 1d47f4ce04554cabb1ccf40a13ee42ec msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 -#: 9a710602e00c4934ae3a3b471aa68458 -msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +#: ../../src/topics/troubleshooting.md:8 0c25602a83e441b48b536eb49568f2b6 +msgid "" +"You can use the `--cachedir` option when running a workflow to tell " +"`cwltool` to cache intermediate files (files that are not input nor " +"output files, but created while your workflow is running). By default, " +"these files are created in a temporary directory but writing them to a " +"separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 -#: 21b5be7270a14f0987240c81d1ec879b -msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +#: ../../src/topics/troubleshooting.md:14 36ec60b80c714357a4274217274136ff +msgid "" +"In the following example `troubleshooting-wf1.cwl` we have two steps, " +"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " +"World\" | rev`, which would print the message \"Hello World\" reversed, " +"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," +" where instead of executing the `rev` command it tries to execute `revv`," +" which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 -#: 0490b1fab86749e49b473949c52bbe8b +#: ../../src/topics/troubleshooting.md:20 6f34038054ac4f4fa0b0ad9cbc3ecdc7 msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 -#: cfe9d8241fe84bd5b74042a5625d933f -msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +#: ../../src/topics/troubleshooting.md:27 b777877c88024c9fb06a6614029ef8d6 +msgid "" +"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " +"value (`cwltool` will create the directory for you if it does not exist " +"already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 -#: 764d933cc4da446abd8dd8f913f05dac -msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +#: ../../src/topics/troubleshooting.md:35 8654b7f2f4464d13be4b47729e1f07e5 +msgid "" +"The workflow is in the `permanentFail` status due to `step_b` failing to " +"execute the non-existent `revv` command. The `step_a` was executed " +"successfully and its output has been cached in your `cachedir` location. " +"You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 -#: c93efc6d4e004859981ee7f5fa28ed03 -msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +#: ../../src/topics/troubleshooting.md:44 04e80f7ce14d4d73bc5d290dcf01bcdb +msgid "" +"Each workflow step has received a unique ID (the long value that looks " +"like a hash). The `${HASH}.status` files display the status of each step " +"executed by the workflow. And the `step_a` output file `stdout.txt` is " +"visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 -#: 546601da44cb49bd9611b1c85807fd90 -msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +#: ../../src/topics/troubleshooting.md:48 719917cb0fd849f5a328671df8726189 +msgid "" +"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" +" in the `step_b`). After fixing the typo, when you execute `cwltool` with" +" the same arguments as the previous time, note that now `cwltool` output " +"contains information about pre-cached outputs for `step_a`, and about a " +"new cache entry for the output of `step_b`. Also note that the status of " +"`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 -#: 7e0bf00f8ce542b9b009cdcf1945a9e5 -msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +#: ../../src/topics/troubleshooting.md:59 2a9dbb3ad7564f5aa103349c45ee7925 +msgid "" +"In this example the workflow step `step_a` was not re-evaluated as it had" +" been cached, and there was no change in its execution or output. " +"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " +"`step_b` after we fixed the executable name. This technique is useful for" +" troubleshooting your CWL documents and also as a way to prevent " +"`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 -#: eff5f28ca83c458a9b07faf7a81f7e91 +#: ../../src/topics/using-containers.md:1 7439fe097aa4459ba1e4c0e28fc59b9a msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 -#: 2e634f3737d04d279ae78ceee4b0a664 +#: ../../src/topics/using-containers.md:3 eff5c6ac1cad44f9862585daf0a91298 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 -#: e07f33d01b804663a25ffb08aad74821 -msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 -#: 7a644506619a4f08958ec7d4540cd557 -msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +#: ../../src/topics/using-containers.md:5 50d1a644bc8c49f78c453e4e0f3c07c8 +msgid "" +"[Docker][docker] containers simplify software installation by providing a" +" complete known-good runtime for software and its dependencies. However," +" containers are also purposefully isolated from the host system, so in " +"order to run a tool inside a Docker container there is additional work to" +" ensure that input files are available inside the container and output " +"files can be recovered from the container. A CWL runner can perform this" +" work automatically, allowing you to use Docker to simplify your software" +" management while avoiding the complexity of invoking and managing Docker" +" containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 4b0f6cfc8a774c77bfbc99e568af2ece +msgid "" +"One of the responsibilities of the CWL runner is to adjust the paths of " +"input files to reflect the location where they appear inside the " +"container." msgstr "" -#: ../../src/topics/using-containers.md:18 -#: b5195b7d8eaa419fb2b90cb33a57783a -msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +#: ../../src/topics/using-containers.md:18 27c02a5d479a420eab7d14888d9fb288 +msgid "" +"This example runs a simple Node.js script inside a Docker container which" +" will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 -#: 7921a837ee744c5aa9a5bda04b0c8db1 +#: ../../src/topics/using-containers.md:21 1a62a93ab20b4f2ca1e13ded3a767dc5 msgid "`docker.cwl`" msgstr "`docker.cwl`" -#: ../../src/topics/using-containers.md:27 -#: 387e9bc9381a4450af54aff77e4df6a2 +#: ../../src/topics/using-containers.md:27 ccc2874840c3476bb714ddf4bdbf0f3e msgid "`docker-job.yml`" msgstr "`docker-job.yml`" -#: ../../src/topics/using-containers.md:33 -#: 2713594c937d4c528fc8d04d9e9819ed -msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 -#: cf94c1424fc2413c85647fd1ee73d951 -msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +#: ../../src/topics/using-containers.md:33 d766b66de4714a5da0cd87ed886cc32f +msgid "" +"Before we run this, let's just break it down and see what some bits do. " +"Most of this has been explained in previous sections, the only part that " +"is really new is the " +"[`dockerRequirement`](https://w3id.org/cwl/CommandLineTool.html#DockerRequirement)" +" section." msgstr "" -#: ../../src/topics/using-containers.md:52 -#: dc0452107c604e29bdf32bb289fe5db8 -msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +#: ../../src/topics/using-containers.md:44 1f02618ab6254459ae71f72844e3cc18 +msgid "" +"`baseCommand: node` tells CWL that we will be running this command using " +"the Node Js runtime that is meant for Javascript files. We then need to " +"specify some `hints` for how to find the container we want. In this case" +" we list just our requirements for the docker container in " +"`DockerRequirements`. The `dockerPull:` parameter takes the same value " +"that you would pass to a `docker pull` command. That is, the name of the " +"container image (you can even specify the tag, which is good idea for " +"best practices when using containers for reproducible research). In this " +"case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 54cade4978ec463bbb5c0d8c08e27adb +msgid "" +"Create a Javascript file named \"hello.js\" and invoke `cwltool` " +"providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 -#: 1a5596243cec4c948d9b6bf0bb12fad0 +#: ../../src/topics/using-containers.md:55 6541d0cd9f6c4c43b8601715cc35e585 msgid "`hello.js`" msgstr "`hello.js`" -#: ../../src/topics/using-containers.md:69 -#: 483181f498fc4d968b5fe6ef427709f7 -msgid "Notice the CWL runner has constructed a Docker command line to run the script." +#: ../../src/topics/using-containers.md:69 6abf220b7fa4479394ed33447cdd070e +msgid "" +"Notice the CWL runner has constructed a Docker command line to run the " +"script." msgstr "" -#: ../../src/topics/using-containers.md:72 -#: 7487485d6aa4458089a4b4bdf107ea64 -msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +#: ../../src/topics/using-containers.md:72 d2dd89a5edde4f2eab4c2baf0cc78745 +msgid "" +"In this example, the path to the script `hello.js` is " +"`/home/me/cwl/user_guide/hello.js` outside the container but " +"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " +"reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 -#: 7394e7690f934043af617436b40845f0 +#: ../../src/topics/workflows.md:1 06281a10592d42509566c8fc51f8d4da msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 -#: b9ae9e9a896048caad7e6c38a5bc1bd1 -msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +#: ../../src/topics/workflows.md:3 325a656f9b8e4c1fa6f699cd8c447d00 +msgid "" +"A workflow is a CWL processing unit that executes command-line tools, " +"expression tools, or workflows (sub-workflows) as steps. It must have " +"`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 -#: f228fb7953ea48ed99d89880205f4620 +#: ../../src/topics/workflows.md:13 b92275181c9e480da64e660b7aca0745 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 -#: 5870ac44e4c24b8daf5f06c49f95ce04 -msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +#: ../../src/topics/workflows.md:41 be2540315f854b8e9a1d257bcabd78db +msgid "" +"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " +"command-line tool, and the expression tool showed in the earlier " +"examples." msgstr "" -#: ../../src/topics/workflows.md:51 -#: a913c76d06164fa18718a8a6a7dcf0d6 +#: ../../src/topics/workflows.md:51 3be900594bb743399854b95baa9ae2f9 msgid "`echo-uppercase.cwl`" msgstr "`echo-uppercase.cwl`" -#: ../../src/topics/workflows.md:81 -#: 93188ed43ee949cc98b3ea679ce14feb -msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +#: ../../src/topics/workflows.md:81 5133c4e062bc4e479ce1dc8abbb08107 +msgid "" +"A command-line tool or expression tool can also be written directly in " +"the same CWL document as the workflow. For example, we can rewrite the " +"`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 -#: 36618126a4df4326b236ebe2ea42cffa +#: ../../src/topics/workflows.md:91 83bc2796889f4dccb713764ac1b3c3ad msgid "`echo-uppercase-single-file.cwl`" msgstr "`echo-uppercase-single-file.cwl`" -#: ../../src/topics/workflows.md:150 -#: 1cc17ad26e9c474b895ba5cd20c8b66a -msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +#: ../../src/topics/workflows.md:150 5a9a1dd6ed1f4ca6803f1d235c4fd392 +msgid "" +"Having separate files helps with modularity and code organization. But it" +" can be helpful writing everything in a single file for development. " +"There are other ways to combine multiple files into a single file (e.g. " +"`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 -#: 24aca0bea4d94e3593b844cf0586cffe -msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +#: ../../src/topics/workflows.md:160 277ed30d4b3a4156a4523e8d10e6ce60 +msgid "" +"For a sub-workflows you need to enable the requirement " +"`SubworkflowFeatureRequirement`. It is covered in another section of this" +" user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 -#: 46cc4859856e4367a9e5e68eecd48b73 +#: ../../src/topics/workflows.md:165 82818ab17aa4403eb982fd81a14a5865 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 -#: 9c56528acd5f49deb139e034dfbfac7c -msgid "This workflow extracts a java source file from a tar file and then compiles it." +#: ../../src/topics/workflows.md:167 3d8b98e8d03548699fadb22198de9b20 +msgid "" +"This workflow extracts a java source file from a tar file and then " +"compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 -#: 55ab007d472f43388e4c77aae8f165e7 +#: ../../src/topics/workflows.md:170 c61097c695424f7195e8205a23b6ecff msgid "`1st-workflow.cwl`" msgstr "`1st-workflow.cwl`" -#: ../../src/topics/workflows.md:179 -#: ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa -#: 307b6618a92948fca4203ccb497c77e6 +#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 +#: 6660c48f51d94d4fbcc05656e154059e bd2bab6c11614fa983ca8dab1408e1d8 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 -#: a2dd833fdca4443181648e41051a5232 -msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" -msgstr "" - -#: ../../src/topics/workflows.md:183 -#: 7e40cc9f9e1341c195e843c009575b94 -msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +#: ../../src/topics/workflows.md:180 f0831481a43548039fbc4fd17555af57 +msgid "" +"[![Visualization of 1st-" +"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" +"workflow-" +"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" +"-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 5ff059fc8ae6471c8ea86dab7e5a93f5 +msgid "" +"Use a YAML or a JSON object in a separate file to describe the input of a" +" run:" msgstr "" -#: ../../src/topics/workflows.md:185 -#: 26c51dcb76364ed780376aecb7cbacda +#: ../../src/topics/workflows.md:185 822e5d0a097b4109960d621a72a3c009 msgid "`1st-workflow-job.yml`" msgstr "`1st-workflow-job.yml`" -#: ../../src/topics/workflows.md:191 -#: 6fcf8ad3d1bd49afa4a105622437bd59 -msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +#: ../../src/topics/workflows.md:191 4a4db7da861547639524083bf35ccfc0 +msgid "" +"Next, create a sample Java file and add it to a tar file to use with the " +"command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 -#: 71cb81fa4511495b80422244849979e4 +#: ../../src/topics/workflows.md:205 ed16b30eaa4747f79b6dd10a19188d8c msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 -#: def35d6021394def80a53ae49a2cdbde -msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +#: ../../src/topics/workflows.md:212 6428bd7bd3be4393bfe5675f8e45ff94 +msgid "" +"The `cwlVersion` field indicates the version of the CWL spec used by the " +"document. The `class` field indicates this document describes a " +"workflow." msgstr "" -#: ../../src/topics/workflows.md:221 -#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 -msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +#: ../../src/topics/workflows.md:221 d6abec8805f649fca668292412263f78 +msgid "" +"The `inputs` section describes the inputs of the workflow. This is a " +"list of input parameters where each parameter consists of an identifier " +"and a data type. These parameters can be used as sources for input to " +"specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 -#: c84d4450bc6a475dbf34e0b22cea9130 -msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +#: ../../src/topics/workflows.md:233 22bf3e4910ef4f86a2e8f6d5a6cf0d42 +msgid "" +"The `outputs` section describes the outputs of the workflow. This is a " +"list of output parameters where each parameter consists of an identifier " +"and a data type. The `outputSource` connects the output parameter " +"`classfile` of the `compile` step to the workflow output parameter " +"`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 -#: cca9665f6daa44b49233baf34ab9fcc7 -msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +#: ../../src/topics/workflows.md:248 e0429688fce445da8083e69323e5b020 +msgid "" +"The `steps` section describes the actual steps of the workflow. In this " +"example, the first step extracts a file from a tar file, and the second " +"step compiles the file from the first step using the java compiler. " +"Workflow steps are not necessarily run in the order they are listed, " +"instead the order is determined by the dependencies between steps (using " +"`source`). In addition, workflow steps which do not depend on one " +"another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 -#: 547edbf5fa424b8286cc21674ff159b0 -msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +#: ../../src/topics/workflows.md:256 980f5eada57c4fadbb783838ded1fa0b +msgid "" +"The first step, `untar` runs `tar-param.cwl` (described previously in " +"[Parameter References](parameter-references.md)). This tool has two input" +" parameters, `tarfile` and `extractfile` and one output parameter " +"`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 -#: 7ca248888b9d484cb544cd76ba538662 -msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +#: ../../src/topics/workflows.md:261 3532e165842f4ebb8db0c78208071555 +msgid "" +"The ``in`` section of the workflow step connects these two input " +"parameters to the inputs of the workflow, `tarball` and " +"`name_of_file_to_extract` using `source`. This means that when the " +"workflow step is executed, the values assigned to `tarball` and " +"`name_of_file_to_extract` will be used for the parameters `tarfile` and " +"`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 -#: ae6b240718104380b08db5552d7355ea -msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +#: ../../src/topics/workflows.md:267 04a4db2f3da94ce29e7999039ee13fde +msgid "" +"The `out` section of the workflow step lists the output parameters that " +"are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 -#: e5a8b7f84be64020b191099f3fad30ed -msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +#: ../../src/topics/workflows.md:278 2651ee113a3d4b79b138854ebe729f48 +msgid "" +"The second step `compile` depends on the results from the first step by " +"connecting the input parameter `src` to the output parameter of `untar` " +"using `untar/extracted_file`. It runs `arguments.cwl` (described " +"previously in [Additional Arguments and Parameters](additional-arguments-" +"and-parameters.md)). The output of this step `classfile` is connected to " +"the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 -#: f0b04849253c4693904512ddd7f9ce84 +#: ../../src/topics/workflows.md:285 177040bf9c0045f2878f42bcdd8cbd2d msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 -#: 12a06d8358534102b202965d4258c18e -msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +#: ../../src/topics/workflows.md:287 e8adc2f7c5ac4464b0711712617b8bbe +msgid "" +"Workflows are ways to combine multiple tools to perform a larger " +"operations. We can also think of a workflow as being a tool itself; a CWL" +" workflow can be used as a step in another CWL workflow, if the workflow " +"engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 -#: 1658cac0de1b47e9b60f6d4a4ad9bb19 -msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +#: ../../src/topics/workflows.md:297 44d281d99cd944478db98446a984c001 +msgid "" +"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " +"workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 -#: 49ed137fe996452a8534c68d100db941 +#: ../../src/topics/workflows.md:300 d7b60ce81ea741ffa08f2c2d9d7cca69 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 -#: b7f93705e5b8416696be01850072e8c0 -msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 -#: e87045829b344089ab59dc27063ddd7a -msgid "\"Visualization \"Visualization" +#: ../../src/topics/workflows.md:309 a5b7a1ab16e34bda8744ffadacdda3e8 +msgid "" +"This two-step workflow starts with the `create-tar` step which is " +"connected to the `compile` step in orange; `compile` is another workflow," +" diagrammed on the right. In purple we see the fixed string " +"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:322 -#: 42ef2f145b824d69b63abc1da175c216 -msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +#: ../../src/topics/workflows.md:314 8654f2d86b644609aaa5b9b73db30bda +msgid "" +" \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 7ce847ab54224452b6425de2a55ec893 +msgid "" +"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " +"its CWL file is included with `run`. The workflow inputs (`tarball` and " +"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " +"mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 -#: c61cedf543664d388183e04b3939cc39 -msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +#: ../../src/topics/workflows.md:336 d621821d2c1b403cb7415b381dd883f6 +msgid "" +"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " +"running it we had to provide a job file to denote the tar file and " +"`*.java` filename. This is generally best-practice, as it means it can be" +" reused in multiple parent workflows, or even in multiple steps within " +"the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 -#: 9e39e3f1501c4fcaab3e8962e090f6be -msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +#: ../../src/topics/workflows.md:341 358c612f175241f7bf148a04d75e00c9 +msgid "" +"Here we use `default:` to hard-code `\"Hello.java\"` as the " +"`name_of_file_to_extract` input, however our workflow also requires a tar" +" file at `tarball`, which we will prepare in the `create-tar` step. At " +"this point it is probably a good idea to refactor `1st-workflow.cwl` to " +"have more specific input/output names, as those also appear in its usage " +"as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 -#: 03e2f767c4da461982fc3c0f3ba94762 -msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +#: ../../src/topics/workflows.md:347 c6297c120e004ae8b52d5b519fbc04d2 +msgid "" +"It is also possible to do a less generic approach and avoid external " +"dependencies in the job file. So in this workflow we can generate a hard-" +"coded `Hello.java` file using the previously mentioned " +"`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 -#: 3bea5822b8694e2aa32c446e1c54a045 -msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +#: ../../src/topics/workflows.md:366 66f76677f4ce42baa8a8813410ea5aee +msgid "" +"In this case our step can assume `Hello.java` rather than be " +"parameterized, so we can use hardcoded values `hello.tar` and " +"`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 -#: 426023bd6e3a471cbb30dbda3d6f9e57 -msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +#: ../../src/topics/workflows.md:383 a8ccb9f9ab4448e087ea8448d620d33c +msgid "" +"Did you notice that we didn't split out the `tar --create` tool to a " +"separate file, but rather embedded it within the CWL Workflow file? This " +"is generally not best practice, as the tool then can't be reused. The " +"reason for doing it in this case is because the command line is hard-" +"coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 -#: 0d498cd4caf54c15891ca1afe58e2727 -msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +#: ../../src/topics/workflows.md:389 afe43b9e92e949a589f493293eff2903 +msgid "" +"In this example we had to prepare a tar file outside, but only because " +"our inner workflow was designed to take that as an input. A better " +"refactoring of the inner workflow would be to take a list of Java files " +"to compile, which would simplify its usage as a tool step in other " +"workflows." msgstr "" -#: ../../src/topics/workflows.md:394 -#: b2d75045e02741b4850f5ff1243f7858 -msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +#: ../../src/topics/workflows.md:394 239eef3a740d42a69208a8f4e716d2b3 +msgid "" +"Nested workflows can be a powerful feature to generate higher-level " +"functional and reusable workflow units - but just like for creating a CWL" +" Tool description, care must be taken to improve its usability in " +"multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 -#: cfa765264a27411ab914de569aa3dac4 +#: ../../src/topics/workflows.md:398 96d1ca78cc324f40b61c4b7330447db2 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 -#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 -msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +#: ../../src/topics/workflows.md:400 eab4437bf9994b649954221375e3dd6d +msgid "" +"Now that we know how to write workflows, we can start utilizing the " +"`ScatterFeatureRequirement`. This feature tells the runner that you wish " +"to run a tool or workflow multiple times over a list of inputs. The " +"workflow then takes the input(s) as an array and will run the specified " +"step(s) on each element of the array as if it were a single input. This " +"allows you to run the same workflow on multiple inputs without having to " +"generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 -#: 5fa79c62049a447c8328ebf9db54ebf4 -msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +#: ../../src/topics/workflows.md:411 c245ba0ae2074fa388ad6c35695033c8 +msgid "" +"The most common reason a new user might want to use scatter is to perform" +" the same analysis on different samples. Let's start with a simple " +"workflow that calls our first example (`hello_world.cwl`) and takes an " +"array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 -#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#: ../../src/topics/workflows.md:415 83537938ce1244709f9b72269b048d63 msgid "`scatter-workflow.cwl`" msgstr "`scatter-workflow.cwl`" -#: ../../src/topics/workflows.md:421 -#: 3a67d77a2e7b4c0bb61cc3585ceae942 -msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +#: ../../src/topics/workflows.md:421 4f507925766e48ae8f713d56051a5e29 +msgid "" +"Aside from the `requirements` section including " +"`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 -#: f1cb55fc59824cc18a95fd6dcb32cf4c -msgid "First of all, notice that the main workflow level input here requires an array of strings." +#: ../../src/topics/workflows.md:429 ccbbba3189404241a44736c970249b84 +msgid "" +"First of all, notice that the main workflow level input here requires an " +"array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 -#: d947c54933d64aad90df392a1cedd63f -msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +#: ../../src/topics/workflows.md:441 31eff13bb8334fc7b6d48ef6c5b1ce33 +msgid "" +"Here we've added a new field to the step `echo` called `scatter`. This " +"field tells the runner that we'd like to scatter over this input for this" +" particular step. Note that the input name listed after scatter is the " +"one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 -#: 651d35997332404186aa6d5711da4a3d -msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +#: ../../src/topics/workflows.md:445 0d5cf8b82dbd47f2abd1ed16b9b3eb61 +msgid "" +"For our first scatter, it's as simple as that! Since our tool doesn't " +"collect any outputs, we still use `outputs: []` in our workflow, but if " +"you expect that the final output of your workflow will now have multiple " +"outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 -#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +#: ../../src/topics/workflows.md:450 38b7042a270043ba82c11cf2e758f0c8 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 -#: 842b926ae34542cb9023021f137b08be +#: ../../src/topics/workflows.md:452 b3fc75c262fe4a3a8e8bfba1abb07b3d msgid "`scatter-job.yml`" msgstr "`scatter-job.yml`" -#: ../../src/topics/workflows.md:458 -#: b662c1a5a4424c8d8350a806356acc61 -msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +#: ../../src/topics/workflows.md:458 f9fa7046c89c417db51dc7c8a026fd5d +msgid "" +"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" +" calls the command `echo` on a message. If we invoke `cwltool scatter-" +"workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 -#: 04d6babfd87343d7a5f13867ea02b65f -msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +#: ../../src/topics/workflows.md:466 b6a33410ee9a45d7bf7b2ba56f786f8f +msgid "" +"You can see that the workflow calls echo multiple times on each element " +"of our `message_array`. Ok, so how about if we want to scatter over two " +"steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 -#: 2eaacf1a90204a2b9bd621344560f2a1 -msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +#: ../../src/topics/workflows.md:469 99b5c8a845ab4beb8524a69c051e2d42 +msgid "" +"Let's perform a simple echo like above, but capturing `stdout` by adding " +"the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 -#: 242993d42b164ee5abe7ca10d45856de +#: ../../src/topics/workflows.md:472 97bf58937d3f4e98af702e3c1a418992 msgid "`hello_world_to_stdout.cwl`" msgstr "`hello_world_to_stdout.cwl`" -#: ../../src/topics/workflows.md:480 -#: 4a94e5f7e1bc4d628702140e4e51d6d3 -msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +#: ../../src/topics/workflows.md:480 173bd28708834f11a2a1366b579b7ad7 +msgid "" +"And add a second step that uses `wc` to count the characters in each " +"file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 -#: e61d93b848184c8e8e573928427b4d0a +#: ../../src/topics/workflows.md:483 4afccfe982ff4be2be96cbe5889e5014 msgid "`wc-tool.cwl`" msgstr "`wc-tool.cwl`" -#: ../../src/topics/workflows.md:489 -#: e3a7182f00f440b8b5461da91194a64b -msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +#: ../../src/topics/workflows.md:489 63595d35dded4911aab0be3a165eec0c +msgid "" +"Now, how do we incorporate scatter? Remember the scatter field is under " +"each step:" msgstr "" -#: ../../src/topics/workflows.md:491 -#: 99fa96caacaa45cb97aded9a24fcac6d +#: ../../src/topics/workflows.md:491 a7f96ec6e4f24c62ac0f5b6edcc9734b msgid "`scatter-two-steps.cwl`" msgstr "`scatter-two-steps.cwl`" -#: ../../src/topics/workflows.md:497 -#: b5338f39e8c74ff28e139da68089a742 -msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 -#: f6d92156d67c4a339bcfd194cff897df -msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +#: ../../src/topics/workflows.md:497 122452b7d7114c3fa53cbea286703023 +msgid "" +"Here we have placed the scatter field under each step. This is fine for " +"this example since it runs quickly, but if you're running many samples " +"for a more complex workflow, you may wish to consider an alternative. " +"Here we are running scatter on each step independently, but since the " +"second step is not dependent on the first step completing all languages, " +"we aren't using the scatter functionality efficiently. The second step " +"expects an array as input from the first step, so it will wait until " +"everything in step one is finished before doing anything. Pretend that " +"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " +"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " +"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " +"could finish in 4 minutes, it will actually finish in 8 minutes because " +"the first step must wait on `echo Hallo welt!`. You can see how this " +"might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 85dd63daf04546b78bdcb68c1d985fa9 +msgid "" +"Ok, so how do we scatter on steps that can proceed independent of other " +"samples? Remember from [Nested Workflows](#nested-workflows), that we can" +" make an entire workflow a single step in another workflow! Convert our " +"two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 -#: 1c9e386922324ec8a59306572c19fb8b +#: ../../src/topics/workflows.md:513 fac138ba275745898b763a7d719a8235 msgid "`scatter-nested-workflow.cwl`" msgstr "`scatter-nested-workflow.cwl`" -#: ../../src/topics/workflows.md:519 -#: d80ab383eec9402faba997b548fe42eb -msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +#: ../../src/topics/workflows.md:519 508ef2240879445594b0f262ed11a01d +msgid "" +"Now the scatter acts on a single step, but that step consists of two " +"steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 -#: f7d2827d97db4bf4ab84b5d6621c3b48 +#: ../../src/topics/workflows.md:522 b0bf01dad1234a1db3c87b10953e42ef msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 -#: 49217c02f58c43ff9ec00f10da8d4e84 -msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +#: ../../src/topics/workflows.md:524 8d933ed1ec6e408589f781e3a425b869 +msgid "" +"This workflow contains a conditional step and is executed based on the " +"input. This allows workflows to skip additional steps based on input " +"parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 -#: 20b9f181420c401d8615c17a10027517 +#: ../../src/topics/workflows.md:527 9ac7b4f71621411da9a4ca3bc277dcb0 msgid "`conditional-workflow.cwl`" msgstr "`conditional-workflow.cwl`" -#: ../../src/topics/workflows.md:566 -#: 8dbd56473f8c40c0bb12a48be06117e3 -msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +#: ../../src/topics/workflows.md:566 4a4a2b2b99b44d449adb246cebce0a26 +msgid "" +"The first thing you'll notice is that this workflow is only compatible " +"for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 -#: 78d7f3ede2c746d482042adef050b2c4 -msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +#: ../../src/topics/workflows.md:573 4742fe09a4264fb8be6f092519de5d72 +msgid "" +"The first step of the workflow (step1) contains two input properties and " +"will execute foo.cwl when the conditions are met. The new property `when`" +" is where the condition validation takes place. In this case only when " +"`in1` from the workflow contains a value `< 1` this step will be " +"executed." msgstr "" -#: ../../src/topics/workflows.md:587 -#: cbbf93c70fe04ba7932ba25758ddc611 -msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +#: ../../src/topics/workflows.md:587 b33ecd2b8af042feb08687e32d4b6bbf +msgid "" +"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" +" will pass the first conditional step and will therefore be executed and " +"is shown in the log by `INFO [step step1] start` whereas the second step " +"is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 -#: cfa1c1fde4454df283f87cc54a9c59ec -msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +#: ../../src/topics/workflows.md:607 7cd80b31a94543358ece7a2d413adce9 +msgid "" +"When a value of 3 is given the first conditional step will not be " +"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 -#: 1a8be2950cbb475bbb2617e005f0fac9 -msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +#: ../../src/topics/workflows.md:627 9679e32f65e0482a8b083387e4a18c1f +msgid "" +"If no conditions are met for example when using `--val 2` the workflow " +"will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 -#: 5f09d4d897cf457d80b9a11b8c01747e +#: ../../src/topics/yaml-guide.md:1 4fa76441f95d45fab76ab7eef8d7d4d2 msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 -#: 5d83c56102e141cc978500f678dd0c1c -msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +#: ../../src/topics/yaml-guide.md:6 705765787eb84ecaae004194225924cb +msgid "" +"[YAML][yaml] is a file format designed to be readable by both computers " +"and humans. This guide introduces the features of YAML that are relevant " +"when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 -#: c38438fbf9a04e729ec2e3c962435289 +#: ../../src/topics/yaml-guide.md:13 cb243f6ab11f48ffb5c91945c4e0d101 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 -#: fdb9cc750cec43ee962517e637dc5fea +#: ../../src/topics/yaml-guide.md:16 cfc95d15e33a492f842649f92ced941d msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 -#: 08da9cd8056b4ddd8f5150cc85ba72ee +#: ../../src/topics/yaml-guide.md:18 f618d44d202f4c2ea6ff72a1dca2c659 msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 -#: b027fc234ed943bbb00d4c6bc03c040a +#: ../../src/topics/yaml-guide.md:19 36bfa6ed40c54bd99826bedff12c759d msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 -#: b8befec0d8684638aaa616a659e0100c +#: ../../src/topics/yaml-guide.md:20 61913753eb0c4c728889b47f1110be24 msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 -#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +#: ../../src/topics/yaml-guide.md:21 0de824a05eea46209aafa6f9e2e8623c msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 -#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +#: ../../src/topics/yaml-guide.md:22 95627bc476b3415ca4d77246125137d2 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 -#: 98056c5cfd5640ad9de0679360797cc7 +#: ../../src/topics/yaml-guide.md:24 3f64a6d33d9a4c22a8a839a8def82686 msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 -#: cda73485875d4c8e9464679a20558616 -msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +#: ../../src/topics/yaml-guide.md:26 2f74f6eaa8d84dc9b4d0a166844dedbe +msgid "" +"Fundamentally, a file written in YAML consists of a set of _key-value " +"pairs_. Each pair is written as `key: value`, where whitespace after the " +"`:` is required. Key names in CWL files should not contain whitespace - " +"[_camelCase_][camelCase] is used for multi-word key names that have " +"special meaning in the CWL specification and underscored key names " +"otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 -#: 98cae24919b74c088a5d89706aec581b -msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +#: ../../src/topics/yaml-guide.md:42 514365e59d9648deb896e2068d967a64 +msgid "" +"The YAML above defines four keys - `first_name`, `last_name`, " +"`age_years`, and `home` - with their four respective values. Values can " +"be character strings, numeric (integer, floating point, or scientific " +"representation), Boolean (`true` or `false`), or more complex nested " +"types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 -#: b4b0940b4b5743c09637b36b964202d0 -msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +#: ../../src/topics/yaml-guide.md:51 6939eb7e783744d7bcf75ea0a7cae129 +msgid "" +"Values may be wrapped in quotation marks, but be aware that this may " +"change the way that they are interpreted i.e. `\"1234\"` will be treated " +"as a character string , while `1234` will be treated as an integer. This " +"distinction can be important, for example when describing parameters to a" +" command: in CWL all parts of `baseCommand` must be strings so, if you " +"want to specify a fixed numeric value to a command, make sure that you " +"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 -#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +#: ../../src/topics/yaml-guide.md:61 96e1776b09e840ebbc9b4b7e01da0e43 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 -#: 9ca3554d771d45998e88aaede525b227 -msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +#: ../../src/topics/yaml-guide.md:63 8b17f7557c3540b2b0d0beca0fe4ebc7 +msgid "" +"You may use `#` to add comments to your CWL and parameter files. Any " +"characters to the right of ` #` will be ignored by the program " +"interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 -#: 3fca839cede94cfd8e4f605c73ba699d -msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +#: ../../src/topics/yaml-guide.md:76 13da997c82c04023a4b7bb36b76e969d +msgid "" +"If there is anything on the line before the comment, be sure to add at " +"least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 -#: da34c635707345b2a5e85a2fcd30bbaf +#: ../../src/topics/yaml-guide.md:79 b9fc191166a64450b64a8182adabad75 msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 -#: 3ded0f125249485c921994b6e6b93ac9 -msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:104 -#: 53ece35d309a4c8d99f1efb2122a7092 -msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +#: ../../src/topics/yaml-guide.md:81 aedf8c4f615845ad91a7947217005d6e +msgid "" +"When describing a tool or workflow with CWL, it is usually necessary to " +"construct more complex, nested representations. Referred to as _maps_, " +"these hierarchical structures are described in YAML by providing " +"additional key-value pairs as the value of any key. These pairs " +"(sometimes referred to as \"children\") are written on new lines under " +"the key to which they belong (the \"parent\"), and should be indented " +"with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:127 -#: d74321b111d84ae7a515f2f17dd39e23 +#: ../../src/topics/yaml-guide.md:104 f0f1f414f74342a89065ba5ded8668e5 +msgid "" +"The YAML above illustrates how to build up complex nested object " +"descriptions relatively quickly. The `inputs` map contains a single key, " +"`example_flag`, which itself contains two keys, `type` and " +"`inputBinding`, while one of these children, `inputBinding`, contains a " +"further two key-value pairs (`position` and `prefix`). See the " +"[Arrays](#arrays) section below for more information about providing " +"multiple values/key-value pairs for a single key. For comparison with the" +" example YAML above, here is a graphical representation of the `inputs` " +"object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 965405e2a45a4cbb8f227bc8ceeb05df msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 -#: 7fc0bdf2489a44f2a29e71b86f7c0055 -msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +#: ../../src/topics/yaml-guide.md:129 5aca9a90fb6149529ed717992746a2f3 +msgid "" +"In certain circumstances, it is necessary to provide multiple values or " +"objects for a single key. As we've already seen in the [Maps](#maps) " +"section above, more than one key-value pair can be mapped to a single " +"key. However, it is also possible to define multiple values for a key " +"without having to provide a unique key for each value. We can achieve " +"this with an _array_, where each value is defined on its own line and " +"preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 -#: fd64dd818ec64bb6aa9a11586a5747f6 +#: ../../src/topics/yaml-guide.md:146 d1c9e72e004b4fb4a6efb7748a15ab6f msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 -#: 8c06e542dd4144fa83388d8142552c8d +#: ../../src/topics/yaml-guide.md:167 9a3d6879404745a48cd394bf86865dbc msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 -#: 87bafb845c714b109874f6137b84462d -msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +#: ../../src/topics/yaml-guide.md:169 6a7cca0339794e679329b00d89e29d2b +msgid "" +"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " +"arrays can also be defined in YAML using the native JSON syntax. For " +"example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 -#: 5ab9ddf613a540a2b8228e37600cc5dc +#: ../../src/topics/yaml-guide.md:177 d8feed2d36d04fe283b9de9784d91941 msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 -#: fcd05b1ef31a4046946a2399c7fc5575 -msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +#: ../../src/topics/yaml-guide.md:184 5156ad32791048f8ace51475d7689575 +msgid "" +"Native JSON can be useful in indicating where a field is intentionally " +"left empty (such as `[]` for an empty array), as well as where it makes " +"more sense for the values to be located on the same line (For example, " +"when providing option flags and their values in a shell command). " +"However, as the second example above shows, it can severely affect the " +"readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 -#: f4b8fc8236044fada420def13a02813d +#: ../../src/topics/yaml-guide.md:194 ce49f80e6fc0498b8ad298fb1f0268f3 msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 -#: 859368c1f25c4a4aad57abfd046c63f5 -msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +#: ../../src/topics/yaml-guide.md:196 180d261392a644fcb8ff47d7a4a160c0 +msgid "" +"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" +" us while we wrote this guide, though it also covers features that are " +"not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 -#: 2203c93f02ac4514a43508ecb98dfcc5 +#: ../../src/tutorials.md:1 d682035afebf4c128755bd4e58780dd2 msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 -#: 5d92464923c245818c070fbef102be89 -msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +#: ../../src/tutorials.md:5 d9adeab63ec54084bc41fb90f264d3ae +msgid "" +"This is a list of tutorials provided by the CWL community. Use the `Edit " +"this page` link in the menu if you would like to add another tutorial to " +"the list." msgstr "" -#: ../../src/tutorials.md:7 -#: 8a5cd557dab5456bb41cdc24af73b50c +#: ../../src/tutorials.md:7 23c81edb650b4f86a60c5e0bcedeac1d msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 -#: 13d7e2e92e96432787c712cf6a595424 -msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +#: ../../src/tutorials.md:9 87ddaa1e5f57445c8f13803722aa146e +msgid "" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" +"tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 -#: 0abdd85c9b964a4e89ba3d80a6c78d6f +#: ../../src/tutorials.md:11 b8ee193ba533498db6263e0f5f4ec45f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 -#: 3cbf1f69a5514fd3bee90e68b201190f +#: ../../src/tutorials.md:13 67c4b3923fce46fdab025495125c91d4 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 -#: 68c97a7065634d02956f3f5c1d4eeb9f +#: ../../src/tutorials.md:15 e640316669104239970794191b6da38b msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 -#: a67c7e0eaf4e4d27b3e5db303333a088 +#: ../../src/tutorials.md:17 efe94af44b874f9b81b245fbdee43f7f msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" + +#~ msgid "In CWL, everything must be directly stated." +#~ msgstr "在CWL中，一切都必须直接说明。" + +#~ msgid "Optional Inputs 💯" +#~ msgstr "可选输入💯" + +#~ msgid "Enum Inputs ⚜️" +#~ msgstr "枚举输入 ⚜️" + +#~ msgid "Record Inputs 📀" +#~ msgstr "记录输入 📀" + +#~ msgid "Debug JavaScript Expressions" +#~ msgstr "调试 JavaScript 表达式" + +#~ msgid "" +#~ "`cwltool` can be installed with `pip`." +#~ " We recommend using a virtual " +#~ "environment like `venv` or `conda`. The" +#~ " following commands will create and " +#~ "activate a Python virtual environment " +#~ "using the `venv` module, and install " +#~ "`cwltool` in that environment:" +#~ msgstr "" +#~ "`cwltool` 可以用 `pip` 命令安装，而且我们推荐使用 `venv` " +#~ "或 `conda` 等虚拟环境。以下命令将使用 `venv` 模块创建并激活一个 " +#~ "Python 虚拟环境，并在该环境中安装 `cwltool`:" + +#~ msgid "Installing `cwltool` with `pip` and `venv`." +#~ msgstr "使用 `pip` 和 `venv` 安装 `cwltool`." + +#~ msgid "Cwl-runner Python Module" +#~ msgstr "Python 模块 cwl-runner" + +#~ msgid "" +#~ "This indicates whether a process " +#~ "requires outgoing IPv4/IPv6 network access." +#~ " If a command-line tool is " +#~ "written manually in CWL v1.1+, there " +#~ "is a need to specify when network" +#~ " access is required." +#~ msgstr "" +#~ "这指的是流程是否需要发起 IPv4/IPv6 网络访问。如果命令行工具是基于 CWL " +#~ "v1.1+ 版本新编写的，则有必要明文指定何时需要访问网络。" + +#~ msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +#~ msgstr "要生成此类文件，我们可以使用 `InitialWorkDirRequirements`." + +#~ msgid "From `Workflow`" +#~ msgstr "来自 `Workflow`" + +#~ msgid "" +#~ "If you try running it with " +#~ "`cwltool`, the command will fail since" +#~ " `cwltool` does not have enough " +#~ "information to know how to execute " +#~ "it:" +#~ msgstr "如果您尝试用 `cwltool` 运行它，该命令会失败，因为 `cwltool` 缺少足够信息，无从知晓如何运行它：" + +#~ msgid "" +#~ "Before we run this, let's just " +#~ "break it down and see what some" +#~ " bits do. Most of this has " +#~ "been explained in previous sections, the" +#~ " only part that is really new " +#~ "is the `dockerRequirement` section." +#~ msgstr "" + From c8666aa2ac3230c4a5d6eb9ed52cc2b090b19cb9 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Wed, 31 Jan 2024 11:50:22 +0100 Subject: [PATCH 122/179] Translations update from Hosted Weblate (#452) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Translated using Weblate (Japanese) Currently translated at 51.9% (311 of 599 strings) Translated using Weblate (Japanese) Currently translated at 51.7% (310 of 599 strings) Translated using Weblate (Japanese) Currently translated at 51.7% (310 of 599 strings) Translated using Weblate (Japanese) Currently translated at 51.7% (310 of 599 strings) Translated using Weblate (Japanese) Currently translated at 51.5% (309 of 599 strings) Translated using Weblate (Japanese) Currently translated at 51.2% (307 of 599 strings) Translated using Weblate (Japanese) Currently translated at 51.0% (306 of 599 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Tamazight (Standard Moroccan)) Currently translated at 0.1% (1 of 598 strings) Added translation using Weblate (Tamazight (Standard Moroccan)) Co-authored-by: ⵣⵓⵀⵉⵔ ⴰⵎⴰⵣⵉⵖ ZOUHIR DEHBI Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zgh/ Translation: Common Workflow Language/CWL User Guide * Added translation using Weblate (Tamazight (Standard Moroccan)) Co-authored-by: Weblate * Translated using Weblate (Chinese (Simplified)) Currently translated at 69.7% (418 of 599 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 69.6% (417 of 599 strings) Co-authored-by: Zoë Ma Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide --------- Co-authored-by: Manabu ISHII Co-authored-by: ⵣⵓⵀⵉⵔ ⴰⵎⴰⵣⵉⵖ ZOUHIR DEHBI Co-authored-by: Zoë Ma --- locales/ja/LC_MESSAGES/user_guide.po | 215 +- locales/zgh/LC_MESSAGES/sphinx.po | 27 + locales/zgh/LC_MESSAGES/user_guide.po | 3125 +++++++++++++++++++++ locales/zh_Hans/LC_MESSAGES/user_guide.po | 31 +- 4 files changed, 3377 insertions(+), 21 deletions(-) create mode 100644 locales/zgh/LC_MESSAGES/sphinx.po create mode 100644 locales/zgh/LC_MESSAGES/user_guide.po diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index ce4d41ef..2aa1d64d 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,15 +9,16 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2023-12-16 02:08+0000\n" +"PO-Revision-Date: 2024-01-31 06:01+0000\n" "Last-Translator: Manabu ISHII \n" +"Language-Team: Japanese \n" "Language: ja\n" -"Language-Team: Japanese \n" -"Plural-Forms: nplurals=1; plural=0;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=1; plural=0;\n" +"X-Generator: Weblate 5.4-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -923,6 +924,7 @@ msgid "Windows" msgstr "Windows" #: ../../src/introduction/prerequisites.md:29 aeeb990abbbd42cca122c342054be29c +#, fuzzy msgid "" "If you are using Windows, you will have to install the Windows Subsystem " "for Linux 2 as documented in the [`cwltool` documentation for Microsoft " @@ -930,6 +932,11 @@ msgid "" "language/cwltool/blob/main/README.rst#ms-windows-users). Your operating " "system also needs internet access and a recent version of Python (3.6+)." msgstr "" +"Windowsを使用している場合は、[`cwltool` documentation for Microsoft Windows " +"users](https://github.com/common-workflow-language/cwltool/blob/main/README." +"rst#ms-windows-users)に記載されているように、Windows Subsystem for Linux 2を" +"インストールする必要があります。インターネットアクセスとPythonの最新バージョ" +"ン(3.6+)も必要です。" #: ../../src/introduction/prerequisites.md:34 21d1f29fb15745c480194eae6acdd031 #, fuzzy @@ -953,6 +960,8 @@ msgid "" "`cwltool` can be installed with `pip`, `apt`, or `conda`. We recommend " "using a virtual environment like `venv` or `conda`." msgstr "" +"`cwltool` は `pip`、`apt` または `conda` でインストールできます。`venv` や " +"`conda` のような仮想環境を使用することを推奨します。" #: ../../src/introduction/prerequisites.md:48 1edf8b8438334ae29dc406dbfd711228 #, fuzzy @@ -1000,8 +1009,9 @@ msgid "Running `true.cwl` with `cwltool`." msgstr "`cwltool` を使って `true.cwl` を実行します。" #: ../../src/introduction/prerequisites.md:78 d2dc809318be49cc996d892e93ad84ac +#, fuzzy msgid "Generic ``cwl-runner`` alias" -msgstr "" +msgstr "一般的な ``cwl-runner`` エイリアス" #: ../../src/introduction/prerequisites.md:80 9809c2e262924ef286b0bd62e0b00995 msgid "" @@ -1453,6 +1463,7 @@ msgstr "ここでは、`arguments` フィールドを使用して、特定の入 #: ../../src/topics/additional-arguments-and-parameters.md:43 #: dc9fa5f2cbb147b1853c4042c54010f3 +#, fuzzy msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1462,6 +1473,13 @@ msgid "" "`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " "Environment][runtime] section of the CWL specification for details." msgstr "" +"この例では、ランタイムパラメータを参照しています。 ランタイムパラメータは、" +"ツールが実際に実行されたときのハードウェアまたはソフトウェア環境に関する情報" +"を提供します。 ` $(runtime.outdir)` " +"パラメータは、指定された出力ディレクトリへのパスです。 その他、`$(runtime." +"tmpdir)`,`$(runtime.ram)`,`$(runtime.cores)`,`$(runtime." +"outdirSize)`,`$(runtime.tmpdirSize)` などがあります。 詳細はCWL仕様書の[" +"Runtime Environment][runtime]の項を参照してください。" #: ../../src/topics/best-practices.md:1 964bf8276dd04b65887448e1386e63fe msgid "Best Practices" @@ -1485,6 +1503,7 @@ msgstr "" "Direcotry` を適宜使用します。" #: ../../src/topics/best-practices.md:11 ae127b776eed4894af8cb680377703e0 +#, fuzzy msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1499,8 +1518,20 @@ msgid "" "license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" "license]." msgstr "" +"CWL 定義（`Dockerfile`のような外部コンポーネントと合わせて）は、ソフトウェア" +"コードです。ワークフロー開発者は、ソフトウェアライセンスに関する通常の規則が" +"このCWL定義に適用されることを認識する必要があります。例えば、ワークフローが一" +"般に共有される場合、将来のユーザーがどのような条件でワークフローを実行、修正" +"、および/または他のワークフローと組み合わせることができるかを理解するために、" +"ライセンス条項は明確でなければなりません。このような理由から、CWL定義にライセ" +"ンスフィールドを含めることを検討してください。このガイドの著者は、独自のライ" +"センスを作成するのではなく、既存のライセンスを選択することをお勧めします（ラ" +"イセンスの選択について詳しくは、以下のリンクを参照してください）。そして、私" +"たちの推奨する実践は、誰でも再利用できるライセンスを選択することです。例えば " +"[Apache 2.0][apache-license]です。" #: ../../src/topics/best-practices.md:20 384eb620dc31468e8c3f5f33a3436200 +#, fuzzy msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1509,6 +1540,11 @@ msgid "" "example snippet below for guidance. For non-standard licenses without an " "SPDX identifier, provide a URL to the license." msgstr "" +"可能であれば、ライセンスは対応する [SPDX 識別子][spdx] " +"と共に指定されるべきです。`https://spdx.org/licenses/[SPDX-ID]` (`SPDX-ID` " +"は、上記のリンク先の識別子のリストから選択) という形式の URL を指定して、ライ" +"センスのメタデータフィールドを構築します。以下の例を参照してください。SPDX識" +"別子のない非標準ライセンスの場合は、そのライセンスへのURLを指定します。" #: ../../src/topics/best-practices.md:26 e8259b43fa6944eda73eae381db6b97b msgid "" @@ -1719,12 +1755,17 @@ msgid "Network Access" msgstr "ネットワークアクセス" #: ../../src/topics/command-line-tool.md:69 201712f3ceee4d4ea56ab96d3fef97b0 +#, fuzzy msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. Starting with CWL v1.1, programs are not granted network access " "by default, so you must include the requirement for network access in the" " specification of your tool." msgstr "" +"これは、プロセスが送信先としてIPv4/" +"IPv6ネットワーク・アクセスを必要とするかどうかを示します。 CWL v1.1以降、プロ" +"グラムにはデフォルトでネットワーク・アクセス権が付与されないため、ツール定義" +"にネットワーク・アクセスの要件を含める必要があります。" #: ../../src/topics/command-line-tool.md:84 3282a357799f4a72a6b8bace206144c4 #, fuzzy @@ -1814,6 +1855,7 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 #: 9aeea5a6a4244bc7a1626e0cb7351068 +#, fuzzy msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1823,6 +1865,13 @@ msgid "" "means that you are using a multiline string (without it, we would need to" " write the whole script on one line)." msgstr "" +"`InitialWorkDirRequirement` は`listing` を必要とします。`listing` は YAML " +"配列なので、配列の各要素の最初の行に`-` が必要です。この場合、要素は 1 " +"つだけです。`entryname:` は任意の値を指定できますが、`baseCommand` " +"で指定したものと一致していなければなりません。最後の部分は`entry:` " +"で、この後に`|-` が続きます。これは YAML の引用構文で、" +"複数行の文字列を使用していることを意味します (これがなければ、" +"スクリプト全体を 1 行で記述する必要があります)." #: ../../src/topics/creating-files-at-runtime.md:51 #: 867239e9ad3d4187a2703662a0ca3976 @@ -1848,6 +1897,7 @@ msgid "Custom Types" msgstr "カスタムタイプ" #: ../../src/topics/custom-types.md:3 e0275ddda8f84207a58d10c17ca99a45 +#, fuzzy msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1855,6 +1905,10 @@ msgid "" "for additional customisation/configuration of a tool/analysis without the" " need to fiddle with the CWL description directly." msgstr "" +"CWL定義で使用・再利用するために、独自のカスタム型を書きたい場合があります。こ" +"のようなカスタムタイプを使用することで、同じタイプを使用する複数の記述の間の" +"冗長性を減らし、また、CWL記述を直接いじらずに、ツールや分析のカスタマイズや設" +"定を追加できるようになります。" #: ../../src/topics/custom-types.md:9 8367e38e5e7c4a298d1d87b9001aaddc msgid "" @@ -1871,6 +1925,7 @@ msgid "`custom-types.yml`" msgstr "`custom-types.yml`" #: ../../src/topics/custom-types.md:24 56b8912a1ea84f28adeb8beaf92ab563 +#, fuzzy msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1878,6 +1933,10 @@ msgid "" "types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " "`wget`:" msgstr "" +"___注意:___ 以下の例に行うには、`wget`などで*rich_sparse_otu_table." +"biom*という入力ファイルを[ダウンロード](https://github.com/" +"common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/" +"rich_sparse_otu_table.biom)する必要があります：" #: ../../src/topics/custom-types.md:30 a48539920c4944898918bc90b2d4e3c9 msgid "" @@ -1917,6 +1976,7 @@ msgstr "" " で定義されており、例として`custom-types.cwl` の定義にあるように、インポートされます：" #: ../../src/topics/custom-types.md:76 dce43b138ba24b22bfa9fa5692a17009 +#, fuzzy msgid "" "Note also that the author of this CWL description has also included " "[`ResourceRequirement`](https://w3id.org/cwl/CommandLineTool.html#ResourceRequirement)s," @@ -1926,6 +1986,13 @@ msgid "" "These features are discussed further in other chapters of this user " "guide." msgstr "" +"また、この CWL 定義には、[`ResourceRequirement`](https://w3id.org/cwl/" +"CommandLineTool." +"html#ResourceRequirement)も含まれていることに注意してください。これは、" +"ツールが正常に動作するために必要な最小限の RAM の量とコアの数、さらにその定義" +"に書かれたソフトウェアのバージョンの詳細やその他の有用なメタデータを指定する" +"ものです。これらの機能については、このユーザーガイドの他の章で詳しく説明する" +"。" #: ../../src/topics/environment-variables.md:1 19737f89f2994815969fa4a88346f49a msgid "Environment Variables" @@ -2511,6 +2578,11 @@ msgid "" " tool with others. You can browse existing [IANA file format " "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" +"ファイルフォーマットについては、既存のオントロジーを参照すること（例ではEDAM" +"）、所属機関のローカルオントロジーを参照すること、またはツールを他者と共有す" +"る前に迅速に開発するために最初はファイルフォーマットを追加しないことを推奨し" +"ています。既存の[IANAファイルフォーマット一覧][IANA]と[EDAMファイルフォーマッ" +"ト一覧][EDAM]は、それぞれのウェブサイトで参照することができます。" #: ../../src/topics/file-formats.md:14 81c441846fc249c58607bacf97095eb8 msgid "" @@ -2675,6 +2747,7 @@ msgid "" msgstr "CWLリファレンスランナー（cwltool）と他のランナーは、ツールが明示的に指定されていないファイルに誤ってアクセスしないように、入力ファイルへの（\"ソフト\"）シンボリックリンクを持つ一時ディレクトリを作成します。" #: ../../src/topics/inputs.md:70 5bdf77c45346445d8f93353c1e73f768 +#, fuzzy msgid "" "The field " "[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)" @@ -2683,6 +2756,10 @@ msgid "" "parameter does not appear on the command line. Let's look at each " "example in detail." msgstr "" +"フィールド[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_bi" +"nding)はオプションであり、入力パラメータをツールのコマンドラインに表示するか" +"どうか、またどのように表示するかを指定します。`inputBinding`がない場合、パラ" +"メータはコマンドラインに表示されません。 それぞれの例を詳しく見てみましょう。" #: ../../src/topics/inputs.md:83 d783fe52e86f4feda33ea0eecb622603 msgid "" @@ -2705,14 +2782,19 @@ msgstr "" " hello` と与えられます。" #: ../../src/topics/inputs.md:109 b106eed01c1744a792368f91f547e553 +#, fuzzy msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " "default value is true), the prefix and value are combined into a single " "argument. In the example above, this is rendered as `-i42`." msgstr "" +"整数型（および浮動小数点型）はコマンドラインに10進数のテキスト表現で表示され" +"ます。 `separate`オプションがfalseの場合（デフォルト値はtrue）、prefixと値は1" +"つの引数にまとめられます。 上の例では `-i42` として表示されます。" #: ../../src/topics/inputs.md:124 1c70336741a842a5b16b687642d1d9b4 +#, fuzzy msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2721,6 +2803,11 @@ msgid "" "parameter were not provided in the input, nothing would appear on the " "command line." msgstr "" +"ファイル型は、コマンドライン上にファイルへのパスとして表示されます。 パラメ" +"ータの型の末尾にクエスチョンマーク`?`がある場合、これは、パラメータがオプショ" +"ンであることを表します。 上記の例では、`--file=/tmp/random/path/whale.txt` " +"と表示されます。 ただし、入力パラメータに \"example_file\" " +"パラメータを指定しなかった場合、コマンドラインには何も表示されません。" #: ../../src/topics/inputs.md:131 9294c07c672b414f9c3895ed70b9b4ee msgid "" @@ -2752,6 +2839,7 @@ msgid "Array Inputs" msgstr "配列入力" #: ../../src/topics/inputs.md:148 b11a5c7a13b345939e4ae15e1e2c0786 +#, fuzzy msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2760,6 +2848,11 @@ msgid "" " be added after the type name to indicate that input parameter is array " "of that type." msgstr "" +"コマンドラインに表現される入力パラメータの配列を簡単に追加することができます" +"。配列パラメータを指定するには、2つの方法があります。1つ目の方法は、`type` " +"に`type: array` と`items` を指定して、配列に現れる可能性のある有効なデータ型" +"を定義する方法です。2つ目の方法は、入力パラメータがその型の配列であることを示" +"すために、型名の後に`[]` という括弧を付けることもできます。" #: ../../src/topics/inputs.md:154 aa00bcfc6c0f4085ae52621a2f4ae8d9 msgid "`array-inputs.cwl`" @@ -2787,8 +2880,13 @@ msgid "" "values should be concatenated into a single argument separated by the " "item separator string." msgstr "" +"`inputBinding` は、外側の配列パラメータ定義と内側の配列要素定義のいずれかに記" +"述することができ、上図のようにコマンドラインを構築する際に異なる挙動を示しま" +"す。また、`itemSeparator` フィールドがあれば、配列の値を項目区切り文字列で区" +"切って1つの引数に連結することを指定することができます。" #: ../../src/topics/inputs.md:185 bb31c6784ea843ec88f185523cfa25df +#, fuzzy msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2798,6 +2896,11 @@ msgid "" "guide.md#arrays). You can specify arrays of arrays, arrays of records, " "and other complex types." msgstr "" +"なお、入力の配列は角括弧の中で指定します `array-inputs-job.yml`の`[]`です.配" +"列は複数行に渡って表現することも可能で、関連するキーで定義されていない配列の" +"値は、先頭の`-` でマークされます。これは次のレッスンで実演され、[YAML Guide" +"](yaml-guide.md#arrays) でより詳細に説明されています。配列の配列、レコードの" +"配列、その他の複雑な型を指定することができます。" #: ../../src/topics/inputs.md:191 53817379078548b2aeb6195cae9cbab7 #, fuzzy @@ -2805,12 +2908,17 @@ msgid "Inclusive and Exclusive Inputs" msgstr "包括的入力と排他的入力" #: ../../src/topics/inputs.md:193 e163c0cfe9694a85b2e42682f42970a5 +#, fuzzy msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " "provided together (they are exclusive). You can use records and type " "unions to group parameters together to describe these two conditions." msgstr "" +"基本的なツールには、一緒に提供しなければならない複数の引数（依存関係あり）や" +"、一緒に提供できない複数の引数（排他関係あり）があることがあります。 record" +"とユニオン型を使ってパラメータをグループ化し、この2つの条件を定義することがで" +"きます。" #: ../../src/topics/inputs.md:198 84e1ab25511c49d1baabb1f80f247b49 msgid "`record.cwl`" @@ -3027,10 +3135,12 @@ msgid "" msgstr "上記のコマンドの出力は、Graphvizレンダラーでレンダリングすることができます。以下の画像は、SphinxのGraphvizディレクティブでレンダリングしたものです（このユーザーガイドはSphinxで構築されています）：" #: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd +#, fuzzy msgid "" "The operation file will fail to run with `cwltool` because `cwltool` " "lacks the necessary information to execute it:" -msgstr "" +msgstr "操作ファイルを `cwltool` で実行しようとすると、`cwltool` " +"が実行に必要な情報を持っていないため、失敗します：" #: ../../src/topics/operations.md:59 e184470550e645f6b9ce658af7e65ecf msgid "`cwltool` does not know how to run operations" @@ -3198,6 +3308,7 @@ msgid "Parameter References" msgstr "パラメータリファレンス" #: ../../src/topics/parameter-references.md:3 f5c0592ca28c46c2a89943f4f6f69a27 +#, fuzzy msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -3209,6 +3320,15 @@ msgid "" "reference the value of input parameters dynamically from other fields, " "which will allow us to then specify the name of the file to extract." msgstr "" +"前の例では、\"tar \"プログラムを使用してファイルを抽出しました" +"。しかし、その例は非常に限定的なものでした。というのも、" +"私たちが興味を持っているファイルは\"hello.txt\"と呼ばれ、これが`.cwl` ファイ" +"ルに書き込まれていると仮定していたからです。これは最良の方法ではありません。" +"なぜなら、\"hello.txt \"というファイル名は" +"、使用する入力ファイルによって異なるか、または依存する可能性があるからです。" +" これを避けるために、ジョブパラメーターファイル(`.yml`)で必要なファイル名を" +"指定することができます。この例では、入力パラメーターの値を他のフィールドから" +"動的に参照し、抽出するファイル名を指定する方法を説明します。" #: ../../src/topics/parameter-references.md:13 50db8add9b1942d986e581b8d21c2ee4 msgid "`tar-param.cwl`" @@ -3393,6 +3513,7 @@ msgstr "ソフトウェア要求事項の指定" #: ../../src/topics/specifying-software-requirements.md:3 #: e708866921ea49d69d3c2a32d63ea468 +#, fuzzy msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -3401,6 +3522,12 @@ msgid "" " field in the `hints` section. This may also help to avoid confusion " "about which version of a tool the description was written for." msgstr "" +"多くの場合、ツール定義はソフトウェアの特定のバージョン用に書かれます。他の人" +"があなたの説明を使いやすくするために、`hints` セクションに " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#SoftwareRequirement) フィールドを含めることができます。これは、ツール定" +"義がどのツールのどのバージョン用に書かれたかについての混乱を避けるのにも役立" +"ちます。" #: ../../src/topics/specifying-software-requirements.md:13 #: 6f722d6fd54f485fa964076c8d08938b @@ -3418,6 +3545,10 @@ msgid "" "enable these checks with the reference implementation, use the " "[dependency resolvers configuration][dependencies]." msgstr "" +"CWLランナーによっては、これらのヒントを使用して、ジョブの実行前に必要なソフト" +"ウェアがインストールされ、利用可能であることをチェックすることができます。リ" +"ファレンス実装でこれらのチェックを有効にするには、[依存性解決のための設定][de" +"pendencies] を使用します。" #: ../../src/topics/specifying-software-requirements.md:29 #: 1a8b8aadf1c64e87b8b670e288bc14bc @@ -3442,6 +3573,7 @@ msgid "Staging Input Files" msgstr "入力ファイルのステージング" #: ../../src/topics/staging-input-files.md:3 ac2ef1fced5f4044861761a11c35e78a +#, fuzzy msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -3452,6 +3584,13 @@ msgid "" "a JavaScript expression to extract the base name of the input file from " "its leading directory path." msgstr "" +"通常、入力ファイルは出力ディレクトリとは別の読み取り専用ディレクトリに置かれ" +"ます。 これは、ツールが同じディレクトリに入力ファイルと一緒に出力ファイルを書" +"き込むことを期待している場合に問題を引き起こします。 入力ファイルを出力ディレ" +"クトリにステージング（配置のこと）するには、[`InitialWorkDirRequirement`](htt" +"ps://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)を使用します" +"。この例では、JavaScript式を使用して、先頭のディレクトリパスから入力ファイル" +"のベース名を抽出しています。" #: ../../src/topics/staging-input-files.md:9 d8ca16f5321e486ebe8ea9f9752b3737 msgid "`linkfile.cwl`" @@ -3482,6 +3621,11 @@ msgid "" "these files are created in a temporary directory but writing them to a " "separate directory makes accessing them easier." msgstr "" +"ワークフロー実行時に`--cachedir` オプションを使用すると、`cwltool` に中間ファ" +"イル（入力ファイルでも出力ファイルでもないが、ワークフロー実行中に作成される" +"ファイル）をキャッシュするよう指示することができます。デフォルトでは、これら" +"のファイルは一時ディレクトリに作成されますが、別のディレクトリに書き込むこと" +"でアクセスが容易になります。" #: ../../src/topics/troubleshooting.md:14 36ec60b80c714357a4274217274136ff msgid "" @@ -3492,6 +3636,13 @@ msgid "" " where instead of executing the `rev` command it tries to execute `revv`," " which fails." msgstr "" +"次の例では、`troubleshooting-wf1.cwl` ` step_a` と`step_b` " +"という2つのステップを用意しています。このワークフローは、`echo \"Hello " +"World\" | rev` と同等で、\"Hello World\" というメッセージを反転して、" +"すなわち \"dlroW olleH\" " +"と表示します。しかし、2番目のステップである`step_b`,**にはタイプミス** " +"があり、`rev` コマンドを実行する代わりに`revv` " +"を実行しようとし、失敗しています。" #: ../../src/topics/troubleshooting.md:20 6f34038054ac4f4fa0b0ad9cbc3ecdc7 msgid "`troubleshooting-wf1.cwl`" @@ -3508,22 +3659,33 @@ msgstr "" "は、ディレクトリがまだ存在しない場合、新規作成します）：" #: ../../src/topics/troubleshooting.md:35 8654b7f2f4464d13be4b47729e1f07e5 +#, fuzzy msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " "successfully and its output has been cached in your `cachedir` location. " "You can inspect the intermediate files created:" msgstr "" +"`step_b` が存在しない `revv` コマンドの実行に失敗したため、ワークフローは " +"`permanentFail` ステータスになっています。`step_a` は正常に実行され、" +"その出力は `cachedir` " +"にキャッシュされました。作成された中間ファイルを確認することができます：" #: ../../src/topics/troubleshooting.md:44 04e80f7ce14d4d73bc5d290dcf01bcdb +#, fuzzy msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " "executed by the workflow. And the `step_a` output file `stdout.txt` is " "visible in the output of the command above." msgstr "" +"各ワークフローのステップには、一意のID（ハッシュのような長い値）が付与されて" +"います。`${HASH}.status` ファイルは、ワークフローによって実行された各ステップ" +"のステータスを表示します。そして、`step_a` 出力ファイル`stdout.txt` " +"は、上記のコマンドの出力で確認できます。" #: ../../src/topics/troubleshooting.md:48 719917cb0fd849f5a328671df8726189 +#, fuzzy msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3532,8 +3694,16 @@ msgid "" "new cache entry for the output of `step_b`. Also note that the status of " "`step_b` is now of success." msgstr "" +"`step_b` が`rev` を実行するように、タイプミスを修正します（すなわち、`step_b`" +" の`revv` を`rev` " +"で置き換えます）。タイプミスを修正した後、前回と同じ引数で`cwltool` " +"を実行すると、`cwltool` の出力に、`step_a` " +"の出力が事前にキャッシュされていることと、`step_b` " +"の出力の新しいキャッシュ・エントリーがあることがわかります。また、`step_b` " +"のステータスは、現在、成功であることに注目してください。" #: ../../src/topics/troubleshooting.md:59 2a9dbb3ad7564f5aa103349c45ee7925 +#, fuzzy msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3542,6 +3712,11 @@ msgid "" " troubleshooting your CWL documents and also as a way to prevent " "`cwltool` to re-evaluate steps unnecessarily." msgstr "" +"この例では、ワークフローのステップ`step_a` はキャッシュされていたため再実行さ" +"れず、その実行や出力に変化はありませんでした。さらに、`cwltool` " +"は、実行ファイル名を修正した後、`step_b` を再実行する必要があることがわかりま" +"した。このテクニックは、CWL文書のトラブルシューティングに役立つだけでなく、`c" +"wltool` が不必要にステップを再実行するのを防ぐ方法としても有効です。" #: ../../src/topics/using-containers.md:1 7439fe097aa4459ba1e4c0e28fc59b9a msgid "Using Containers" @@ -3690,19 +3865,28 @@ msgid "`echo-uppercase-single-file.cwl`" msgstr "`echo-uppercase-single-file.cwl`" #: ../../src/topics/workflows.md:150 5a9a1dd6ed1f4ca6803f1d235c4fd392 +#, fuzzy msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " "There are other ways to combine multiple files into a single file (e.g. " "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" +"ファイルを分けることは、モジュール化やコードの整理に役立ちます。しかし、開発" +"のためにすべてを1つのファイルに書いておくと便利なことがあります。複数のファイ" +"ルを1つのファイルにまとめる方法は他にもあります（例：`cwltool --pack` " +"）このユーザーガイドの他のセクションで詳しく説明します。" #: ../../src/topics/workflows.md:160 277ed30d4b3a4156a4523e8d10e6ce60 +#, fuzzy msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" +"サブワークフローでは、Requirement、`SubworkflowFeatureRequirement` を有効にす" +"る必要があります。このユーザーガイドの別のセクションで、より詳しく説明してい" +"ます。" #: ../../src/topics/workflows.md:165 82818ab17aa4403eb982fd81a14a5865 msgid "Writing Workflows" @@ -3914,6 +4098,7 @@ msgstr "" "）と出力（`compiled_class` ）は、ステップの入力/出力になるようにマッピングすることができます。" #: ../../src/topics/workflows.md:336 d621821d2c1b403cb7415b381dd883f6 +#, fuzzy msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3921,8 +4106,13 @@ msgid "" " reused in multiple parent workflows, or even in multiple steps within " "the same workflow." msgstr "" +"`1st-workflow.cwl` はワークフロー入力でパラメータ化されているため、" +"実行時には tar ファイルと`*.java` ファイル名を示すジョブファイルを提供する必" +"要がありました。これは、複数の親ワークフローや、同じワークフロー内の複数のス" +"テップで再利用できることを意味するため、一般的にベストプラクティスです。" #: ../../src/topics/workflows.md:341 358c612f175241f7bf148a04d75e00c9 +#, fuzzy msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3931,6 +4121,11 @@ msgid "" "have more specific input/output names, as those also appear in its usage " "as a tool." msgstr "" +"ここでは、`default:` を使って、`\"Hello.java\"` を`name_of_file_to_extract` " +"input として固定しています。しかし、このワークフローでは`tarball` の tar " +"ファイルも必要です。これは`create-tar` ステップで用意します。この時点で" +"、`1st-workflow.cwl` 、より具体的な入力/出力名を持つようにリファクタリングす" +"るのがよいでしょう。これらは、ツールとしての使用法にも現れるからです。" #: ../../src/topics/workflows.md:347 c6297c120e004ae8b52d5b519fbc04d2 #, fuzzy @@ -4358,6 +4553,7 @@ msgid "Arrays" msgstr "配列" #: ../../src/topics/yaml-guide.md:129 5aca9a90fb6149529ed717992746a2f3 +#, fuzzy msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -4367,6 +4563,12 @@ msgid "" "this with an _array_, where each value is defined on its own line and " "preceded by `-`. For example:" msgstr "" +"ある状況下では、1つのキーに対して複数の値やオブジェクトを提供する必要がありま" +"す。上記の[Maps](#maps)のセクションですでに見たように、1つのキーに複数のキー" +"と値のペアをマッピングすることができます。しかし、各値にユニークなキーを用意" +"しなくても、キーに対して複数の値を定義することも可能です。この場合、_array_ " +"を用いて、各値を独自の行で定義し、その前に`-` " +"を置くことで実現できます。例えば、次のようになります：" #: ../../src/topics/yaml-guide.md:146 d1c9e72e004b4fb4a6efb7748a15ab6f #, fuzzy @@ -4629,4 +4831,3 @@ msgstr "[CWLでrnaseq](https://arvados.github.io/rnaseq-cwl-training/)" #~ " file from its leading directory " #~ "path." #~ msgstr "" - diff --git a/locales/zgh/LC_MESSAGES/sphinx.po b/locales/zgh/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..fa449b56 --- /dev/null +++ b/locales/zgh/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: zgh\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "" diff --git a/locales/zgh/LC_MESSAGES/user_guide.po b/locales/zgh/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..702fb704 --- /dev/null +++ b/locales/zgh/LC_MESSAGES/user_guide.po @@ -0,0 +1,3125 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: 2023-12-24 21:09+0000\n" +"Last-Translator: ⵣⵓⵀⵉⵔ ⴰⵎⴰⵣⵉⵖ ZOUHIR DEHBI \n" +"Language-Team: Tamazight (Standard Moroccan) \n" +"Language: zgh\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 5.4-dev\n" + +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "ⵜⵓⵔⴰⴳⵉⵏ" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 4dee8504a8e5496081dadc386ab45540 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 674c238b25e240eda05e22e399f2f78f +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: b651f80f47b4442fbf29454a233697fc +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: ecf2b9c0b1664afe9c4e180610610021 +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: e24cb13d98014e558b6a6946758359e0 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: 928e3df7ca3e479ca6474a8e72cf36eb +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: d355f035676446c88b028f327aeb4829 +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 339b852df24242189d6efcd2898a3396 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: 3ef57e6862f240bebcf193a52397af0a +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: fae385da16aa443da996fa23ac03d6ae +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: 92430be71ecc40e18bbbb80d5576c613 +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 387d83db81024f65aa9a890c2d07874a +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: d8e2280a75a74916a1630afaa2fe2ae3 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: f1c1340f9745458980e0fbd641738687 +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 5424e5472c3d466fa2a3d2022c6cb475 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: 12f57b2ba76b492abe1816e06bfb1417 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: e1f657a46ce94a0d83671540e2cc2dab +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a5eacdbc9aa142c890b177869da4143d +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: e3bdaceae8784ab0807b2cf356a98580 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: ed521ac365db4a6ba5a1051fbaa2932e +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 67573252cc064b27ab13eebc468ac58a +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 73e68b3af9cf41338d843c0c40e50cdc +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: a999b1acda2641598086648c64aa3831 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: f8c12a58cb0b46a488823c6ae95f25ea +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: f25a63e0926d4932bbe64b2e4bdabf9e +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: d718630a296545f3a989c8c71e9ddc77 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 9a97acd430064710bcdf76edbd9f711c +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: 48deb71f361a43e48a56ed483075bca8 +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 716b56506ca7470299899c5d820a9ea2 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: e3ecac0a8e604f2b98a2a12b0579990a +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 007a345b4bad49cf996c4301b8386473 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: efb5fd14988c4e2a8f834ee5369d4102 +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: 276f688ba7cc471a842f085ca852b1d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 8b70a1ad70514039b97164fa630c12e4 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 2f28ab412d2843ffa5f14acdc01fc732 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: cbec9277b5004e50af2728cbda0df740 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: e259f55f8000479bbd8009e25cf0ca6c +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 8210b36347a749889450529ecdf4ff0e +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 23088850ad02459696f6bbd385109aac +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: f02257a822ad46ac93c5981531cc85d5 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: d289541e460147aa933f7878996f8649 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: f495da32f05a4a5ba9539be0a54c1a59 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: bdb4c68a175047ddbe141ca24960127f +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 97b61352363f47cb890e8937c5613fa3 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: 0bc424ef2ca346099f29b937379908a0 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 29b73e1dd72744f68377f0a38c10f062 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 38a2afaf4a6c4d04909af22c93f2808d +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: cd74f34b21af4de9be96fd897efc469b +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: f12e371f3f1a4b0cb2cff9800352d48c +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 8f0e8f050e334ac08334e9215e1dcf61 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 7a6be0005a6441feb67f036d005d7885 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 06635145b441418aaae84dc804f3d6ac +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 04eaf1f7c630450db318dcd8b7626e15 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: fd4579a3c9844492b314b5c3c1775fc7 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: e024bcb70e04412e90e1838426d1b69a +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: a3db21c0b3114802a8a5b610e252ef13 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 0f5bc8520d6a4dafa37c65343da9702a +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 5cb830da47464a8b9c3950983fa4d56f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: a2ce43b391864e8bbde16328cc19b32b +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 56ee4dcfff6141d5bef80eb96559876d +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 96671c56523c4ea9992fb5dfcfa6490e +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: bcc6246742cb46bfb185e415c4a3431a +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 86dce36de687449c88fb5eb9d64eb045 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 7dc630ea86464b1dba3a4e5079260b3b +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: 651e032007ea4a119d20c820bb61f86b +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 0b056dde9e87428996e47870b12119da +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 628124a1670b4b058bb0fb6e495a099c +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: ec2adb3912bc46e28891229e9e0d9a1c +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: a519be60726a44af9941fdce04735353 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: cb8fc8c4c79e467eac5fab4ca685201e +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: a26cc105716f47cb807174c9003153b0 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: cc159dd5fe5748caac838862f5b8c4d1 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 6812698e9ad84d3385de5e88e9dde0b3 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: d1f02be278754267893dfce5a940997d +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: 75d59e395c66416cae9b352db5081516 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 874c6f19abbf45d7ab7d30a378c4048d +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: dea0d4b681f94e73b13965dcfe75cf7d +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: 750474486a84482292eeba45f118287f +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 1eb0e39bb6d04b8cab300f44a79f3add +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 4b2ab812f62c4f949dd25c8527f2411c +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 2c3b884cb1c54521900cc90782e8a58d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: a1073b6306044dffb414319ae01f68bb +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: 9a1d92334685449386dfa3b3a899ed48 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: fb623af4c480411b8fde28d01c981411 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: e98e165f6bba40809c90473d72f9d592 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 5565c1b2d8a349169a305a9b26b4574d +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: 88160cef4cfa4add9020aa89511a5749 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 730ba1434a1445ae847ec6153b6a3b72 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: a25d0b1e13324b40a6b8fcd227948c4f +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: d661df070e3040869da412d07a71f716 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: a11585474d3849cca5467512ed964743 +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 2682f9ca8e604a0c9986f7746fdec960 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 22447a560f6f4317bf67bd7c4336126c +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 52703d6b7f914097934bfad13663abeb +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 5e1c79df657d4a6e84e055dd6b300a5d +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 329d2809dfae4f90bc638f5f03a47ee3 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 9647019d8c37466886e7aab6f176634d +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: cc067051f22f433bbece08f60933e002 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: dbfe2c1123144316aa026374b0f353d3 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: 074cf5d912854d8c864607cc24b15302 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: b54240bb94f746bba7511633aa969db0 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 8b70a072aa87414c88e89a3e19af0a51 +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: eea20f89c45f424a888178df53713b28 +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7647e0229a924f988cf02b7812a55c06 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 9d663249666045618a0d3acddb85a9a9 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: dbf6153cd02542a6a01c172803122b7f +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: b6250cf6fa8a4a0c94b33302e0decca5 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: fa6ca3bbc6784380a03a950a6f49a180 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: b92b516e537a4773ad67b4af586e7a25 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: 467a701228504d06b971b79a59c69064 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: 2634f989eb304009a8568d70ed42786c +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: fbe0c65b444441f785d0054176d036a6 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 9a710602e00c4934ae3a3b471aa68458 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: 21b5be7270a14f0987240c81d1ec879b +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: cfe9d8241fe84bd5b74042a5625d933f +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 764d933cc4da446abd8dd8f913f05dac +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: c93efc6d4e004859981ee7f5fa28ed03 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: 546601da44cb49bd9611b1c85807fd90 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: e07f33d01b804663a25ffb08aad74821 +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: 7a644506619a4f08958ec7d4540cd557 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: b5195b7d8eaa419fb2b90cb33a57783a +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: 2713594c937d4c528fc8d04d9e9819ed +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: cf94c1424fc2413c85647fd1ee73d951 +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: dc0452107c604e29bdf32bb289fe5db8 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 483181f498fc4d968b5fe6ef427709f7 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 7487485d6aa4458089a4b4bdf107ea64 +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 93188ed43ee949cc98b3ea679ce14feb +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 24aca0bea4d94e3593b844cf0586cffe +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 9c56528acd5f49deb139e034dfbfac7c +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: a2dd833fdca4443181648e41051a5232 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: 7e40cc9f9e1341c195e843c009575b94 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: def35d6021394def80a53ae49a2cdbde +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: c84d4450bc6a475dbf34e0b22cea9130 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: cca9665f6daa44b49233baf34ab9fcc7 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: 547edbf5fa424b8286cc21674ff159b0 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 7ca248888b9d484cb544cd76ba538662 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: ae6b240718104380b08db5552d7355ea +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: e5a8b7f84be64020b191099f3fad30ed +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 12a06d8358534102b202965d4258c18e +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: b7f93705e5b8416696be01850072e8c0 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: e87045829b344089ab59dc27063ddd7a +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: 42ef2f145b824d69b63abc1da175c216 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: c61cedf543664d388183e04b3939cc39 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: 9e39e3f1501c4fcaab3e8962e090f6be +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: 03e2f767c4da461982fc3c0f3ba94762 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 3bea5822b8694e2aa32c446e1c54a045 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: 0d498cd4caf54c15891ca1afe58e2727 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: b2d75045e02741b4850f5ff1243f7858 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: 5fa79c62049a447c8328ebf9db54ebf4 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: d947c54933d64aad90df392a1cedd63f +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 651d35997332404186aa6d5711da4a3d +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: b662c1a5a4424c8d8350a806356acc61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 04d6babfd87343d7a5f13867ea02b65f +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 2eaacf1a90204a2b9bd621344560f2a1 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: e3a7182f00f440b8b5461da91194a64b +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: b5338f39e8c74ff28e139da68089a742 +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: f6d92156d67c4a339bcfd194cff897df +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: d80ab383eec9402faba997b548fe42eb +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: 49217c02f58c43ff9ec00f10da8d4e84 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 8dbd56473f8c40c0bb12a48be06117e3 +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 78d7f3ede2c746d482042adef050b2c4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: cbbf93c70fe04ba7932ba25758ddc611 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: cfa1c1fde4454df283f87cc54a9c59ec +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 1a8be2950cbb475bbb2617e005f0fac9 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: 5d83c56102e141cc978500f678dd0c1c +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: cda73485875d4c8e9464679a20558616 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 98cae24919b74c088a5d89706aec581b +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: b4b0940b4b5743c09637b36b964202d0 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 9ca3554d771d45998e88aaede525b227 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 3fca839cede94cfd8e4f605c73ba699d +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: 3ded0f125249485c921994b6e6b93ac9 +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 53ece35d309a4c8d99f1efb2122a7092 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 87bafb845c714b109874f6137b84462d +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: fcd05b1ef31a4046946a2399c7fc5575 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: 859368c1f25c4a4aad57abfd046c63f5 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index e55e61c3..e0316d50 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -9,15 +9,16 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2023-07-05 09:51+0000\n" -"Last-Translator: Michael Crusoe \n" +"PO-Revision-Date: 2024-01-27 01:01+0000\n" +"Last-Translator: Zoë Ma \n" +"Language-Team: Chinese (Simplified) \n" "Language: zh_Hans\n" -"Language-Team: Chinese (Simplified) " -"\n" -"Plural-Forms: nplurals=1; plural=0;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=1; plural=0;\n" +"X-Generator: Weblate 5.4-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -3397,12 +3398,11 @@ msgid "" "enable these checks with the reference implementation, use the " "[dependency resolvers configuration][dependencies]." msgstr "" -"您的 CWL " -"运行程序有可能支持在运行作业之前，根据提示检查所需软件是否已安装就绪。如果要让参考实现启用这些检查，请使用[依赖项解析配置][dependencies]。" +"您的 CWL 运行程序有可能支持在运行作业前根据提示检查所需软件是否已安装就绪。如" +"果要让参考实现启用此类检查，请使用[依赖项解析配置][dependencies]。" #: ../../src/topics/specifying-software-requirements.md:29 #: 1a8b8aadf1c64e87b8b670e288bc14bc -#, fuzzy msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -3418,11 +3418,15 @@ msgid "" "preference, are to include the DOI for the main tool citation and the URL" " to the tool." msgstr "" -"除了版本号之外，该工具的唯一资源标识符 (URI) 以 [RRID][rrid] 的形式给出。可以在 [SciCrunch][scicrunch]" -" 注册表中查找具有 RRID 的资源，该注册表提供了一个用于查找、跟踪和一致引用科学资源的门户。如果要将工具指定为 " -"`SoftwareRequirement`，请在 SciCrunch 上搜索该工具并使用在注册表中分配的 RRID。 （按照 [添加资源教程" -"][scicrunch-add-tool] 将工具添加到 SciCrunch）。您可以使用此 RRID 在需求描述的 `specs` " -"字段中引用该工具（通过 [identifiers.org][identifiers]）。其他不错的选择（按优先顺序）包括主要工具引用的 DOI " +"此处我们不仅给出了工具的版本号，还以 [RRID][rrid] " +"的形式给出了该工具的统一资源标识符 (URI) 。查找以 RRID 标识的资源可以使用 " +"[SciCrunch][scicrunch] " +"注册表。该信息门户网站可供查询、跟踪和一致引用科学资源。如果要将工具指定为 " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#SoftwareRequirement)，请在 SciCrunch 上搜索该工具并使用在注册表中分配的 " +"RRID。 （按照 [添加资源教程][scicrunch-add-tool] 将工具添加到 SciCrunch）。" +"您可以使用此 RRID 在需求描述的 `specs` 字段中引用该工具（通过 [identifiers." +"org][identifiers]）。其他不错的选择（按优先顺序）包括主要工具引用的 DOI " "和工具的 URL。" #: ../../src/topics/staging-input-files.md:1 d10c792550e8498c8ee384d3093da306 @@ -4374,4 +4378,3 @@ msgstr "" #~ " only part that is really new " #~ "is the `dockerRequirement` section." #~ msgstr "" - From 68ed6645d008b45151273b712ebf84c1ab1ba454 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Fri, 9 Feb 2024 15:23:32 +0100 Subject: [PATCH 123/179] Translated using Weblate (Japanese) (#453) Currently translated at 53.9% (323 of 599 strings) Translated using Weblate (Japanese) Currently translated at 52.2% (313 of 599 strings) Translated using Weblate (Japanese) Currently translated at 52.0% (312 of 599 strings) Translated using Weblate (Japanese) Currently translated at 51.9% (311 of 599 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 158 ++++++++++++++++++++++++--- 1 file changed, 144 insertions(+), 14 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 2aa1d64d..42482185 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-01-31 06:01+0000\n" +"PO-Revision-Date: 2024-02-09 14:02+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -117,13 +117,16 @@ msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 #: 08aa9181d5304e0fa96b28db15718559 d37fc100eb6948bba8b5e757574b2aaf #: ecdd0f28d5b048d69dd1ffae2fa1f6c0 -#, fuzzy msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" " of software, tools and workflows described using CWL are portable across" " a variety of platforms that support the CWL standard." -msgstr "CWLは、コマンドラインツールを定義し、それらを結びつけてワークフローを作成するための方法です。CWLは仕様であり、特定のソフトウェアではないため、CWLを使用して記述されたツールやワークフローは、CWL標準をサポートするさまざまなプラットフォームで利用可能です。" +msgstr "" +"CWLは、コマンドラインツールを定義し、それらのツールを繋げてワークフローを作成" +"するための方法です。CWLは仕様であり、特定のソフトウェアではないため、CWLを使" +"用して定義されたツールやワークフローは、CWL標準をサポートするさまざまなプラッ" +"トフォームで利用可能です。" #: ../../src/episodes.md:5 ../../src/setup.md:5 #: 1361ff6bf4924efc9ce9a85785a6b381 eb254514301c491e81f72ae19c407261 @@ -144,14 +147,12 @@ msgid "FAQ" msgstr "よくある質問" #: ../../src/faq.md:11 370a9659c7904ef6b5e1ae7480f82ef6 -#, fuzzy msgid "How do I create non \"`File`\" types using `evalFrom`?" msgstr "\"`File`\" 型をつかわず `evalFrom`を使う方法" #: ../../src/faq.md:41 8333f51e3f5945fe8963adfc6685bcb1 -#, fuzzy msgid "How do I rename an input file?" -msgstr "入力ファイルの名前を変更する" +msgstr "入力ファイルの名前を変更するにはどうしたらよいですか？" #: ../../src/faq.md:43 f6b88d9154d049d7807afa9bb0f1ac98 msgid "" @@ -162,9 +163,8 @@ msgid "" msgstr "この例では、ツール定義の一部として、入力ファイルの名前を変更する方法を説明します。これは、ワークフローの別のステップで作成されたファイルを使用する場合に、これらのファイルが作成されたときに与えられたデフォルトの名前を使用して作業したくない場合に便利です。" #: ../../src/faq.md:59 833510f5896b4a6eb5875d25eca5b047 -#, fuzzy msgid "How do I rename an output file?" -msgstr "出力ファイルの名前を変更する" +msgstr "出力ファイルの名前を変更するにはどうしたらよいですか？" #: ../../src/faq.md:61 207e2f97d1c44233ae3f109c5a6ec944 msgid "" @@ -178,25 +178,27 @@ msgid "" " engines will rename the file using the new name for subsequent steps or " "as a workflow-level output." msgstr "" +"`outputEval`フィールドの`basename`フィールドを変更することで、CWLワークフロー" +"エンジンは、後続のステップまたはワークフローレベルの出力として、新しい名前を" +"使用してファイル名を変更します。" #: ../../src/faq.md:86 8641f105131b4ac1bca7e0a46756ef79 -#, fuzzy msgid "How do I reference a local script?" -msgstr "ローカルスクリプトを参照する" +msgstr "ローカルスクリプトを参照するにはどうしたらよいですか？" #: ../../src/faq.md:88 d3e43b40d6994b32bc37067ee116418e msgid "There are two ways to reference a local script:" msgstr "ローカルスクリプトを参照するには、2つの方法があります：" #: ../../src/faq.md:90 64b140a321ca4087945339c523cc24dd -#, fuzzy msgid "" "The first method involves adding the path to a folder containing your " "scripts to the `PATH` environment variable. This allows you to execute " "the shell script directly (without explicitly using the `sh` or `bash` " "commands)." msgstr "" -"最初の方法は、スクリプトの入ったフォルダを`PATH` 環境変数に追加する方法です。これにより、`sh` や`bash` " +"最初の方法は、スクリプトの入ったフォルダを " +"環境変数`PATH`に追加する方法です。これにより、`sh` や`bash` " "コマンドを使用せずに、シェルスクリプトを直接実行することができます。" #: ../../src/faq.md:93 34ebca4487a54ceab5d087105820e945 @@ -223,11 +225,11 @@ msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "これで、`baseCommand: scriptname.sh` を使って、スクリプトを直接実行できるようになりました。" #: ../../src/faq.md:117 844938d5d2304c6cb03184b4b4b0b024 -#, fuzzy msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." -msgstr "後で作ったものを共有したいときは、スクリプトをDockerコンテナに入れることができます。" +msgstr "後で作ったものを共有したいときは、スクリプトをDockerコンテナに入れることがで" +"きます。" #: ../../src/faq.md:119 796ce8155e32486d9651f8f13bfa3148 #, fuzzy @@ -1614,6 +1616,7 @@ msgstr "" "の下に、このツール定義で動作することが確認されているツールのバージョンのリストを含めるます。" #: ../../src/topics/best-practices.md:58 88806cb0462f4359801c1fa0ff0ebcc0 +#, fuzzy msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1624,6 +1627,14 @@ msgid "" "ontology/controlled vocabulary in the same way. Please edit this page to " "let us know about it." msgstr "" +"`format` は、すべての入力および出力`File`に指定する必要があります。バイオイン" +"フォマティクスツールは、[EDAM][edam-" +"example]のフォーマット識別子を使用するのが良いです。`iana:text/plain`,`iana:" +"text/tab-separated-values`、`$namespaces：{ iana: \"https://www.iana.org/" +"assignments/media-types/\" }もご参照ください`.[IANA メディアタイプ一覧][iana-" +"types]（MIME タイプとしても知られています）。バイオインフォマティクス以外のツ" +"ールについては、同様に適切なオントロジー/統制語彙を使用または構築してください" +"。このページを編集して私たちに知らせてください。" #: ../../src/topics/best-practices.md:66 b178c7296ed5491782a4180c76883c14 #, fuzzy @@ -1947,6 +1958,7 @@ msgstr "" "で、テーブル変換で使用できるテーブルオプションのリストがカスタムオブジェクトとしてインポートされます：" #: ../../src/topics/custom-types.md:46 c791096f537141e8bd7cc941d711d108 +#, fuzzy msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1956,6 +1968,14 @@ msgid "" "`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" " to create an OTU table in hdf5 format." msgstr "" +"カスタムタイプの参照は、そのオブジェクトが定義されているファイル名（`biom-" +"convert-table.yaml` " +"）と、カスタムタイプを定義するそのファイル内のオブジェクト名（`table_type` " +"）を組み合わせたものです。この場合、インポートされた`biom-convert-table.yaml`" +" ファイルからの`symbols` " +"配列が、許容されるテーブルオプションを定義します。例えば、`custom-types.yml` " +"では、`OTU table` を`input` として渡し、hdf5 形式の OTU table " +"を作成するようツールに指示しています。" #: ../../src/topics/custom-types.md:53 5f6bc6ed72334a74b9a4c46c29ddda46 msgid "The contents of the YAML file describing the custom type are given below:" @@ -2827,6 +2847,13 @@ msgid "" "broken using the parameter name), and the position field itself is " "optional. The default position is 0." msgstr "" +"`position` の値は、パラメータがコマンドライン上のどこに表示されるかを決定する" +"ために使用されます。 " +"Positionは、絶対的なものではなく、互いに相対的なものです。 そのため、位置は" +"連続である必要はなく、1、3、5の位置にある3つのパラメータは、1、2、3と同じコマ" +"ンドラインになります。 複数のパラメータが同じ位置を持つことも可能です（パラ" +"メータ名で紐付けを行います）。また、位置フィールドは任意です。 " +"デフォルトの位置は0です。" #: ../../src/topics/inputs.md:142 7513adabd3ae4701b17f578ac9f321d7 msgid "" @@ -3024,6 +3051,7 @@ msgstr "" "に変更すると、コマンドラインやジョブ入力ファイルで何も指定されていない場合にデフォルト値を持つようになります。" #: ../../src/topics/inputs.md:295 b5055c77f85e43609fe3e9b9839778e3 +#, fuzzy msgid "" "Here, the boolean “or” operator `||` in JavaScript is used for its " "_short-circuiting_ property. If `inputs.file_format` is “true” in a " @@ -3033,6 +3061,12 @@ msgid "" "expression’s value becomes that of the second operand, which is why a " "reasonable default can be provided there." msgstr "" +"ここでは、JavaScriptのブール値 \"or\"、 \"演算子 `||` は、その_short-" +"circuiting_プロパティに使用されます。`inputs.file_format`がブール値の \"true " +"\"である場合（例えば、列挙された有効な空でない文字列）、式の評価は`||`の最初" +"のオペランドで停止します。しかし、`inputs.file_format`が`null`の場合、式全体" +"の値は2番目のオペランドの値になります。これにより合理的なデフォルト値を提供し" +"ます。" #: ../../src/topics/metadata-and-authorship.md:1 #: 723c2232310c4276aeac2bd6728d2912 @@ -3053,6 +3087,15 @@ msgid "" "anywhere in the document as shown below. Otherwise, one must use full " "URLs: `format: http://edamontology.org/format_2572`." msgstr "" +"正しい実行に必須でない実装拡張（例えば、GUI表示に関するフィールド）およびツー" +"ルまたはワークフロー自体に関するメタデータ（例えば、引用で使用するための著者" +"名）は、任意のオブジェクトの追加フィールドとして提供できます。このような拡張" +"フィールド（例：`format: edam:format_2572` ）は、[Schema Salad仕様][schema-" +"salad]で説明されているように、文書の`$namespaces` セクション（例： edam: " +"http://edamontology.org/%20%EF%BC%89%E3%81%AB%E8%A8%98%E8%BC%89%E3%81%95%E3%82%8C%E3%81%A6%E3%81%84%E3%82%8B%E5%90%8D%E5%89%8D%E7%A9%BA%E9%96%93%E3%83%97%E3%83%AC%E3%83%95%E3%82%A3%E3%83%83%E3%82%AF%E3%82%B9%E3%82%92%E4%BD%BF%E7%94%A8%E3%81%A7%E3%81%8D%E3%81%BE" +"す。一度名前空間プレフィックスを追加すれば、以下のように定義内のどこにでもア" +"クセスできるようになります。それ以外の場合は、完全なURLを使用しなければなりま" +"せん。`format: http://edamontology.org/format_2572`." #: ../../src/topics/metadata-and-authorship.md:13 #: 368f8993ae9d401488081d74ae5acd49 @@ -3738,6 +3781,14 @@ msgid "" " management while avoiding the complexity of invoking and managing Docker" " containers." msgstr "" +"[Docker][docker]コンテナは、ソフトウェアとその依存関係のための完全な既知の良" +"いランタイムを提供することによって、ソフトウェアのインストールを簡素化します" +"。 しかし、コンテナはホストシステムから意図的に隔離されているため、Dockerコ" +"ンテナ内でツールを実行するには、入力ファイルがコンテナ内で利用可能で、出力フ" +"ァイルがコンテナから回収できることを確認するための追加作業が必要です。 CWLラ" +"ンナーはこの作業を自動的に行うことができるため、Dockerコンテナの呼び出しや管" +"理の複雑さを回避しながら、Dockerを使用してソフトウェア管理を簡素化することが" +"できます。" #: ../../src/topics/using-containers.md:15 4b0f6cfc8a774c77bfbc99e568af2ece #, fuzzy @@ -3774,6 +3825,7 @@ msgstr "" "この大部分は以前のセクションで説明したもので、本当に新しいのは`dockerRequirement` の部分だけです。" #: ../../src/topics/using-containers.md:44 1f02618ab6254459ae71f72844e3cc18 +#, fuzzy msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3785,6 +3837,15 @@ msgid "" "best practices when using containers for reproducible research). In this " "case we have used a container called `node:slim`." msgstr "" +"`baseCommand: node` は、Javascript ファイル用の Node Js " +"ランタイムを使用してこのコマンドを実行することを CWL " +"に指示します。次に、必要なコンテナを見つける方法について、`hints` " +"をいくつか指定する必要があります。 この場合、`DockerRequirements` に docker " +"コンテナに関する要件だけを列挙します。 ` dockerPull:` パラメータは、`docker " +"pull` コマンドに渡すのと同じ値を取ります。つまり、コンテナイメージの名前です" +"（タグを指定することも可能で、再現可能な研究にコンテナを使用する際のベストプ" +"ラクティスに適しています）。この場合、`node:slim` " +"というコンテナを使用しました。" #: ../../src/topics/using-containers.md:52 54cade4978ec463bbb5c0d8c08e27adb msgid "" @@ -3987,6 +4048,7 @@ msgstr "" "ステップの出力パラメータ`classfile` を、ワークフロー出力パラメータ`compiled_class` に接続します。" #: ../../src/topics/workflows.md:248 e0429688fce445da8083e69323e5b020 +#, fuzzy msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3996,6 +4058,13 @@ msgid "" "`source`). In addition, workflow steps which do not depend on one " "another may run in parallel." msgstr "" +"`steps` セクションでは、ワークフローの実際のステップを説明しています。 " +"この例では、最初のステップで tar ファイルからファイルを抽出し、2 " +"番目のステップで java コンパイラを使用して最初のステップで抽出されたファイル" +"をコンパイルしています。ワークフローのステップは、必ずしもリストされた順序で" +"実行されるわけではなく、ステップ間の依存関係によって順序が決定されます（`sour" +"ce` を使用）。 また、互いに依存しないワークフロー・ステップは、並行して実行" +"されることがあります。" #: ../../src/topics/workflows.md:256 980f5eada57c4fadbb783838ded1fa0b #, fuzzy @@ -4010,6 +4079,7 @@ msgstr "" "と1つの出力パラメータ`extracted_file` を持ちます。" #: ../../src/topics/workflows.md:261 3532e165842f4ebb8db0c78208071555 +#, fuzzy msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -4018,6 +4088,13 @@ msgid "" "`name_of_file_to_extract` will be used for the parameters `tarfile` and " "`extractfile` in order to run the tool." msgstr "" +"ワークフローステップの``in`` " +"セクションは、これらの2つの入力パラメータを、`source` " +"を使用してワークフローの入力である`tarball` および`name_of_file_to_extract` " +"に接続しています。 つまり、ワークフローステップが実行されると、`tarball` " +"と`name_of_file_to_extract` " +"に割り当てられた値が、ツールを実行するために`tarfile` と`extractfile` " +"のパラメータに使用されることになり ます。" #: ../../src/topics/workflows.md:267 04a4db2f3da94ce29e7999039ee13fde #, fuzzy @@ -4027,6 +4104,7 @@ msgid "" msgstr "ワークフローステップの`out` セクションには、ツールから期待される出力パラメータが記載されています。" #: ../../src/topics/workflows.md:278 2651ee113a3d4b79b138854ebe729f48 +#, fuzzy msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -4035,6 +4113,12 @@ msgid "" "and-parameters.md)). The output of this step `classfile` is connected to " "the `outputs` section for the Workflow, described above." msgstr "" +"第2ステップ `compile` は、第1ステップの結果に依存し、入力パラメータ`src` " +"を`untar` の出力パラメータに接続し、`untar/extracted_file` を使用します。 " +"これは、`arguments.cwl` (以前に [追加の引数とパラメータ](additional-" +"arguments-and-parameters.md)で説明) " +"を実行します。このステップの出力`classfile` は、前述のワークフローの`outputs`" +" セクションに接続されています。" #: ../../src/topics/workflows.md:285 177040bf9c0045f2878f42bcdd8cbd2d msgid "Nested Workflows" @@ -4084,6 +4168,16 @@ msgid "" "/common-workflow-language/user_guide/blob/main/_includes/cwl/workflows" "/1st-workflow.cwl\" alt=\"Visualization of 1st-workflow.cwl\" />" msgstr "" +"\"Visualization \"Visualization" #: ../../src/topics/workflows.md:322 7ce847ab54224452b6425de2a55ec893 #, fuzzy @@ -4185,6 +4279,7 @@ msgid "Scattering Steps" msgstr "Scatter ステップ" #: ../../src/topics/workflows.md:400 eab4437bf9994b649954221375e3dd6d +#, fuzzy msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -4194,6 +4289,12 @@ msgid "" "allows you to run the same workflow on multiple inputs without having to " "generate many different commands or input yaml files." msgstr "" +"ワークフローの書き方がわかったので、`ScatterFeatureRequirement` を利用し始め" +"ることができます。この機能は、ツールやワークフローを入力のリストに対して複数" +"回実行したいことをランナーに伝えます。ワークフローは、入力を配列として受け取" +"り、配列の各要素に対して、あたかも1つの入力であるかのように、指定されたステッ" +"プを実行します。これにより、多くの異なるコマンドや入力 yaml ファイルを生成す" +"ることなく、複数の入力に対して同じワークフローを実行することができます。" #: ../../src/topics/workflows.md:411 c245ba0ae2074fa388ad6c35695033c8 msgid "" @@ -4307,6 +4408,7 @@ msgid "`scatter-two-steps.cwl`" msgstr "`scatter-two-steps.cwl`" #: ../../src/topics/workflows.md:497 122452b7d7114c3fa53cbea286703023 +#, fuzzy msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -4323,6 +4425,18 @@ msgid "" "the first step must wait on `echo Hallo welt!`. You can see how this " "might not scale well." msgstr "" +"ここでは、各ステップの下にscatterフィールドを配置しました。この例では素早く実" +"行されるので問題ありませんが、より複雑なワークフローのために多くのサンプルを" +"実行する場合は、別の方法を検討することをお勧めします。ここでは、各ステップで" +"独立してscatterを実行していますが、2番目のステップはすべての言語を完了する最" +"初のステップに依存していないため、scatter機能を効率的に使用することはできませ" +"ん。第2ステップは第1ステップからの入力として配列を期待するので、何かをする前" +"に第1ステップのすべてが終了するまで待つことになります。`echo Hello World!` " +"の実行に1分、出力の`wc -c` に3分、`echo Hallo welt!` の実行に5分、出力の`wc` " +"に3分かかると仮定してください。`echo Hello World!` " +"が4分で終了しても、最初のステップは`echo Hallo welt!` を待つ必要があるので、" +"実際には8分で終了することになります。このように、うまくスケールしないことがお" +"わかりいただけると思います。" #: ../../src/topics/workflows.md:509 85dd63daf04546b78bdcb68c1d985fa9 msgid "" @@ -4524,6 +4638,7 @@ msgid "Maps" msgstr "マップ" #: ../../src/topics/yaml-guide.md:81 aedf8c4f615845ad91a7947217005d6e +#, fuzzy msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -4533,8 +4648,15 @@ msgid "" "the key to which they belong (the \"parent\"), and should be indented " "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" +"CWLでツールやワークフローを定義する場合、通常、より複雑で入れ子の表現を構築す" +"る必要があります。_maps_ と呼ばれるこれらの階層構造は、キーの値として追加のキ" +"ーと値のペアを提供することでYAMLで記述されます。これらのペア（「子」と呼ばれ" +"ることもあります）は、属するキー（「親」）の下の新しい行に書かれ、2つのスペー" +"スでインデントされます（⇥タブ文字は許可されていません）。例えば、次のようにな" +"ります：" #: ../../src/topics/yaml-guide.md:104 f0f1f414f74342a89065ba5ded8668e5 +#, fuzzy msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -4546,6 +4668,14 @@ msgid "" " example YAML above, here is a graphical representation of the `inputs` " "object it describes." msgstr "" +"上記のYAMLは、複雑なネストされたオブジェクトの記述を比較的素早く構築する方法" +"を示しています。`inputs` マップは単一のキー、`example_flag` " +"を含み、それ自体が2つのキー、`type` と`inputBinding` " +"を含み、これらの子の1つ、`inputBinding` はさらに2つのキーと値のペア " +"(`position` と`prefix`) を含みます。1つのキーに対して複数の値/キーバリューペ" +"アを提供することについての詳細は、以下の[配列](#arrays)のセクションを参照して" +"ください。上記のYAMLの例と比較するために、`inputs` " +"オブジェクトを図式化したものを示します。" #: ../../src/topics/yaml-guide.md:127 965405e2a45a4cbb8f227bc8ceeb05df #, fuzzy From 41aac65c5cf3d7f011986a24b5702b2279edcbeb Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Wed, 14 Feb 2024 15:10:14 +0100 Subject: [PATCH 124/179] novice tutorial is for novices, not contributors (#456) --- src/tutorials.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tutorials.md b/src/tutorials.md index 113b2368..750e5454 100644 --- a/src/tutorials.md +++ b/src/tutorials.md @@ -6,7 +6,7 @@ This is a list of tutorials provided by the CWL community. Use the `Edit this pa ## Beginner Tutorials -- [Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/) +- [Introduction to Workflows with Common Workflow Language: For novices.](https://carpentries-incubator.github.io/cwl-novice-tutorial/) ## Advanced Tutorials From 63d26c2d828b1458478561ec1ceb02b0e5c16a2f Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Sun, 18 Feb 2024 09:00:07 +0100 Subject: [PATCH 125/179] Translations update from Hosted Weblate (#455) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Translated using Weblate (Chinese (Simplified)) Currently translated at 71.1% (426 of 599 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 69.9% (419 of 599 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 69.7% (418 of 599 strings) Co-authored-by: Zoë Ma Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 55.9% (335 of 599 strings) Translated using Weblate (Japanese) Currently translated at 55.4% (332 of 599 strings) Translated using Weblate (Japanese) Currently translated at 100.0% (2 of 2 strings) Translated using Weblate (Japanese) Currently translated at 55.0% (330 of 599 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-sphinx/ja/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Translation: Common Workflow Language/CWL User Guide: Sphinx --------- Co-authored-by: Zoë Ma Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/sphinx.po | 13 +++--- locales/ja/LC_MESSAGES/user_guide.po | 54 +++++++++++++++++------ locales/zh_Hans/LC_MESSAGES/user_guide.po | 44 ++++++++++++------ 3 files changed, 78 insertions(+), 33 deletions(-) diff --git a/locales/ja/LC_MESSAGES/sphinx.po b/locales/ja/LC_MESSAGES/sphinx.po index e0513de9..0a256b46 100644 --- a/locales/ja/LC_MESSAGES/sphinx.po +++ b/locales/ja/LC_MESSAGES/sphinx.po @@ -8,20 +8,23 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" +"PO-Revision-Date: 2024-02-13 04:02+0000\n" +"Last-Translator: Manabu ISHII \n" +"Language-Team: Japanese \n" "Language: ja\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=1; plural=0;\n" +"X-Generator: Weblate 5.4-dev\n" #: ../../src/_templates/sidebar-nav-bs.html:1 #: d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" -msgstr "" +msgstr "メインナビゲーション" #: ../../src/_templates/sidebar-nav-bs.html:3 #: 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" -msgstr "" +msgstr "セクションナビゲーション" diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 42482185..a6fac25c 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-02-09 14:02+0000\n" +"PO-Revision-Date: 2024-02-18 03:01+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -18,7 +18,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.4-dev\n" +"X-Generator: Weblate 5.4\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -26,7 +26,6 @@ msgid "Licenses" msgstr "ライセンス" #: ../../LICENSE.md:4 9dd9705700664b31a3f296d263b4028b -#, fuzzy msgid "Instructional Material" msgstr "指導資料" @@ -38,6 +37,11 @@ msgid "" "summary of (and not a substitute for) the [full legal text of the CC BY " "4.0 license][cc-by-legal]." msgstr "" +"Common Workflow Languageプロジェクトのすべての説明資料と構造の変更は、[" +"Creative Commons Attribution license][cc-by-human] " +"の下でも利用できるようになっています。以下は、[CC BY 4.0 ライセンスの法的全文" +"][cc-by-legal]を人間が読めるようにまとめたものです（ライセンス全文に代わるも" +"のではありません）。" #: ../../LICENSE.md:12 754f3f54aa4142ef9dac27f508dd0bca msgid "You are free:" @@ -53,7 +57,7 @@ msgstr "" #: ../../LICENSE.md:17 247db3bcc7024c44a044886a29ef1414 msgid "for any purpose, even commercially." -msgstr "" +msgstr "営利目的であっても、いかなる目的であっても。" #: ../../LICENSE.md:19 c04d906124854afc917707b7b4e45bb2 msgid "" @@ -104,6 +108,9 @@ msgid "" "provided by Common Workflow Language project are made available under the" " [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" +"Common Workflow Languageプロジェクトが提供するサンプルプログラムおよびその他" +"のソフトウェアは、特に断りのない限り、[OSI][osi]が承認した[Apache 2.0 " +"license][apache-2.0-license] の下で提供されています。" #: ../../LICENSE.md:51 96f1e5be3e1e48db8d9a4c7693008715 msgid "" @@ -244,19 +251,18 @@ msgid "How can I set `self`-based input bindings for optional inputs?" msgstr "オプショナル入力のために `self`-形式のInput Bindings を設定します" #: ../../src/faq.md:140 6169b7be9af7448abcb57eaf91e1cc91 -#, fuzzy msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -"現在、`cwltool` は、入力バインディングが`self` " -"を使用している場合、見つからないオプション入力に対処することができません。以下は、より洗練された修正を待つ間の回避策の例です。" +"現在、`cwltool` は、入力バインディングが`self` を使用している場合、オプション" +"入力が見つからない事に対処することができません。以下は、より洗練された修正を" +"待つ間の回避策の例です。" #: ../../src/faq.md:165 6c98b7948059411b8e09cf03a552c5ab -#, fuzzy msgid "How can I model a \"one-or-the-other\" parameter?" -msgstr "「一か八か」のパラメータをモデル化する" +msgstr "「一か八か」のパラメータをモデル化するにはどうしたらよいですか?" #: ../../src/faq.md:167 d1424da3f43c4519a4c4735f4a720341 msgid "" @@ -315,7 +321,7 @@ msgstr "" #: ../../src/faq.md:229 2f1bbb611c9c4f80b7ae0566432f2f35 msgid "How do make an input optional? 💯" -msgstr "" +msgstr "入力パラメータをオプショナルにするにはどうしたらよいですか? 💯" #: ../../src/faq.md:231 08a226efe5d141e68215ac77725033db msgid "" @@ -469,7 +475,7 @@ msgstr "" #: ../../src/faq.md:450 61641314d82b43e982e54c64c73232c5 msgid "How do I debug the JavaScript in my CWL tool?" -msgstr "" +msgstr "CWLツールのJavaScriptをデバッグするには?" #: ../../src/faq.md:452 5556d3c323664edea55cfb777f4efb3b #, fuzzy @@ -523,13 +529,15 @@ msgid "Navigating the User Guide" msgstr "ユーザーガイドの使い方" #: ../../src/index.md:18 9431edcf4e344fb89b6a251e627279d2 -#, fuzzy msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " "subsections of the [Topics](/topics/index.md) have detailed information " "about the most common topics for CWL." -msgstr "初心者の方は、[はじめに](/introduction/index.md)のセクションから始めてください。上級者向けには、[Topics](/topics/index.md)のサブセクションに、CWLで最も一般的なトピックに関する詳細情報があります。" +msgstr "" +"初心者の方は、[はじめに](/introduction/index." +"md)のセクションから始めてください。上級者向けには、[Topics](/topics/index." +"md)のサブセクションに、CWLで最も一般的なトピックに関する詳細情報があります。" #: ../../src/index.md:23 61cf57e61a9f46e5a1bff6368c5ad5e3 msgid "" @@ -557,6 +565,12 @@ msgid "" "already familiar with CWL or you are looking for more advanced content, " "you may want to skip this section." msgstr "" +"このセクションでは、Common Workflow Language（CWL）ワークフローの使用を開始す" +"るための基本的な概念について説明します。読者は、ワークフローマネージャー、" +"YAML に精通し、コマンドラインの指示に従うことに慣れていることが期待されます。" +"このユーザーガイドの他のセクションは、同じ概念をカバーしていますが、より詳細" +"に説明されています。すでにCWLに精通している場合、またはより高度なコンテンツを" +"探している場合は、このセクションをスキップすることができます。" #: ../../src/introduction/basic-concepts.md:10 7a56d394fb244431aefce7ebbb834ecf msgid "The CWL Specification" @@ -580,6 +594,11 @@ msgid "" "that are backward-compatible. The last number is used for bug fixes, like" " typos and other corrections to the specification." msgstr "" +"仕様のバージョンは、`.`s（ドット）で区切られた最大3つの数字を持つことができま" +"す。最初の番号はメジャーリリースで、非推奨機能の削除など、後方互換性のない変" +"更に使用されます。2番目の番号はマイナーリリースで、新機能や後方互換性のある小" +"さな変更に使用されます。最後の番号は、仕様の誤字やその他の修正など、バグフィ" +"ックスに使用される番号です。" #: ../../src/introduction/basic-concepts.md:33 72ae1fb763a34c41b1b06adcbe1522c3 #, fuzzy @@ -879,6 +898,7 @@ msgid "Prerequisites" msgstr "前提条件" #: ../../src/introduction/prerequisites.md:6 ab9e21b3e99641d096ba70012b4eb035 +#, fuzzy msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -887,6 +907,13 @@ msgid "" "compatible runner or workflow system, but the results and interface may " "look different (though the exact workflow outputs should be identical)." msgstr "" +"このセクションに記載されているソフトウェアと構成は、このユーザーガイドに従う" +"ための前提条件となるものです。CWL標準は、多くの異なるワークフローランナー(訳" +"注:ワークフローを実行するためのソフトウェア)やプラットフォームによって実装さ" +"れています。この要件のリストは、CWL参照ランナー、`cwltool` に焦点を当てていま" +"す。他のCWL互換ランナーやワークフローシステムを使用することもできますが、結果" +"やインターフェイスは異なるかもしれません（ただし、正確なワークフロー出力は同" +"一でなければなりません）。" #: ../../src/introduction/prerequisites.md:12 8ed426ebcb744839915e7c414d69b1e9 msgid "CWL Implementations" @@ -3702,7 +3729,6 @@ msgstr "" "は、ディレクトリがまだ存在しない場合、新規作成します）：" #: ../../src/topics/troubleshooting.md:35 8654b7f2f4464d13be4b47729e1f07e5 -#, fuzzy msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index e0316d50..f0430fd8 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-01-27 01:01+0000\n" +"PO-Revision-Date: 2024-02-18 03:01+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified) \n" @@ -18,7 +18,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.4-dev\n" +"X-Generator: Weblate 5.4\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -3423,18 +3423,17 @@ msgstr "" "[SciCrunch][scicrunch] " "注册表。该信息门户网站可供查询、跟踪和一致引用科学资源。如果要将工具指定为 " "[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool." -"html#SoftwareRequirement)，请在 SciCrunch 上搜索该工具并使用在注册表中分配的 " -"RRID。 （按照 [添加资源教程][scicrunch-add-tool] 将工具添加到 SciCrunch）。" -"您可以使用此 RRID 在需求描述的 `specs` 字段中引用该工具（通过 [identifiers." -"org][identifiers]）。其他不错的选择（按优先顺序）包括主要工具引用的 DOI " -"和工具的 URL。" +"html#SoftwareRequirement)，请在 SciCrunch " +"上找到该工具并使用该注册表中为其分配的 RRID（如需将工具添加到 SciCrunch " +"请参考 [添加资源教程][scicrunch-add-tool] ）。您可以使用此 RRID, 通过 " +"[identifiers.org][identifiers] 在需求描述的 `specs` 字段中引用该工具。此外，" +"加入主要工具参考文献的 DOI 以及工具的 URL, 也是合适的选择。" #: ../../src/topics/staging-input-files.md:1 d10c792550e8498c8ee384d3093da306 msgid "Staging Input Files" msgstr "暂存输入文件" #: ../../src/topics/staging-input-files.md:3 ac2ef1fced5f4044861761a11c35e78a -#, fuzzy msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -3445,9 +3444,12 @@ msgid "" "a JavaScript expression to extract the base name of the input file from " "its leading directory path." msgstr "" -"通常，输入文件位于独立于输出目录的只读目录中。 如果基础工具希望将其输出文件与输入文件一起写入同一目录中，则会导致问题。 使用 " -"`InitialWorkDirRequirement` 将输入文件暂存到输出目录中。在此示例中，我们使用 JavaScript " -"表达式从输入文件的前导目录路径中提取该文件的基本名称。" +"通常，输入文件存放于只读目录中，而且位于输出目录之外。 然而，如果基础工具工作" +"的惯例是将输出文件写到输入文件所在的同一目录，则会导致问题。 使用 " +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#InitialWorkDirRequirement) " +"可以实现在输出目录中暂存输入文件。在此示例中，我们使用 JavaScript 表达式，" +"提取输入文件去除前导目录路径后的基本文件名 (base name)." #: ../../src/topics/staging-input-files.md:9 d8ca16f5321e486ebe8ea9f9752b3737 msgid "`linkfile.cwl`" @@ -3455,7 +3457,7 @@ msgstr "`linkfile.cwl`" #: ../../src/topics/troubleshooting.md:1 aa3eddcaa0684f86ba67aafcd57872e7 msgid "Troubleshooting" -msgstr "疑难解答" +msgstr "故障排除" #: ../../src/topics/troubleshooting.md:3 3207f476afa04158bd26db39a16a2df5 msgid "" @@ -3463,10 +3465,12 @@ msgid "" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" +"本节将介绍执行 CWL 程序遇到问题时的排查、解决方法。此处我们重点介绍 `cwltool`" +", 不过同样的技巧也可能适用于其他 CWL 运行程序。" #: ../../src/topics/troubleshooting.md:6 1d47f4ce04554cabb1ccf40a13ee42ec msgid "Run `cwltool` with `cachedir`" -msgstr "" +msgstr "制定 `cachedir`（缓存目录）运行 `cwltool`" #: ../../src/topics/troubleshooting.md:8 0c25602a83e441b48b536eb49568f2b6 msgid "" @@ -3476,6 +3480,9 @@ msgid "" "these files are created in a temporary directory but writing them to a " "separate directory makes accessing them easier." msgstr "" +"运行工作流时，您可使用 `--cachedir` 选项令 `cwltool` 缓存中间文件（不属于输入" +"输出文件，而是工作流运行过程中创建）。默认情况下这些文件创建于一个临时目录下" +"，不过将其写入指定的独立目录可以更方便地访问。" #: ../../src/topics/troubleshooting.md:14 36ec60b80c714357a4274217274136ff msgid "" @@ -3486,10 +3493,14 @@ msgid "" " where instead of executing the `rev` command it tries to execute `revv`," " which fails." msgstr "" +"以下示例 `troubleshooting-wf1.cwl` 中设有两个步骤 `step_a` 和 `step_b`. " +"该工作流相当于执行命令 `echo \"Hello World\" | rev`, 将 \"Hello World\" " +"反向输出为 \"dlroW olleH\". 但是第二个步骤 `step_b` **有一处错误**：本该执行 " +"`rev` 命令，却成了 `revv`, 于是失败。" #: ../../src/topics/troubleshooting.md:20 6f34038054ac4f4fa0b0ad9cbc3ecdc7 msgid "`troubleshooting-wf1.cwl`" -msgstr "" +msgstr "`troubleshooting-wf1.cwl`" #: ../../src/topics/troubleshooting.md:27 b777877c88024c9fb06a6614029ef8d6 msgid "" @@ -3497,6 +3508,8 @@ msgid "" "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" +"我们来以 `/tmp/cachedir/` 为 `--cachedir` " +"选项的值重新执行这个工作流（如果这个目录不存在，`cwltool` 会为你创建之）：" #: ../../src/topics/troubleshooting.md:35 8654b7f2f4464d13be4b47729e1f07e5 msgid "" @@ -3505,6 +3518,9 @@ msgid "" "successfully and its output has been cached in your `cachedir` location. " "You can inspect the intermediate files created:" msgstr "" +"该工作流处于 `permanentFail` 状态，因为 `step_b` 中执行不存在的命令 `revv` " +"失败。`step_a` 得到了成功执行，其输出换存在了你通过 `cachedir` " +"选项指定的位置。你可以检查它创建的中间文件：" #: ../../src/topics/troubleshooting.md:44 04e80f7ce14d4d73bc5d290dcf01bcdb msgid "" From 3dd41559b881c43552ad96ae6e6105b8234b53ed Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Sat, 24 Feb 2024 08:57:30 +0100 Subject: [PATCH 126/179] Translated using Weblate (Japanese) (#457) Currently translated at 58.2% (349 of 599 strings) Translated using Weblate (Japanese) Currently translated at 57.2% (343 of 599 strings) Translated using Weblate (Japanese) Currently translated at 56.5% (339 of 599 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 62 +++++++++++++++------------- 1 file changed, 33 insertions(+), 29 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index a6fac25c..87208b7a 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-02-18 03:01+0000\n" +"PO-Revision-Date: 2024-02-24 01:02+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -18,7 +18,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.4\n" +"X-Generator: Weblate 5.5-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -356,7 +356,8 @@ msgstr "" msgid "" "How do I describe dependent or exclusive input parameters(e.g. How do I " "use record inputs)?" -msgstr "" +msgstr "依存的または排他的な入力パラメータはどのように記述すればよいですか（例えば、" +"レコード入力をどのように使用すればよいですか）？" #: ../../src/faq.md:270 949ce95c082f4a05891a55fee25d4873 #, fuzzy @@ -374,6 +375,7 @@ msgid "How do I set mutually exclusive parameters?" msgstr "相互に排他的なパラメータを設定する" #: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f +#, fuzzy msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -381,6 +383,10 @@ msgid "" "field you want to set. The source field is set to indicate the input from" " the workflow to be used as the value." msgstr "" +"レコード入力タイプのフィールドを適切に設定するには、入力に辞書を渡してパラメ" +"ータを適切に設定する必要があります。これは、インラインJavaScriptを使用し、設" +"定したいフィールドのキーを持つ辞書を返すことで実現します。ソースフィールドに" +"は、値として使用するワークフローからの入力を示すものが設定されます。" #: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 #, fuzzy @@ -460,9 +466,8 @@ msgid "" msgstr "入力識別子を変更することができない場合は、別のCWLパラメータリファレンス構文を使用することができます：" #: ../../src/faq.md:442 fc407a9e8d8c4b699d9cd14b369343b5 -#, fuzzy msgid "How do I use CWL and cwltool with Singularity?" -msgstr "CWLとcwltoolをSingularityで使う" +msgstr "SingularityをCWLとcwltoolで使うにはどうしたらよいでしょうか？" #: ../../src/faq.md:445 239f5f81cef042b08fb8015c36b3ecad msgid "" @@ -472,6 +477,10 @@ msgid "" "Directly specifying a Singularity format container is not part of the CWL" " standards." msgstr "" +"CWL標準は、（オプションの）Docker形式のコンテナを中心に構築されています。リフ" +"ァレンスランナーや他のいくつかのCWL実装は、Singularityエンジンを使用してそれ" +"らのDockerフォーマットコンテナを実行することをサポートしています。Singularity" +"フォーマットコンテナを直接指定することは、CWL標準ではありません。" #: ../../src/faq.md:450 61641314d82b43e982e54c64c73232c5 msgid "How do I debug the JavaScript in my CWL tool?" @@ -601,13 +610,13 @@ msgstr "" "ックスに使用される番号です。" #: ../../src/introduction/basic-concepts.md:33 72ae1fb763a34c41b1b06adcbe1522c3 -#, fuzzy msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -"仕様のバージョンアップに使われるモデルは、セマンティックバージョニングを利用しています。それについて[もっと知りたい](#learn-" +"仕様のバージョンアップに使われるモデルは、セマンティックバージョニングです。" +"それについて[もっと知りたい](#learn-" "more)方は、このセクションの最後をご覧ください。" #: ../../src/introduction/basic-concepts.md:37 5aa7d3ee6cb048d888f1e1f49d0e08be @@ -625,12 +634,14 @@ msgid "" msgstr "CWL仕様の実装とは、あるバージョンの仕様書で定義された内容に従って書かれたソフトウェアのことです。ただし、実装は仕様のすべての側面を実装するわけではありません。CWLの実装は、オープンソース・ライセンスと商用ライセンスの両方でライセンスされています。" #: ../../src/introduction/basic-concepts.md:44 c995e699ae2949219af252f9d802a43d -#, fuzzy msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." -msgstr "CWLは、多くのノードでタスクが並列にスケジューリングされるクラスタ、クラウド、ハイパフォーマンスコンピューティング環境における大規模なワークフローを記述するのに適しています。" +msgstr "" +"CWLは、多くのノードでタスクが並列にスケジューリングされるクラスタ、クラウド、" +"ハイパフォーマンスコンピューティング環境における大規模なワークフローを記述す" +"るのに適しています。" #: ../../src/introduction/basic-concepts.md:51 09171f48a3d841b2acb6d803b2340c8e msgid "CWL specification, implementations, and other tools." @@ -638,21 +649,20 @@ msgstr "CWL仕様、実装、その他ツール。" #: ../../src/introduction/basic-concepts.md:105 #: 1c1647a3496c4251a3193f94ee4e78c8 -#, fuzzy msgid "Processes and Requirements" msgstr "Processes 及び Requirements" #: ../../src/introduction/basic-concepts.md:107 #: 854633336f4d4fc394e62c53ce022c6b -#, fuzzy msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " "hints. There are four types of processes defined in the CWL specification" " {{ cwl_version }}:" msgstr "" -"Processとは、入力を受けて出力を生成する計算のユニットです。Processの動作は、inputs、requirements、hintsに影響されることがあります。CWL仕様{{" -" cwl_version }}では、4種類のProcessが定義されています：" +"Processとは、入力を受けて出力を生成する計算のユニットです。Processの動作は、i" +"nputs、requirements、hintsに影響されることがあります。CWL仕様{{ cwl_version " +"}}では、4種類のProcessが定義されています：" #: ../../src/introduction/basic-concepts.md:112 #: 142a847f11d7462f8bf77bfe789410ca @@ -2940,7 +2950,6 @@ msgstr "" "切って1つの引数に連結することを指定することができます。" #: ../../src/topics/inputs.md:185 bb31c6784ea843ec88f185523cfa25df -#, fuzzy msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2950,19 +2959,17 @@ msgid "" "guide.md#arrays). You can specify arrays of arrays, arrays of records, " "and other complex types." msgstr "" -"なお、入力の配列は角括弧の中で指定します `array-inputs-job.yml`の`[]`です.配" +"なお、入力の配列は大括弧の中で指定します `array-inputs-job.yml`の`[]`です.配" "列は複数行に渡って表現することも可能で、関連するキーで定義されていない配列の" -"値は、先頭の`-` でマークされます。これは次のレッスンで実演され、[YAML Guide" -"](yaml-guide.md#arrays) でより詳細に説明されています。配列の配列、レコードの" -"配列、その他の複雑な型を指定することができます。" +"値は、先頭の`-` でマークされます。これは次のレッスンで実際に確認し、[YAML " +"Guide](yaml-guide.md#arrays) でより詳細に説明されています。配列の配列、レコー" +"ドの配列、その他の複雑な型を指定することができます。" #: ../../src/topics/inputs.md:191 53817379078548b2aeb6195cae9cbab7 -#, fuzzy msgid "Inclusive and Exclusive Inputs" msgstr "包括的入力と排他的入力" #: ../../src/topics/inputs.md:193 e163c0cfe9694a85b2e42682f42970a5 -#, fuzzy msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -3012,7 +3019,6 @@ msgid "" msgstr "3番目の例では、`itemD` のみが提供されているので、コマンドラインに表示されます。" #: ../../src/topics/inputs.md:255 ffddeeda8f04408ba73f7a59a4618da5 -#, fuzzy msgid "Exclusive Input Parameters with Expressions" msgstr "式で入力パラメータを排他的に指定する" @@ -3754,7 +3760,6 @@ msgstr "" "は、上記のコマンドの出力で確認できます。" #: ../../src/topics/troubleshooting.md:48 719917cb0fd849f5a328671df8726189 -#, fuzzy msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3769,10 +3774,9 @@ msgstr "" "を実行すると、`cwltool` の出力に、`step_a` " "の出力が事前にキャッシュされていることと、`step_b` " "の出力の新しいキャッシュ・エントリーがあることがわかります。また、`step_b` " -"のステータスは、現在、成功であることに注目してください。" +"のステータスは、今度は、成功であることに注目してください。" #: ../../src/topics/troubleshooting.md:59 2a9dbb3ad7564f5aa103349c45ee7925 -#, fuzzy msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3783,9 +3787,9 @@ msgid "" msgstr "" "この例では、ワークフローのステップ`step_a` はキャッシュされていたため再実行さ" "れず、その実行や出力に変化はありませんでした。さらに、`cwltool` " -"は、実行ファイル名を修正した後、`step_b` を再実行する必要があることがわかりま" -"した。このテクニックは、CWL文書のトラブルシューティングに役立つだけでなく、`c" -"wltool` が不必要にステップを再実行するのを防ぐ方法としても有効です。" +"は、実行したいコマンド名を修正した後、`step_b` を再実行する必要があることがわ" +"かりました。このテクニックは、CWL文書のトラブルシューティングに役立つだけでな" +"く、`cwltool` が不必要にステップを再実行するのを防ぐ方法としても有効です。" #: ../../src/topics/using-containers.md:1 7439fe097aa4459ba1e4c0e28fc59b9a msgid "Using Containers" @@ -3817,12 +3821,12 @@ msgstr "" "できます。" #: ../../src/topics/using-containers.md:15 4b0f6cfc8a774c77bfbc99e568af2ece -#, fuzzy msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." -msgstr "CWLランナーの役割のひとつに、入力ファイルのパスをコンテナ内のでの配置位置に合わせて調整することがあります。" +msgstr "CWLランナーの役割のひとつに、入力ファイルのパスをコンテナ内のでの配置位置に合" +"わせることがあります。" #: ../../src/topics/using-containers.md:18 27c02a5d479a420eab7d14888d9fb288 msgid "" From 8a045a81a482c2b822cab120f4c795f975e04ef1 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Thu, 29 Feb 2024 11:44:02 +0100 Subject: [PATCH 127/179] Translated using Weblate (Japanese) (#458) Currently translated at 62.2% (373 of 599 strings) Translated using Weblate (Japanese) Currently translated at 61.6% (369 of 599 strings) Translated using Weblate (Japanese) Currently translated at 59.5% (357 of 599 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 111 ++++++++++++++------------- 1 file changed, 58 insertions(+), 53 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 87208b7a..7d69806c 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-02-24 01:02+0000\n" +"PO-Revision-Date: 2024-02-29 05:02+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -337,7 +337,8 @@ msgstr "" msgid "" "How do I specify an input that must come from a list of predefined values" " (i.e. How do I use enum inputs) ?" -msgstr "" +msgstr "どうやってあらかじめ定義された値のリストから入力を指定できますか(つまり、入力" +"でenumを使うにはどうしたらよいですか)?" #: ../../src/faq.md:250 b1934a82553b4da3b7f981e576245dd8 #, fuzzy @@ -720,14 +721,17 @@ msgstr "Operationは、入力を受け、出力を出す抽象的なプロセス #: ../../src/introduction/basic-concepts.md:131 #: 44aac23f302c4178accf7e431cfbb96c -#, fuzzy msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " "The inputs of a workflow can be passed to any of its steps, while the " "outputs produced by its steps can be used in the final output of the " "workflow." -msgstr "Workflowは、ステップを含むプロセスである。ステップには、他のWorkflow（ネストされたWorkflow）、CommandLineTool、またはExpressionToolを使用することができます。Workflowの入力は、そのステップのいずれかに渡すことができ、ステップによって生成された出力は、Workflowの最終出力に使用することができます。" +msgstr "" +"Workflowは、ステップを含むプロセスです。ステップには、他のWorkflow（ネストさ" +"れたWorkflow）、CommandLineTool、ExpressionToolを使用することができます。Work" +"flowの入力は、そのステップのいずれかに渡すことができ、ステップによって生成さ" +"れた出力は、Workflowの最終出力に使用することができます。" #: ../../src/introduction/basic-concepts.md:137 #: 5afdb7aaf0bf4c1abf4c22cdbdd58be9 @@ -742,27 +746,31 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:141 #: 07c5789c59224ed78a3ecd03cfe872e9 -#, fuzzy msgid "" "[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement)" " - enables JavaScript in expressions." -msgstr "`InlineJavascriptWorkflow` - でJavaScriptを有効にします。" +msgstr "" +"[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow." +"html#InlineJavascriptRequirement) - でJavaScriptを有効にします。" #: ../../src/introduction/basic-concepts.md:142 #: 6f9854ae1b884ad39f88d2f39d66cb98 -#, fuzzy msgid "" "[`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow.html#SubworkflowFeatureRequirement)" " - enables nested workflows." -msgstr "`SubworkflowFeatureRequirement` - ネストしたワークフローを有効にします。" +msgstr "" +"[`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow." +"html#SubworkflowFeatureRequirement) - ネストしたワークフローを有効にします。" #: ../../src/introduction/basic-concepts.md:143 #: 23fef6de073f4da18118e4d0512670fe -#, fuzzy msgid "" "[`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow.html#InitialWorkDirRequirement)" " - controls staging files in the input directory." -msgstr "`InitialWorkDirRequirement` - 入力ディレクトリのステージングファイルを制御します。" +msgstr "" +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow." +"html#InitialWorkDirRequirement) - " +"入力ディレクトリのステージングファイルを制御します。" #: ../../src/introduction/basic-concepts.md:145 #: fb3762f91177401ea624d1e716d67ae6 @@ -1170,13 +1178,12 @@ msgstr "" "CodeとWebStormには、CWLとの統合を実現する拡張機能があり、カスタマイズされたシンタックスハイライトやより優れた自動補完などの機能が用意されています：" #: ../../src/introduction/prerequisites.md:158 73c08e11e90d4c7f952307a1cdaa360b -#, fuzzy msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -"Benten(弁天)（CWL）プラグインを使ったVisual Studio Code " -"-" +"Benten(弁天)（CWL）プラグインを使ったVisual Studio Code -" #: ../../src/introduction/prerequisites.md:159 a5b788252a924338963f0ed198fc22ca msgid "" @@ -1197,7 +1204,6 @@ msgid "Docker" msgstr "Docker" #: ../../src/introduction/prerequisites.md:168 eff13997c1ce43d1ad2d7a4d927394fe -#, fuzzy msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1206,26 +1212,29 @@ msgid "" msgstr "" "`cwltool` は、ツール、ワークフロー、およびワークフロー " "ステップで指定されたソフトウェアコンテナをDockerを使用して実行します。Docker " -"ドキュメントの指示に従って、お使いのオペレーティングシステム用にインストールしてください：." +"ドキュメントの指示に従って、お使いのオペレーティングシステム用にインストール" +"してください：." #: ../../src/introduction/prerequisites.md:172 2872503638624b7e904ae407375ac165 -#, fuzzy msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " "examples, and to clarify the differences between the execution models " "with and without containers." -msgstr "Dockerコンテナの書き方や構築方法を知っておく必要はありません。このユーザーガイドの残りの部分では、実行例として既存のDockerイメージを使用し、コンテナのある実行モデルとない実行モデルの違いを明確にすることにします。" +msgstr "" +"Dockerコンテナの書き方や構築方法を知っておく必要はありません。このユーザーガ" +"イドの残りの部分では、実行例として既存のDockerイメージを使用し、コンテナのあ" +"る実行モデルとない実行モデルの違いを明確にすることにします。" #: ../../src/introduction/prerequisites.md:178 52ddcc9bc1554d809371fc0a503c40bc -#, fuzzy msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -"`cwltool` " -"Docker、Podman、udocker、Singularityによるコンテナの実行をサポートしています。また、コンテナイメージを取得するために代替のコンテナレジストリを使用することもできます。" +"`cwltool` は、Docker、Podman、udocker、Singularityによるコンテナの実行をサポ" +"ートしています。また、コンテナイメージを取得するために代替のコンテナレジスト" +"リを使用することもできます。" #: ../../src/introduction/prerequisites.md:185 f3bbfa17f31a459386461951de157dd2 msgid "" @@ -1973,7 +1982,6 @@ msgid "`custom-types.yml`" msgstr "`custom-types.yml`" #: ../../src/topics/custom-types.md:24 56b8912a1ea84f28adeb8beaf92ab563 -#, fuzzy msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1982,7 +1990,7 @@ msgid "" "`wget`:" msgstr "" "___注意:___ 以下の例に行うには、`wget`などで*rich_sparse_otu_table." -"biom*という入力ファイルを[ダウンロード](https://github.com/" +"biom*という[入力ファイルをダウンロード](https://github.com/" "common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/" "rich_sparse_otu_table.biom)する必要があります：" @@ -2033,7 +2041,6 @@ msgstr "" " で定義されており、例として`custom-types.cwl` の定義にあるように、インポートされます：" #: ../../src/topics/custom-types.md:76 dce43b138ba24b22bfa9fa5692a17009 -#, fuzzy msgid "" "Note also that the author of this CWL description has also included " "[`ResourceRequirement`](https://w3id.org/cwl/CommandLineTool.html#ResourceRequirement)s," @@ -2048,8 +2055,8 @@ msgstr "" "html#ResourceRequirement)も含まれていることに注意してください。これは、" "ツールが正常に動作するために必要な最小限の RAM の量とコアの数、さらにその定義" "に書かれたソフトウェアのバージョンの詳細やその他の有用なメタデータを指定する" -"ものです。これらの機能については、このユーザーガイドの他の章で詳しく説明する" -"。" +"ものです。これらの機能については、このユーザーガイドの他の章で詳しく説明しま" +"す。" #: ../../src/topics/environment-variables.md:1 19737f89f2994815969fa4a88346f49a msgid "Environment Variables" @@ -2073,40 +2080,37 @@ msgid "Expression Tool" msgstr "Expression Tool" #: ../../src/topics/expression-tool.md:3 b267056eae704737af5aaada3ea7e6e2 -#, fuzzy msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " "be used as a way to isolate complex JavaScript expressions that need to " "operate on input data and produce some result as output." msgstr "" -"ExpressionToolは、それ自体またはワークフローのステップとして実行することができるProcessの一種です。純粋な " -"JavaScript 式を実行します。入力データを操作し、出力として結果を生成する必要がある複雑な JavaScript " +"ExpressionToolは、それ自体またはワークフローのステップとして実行することがで" +"きるProcessの一種です。純粋な JavaScript 式を実行します。入力データを操作し、" +"出力として結果を生成する必要がある複雑な JavaScript " "式を分離する方法として使用されることを意図しています。" #: ../../src/topics/expression-tool.md:8 7e930144163e4d6e9f0bcaa764497ccf -#, fuzzy msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an " "[`expression`](https://w3id.org/cwl/CommandLineTool.html#Expressions_(Optional))" " attribute." msgstr "" -"CommandLinetToolと同様に、`inputs` と`outputs` が必要です。しかし、`baseCommand` " -"の代わりに、`expression` 属性を必要とします。" +"CommandLinetToolと同様に、`inputs` と`outputs` " +"が必要です。しかし、`baseCommand` の代わりに、[`expression`](https://w3id." +"org/cwl/CommandLineTool.html#Expressions_(Optional)) 属性を必要とします。" #: ../../src/topics/expression-tool.md:17 f172488c19a94d688036197117d30b38 -#, fuzzy msgid "CWL expression tool." msgstr "CWL expression tool." #: ../../src/topics/expression-tool.md:48 ef978c951f1a4b7d9280d31367e5bae7 -#, fuzzy msgid "`uppercase.cwl`" msgstr "`uppercase.cwl`" #: ../../src/topics/expression-tool.md:67 0b63da31bc274b3cad798b07149592ab -#, fuzzy msgid "" "We had to use an " "[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" @@ -2114,12 +2118,12 @@ msgid "" "means to tools using the expression tool that JavaScript is a " "requirement." msgstr "" -"`InlineJavascriptRequirement` を使用する必要がありました。この式には`.toUpperCase()` で " -"JavaScript " -"の呼び出しが含まれているからです。これは、ExpressionToolを使用するツールにとって、JavaScriptが必要であることを意味します。" +"この式には`.toUpperCase()` で JavaScript の呼び出しが含まれているため、 " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#InlineJavascriptRequirement) を使用する必要があります。これは、Expressio" +"nToolを使用するツールにとって、JavaScriptが必要であることを意味します。" #: ../../src/topics/expressions.md:1 b0e567a985f748538552bdb486a47998 -#, fuzzy msgid "Expressions" msgstr "Expressions" @@ -3203,12 +3207,14 @@ msgstr "" "を使ってプロットすることもできます：" #: ../../src/topics/operations.md:24 61e4ae6ed18e41708270eb358cd55277 -#, fuzzy msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx `{graphviz}` directive " "(this user guide is built with Sphinx):" -msgstr "上記のコマンドの出力は、Graphvizレンダラーでレンダリングすることができます。以下の画像は、SphinxのGraphvizディレクティブでレンダリングしたものです（このユーザーガイドはSphinxで構築されています）：" +msgstr "" +"上記のコマンドの出力は、Graphvizを使ってレンダリングすることができます。以下" +"の画像は、SphinxのGraphvizディレクティブでレンダリングしたものです（このユー" +"ザーガイドはSphinxで構築されています）：" #: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd #, fuzzy @@ -3229,27 +3235,29 @@ msgid "" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -"CWL runnerは、操作を具体的なステップにバインドする方法を思いつくかもしれません。例えば、CWL " -"runnerは、異なるワークフローエンジンで実行されるステップに対応するIDを持つ抽象的な operation を使用することができます。" +"CWL runnerは、operations " +"を具体的なステップにバインドする見出すかもしれません。例えば、CWL runnerは、" +"ワークフローエンジンで実行される異なるステップに対応するIDを持つ抽象的な " +"operation を使用することができます。" #: ../../src/topics/outputs.md:1 35e7bad6fdc04bcf9bbfbb2d8d42cfa5 msgid "Outputs" msgstr "Outputs" #: ../../src/topics/outputs.md:3 6d912d40359c4d33a4f08abca83c00be -#, fuzzy msgid "Returning Output Files" msgstr "出力ファイルの回収" #: ../../src/topics/outputs.md:5 a6bd3f9e23de488394958fe7b59a61e0 -#, fuzzy msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" " of parameter, and `type` describing what types of values are valid for " "that parameter." msgstr "" -"ツールの`outputs` は、ツールの実行後に返されるべき出力パラメータのリストです。 各パラメーターには、パラメーター名を示す`id` " +"ツールの`outputs` " +"は、ツールの実行後に返されるべき出力パラメータのリストです。 " +"各パラメーターには、パラメーター名を示す`id` " "と、そのパラメーターに有効な値の型を示す`type` があります。" #: ../../src/topics/outputs.md:10 a229d8d983344e51a231edb5f667d84b @@ -3343,7 +3351,6 @@ msgstr "" "次に、対応する出力パラメータに`type: stdout` を追加します。" #: ../../src/topics/outputs.md:75 cf2ef8dc7fda49308c09efe4f4ef5d7b -#, fuzzy msgid "`stdout.cwl`" msgstr "`stdout.cwl`" @@ -3358,7 +3365,6 @@ msgid "" msgstr "また、`glob` を使って、複数の出力ファイルを配列に取り込むことができます。" #: ../../src/topics/outputs.md:97 b34e30481fbd489d95fb7f8d5b5ab50c -#, fuzzy msgid "`array-outputs.cwl`" msgstr "`array-outputs.cwl`" @@ -3384,7 +3390,6 @@ msgid "Parameter References" msgstr "パラメータリファレンス" #: ../../src/topics/parameter-references.md:3 f5c0592ca28c46c2a89943f4f6f69a27 -#, fuzzy msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -3399,12 +3404,12 @@ msgstr "" "前の例では、\"tar \"プログラムを使用してファイルを抽出しました" "。しかし、その例は非常に限定的なものでした。というのも、" "私たちが興味を持っているファイルは\"hello.txt\"と呼ばれ、これが`.cwl` ファイ" -"ルに書き込まれていると仮定していたからです。これは最良の方法ではありません。" -"なぜなら、\"hello.txt \"というファイル名は" +"ルに直接書き込まれていると仮定していたからです。これは最良の方法ではありませ" +"ん。なぜなら、\"hello.txt \"というファイル名は" "、使用する入力ファイルによって異なるか、または依存する可能性があるからです。" " これを避けるために、ジョブパラメーターファイル(`.yml`)で必要なファイル名を" "指定することができます。この例では、入力パラメーターの値を他のフィールドから" -"動的に参照し、抽出するファイル名を指定する方法を説明します。" +"動的に参照して、抽出するファイル名を指定する方法を説明します。" #: ../../src/topics/parameter-references.md:13 50db8add9b1942d986e581b8d21c2ee4 msgid "`tar-param.cwl`" @@ -3415,11 +3420,11 @@ msgid "`tar-param-job.yml`" msgstr "`tar-param-job.yml`" #: ../../src/topics/parameter-references.md:25 9b1e2f1a23ea4fe2af97ef5108f33376 -#, fuzzy msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" -msgstr "入力ファイル(入力オブジェクト)を作成し、コマンドラインでツール定義と入力オブジェクトを指定して`cwltool` を呼び出します：" +msgstr "入力ファイル(入力オブジェクト)を作成し、コマンドラインでツール定義と入力オブ" +"ジェクトを指定して`cwltool` を呼び出します：" #: ../../src/topics/parameter-references.md:36 06926a516ae6432d96e3eaa62202cd86 #, fuzzy From d6bcbc7537ba9bf1f0315fbf475f1d8bfcc1d9d5 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Thu, 7 Mar 2024 08:05:14 +0100 Subject: [PATCH 128/179] Translations update from Hosted Weblate (#459) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Translated using Weblate (Chinese (Simplified)) Currently translated at 72.7% (436 of 599 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 71.9% (431 of 599 strings) Co-authored-by: Zoë Ma Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 64.1% (384 of 599 strings) Translated using Weblate (Japanese) Currently translated at 63.4% (380 of 599 strings) Translated using Weblate (Japanese) Currently translated at 62.7% (376 of 599 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide --------- Co-authored-by: Zoë Ma Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 42 ++++++++++------------- locales/zh_Hans/LC_MESSAGES/user_guide.po | 40 +++++++++++++++++---- 2 files changed, 53 insertions(+), 29 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 7d69806c..1c39d0b1 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-02-29 05:02+0000\n" +"PO-Revision-Date: 2024-03-07 01:01+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -938,15 +938,15 @@ msgid "CWL Implementations" msgstr "CWL実装" #: ../../src/introduction/prerequisites.md:14 ff74d48407464c4b9d451fa419137144 -#, fuzzy msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " "engines. We have a better explanation in the [Implementations](basic-" "concepts.md#implementations) section." msgstr "" -"CWL規格の実装は数多く存在します。あるものは完全なCWL実装であり、他のものはワークフローエンジンのプラグインや拡張になり得ます。[実装" -"](basic-concepts.md#implementations)のセクションでより詳しいをしています。" +"CWL標準規格の実装は数多く存在します。あるものは完全なCWL実装であり、他のもの" +"はワークフローエンジンのプラグインや拡を含むことがあります。[実装](basic-" +"concepts.md#implementations)のセクションでより詳しい説明をしています。" #: ../../src/introduction/prerequisites.md:19 eb98aa9c71d746a69e9610996ffc5b47 msgid "Operating System" @@ -971,7 +971,6 @@ msgid "Windows" msgstr "Windows" #: ../../src/introduction/prerequisites.md:29 aeeb990abbbd42cca122c342054be29c -#, fuzzy msgid "" "If you are using Windows, you will have to install the Windows Subsystem " "for Linux 2 as documented in the [`cwltool` documentation for Microsoft " @@ -979,14 +978,13 @@ msgid "" "language/cwltool/blob/main/README.rst#ms-windows-users). Your operating " "system also needs internet access and a recent version of Python (3.6+)." msgstr "" -"Windowsを使用している場合は、[`cwltool` documentation for Microsoft Windows " -"users](https://github.com/common-workflow-language/cwltool/blob/main/README." +"Windowsを使用している場合は、[Microsoft Windows ユーザのための`cwltool` " +"文書](https://github.com/common-workflow-language/cwltool/blob/main/README." "rst#ms-windows-users)に記載されているように、Windows Subsystem for Linux 2を" "インストールする必要があります。インターネットアクセスとPythonの最新バージョ" "ン(3.6+)も必要です。" #: ../../src/introduction/prerequisites.md:34 21d1f29fb15745c480194eae6acdd031 -#, fuzzy msgid "CWL Runner" msgstr "CWL Runner" @@ -3170,20 +3168,19 @@ msgid "`metadata_example3.cwl`" msgstr "`metadata_example3.cwl`" #: ../../src/topics/operations.md:1 a79974b2f4534fcd8c7a04401e8a5556 -#, fuzzy msgid "Operations" msgstr "Operations" #: ../../src/topics/operations.md:3 b6507c8e1625476b97708423acb4fd0e -#, fuzzy msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " "specifies inputs and outputs, but it does not provide enough information " "to be executed." msgstr "" -"Operationは、Workflow、CommandLineTool、ExpressionToolと同様に、CWL " -"Processの一種です。Workflowのステップで、入力と出力を指定しますが、実行するのに十分な情報を提供しません。" +"Operationは、Workflow、CommandLineTool、ExpressionToolと同様に、CWL Processの" +"一種です。Workflowのステップで、入力と出力を指定しますが、実行するのに十分な" +"情報を提供しません。" #: ../../src/topics/operations.md:7 047b09455db64524a71c47ab5192039f msgid "" @@ -3196,15 +3193,14 @@ msgid "`operations.cwl`" msgstr "`operations.cwl`" #: ../../src/topics/operations.md:16 d21e9444182d4e27bae934db4573ae99 -#, fuzzy msgid "" "The `uppercase` step of the workflow is an operation. It can appear where" " a command line tool or an expression is expected. You can also plot it " "with the CWL Viewer or `cwltool`:" msgstr "" "ワークフローの`uppercase` ステップは Operation " -"です。CommandLineToolやExpressionToolのように使用することができます。また、CWL Viewerや`cwltool` " -"を使ってプロットすることもできます：" +"です。CommandLineToolやExpressionToolのように使用することができます。また、" +"CWL Viewerや`cwltool` を使って可視化することもできます：" #: ../../src/topics/operations.md:24 61e4ae6ed18e41708270eb358cd55277 msgid "" @@ -3217,11 +3213,11 @@ msgstr "" "ザーガイドはSphinxで構築されています）：" #: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd -#, fuzzy msgid "" "The operation file will fail to run with `cwltool` because `cwltool` " "lacks the necessary information to execute it:" -msgstr "操作ファイルを `cwltool` で実行しようとすると、`cwltool` " +msgstr "" +"operation ファイルを `cwltool` で実行しようとすると、`cwltool` " "が実行に必要な情報を持っていないため、失敗します：" #: ../../src/topics/operations.md:59 e184470550e645f6b9ce658af7e65ecf @@ -4484,7 +4480,6 @@ msgstr "" "workflows)で、ワークフロー全体を別のワークフローの1ステップにすることができることを思い出しましょう！2ステップのワークフローを1ステップのサブワークフローに変換してみましょう：" #: ../../src/topics/workflows.md:513 fac138ba275745898b763a7d719a8235 -#, fuzzy msgid "`scatter-nested-workflow.cwl`" msgstr "`scatter-nested-workflow.cwl`" @@ -4496,28 +4491,29 @@ msgid "" msgstr "今、scatter は1つのステップに作用しますが、そのステップは2つのステップで構成されているので、各ステップは並行して実行されます。" #: ../../src/topics/workflows.md:522 b0bf01dad1234a1db3c87b10953e42ef -#, fuzzy msgid "Conditional Workflows" msgstr "条件分岐ワークフロー" #: ../../src/topics/workflows.md:524 8d933ed1ec6e408589f781e3a425b869 -#, fuzzy msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." -msgstr "このワークフローは、条件付きステップを含み、入力に基づき実行されます。これにより、ワークフローは、プログラムの開始時に与えられた入力パラメータや以前のステップによって、追加のステップをスキップすることができます。" +msgstr "" +"このワークフローは、条件付きステップを含み、入力に基づき実行されます。これに" +"より、ワークフローは、プログラムの開始時に与えられた入力パラメータや以前のス" +"テップによって、追加のステップをスキップすることができます。" #: ../../src/topics/workflows.md:527 9ac7b4f71621411da9a4ca3bc277dcb0 msgid "`conditional-workflow.cwl`" msgstr "`conditional-workflow.cwl`" #: ../../src/topics/workflows.md:566 4a4a2b2b99b44d449adb246cebce0a26 -#, fuzzy msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." -msgstr "まず、このワークフローはCWL仕様のバージョン1.2以降でしか対応していないことがわかります。" +msgstr "まず、このワークフローはCWL仕様のバージョン1." +"2以降から対応しているがわかります。" #: ../../src/topics/workflows.md:573 4742fe09a4264fb8be6f092519de5d72 #, fuzzy diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index f0430fd8..5bbe5fd4 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-02-18 03:01+0000\n" +"PO-Revision-Date: 2024-03-07 01:01+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified) \n" @@ -18,7 +18,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.4\n" +"X-Generator: Weblate 5.5-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -3529,6 +3529,9 @@ msgid "" "executed by the workflow. And the `step_a` output file `stdout.txt` is " "visible in the output of the command above." msgstr "" +"工作流中的每一步骤均有唯一的 ID（即形如散列/哈希值的一长串字符）。文件 " +"`${HASH}.status` 包含工作流各步骤的执行状态。在上例命令的输出结果中可以看到 " +"`step_a` 这一步骤的输出文件 `stdout.txt`." #: ../../src/topics/troubleshooting.md:48 719917cb0fd849f5a328671df8726189 msgid "" @@ -3539,6 +3542,10 @@ msgid "" "new cache entry for the output of `step_b`. Also note that the status of " "`step_b` is now of success." msgstr "" +"现在，将 `step_b` 中的错误（即 `revv`）改正过来，使之执行 `rev` 命令。然后，" +"用与之前相同的命令行选项执行 `cwltool`. 注意这时 `cwltool` 的输出包含 " +"`step_a` 经缓存的输出，而 `step_b` 的输出有了新的缓存项。同时，可以注意到 " +"`step_b` 的状态已经是“成功”。" #: ../../src/topics/troubleshooting.md:59 2a9dbb3ad7564f5aa103349c45ee7925 msgid "" @@ -3549,14 +3556,18 @@ msgid "" " troubleshooting your CWL documents and also as a way to prevent " "`cwltool` to re-evaluate steps unnecessarily." msgstr "" +"此例子中，工作流步骤 `step_a` 并没有得到重新计算，因为它仍在缓存中，而且其执" +"行或输出都没有改变。另外，`cwltool` 能够认识到我们修改了 `step_b` " +"中可执行文件的名称后，它必须重新计算这一步骤。这一技巧十分适用于排查 CWL " +"程序中的错误时，而且可以避免 `cwltool` 无谓地重复运算每一步骤。" #: ../../src/topics/using-containers.md:1 7439fe097aa4459ba1e4c0e28fc59b9a msgid "Using Containers" -msgstr "" +msgstr "使用容器" #: ../../src/topics/using-containers.md:3 eff5c6ac1cad44f9862585daf0a91298 msgid "Running Tools Inside Docker" -msgstr "" +msgstr "在 Docker 中运行工具" #: ../../src/topics/using-containers.md:5 50d1a644bc8c49f78c453e4e0f3c07c8 msgid "" @@ -3570,19 +3581,25 @@ msgid "" " management while avoiding the complexity of invoking and managing Docker" " containers." msgstr "" +"[Docker][docker] 容器可以为软件及其依赖的组件提供确知可正常使用的完整运行环境" +"，进而简化软件的安装。不过，容器与宿主系统是刻意隔离开来的。因此，要在 " +"Docker 容器中运行某个工具，需进行额外操作，以使输入文件在容器内可用，而输出文" +"件可从容器中提取。CWL 运行程序可以自动完成这个任务，从而帮助您使用 Docker " +"简化对软件的管理，同时避免调用和管理 Docker 容器等复杂操作。" #: ../../src/topics/using-containers.md:15 4b0f6cfc8a774c77bfbc99e568af2ece msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." -msgstr "" +msgstr "CWL 运行程序的任务之一，就是调整输入文件的路径，以反映它们在容器内的位置。" #: ../../src/topics/using-containers.md:18 27c02a5d479a420eab7d14888d9fb288 msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." -msgstr "" +msgstr "本示例在 Docker 容器中运行一个简单的 Node.js 脚本，将 \"Hello World\" " +"写入标准输出。" #: ../../src/topics/using-containers.md:21 1a62a93ab20b4f2ca1e13ded3a767dc5 msgid "`docker.cwl`" @@ -3600,6 +3617,9 @@ msgid "" "[`dockerRequirement`](https://w3id.org/cwl/CommandLineTool.html#DockerRequirement)" " section." msgstr "" +"运行这个例子前，我们先来看看代码各部分都是为了做什么。这里，多数内容已在此前" +"的章节中讲授，而算得上新内容的就是 [`dockerRequirement`](https://w3id.org/" +"cwl/CommandLineTool.html#DockerRequirement) 这一段代码。" #: ../../src/topics/using-containers.md:44 1f02618ab6254459ae71f72844e3cc18 msgid "" @@ -3613,6 +3633,14 @@ msgid "" "best practices when using containers for reproducible research). In this " "case we have used a container called `node:slim`." msgstr "" +"`baseCommand: node` 告诉 CWL, 我们打算为了这个命令使用 Node.js 运行环境，" +"意在运行 JavaScript 程序。然后，我们需要给出一点“提示” (`hints`), " +"以便找到我们想要的容器。这个例子里，我们只需要在 `DockerRequirements` " +"下列出我们 Docker 容器的需求。`dockerPull:` 参数应赋予的值，就是您假如使用 `" +"docker pull` 命令的话应该给出的参数，也就是容器映像 (image) 的名称（" +"您可进一步标明容器的标签即 tag, " +"用容器从事可复现研究工作时这是个好习惯）。这里，我们使用的容器名为 " +"`node:slim`." #: ../../src/topics/using-containers.md:52 54cade4978ec463bbb5c0d8c08e27adb msgid "" From 2773ed5c77427f84240940ba073a12d071d9484f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 7 Mar 2024 13:42:37 +0100 Subject: [PATCH 129/179] Update sphinx-autobuild requirement from ==2021.3.* to ==2024.2.* (#454) Updates the requirements on [sphinx-autobuild](https://github.com/sphinx-doc/sphinx-autobuild) to permit the latest version. - [Release notes](https://github.com/sphinx-doc/sphinx-autobuild/releases) - [Changelog](https://github.com/sphinx-doc/sphinx-autobuild/blob/main/NEWS.rst) - [Commits](https://github.com/sphinx-doc/sphinx-autobuild/compare/2021.03.14...2024.02.04) --- updated-dependencies: - dependency-name: sphinx-autobuild dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index b039f887..748cf83d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -53,7 +53,7 @@ test = [ "cwltest==2.*", "cwltool==3.1.*", ] -watch = ["sphinx-autobuild==2021.3.*"] +watch = ["sphinx-autobuild==2024.2.*"] rtd = ["udocker"] all = ["cwl-user-guide[test,watch,rtd]"] From 515c21387daaa886c7d520b25bd4ec2b201f6296 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Thu, 7 Mar 2024 14:07:07 +0100 Subject: [PATCH 130/179] update cwl testing (#460) * CWL tests: add IDs. * custom-types example: don't use Docker Image Format v1 container. --- .../cwl/custom-types/custom-types.cwl | 4 ++-- src/_includes/cwl/cwl_tests.yml | 23 ++++++++++++++++++- 2 files changed, 24 insertions(+), 3 deletions(-) diff --git a/src/_includes/cwl/custom-types/custom-types.cwl b/src/_includes/cwl/custom-types/custom-types.cwl index d60e6e92..bc55213c 100755 --- a/src/_includes/cwl/custom-types/custom-types.cwl +++ b/src/_includes/cwl/custom-types/custom-types.cwl @@ -13,12 +13,12 @@ requirements: hints: DockerRequirement: - dockerPull: 'quay.io/biocontainers/biom-format:2.1.6--py27_0' + dockerPull: 'quay.io/biocontainers/biom-format:2.1.15' SoftwareRequirement: packages: biom-format: specs: [ "https://doi.org/10.1186/2047-217X-1-7" ] - version: [ "2.1.6" ] + version: [ "2.1.15" ] inputs: biom: diff --git a/src/_includes/cwl/cwl_tests.yml b/src/_includes/cwl/cwl_tests.yml index bb27f087..e95d61e3 100644 --- a/src/_includes/cwl/cwl_tests.yml +++ b/src/_includes/cwl/cwl_tests.yml @@ -1,5 +1,6 @@ # Expressions - doc: Test for Expressions section + id: expressions job: expressions/empty.yml tool: expressions/expression.cwl output: @@ -12,12 +13,14 @@ # Inputs - doc: Test for Essential Inputs section + id: essential-inputs job: inputs/inp-job.yml tool: inputs/inp.cwl should_fail: false output: {} - doc: Test for Array Inputs section + id: array-inputs job: inputs/array-inputs-job.yml tool: inputs/array-inputs.cwl output: @@ -29,11 +32,13 @@ size: 60 - doc: Test for Include and Exclusive Inputs section (1st example) + id: include-exclusive-inputs1 job: inputs/record-job1.yml tool: inputs/record.cwl should_fail: true - doc: Test for Include and Exclusive Inputs section (2nd example) + id: include-exclusive-inputs2 job: inputs/record-job2.yml tool: inputs/record.cwl output: @@ -45,6 +50,7 @@ size: 23 - doc: Test for Include and Exclusive Inputs section (3rd example) + id: include-exclusive-inputs3 job: inputs/record-job3.yml tool: inputs/record.cwl output: @@ -57,6 +63,7 @@ # Additional Arguments and Parameters - doc: Test for Additional Arguments and Parameters section + id: additional-arguments-and-parameters job: additional-arguments-and-parameters/arguments-job.yml tool: additional-arguments-and-parameters/arguments.cwl output: @@ -69,6 +76,7 @@ # Parameter References - doc: Test for Parameter References section + id: parameter-references job: parameter-references/tar-param-job.yml tool: parameter-references/tar-param.cwl output: @@ -81,6 +89,7 @@ # Outputs - doc: Test for Outputs section + id: outputs-section job: outputs/tar-job.yml tool: outputs/tar.cwl output: @@ -92,6 +101,7 @@ size: 0 - doc: Test for Outputs, Capturing Standard Output section + id: outputs-capturing-stdout job: outputs/echo-job.yml tool: outputs/stdout.cwl output: @@ -103,6 +113,7 @@ size: 13 - doc: Test for Outputs, Array Outputs section + id: outputs-array-outputs job: outputs/array-outputs-job.yml tool: outputs/array-outputs.cwl output: @@ -121,6 +132,7 @@ # Custom Types # NOTE: The checksum is always changed for every execution - doc: Test for Custom Types section + id: custom-types job: custom-types/custom-types.yml tool: custom-types/custom-types.cwl output: @@ -128,10 +140,11 @@ class: File basename: rich_sparse_otu_table.hdf5 location: Any - size: 46992 + size: 46936 # Workflows - doc: Test for Workflows section + id: workflows-1st-workflow job: workflows/1st-workflow-job.yml tool: workflows/1st-workflow.cwl output: @@ -144,6 +157,7 @@ - doc: Test for Workflows, Nested Workflows section tool: workflows/nestedworkflows.cwl + id: workflows-nestedworkflows output: classout: class: File @@ -164,6 +178,7 @@ # Environment Variables - doc: Test for Environment Variables section + id: environment-variables job: environment-variables/echo-job.yml tool: environment-variables/env.cwl output: @@ -174,6 +189,7 @@ # Using Containers - doc: Test for Using Containers section + id: using-containers job: using-containers/docker-job.yml tool: using-containers/docker.cwl output: @@ -186,6 +202,7 @@ # Creating files at runtime - doc: Test for Creating files at runtime section + id: creating-files-at-runtime job: creating-files-at-runtime/echo-job.yml tool: creating-files-at-runtime/createfile.cwl output: @@ -198,6 +215,7 @@ # Staging input files - doc: Test for Staging input files section + id: staging-input-files job: staging-input-files/arguments-job.yml tool: staging-input-files/linkfile.cwl output: @@ -211,6 +229,7 @@ # File formats # NOTE: The checksum and size is always changed for every execution - doc: Test for File formats section + id: file-formats job: file-formats/sample.yml tool: file-formats/metadata_example.cwl output: @@ -222,6 +241,7 @@ # Metadata and authorship # NOTE: The checksum and size is always changed for every executions - doc: Test for Metadata and authorship section (1st example) + id: metadata-and-authorship job: metadata-and-authorship/sample.yml tool: metadata-and-authorship/metadata_example2.cwl output: @@ -231,6 +251,7 @@ location: Any - doc: Test for Metadata and authorship section (extended example) + id: metadata-and-authorship-extended job: metadata-and-authorship/sample.yml tool: metadata-and-authorship/metadata_example3.cwl output: From 15be3a5cd86b7a9d32a07cf68cefe42cf2aff351 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Wed, 13 Mar 2024 08:09:52 +0100 Subject: [PATCH 131/179] Translations update from Hosted Weblate (#461) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Translated using Weblate (Chinese (Simplified)) Currently translated at 73.7% (442 of 599 strings) Co-authored-by: Zoë Ma Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 66.2% (397 of 599 strings) Translated using Weblate (Japanese) Currently translated at 64.4% (386 of 599 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide --------- Co-authored-by: Zoë Ma Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 82 ++++++++++++----------- locales/zh_Hans/LC_MESSAGES/user_guide.po | 29 +++++--- 2 files changed, 60 insertions(+), 51 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 1c39d0b1..53e71d91 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-03-07 01:01+0000\n" +"PO-Revision-Date: 2024-03-13 02:01+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -989,16 +989,17 @@ msgid "CWL Runner" msgstr "CWL Runner" #: ../../src/introduction/prerequisites.md:39 89f0bf6ff8544a6d87114085be8e0bb6 -#, fuzzy msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " "community. It is also the CWL reference runner, which means it must " "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -"CWL ワークフローを実行するために最初に必要なものは、CWL runnerです。`cwltool` は、CWL " -"コミュニティによって維持されている Python オープンソース・プロジェクトです。これはCWL reference runner(訳注: " -"CWLの参照実装)でもあり、現在のCWL仕様{{ cwl_version }}のすべてをサポートしなければならないことを意味します。" +"CWL ワークフローを実行するために最初に必要なものは、CWL runnerです。`cwltool`" +" は、CWL コミュニティによって維持されている Python " +"オープンソース・プロジェクトです。これはCWL reference runner(訳注: " +"CWLの参照実装)でもあり、`cwltool`は現在のCWL仕様{{ cwl_version " +"}}のすべてをサポートしなければならないことを意味します。" #: ../../src/introduction/prerequisites.md:44 068f09d4d66547448693f7b9dadef497 msgid "" @@ -1009,15 +1010,15 @@ msgstr "" "`conda` のような仮想環境を使用することを推奨します。" #: ../../src/introduction/prerequisites.md:48 1edf8b8438334ae29dc406dbfd711228 -#, fuzzy msgid "" "Visit the `cwltool` " "[documentation](https://cwltool.readthedocs.io/en/latest/#install) for " "details on installing `cwltool`." msgstr "" -"`cwltool` を`apt` と`conda` とともにインストールする他の方法については、`cwltool` " -"[documentation](https://github.com/common-workflow-" -"language/cwltool#install) を参照してください。" +"`cwltool` を`apt` と`conda` " +"とともにインストールする他の方法については、`cwltool` " +"[ドキュメント](https://github.com/common-workflow-language/cwltool#install) " +"を参照してください。" #: ../../src/introduction/prerequisites.md:52 5e300141ce43435f9437507374987213 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." @@ -1054,7 +1055,6 @@ msgid "Running `true.cwl` with `cwltool`." msgstr "`cwltool` を使って `true.cwl` を実行します。" #: ../../src/introduction/prerequisites.md:78 d2dc809318be49cc996d892e93ad84ac -#, fuzzy msgid "Generic ``cwl-runner`` alias" msgstr "一般的な ``cwl-runner`` エイリアス" @@ -1074,13 +1074,13 @@ msgstr "" "は、システム管理者またはユーザーによってインストールされ、好みのCWL実装を指し示す。これは、複数のCWLランナーがある環境では便利です。" #: ../../src/introduction/prerequisites.md:88 6dd6aa836099469381fb564d63b84f3d -#, fuzzy msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`." msgstr "" -"CWLコミュニティは、`cwlref-runner` という名前のPythonパッケージを公開しており、`cwltool` のエイリアスを" -"`cwl-runner` という名前でインストールします" +"CWLコミュニティは、`cwlref-runner` " +"という名前のPythonパッケージを公開しており、`cwltool` のエイリアスを`cwl-" +"runner` という名前でインストールします" #: ../../src/introduction/prerequisites.md:91 cc1a9b95508e44a1bf08ae75d990c301 msgid "Installing `cwl-runner` alias for cwltool with `pip`." @@ -1148,10 +1148,12 @@ msgid "" " using a hard-coded location, since `/usr/bin/env [executable]` looks for" " the `[executable]` program in the system `PATH`," msgstr "" -"*shebang* は、スクリプトの冒頭の2文字列`#!` " -"のことです。スクリプトが実行可能な場合、オペレーティングシステムは、shebangの後に指定された実行可能ファイルを使用してスクリプトを実行します。`/usr/bin/env" -" ` は` ` プログラムをシステムの`PATH` " -"で探すので、ハードコードされた場所を使うよりも`/usr/bin/env ` を使うことが良い習慣と考えられています" +"*shebang* は、スクリプトの冒頭の2文字列`#!` のことです。スクリプトが実行可能" +"な場合、オペレーティングシステムは、shebangの後に指定された実行可能ファイルを" +"使用してスクリプトを実行します。`/usr/bin/env ` は` `" +" プログラムを設定されている環境変数`PATH` " +"の中で探すので、ハードコードされた場所を使うよりも`/usr/bin/env `" +" を使うことが良い習慣と考えられています" #: ../../src/introduction/prerequisites.md:148 854736eef2ac4b63b187a4cea9660ae4 msgid "Text Editor" @@ -1249,12 +1251,14 @@ msgid "Quick Start" msgstr "クイックスタート" #: ../../src/introduction/quick-start.md:3 733db5702c774f32b8c91d13f74f3720 -#, fuzzy msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." -msgstr "このセクションでは、CWLとは何か、またCWLについてもっと詳しく知ることができる場所について、簡単に紹介します。CWLに関する予備知識は必要ありませんが、コマンドラインを使用することに慣れていると良いです。" +msgstr "" +"このセクションでは、CWLとは何か、またCWLについてもっと詳しく知ることができる" +"場所について、簡単に紹介します。CWLに関する予備知識は必要ありませんが、コマン" +"ドラインを使用することに慣れていると良いです。" #: ../../src/introduction/quick-start.md:7 0b164074dd0849c3b2c8d2f78ea99e95 msgid "“Hello World”" @@ -1860,15 +1864,14 @@ msgstr "`createfile.cwl`" #: ../../src/topics/creating-files-at-runtime.md:15 #: 252f8e897b0942a8be098481890005f3 -#, fuzzy msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " "value at the input `message`." msgstr "" -"`$(inputs.message)` のような " -"[Expressions](../topics/expressions.md)は、ファイルを作成する前にCWLエンジンによって展開されます。ここでは、入力パラメータ`message`" -" に値を挿入します。" +"`$(inputs.message)` のような [Expressions](../topics/expressions.md)は、ファ" +"イルを作成する前にCWL実行エンジンによって展開されます。ここでは、入力パラメー" +"タ`message` に値を挿入します。" #: ../../src/topics/creating-files-at-runtime.md:20 #: aca24b72687c4d4d84bf9de8b71413f7 @@ -1952,7 +1955,6 @@ msgid "Custom Types" msgstr "カスタムタイプ" #: ../../src/topics/custom-types.md:3 e0275ddda8f84207a58d10c17ca99a45 -#, fuzzy msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1962,7 +1964,7 @@ msgid "" msgstr "" "CWL定義で使用・再利用するために、独自のカスタム型を書きたい場合があります。こ" "のようなカスタムタイプを使用することで、同じタイプを使用する複数の記述の間の" -"冗長性を減らし、また、CWL記述を直接いじらずに、ツールや分析のカスタマイズや設" +"冗長性を減らし、また、CWL定義を直接いじらずに、ツールや分析のカスタマイズや設" "定を追加できるようになります。" #: ../../src/topics/custom-types.md:9 8367e38e5e7c4a298d1d87b9001aaddc @@ -4561,12 +4563,14 @@ msgid "YAML Guide" msgstr "YAMLガイド" #: ../../src/topics/yaml-guide.md:6 705765787eb84ecaae004194225924cb -#, fuzzy msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." -msgstr "[YAML][yaml]は、コンピュータと人間の両方が読むことができるように設計されたファイル形式です。本ガイドでは、CWL定義や入力パラメータファイルを書く際に関連するYAMLの機能を紹介します。" +msgstr "" +"[YAML][yaml]は、コンピュータと人間の両方が読むことができるように設計されたフ" +"ァイル形式です。本ガイドでは、CWL定義や入力パラメータファイルを書く際に関連す" +"るYAMLの機能を紹介します。" #: ../../src/topics/yaml-guide.md:13 cb243f6ab11f48ffb5c91945c4e0d101 msgid "You can skip this section if you are already comfortable with YAML." @@ -4614,7 +4618,6 @@ msgstr "" "は、CWL仕様で特別な意味を持つ複数語のキー名、それ以外はアンダースコアのキー名として使用します。例えば：" #: ../../src/topics/yaml-guide.md:42 514365e59d9648deb896e2068d967a64 -#, fuzzy msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -4622,12 +4625,12 @@ msgid "" "representation), Boolean (`true` or `false`), or more complex nested " "types (see below)." msgstr "" -"上記のYAMLは4つのキー -`first_name`,`last_name`,`age_years`, `home` - " -"と4つのそれぞれの値を定義しています。値は、文字列、数値（整数、浮動小数点、科学的表現）、ブール値（`true` または`false` " +"上記のYAMLは4つのキー -`first_name`,`last_name`,`age_years`, `home` - 及びそ" +"れぞれの値を定義しています。値は、文字列、数値（整数、浮動小数点、科学的表現" +"）、ブール値（`true` または`false` " "）、またはより複雑な入れ子型（下記参照）にすることができます。" #: ../../src/topics/yaml-guide.md:51 6939eb7e783744d7bcf75ea0a7cae129 -#, fuzzy msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -4637,34 +4640,33 @@ msgid "" "want to specify a fixed numeric value to a command, make sure that you " "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -"値は引用符で括ることができますが、意味が変わってきます。例えば、`\"1234\"` は文字列として扱われ、`1234` " -"は整数値として扱われます。CWLでは、`baseCommand` " -"のすべての部分が文字列でなければならないので、コマンドに固定した数値を指定する場合は、その数値を引用符で囲むようにしてください：[echo, " -"\"42\"]`." +"値は引用符で括ることができますが、意味が変わってきます。例えば、`\"1234\"` " +"は文字列として扱われ、`1234` は整数値として扱われます。CWLでは、`baseCommand`" +" のすべての部分が文字列でなければならないので、コマンドに固定した数値を指定す" +"る場合は、その数値を引用符で囲むようにしてください：[echo, \"42\"]`." #: ../../src/topics/yaml-guide.md:61 96e1776b09e840ebbc9b4b7e01da0e43 msgid "Comments" msgstr "コメント" #: ../../src/topics/yaml-guide.md:63 8b17f7557c3540b2b0d0beca0fe4ebc7 -#, fuzzy msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -"`#` を使って、CWL定義と入力パラメータファイルにコメントを追加することができます。` #` の右側にある文字は、YAML " +"`#` を使うと、CWL定義や入力パラメータファイルにコメントを追加することができま" +"す。` #` の右側にある文字は、YAML " "を解釈するプログラムによって無視されます。たとえば、次のようになります：" #: ../../src/topics/yaml-guide.md:76 13da997c82c04023a4b7bb36b76e969d -#, fuzzy msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" -msgstr "同じ行内のコメントの前に何かある場合は、必ず`#` の前に少なくとも1つのスペースを追加してください！" +msgstr "同じ行の中でコメントの前に何かある場合は、必ず`#` " +"の前に少なくとも1つのスペースを追加してください！" #: ../../src/topics/yaml-guide.md:79 b9fc191166a64450b64a8182adabad75 -#, fuzzy msgid "Maps" msgstr "マップ" diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 5bbe5fd4..1ff0ee46 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-03-07 01:01+0000\n" +"PO-Revision-Date: 2024-03-08 11:01+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified) \n" @@ -3633,20 +3633,21 @@ msgid "" "best practices when using containers for reproducible research). In this " "case we have used a container called `node:slim`." msgstr "" -"`baseCommand: node` 告诉 CWL, 我们打算为了这个命令使用 Node.js 运行环境，" -"意在运行 JavaScript 程序。然后，我们需要给出一点“提示” (`hints`), " -"以便找到我们想要的容器。这个例子里，我们只需要在 `DockerRequirements` " -"下列出我们 Docker 容器的需求。`dockerPull:` 参数应赋予的值，就是您假如使用 `" -"docker pull` 命令的话应该给出的参数，也就是容器映像 (image) 的名称（" +"`baseCommand: node` 告诉 CWL, 我们运行命令打算使用 Node.js 环境，意在执行 " +"JavaScript 程序。然后，我们需要给出一点“提示” (`hints`), " +"以便找到我们需要的容器。这个例子里，我们只需要在 `DockerRequirements` " +"下列出我们 Docker 容器的需求即可。`dockerPull:` 参数应赋予的值，" +"就是您假如使用 `docker pull` 命令时会给出的参数，即容器映像 (image) 的名称（" "您可进一步标明容器的标签即 tag, " -"用容器从事可复现研究工作时这是个好习惯）。这里，我们使用的容器名为 " +"用容器从事可复现研究工作时这是个好习惯）。这个例子里，我们使用的容器名为 " "`node:slim`." #: ../../src/topics/using-containers.md:52 54cade4978ec463bbb5c0d8c08e27adb msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" -msgstr "" +msgstr "创建一个名为 \"hello.js\" 的 JavaScript " +"文件，然后在命令行中，以工具描述和输入对象为参数，调用 `cwltool`:" #: ../../src/topics/using-containers.md:55 6541d0cd9f6c4c43b8601715cc35e585 msgid "`hello.js`" @@ -3656,7 +3657,7 @@ msgstr "`hello.js`" msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." -msgstr "" +msgstr "请注意，CWL 运行程序构建出了一行 Docker 命令，用来运行脚本。" #: ../../src/topics/using-containers.md:72 d2dd89a5edde4f2eab4c2baf0cc78745 msgid "" @@ -3665,10 +3666,13 @@ msgid "" "`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " "reflected in the invocation of the `node` command." msgstr "" +"这个例子中，在容器外部，脚本 `hello.js` 的路径位于 `/home/me/cwl/user_guide/" +"hello.js`, 而它在容器内的路径为 `/var/lib/cwl/job369354770_examples/hello.js`" +", 这从 `node` 命令的调用参数可见。" #: ../../src/topics/workflows.md:1 06281a10592d42509566c8fc51f8d4da msgid "Workflows" -msgstr "" +msgstr "工作流" #: ../../src/topics/workflows.md:3 325a656f9b8e4c1fa6f699cd8c447d00 msgid "" @@ -3676,10 +3680,13 @@ msgid "" "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" +"工作流 (workflow) 指的是将命令行工具、表达式工具或（子）" +"工作流等作为步骤进行执行的 CWL 处理单元。一个工作流必须具备 CWL 程序所定义的 " +"`inputs`（输入）, `outputs`（输出）, 以及 `step`（步骤）." #: ../../src/topics/workflows.md:13 b92275181c9e480da64e660b7aca0745 msgid "CWL workflow." -msgstr "" +msgstr "CWL 工作流" #: ../../src/topics/workflows.md:41 be2540315f854b8e9a1d257bcabd78db msgid "" From c3c4e32d637b781020cfdf6b2dd00624e03a5fb6 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Sat, 16 Mar 2024 11:08:02 +0100 Subject: [PATCH 132/179] Translated using Weblate (Japanese) (#463) Currently translated at 68.6% (411 of 599 strings) Translated using Weblate (Japanese) Currently translated at 67.4% (404 of 599 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 86 +++++++++++++++------------- 1 file changed, 47 insertions(+), 39 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 53e71d91..a880629d 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-03-13 02:01+0000\n" +"PO-Revision-Date: 2024-03-16 02:01+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -1468,7 +1468,6 @@ msgstr "ツールには、入力パラメータに正確に対応しない追加 #: ../../src/topics/additional-arguments-and-parameters.md:6 #: dfed0747ed544547afd364086d828c9b -#, fuzzy msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1477,9 +1476,12 @@ msgid "" "instruct \"javac\" to write the class file to the designated output " "directory instead." msgstr "" -"この例では、Javaコンパイラを使用して、javaソースファイルをクラスファイルにコンパイルするようにラップします。 " -"デフォルトでは、\"javac \"はソース・ファイルと同じディレクトリにクラス・ファイルを作成します。 " -"しかし、CWLの入力ファイル（およびそのディレクトリ）は読み取り専用である場合があるので、代わりに指定された出力ディレクトリにクラスファイルを書き込むように「javac」に指示する必要があります。" +"この例では、Javaコンパイラを使用して、javaソースファイルをclassファイルにコン" +"パイルするようにラップします。 デフォルトでは、\"javac " +"\"はjavaファイルと同じディレクトリにclassファイルを作成します。 しかし、CWL" +"の入力ファイル（およびそのディレクトリ）は読み取り専用である場合があるので、" +"代わりに指定された出力ディレクトリにclassファイルを書き込むように「javac」に" +"指示する必要があります。" #: ../../src/topics/additional-arguments-and-parameters.md:13 #: e690b567eae34f3f8dbdd7760e51449a @@ -1513,7 +1515,6 @@ msgstr "ここでは、`arguments` フィールドを使用して、特定の入 #: ../../src/topics/additional-arguments-and-parameters.md:43 #: dc9fa5f2cbb147b1853c4042c54010f3 -#, fuzzy msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1523,9 +1524,9 @@ msgid "" "`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " "Environment][runtime] section of the CWL specification for details." msgstr "" -"この例では、ランタイムパラメータを参照しています。 ランタイムパラメータは、" -"ツールが実際に実行されたときのハードウェアまたはソフトウェア環境に関する情報" -"を提供します。 ` $(runtime.outdir)` " +"この例では、runtimeパラメータを参照しています。 runtimeパラメータは、ツール" +"が実際に実行されたときのハードウェアまたはソフトウェア環境に関する情報を提供" +"します。 ` $(runtime.outdir)` " "パラメータは、指定された出力ディレクトリへのパスです。 その他、`$(runtime." "tmpdir)`,`$(runtime.ram)`,`$(runtime.cores)`,`$(runtime." "outdirSize)`,`$(runtime.tmpdirSize)` などがあります。 詳細はCWL仕様書の[" @@ -1536,13 +1537,15 @@ msgid "Best Practices" msgstr "ベストプラクティス" #: ../../src/topics/best-practices.md:3 7b59377bd56c47b8a71c18acfba4d3bb -#, fuzzy msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " "workflow. These guidelines are presented for consideration on a scale of " "usefulness: although more is better, not all are required." -msgstr "以下は、ツールやワークフローのCWL定義を書く際に留意すべき推奨グッドプラクティスのセットです。これらのガイドラインは、有用性の尺度で検討するために提示されています：多ければ多いほど良いが、すべてが必要なわけではありません。" +msgstr "" +"以下は、ツールやワークフローのCWL定義を書く際に留意すべき推奨グッドプラクティ" +"スのセットです。これらのガイドラインは、有用性の尺度で検討するために提示され" +"ています：多ければ多いほど良いが、すべてが必要なわけではありません。" #: ../../src/topics/best-practices.md:8 2292670347cd4549bc6a51e972de0ef4 msgid "" @@ -1607,13 +1610,13 @@ msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "_SPDX 識別子を持つライセンスのメタデータフィールドの例：_" #: ../../src/topics/best-practices.md:37 924b8df24deb4c82b32732f491c9a246 -#, fuzzy msgid "" "For more examples of providing metadata within CWL descriptions, see [the" " Metadata and Authorship section of this User Guide](../topics/metadata-" "and-authorship.md)." msgstr "" -"CW定義にメタデータを与える例については、 [このユーザーガイドのメタデータと著者名のセクション](../topics/metadata-and-" +"CW定義にメタデータを与える例については、 " +"[このユーザーガイドのメタデータと著者名のセクション](../topics/metadata-and-" "authorship.md)を参照してください。" #: ../../src/topics/best-practices.md:40 9e64a9fc89cb45cfbff0e925cc91b1be @@ -1626,20 +1629,21 @@ msgstr "" "example]を含みます。[ORCID][orcid]のような曖昧でない識別子を使用してください。" #: ../../src/topics/best-practices.md:44 87030aef02044b8283c76debab4772bf -#, fuzzy msgid "" "In tool descriptions, list dependencies using short name(s) under " "[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." -msgstr "ツール定義では、`SoftwareRequirement` の下に、短い名前を使用して依存関係をリストアップします。" +msgstr "" +"ツール定義では、[`SoftwareRequirement`] (https://w3id.org/cwl/CommandLineTool" +".html#SoftwareRequirement)." +"の下に、短い名前を使用して依存関係をリストアップします。" #: ../../src/topics/best-practices.md:47 6c9eaae099fa4ca4b0986b1c4146df50 -#, fuzzy msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` フォーマットで依存関係のための " -"[SciCrunch][scicrunch] 識別子を含みます。" +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` 形式で依存関係のための " +"[SciCrunch][scicrunch] 識別子を書きます。" #: ../../src/topics/best-practices.md:50 5ae8950fd31541399c2fe59096581dbc msgid "" @@ -1654,14 +1658,14 @@ msgstr "" "または`aligned_sequences` などの情報量の多い名称を使ってください。" #: ../../src/topics/best-practices.md:55 b0493895105e43849bff2026763e472a -#, fuzzy msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under " "[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "" -"ツール定義では、`SoftwareRequirement` " -"の下に、このツール定義で動作することが確認されているツールのバージョンのリストを含めるます。" +"ツール定義では、[`SoftwareRequirement`] (https://w3id.org/cwl/CommandLineTool" +".html#SoftwareRequirement)の下に、このツール定義で動作することが確認されてい" +"るツールのバージョンのリストを書きます。" #: ../../src/topics/best-practices.md:58 88806cb0462f4359801c1fa0ff0ebcc0 #, fuzzy @@ -3027,7 +3031,6 @@ msgid "Exclusive Input Parameters with Expressions" msgstr "式で入力パラメータを排他的に指定する" #: ../../src/topics/inputs.md:257 cf22f21ec44c483986979316544a7c3b -#, fuzzy msgid "" "If you use exclusive input parameters and reference them in expressions, " "you need to be aware that the `inputs` JavaScript object will contain one" @@ -3035,18 +3038,18 @@ msgid "" "these exclusive values may differ, you may need to check which type is in" " use when you reference the properties of the `input` object." msgstr "" -"排他的入力パラメータを式と組み合わせて使用する場合、`inputs` JavaScript " -"オブジェクトに排他的入力値のいずれかが含まれることを意識する必要があります。つまり、**or** " -"のブーリアン演算子を使用して、どの値が存在するかをチェックする必要がある場合があります。" +"排他的入力パラメータを式と組み合わせて使用する場合、JavaScript " +"オブジェクトの`inputs` に排他的入力値のいずれかが含まれることを意識する必要が" +"あります。つまり、**or** のブーリアン演算子を使用して、`inputs`にどの値が存在" +"するかをチェックする必要がある場合があります。" #: ../../src/topics/inputs.md:263 0fecb128b19b44d796b6c1b6de4f7166 -#, fuzzy msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -"`file_format` 入力パラメータに、`null` (つまり、値が提供されていない)、または enum " +"`file_format` 入力パラメータに、`null` (つまり、値がない)、または enum " "の任意の値を受け入れる排他的なものを含む例を使ってみましょう。" #: ../../src/topics/inputs.md:266 7f1941698a6046e9b9e8a53736af949a @@ -3054,15 +3057,15 @@ msgid "`exclusive-parameter-expressions.cwl`" msgstr "`exclusive-parameter-expressions.cwl`" #: ../../src/topics/inputs.md:272 60b585142f06489d9f48090b664b6d32 -#, fuzzy msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " "provide a valid value, such as `fasta` (one of the possible values of the" " enum), your command should execute successfully:" msgstr "" -"JavaScriptの式では、`null` " -"の値を考慮せずに、排他的入力パラメータの値を使用していることに注意してください。\"fasta\"（enumの値の1つ）のような有効な値を指定すると、コマンドは正常に実行されるはずです：" +"JavaScriptの式では、`null` の値を考慮せずに、排他的入力パラメータの値を使用し" +"ていることに注意してください。`fasta`（enumの値の1つ）のような有効な値を指定" +"すると、コマンドは正常に実行されるはずです：" #: ../../src/topics/inputs.md:281 11fdeb057d674f118830f431ff019c15 #, fuzzy @@ -3282,7 +3285,6 @@ msgid "Passing mandatory arguments to the `baseCommand`" msgstr "`baseCommand` に必須引数を渡します。" #: ../../src/topics/outputs.md:21 553d535b023e4d69a888fe5b24bb8c5b -#, fuzzy msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string, we can use an" @@ -3290,8 +3292,10 @@ msgid "" "the array is the command to run, and any subsequent elements are " "mandatory command line arguments" msgstr "" -"これまでの例では、`baseCommand` は単なる文字列で、引数はCWL入力として渡していました。単一の文字列の代わりに、文字列の配列__ " -"を使用することができます。 最初の要素は実行するコマンドで、それ以降の要素は必須のコマンドライン引数です" +"これまでの例では、`baseCommand` " +"は単なる文字列で、引数はCWL入力として渡していました。単一の文字列の代わりに、" +"_文字列の配列_ を使用することができます。 配列の最初の要素は実行するコマンド" +"で、それ以降の要素は必須のコマンドライン引数です" #: ../../src/topics/outputs.md:28 9b65071222c94951bed12ac53e964ee3 msgid "`tar.cwl`" @@ -3302,7 +3306,6 @@ msgid "`tar-job.yml`" msgstr "`tar-job.yml`" #: ../../src/topics/outputs.md:40 f9752ec303ab419c8db8adef3fa2466f -#, fuzzy msgid "Next, create a tar file for the example." msgstr "次に、サンプルとなるtarファイルを作成します。" @@ -3313,15 +3316,16 @@ msgid "" msgstr "そして、今度はコマンドラインにツール定義と入力オブジェクトを指定して`cwltool` を呼び出します：" #: ../../src/topics/outputs.md:53 707803bec0cb42919905c7c321bd9d30 -#, fuzzy msgid "" "The field " "[`outputBinding`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding)" " describes how to set the value of each output parameter." -msgstr "`outputBinding` フィールドには、各出力パラメータの値の設定方法が記述されています。" +msgstr "" +"[`outputBinding`](https://w3id.org/cwl/CommandLineTool." +"html#CommandOutputBinding) " +"フィールドには、各出力パラメータの値の設定方法が記述されています。" #: ../../src/topics/outputs.md:64 cbaec50871e04718883c8c91ff475d20 -#, fuzzy msgid "" "The " "[`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) " @@ -3330,7 +3334,9 @@ msgid "" "know the name of the file in advance, you can use a wildcard pattern like" " `glob: '*.txt'`." msgstr "" -"`glob` フィールドは、出力ディレクトリ内のファイル名で構成されます。ファイル名が予め分からない場合は、`glob: '*.txt'` " +"[`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) フィ" +"ールドは、出力ディレクトリ内のファイル名で構成されます。前もって出力ファイル" +"名が分からない場合は、`glob: '*.txt'` " "のようにワイルドカードパターンを使用することができます。" #: ../../src/topics/outputs.md:69 8a6e9173198241429effd911c3a7c4d7 @@ -3345,7 +3351,9 @@ msgid "" "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -"ツールの標準出力をキャプチャするには、`stdout` フィールドに、標準出力を保存したいファイル名を追加します。 " +"ツールの標準出力をキャプチャするには、[`stdout`](https://w3id.org/cwl/" +"CommandLineTool.html#stdout) " +"フィールドに、標準出力を保存したいファイル名を追加します。 " "次に、対応する出力パラメータに`type: stdout` を追加します。" #: ../../src/topics/outputs.md:75 cf2ef8dc7fda49308c09efe4f4ef5d7b From 9ea16ff78151d6cf71d8706f4ea4a1912c679276 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Wed, 20 Mar 2024 18:12:08 +0100 Subject: [PATCH 133/179] Translations update from Hosted Weblate (#464) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Translated using Weblate (Japanese) Currently translated at 70.9% (425 of 599 strings) Translated using Weblate (Japanese) Currently translated at 70.2% (421 of 599 strings) Translated using Weblate (Japanese) Currently translated at 69.2% (415 of 599 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Chinese (Simplified)) Currently translated at 75.6% (453 of 599 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 75.2% (451 of 599 strings) Co-authored-by: Zoë Ma Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide * Deleted translation using Weblate (Russian) * Deleted translation using Weblate (Russian) --------- Co-authored-by: Manabu ISHII Co-authored-by: Zoë Ma Co-authored-by: Michael Crusoe --- locales/ja/LC_MESSAGES/user_guide.po | 79 +- locales/ru/LC_MESSAGES/sphinx.po | 27 - locales/ru/LC_MESSAGES/user_guide.po | 4336 --------------------- locales/zh_Hans/LC_MESSAGES/user_guide.po | 32 +- 4 files changed, 66 insertions(+), 4408 deletions(-) delete mode 100644 locales/ru/LC_MESSAGES/sphinx.po delete mode 100644 locales/ru/LC_MESSAGES/user_guide.po diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index a880629d..71137498 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-03-16 02:01+0000\n" +"PO-Revision-Date: 2024-03-20 01:01+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -625,14 +625,17 @@ msgid "Implementations" msgstr "実装" #: ../../src/introduction/basic-concepts.md:39 c87e6daefda74579a39924777b2e6809 -#, fuzzy msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " "However, implementations may not implement every aspect of the " "specification. CWL implementations are licensed under both Open Source " "and commercial licenses." -msgstr "CWL仕様の実装とは、あるバージョンの仕様書で定義された内容に従って書かれたソフトウェアのことです。ただし、実装は仕様のすべての側面を実装するわけではありません。CWLの実装は、オープンソース・ライセンスと商用ライセンスの両方でライセンスされています。" +msgstr "" +"CWL仕様の実装とは、あるバージョンの仕様書で定義された内容に従って書かれたソフ" +"トウェアのことです。ただし、実装は仕様にあるすべてを実装するわけではありませ" +"ん。CWLの実装は、オープンソース・ライセンスと商用ライセンスの両方でライセンス" +"されています。" #: ../../src/introduction/basic-concepts.md:44 c995e699ae2949219af252f9d802a43d msgid "" @@ -701,23 +704,27 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:122 #: c88ad26efa794cbeb6f0690aa0cad5ea -#, fuzzy msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" " a workflow execution into reusable JavaScript code that takes inputs and" " produces outputs like a command-line tool." -msgstr "ExpressionToolは、JavaScriptの式のラッパーです。WorkflowやCommandLineToolの簡略化に使用でき、ワークフロー実行の共通部分を、CommandLineToolのように入力を受けて出力を生成する再利用可能なJavaScriptコードに移動させることができます。" +msgstr "" +"ExpressionToolは、JavaScriptの式のラッパーです。WorkflowやCommandLineToolの簡" +"略化に使用でき、ワークフロー実行の共通部分を、CommandLineToolのように入力を受" +"けて出力を生成する再利用可能なJavaScriptコードに移動させることができます。" #: ../../src/introduction/basic-concepts.md:127 #: 946825a7ea2c450eb3e41b5548670fb7 -#, fuzzy msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" " so commonly used. It is discussed in the [Operations " "section](../topics/operations.md) of this user guide." -msgstr "Operationは、入力を受け、出力を出す抽象的なプロセスでもあり、ワークフローで使用することができます。しかし、あまり一般的に使われていない特別な処理です。このユーザーガイドの[Operation編](../topics/operations.md)で説明します。" +msgstr "" +"Operationは、入力を受け、出力を出す抽象的なプロセスでもあり、ワークフローで使" +"用することができます。しかし、あまり一般的に使われていない特別な処理です。こ" +"のユーザーガイドの[Operation編](../topics/operations.md)で説明します。" #: ../../src/introduction/basic-concepts.md:131 #: 44aac23f302c4178accf7e431cfbb96c @@ -774,7 +781,6 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:145 #: fb3762f91177401ea624d1e716d67ae6 -#, fuzzy msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -782,9 +788,10 @@ msgid "" "the {{ cwl_version }} specification and may not be supported by other CWL" " runners." msgstr "" -"いくつかのCWLランナーは、仕様にないrequirementsを提供することがあります。例えば、GPUに関するrequirementsは`cwltool`" -" で`cwltool:CUDARequirement` を通してサポートされていますが、{{ cwl_version " -"}}仕様の一部ではないので、他のCWLランナーではサポートされていないかもしれません。" +"いくつかのCWLランナーは、仕様にないrequirementsを提供することがあります。例え" +"ば、GPUに関するrequirementsは`cwltool` で`cwltool:CUDARequirement` " +"を通してサポートされていますが、{{ cwl_version }}仕様の一部ではないので、他の" +"CWLランナーではサポートされていないかもしれません。" #: ../../src/introduction/basic-concepts.md:151 #: b6a5cd431c324078a9a4e1513a14ee28 @@ -1304,7 +1311,6 @@ msgid "Installing a CWL Runner" msgstr "CWL Runnerのインストール" #: ../../src/introduction/quick-start.md:34 73a42cd9e0e54296985088b7221a8a93 -#, fuzzy msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1312,8 +1318,8 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" "`cwltool` は、CWL仕様の実装の１つです。また、同仕様のCWL*Reference Runner* " -"でもあり、同仕様の最新バージョンに準拠しています：{cwl_version }}に準拠しています。`cwltool` は、`pip` " -"を使ってインストールできます：" +"でもあり、同仕様の最新バージョンに準拠しています：{{cwl_version " +"}}に準拠しています。`cwltool` は、`pip` を使ってインストールできます：" #: ../../src/introduction/quick-start.md:39 57aea587ade24610be62f5d993b0b755 msgid "Installing `cwltool` with `pip`." @@ -1334,14 +1340,14 @@ msgid "Running \"Hello World\"" msgstr "\"Hello World\"を実行する" #: ../../src/introduction/quick-start.md:53 0595e96912dc40e5a09f2ced2d2b7bcd -#, fuzzy msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [CWL_DOCUMENT] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -"`cwltool` コマンドライン実行ファイルの使い方は、基本的に`cwltool [OPTIONS] " -"[INPUTS_OBJECT]`です。`hello_world.cwl` Workflowは、オプションを指定せずに実行することができます：" +"基本的に `cwltool` の使い方は、`cwltool [OPTIONS] [cwl_document] " +"[INPUTS_OBJECT]`です。`hello_world.cwl` " +"Workflowは、オプションを指定せずに実行することができます：" #: ../../src/introduction/quick-start.md:57 5b393c69816549b084516dda4d4274f5 msgid "Running `hello_world.cwl` with `cwltool`." @@ -1383,15 +1389,16 @@ msgid "Passing an Inputs Object file to `cwltool`." msgstr "`cwltool` に Inputs Object ファイルをします。" #: ../../src/introduction/quick-start.md:88 52b1602b5c8d48db88d0b16f788e7703 -#, fuzzy msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " "it is not a requirement. You can choose any name for your workflows and " "Inputs Object files." msgstr "" -"ワークフローとInputs Objectファイルには、同様のファイル名を使用しました。*-job.json* という接尾辞は、Inputs " -"Object ファイルでは非常に一般的ですが必須ではありません。ワークフローとInputs " +"ワークフローとInputs " +"Objectファイルには、同様のファイル名を使用しました。*-job.json* " +"という接尾辞は、Inputs Object " +"ファイルでは非常に一般的ですが必須ではありません。ワークフローとInputs " "Objectファイルには、任意の名前を付けることができます。" #: ../../src/introduction/quick-start.md:96 3b06faf5f3194bd8a96118d9f050f61e @@ -1427,14 +1434,13 @@ msgstr "" "[WikipediaにあるYAML](https://en.wikipedia.org/wiki/YAML) です。" #: ../../src/introduction/quick-start.md:101 2bf7b924182f4f2bab88edef5ef85baa -#, fuzzy msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -"{{'[CWL 仕様 VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION'," -" cwl_version_text) }} のことです。" +"{{'[CWL 仕様 VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " +"cwl_version_text) }} のことです。" #: ../../src/introduction/quick-start.md:102 936a7dfab11a4f2c82c0b59964e3ea28 msgid "" @@ -1443,28 +1449,27 @@ msgid "" msgstr "[Wikipediaの項目としてのワークフロー管理システム](https://en.wikipedia.org/wiki/Workflow_management_system)。" #: ../../src/setup.md:9 24ea9c5144664d9599d7aca767b4730a -#, fuzzy msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " "[FAQ](/faq.md) section of the new user guide." msgstr "" -"このページは古いもので、旧ユーザーガイドのリンクを保存するためにここに残されていました。このページの情報は、新しいユーザーガイドの " -"[FAQ](/faq.md) セクションに移行されました。" +"このページは古いもので、旧ユーザーガイドのリンクを保存するためにここに残され" +"ていました。このページの情報は、新しいユーザーガイドの [FAQ](/faq.md) " +"セクションに移行されました。" #: ../../src/topics/additional-arguments-and-parameters.md:1 #: 3843684b039a40dea163de951ca56738 -#, fuzzy msgid "Additional Arguments and Parameters" msgstr "追加の引数とパラメータ" #: ../../src/topics/additional-arguments-and-parameters.md:3 #: a6fd1842b938435aa2a3c889019eec71 -#, fuzzy msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." -msgstr "ツールには、入力パラメータに正確に対応しない追加のコマンドラインオプションが必要な場合があります。" +msgstr "ツールには、入力パラメータに正確に対応しない追加のコマンドラインオプションが" +"必要な場合があります。" #: ../../src/topics/additional-arguments-and-parameters.md:6 #: dfed0747ed544547afd364086d828c9b @@ -1689,17 +1694,16 @@ msgstr "" "。このページを編集して私たちに知らせてください。" #: ../../src/topics/best-practices.md:66 b178c7296ed5491782a4180c76883c14 -#, fuzzy msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -"`File`の入出力のうち、ストリーミング互換の方法（一度だけ、ランダムアクセスなし）で読み書きされるものを、`streamable: true`" -" としてマークします。" +"`File`の入出力のうち、ストリーミング互換の方法（一度だけ利用されて、ランダム" +"アクセスなし、訳注標準入出力のイメージ）で読み書きされるものを、`streamable: " +"true` としてマークします。" #: ../../src/topics/best-practices.md:69 886d15c1972243acadccff5760f842f1 -#, fuzzy msgid "" "Each " "[`CommandLineTool`](https://w3id.org/cwl/CommandLineTool.html#CommandLineTool)" @@ -1707,18 +1711,19 @@ msgid "" "(sub)command is capable of more. Don't overcomplicate your tool " "descriptions with options that you don't need or use." msgstr "" -"各`CommandLineTool` " -"の定義は、たとえ（サブ）コマンドがそれ以上の機能を備えていたとしても、単一の操作のみに焦点を当てるべきです。必要でない、または使用しないオプションでツールの定義を複雑にし過ぎないようにしましょう。" +"各`CommandLineTool` の定義は、たとえ（サブ）コマンドがそれ以上の機能を備えて" +"いたとしても、一つの使用方法のみに焦点を当てるべきです。必要ないまたは、使用" +"しないオプションでツールの定義を複雑にし過ぎないようにしましょう。" #: ../../src/topics/best-practices.md:73 ef5a5f9b253c4ca3916802a695fb7c6d #, fuzzy msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." -msgstr "カスタム型は、再利用のため、タイプ定義ごとに1つの外部YAMLで定義する必要があります。" +msgstr "カスタム型は、再利用のため、タイプ定義ごとに1つの外部YAMLで定義した方が良いで" +"す。" #: ../../src/topics/best-practices.md:76 ff59f40e84004523904e3094be07cc80 -#, fuzzy msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "ツール/ワークフローを要約したトップレベルの短い`label` を含めます。" diff --git a/locales/ru/LC_MESSAGES/sphinx.po b/locales/ru/LC_MESSAGES/sphinx.po deleted file mode 100644 index 13426aa9..00000000 --- a/locales/ru/LC_MESSAGES/sphinx.po +++ /dev/null @@ -1,27 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: ru\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/_templates/sidebar-nav-bs.html:1 -#: d65b012160e9455eb4d2628279fffc42 -msgid "Main navigation" -msgstr "" - -#: ../../src/_templates/sidebar-nav-bs.html:3 -#: 4b3441eb77f448daa60718b7bfa862db -msgid "Section Navigation" -msgstr "" diff --git a/locales/ru/LC_MESSAGES/user_guide.po b/locales/ru/LC_MESSAGES/user_guide.po deleted file mode 100644 index 2ccbe00b..00000000 --- a/locales/ru/LC_MESSAGES/user_guide.po +++ /dev/null @@ -1,4336 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow -# Language User Guide package. -# FIRST AUTHOR , 2023. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language: ru\n" -"Language-Team: none\n" -"Plural-Forms: nplurals=3; plural=(n%10==1 && n%100!=11 ? 0 : n%10>=2 && " -"n%10<=4 && (n%100<10 || n%100>=20) ? 1 : 2);\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.12.1\n" - -#: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac -msgid "Licenses" -msgstr "" - -#: ../../LICENSE.md:4 9dd9705700664b31a3f296d263b4028b -msgid "Instructional Material" -msgstr "" - -#: ../../LICENSE.md:6 e54324bd39cd431d91b32e338217b8c7 -msgid "" -"All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the [Creative Commons " -"Attribution license][cc-by-human]. The following is a human-readable " -"summary of (and not a substitute for) the [full legal text of the CC BY " -"4.0 license][cc-by-legal]." -msgstr "" - -#: ../../LICENSE.md:12 754f3f54aa4142ef9dac27f508dd0bca -msgid "You are free:" -msgstr "" - -#: ../../LICENSE.md:14 d2b1d5e965ef4e71b64c359549919975 -msgid "to **Share**---copy and redistribute the material in any medium or format" -msgstr "" - -#: ../../LICENSE.md:15 fe9551ffef8149bf8da50e70318e8de8 -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" - -#: ../../LICENSE.md:17 247db3bcc7024c44a044886a29ef1414 -msgid "for any purpose, even commercially." -msgstr "" - -#: ../../LICENSE.md:19 c04d906124854afc917707b7b4e45bb2 -msgid "" -"The licensor cannot revoke these freedoms as long as you follow the " -"license terms:" -msgstr "" - -#: ../../LICENSE.md:24 551cb5ab59dd4737b1042a4ef79ffab7 -msgid "" -"**Attribution**---You must give appropriate credit (mentioning that your " -"work is derived from work that is Copyright © the Common Workflow " -"Language project, and, where practical, linking to " -"https://www.commonwl.org/%20),%20provide%20a%20[link%20to%20the%20license][cc-by-" -"human], and indicate if changes were made. You may do so in any " -"reasonable manner, but not in any way that suggests the licensor endorses" -" you or your use." -msgstr "" - -#: ../../LICENSE.md:32 f6c3b2ccad494ed6811a35537fc1fb0d -msgid "" -"**No additional restrictions**---You may not apply legal terms or " -"technological measures that legally restrict others from doing anything " -"the license permits. With the understanding that:" -msgstr "" - -#: ../../LICENSE.md:36 91c95248cd7f435c909ee263a9a8bf3f -msgid "" -"You do not have to comply with the license for elements of the material " -"in the public domain or where your use is permitted by an applicable " -"exception or limitation." -msgstr "" - -#: ../../LICENSE.md:39 27f79b0b648b4de4b0eb3172b2dc4ae8 -msgid "" -"No warranties are given. The license may not give you all of the " -"permissions necessary for your intended use. For example, other rights " -"such as publicity, privacy, or moral rights may limit how you use the " -"material." -msgstr "" - -#: ../../LICENSE.md:44 1e367d07720d4f9fb7ebc3149052e823 -msgid "Software" -msgstr "" - -#: ../../LICENSE.md:46 cf8b58d02b6943a48cb70aa78a27bea4 -msgid "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the" -" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." -msgstr "" - -#: ../../LICENSE.md:51 96f1e5be3e1e48db8d9a4c7693008715 -msgid "" -"Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an \"AS IS\" BASIS, " -"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " -"See the License for the specific language governing permissions and " -"limitations under the License." -msgstr "" - -#: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 08aa9181d5304e0fa96b28db15718559 d37fc100eb6948bba8b5e757574b2aaf -#: ecdd0f28d5b048d69dd1ffae2fa1f6c0 -msgid "" -"CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece" -" of software, tools and workflows described using CWL are portable across" -" a variety of platforms that support the CWL standard." -msgstr "" - -#: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 1361ff6bf4924efc9ce9a85785a6b381 eb254514301c491e81f72ae19c407261 -msgid "This page has moved" -msgstr "" - -#: ../../src/episodes.md:9 f03d7cbe6670451db0896f1b674d56c7 -msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. Please use the new [Table of Contents](index.md#table-of-" -"contents) to browse the User Guide." -msgstr "" - -#: ../../src/faq.md:1 d65ad48ac6314bf0a74c34a6766561fc -msgid "FAQ" -msgstr "" - -#: ../../src/faq.md:11 370a9659c7904ef6b5e1ae7480f82ef6 -msgid "How do I create non \"`File`\" types using `evalFrom`?" -msgstr "" - -#: ../../src/faq.md:41 8333f51e3f5945fe8963adfc6685bcb1 -msgid "How do I rename an input file?" -msgstr "" - -#: ../../src/faq.md:43 f6b88d9154d049d7807afa9bb0f1ac98 -msgid "" -"This example demonstrates how to change the name of an input file as part" -" of a tool description. This could be useful when you are taking files " -"produced from another step in a workflow, and don't want to work with the" -" default names that these files were given when they were created." -msgstr "" - -#: ../../src/faq.md:59 833510f5896b4a6eb5875d25eca5b047 -msgid "How do I rename an output file?" -msgstr "" - -#: ../../src/faq.md:61 207e2f97d1c44233ae3f109c5a6ec944 -msgid "" -"This example demonstrates how to change the name of an output file from " -"the default name given to it by a tool:" -msgstr "" - -#: ../../src/faq.md:83 d66acc583da24273980a52be03e79e91 -msgid "" -"By modifying the `basename` field in the `outputEval` field, CWL workflow" -" engines will rename the file using the new name for subsequent steps or " -"as a workflow-level output." -msgstr "" - -#: ../../src/faq.md:86 8641f105131b4ac1bca7e0a46756ef79 -msgid "How do I reference a local script?" -msgstr "" - -#: ../../src/faq.md:88 d3e43b40d6994b32bc37067ee116418e -msgid "There are two ways to reference a local script:" -msgstr "" - -#: ../../src/faq.md:90 64b140a321ca4087945339c523cc24dd -msgid "" -"The first method involves adding the path to a folder containing your " -"scripts to the `PATH` environment variable. This allows you to execute " -"the shell script directly (without explicitly using the `sh` or `bash` " -"commands)." -msgstr "" - -#: ../../src/faq.md:93 34ebca4487a54ceab5d087105820e945 -msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" - -#: ../../src/faq.md:99 6b04a4dcdada4515b28d74aacff3537a -msgid "" -"After that, make the script executable with the command `chmod +x " -"scriptname.sh`" -msgstr "" - -#: ../../src/faq.md:101 756ab4f7edcf42d3872bb86818e088c3 -msgid "" -"Finally, modify your `PATH` to add the directory where your script is " -"located. (It is good practice to use `$HOME/bin` for storing your own " -"scripts)." -msgstr "" - -#: ../../src/faq.md:108 efb46b3a2d7c4c51b65998602bfa6f18 -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "" - -#: ../../src/faq.md:117 844938d5d2304c6cb03184b4b4b0b024 -msgid "" -"When you wish to share your work later, you can place your script in a " -"software container in the Docker format." -msgstr "" - -#: ../../src/faq.md:119 796ce8155e32486d9651f8f13bfa3148 -msgid "" -"The second method involves including an input of `type: File` in the " -"script itself:" -msgstr "" - -#: ../../src/faq.md:138 ba246320fdd94a1aab4736f83718d793 -msgid "How can I set `self`-based input bindings for optional inputs?" -msgstr "" - -#: ../../src/faq.md:140 6169b7be9af7448abcb57eaf91e1cc91 -msgid "" -"Currently, `cwltool` can't cope with missing optional inputs if their " -"input binding makes use of `self`. Below is an example workaround for " -"this, pending a more sophisticated fix." -msgstr "" - -#: ../../src/faq.md:165 6c98b7948059411b8e09cf03a552c5ab -msgid "How can I model a \"one-or-the-other\" parameter?" -msgstr "" - -#: ../../src/faq.md:167 d1424da3f43c4519a4c4735f4a720341 -msgid "" -"Below is an example showing how to specify different strings to be added " -"to a command line, based on the value given to a Boolean parameter." -msgstr "" - -#: ../../src/faq.md:188 5c9980839f404ba6aef92ef23034500f -msgid "" -"How do I connect a solo value to an input that expects an array of that " -"type?" -msgstr "" - -#: ../../src/faq.md:190 2525baf16c1f4725b096f33fd99009cf -msgid "" -"Add a " -"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" -" along with [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput):" -msgstr "" - -#: ../../src/faq.md:194 a00d5d96b15048a79ae099d22d63bb42 -msgid "merge_nested" -msgstr "" - -#: ../../src/faq.md:196 3a92c6cc5c2b40ffa0d692d03bad5c87 -msgid "" -"The input must be an array consisting of exactly one entry for each input" -" link. If \"merge_nested\" is specified with a single link, the value " -"from the link must be wrapped in a single-item list." -msgstr "" - -#: ../../src/faq.md:199 3af16c07e3f148ddb8849c94a3864158 -msgid "Which means \"create a list with exactly these sources as elements\"." -msgstr "" - -#: ../../src/faq.md:201 0ea3de393d2f42aeb82658c85a19ec45 -msgid "" -"Or in other words: if the destination is of type `File[]` (an array of " -"`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` " -"and add `linkMerge: merge_nested` under the appropriate `in` entry of the" -" destination step." -msgstr "" - -#: ../../src/faq.md:229 2f1bbb611c9c4f80b7ae0566432f2f35 -msgid "How do make an input optional? 💯" -msgstr "" - -#: ../../src/faq.md:231 08a226efe5d141e68215ac77725033db -msgid "" -"To make an input parameter optional, add a question mark to the type " -"declaration." -msgstr "" - -#: ../../src/faq.md:247 06e70a855a8f455ca0536eead77073c2 -msgid "" -msgstr "" - -#: ../../src/faq.md:248 7fda8eeb6a7f4689993ed0118c77f023 -msgid "" -"How do I specify an input that must come from a list of predefined values" -" (i.e. How do I use enum inputs) ?" -msgstr "" - -#: ../../src/faq.md:250 b1934a82553b4da3b7f981e576245dd8 -msgid "" -"For command line flags that require a specific input as the argument an " -"enum type can be declared in CWL. **Specifying null here is known as long" -" form style. It does the same thing as the question mark on the other " -"inputs.**" -msgstr "" - -#: ../../src/faq.md:267 17fc34fad2094f5ea60e963dabd632b8 -msgid "" -msgstr "" - -#: ../../src/faq.md:268 4d7acfbeba5b4e9cb31f08ef4b280447 -msgid "" -"How do I describe dependent or exclusive input parameters(e.g. How do I " -"use record inputs)?" -msgstr "" - -#: ../../src/faq.md:270 949ce95c082f4a05891a55fee25d4873 -msgid "" -"For commandline flags that are either **mutually exclusive** or " -"**dependent** a special record type can be defined. You can also specify " -"null here to create optional inputs." -msgstr "" - -#: ../../src/faq.md:322 6fd3c469d11d4d52b9fbb7a3d443a8db -msgid "How do I set mutually exclusive parameters?" -msgstr "" - -#: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f -msgid "" -"To properly set fields in a record input type, you need to pass a " -"dictionary to the input to properly set the parameters. This is done by " -"using inline JavaScript and returning the dictionary with the key of the " -"field you want to set. The source field is set to indicate the input from" -" the workflow to be used as the value." -msgstr "" - -#: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 -msgid "How can I set Booleans?" -msgstr "" - -#: ../../src/faq.md:344 8dcb88744e5840029de0e1bbf1c4b967 -msgid "These can be set by using the default field" -msgstr "" - -#: ../../src/faq.md:349 972b7a5551bb43e6b9fa30e0cb713ff7 -msgid "What should I do when concatenating strings in inputs?" -msgstr "" - -#: ../../src/faq.md:351 68f74afc21d846dd9070d45dec0cc1d8 -msgid "The valueFrom field must be used instead of default." -msgstr "" - -#: ../../src/faq.md:359 53b633c6f8644106beb95ae567eb0708 -msgid "" -"I get `cwltool` errors due to filenames with space characters inside. " -"What should I do?" -msgstr "" - -#: ../../src/faq.md:361 7101bb5cb69e4faca4e60eabb4eb258e -msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "" - -#: ../../src/faq.md:363 0eaf834b0ca847cca6736794895f5f81 -msgid "" -"For example, the filename `a space is here.txt` includes 3 space " -"characters." -msgstr "" - -#: ../../src/faq.md:371 7dabd8aab7a5423b842433616640bac0 -msgid "" -"If you can not avoid these dangerous characters, then pass `--relax-path-" -"checks` to `cwltool`." -msgstr "" - -#: ../../src/faq.md:373 b7ec33f38ce74ceb890f4379e4c41054 -msgid "" -"What should I do when I get CWL Parameter Reference error due to hyphen " -"in an input identifier?" -msgstr "" - -#: ../../src/faq.md:375 e39b65947b294b20a444f18d780246f4 -msgid "If `cwltool --validate` returns valid" -msgstr "" - -#: ../../src/faq.md:384 dcd42c65681b438bb541fb38ddebb536 -msgid "But executing it causes an error like:" -msgstr "" - -#: ../../src/faq.md:396 2b96665acac449758b852bbe7600e007 -msgid "The file is here" -msgstr "" - -#: ../../src/faq.md:410 f59751d2f0014e59af7879a748062cec -msgid "Problem caused by `-` (hyphen character)." -msgstr "" - -#: ../../src/faq.md:423 7780f461ca4c478b92fca893c0b0894a -msgid "To fix this error, change `-` (hyphen) to `_` (underscore):" -msgstr "" - -#: ../../src/faq.md:436 88df56dfff854fc68fb6ad3835a846e4 -msgid "" -"If it is not possible to change the input identifier, then you can use an" -" alternative CWL Parameter Reference syntax:" -msgstr "" - -#: ../../src/faq.md:442 fc407a9e8d8c4b699d9cd14b369343b5 -msgid "How do I use CWL and cwltool with Singularity?" -msgstr "" - -#: ../../src/faq.md:445 239f5f81cef042b08fb8015c36b3ecad -msgid "" -"The CWL standards are built around (optional) Docker format containers. " -"The reference runner and several other CWL implementations support " -"running those Docker format containers using the Singularity engine. " -"Directly specifying a Singularity format container is not part of the CWL" -" standards." -msgstr "" - -#: ../../src/faq.md:450 61641314d82b43e982e54c64c73232c5 -msgid "How do I debug the JavaScript in my CWL tool?" -msgstr "" - -#: ../../src/faq.md:452 5556d3c323664edea55cfb777f4efb3b -msgid "" -"You can use the --js-console option of cwltool," -" or you can try creating a JavaScript or TypeScript project for your " -"code, and load it using expressionLib, e.g.: " -"https://github.com/common-workflow-language/common-workflow-" -"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" -msgstr "" - -#: ../../src/index.md:1 1c9fb72b83c9467a9672943fb47ffe32 -msgid "Common Workflow Language User Guide" -msgstr "" - -#: ../../src/index.md:3 aaa44578e27345e682ab44686b4da159 -msgid "" -"This guide will introduce you to writing workflows using the [Common " -"Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " -"guide describes the latest specification {{ cwl_version }}." -msgstr "" - -#: ../../src/index.md:7 0adfc2adb0c74372b25d197dd3a73b8b -msgid "Contributions and Feedback are Welcome!" -msgstr "" - -#: ../../src/index.md:9 96c8dca812f1415db7c5c006b0c0e022 -msgid "" -"If you find that something is missing from this guide, or if you would " -"like to provide other feedback, file an Issue on the [project repository " -"for this guide][repo]. You can also suggest changes directly in a Pull " -"Request by clicking the \"Edit this page\" button at the right sidebar of" -" each page." -msgstr "" - -#: ../../src/index.md:16 35c50bb5c3a345b4a4ae66b2df065376 -msgid "Navigating the User Guide" -msgstr "" - -#: ../../src/index.md:18 9431edcf4e344fb89b6a251e627279d2 -msgid "" -"If you are a beginner user get started with the " -"[Introduction](/introduction/index.md) section. For advanced users the " -"subsections of the [Topics](/topics/index.md) have detailed information " -"about the most common topics for CWL." -msgstr "" - -#: ../../src/index.md:23 61cf57e61a9f46e5a1bff6368c5ad5e3 -msgid "" -"The Table of Contents is displayed at the top menu and also on the left " -"sidebar. It also appears further down this page but with links to " -"subsections. The right sidebar contains links to the sections of each " -"page, and the Search form is on the left sidebar." -msgstr "" - -#: ../../src/index.md:28 94381840d8a848c4a02fa97bfe83566d -msgid "Table of Contents" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:1 c1271d88e203454688a22e61ee88f02a -msgid "Basic Concepts" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:3 dd462818cc9a4205b38866d0c5137ece -msgid "" -"This section describes the basic concepts for users to get started on " -"working with Common Workflow Language (CWL) workflows. Readers are " -"expected to be familiar with workflow managers, YAML, and comfortable " -"with following instructions for the command-line. The other sections of " -"the user guide cover the same concepts, but in more detail. If you are " -"already familiar with CWL or you are looking for more advanced content, " -"you may want to skip this section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:10 7a56d394fb244431aefce7ebbb834ecf -msgid "The CWL Specification" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:21 35800ed2c56d489190d3702d9ad20fd7 -msgid "" -"The CWL specification is a document written and maintained by the CWL " -"community. The specification has different versions. The version covered " -"in this user guide is the {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:25 3ab6dd6b2f694afeb08f3984a74f3efb -msgid "" -"The specification version can have up to three numbers separated by `.`s " -"(dots). The first number is the major release, used for backward-" -"incompatible changes like the removal of deprecated features. The second " -"number is the minor release, used for new features or smaller changes " -"that are backward-compatible. The last number is used for bug fixes, like" -" typos and other corrections to the specification." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:33 72ae1fb763a34c41b1b06adcbe1522c3 -msgid "" -"The model used for the specification version is called Semantic " -"Versioning. See the end of this section to [learn more](#learn-more) " -"about it." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:37 5aa7d3ee6cb048d888f1e1f49d0e08be -msgid "Implementations" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:39 c87e6daefda74579a39924777b2e6809 -msgid "" -"An implementation of the CWL specification is any software written " -"following what is defined in a version of the specification document. " -"However, implementations may not implement every aspect of the " -"specification. CWL implementations are licensed under both Open Source " -"and commercial licenses." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:44 c995e699ae2949219af252f9d802a43d -msgid "" -"CWL is well suited for describing large-scale workflows in cluster, cloud" -" and high performance computing environments where tasks are scheduled in" -" parallel across many nodes." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:51 09171f48a3d841b2acb6d803b2340c8e -msgid "CWL specification, implementations, and other tools." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:105 -#: 1c1647a3496c4251a3193f94ee4e78c8 -msgid "Processes and Requirements" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:107 -#: 854633336f4d4fc394e62c53ce022c6b -msgid "" -"A process is a computing unit that takes inputs and produces outputs. The" -" behavior of a process can be affected by the inputs, requirements, and " -"hints. There are four types of processes defined in the CWL specification" -" {{ cwl_version }}:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:112 -#: 142a847f11d7462f8bf77bfe789410ca -msgid "A command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:113 -#: 7c7567fa690043f9b4b89bdf8ca60cad -msgid "An expression tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:114 -#: 7afcf087d3ea49dabf1a641a2bb71b35 -msgid "An operation." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:115 -#: 6399939602334819a20b92b957352a8a -msgid "A workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:118 -#: 8c55b15cebf142899045f229ccc86b1e -msgid "The processing units available in the CWL objects model." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:119 -#: ec54c0e67e894bfba2d0fbb0f87ffdf4 -msgid "" -"A command-line tool is a wrapper for a command-line utility like `echo`, " -"`ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:122 -#: c88ad26efa794cbeb6f0690aa0cad5ea -msgid "" -"An expression tool is a wrapper for a JavaScript expression. It can be " -"used to simplify workflows and command-line tools, moving common parts of" -" a workflow execution into reusable JavaScript code that takes inputs and" -" produces outputs like a command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:127 -#: 946825a7ea2c450eb3e41b5548670fb7 -msgid "" -"Operation is an abstract process that also takes inputs, produces " -"outputs, and can be used in a workflow. But it is a special operation not" -" so commonly used. It is discussed in the [Operations " -"section](../topics/operations.md) of this user guide." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:131 -#: 44aac23f302c4178accf7e431cfbb96c -msgid "" -"The workflow is a process that contains steps. Steps can be other " -"workflows (nested workflows), command-line tools, or expression tools. " -"The inputs of a workflow can be passed to any of its steps, while the " -"outputs produced by its steps can be used in the final output of the " -"workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:137 -#: 5afdb7aaf0bf4c1abf4c22cdbdd58be9 -msgid "" -"The CWL specification allows for implementations to provide extra " -"functionality and specify prerequisites to workflows through " -"*requirements*. There are many requirements defined in the CWL " -"specification, for instance:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:141 -#: 07c5789c59224ed78a3ecd03cfe872e9 -msgid "" -"[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement)" -" - enables JavaScript in expressions." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:142 -#: 6f9854ae1b884ad39f88d2f39d66cb98 -msgid "" -"[`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow.html#SubworkflowFeatureRequirement)" -" - enables nested workflows." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:143 -#: 23fef6de073f4da18118e4d0512670fe -msgid "" -"[`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow.html#InitialWorkDirRequirement)" -" - controls staging files in the input directory." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:145 -#: fb3762f91177401ea624d1e716d67ae6 -msgid "" -"Some CWL runners may provide requirements that are not in the " -"specification. For example, GPU requirements are supported in `cwltool` " -"through the `cwltool:CUDARequirement` requirement, but it is not part of " -"the {{ cwl_version }} specification and may not be supported by other CWL" -" runners." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:151 -#: b6a5cd431c324078a9a4e1513a14ee28 -msgid "" -"Hints are similar to requirements, but while requirements list features " -"that are required, hints list optional features. Requirements are " -"explained in detail in the [Requirements](../topics/requirements-and-" -"hints.md) section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:155 -#: 88d7bad84dd341d2abb33673b8b8f250 -msgid "FAIR Workflows" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:157 -#: bcbf5d76cf5f47b2a9691b7d2d8ef891 -msgid "" -"The FAIR principles have laid a foundation for sharing and publishing " -"digital assets, and in particular, data. The FAIR principles emphasize " -"machine accessibility and that all digital assets should be Findable, " -"Accessible, Interoperable, and Reusable. Workflows encode the methods by " -"which the scientific process is conducted and via which data are created." -" It is thus important that workflows both support the creation of FAIR " -"data and themselves adhere to the FAIR principles. — [FAIR Computational " -"Workflows](https://workflows.community/groups/fair/), Workflows Community" -" Initiative." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:167 -#: 4ea1d3bf04dc42f0bc6735a45b9e0dc0 -msgid "" -"CWL has roots in \"make\" and many similar tools that determine order of " -"execution, based on dependencies between tasks. However, unlike \"make\"," -" CWL tasks are isolated, and you must be explicit about your inputs and " -"outputs." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:171 -#: c0f53138bf084939a54b0a576b44199f -msgid "" -"The benefit of explicitness and isolation are flexibility, portability, " -"and scalability; tools and workflows described with CWL can transparently" -" leverage technologies such as Docker and be used with CWL " -"implementations from different vendors." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:176 -#: 91d6eb4984a6410ba99616b6617ba9af -msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:183 -#: ../../src/introduction/quick-start.md:94 0d7e607b00b9485aa2e3c5fb0a931bc6 -#: 161697ed3e864155bb89d8be794fc139 b4a7563eabf547c3bf7eab2567a27b51 -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:180 -#: 7221a89559944627b4c3db37f468f72c -msgid "Semantic Versioning - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:181 -#: bccf086fc9514f76b60dc161e3a09da3 -msgid "" -"The CWL Specification page in the CWL website: " -"" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:182 -#: a5b37924c7d04ab984ff2542847afc4a -msgid "" -"The Command Line Tool Description Standard: " -"<[https://www.commonwl.org/v1.2/CommandLineTool.html](https://w3id.org/cwl/CommandLineTool.html)>" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:183 -#: 44af015fa36644b99f07338d241d29c1 -msgid "" -"The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:184 -#: bffca993172048a4b7ab7c62637662e2 -msgid "" -"The list of Implementations in the CWL website: " -"" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:185 -#: 84c61946406347c8b138772909110d54 -msgid "PROV-O: The PROV Ontology - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:186 -#: eb0b6a62e06143eabc7b92acff9643ea -msgid "" -"CWL Operations are covered in the [Operations](../topics/operations.md) " -"section of this user guide." -msgstr "" - -#: ../../src/introduction/index.md:1 48532f7701c54166859098e521a43db0 -msgid "Introduction" -msgstr "" - -#: ../../src/introduction/index.md:3 08db628a949b4513b824ee334e70a7df -msgid "" -"This section will guide you through a short introduction to CWL, the " -"prerequisites for following this user guide, and some basic concepts that" -" are useful to know before reading the rest of the user guide." -msgstr "" - -#: ../../src/introduction/prerequisites.md:1 d3f5749a76c14fdf8052f5f683d11b9e -msgid "Prerequisites" -msgstr "" - -#: ../../src/introduction/prerequisites.md:6 ab9e21b3e99641d096ba70012b4eb035 -msgid "" -"The software and configurations listed in this section are prerequisites " -"for following this user guide. The CWL standards are implemented by many " -"different workflow runners and platforms. This list of requirements " -"focuses on the CWL reference runner, `cwltool`. You can use another CWL-" -"compatible runner or workflow system, but the results and interface may " -"look different (though the exact workflow outputs should be identical)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:12 8ed426ebcb744839915e7c414d69b1e9 -msgid "CWL Implementations" -msgstr "" - -#: ../../src/introduction/prerequisites.md:14 ff74d48407464c4b9d451fa419137144 -msgid "" -"There are many implementations of the CWL standards. Some are complete " -"CWL runners, while others could be plug-ins or extensions to workflow " -"engines. We have a better explanation in the [Implementations](basic-" -"concepts.md#implementations) section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:19 eb98aa9c71d746a69e9610996ffc5b47 -msgid "Operating System" -msgstr "" - -#: ../../src/introduction/prerequisites.md:21 209a0018e7da48f09b27dc507ba14d24 -msgid "" -"We recommend using an up-to-date operating system. You can choose any of " -"the following options for your operating system:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:24 8baf869537ea478791356320280df928 -msgid "Linux" -msgstr "" - -#: ../../src/introduction/prerequisites.md:25 248e9760ce60442eb10ab7247d6af23b -msgid "macOS" -msgstr "" - -#: ../../src/introduction/prerequisites.md:26 d89306bbadf44b6bba8959f1f68cc2f0 -msgid "Windows" -msgstr "" - -#: ../../src/introduction/prerequisites.md:29 aeeb990abbbd42cca122c342054be29c -msgid "" -"If you are using Windows, you will have to install the Windows Subsystem " -"for Linux 2 as documented in the [`cwltool` documentation for Microsoft " -"Windows users](https://github.com/common-workflow-" -"language/cwltool/blob/main/README.rst#ms-windows-users). Your operating " -"system also needs internet access and a recent version of Python (3.6+)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:34 21d1f29fb15745c480194eae6acdd031 -msgid "CWL Runner" -msgstr "" - -#: ../../src/introduction/prerequisites.md:39 89f0bf6ff8544a6d87114085be8e0bb6 -msgid "" -"The first thing you will need for running CWL workflows is a CWL runner. " -"`cwltool` is a Python Open Source project maintained by the CWL " -"community. It is also the CWL reference runner, which means it must " -"support everything in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/prerequisites.md:44 068f09d4d66547448693f7b9dadef497 -msgid "" -"`cwltool` can be installed with `pip`, `apt`, or `conda`. We recommend " -"using a virtual environment like `venv` or `conda`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:48 1edf8b8438334ae29dc406dbfd711228 -msgid "" -"Visit the `cwltool` " -"[documentation](https://cwltool.readthedocs.io/en/latest/#install) for " -"details on installing `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:52 5e300141ce43435f9437507374987213 -msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:54 282ac7ba2a2346feac2456bcda0f214a -msgid "`true.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:60 0b36f94f479a4bce9bd9be9983894421 -msgid "" -"The `cwltool` command has an option to validate CWL tool and workflow " -"descriptions. This option will parse the CWL document, look for syntax " -"errors, and verify that the workflow descriptions are compliant with the " -"CWL standards. However, these actions will be performed without running " -"the document. To validate CWL workflows (or even a standalone command " -"line tool description like the above) pass the `--validate` option to the" -" `cwltool` command:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:66 5fce122794e34892b430ca4bdba5ba50 -msgid "Validating `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:71 73f074f47d1449dcb40ff960a84851fd -msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:73 2dd5a67870ca41b48e17c468ba15888b -msgid "Running `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:78 d2dc809318be49cc996d892e93ad84ac -msgid "Generic ``cwl-runner`` alias" -msgstr "" - -#: ../../src/introduction/prerequisites.md:80 9809c2e262924ef286b0bd62e0b00995 -msgid "" -"`cwl-runner` is an implementation-agnostic alias for any CWL compliant " -"runner. This simply means that the `cwl-runner` alias command can be " -"invoked independently, and is not reliant on a particular CWL runner " -"program name. Users can invoke `cwl-runner` instead of invoking a CWL " -"runner like `cwltool` directly. The `cwl-runner` is installed by a system" -" administrator or user to point to the preferred CWL implementation. This" -" is convenient for environments with multiple CWL runners." -msgstr "" - -#: ../../src/introduction/prerequisites.md:88 6dd6aa836099469381fb564d63b84f3d -msgid "" -"The CWL community publishes a Python package with the name `cwlref-" -"runner` that installs an alias for `cwltool` under the name `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:91 cc1a9b95508e44a1bf08ae75d990c301 -msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:98 8f8c80f705d94d4899b250bbf9c54562 -msgid "" -"Now you can validate and run your workflow with the `cwl-runner` " -"executable, which will invoke `cwltool`. You should have the same results" -" and output as in the previous section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:102 176e4214d18149f3ba0bda692bcf760f -msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:107 4890bf20bc3842d3a7421b555bcda94a -msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:112 2475a83cf6ed4389bb680fa37e8fe69c -msgid "" -"Another way to execute `cwl-runner` is by invoking the file directly. For" -" that, the first thing you need to do is copy `true.cwl` workflow into a " -"new file: `true_shebang.cwl`, and include a special first line, a " -"*shebang*:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:116 24da787aa76c4480838a93ba0533898d -msgid "`true_shebang.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:122 4f3cb8d1f9ce4e3d852e81aa4e0f60be -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:124 27693d62faa045d9b03143d9bd2afcdf -msgid "Making `true.cwl` executable." -msgstr "" - -#: ../../src/introduction/prerequisites.md:131 703531514abe4fd48015c472005dbffa -msgid "" -"And finally, you can execute it directly in the command-line. On " -"execution, the program specified in the shebang (`cwl-runner`) will be " -"used to execute the rest of the file." -msgstr "" - -#: ../../src/introduction/prerequisites.md:135 abba2e14c4e54252bb75983274663a7a -msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" - -#: ../../src/introduction/prerequisites.md:141 11fea992c00940d29eb29ccf4b9370e9 -msgid "" -"The *shebang* is the two-character sequence `#!` at the beginning of a " -"script. When the script is executable, the operating system will execute " -"the script using the executable specified after the shebang. It is " -"considered a good practice to use `/usr/bin/env [executable]` rather than" -" using a hard-coded location, since `/usr/bin/env [executable]` looks for" -" the `[executable]` program in the system `PATH`," -msgstr "" - -#: ../../src/introduction/prerequisites.md:148 854736eef2ac4b63b187a4cea9660ae4 -msgid "Text Editor" -msgstr "" - -#: ../../src/introduction/prerequisites.md:150 480fbb7a743046068c114fff5b396a9f -msgid "" -"You can use any text editor with CWL, but for syntax highlighting we " -"recommend an editor with YAML support. Popular editors are Visual Studio " -"Code, Sublime, WebStorm, vim/neovim, and Emacs." -msgstr "" - -#: ../../src/introduction/prerequisites.md:154 28da3eea8fd245d1936013d021c25164 -msgid "" -"There are extensions for Visual Studio Code and WebStorm that provide " -"integration with CWL, and features such as customized syntax highlighting" -" and better auto-complete:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:158 73c08e11e90d4c7f952307a1cdaa360b -msgid "" -"Visual Studio Code with the Benten (CWL) plugin - " -"" -msgstr "" - -#: ../../src/introduction/prerequisites.md:159 a5b788252a924338963f0ed198fc22ca -msgid "" -"cwl-plugin for IntelliJ - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:161 ee705b919acd461a8d9622821da246b6 -msgid "" -"The CWL community also maintains a list of editors and viewers: " -"" -msgstr "" - -#: ../../src/introduction/prerequisites.md:164 7724b63db3cc45139379898d047c0f83 -msgid "Docker" -msgstr "" - -#: ../../src/introduction/prerequisites.md:168 eff13997c1ce43d1ad2d7a4d927394fe -msgid "" -"`cwltool` uses Docker to run tools, workflows, and workflow steps that " -"specify a software container. Follow the instructions in the Docker " -"documentation to install it for your operating system: " -"." -msgstr "" - -#: ../../src/introduction/prerequisites.md:172 2872503638624b7e904ae407375ac165 -msgid "" -"You do not need to know how to write and build Docker containers. In the " -"rest of the user guide, we will use existing Docker images for running " -"examples, and to clarify the differences between the execution models " -"with and without containers." -msgstr "" - -#: ../../src/introduction/prerequisites.md:178 52ddcc9bc1554d809371fc0a503c40bc -msgid "" -"`cwltool` supports running containers with Docker, Podman, udocker, and " -"Singularity. You can also use alternative container registries for " -"pulling images." -msgstr "" - -#: ../../src/introduction/prerequisites.md:185 f3bbfa17f31a459386461951de157dd2 -msgid "" -"The [Implementations](basic-concepts.md#implementations) topic in the " -"next section, Basic Concepts." -msgstr "" - -#: ../../src/introduction/prerequisites.md:186 e22b9e7c56104e018e6d2f3d547c01ea -msgid "The Python `venv` module: " -msgstr "" - -#: ../../src/introduction/quick-start.md:1 9ca367e3ca754a0fa88dab64724b95b6 -msgid "Quick Start" -msgstr "" - -#: ../../src/introduction/quick-start.md:3 733db5702c774f32b8c91d13f74f3720 -msgid "" -"This section will show you a brief overview of what CWL is, and where you" -" can learn more about it. No previous knowledge of CWL is required, but " -"you must be comfortable following instructions for the command-line." -msgstr "" - -#: ../../src/introduction/quick-start.md:7 0b164074dd0849c3b2c8d2f78ea99e95 -msgid "“Hello World”" -msgstr "" - -#: ../../src/introduction/quick-start.md:12 6485f96f638548fbb7addc57f6cde92b -msgid "" -"CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " -"The example below shows a simple CWL “Hello World” workflow annotated " -"with comments. Note that comments start with `#`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:16 5e06f9c4754347b8bac88d24c21e0f67 -msgid "`hello_world.cwl`" -msgstr "" - -#: ../../src/introduction/quick-start.md:22 6a13fb9112ab41acb60dc65b3656f63e -msgid "" -"The example above is just a wrapper for the `echo` command-line tool. " -"Running the workflow above with the default input values will produce the" -" same result as the command-line `echo \"Hello World\"`." -msgstr "" - -#: ../../src/introduction/quick-start.md:27 7b2ae93353184faea0ae4f4acdfc3350 -msgid "" -"In CWL, there is a distinction between a command-line tool and a " -"workflow. But for the sake of simplicity, we are using the term " -"“workflow” here. You will learn more about this in the [basic concepts" -"](basic-concepts.md) section." -msgstr "" - -#: ../../src/introduction/quick-start.md:32 1ed30b04073d47a9893774746479fb5d -msgid "Installing a CWL Runner" -msgstr "" - -#: ../../src/introduction/quick-start.md:34 73a42cd9e0e54296985088b7221a8a93 -msgid "" -"`cwltool` is an implementation of the CWL specification. It is also the " -"CWL *Reference Runner* for the specification, and it is compliant with " -"the latest version of the specification: {{ cwl_version }}. You can " -"install `cwltool` using `pip`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:39 57aea587ade24610be62f5d993b0b755 -msgid "Installing `cwltool` with `pip`." -msgstr "" - -#: ../../src/introduction/quick-start.md:47 51183fc986014edbb026a53f222e6c2e -msgid "" -"If installing the cwltool using the pip command doesn't work for you, the" -" [prerequisites](prerequisites.md) section contains other ways to install" -" `cwltool` and a more detailed list of software and libraries used for " -"following the rest of this user guide." -msgstr "" - -#: ../../src/introduction/quick-start.md:51 a7582c3ae37a462a8ae1e72b3f321534 -msgid "Running \"Hello World\"" -msgstr "" - -#: ../../src/introduction/quick-start.md:53 0595e96912dc40e5a09f2ced2d2b7bcd -msgid "" -"The usage of the `cwltool` command-line executable is basically `cwltool " -"[OPTIONS] [CWL_DOCUMENT] [INPUTS_OBJECT]`. You can run the " -"`hello_world.cwl` workflow without specifying any option:" -msgstr "" - -#: ../../src/introduction/quick-start.md:57 5b393c69816549b084516dda4d4274f5 -msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:62 4306d8ad802f45c18487d932d04492fa -msgid "" -"Or you can override the default value of the input parameter `message`, " -"similar to how you would change the argument of the `echo` base command:" -msgstr "" - -#: ../../src/introduction/quick-start.md:65 8339ec411ad04c70ab8d795eb154fc38 -msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" - -#: ../../src/introduction/quick-start.md:70 3ecca6985e754951aee00c93effe9517 -msgid "" -"Another way of passing values to your workflow input parameters is via an" -" *Inputs Object*. This is a file containing the input fields with their " -"corresponding values. The Inputs Objects file can be written in JSON or " -"YAML. For example:" -msgstr "" - -#: ../../src/introduction/quick-start.md:74 d05e8e016b1d40c28c4b6091103fe920 -msgid "`hello_world-job.json`" -msgstr "" - -#: ../../src/introduction/quick-start.md:80 c5983ba6c86f4b749522c11cb3843911 -msgid "" -"You can use this Inputs Object file now to execute the “Hello World” " -"workflow:" -msgstr "" - -#: ../../src/introduction/quick-start.md:82 4065124edf3a4678a37c82e3070595cb -msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:88 52b1602b5c8d48db88d0b16f788e7703 -msgid "" -"We used a similar file name for the workflow and for the Inputs Object " -"files. The *-job.json* suffix is very common in Inputs Object files, but " -"it is not a requirement. You can choose any name for your workflows and " -"Inputs Object files." -msgstr "" - -#: ../../src/introduction/quick-start.md:96 3b06faf5f3194bd8a96118d9f050f61e -msgid "Continue reading the next sections of this User Guide!" -msgstr "" - -#: ../../src/introduction/quick-start.md:97 669b8ac154e74181830a430b1dc7684b -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" - -#: ../../src/introduction/quick-start.md:98 1c888f1b771d49b3a257ed534b5afa0a -msgid "" -"The [`common-workflow-language` organization](https://github.com/common-" -"workflow-language) at GitHub." -msgstr "" - -#: ../../src/introduction/quick-start.md:99 dbce82b7a930493486a585ecb8891121 -msgid "" -"[Common Workflow Language at " -"Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -msgstr "" - -#: ../../src/introduction/quick-start.md:100 dc714ffd4278421b9f2417f41627722c -msgid "" -"[YAML.org](http://yaml.org/) and [YAML at " -"Wikipedia](https://en.wikipedia.org/wiki/YAML)." -msgstr "" - -#: ../../src/introduction/quick-start.md:101 2bf7b924182f4f2bab88edef5ef85baa -msgid "" -"The {{'[CWL Specification " -"VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " -"cwl_version_text) }}." -msgstr "" - -#: ../../src/introduction/quick-start.md:102 936a7dfab11a4f2c82c0b59964e3ea28 -msgid "" -"[Workflow management system at " -"Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -msgstr "" - -#: ../../src/setup.md:9 24ea9c5144664d9599d7aca767b4730a -msgid "" -"This page is out-of-date and was kept here to preserve the links of the " -"old User Guide. The information on this page has been migrated to the " -"[FAQ](/faq.md) section of the new user guide." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 3843684b039a40dea163de951ca56738 -msgid "Additional Arguments and Parameters" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:3 -#: a6fd1842b938435aa2a3c889019eec71 -msgid "" -"Sometimes tools require additional command line options that don't " -"correspond exactly to input parameters." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:6 -#: dfed0747ed544547afd364086d828c9b -msgid "" -"In this example, we will wrap the Java compiler to compile a java source " -"file to a class file. By default, \"javac\" will create the class files " -"in the same directory as the source file. However, CWL input files (and " -"the directories in which they appear) may be read-only, so we need to " -"instruct \"javac\" to write the class file to the designated output " -"directory instead." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:13 -#: e690b567eae34f3f8dbdd7760e51449a -msgid "`arguments.cwl`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 4cee519b108143be89a0e47a75d7d649 -#: 79585673fd654bab9ba7c1927d7e153b -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:24 -#: ef070ebe5f7245489b05660fb6d7c178 -msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 4ae43e3e841442039e4bb8c740096c56 -msgid "" -"And now invoke `cwltool` providing the tool description and the input " -"object on the command line:" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 8497291577914eb3a172c1ffb736d95d -msgid "" -"Here we use the `arguments` field to add an additional argument to the " -"command line that isn't tied to a specific input parameter." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:43 -#: dc9fa5f2cbb147b1853c4042c54010f3 -msgid "" -"This example references a runtime parameter. Runtime parameters provide " -"information about the hardware or software environment when the tool is " -"actually executed. The `$(runtime.outdir)` parameter is the path to the " -"designated output directory. Other parameters include " -"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " -"`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " -"Environment][runtime] section of the CWL specification for details." -msgstr "" - -#: ../../src/topics/best-practices.md:1 964bf8276dd04b65887448e1386e63fe -msgid "Best Practices" -msgstr "" - -#: ../../src/topics/best-practices.md:3 7b59377bd56c47b8a71c18acfba4d3bb -msgid "" -"The following are a set of recommended good practices to keep in mind " -"when writing a Common Workflow Language description for a tool or " -"workflow. These guidelines are presented for consideration on a scale of " -"usefulness: although more is better, not all are required." -msgstr "" - -#: ../../src/topics/best-practices.md:8 2292670347cd4549bc6a51e972de0ef4 -msgid "" -"No `type: string` parameters for names of input or reference " -"files/directories; use `type: File` or `type: Directory` as appropriate." -msgstr "" - -#: ../../src/topics/best-practices.md:11 ae127b776eed4894af8cb680377703e0 -msgid "" -"A CWL document (in conjunction with any external components like " -"`Dockerfile`s) is software code. Workflow developers should be aware that" -" the usual rules of software licensing apply to this document. For " -"example, if the workflow is shared publicly, licensing terms must be " -"clear so that a future user understands under what conditions they can " -"run the workflow, modify it and/or combine it with other workflows. For " -"this reason, please consider including a license field in the document. " -"The authors of this guide urge you to choose a pre-existing license " -"rather than trying to write your own (see the link below to learn more " -"about choosing a license), and our recommended practice is to choose a " -"license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" -"license]." -msgstr "" - -#: ../../src/topics/best-practices.md:20 384eb620dc31468e8c3f5f33a3436200 -msgid "" -"If possible, the license should be specified with its corresponding [SPDX" -" identifier][spdx]. Construct the metadata field for the license by " -"providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where " -"`SPDX-ID` is taken from the list of identifiers linked above. See the " -"example snippet below for guidance. For non-standard licenses without an " -"SPDX identifier, provide a URL to the license." -msgstr "" - -#: ../../src/topics/best-practices.md:26 e8259b43fa6944eda73eae381db6b97b -msgid "" -"Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" -"Programmer][sci-license]\"" -msgstr "" - -#: ../../src/topics/best-practices.md:28 5b976a5aec7d44bda55b0a019e955416 -msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" - -#: ../../src/topics/best-practices.md:37 924b8df24deb4c82b32732f491c9a246 -msgid "" -"For more examples of providing metadata within CWL descriptions, see [the" -" Metadata and Authorship section of this User Guide](../topics/metadata-" -"and-authorship.md)." -msgstr "" - -#: ../../src/topics/best-practices.md:40 9e64a9fc89cb45cfbff0e925cc91b1be -msgid "" -"Include [attribution information][license-example] for the author(s) of " -"the CWL tool or workflow description. Use unambiguous identifiers like " -"[ORCID][orcid]." -msgstr "" - -#: ../../src/topics/best-practices.md:44 87030aef02044b8283c76debab4772bf -msgid "" -"In tool descriptions, list dependencies using short name(s) under " -"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." -msgstr "" - -#: ../../src/topics/best-practices.md:47 6c9eaae099fa4ca4b0986b1c4146df50 -msgid "" -"Include [SciCrunch][scicrunch] identifiers for dependencies in " -"`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." -msgstr "" - -#: ../../src/topics/best-practices.md:50 5ae8950fd31541399c2fe59096581dbc -msgid "" -"All `input` and `output` identifiers should reflect their conceptual " -"identity. Use informative names like `unaligned_sequences`, " -"`reference_genome`, `phylogeny`, or `aligned_sequences` instead of " -"`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." -msgstr "" - -#: ../../src/topics/best-practices.md:55 b0493895105e43849bff2026763e472a -msgid "" -"In tool descriptions, include a list of version(s) of the tool that are " -"known to work with this description under " -"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." -msgstr "" - -#: ../../src/topics/best-practices.md:58 88806cb0462f4359801c1fa0ff0ebcc0 -msgid "" -"`format` should be specified for all input and output `File`s. " -"Bioinformatics tools should use format identifiers from [EDAM][edam-" -"example]. See also `iana:text/plain`, `iana:text/tab-separated-values` " -"with `$namespaces: { iana: \"https://www.iana.org/assignments/media-" -"types/\" }`. [Full IANA media type list][iana-types] (also known as MIME " -"types). For non-bioinformatics tools, use or build an appropriate " -"ontology/controlled vocabulary in the same way. Please edit this page to " -"let us know about it." -msgstr "" - -#: ../../src/topics/best-practices.md:66 b178c7296ed5491782a4180c76883c14 -msgid "" -"Mark all input and output `File`s that are read from or written to in a " -"streaming compatible way (only once, no random-access), as `streamable: " -"true`." -msgstr "" - -#: ../../src/topics/best-practices.md:69 886d15c1972243acadccff5760f842f1 -msgid "" -"Each " -"[`CommandLineTool`](https://w3id.org/cwl/CommandLineTool.html#CommandLineTool)" -" description should focus on a single operation only, even if the " -"(sub)command is capable of more. Don't overcomplicate your tool " -"descriptions with options that you don't need or use." -msgstr "" - -#: ../../src/topics/best-practices.md:73 ef5a5f9b253c4ca3916802a695fb7c6d -msgid "" -"Custom types should be defined with one external YAML per type definition" -" for re-use." -msgstr "" - -#: ../../src/topics/best-practices.md:76 ff59f40e84004523904e3094be07cc80 -msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "" - -#: ../../src/topics/best-practices.md:78 78d73fde24e24beeab541a623d9530b6 -msgid "" -"If useful, include a top-level `doc` as well. This should provide a " -"longer, more detailed description than was provided in the top-level " -"`label` (see above)." -msgstr "" - -#: ../../src/topics/best-practices.md:82 d92013d662b44dbf8875e06c9dfbfd79 -msgid "" -"Use `type: enum` instead of `type: string` for elements with a fixed list" -" of valid values." -msgstr "" - -#: ../../src/topics/best-practices.md:85 c100d5192a52497fb6a890b81a388fcf -msgid "" -"Evaluate all use of JavaScript for possible elimination or replacement. " -"One common example: manipulating `File` names and paths? Consider whether" -" one of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc., could be used instead." -msgstr "" - -#: ../../src/topics/best-practices.md:90 e22fbacdb2fb4202b1bd69cfc24af5cd -msgid "" -"Give the tool description to a colleague (preferably at a different " -"institution) to test and provide feedback." -msgstr "" - -#: ../../src/topics/best-practices.md:93 0060a863362140f6bb3932cb5da1df04 -msgid "" -"Complex workflows with individual components which can be abstracted " -"should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" -" their workflow modular and allow sections of them to be easily reused." -msgstr "" - -#: ../../src/topics/best-practices.md:97 93f6d6b544c24ce780184272f66bacab -msgid "" -"Software containers should be made to be conformant to the " -"[\"Recommendations for the packaging and containerizing of bioinformatics" -" software\"][containers] (also useful to other disciplines)." -msgstr "" - -#: ../../src/topics/command-line-tool.md:1 a378a2f7d268401abfbbbe6e5090a952 -msgid "Command Line Tool" -msgstr "" - -#: ../../src/topics/command-line-tool.md:3 cf0f1c00c0b34c94a8e2460a700c303e -msgid "" -"A command-line tool is a type of Process object that can be run by itself" -" or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " -"`tar`, etc. The command-line tool is defined in the `baseCommand` " -"attribute of the command-line tool CWL document." -msgstr "" - -#: ../../src/topics/command-line-tool.md:8 7a180ba1f2d746a78b79be7e899cbad6 -msgid "" -"A CWL command-line tool must also have `inputs` and `outputs`. The " -"following example contains a minimal example of a CWL command-line tool " -"for the `echo` Linux command, using inputs and outputs." -msgstr "" - -#: ../../src/topics/command-line-tool.md:19 128bd8cd6788431da54fa07a8dc87f99 -msgid "CWL command-line tool." -msgstr "" - -#: ../../src/topics/command-line-tool.md:50 d742e9e59ea44ca1a1df2de85059343f -msgid "`echo.cwl`" -msgstr "" - -#: ../../src/topics/command-line-tool.md:57 e3a06ebe51b64b0183673a8acc04969f -msgid "" -"The example above uses a simplified form to define inputs and outputs. " -"You will learn more about in the [Inputs](../topics/inputs.md) and in the" -" [Outputs](../topics/outputs.md) sections." -msgstr "" - -#: ../../src/topics/command-line-tool.md:68 2bab464d19d14562a6501373aff13905 -msgid "Network Access" -msgstr "" - -#: ../../src/topics/command-line-tool.md:69 201712f3ceee4d4ea56ab96d3fef97b0 -msgid "" -"This indicates whether a process requires outgoing IPv4/IPv6 network " -"access. Starting with CWL v1.1, programs are not granted network access " -"by default, so you must include the requirement for network access in the" -" specification of your tool." -msgstr "" - -#: ../../src/topics/command-line-tool.md:84 3282a357799f4a72a6b8bace206144c4 -msgid "" -"CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 or v1.2 " -"will have `networkAccess: true` set automatically." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:1 -#: 17c5b4ee43cc4a979676ad27e473d046 -msgid "Creating Files at Runtime" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:3 -#: cd0dff10471c4ad2b84e3a0e4d7767ea -msgid "" -"Sometimes you need to create a file on the fly from input parameters, " -"such as tools that expect to read their input configuration from a file " -"rather than the command line parameters, or need a small wrapper shell " -"script." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:7 -#: bf4aea0a22334a1ca75cc20e937e6581 -msgid "" -"To generate such files, we can use the " -"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:9 -#: 008f768d56b8465bb4e8f4fde15853a7 -msgid "`createfile.cwl`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:15 -#: 252f8e897b0942a8be098481890005f3 -msgid "" -"Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " -"expanded by the CWL engine before creating the file. Here, insert the " -"value at the input `message`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:20 -#: aca24b72687c4d4d84bf9de8b71413f7 -msgid "" -"The _CWL expressions_ are independent of any _shell variables_ used later" -" during command line tool invocation. That means that any genuine need " -"for the character `$` must be **escaped** with `\\`. For instance, " -"`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " -"be evaluated by the shell script instead of the CWL engine." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:27 -#: 750b3232e8754448bc2b5913539495b8 -msgid "" -"To test the above CWL tool, use this job to provide the input value " -"`message`:" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:81 -#: 687c8a84bade43269f3cd767d32f9f47 81da7a18fe8d4659abc883cf43009f1f -#: d5d67eae63304ebb9b242133feacb0d1 -msgid "`echo-job.yml`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:35 -#: c4f964450d014734877fb3c968353a74 -msgid "" -"Before we run this, let us look at each step in a little more detail. The" -" base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " -"command `sh example.sh`. This will run the file we create in the shell." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:40 -#: 9aeea5a6a4244bc7a1626e0cb7351068 -msgid "" -"`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " -"YAML array, we need a `-` on the first line of each element of the array," -" in this case we have just one element. `entryname:` can have any value, " -"but it must match what was specified in the `baseCommand`. The final part" -" is `entry:`, this is followed by `|-` which is YAML quoting syntax, and " -"means that you are using a multiline string (without it, we would need to" -" write the whole script on one line)." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:51 -#: 867239e9ad3d4187a2703662a0ca3976 -msgid "" -"See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " -"formatting." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:54 -#: ../../src/topics/environment-variables.md:18 -#: ../../src/topics/file-formats.md:52 -#: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 0d7151b9f0194197bd686fe6c9c47afd 78bb40eeeda24d7b923162daa45d51a7 -#: 7b341a317347482ca86fc56119c3686f 7c637fa62cab4d0dbe670a3b72737cc9 -#: cfb4605a01dd4475aabcc086a4e65957 -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line:" -msgstr "" - -#: ../../src/topics/custom-types.md:1 252a3a17b1ec4d5a9a82ebbf6c2f314c -msgid "Custom Types" -msgstr "" - -#: ../../src/topics/custom-types.md:3 e0275ddda8f84207a58d10c17ca99a45 -msgid "" -"Sometimes you may want to write your own custom types for use and reuse " -"in CWL descriptions. Use of such custom types can reduce redundancy " -"between multiple descriptions that all use the same type, and also allow " -"for additional customisation/configuration of a tool/analysis without the" -" need to fiddle with the CWL description directly." -msgstr "" - -#: ../../src/topics/custom-types.md:9 8367e38e5e7c4a298d1d87b9001aaddc -msgid "" -"The example below is a CWL description of the [biom convert format][biom]" -" tool for converting a standard biom table file to hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:12 18b802f45ce0454ab7aa2a21812863c6 -msgid "`custom-types.cwl`" -msgstr "" - -#: ../../src/topics/custom-types.md:18 66d1953f5dd54d448bddd0f30c330402 -msgid "`custom-types.yml`" -msgstr "" - -#: ../../src/topics/custom-types.md:24 56b8912a1ea84f28adeb8beaf92ab563 -msgid "" -"___Note:___ To follow the example below, you need to [download the " -"example input file](https://github.com/common-workflow-" -"language/user_guide/blob/main/src/_includes/cwl/custom-" -"types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " -"`wget`:" -msgstr "" - -#: ../../src/topics/custom-types.md:30 a48539920c4944898918bc90b2d4e3c9 -msgid "" -"On line 29, in `inputs:table_type`, a list of allowable table options to " -"be used in the table conversion are imported as a custom object:" -msgstr "" - -#: ../../src/topics/custom-types.md:46 c791096f537141e8bd7cc941d711d108 -msgid "" -"The reference to a custom type is a combination of the name of the file " -"in which the object is defined (`biom-convert-table.yaml`) and the name " -"of the object within that file (`table_type`) that defines the custom " -"type. In this case the `symbols` array from the imported `biom-convert-" -"table.yaml` file define the allowable table options. For example, in " -"`custom-types.yml`, we pass `OTU table` as an `input` that tells the tool" -" to create an OTU table in hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:53 5f6bc6ed72334a74b9a4c46c29ddda46 -msgid "The contents of the YAML file describing the custom type are given below:" -msgstr "" - -#: ../../src/topics/custom-types.md:55 3b55419088e8446994703220bd8e8480 -msgid "`biom-convert-table.yaml`" -msgstr "" - -#: ../../src/topics/custom-types.md:61 fe6f4ce5e7344af0abea9d5c03e32ecd -msgid "" -"In order for the custom type to be used in the CWL description, it must " -"be imported. Imports are described in " -"`requirements:SchemaDefRequirement`, as below in the example `custom-" -"types.cwl` description:" -msgstr "" - -#: ../../src/topics/custom-types.md:76 dce43b138ba24b22bfa9fa5692a17009 -msgid "" -"Note also that the author of this CWL description has also included " -"[`ResourceRequirement`](https://w3id.org/cwl/CommandLineTool.html#ResourceRequirement)s," -" specifying the minimum amount of RAM and number of cores required for " -"the tool to run successfully, as well as details of the version of the " -"software that the description was written for and other useful metadata. " -"These features are discussed further in other chapters of this user " -"guide." -msgstr "" - -#: ../../src/topics/environment-variables.md:1 19737f89f2994815969fa4a88346f49a -msgid "Environment Variables" -msgstr "" - -#: ../../src/topics/environment-variables.md:3 ad965f75aa0c41cda8b82c46af49774d -msgid "" -"Tools run in a restricted environment and do not inherit most environment" -" variables from the parent process. You can set environment variables " -"for the tool using `EnvVarRequirement`." -msgstr "" - -#: ../../src/topics/environment-variables.md:7 38b276f9b0114a0bb87734f0a07a736f -msgid "`env.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:1 9f33532119dc47ffb6ade20fb1d950bd -msgid "Expression Tool" -msgstr "" - -#: ../../src/topics/expression-tool.md:3 b267056eae704737af5aaada3ea7e6e2 -msgid "" -"An expression tool is a type of Process that can be run by itself or as a" -" Workflow step. It executes a pure JavaScript expression. It is meant to " -"be used as a way to isolate complex JavaScript expressions that need to " -"operate on input data and produce some result as output." -msgstr "" - -#: ../../src/topics/expression-tool.md:8 7e930144163e4d6e9f0bcaa764497ccf -msgid "" -"Similar to the command-line tool it requires `inputs` and `outputs`. But " -"instead of `baseCommand`, it requires an " -"[`expression`](https://w3id.org/cwl/CommandLineTool.html#Expressions_(Optional))" -" attribute." -msgstr "" - -#: ../../src/topics/expression-tool.md:17 f172488c19a94d688036197117d30b38 -msgid "CWL expression tool." -msgstr "" - -#: ../../src/topics/expression-tool.md:48 ef978c951f1a4b7d9280d31367e5bae7 -msgid "`uppercase.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:67 0b63da31bc274b3cad798b07149592ab -msgid "" -"We had to use an " -"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" -" as our expression contains a JavaScript call in `.toUpperCase()`. This " -"means to tools using the expression tool that JavaScript is a " -"requirement." -msgstr "" - -#: ../../src/topics/expressions.md:1 b0e567a985f748538552bdb486a47998 -msgid "Expressions" -msgstr "" - -#: ../../src/topics/expressions.md:3 24d05cbbab8e460e99f2edc97ab0dcec -msgid "" -"If you need to manipulate input parameters, include the requirement " -"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" -" and then anywhere a parameter reference is legal you can provide a " -"fragment of Javascript that will be evaluated by the CWL runner." -msgstr "" - -#: ../../src/topics/expressions.md:9 3d48d1a8f7f74bc1886e41653cb53a22 -msgid "" -"JavaScript expressions should only be used when absolutely necessary. " -"When manipulating file names, extensions, paths etc, consider whether one" -" of the [built in `File` properties][file-prop] like `basename`, " -"`nameroot`, `nameext`, etc, could be used instead. See the [list of best " -"practices](best-practices.md)." -msgstr "" - -#: ../../src/topics/expressions.md:16 7d444aacd418466bbe588fa964b45179 -msgid "`expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:22 72a0558a83964796a8c1a0eb55fd78e8 -msgid "" -"As this tool does not require any `inputs` we can run it with an (almost)" -" empty job file:" -msgstr "" - -#: ../../src/topics/expressions.md:25 d679fd1363b24c81979c68e7342159cf -msgid "`empty.yml`" -msgstr "" - -#: ../../src/topics/expressions.md:31 d2ee4fcece744b6681f29322b5305111 -msgid "" -"`empty.yml` contains a description of an empty JSON object. JSON objects " -"descriptions are contained inside curly brackets `{}`, so an empty object" -" is represented simply by a set of empty brackets." -msgstr "" - -#: ../../src/topics/expressions.md:35 624e4a270e374b1699b780df508b9184 -msgid "We can then run `expression.cwl`:" -msgstr "" - -#: ../../src/topics/expressions.md:37 c252eac9a35e46aab08bd07bc1cdb57d -msgid "Running `expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:47 f6f64d57a50742b19b801c14806ee18a -msgid "" -"Note that requirements can be provided with the map syntax, as in the " -"example above:" -msgstr "" - -#: ../../src/topics/expressions.md:54 052e24e2ad044cc28f04d7f39be871d6 -msgid "" -"Or as an array, with each entry (in this case, only `class: " -"InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" -" describe the additional command line arguments." -msgstr "" - -#: ../../src/topics/expressions.md:62 84b31c076d4b4826aae35e8c23fe6a25 -msgid "Where are JavaScript expressions allowed?" -msgstr "" - -#: ../../src/topics/expressions.md:64 8c3b402c40f64880a4bd42c47b910254 -msgid "" -"Just like [parameter references](parameter-references.md), you can use " -"JavaScript Expressions only in certain fields. These are:" -msgstr "" - -#: ../../src/topics/expressions.md:66 9bf5ca0e769147c6a9705bc40bd1febc -msgid "" -"From " -"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 7ab0dbd54c1441539673fa12ef96b89e -#: e76c6ece0c594fefa86b190879c5acaa -msgid "`arguments`" -msgstr "" - -#: ../../src/topics/expressions.md:68 ../../src/topics/expressions.md:76 -#: ../../src/topics/expressions.md:89 -#: ../../src/topics/parameter-references.md:65 -#: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 0209558b1013471eb708698537edaf06 -#: 4458393fdb0e451f9806e91122ea2534 594a163e08f04aa5a04a44a303a1c643 -#: a6fddc160afc4ef09717f69de72c11ce a9ec99ddcb344bcbbe5c1f59af0bcff2 -#: af2cdb5f66ac4fd5b8f91258f005cc62 -msgid "`valueFrom`" -msgstr "" - -#: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 afb175f182354cb19e23b1cad241437e -#: f9a6718845e24f46b76fcc8ab26eec7a -msgid "`stdin`" -msgstr "" - -#: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 3bce21dcc2da439daca80c4fcdf4c343 -#: 7f5ce097ca0442a6a200599342a6e24b -msgid "`stdout`" -msgstr "" - -#: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 3397e8816f6a4d4b9af728c175f04917 -#: 7b14686e16eb4f488659b22d67ec3bfa -msgid "`stderr`" -msgstr "" - -#: ../../src/topics/expressions.md:72 7a2d74aa018f4cab8c68e8775d83dd01 -msgid "" -"From " -"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 -#: ../../src/topics/parameter-references.md:70 -#: ../../src/topics/parameter-references.md:75 -#: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 24f27702d0684bc98e3232103510232e -#: 26a8dff7b80c4e059f1e20eef9da6203 476aa37af5214bcf963c7aab1f859273 -#: 4b0a0cd934bd41b4b55c034b91392bc7 5182e2165e44429287b4d924c2f896a4 -#: 7de500d3be6b4c3e8f274fd6a092109f 953d824a494947a3ab0ca2988717ee01 -#: b301751f90af4700bbada5e5b166be35 -msgid "`format`" -msgstr "" - -#: ../../src/topics/expressions.md:74 ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 ../../src/topics/expressions.md:94 -#: ../../src/topics/parameter-references.md:71 -#: ../../src/topics/parameter-references.md:76 -#: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 2c2b8db396b04ace8aa396c0a5a4858f -#: 33a9b77ce15b4910962a7f08bd2f47a3 57cba0191de3470bbe112ed2a0d3f252 -#: 6efe998094b3469eae61cfff551b1eb1 776de1ecfafc41ada7e916addd7229fd -#: 8595d62eb0274b3a8a7f0adf058b51d3 988966a2d4844e73961b0358aff8f6e1 -#: faa7d521fec240748407d03ffdb93aa0 -msgid "`secondaryFiles`" -msgstr "" - -#: ../../src/topics/expressions.md:75 d737a9e9bf1c45d695bf584bc3241d9a -msgid "" -"From " -"[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:77 0e2052e16f6a41b8983dc64b4b3a7586 -msgid "" -"From " -"[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:80 dff31dd961d540e3b8cd1247e978d60e -msgid "" -"From " -"[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 249aba7c38ce49379b9d35e7ad81a0bf -#: 5a354eb4883948e0a2b5c96b5ae12da7 -msgid "`glob`" -msgstr "" - -#: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 2325a310f2bc4d09b53b32c54efae2df -#: 9e477e2cfab24861b517fe2fb52962f4 -msgid "`outputEval`" -msgstr "" - -#: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 9448462d104b4be5904623c85a9e16b7 -#: bf11a7a72147445c9b8e44b541e09f36 -msgid "From [`Workflow`](https://w3id.org/cwl/Workflow.html)" -msgstr "" - -#: ../../src/topics/expressions.md:84 0d54a777a33d4f17a2f3390384a3c0c5 -msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 7918d0661be746faaddf25ad49172f30 -#: b8439dbaa949427097e25ccb48fe15ee -msgid "From `steps`" -msgstr "" - -#: ../../src/topics/expressions.md:88 7b37eb600c9b4847a58a7e5077bef4c3 -msgid "" -"From " -"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 368ef005c2ca4b8599f76242f7178375 -#: ab1ba7626eae483a8b614ee4cd5bab6f -msgid "" -"From " -"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 595b9ddcee734d6595c1b4b2d169dcb8 -#: 80b55c77a4384644acfc9472c3cedee0 -msgid "`expression`" -msgstr "" - -#: ../../src/topics/expressions.md:92 fd504478a6c641e0a72321fa80ad1c9c -msgid "" -"From " -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:95 32b1a39cca1a4402af9bdc0abc4d70c8 -msgid "" -"From " -"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 2518d499801e4bcf82e9e4666280504d -#: 98a511d138e9497c923963c2ca5f0a0b -msgid "`coresMin`" -msgstr "" - -#: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 57a055b125f742dc8842b798b034161b -#: e84bc5505a6549ae9aacde8cb9225403 -msgid "`coresMax`" -msgstr "" - -#: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 98cd455e080f43749090270e7a61cb42 -#: e698ea756fe94e99837312fb30c9f9bf -msgid "`ramMin`" -msgstr "" - -#: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 8dfae10004a641fdb95c456c90a48d94 -#: bef90c153d4f4397b1f69f9beb38f7e6 -msgid "`ramMax`" -msgstr "" - -#: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 47fddc711ce44086a7811bdfbd9167dd -#: e2bdf4fe676346cbb4443ee54fb7419b -msgid "`tmpdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 7d143ba98f1f4dfcbe08b70389d43092 -#: 8f1665baca2e4e3b96026b50d132709a -msgid "`tmpdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 79bea45c2a484eda92c8578130b0b982 -#: d169949866a24e31947dffcb94620c5f -msgid "`outdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:103 -#: ../../src/topics/parameter-references.md:100 -#: 8d2e01f2aa314f1cb1231f2e08f89ce5 d5417397b1e242ef9878ac77d2f65005 -msgid "`outdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:104 08a66b2ab271494d810ff5834ca5c1bc -msgid "" -"From " -"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:105 -#: ../../src/topics/parameter-references.md:102 -#: 21e9582891cf4b87a7ee4693663040fa 51bc6d1ccef14729a0d5e63b56d73d20 -msgid "`listing`" -msgstr "" - -#: ../../src/topics/expressions.md:106 7d8755f05d6541439f72ec9d6806d3fc -msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/expressions.md:107 -#: ../../src/topics/parameter-references.md:104 -#: 29c2424fc7dc43e68c9bfee179167bb3 30f25141bcce4670882e4a5bbe4fc3e2 -msgid "`entry`" -msgstr "" - -#: ../../src/topics/expressions.md:108 -#: ../../src/topics/parameter-references.md:105 -#: 02cfd4f1c3014e1eaa598a329dc5a95d d76fb015595e4194a7e15d714baaaf98 -msgid "`entryname`" -msgstr "" - -#: ../../src/topics/expressions.md:109 -#: ../../src/topics/parameter-references.md:106 -#: 408f69a2df1343a78f93ff2ac0a994ea d37c78309e8b427f835af4fbd367e643 -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../src/topics/expressions.md:110 53752bdff0974e39b2a86e8f2d96455f -msgid "" -"From " -"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/expressions.md:111 -#: ../../src/topics/parameter-references.md:108 -#: 242a12ec757947db894195c9aefba818 7b26b9972f7141bf950b3bb024b0e369 -msgid "`envValue`" -msgstr "" - -#: ../../src/topics/expressions.md:116 93d6c90b49d8424f9283c384062ce333 -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" - -#: ../../src/topics/expressions.md:118 ea6cbaa5dae647538c0bd9a4d5cad3f9 -msgid "" -"The requirement " -"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" -" supports an `expressionLib` attribute that allows users to load external" -" JavaScript files, or to provide inline JavaScript code." -msgstr "" - -#: ../../src/topics/expressions.md:122 484dc17440524cfda4dc486a7c5d5f63 -msgid "" -"Entries added to the `expressionLib` attribute are parsed with the " -"JavaScript engine of a CWL runner. This can be used to include external " -"files or to create JavaScript functions that can be called in other parts" -" of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:128 5b2336cae1ef4cae8ed187d3f33cff25 -msgid "" -"The CWL standards (versions 1.0 through 1.2) " -"[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" -" that the only version of JavaScript valid in CWL expressions is " -"[ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means " -"that any code that you include or write in your CWL Document must be " -"compliant with ECMAScript 5.1." -msgstr "" - -#: ../../src/topics/expressions.md:135 32eca3a47efc4685bf7be706e123adbe -msgid "" -"For example, we can use `InlineJavascriptRequirement` and write a " -"JavaScript function inline in `expressionLib`. That function can then be " -"used in other parts of the CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:139 6839a02fb82d45c29ae518f2b00cb9d5 -msgid "`hello-world-expressionlib-inline.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:146 5b5e59fa1688499ea4560ee6f8023227 -msgid "" -"Running this CWL workflow will invoke the JavaScript function and result " -"in the `echo` command printing the input message with capital initial " -"letters:" -msgstr "" - -#: ../../src/topics/expressions.md:149 a1e57c6833c848d3974cf448493ab924 -msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:155 1a4dfef06b5c4402bdb7e7dbd79eeb5d -msgid "" -"Let's move the `capitalizeWords` function to an external file, `custom-" -"functions.js`, and import it in our CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:158 71ac99c65d15451cbbf58d1e81934010 -msgid "`custom-functions.js`" -msgstr "" - -#: ../../src/topics/expressions.md:164 60918e53189243d3872e61c7a4de20fc -msgid "`hello-world-expressionlib-external.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:171 ad2a74bd983b47869dc78b2eb7b6fce1 -msgid "" -"The `custom-functions.js` file is included in the CWL document with the " -"`$include: custom-functions.js` statement. That makes the functions and " -"variables available to be used in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:175 82c02dd2446b4de9a4c4b87736107b30 -msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:181 6fa7ebeffc7b44c6a12cd84897d186a1 -msgid "" -"Finally, note that you can have both inline and external JavaScript code " -"in your CWL document. In this final example we have added another entry " -"to the `expressionLib` attribute with the new function " -"`createHelloWorldMessage`, that calls the `capitalizeWords` function from" -" the external file `custom-functions.js`." -msgstr "" - -#: ../../src/topics/expressions.md:186 d34f3e688d2d49b6bfcda4c962895d8c -msgid "`hello-world-expressionlib.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:193 9e2774fc35b14832a0f92b7afaafd537 -msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:200 8b797cfb232f4e5da51f6c21e9a8e7e3 -msgid "" -"The `$include` statement can be used to include a file from the local " -"disk or from a remote location. It works with both relative and absolute " -"paths. Read the [text about " -"`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " -"the CWL specification to learn more about it." -msgstr "" - -#: ../../src/topics/file-formats.md:1 ac906f26116c45d882e1afa42ae38e34 -msgid "File Formats" -msgstr "" - -#: ../../src/topics/file-formats.md:3 d99dab4f2f264c68b839b59b80d570e0 -msgid "" -"Tools and workflows can take " -"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types as input " -"and produce them as output. We also recommend indicating the format for " -"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types. This " -"helps document for others how to use your tool while allowing you to do " -"some simple type-checking when creating parameter files." -msgstr "" - -#: ../../src/topics/file-formats.md:8 23ba3dd26f5543119e2c152105b58e98 -msgid "" -"For file formats, we recommend referencing existing ontologies (like EDAM" -" in our example), reference a local ontology for your institution, or do " -"not add a file format initially for quick development before sharing your" -" tool with others. You can browse existing [IANA file format " -"listings][IANA] and [EDAM file format listings][EDAM] on their websites." -msgstr "" - -#: ../../src/topics/file-formats.md:14 81c441846fc249c58607bacf97095eb8 -msgid "" -"In the next tutorial, we explain the `$namespaces` and `$schemas` " -"section of the document in greater detail, so don't worry about these for" -" now." -msgstr "" - -#: ../../src/topics/file-formats.md:17 c04841dbf4be4cf8a22cceca8b08bd14 -msgid "" -"Note that for added value `cwltool` can do some basic reasoning based on " -"file formats and warn you if there seem to be some obvious mismatches." -msgstr "" - -#: ../../src/topics/file-formats.md:20 c5f6f6e4c23e4bf19dee69acb8ebed8e -msgid "`metadata_example.cwl`" -msgstr "" - -#: ../../src/topics/file-formats.md:26 -#: ../../src/topics/metadata-and-authorship.md:22 -#: 20e97d58596a4a959ad76ec6128ac414 4e070ae9110d437bbf008b0c60a00cd5 -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../src/topics/file-formats.md:32 632e441919094610b97afc17e9c5e625 -msgid "Sample Parameter Files" -msgstr "" - -#: ../../src/topics/file-formats.md:34 afd8633db1904897aa3e499354b1c376 -msgid "" -"Below is an example of a parameter file for the example above. We " -"encourage checking in working examples of parameter files for your tool. " -"This allows others to quickly work with your tool, starting from a " -"\"known good\" parameterization." -msgstr "" - -#: ../../src/topics/file-formats.md:39 bb69d6963c174191bf527335c3f665b7 -msgid "`sample.yml`" -msgstr "" - -#: ../../src/topics/file-formats.md:45 ddb4f6f81c7d462b974e98c88dd3f558 -msgid "" -"___Note:___ To follow the example below, you need to download the example" -" input file, *file-formats.bam*. The file is available from " -" and can be downloaded e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/index.md:1 2995cd4fb85c423dba021611dac4a137 -msgid "Topics" -msgstr "" - -#: ../../src/topics/inputs.md:1 3bac021fe7614d74ae701fb3c3765b93 -msgid "Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:3 8bb3ee0cd0fc4d85ba007431fc541973 -msgid "Essential Input Parameters" -msgstr "" - -#: ../../src/topics/inputs.md:5 17365707f58242369dd6aa73fc8d7242 -msgid "" -"The `inputs` of a tool is a list of input parameters that control how to " -"run the tool. Each parameter has an `id` for the name of parameter, and " -"`type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/inputs.md:9 521cb5dead5d4e9ab5ff037fb4b683cb -msgid "" -"Available primitive types are *string*, *boolean*, *int*, *long*, " -"*float*, *double*, and *null*; complex types are *array* and *record*; in" -" addition there are special types *File*, *Directory* and *Any*." -msgstr "" - -#: ../../src/topics/inputs.md:13 fbdf2c1bed3e41d7a41ec6b14d134a98 -msgid "" -"The following example demonstrates some input parameters with different " -"types and appearing on the command line in different ways." -msgstr "" - -#: ../../src/topics/inputs.md:16 008f79cdf0074c73948bf50deb0a8a47 -msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "" - -#: ../../src/topics/inputs.md:18 94cd3f10e94f4735bd3ae7dc168e5deb -msgid "`inp.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:24 b339be370e8742b69400c8040ad7d15b -msgid "Create a file called `inp-job.yml`:" -msgstr "" - -#: ../../src/topics/inputs.md:26 78974fb2475947ccb8b8c55e34df5fa6 -msgid "`inp-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:33 9cc4a60d01f945aa9b4c43afcf20098b -msgid "" -"You can use `cwltool` to create a template input object. That saves you " -"from having to type all the input parameters in an input object file:" -msgstr "" - -#: ../../src/topics/inputs.md:40 5ac6da11d56446de97c251a37d997671 -msgid "" -"You can redirect the output to a file, i.e. `cwltool --make-template " -"inp.cwl > inp-job.yml`, and then modify the default values with your " -"desired input values." -msgstr "" - -#: ../../src/topics/inputs.md:44 6a3edb0d259d4d7c900dd9811f978d4e -msgid "" -"Notice that \"example_file\", as a `File` type, must be provided as an " -"object with the fields `class: File` and `path`." -msgstr "" - -#: ../../src/topics/inputs.md:47 f1d76be7ba0b48f4b605581d0a9a5c72 -msgid "" -"Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" -" command line." -msgstr "" - -#: ../../src/topics/inputs.md:53 8cabfa0cbcfd4a5aa30d1aabd412136d -msgid "" -"Now invoke `cwltool` with the tool description and the input object on " -"the command line, using the command `cwltool inp.cwl inp-job.yml`. The " -"following boxed text describes these two commands and the expected output" -" from the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:64 5c78d7824ef34636ae2ed68d524d79e8 -msgid "" -"The CWL reference runner (cwltool) and other runners create temporary " -"directories with symbolic (\"soft\") links to your input files to ensure " -"that the tools aren't accidentally accessing files that were not " -"explicitly specified" -msgstr "" - -#: ../../src/topics/inputs.md:70 5bdf77c45346445d8f93353c1e73f768 -msgid "" -"The field " -"[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)" -" is optional and indicates whether and how the input parameter should " -"appear on the tool's command line. If `inputBinding` is missing, the " -"parameter does not appear on the command line. Let's look at each " -"example in detail." -msgstr "" - -#: ../../src/topics/inputs.md:83 d783fe52e86f4feda33ea0eecb622603 -msgid "" -"Boolean types are treated as a flag. If the input parameter " -"\"example_flag\" is \"true\", then `prefix` will be added to the command " -"line. If false, no flag is added." -msgstr "" - -#: ../../src/topics/inputs.md:95 f99fb9a6d0374ef78503815d4db9006d -msgid "" -"String types appear on the command line as literal values. The `prefix` " -"is optional, if provided, it appears as a separate argument on the " -"command line before the parameter . In the example above, this is " -"rendered as `--example-string hello`." -msgstr "" - -#: ../../src/topics/inputs.md:109 b106eed01c1744a792368f91f547e553 -msgid "" -"Integer (and floating point) types appear on the command line with " -"decimal text representation. When the option `separate` is false (the " -"default value is true), the prefix and value are combined into a single " -"argument. In the example above, this is rendered as `-i42`." -msgstr "" - -#: ../../src/topics/inputs.md:124 1c70336741a842a5b16b687642d1d9b4 -msgid "" -"File types appear on the command line as the path to the file. When the " -"parameter type ends with a question mark `?` it indicates that the " -"parameter is optional. In the example above, this is rendered as " -"`--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" " -"parameter were not provided in the input, nothing would appear on the " -"command line." -msgstr "" - -#: ../../src/topics/inputs.md:131 9294c07c672b414f9c3895ed70b9b4ee -msgid "" -"Input files are read-only. If you wish to update an input file, you must" -" [first copy it to the output directory](staging-input-files.md)." -msgstr "" - -#: ../../src/topics/inputs.md:134 a07137c36e63495f836c483fd472904f -msgid "" -"The value of `position` is used to determine where parameter should " -"appear on the command line. Positions are relative to one another, not " -"absolute. As a result, positions do not have to be sequential, three " -"parameters with positions 1, 3, 5 will result in the same command line as" -" 1, 2, 3. More than one parameter can have the same position (ties are " -"broken using the parameter name), and the position field itself is " -"optional. The default position is 0." -msgstr "" - -#: ../../src/topics/inputs.md:142 7513adabd3ae4701b17f578ac9f321d7 -msgid "" -"The `baseCommand` field will always appear in the final command line " -"before the parameters." -msgstr "" - -#: ../../src/topics/inputs.md:146 c3c82d25a75941b0b50a4a6bb826568f -msgid "Array Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:148 b11a5c7a13b345939e4ae15e1e2c0786 -msgid "" -"It is easy to add arrays of input parameters represented to the command " -"line. There are two ways to specify an array parameter. First is to " -"provide `type` field with `type: array` and `items` defining the valid " -"data types that may appear in the array. Alternatively, brackets `[]` may" -" be added after the type name to indicate that input parameter is array " -"of that type." -msgstr "" - -#: ../../src/topics/inputs.md:154 aa00bcfc6c0f4085ae52621a2f4ae8d9 -msgid "`array-inputs.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:160 e730b2b9bace4427bdd045556963634f -msgid "`array-inputs-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:86 -#: ../../src/topics/outputs.md:109 015a0f00c2b245e2b0e87735926da736 -#: 390384208d7b4771888f164b587c7b9a edb3ae59c48945f29c3086b16a5265d3 -msgid "" -"Now invoke `cwltool` providing the tool description and the input object " -"on the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:178 13e59751d43b49f0ac366538a14f9c84 -msgid "" -"The `inputBinding` can appear either on the outer array parameter " -"definition or the inner array element definition, and these produce " -"different behavior when constructing the command line, as shown above. In" -" addition, the `itemSeparator` field, if provided, specifies that array " -"values should be concatenated into a single argument separated by the " -"item separator string." -msgstr "" - -#: ../../src/topics/inputs.md:185 bb31c6784ea843ec88f185523cfa25df -msgid "" -"Note that the arrays of inputs are specified inside square brackets `[]` " -"in `array-inputs-job.yml`. Arrays can also be expressed over multiple " -"lines, where array values that are not defined with an associated key are" -" marked by a leading `-`. This will be demonstrated in the next lesson " -"and is discussed in more detail in the [YAML Guide](yaml-" -"guide.md#arrays). You can specify arrays of arrays, arrays of records, " -"and other complex types." -msgstr "" - -#: ../../src/topics/inputs.md:191 53817379078548b2aeb6195cae9cbab7 -msgid "Inclusive and Exclusive Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:193 e163c0cfe9694a85b2e42682f42970a5 -msgid "" -"Sometimes an underlying tool has several arguments that must be provided " -"together (they are dependent) or several arguments that cannot be " -"provided together (they are exclusive). You can use records and type " -"unions to group parameters together to describe these two conditions." -msgstr "" - -#: ../../src/topics/inputs.md:198 84e1ab25511c49d1baabb1f80f247b49 -msgid "`record.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:204 3d5dfc8ee47b458db638a9eed84b4938 -msgid "`record-job1.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:215 ecfb1d911a84400ba3db12fd0adf9279 -msgid "" -"In the first example, you can't provide `itemA` without also providing " -"`itemB`." -msgstr "" - -#: ../../src/topics/inputs.md:217 24ba804374b4471d8e925d80670f9dff -msgid "`record-job2.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:233 436707d9c7634732ad1e60d8294bd4ba -msgid "" -"In the second example, `itemC` and `itemD` are exclusive, so only the " -"first matching item (`itemC`) is added to the command line and remaining " -"item (`itemD`) is ignored." -msgstr "" - -#: ../../src/topics/inputs.md:236 01b168c5faf94ead8d836dfe39e4c592 -msgid "`record-job3.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:252 e6d81d6549984689bae4533c6d01bd5b -msgid "" -"In the third example, only `itemD` is provided, so it appears on the " -"command line." -msgstr "" - -#: ../../src/topics/inputs.md:255 ffddeeda8f04408ba73f7a59a4618da5 -msgid "Exclusive Input Parameters with Expressions" -msgstr "" - -#: ../../src/topics/inputs.md:257 cf22f21ec44c483986979316544a7c3b -msgid "" -"If you use exclusive input parameters and reference them in expressions, " -"you need to be aware that the `inputs` JavaScript object will contain one" -" of the possible, mutually-exclusive input values. Because the types of " -"these exclusive values may differ, you may need to check which type is in" -" use when you reference the properties of the `input` object." -msgstr "" - -#: ../../src/topics/inputs.md:263 0fecb128b19b44d796b6c1b6de4f7166 -msgid "" -"Let's use an example that contains an exclusive `file_format` input " -"parameter that accepts `null` (i.e. no value provided), or any value from" -" an enum." -msgstr "" - -#: ../../src/topics/inputs.md:266 7f1941698a6046e9b9e8a53736af949a -msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:272 60b585142f06489d9f48090b664b6d32 -msgid "" -"Note how the JavaScript expression uses the value of the exclusive input " -"parameter without taking into consideration a `null` value. If you " -"provide a valid value, such as `fasta` (one of the possible values of the" -" enum), your command should execute successfully:" -msgstr "" - -#: ../../src/topics/inputs.md:281 11fdeb057d674f118830f431ff019c15 -msgid "" -"However, if you do not provide any input value, then `file_format` will " -"be evaluated to `null`, which does not match the expected type for the " -"output field (a `string`), resulting in failure when running your " -"workflow." -msgstr "" - -#: ../../src/topics/inputs.md:290 8594cca9d93b4280b6cfee64c8a7c578 -msgid "" -"To correct it, you should explicitly handle the possibility of a `null` " -"value. For example, the expression could be changed to " -"`$(inputs.file_format || 'auto')`, to have a default value `\"auto\"` if " -"none was provided in the command line or job input file." -msgstr "" - -#: ../../src/topics/inputs.md:295 b5055c77f85e43609fe3e9b9839778e3 -msgid "" -"Here, the boolean “or” operator `||` in JavaScript is used for its " -"_short-circuiting_ property. If `inputs.file_format` is “true” in a " -"boolean context (e.g. a valid non-empty string from the enum), the " -"evaluation of the expression stops at the first operand of `||`; it " -"“short-circuits”. If however `inputs.file_format` is `null`, the whole " -"expression’s value becomes that of the second operand, which is why a " -"reasonable default can be provided there." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:1 -#: 723c2232310c4276aeac2bd6728d2912 -msgid "Metadata and Authorship" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:3 -#: 4d81aac1830045229e5c60c7959074d8 -msgid "" -"Implementation extensions not required for correct execution (for " -"example, fields related to GUI presentation) and metadata about the tool " -"or workflow itself (for example, authorship for use in citations) may be " -"provided as additional fields on any object. Such extensions fields (e.g." -" `format: edam:format_2572`) can use a namespace prefix listed in the " -"`$namespaces` section of the document (e.g. edam: " -"http://edamontology.org/)%20as%20described%20in%20the%20[Schema%20Salad%20specification" -"][schema-salad]. Once you add the namespace prefix, you can access it " -"anywhere in the document as shown below. Otherwise, one must use full " -"URLs: `format: http://edamontology.org/format_2572`." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:13 -#: 368f8993ae9d401488081d74ae5acd49 -msgid "" -"For all developers, we recommend the following minimal metadata for your " -"tool and workflows. This example includes metadata allowing others to " -"cite your tool." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:16 -#: c80f2b180ca74afb8a1fc18f8686304b -msgid "`metadata_example2.cwl`" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:28 -#: 37b07ea9b7124842b8ba3040f70308e9 -msgid "Extended Example" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:30 -#: 1cd5989ade6741aabe625c13bed3c8ed -msgid "" -"For those that are highly motivated, it is also possible to annotate your" -" tool with a much larger amount of metadata. This example includes EDAM " -"ontology tags as keywords (allowing the grouping of related tools), hints" -" at hardware requirements in order to use the tool, and a few more " -"metadata fields." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:35 -#: ae7369ba14404d23b72d1ef30dcd4153 -msgid "`metadata_example3.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:1 a79974b2f4534fcd8c7a04401e8a5556 -msgid "Operations" -msgstr "" - -#: ../../src/topics/operations.md:3 b6507c8e1625476b97708423acb4fd0e -msgid "" -"An Operation is a type of CWL process, just like a workflow, a command-" -"line tool, or an expression tool. It is a step of a workflow that " -"specifies inputs and outputs, but it does not provide enough information " -"to be executed." -msgstr "" - -#: ../../src/topics/operations.md:7 047b09455db64524a71c47ab5192039f -msgid "" -"You can create operations to visualize a workflow during development, " -"before you are ready to submit the workflow to a CWL runner:" -msgstr "" - -#: ../../src/topics/operations.md:10 e9b2b97f3059460b867577a49934a338 -msgid "`operations.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:16 d21e9444182d4e27bae934db4573ae99 -msgid "" -"The `uppercase` step of the workflow is an operation. It can appear where" -" a command line tool or an expression is expected. You can also plot it " -"with the CWL Viewer or `cwltool`:" -msgstr "" - -#: ../../src/topics/operations.md:24 61e4ae6ed18e41708270eb358cd55277 -msgid "" -"The output of the command above can be rendered with a Graphviz renderer." -" The following image is rendered with the Sphinx `{graphviz}` directive " -"(this user guide is built with Sphinx):" -msgstr "" - -#: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd -msgid "" -"The operation file will fail to run with `cwltool` because `cwltool` " -"lacks the necessary information to execute it:" -msgstr "" - -#: ../../src/topics/operations.md:59 e184470550e645f6b9ce658af7e65ecf -msgid "`cwltool` does not know how to run operations" -msgstr "" - -#: ../../src/topics/operations.md:67 3b90445d3428444cafd7d5c0e5884980 -msgid "" -"CWL runners may come up with ways to bind operations to concrete steps. A" -" CWL runner could, for instance, use abstract operations with ID's that " -"correspond to steps executed by a different workflow engine." -msgstr "" - -#: ../../src/topics/outputs.md:1 35e7bad6fdc04bcf9bbfbb2d8d42cfa5 -msgid "Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:3 6d912d40359c4d33a4f08abca83c00be -msgid "Returning Output Files" -msgstr "" - -#: ../../src/topics/outputs.md:5 a6bd3f9e23de488394958fe7b59a61e0 -msgid "" -"The `outputs` of a tool is a list of output parameters that should be " -"returned after running the tool. Each parameter has an `id` for the name" -" of parameter, and `type` describing what types of values are valid for " -"that parameter." -msgstr "" - -#: ../../src/topics/outputs.md:10 a229d8d983344e51a231edb5f667d84b -msgid "" -"When a tool runs under CWL, the starting working directory is the " -"designated output directory. The underlying tool or script must record " -"its results in the form of files created in the output directory. The " -"output parameters returned by the CWL tool are either the output files " -"themselves, or the result of examining the content of those files." -msgstr "" - -#: ../../src/topics/outputs.md:16 9845e517f7d848e5b59a97880ca6999f -msgid "" -"The following example demonstrates how to return a file that has been " -"extracted from a tar file." -msgstr "" - -#: ../../src/topics/outputs.md:19 0bf1ad2c43174e57a3ba8dd86f7c96b2 -msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "" - -#: ../../src/topics/outputs.md:21 553d535b023e4d69a888fe5b24bb8c5b -msgid "" -"In previous examples, the `baseCommand` was just a string, with any " -"arguments passed as CWL inputs. Instead of a single string, we can use an" -" _array of strings_ as the value of `baseCommand`. The first element of " -"the array is the command to run, and any subsequent elements are " -"mandatory command line arguments" -msgstr "" - -#: ../../src/topics/outputs.md:28 9b65071222c94951bed12ac53e964ee3 -msgid "`tar.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:34 759ab0847b97479fb4a15e4b7d4e6565 -msgid "`tar-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:40 f9752ec303ab419c8db8adef3fa2466f -msgid "Next, create a tar file for the example." -msgstr "" - -#: ../../src/topics/outputs.md:47 4f96576528684f28a72b805f777769e6 -msgid "" -"And now invoke `cwltool` with the tool description and the input object " -"on the command line:" -msgstr "" - -#: ../../src/topics/outputs.md:53 707803bec0cb42919905c7c321bd9d30 -msgid "" -"The field " -"[`outputBinding`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding)" -" describes how to set the value of each output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:64 cbaec50871e04718883c8c91ff475d20 -msgid "" -"The " -"[`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) " -"field consists of the pattern to match file names in the output " -"directory. This can simply be the file's exact name. But if you don't " -"know the name of the file in advance, you can use a wildcard pattern like" -" `glob: '*.txt'`." -msgstr "" - -#: ../../src/topics/outputs.md:69 8a6e9173198241429effd911c3a7c4d7 -msgid "Capturing Standard Output" -msgstr "" - -#: ../../src/topics/outputs.md:71 a7c4fdaeda3e411fbeb802c5fa529ce9 -msgid "" -"To capture a tool's standard output stream, add the " -"[`stdout`](https://w3id.org/cwl/CommandLineTool.html#stdout) field with " -"the name of the file where the output stream should go. Then add `type: " -"stdout` on the corresponding output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:75 cf2ef8dc7fda49308c09efe4f4ef5d7b -msgid "`stdout.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:93 cbe236266dd148aaa96355e490a87cbe -msgid "Array Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:95 77f86a7b94924a08b6ea2660218fe3c5 -msgid "" -"You can also capture multiple output files into an array of files using " -"`glob`." -msgstr "" - -#: ../../src/topics/outputs.md:97 b34e30481fbd489d95fb7f8d5b5ab50c -msgid "`array-outputs.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:103 3aab0e0c9a78430f9caaa29a93303b56 -msgid "`array-outputs-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:116 9a14271c3180429988aaa14869f783a0 -msgid "" -"As described in the [YAML Guide](yaml-guide.md#arrays), the array of " -"expected outputs is specified in `array-outputs-job.yml` with each entry " -"marked by a leading `-`. This format can also be used in CWL descriptions" -" to mark entries in arrays, as demonstrated in several of the upcoming " -"sections." -msgstr "" - -#: ../../src/topics/parameter-references.md:1 c8a6ea340e6a43398e97b68e03a8bb3b -msgid "Parameter References" -msgstr "" - -#: ../../src/topics/parameter-references.md:3 f5c0592ca28c46c2a89943f4f6f69a27 -msgid "" -"In a previous example, we extracted a file using the \"tar\" program. " -"However, that example was very limited because it assumed that the file " -"we were interested in was called \"hello.txt\", and this was written into" -" the `.cwl` file. This is not the best way to do this, as the " -"\"hello.txt\" filename may vary or be dependent on the input file(s) " -"used. To avoid this we can specify the name of the file we want in the " -"job parameters file (`.yml`). In this example, you will see how to " -"reference the value of input parameters dynamically from other fields, " -"which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../src/topics/parameter-references.md:13 50db8add9b1942d986e581b8d21c2ee4 -msgid "`tar-param.cwl`" -msgstr "" - -#: ../../src/topics/parameter-references.md:19 d01ad5fd9fea462cab0d4d776824b4e1 -msgid "`tar-param-job.yml`" -msgstr "" - -#: ../../src/topics/parameter-references.md:25 9b1e2f1a23ea4fe2af97ef5108f33376 -msgid "" -"Create your input files and invoke `cwltool` with the tool description " -"and the input object on the command line:" -msgstr "" - -#: ../../src/topics/parameter-references.md:36 06926a516ae6432d96e3eaa62202cd86 -msgid "" -"Certain fields permit parameter references which are enclosed in " -"`$(...)`. These are evaluated and replaced with value being referenced." -msgstr "" - -#: ../../src/topics/parameter-references.md:47 384fe8188f414eafbbb8d6b81bdfd779 -msgid "" -"References are written using a subset of Javascript syntax. In this " -"example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " -"`$(inputs['extractfile'])` are equivalent." -msgstr "" - -#: ../../src/topics/parameter-references.md:51 56ead1c8d45c43bdbcbc6f7cbb8e1e92 -msgid "" -"The value of the \"inputs\" variable is the input object provided when " -"the CWL tool was invoked." -msgstr "" - -#: ../../src/topics/parameter-references.md:54 56bca89e314c4223b33d7fe63c9b771d -msgid "" -"Note that because `File` parameters are objects, to get the path to an " -"input file you must reference the path field on a file object; to " -"reference the path to the tar file in the above example you would write " -"`$(inputs.tarfile.path)`." -msgstr "" - -#: ../../src/topics/parameter-references.md:59 1c1ab240c4114572bb4e42955baad361 -msgid "Where are parameter references allowed?" -msgstr "" - -#: ../../src/topics/parameter-references.md:61 055d3268859c46c4b7db5005608bae05 -msgid "You can only use parameter references in certain fields. These are:" -msgstr "" - -#: ../../src/topics/parameter-references.md:63 2ed66835bd9044adbfdd0b5097787f22 -msgid "" -"From " -"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/parameter-references.md:69 f592619e4b2c497e80cd75da0548cf07 -msgid "" -"From " -"[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:72 81ea71a35020421187dc18ddd151c62f -msgid "" -"From " -"[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:74 ea0117748adc4324901024f21eed04ac -msgid "" -"From " -"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:77 3a30e73176cf4e4eb9f26770a176b9c9 -msgid "" -"From " -"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:81 551c199c9a6344fca9bfacfb69fc4e53 -msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:85 7008a1ff1af54fda827637e787e5c7dd -msgid "" -"From " -"[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/parameter-references.md:89 45743e1b261c4195856de0c2e30ea72e -msgid "" -"From " -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" and " -"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:92 0ae32d1db5f9452bbfcbbc4719b0b9f1 -msgid "" -"From " -"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:101 -#: 7e1907ff15c74f488187531de336eccf -msgid "" -"From " -"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:103 -#: 678874668fed4f4d80a1b0990e183e2f -msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/parameter-references.md:107 -#: e2882880886046ac88ae1c0d414366d1 -msgid "" -"From " -"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/requirements-and-hints.md:5 -#: 05324169d8ae48d4a1abe3a0ac07c891 -msgid "Requirements and Hints" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:1 -#: 1f5b72d7ec82442ba29baa14a03f061b -msgid "Specifying Software Requirements" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:3 -#: e708866921ea49d69d3c2a32d63ea468 -msgid "" -"Often, tool descriptions will be written for a specific version of a " -"software. To make it easier for others to use your descriptions, you can " -"include a " -"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)" -" field in the `hints` section. This may also help to avoid confusion " -"about which version of a tool the description was written for." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:13 -#: 6f722d6fd54f485fa964076c8d08938b -msgid "" -"In this example, the software requirement being described is InterProScan" -" version 5.21-60." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:25 -#: 5c1236ec57c64079bfb7c779524b12ad -msgid "" -"Depending on your CWL runner, these hints may be used to check that the " -"required software is installed and available before the job is run. To " -"enable these checks with the reference implementation, use the " -"[dependency resolvers configuration][dependencies]." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:29 -#: 1a8b8aadf1c64e87b8b670e288bc14bc -msgid "" -"As well as a version number, a unique resource identifier (URI) for the " -"tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" -" looked up in the [SciCrunch][scicrunch] registry, which provides a " -"portal for finding, tracking, and referring to scientific resources " -"consistently. If you want to specify a tool as a " -"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)," -" search for the tool on SciCrunch and use the RRID that it has been " -"assigned in the registry. (Follow this [Adding a Resource Tutorial" -"][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID " -"to refer to the tool (via [identifiers.org][identifiers]) in the `specs` " -"field of your requirement description. Other good choices, in order of " -"preference, are to include the DOI for the main tool citation and the URL" -" to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 d10c792550e8498c8ee384d3093da306 -msgid "Staging Input Files" -msgstr "" - -#: ../../src/topics/staging-input-files.md:3 ac2ef1fced5f4044861761a11c35e78a -msgid "" -"Normally, input files are located in a read-only directory separate from " -"the output directory. This causes problems if the underlying tool " -"expects to write its output files alongside the input file in the same " -"directory. You use " -"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)" -" to stage input files into the output directory. In this example, we use " -"a JavaScript expression to extract the base name of the input file from " -"its leading directory path." -msgstr "" - -#: ../../src/topics/staging-input-files.md:9 d8ca16f5321e486ebe8ea9f9752b3737 -msgid "`linkfile.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:1 aa3eddcaa0684f86ba67aafcd57872e7 -msgid "Troubleshooting" -msgstr "" - -#: ../../src/topics/troubleshooting.md:3 3207f476afa04158bd26db39a16a2df5 -msgid "" -"In this section you will find ways to troubleshoot when you have problems" -" executing CWL. We focus on `cwltool` here but some of these techniques " -"may apply to other CWL Runners." -msgstr "" - -#: ../../src/topics/troubleshooting.md:6 1d47f4ce04554cabb1ccf40a13ee42ec -msgid "Run `cwltool` with `cachedir`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:8 0c25602a83e441b48b536eb49568f2b6 -msgid "" -"You can use the `--cachedir` option when running a workflow to tell " -"`cwltool` to cache intermediate files (files that are not input nor " -"output files, but created while your workflow is running). By default, " -"these files are created in a temporary directory but writing them to a " -"separate directory makes accessing them easier." -msgstr "" - -#: ../../src/topics/troubleshooting.md:14 36ec60b80c714357a4274217274136ff -msgid "" -"In the following example `troubleshooting-wf1.cwl` we have two steps, " -"`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " -"World\" | rev`, which would print the message \"Hello World\" reversed, " -"i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**," -" where instead of executing the `rev` command it tries to execute `revv`," -" which fails." -msgstr "" - -#: ../../src/topics/troubleshooting.md:20 6f34038054ac4f4fa0b0ad9cbc3ecdc7 -msgid "`troubleshooting-wf1.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:27 b777877c88024c9fb06a6614029ef8d6 -msgid "" -"Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " -"value (`cwltool` will create the directory for you if it does not exist " -"already):" -msgstr "" - -#: ../../src/topics/troubleshooting.md:35 8654b7f2f4464d13be4b47729e1f07e5 -msgid "" -"The workflow is in the `permanentFail` status due to `step_b` failing to " -"execute the non-existent `revv` command. The `step_a` was executed " -"successfully and its output has been cached in your `cachedir` location. " -"You can inspect the intermediate files created:" -msgstr "" - -#: ../../src/topics/troubleshooting.md:44 04e80f7ce14d4d73bc5d290dcf01bcdb -msgid "" -"Each workflow step has received a unique ID (the long value that looks " -"like a hash). The `${HASH}.status` files display the status of each step " -"executed by the workflow. And the `step_a` output file `stdout.txt` is " -"visible in the output of the command above." -msgstr "" - -#: ../../src/topics/troubleshooting.md:48 719917cb0fd849f5a328671df8726189 -msgid "" -"Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" -" in the `step_b`). After fixing the typo, when you execute `cwltool` with" -" the same arguments as the previous time, note that now `cwltool` output " -"contains information about pre-cached outputs for `step_a`, and about a " -"new cache entry for the output of `step_b`. Also note that the status of " -"`step_b` is now of success." -msgstr "" - -#: ../../src/topics/troubleshooting.md:59 2a9dbb3ad7564f5aa103349c45ee7925 -msgid "" -"In this example the workflow step `step_a` was not re-evaluated as it had" -" been cached, and there was no change in its execution or output. " -"Furthermore, `cwltool` was able to recognize when it had to re-evaluate " -"`step_b` after we fixed the executable name. This technique is useful for" -" troubleshooting your CWL documents and also as a way to prevent " -"`cwltool` to re-evaluate steps unnecessarily." -msgstr "" - -#: ../../src/topics/using-containers.md:1 7439fe097aa4459ba1e4c0e28fc59b9a -msgid "Using Containers" -msgstr "" - -#: ../../src/topics/using-containers.md:3 eff5c6ac1cad44f9862585daf0a91298 -msgid "Running Tools Inside Docker" -msgstr "" - -#: ../../src/topics/using-containers.md:5 50d1a644bc8c49f78c453e4e0f3c07c8 -msgid "" -"[Docker][docker] containers simplify software installation by providing a" -" complete known-good runtime for software and its dependencies. However," -" containers are also purposefully isolated from the host system, so in " -"order to run a tool inside a Docker container there is additional work to" -" ensure that input files are available inside the container and output " -"files can be recovered from the container. A CWL runner can perform this" -" work automatically, allowing you to use Docker to simplify your software" -" management while avoiding the complexity of invoking and managing Docker" -" containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 4b0f6cfc8a774c77bfbc99e568af2ece -msgid "" -"One of the responsibilities of the CWL runner is to adjust the paths of " -"input files to reflect the location where they appear inside the " -"container." -msgstr "" - -#: ../../src/topics/using-containers.md:18 27c02a5d479a420eab7d14888d9fb288 -msgid "" -"This example runs a simple Node.js script inside a Docker container which" -" will then print \"Hello World\" to the standard output." -msgstr "" - -#: ../../src/topics/using-containers.md:21 1a62a93ab20b4f2ca1e13ded3a767dc5 -msgid "`docker.cwl`" -msgstr "" - -#: ../../src/topics/using-containers.md:27 ccc2874840c3476bb714ddf4bdbf0f3e -msgid "`docker-job.yml`" -msgstr "" - -#: ../../src/topics/using-containers.md:33 d766b66de4714a5da0cd87ed886cc32f -msgid "" -"Before we run this, let's just break it down and see what some bits do. " -"Most of this has been explained in previous sections, the only part that " -"is really new is the " -"[`dockerRequirement`](https://w3id.org/cwl/CommandLineTool.html#DockerRequirement)" -" section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 1f02618ab6254459ae71f72844e3cc18 -msgid "" -"`baseCommand: node` tells CWL that we will be running this command using " -"the Node Js runtime that is meant for Javascript files. We then need to " -"specify some `hints` for how to find the container we want. In this case" -" we list just our requirements for the docker container in " -"`DockerRequirements`. The `dockerPull:` parameter takes the same value " -"that you would pass to a `docker pull` command. That is, the name of the " -"container image (you can even specify the tag, which is good idea for " -"best practices when using containers for reproducible research). In this " -"case we have used a container called `node:slim`." -msgstr "" - -#: ../../src/topics/using-containers.md:52 54cade4978ec463bbb5c0d8c08e27adb -msgid "" -"Create a Javascript file named \"hello.js\" and invoke `cwltool` " -"providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/using-containers.md:55 6541d0cd9f6c4c43b8601715cc35e585 -msgid "`hello.js`" -msgstr "" - -#: ../../src/topics/using-containers.md:69 6abf220b7fa4479394ed33447cdd070e -msgid "" -"Notice the CWL runner has constructed a Docker command line to run the " -"script." -msgstr "" - -#: ../../src/topics/using-containers.md:72 d2dd89a5edde4f2eab4c2baf0cc78745 -msgid "" -"In this example, the path to the script `hello.js` is " -"`/home/me/cwl/user_guide/hello.js` outside the container but " -"`/var/lib/cwl/job369354770_examples/hello.js` inside the container, as " -"reflected in the invocation of the `node` command." -msgstr "" - -#: ../../src/topics/workflows.md:1 06281a10592d42509566c8fc51f8d4da -msgid "Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:3 325a656f9b8e4c1fa6f699cd8c447d00 -msgid "" -"A workflow is a CWL processing unit that executes command-line tools, " -"expression tools, or workflows (sub-workflows) as steps. It must have " -"`inputs`, `outputs`, and `steps` defined in the CWL document." -msgstr "" - -#: ../../src/topics/workflows.md:13 b92275181c9e480da64e660b7aca0745 -msgid "CWL workflow." -msgstr "" - -#: ../../src/topics/workflows.md:41 be2540315f854b8e9a1d257bcabd78db -msgid "" -"The CWL document `echo-uppercase.cwl` defines a workflow that runs the " -"command-line tool, and the expression tool showed in the earlier " -"examples." -msgstr "" - -#: ../../src/topics/workflows.md:51 3be900594bb743399854b95baa9ae2f9 -msgid "`echo-uppercase.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:81 5133c4e062bc4e479ce1dc8abbb08107 -msgid "" -"A command-line tool or expression tool can also be written directly in " -"the same CWL document as the workflow. For example, we can rewrite the " -"`echo-uppercase.cwl` workflow as a single file:" -msgstr "" - -#: ../../src/topics/workflows.md:91 83bc2796889f4dccb713764ac1b3c3ad -msgid "`echo-uppercase-single-file.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:150 5a9a1dd6ed1f4ca6803f1d235c4fd392 -msgid "" -"Having separate files helps with modularity and code organization. But it" -" can be helpful writing everything in a single file for development. " -"There are other ways to combine multiple files into a single file (e.g. " -"`cwltool --pack`) discussed further in other sections of this user guide." -msgstr "" - -#: ../../src/topics/workflows.md:160 277ed30d4b3a4156a4523e8d10e6ce60 -msgid "" -"For a sub-workflows you need to enable the requirement " -"`SubworkflowFeatureRequirement`. It is covered in another section of this" -" user guide in more detail." -msgstr "" - -#: ../../src/topics/workflows.md:165 82818ab17aa4403eb982fd81a14a5865 -msgid "Writing Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:167 3d8b98e8d03548699fadb22198de9b20 -msgid "" -"This workflow extracts a java source file from a tar file and then " -"compiles it." -msgstr "" - -#: ../../src/topics/workflows.md:170 c61097c695424f7195e8205a23b6ecff -msgid "`1st-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 6660c48f51d94d4fbcc05656e154059e bd2bab6c11614fa983ca8dab1408e1d8 -msgid "Visualization of 1st-workflow.cwl" -msgstr "" - -#: ../../src/topics/workflows.md:180 f0831481a43548039fbc4fd17555af57 -msgid "" -"[![Visualization of 1st-" -"workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-" -"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-workflow.cwl)" -msgstr "" - -#: ../../src/topics/workflows.md:183 5ff059fc8ae6471c8ea86dab7e5a93f5 -msgid "" -"Use a YAML or a JSON object in a separate file to describe the input of a" -" run:" -msgstr "" - -#: ../../src/topics/workflows.md:185 822e5d0a097b4109960d621a72a3c009 -msgid "`1st-workflow-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:191 4a4db7da861547639524083bf35ccfc0 -msgid "" -"Next, create a sample Java file and add it to a tar file to use with the " -"command-line tool." -msgstr "" - -#: ../../src/topics/workflows.md:205 ed16b30eaa4747f79b6dd10a19188d8c -msgid "What's going on here? Let's break it down:" -msgstr "" - -#: ../../src/topics/workflows.md:212 6428bd7bd3be4393bfe5675f8e45ff94 -msgid "" -"The `cwlVersion` field indicates the version of the CWL spec used by the " -"document. The `class` field indicates this document describes a " -"workflow." -msgstr "" - -#: ../../src/topics/workflows.md:221 d6abec8805f649fca668292412263f78 -msgid "" -"The `inputs` section describes the inputs of the workflow. This is a " -"list of input parameters where each parameter consists of an identifier " -"and a data type. These parameters can be used as sources for input to " -"specific workflows steps." -msgstr "" - -#: ../../src/topics/workflows.md:233 22bf3e4910ef4f86a2e8f6d5a6cf0d42 -msgid "" -"The `outputs` section describes the outputs of the workflow. This is a " -"list of output parameters where each parameter consists of an identifier " -"and a data type. The `outputSource` connects the output parameter " -"`classfile` of the `compile` step to the workflow output parameter " -"`compiled_class`." -msgstr "" - -#: ../../src/topics/workflows.md:248 e0429688fce445da8083e69323e5b020 -msgid "" -"The `steps` section describes the actual steps of the workflow. In this " -"example, the first step extracts a file from a tar file, and the second " -"step compiles the file from the first step using the java compiler. " -"Workflow steps are not necessarily run in the order they are listed, " -"instead the order is determined by the dependencies between steps (using " -"`source`). In addition, workflow steps which do not depend on one " -"another may run in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:256 980f5eada57c4fadbb783838ded1fa0b -msgid "" -"The first step, `untar` runs `tar-param.cwl` (described previously in " -"[Parameter References](parameter-references.md)). This tool has two input" -" parameters, `tarfile` and `extractfile` and one output parameter " -"`extracted_file`." -msgstr "" - -#: ../../src/topics/workflows.md:261 3532e165842f4ebb8db0c78208071555 -msgid "" -"The ``in`` section of the workflow step connects these two input " -"parameters to the inputs of the workflow, `tarball` and " -"`name_of_file_to_extract` using `source`. This means that when the " -"workflow step is executed, the values assigned to `tarball` and " -"`name_of_file_to_extract` will be used for the parameters `tarfile` and " -"`extractfile` in order to run the tool." -msgstr "" - -#: ../../src/topics/workflows.md:267 04a4db2f3da94ce29e7999039ee13fde -msgid "" -"The `out` section of the workflow step lists the output parameters that " -"are expected from the tool." -msgstr "" - -#: ../../src/topics/workflows.md:278 2651ee113a3d4b79b138854ebe729f48 -msgid "" -"The second step `compile` depends on the results from the first step by " -"connecting the input parameter `src` to the output parameter of `untar` " -"using `untar/extracted_file`. It runs `arguments.cwl` (described " -"previously in [Additional Arguments and Parameters](additional-arguments-" -"and-parameters.md)). The output of this step `classfile` is connected to " -"the `outputs` section for the Workflow, described above." -msgstr "" - -#: ../../src/topics/workflows.md:285 177040bf9c0045f2878f42bcdd8cbd2d -msgid "Nested Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:287 e8adc2f7c5ac4464b0711712617b8bbe -msgid "" -"Workflows are ways to combine multiple tools to perform a larger " -"operations. We can also think of a workflow as being a tool itself; a CWL" -" workflow can be used as a step in another CWL workflow, if the workflow " -"engine supports the `SubworkflowFeatureRequirement`:" -msgstr "" - -#: ../../src/topics/workflows.md:297 44d281d99cd944478db98446a984c001 -msgid "" -"Here's an example workflow that uses our `1st-workflow.cwl` as a nested " -"workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:300 d7b60ce81ea741ffa08f2c2d9d7cca69 -msgid "`nestedworkflows.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:309 a5b7a1ab16e34bda8744ffadacdda3e8 -msgid "" -"This two-step workflow starts with the `create-tar` step which is " -"connected to the `compile` step in orange; `compile` is another workflow," -" diagrammed on the right. In purple we see the fixed string " -"`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 8654f2d86b644609aaa5b9b73db30bda -msgid "" -" \"Visualization" -msgstr "" - -#: ../../src/topics/workflows.md:322 7ce847ab54224452b6425de2a55ec893 -msgid "" -"A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " -"its CWL file is included with `run`. The workflow inputs (`tarball` and " -"`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " -"mapped to become the step's input/outputs." -msgstr "" - -#: ../../src/topics/workflows.md:336 d621821d2c1b403cb7415b381dd883f6 -msgid "" -"Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " -"running it we had to provide a job file to denote the tar file and " -"`*.java` filename. This is generally best-practice, as it means it can be" -" reused in multiple parent workflows, or even in multiple steps within " -"the same workflow." -msgstr "" - -#: ../../src/topics/workflows.md:341 358c612f175241f7bf148a04d75e00c9 -msgid "" -"Here we use `default:` to hard-code `\"Hello.java\"` as the " -"`name_of_file_to_extract` input, however our workflow also requires a tar" -" file at `tarball`, which we will prepare in the `create-tar` step. At " -"this point it is probably a good idea to refactor `1st-workflow.cwl` to " -"have more specific input/output names, as those also appear in its usage " -"as a tool." -msgstr "" - -#: ../../src/topics/workflows.md:347 c6297c120e004ae8b52d5b519fbc04d2 -msgid "" -"It is also possible to do a less generic approach and avoid external " -"dependencies in the job file. So in this workflow we can generate a hard-" -"coded `Hello.java` file using the previously mentioned " -"`InitialWorkDirRequirement` requirement, before adding it to a tar file." -msgstr "" - -#: ../../src/topics/workflows.md:366 66f76677f4ce42baa8a8813410ea5aee -msgid "" -"In this case our step can assume `Hello.java` rather than be " -"parameterized, so we can use hardcoded values `hello.tar` and " -"`Hello.java` in a `baseCommand` and the resulting `outputs`:" -msgstr "" - -#: ../../src/topics/workflows.md:383 a8ccb9f9ab4448e087ea8448d620d33c -msgid "" -"Did you notice that we didn't split out the `tar --create` tool to a " -"separate file, but rather embedded it within the CWL Workflow file? This " -"is generally not best practice, as the tool then can't be reused. The " -"reason for doing it in this case is because the command line is hard-" -"coded with filenames that only make sense within this workflow." -msgstr "" - -#: ../../src/topics/workflows.md:389 afe43b9e92e949a589f493293eff2903 -msgid "" -"In this example we had to prepare a tar file outside, but only because " -"our inner workflow was designed to take that as an input. A better " -"refactoring of the inner workflow would be to take a list of Java files " -"to compile, which would simplify its usage as a tool step in other " -"workflows." -msgstr "" - -#: ../../src/topics/workflows.md:394 239eef3a740d42a69208a8f4e716d2b3 -msgid "" -"Nested workflows can be a powerful feature to generate higher-level " -"functional and reusable workflow units - but just like for creating a CWL" -" Tool description, care must be taken to improve its usability in " -"multiple workflows." -msgstr "" - -#: ../../src/topics/workflows.md:398 96d1ca78cc324f40b61c4b7330447db2 -msgid "Scattering Steps" -msgstr "" - -#: ../../src/topics/workflows.md:400 eab4437bf9994b649954221375e3dd6d -msgid "" -"Now that we know how to write workflows, we can start utilizing the " -"`ScatterFeatureRequirement`. This feature tells the runner that you wish " -"to run a tool or workflow multiple times over a list of inputs. The " -"workflow then takes the input(s) as an array and will run the specified " -"step(s) on each element of the array as if it were a single input. This " -"allows you to run the same workflow on multiple inputs without having to " -"generate many different commands or input yaml files." -msgstr "" - -#: ../../src/topics/workflows.md:411 c245ba0ae2074fa388ad6c35695033c8 -msgid "" -"The most common reason a new user might want to use scatter is to perform" -" the same analysis on different samples. Let's start with a simple " -"workflow that calls our first example (`hello_world.cwl`) and takes an " -"array of strings as input to the workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:415 83537938ce1244709f9b72269b048d63 -msgid "`scatter-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:421 4f507925766e48ae8f713d56051a5e29 -msgid "" -"Aside from the `requirements` section including " -"`ScatterFeatureRequirement`, what is going on here?" -msgstr "" - -#: ../../src/topics/workflows.md:429 ccbbba3189404241a44736c970249b84 -msgid "" -"First of all, notice that the main workflow level input here requires an " -"array of strings." -msgstr "" - -#: ../../src/topics/workflows.md:441 31eff13bb8334fc7b6d48ef6c5b1ce33 -msgid "" -"Here we've added a new field to the step `echo` called `scatter`. This " -"field tells the runner that we'd like to scatter over this input for this" -" particular step. Note that the input name listed after scatter is the " -"one of the step's input, not a workflow level input." -msgstr "" - -#: ../../src/topics/workflows.md:445 0d5cf8b82dbd47f2abd1ed16b9b3eb61 -msgid "" -"For our first scatter, it's as simple as that! Since our tool doesn't " -"collect any outputs, we still use `outputs: []` in our workflow, but if " -"you expect that the final output of your workflow will now have multiple " -"outputs to collect, be sure to update that to an array type as well!" -msgstr "" - -#: ../../src/topics/workflows.md:450 38b7042a270043ba82c11cf2e758f0c8 -msgid "Using the following input file:" -msgstr "" - -#: ../../src/topics/workflows.md:452 b3fc75c262fe4a3a8e8bfba1abb07b3d -msgid "`scatter-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:458 f9fa7046c89c417db51dc7c8a026fd5d -msgid "" -"As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" -" calls the command `echo` on a message. If we invoke `cwltool scatter-" -"workflow.cwl scatter-job.yml` on the command line:" -msgstr "" - -#: ../../src/topics/workflows.md:466 b6a33410ee9a45d7bf7b2ba56f786f8f -msgid "" -"You can see that the workflow calls echo multiple times on each element " -"of our `message_array`. Ok, so how about if we want to scatter over two " -"steps in a workflow?" -msgstr "" - -#: ../../src/topics/workflows.md:469 99b5c8a845ab4beb8524a69c051e2d42 -msgid "" -"Let's perform a simple echo like above, but capturing `stdout` by adding " -"the following lines instead of `outputs: []`" -msgstr "" - -#: ../../src/topics/workflows.md:472 97bf58937d3f4e98af702e3c1a418992 -msgid "`hello_world_to_stdout.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:480 173bd28708834f11a2a1366b579b7ad7 -msgid "" -"And add a second step that uses `wc` to count the characters in each " -"file. See the tool below:" -msgstr "" - -#: ../../src/topics/workflows.md:483 4afccfe982ff4be2be96cbe5889e5014 -msgid "`wc-tool.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:489 63595d35dded4911aab0be3a165eec0c -msgid "" -"Now, how do we incorporate scatter? Remember the scatter field is under " -"each step:" -msgstr "" - -#: ../../src/topics/workflows.md:491 a7f96ec6e4f24c62ac0f5b6edcc9734b -msgid "`scatter-two-steps.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:497 122452b7d7114c3fa53cbea286703023 -msgid "" -"Here we have placed the scatter field under each step. This is fine for " -"this example since it runs quickly, but if you're running many samples " -"for a more complex workflow, you may wish to consider an alternative. " -"Here we are running scatter on each step independently, but since the " -"second step is not dependent on the first step completing all languages, " -"we aren't using the scatter functionality efficiently. The second step " -"expects an array as input from the first step, so it will wait until " -"everything in step one is finished before doing anything. Pretend that " -"`echo Hello World!` takes 1 minute to perform, `wc -c` on the output " -"takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, " -"and `wc` on that output takes 3 minutes. Even though `echo Hello World!` " -"could finish in 4 minutes, it will actually finish in 8 minutes because " -"the first step must wait on `echo Hallo welt!`. You can see how this " -"might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 85dd63daf04546b78bdcb68c1d985fa9 -msgid "" -"Ok, so how do we scatter on steps that can proceed independent of other " -"samples? Remember from [Nested Workflows](#nested-workflows), that we can" -" make an entire workflow a single step in another workflow! Convert our " -"two-step workflow to a single step subworkflow:" -msgstr "" - -#: ../../src/topics/workflows.md:513 fac138ba275745898b763a7d719a8235 -msgid "`scatter-nested-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:519 508ef2240879445594b0f262ed11a01d -msgid "" -"Now the scatter acts on a single step, but that step consists of two " -"steps so each step is performed in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:522 b0bf01dad1234a1db3c87b10953e42ef -msgid "Conditional Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:524 8d933ed1ec6e408589f781e3a425b869 -msgid "" -"This workflow contains a conditional step and is executed based on the " -"input. This allows workflows to skip additional steps based on input " -"parameters given at the start of the program or by previous steps." -msgstr "" - -#: ../../src/topics/workflows.md:527 9ac7b4f71621411da9a4ca3bc277dcb0 -msgid "`conditional-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:566 4a4a2b2b99b44d449adb246cebce0a26 -msgid "" -"The first thing you'll notice is that this workflow is only compatible " -"for version 1.2 or greater of the CWL standards." -msgstr "" - -#: ../../src/topics/workflows.md:573 4742fe09a4264fb8be6f092519de5d72 -msgid "" -"The first step of the workflow (step1) contains two input properties and " -"will execute foo.cwl when the conditions are met. The new property `when`" -" is where the condition validation takes place. In this case only when " -"`in1` from the workflow contains a value `< 1` this step will be " -"executed." -msgstr "" - -#: ../../src/topics/workflows.md:587 b33ecd2b8af042feb08687e32d4b6bbf -msgid "" -"Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" -" will pass the first conditional step and will therefore be executed and " -"is shown in the log by `INFO [step step1] start` whereas the second step " -"is skipped as indicated by `INFO [step step2] will be skipped`." -msgstr "" - -#: ../../src/topics/workflows.md:607 7cd80b31a94543358ece7a2d413adce9 -msgid "" -"When a value of 3 is given the first conditional step will not be " -"executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." -msgstr "" - -#: ../../src/topics/workflows.md:627 9679e32f65e0482a8b083387e4a18c1f -msgid "" -"If no conditions are met for example when using `--val 2` the workflow " -"will raise a permanentFail." -msgstr "" - -#: ../../src/topics/yaml-guide.md:1 4fa76441f95d45fab76ab7eef8d7d4d2 -msgid "YAML Guide" -msgstr "" - -#: ../../src/topics/yaml-guide.md:6 705765787eb84ecaae004194225924cb -msgid "" -"[YAML][yaml] is a file format designed to be readable by both computers " -"and humans. This guide introduces the features of YAML that are relevant " -"when writing CWL descriptions and input parameter files." -msgstr "" - -#: ../../src/topics/yaml-guide.md:13 cb243f6ab11f48ffb5c91945c4e0d101 -msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" - -#: ../../src/topics/yaml-guide.md:16 cfc95d15e33a492f842649f92ced941d -msgid "Contents" -msgstr "" - -#: ../../src/topics/yaml-guide.md:18 f618d44d202f4c2ea6ff72a1dca2c659 -msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:19 36bfa6ed40c54bd99826bedff12c759d -msgid "[Comments](#comments)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:20 61913753eb0c4c728889b47f1110be24 -msgid "[Maps](#maps)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:21 0de824a05eea46209aafa6f9e2e8623c -msgid "[Arrays](#arrays)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:22 95627bc476b3415ca4d77246125137d2 -msgid "[JSON Style](#json-style)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:24 3f64a6d33d9a4c22a8a839a8def82686 -msgid "Key-Value Pairs" -msgstr "" - -#: ../../src/topics/yaml-guide.md:26 2f74f6eaa8d84dc9b4d0a166844dedbe -msgid "" -"Fundamentally, a file written in YAML consists of a set of _key-value " -"pairs_. Each pair is written as `key: value`, where whitespace after the " -"`:` is required. Key names in CWL files should not contain whitespace - " -"[_camelCase_][camelCase] is used for multi-word key names that have " -"special meaning in the CWL specification and underscored key names " -"otherwise. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:42 514365e59d9648deb896e2068d967a64 -msgid "" -"The YAML above defines four keys - `first_name`, `last_name`, " -"`age_years`, and `home` - with their four respective values. Values can " -"be character strings, numeric (integer, floating point, or scientific " -"representation), Boolean (`true` or `false`), or more complex nested " -"types (see below)." -msgstr "" - -#: ../../src/topics/yaml-guide.md:51 6939eb7e783744d7bcf75ea0a7cae129 -msgid "" -"Values may be wrapped in quotation marks, but be aware that this may " -"change the way that they are interpreted i.e. `\"1234\"` will be treated " -"as a character string , while `1234` will be treated as an integer. This " -"distinction can be important, for example when describing parameters to a" -" command: in CWL all parts of `baseCommand` must be strings so, if you " -"want to specify a fixed numeric value to a command, make sure that you " -"wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." -msgstr "" - -#: ../../src/topics/yaml-guide.md:61 96e1776b09e840ebbc9b4b7e01da0e43 -msgid "Comments" -msgstr "" - -#: ../../src/topics/yaml-guide.md:63 8b17f7557c3540b2b0d0beca0fe4ebc7 -msgid "" -"You may use `#` to add comments to your CWL and parameter files. Any " -"characters to the right of ` #` will be ignored by the program " -"interpreting the YAML. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:76 13da997c82c04023a4b7bb36b76e969d -msgid "" -"If there is anything on the line before the comment, be sure to add at " -"least one space before the `#`!" -msgstr "" - -#: ../../src/topics/yaml-guide.md:79 b9fc191166a64450b64a8182adabad75 -msgid "Maps" -msgstr "" - -#: ../../src/topics/yaml-guide.md:81 aedf8c4f615845ad91a7947217005d6e -msgid "" -"When describing a tool or workflow with CWL, it is usually necessary to " -"construct more complex, nested representations. Referred to as _maps_, " -"these hierarchical structures are described in YAML by providing " -"additional key-value pairs as the value of any key. These pairs " -"(sometimes referred to as \"children\") are written on new lines under " -"the key to which they belong (the \"parent\"), and should be indented " -"with two spaces (⇥tab characters are not allowed). For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:104 f0f1f414f74342a89065ba5ded8668e5 -msgid "" -"The YAML above illustrates how to build up complex nested object " -"descriptions relatively quickly. The `inputs` map contains a single key, " -"`example_flag`, which itself contains two keys, `type` and " -"`inputBinding`, while one of these children, `inputBinding`, contains a " -"further two key-value pairs (`position` and `prefix`). See the " -"[Arrays](#arrays) section below for more information about providing " -"multiple values/key-value pairs for a single key. For comparison with the" -" example YAML above, here is a graphical representation of the `inputs` " -"object it describes." -msgstr "" - -#: ../../src/topics/yaml-guide.md:127 965405e2a45a4cbb8f227bc8ceeb05df -msgid "Arrays" -msgstr "" - -#: ../../src/topics/yaml-guide.md:129 5aca9a90fb6149529ed717992746a2f3 -msgid "" -"In certain circumstances, it is necessary to provide multiple values or " -"objects for a single key. As we've already seen in the [Maps](#maps) " -"section above, more than one key-value pair can be mapped to a single " -"key. However, it is also possible to define multiple values for a key " -"without having to provide a unique key for each value. We can achieve " -"this with an _array_, where each value is defined on its own line and " -"preceded by `-`. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:146 d1c9e72e004b4fb4a6efb7748a15ab6f -msgid "and a more complex example combining maps and arrays:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:167 9a3d6879404745a48cd394bf86865dbc -msgid "JSON Style" -msgstr "" - -#: ../../src/topics/yaml-guide.md:169 6a7cca0339794e679329b00d89e29d2b -msgid "" -"YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " -"arrays can also be defined in YAML using the native JSON syntax. For " -"example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:177 d8feed2d36d04fe283b9de9784d91941 -msgid "and:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:184 5156ad32791048f8ace51475d7689575 -msgid "" -"Native JSON can be useful in indicating where a field is intentionally " -"left empty (such as `[]` for an empty array), as well as where it makes " -"more sense for the values to be located on the same line (For example, " -"when providing option flags and their values in a shell command). " -"However, as the second example above shows, it can severely affect the " -"readability of a YAML file, and should be used sparingly." -msgstr "" - -#: ../../src/topics/yaml-guide.md:194 ce49f80e6fc0498b8ad298fb1f0268f3 -msgid "Reference" -msgstr "" - -#: ../../src/topics/yaml-guide.md:196 180d261392a644fcb8ff47d7a4a160c0 -msgid "" -"The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" -" us while we wrote this guide, though it also covers features that are " -"not valid in CWL." -msgstr "" - -#: ../../src/tutorials.md:1 d682035afebf4c128755bd4e58780dd2 -msgid "Tutorials" -msgstr "" - -#: ../../src/tutorials.md:5 d9adeab63ec54084bc41fb90f264d3ae -msgid "" -"This is a list of tutorials provided by the CWL community. Use the `Edit " -"this page` link in the menu if you would like to add another tutorial to " -"the list." -msgstr "" - -#: ../../src/tutorials.md:7 23c81edb650b4f86a60c5e0bcedeac1d -msgid "Beginner Tutorials" -msgstr "" - -#: ../../src/tutorials.md:9 87ddaa1e5f57445c8f13803722aa146e -msgid "" -"[Introduction to Workflows with Common Workflow Language: For " -"Contributors.](https://carpentries-incubator.github.io/cwl-novice-" -"tutorial/)" -msgstr "" - -#: ../../src/tutorials.md:11 b8ee193ba533498db6263e0f5f4ec45f -msgid "Advanced Tutorials" -msgstr "" - -#: ../../src/tutorials.md:13 67c4b3923fce46fdab025495125c91d4 -msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" - -#: ../../src/tutorials.md:15 e640316669104239970794191b6da38b -msgid "Bioinformatics Tutorials" -msgstr "" - -#: ../../src/tutorials.md:17 efe94af44b874f9b81b245fbdee43f7f -msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" - -#~ msgid "Non \"`File`\" Types Using `evalFrom`" -#~ msgstr "" - -#~ msgid "Rename an Input File" -#~ msgstr "" - -#~ msgid "Rename an Output File" -#~ msgstr "" - -#~ msgid "Referencing a Local Script" -#~ msgstr "" - -#~ msgid "" -#~ "The first method involves adding the " -#~ "folder containing your scripts to the" -#~ " `PATH` environment variable. This allows" -#~ " you to run the shell script " -#~ "directly without using `sh` or `bash`" -#~ " commands." -#~ msgstr "" - -#~ msgid "In CWL, everything must be directly stated." -#~ msgstr "" - -#~ msgid "Setting `self`-based Input Bindings for Optional Inputs" -#~ msgstr "" - -#~ msgid "Model a \"one-or-the-other\" Parameter" -#~ msgstr "" - -#~ msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -#~ msgstr "" - -#~ msgid "" -#~ "Using " -#~ "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" -#~ " along with [`linkMerge: " -#~ "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -#~ msgstr "" - -#~ msgid "Which means \"create a list with exactly these sources as elements\"" -#~ msgstr "" - -#~ msgid "Optional Inputs 💯" -#~ msgstr "" - -#~ msgid "Enum Inputs ⚜️" -#~ msgstr "" - -#~ msgid "Record Inputs 📀" -#~ msgstr "" - -#~ msgid "Setting Mutually Exclusive Parameters" -#~ msgstr "" - -#~ msgid "Setting Booleans" -#~ msgstr "" - -#~ msgid "Concatenating Strings in Inputs" -#~ msgstr "" - -#~ msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -#~ msgstr "" - -#~ msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -#~ msgstr "" - -#~ msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -#~ msgstr "" - -#~ msgid "Use CWL and cwltool with Singularity" -#~ msgstr "" - -#~ msgid "Debug JavaScript Expressions" -#~ msgstr "" - -#~ msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -#~ msgstr "" - -#~ msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -#~ msgstr "" - -#~ msgid "" -#~ "`InitialWorkDirRequirement` - controls staging " -#~ "files in the input directory." -#~ msgstr "" - -#~ msgid "" -#~ "The FAIR principles have laid a " -#~ "foundation for sharing and publishing " -#~ "digital assets, and in particular, data." -#~ " The FAIR principles emphasize machine " -#~ "accessibility and that all digital " -#~ "assets should be Findable, Accessible, " -#~ "Interoperable, and Reusable. Workflows encode" -#~ " the methods by which the scientific" -#~ " process is conducted and via which" -#~ " data are created. It is thus " -#~ "important that workflows support the " -#~ "creation of FAIR data and adhere " -#~ "to the FAIR principles. — [FAIR " -#~ "Computational " -#~ "Workflows](https://workflows.community/groups/fair/), Workflows" -#~ " Community Initiative." -#~ msgstr "" - -#~ msgid "" -#~ "If you are using Windows, you will" -#~ " have to install the [Windows " -#~ "Subsystem for Linux 2](https://learn.microsoft.com" -#~ "/en-us/windows/wsl/install) (WSL2). Visit the " -#~ "`cwltool` [documentation](https://github.com/common-" -#~ "workflow-language/cwltool/blob/main/README.rst#ms-windows-" -#~ "users) for details on installing WSL2." -#~ " Your operating system also needs " -#~ "internet access and a recent version " -#~ "of Python (3.6+)." -#~ msgstr "" - -#~ msgid "" -#~ "`cwltool` can be installed with `pip`." -#~ " We recommend using a virtual " -#~ "environment like `venv` or `conda`. The" -#~ " following commands will create and " -#~ "activate a Python virtual environment " -#~ "using the `venv` module, and install " -#~ "`cwltool` in that environment:" -#~ msgstr "" - -#~ msgid "Installing `cwltool` with `pip` and `venv`." -#~ msgstr "" - -#~ msgid "" -#~ "Visit the `cwltool` " -#~ "[documentation](https://github.com/common-workflow-" -#~ "language/cwltool#install) for other ways to" -#~ " install `cwltool` with `apt` and " -#~ "`conda`." -#~ msgstr "" - -#~ msgid "Cwl-runner Python Module" -#~ msgstr "" - -#~ msgid "" -#~ "The CWL community publishes a Python " -#~ "package with the name `cwlref-runner`" -#~ " that installs an alias for `cwltool`" -#~ " under the name `cwl-runner`" -#~ msgstr "" - -#~ msgid "" -#~ "The *shebang* is the two-character " -#~ "sequence `#!` at the beginning of " -#~ "a script. When the script is " -#~ "executable, the operating system will " -#~ "execute the script using the executable" -#~ " specified after the shebang. It is" -#~ " considered a good practice to use" -#~ " `/usr/bin/env ` rather than " -#~ "using a hard-coded location, since " -#~ "`/usr/bin/env ` looks for the " -#~ "`` program in the system " -#~ "`PATH`," -#~ msgstr "" - -#~ msgid "" -#~ "The usage of the `cwltool` command-" -#~ "line executable is basically `cwltool " -#~ "[OPTIONS] [INPUTS_OBJECT]`. You " -#~ "can run the `hello_world.cwl` workflow " -#~ "without specifying any option:" -#~ msgstr "" - -#~ msgid "" -#~ "For more examples of providing metadata" -#~ " within CWL descriptions, see [the " -#~ "Metadata and Authorship section of this" -#~ " User Guide](../topics/metadata-and-" -#~ "authorship.md)." -#~ msgstr "" - -#~ msgid "" -#~ "In tool descriptions, list dependencies " -#~ "using short name(s) under " -#~ "`SoftwareRequirement`." -#~ msgstr "" - -#~ msgid "" -#~ "In tool descriptions, include a list " -#~ "of version(s) of the tool that are" -#~ " known to work with this description" -#~ " under `SoftwareRequirement`." -#~ msgstr "" - -#~ msgid "" -#~ "Each `CommandLineTool` description should " -#~ "focus on a single operation only, " -#~ "even if the (sub)command is capable " -#~ "of more. Don't overcomplicate your tool" -#~ " descriptions with options that you " -#~ "don't need or use." -#~ msgstr "" - -#~ msgid "" -#~ "This indicates whether a process " -#~ "requires outgoing IPv4/IPv6 network access." -#~ " If a command-line tool is " -#~ "written manually in CWL v1.1+, there " -#~ "is a need to specify when network" -#~ " access is required." -#~ msgstr "" - -#~ msgid "" -#~ "CWL v1.0 command-line tools that " -#~ "are upgraded to v1.1 or v1.2 get" -#~ " Network Access automatically." -#~ msgstr "" - -#~ msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -#~ msgstr "" - -#~ msgid "" -#~ "Note also that the author of this" -#~ " CWL description has also included " -#~ "`ResourceRequirement`s, specifying the minimum " -#~ "amount of RAM and number of cores" -#~ " required for the tool to run " -#~ "successfully, as well as details of " -#~ "the version of the software that " -#~ "the description was written for and " -#~ "other useful metadata. These features " -#~ "are discussed further in other chapters" -#~ " of this user guide." -#~ msgstr "" - -#~ msgid "" -#~ "Similar to the command-line tool " -#~ "it requires `inputs` and `outputs`. But" -#~ " instead of `baseCommand`, it requires " -#~ "an `expression` attribute." -#~ msgstr "" - -#~ msgid "" -#~ "We had to use an " -#~ "`InlineJavascriptRequirement` as our expression " -#~ "contains a JavaScript call in " -#~ "`.toUpperCase()`. This means to tools " -#~ "using the expression tool that " -#~ "JavaScript is a requirement." -#~ msgstr "" - -#~ msgid "" -#~ "If you need to manipulate input " -#~ "parameters, include the requirement " -#~ "`InlineJavascriptRequirement` and then anywhere " -#~ "a parameter reference is legal you " -#~ "can provide a fragment of Javascript " -#~ "that will be evaluated by the CWL" -#~ " runner." -#~ msgstr "" - -#~ msgid "From `Workflow`" -#~ msgstr "" - -#~ msgid "" -#~ "The requirement `InlineJavascriptRequirement` " -#~ "supports an `expressionLib` attribute that " -#~ "allows users to load external JavaScript" -#~ " files, or to provide inline " -#~ "JavaScript code." -#~ msgstr "" - -#~ msgid "" -#~ "Tools and workflows can take `File` " -#~ "types as input and produce them as" -#~ " output. We also recommend indicating " -#~ "the format for `File` types. This " -#~ "helps document for others how to " -#~ "use your tool while allowing you " -#~ "to do some simple type-checking " -#~ "when creating parameter files." -#~ msgstr "" - -#~ msgid "" -#~ "Available primitive types are *string*, " -#~ "*int*, *long*, *float*, *double*, and " -#~ "*null*; complex types are *array* and" -#~ " *record*; in addition there are " -#~ "special types *File*, *Directory* and " -#~ "*Any*." -#~ msgstr "" - -#~ msgid "" -#~ "You can use `cwltool` to create a" -#~ " template input object. That saves " -#~ "you from having to type all the" -#~ " input parameters in a input object" -#~ " file:" -#~ msgstr "" - -#~ msgid "" -#~ "The field `inputBinding` is optional and" -#~ " indicates whether and how the input" -#~ " parameter should appear on the " -#~ "tool's command line. If `inputBinding` " -#~ "is missing, the parameter does not " -#~ "appear on the command line. Let's " -#~ "look at each example in detail." -#~ msgstr "" - -#~ msgid "" -#~ "If you use exclusive input parameters" -#~ " combined with expressions, you need " -#~ "to be aware that the `inputs` " -#~ "JavaScript object will contain one of" -#~ " the exclusive input values. This " -#~ "means that you might need to use" -#~ " an **or** boolean operator to check" -#~ " which values are present." -#~ msgstr "" - -#~ msgid "" -#~ "Note how the JavaScript expression uses" -#~ " the value of the exclusive input " -#~ "parameter without taking into consideration" -#~ " a `null` value. If you provide " -#~ "a valid value, such as “fasta” " -#~ "(one of the values of the enum)," -#~ " your command should execute successfully:" -#~ msgstr "" - -#~ msgid "" -#~ "However, if you do not provide any" -#~ " input value, then `file_format` will " -#~ "be evaluated to a `null` value, " -#~ "which does not match the expected " -#~ "type for the output field (a " -#~ "`string`), resulting in failure when " -#~ "running your workflow." -#~ msgstr "" - -#~ msgid "" -#~ "To correct it, you must remember " -#~ "to use an or operator in your " -#~ "JavaScript expression when using exclusive " -#~ "parameters, or any parameter that allows" -#~ " `null`. For example, the expression " -#~ "could be changed to `$(inputs.file_format " -#~ "|| 'auto')`, to have a default " -#~ "value if none was provided in the" -#~ " command line or job input file." -#~ msgstr "" - -#~ msgid "" -#~ "The `uppercase` step of the workflow " -#~ "is an operation. It can be used" -#~ " like a command line tool or an" -#~ " expression. You can also plot it " -#~ "with the CWL Viewer or `cwltool`:" -#~ msgstr "" - -#~ msgid "" -#~ "The output of the command above " -#~ "can be rendered with a Graphviz " -#~ "renderer. The following image is " -#~ "rendered with the Sphinx Graphviz " -#~ "directive (this user guide is built " -#~ "with Sphinx):" -#~ msgstr "" - -#~ msgid "" -#~ "If you try running it with " -#~ "`cwltool`, the command will fail since" -#~ " `cwltool` does not have enough " -#~ "information to know how to execute " -#~ "it:" -#~ msgstr "" - -#~ msgid "" -#~ "When a tool runs under CWL, the" -#~ " starting working directory is the " -#~ "designated output directory. The underlying" -#~ " tool or script must record its " -#~ "results in the form of files " -#~ "created in the output directory. The" -#~ " output parameters returned by the " -#~ "CWL tool are either the output " -#~ "files themselves, or come from examining" -#~ " the content of those files." -#~ msgstr "" - -#~ msgid "" -#~ "In previous examples, the `baseCommand` " -#~ "was just a string, with any " -#~ "arguments passed as CWL inputs. Instead" -#~ " of a single string we can use" -#~ " an _array of strings_. The first" -#~ " element is the command to run, " -#~ "and any subsequent elements are " -#~ "mandatory command line arguments" -#~ msgstr "" - -#~ msgid "" -#~ "The field `outputBinding` describes how " -#~ "to set the value of each output" -#~ " parameter." -#~ msgstr "" - -#~ msgid "" -#~ "The `glob` field consists of the " -#~ "name of a file in the output " -#~ "directory. If you don't know name " -#~ "of the file in advance, you can" -#~ " use a wildcard pattern like `glob:" -#~ " '*.txt'`." -#~ msgstr "" - -#~ msgid "" -#~ "To capture a tool's standard output " -#~ "stream, add the `stdout` field with " -#~ "the name of the file where the " -#~ "output stream should go. Then add " -#~ "`type: stdout` on the corresponding " -#~ "output parameter." -#~ msgstr "" - -#~ msgid "" -#~ "Often, tool descriptions will be written" -#~ " for a specific version of a " -#~ "software. To make it easier for " -#~ "others to use your descriptions, you " -#~ "can include a `SoftwareRequirement` field " -#~ "in the `hints` section. This may " -#~ "also help to avoid confusion about " -#~ "which version of a tool the " -#~ "description was written for." -#~ msgstr "" - -#~ msgid "" -#~ "As well as a version number, a " -#~ "unique resource identifier (URI) for the" -#~ " tool is given in the form of" -#~ " an [RRID][rrid]. Resources with RRIDs " -#~ "can be looked up in the " -#~ "[SciCrunch][scicrunch] registry, which provides " -#~ "a portal for finding, tracking, and " -#~ "referring to scientific resources " -#~ "consistently. If you want to specify " -#~ "a tool as a `SoftwareRequirement`, " -#~ "search for the tool on SciCrunch " -#~ "and use the RRID that it has " -#~ "been assigned in the registry. (Follow" -#~ " this [Adding a Resource Tutorial" -#~ "][scicrunch-add-tool] to add a tool" -#~ " to SciCrunch). You can use this " -#~ "RRID to refer to the tool (via " -#~ "[identifiers.org][identifiers]) in the `specs` " -#~ "field of your requirement description. " -#~ "Other good choices, in order of " -#~ "preference, are to include the DOI " -#~ "for the main tool citation and the" -#~ " URL to the tool." -#~ msgstr "" - -#~ msgid "" -#~ "Normally, input files are located in " -#~ "a read-only directory separate from " -#~ "the output directory. This causes " -#~ "problems if the underlying tool expects" -#~ " to write its output files alongside" -#~ " the input file in the same " -#~ "directory. You use `InitialWorkDirRequirement` " -#~ "to stage input files into the " -#~ "output directory. In this example, we" -#~ " use a JavaScript expression to " -#~ "extract the base name of the input" -#~ " file from its leading directory " -#~ "path." -#~ msgstr "" - -#~ msgid "" -#~ "Before we run this, let's just " -#~ "break it down and see what some" -#~ " bits do. Most of this has " -#~ "been explained in previous sections, the" -#~ " only part that is really new " -#~ "is the `dockerRequirement` section." -#~ msgstr "" - diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 1ff0ee46..8a75ef39 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-03-08 11:01+0000\n" +"PO-Revision-Date: 2024-03-20 01:01+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified) \n" @@ -3693,7 +3693,8 @@ msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." -msgstr "" +msgstr "CWL 文件 `echo-uppercase.cwl` " +"定义了之前的例子中运行命令行工具的工作流以及表达式工具。" #: ../../src/topics/workflows.md:51 3be900594bb743399854b95baa9ae2f9 msgid "`echo-uppercase.cwl`" @@ -3705,6 +3706,8 @@ msgid "" "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" +"命令行工具或表达式工具亦可直接写在定义工作流的单一 CWL 文件里。例如，" +"我们可以将 `echo-uppercase.cwl` 改写成一个单独的文件如下：" #: ../../src/topics/workflows.md:91 83bc2796889f4dccb713764ac1b3c3ad msgid "`echo-uppercase-single-file.cwl`" @@ -3717,6 +3720,9 @@ msgid "" "There are other ways to combine multiple files into a single file (e.g. " "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" +"将代码分为多个独立的文件有助于模块化和代码的组织条理。不过，把全部代码集中在" +"一个文件，可能对开发更有利。将多个文件整合为一个，还有其他手段（如 `cwltool " +"--pack`），将在本《指南》的其他章节进一步讨论。" #: ../../src/topics/workflows.md:160 277ed30d4b3a4156a4523e8d10e6ce60 msgid "" @@ -3724,16 +3730,18 @@ msgid "" "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" +"子工作流 (sub-workflow) 需要启用 `SubworkflowFeatureRequirement` " +"这一要求，这在另一章节中将有更详细的教程。" #: ../../src/topics/workflows.md:165 82818ab17aa4403eb982fd81a14a5865 msgid "Writing Workflows" -msgstr "" +msgstr "编写工作流" #: ../../src/topics/workflows.md:167 3d8b98e8d03548699fadb22198de9b20 msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." -msgstr "" +msgstr "这个工作流从 tar 文件中提取一个 Java 源文件，然后编译。" #: ../../src/topics/workflows.md:170 c61097c695424f7195e8205a23b6ecff msgid "`1st-workflow.cwl`" @@ -3742,7 +3750,7 @@ msgstr "`1st-workflow.cwl`" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 #: 6660c48f51d94d4fbcc05656e154059e bd2bab6c11614fa983ca8dab1408e1d8 msgid "Visualization of 1st-workflow.cwl" -msgstr "" +msgstr "1st-workflow.cwl 的图示" #: ../../src/topics/workflows.md:180 f0831481a43548039fbc4fd17555af57 msgid "" @@ -3756,12 +3764,19 @@ msgid "" "language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" "-1st-workflow/1st-workflow.cwl)" msgstr "" +"[![1st-workflow.cwl 的图示](https://view.commonwl.org/graph/png/github.com/" +"common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/" +"common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)" #: ../../src/topics/workflows.md:183 5ff059fc8ae6471c8ea86dab7e5a93f5 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" -msgstr "" +msgstr "在分立的文件中通过 YAML 或 JSON 对象来描述一次运行的输入：" #: ../../src/topics/workflows.md:185 822e5d0a097b4109960d621a72a3c009 msgid "`1st-workflow-job.yml`" @@ -3771,11 +3786,12 @@ msgstr "`1st-workflow-job.yml`" msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." -msgstr "" +msgstr "接下来，创建一个 Java 文件样本，将其打包到一个 tar " +"文件，以供运行命令行工具时使用。" #: ../../src/topics/workflows.md:205 ed16b30eaa4747f79b6dd10a19188d8c msgid "What's going on here? Let's break it down:" -msgstr "" +msgstr "这是怎么一回事呢？我们一一道来：" #: ../../src/topics/workflows.md:212 6428bd7bd3be4393bfe5675f8e45ff94 msgid "" From d4c3990aba8b0efd8df1e8c13bf19f8767fad200 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Sat, 6 Apr 2024 08:01:14 +0200 Subject: [PATCH 134/179] Translations update from Hosted Weblate (#465) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Translated using Weblate (Ainu (Japan)) Currently translated at 7.3% (44 of 598 strings) Added translation using Weblate (Ainu (Japan)) Co-authored-by: Mohd Hafez Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ain/ Translation: Common Workflow Language/CWL User Guide * Added translation using Weblate (Ainu (Japan)) Co-authored-by: Languages add-on * Deleted translation using Weblate (Ainu (Japan)) Deleted translation using Weblate (Ainu (Japan)) Co-authored-by: Michael Crusoe * Translated using Weblate (Chinese (Simplified)) Currently translated at 77.6% (465 of 599 strings) Translated using Weblate (Chinese (Simplified)) Currently translated at 76.2% (457 of 599 strings) Co-authored-by: Zoë Ma Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 74.4% (446 of 599 strings) Translated using Weblate (Japanese) Currently translated at 74.2% (445 of 599 strings) Translated using Weblate (Japanese) Currently translated at 73.6% (441 of 599 strings) Translated using Weblate (Japanese) Currently translated at 72.9% (437 of 599 strings) Translated using Weblate (Japanese) Currently translated at 72.4% (434 of 599 strings) Translated using Weblate (Japanese) Currently translated at 71.9% (431 of 599 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide --------- Co-authored-by: Mohd Hafez Co-authored-by: Languages add-on Co-authored-by: Michael Crusoe Co-authored-by: Zoë Ma Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 108 +++++++++++----------- locales/zh_Hans/LC_MESSAGES/user_guide.po | 37 ++++++-- 2 files changed, 83 insertions(+), 62 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 71137498..a55d3d7a 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-03-20 01:01+0000\n" +"PO-Revision-Date: 2024-04-06 01:01+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -795,15 +795,15 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:151 #: b6a5cd431c324078a9a4e1513a14ee28 -#, fuzzy msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " "explained in detail in the [Requirements](../topics/requirements-and-" "hints.md) section." msgstr "" -"Hintsはrequirementsと似ていますが、requirementsが必須の機能を列挙するのに対し、hintsはオプションの機能を列挙します。requirementsについては、[requirements](../topics" -"/requirements-and-hints.md) セクションで詳しく説明しています。" +"HintsはRequirementsと似ていますが、Requirementsが必須機能を列挙するのに対し、" +"Hintsはオプションの機能を列挙します。Requirementsについては、[Requirements](." +"./topics/requirements-and-hints.md) セクションで詳しく説明しています。" #: ../../src/introduction/basic-concepts.md:155 #: 88d7bad84dd341d2abb33673b8b8f250 @@ -826,14 +826,14 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:167 #: 4ea1d3bf04dc42f0bc6735a45b9e0dc0 -#, fuzzy msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," " CWL tasks are isolated, and you must be explicit about your inputs and " "outputs." msgstr "" -"CWLのルーツは、タスク間の依存関係に基づき、実行順序を決定する \"make\" や多くの類似ツールにあります。しかし、\"make\" " +"CWLのルーツは、タスク間の依存関係に基づき、実行順序を決定する \"make\" " +"や多くの類似ツールにあります。しかし、\"make\" " "とは異なり、CWLのタスクは分離されており、入力と出力を明示する必要があります。" #: ../../src/introduction/basic-concepts.md:171 @@ -911,12 +911,14 @@ msgid "Introduction" msgstr "はじめに" #: ../../src/introduction/index.md:3 08db628a949b4513b824ee334e70a7df -#, fuzzy msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." -msgstr "このセクションでは、CWLの簡単な紹介、このユーザーガイドに従うための前提条件、そしてユーザーガイドの他の部分を読む前に知っておくと便利な基本概念について案内します。" +msgstr "" +"このセクションでは、CWLの簡単な紹介、このユーザーガイドに従うための前提条件、" +"そしてユーザーガイドの他の部分を読む前に知っておくと便利な基本概念について案" +"内します。" #: ../../src/introduction/prerequisites.md:1 d3f5749a76c14fdf8052f5f683d11b9e msgid "Prerequisites" @@ -1285,15 +1287,14 @@ msgid "`hello_world.cwl`" msgstr "`hello_world.cwl`" #: ../../src/introduction/quick-start.md:22 6a13fb9112ab41acb60dc65b3656f63e -#, fuzzy msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -"上記の例は、`echo` " -"のコマンドラインツールのラッパーに過ぎません。デフォルトの入力値で上記のワークフローを実行すると、コマンドラインと同じ結果が得られます`echo " -"\"Hello World\"`." +"上記の例は、`echo` のCommandLineToolのラッパーに過ぎません。デフォルトの入力" +"値で上記のワークフローを実行すると、コマンドラインと同じ結果が得られます`" +"echo \"Hello World\"`." #: ../../src/introduction/quick-start.md:27 7b2ae93353184faea0ae4f4acdfc3350 #, fuzzy @@ -1716,12 +1717,10 @@ msgstr "" "しないオプションでツールの定義を複雑にし過ぎないようにしましょう。" #: ../../src/topics/best-practices.md:73 ef5a5f9b253c4ca3916802a695fb7c6d -#, fuzzy msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." -msgstr "カスタム型は、再利用のため、タイプ定義ごとに1つの外部YAMLで定義した方が良いで" -"す。" +msgstr "カスタム型は、型定義ごとに1つの外部YAMLで定義すると再利用しやすくなります。" #: ../../src/topics/best-practices.md:76 ff59f40e84004523904e3094be07cc80 msgid "Include a top-level short `label` summarising the tool/workflow." @@ -2565,27 +2564,24 @@ msgid "" msgstr "`capitalizeWords` 関数を外部ファイル`custom-functions.js` に移動し、CWL 定義でインポートしてみましょう：" #: ../../src/topics/expressions.md:158 71ac99c65d15451cbbf58d1e81934010 -#, fuzzy msgid "`custom-functions.js`" msgstr "`custom-functions.js`" #: ../../src/topics/expressions.md:164 60918e53189243d3872e61c7a4de20fc -#, fuzzy msgid "`hello-world-expressionlib-external.cwl`" msgstr "`hello-world-expressionlib-external.cwl`" #: ../../src/topics/expressions.md:171 ad2a74bd983b47869dc78b2eb7b6fce1 -#, fuzzy msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -"`custom-functions.js` ファイルは、`$include: custom-functions.js` " -"という記述でCWL定義に含まれます。これにより、関数と変数がCWL定義の他の部分で使用できるようになります。" +"`custom-functions.js` ファイルは、`$include: custom-functions.js` という記述" +"でCWL定義に含まれます。これにより、関数と変数がCWL定義の他の部分で使用できる" +"ようになります。" #: ../../src/topics/expressions.md:175 82c02dd2446b4de9a4c4b87736107b30 -#, fuzzy msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "`hello-world-expressionlib-external.cwl`実行しています。" @@ -2610,7 +2606,6 @@ msgid "Running `hello-world-expressionlib.cwl`." msgstr "`hello-world-expressionlib.cwl`を実行する。" #: ../../src/topics/expressions.md:200 8b797cfb232f4e5da51f6c21e9a8e7e3 -#, fuzzy msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2618,10 +2613,10 @@ msgid "" "`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from " "the CWL specification to learn more about it." msgstr "" -"`$include` " -"ステートメントを使用すると、ローカルディスクまたはリモートロケーションからファイルをインクルードすることができます。相対パスと絶対パスの両方で動作します。CWL仕様の[text" -" " -"about`$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include)を読むと、より詳しく知ることができます。" +"`$include` ステートメントを使用すると、ローカルディスクまたはリモートロケーシ" +"ョンからファイルをインクルードすることができます。相対パスと絶対パスの両方で" +"動作します。CWL仕様の[`$include`について](https://www.commonwl.org/v1.0/" +"SchemaSalad.html#Include)を読むと、より詳しく知ることができます。" #: ../../src/topics/file-formats.md:1 ac906f26116c45d882e1afa42ae38e34 msgid "File Formats" @@ -2662,11 +2657,11 @@ msgid "" msgstr "次のチュートリアルで、`$namespaces` と`$schemas` の部分をより詳しく説明しますので、今は気にしないでください。" #: ../../src/topics/file-formats.md:17 c04841dbf4be4cf8a22cceca8b08bd14 -#, fuzzy msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." -msgstr "なお、さらなる利点として`cwltool` は、ファイル形式に基づく基本的な推論を行い、明らかな不一致があるようであれば警告を発します。" +msgstr "なお、さらなる利点として`cwltool` は、ファイル形式に基づく基本的な推論を行い" +"、明らかな不一致があるようであれば警告を発します。" #: ../../src/topics/file-formats.md:20 c5f6f6e4c23e4bf19dee69acb8ebed8e msgid "`metadata_example.cwl`" @@ -4059,29 +4054,26 @@ msgid "What's going on here? Let's break it down:" msgstr "どうなっているのでしょう？ 分解してみましょう：" #: ../../src/topics/workflows.md:212 6428bd7bd3be4393bfe5675f8e45ff94 -#, fuzzy msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -"`cwlVersion` フィールドは、この文書が使用するCWL仕様のバージョンを示します。 ` class` " -"フィールドは、この文書がワークフローを記述していることを示します。" +"`cwlVersion` フィールドは、この文書が使用するCWL仕様のバージョンを示します。" +" ` class` フィールドは、この文書がワークフローを記述していることを示します。" #: ../../src/topics/workflows.md:221 d6abec8805f649fca668292412263f78 -#, fuzzy msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " "and a data type. These parameters can be used as sources for input to " "specific workflows steps." msgstr "" -"`inputs` セクションでは、ワークフローの入力について記述します。 " -"これは入力パラメータのリストであり、各パラメータは識別子とデータ型から構成されます。 " -"これらのパラメータは、特定のワークフロー・ステップへの入力ソースとして使用できます。" +"`inputs` セクションでは、ワークフローの入力について記述します。 これは入力パ" +"ラメータのリストであり、各パラメータは識別子とデータ型から構成されます。 こ" +"れらのパラメータは、特定のワークフロー・ステップへの入力として使用できます。" #: ../../src/topics/workflows.md:233 22bf3e4910ef4f86a2e8f6d5a6cf0d42 -#, fuzzy msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -4089,9 +4081,10 @@ msgid "" "`classfile` of the `compile` step to the workflow output parameter " "`compiled_class`." msgstr "" -"`outputs` セクションでは、ワークフローの出力について記述します。 " -"これは出力パラメータのリストであり、各パラメータは識別子とデータ型から構成されます。 ` outputSource` は、`compile` " -"ステップの出力パラメータ`classfile` を、ワークフロー出力パラメータ`compiled_class` に接続します。" +"`outputs` セクションでは、ワークフローの出力について記述します。 これは出力" +"パラメータのリストであり、各パラメータは識別子とデータ型から構成されます。 `" +" outputSource` は、`compile` ステップの出力パラメータ`classfile` " +"を、ワークフロー出力パラメータ`compiled_class` とします。" #: ../../src/topics/workflows.md:248 e0429688fce445da8083e69323e5b020 #, fuzzy @@ -4301,26 +4294,31 @@ msgstr "" "定義の中に埋め込んだことにお気づきでしょうか。これは一般的にベストプラクティスではありません。なぜなら、そのツールを再利用できないからです。このケースでそれを行う理由は、コマンドラインに、このワークフロー定義内でしか意味をなさないファイル名がハードコーディングされているためです。" #: ../../src/topics/workflows.md:389 afe43b9e92e949a589f493293eff2903 -#, fuzzy msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " "refactoring of the inner workflow would be to take a list of Java files " "to compile, which would simplify its usage as a tool step in other " "workflows." -msgstr "この例では、外部にtarファイルを用意する必要がありましたが、これは内部のワークフローがそれを入力として受け取るように設計されているためです。内部ワークフローのリファクタリングとしては、コンパイルするJavaファイルのリストを受け取るようにすれば、他のワークフローにおけるツールステップとしての使い方が簡単になります。" +msgstr "" +"この例では、外部にtarファイルを用意する必要がありました。これは内部ワークフロ" +"ーがそれを入力として受け取るように設計されているためです。内部ワークフローの" +"リファクタリングとしては、コンパイルするjavaファイルのリストを受け取るように" +"すれば、他のワークフローにおいてもツールステップとしての使い方が簡単になりま" +"す。" #: ../../src/topics/workflows.md:394 239eef3a740d42a69208a8f4e716d2b3 -#, fuzzy msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" " Tool description, care must be taken to improve its usability in " "multiple workflows." -msgstr "ネストされたワークフローは、より高機能で再利用可能なワークフローユニットを生成する強力な機能ですが、CWLツール定義の作成と同様に、複数のワークフローでの使い勝手を向上させるための配慮が必要です。" +msgstr "" +"ネストされたワークフローは、より高機能で再利用可能なワークフローユニットを生" +"成する強力な機能ですが、CWLツール定義の作成と同様に、複数のワークフローでの使" +"い勝手を向上させるための配慮が必要です。" #: ../../src/topics/workflows.md:398 96d1ca78cc324f40b61c4b7330447db2 -#, fuzzy msgid "Scattering Steps" msgstr "Scatter ステップ" @@ -4499,11 +4497,11 @@ msgid "`scatter-nested-workflow.cwl`" msgstr "`scatter-nested-workflow.cwl`" #: ../../src/topics/workflows.md:519 508ef2240879445594b0f262ed11a01d -#, fuzzy msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." -msgstr "今、scatter は1つのステップに作用しますが、そのステップは2つのステップで構成されているので、各ステップは並行して実行されます。" +msgstr "今、scatter は1つのステップに作用しますが、そのステップは2つのステップで構成" +"されているので、各ステップは並行して実行されます。" #: ../../src/topics/workflows.md:522 b0bf01dad1234a1db3c87b10953e42ef msgid "Conditional Workflows" @@ -4543,33 +4541,31 @@ msgstr "" " は、条件の検証が行われる場所です。この場合、ワークフローから`in1` に値`< 1` が含まれるときのみ、このステップが実行されます。" #: ../../src/topics/workflows.md:587 b33ecd2b8af042feb08687e32d4b6bbf -#, fuzzy msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " "is shown in the log by `INFO [step step1] start` whereas the second step " "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -"次のコマンドを実行します。`cwltool cond-wf-003.1.cwl --val 0` " -"この値は最初の条件ステップを通過するため実行され、ログには`INFO [step step1] start` " -"で示されています。一方、2番目のステップは`INFO [step step2] will be skipped` で示されているようにスキップされ" -" ます。" +"次のコマンド`cwltool cond-wf-003.1.cwl --val 0` を実行します。この値(val)は最" +"初の条件ステップを通過するため実行され、ログには`INFO [step step1] start` " +"で示されています。一方、2番目のステップは`INFO [step step2] will be skipped` " +"で示されているようにスキップされ ます。" #: ../../src/topics/workflows.md:607 7cd80b31a94543358ece7a2d413adce9 -#, fuzzy msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -"値3が与えられた場合、最初の条件ステップは実行されませんが、2番目の条件ステップは実行されます`cwltool cond-wf-003.1.cwl" -" --val 3`." +"`cwltool cond-wf-003.1.cwl --val 3`のように値(val)として3が与えられた場合、最" +"初の条件ステップは実行されませんが、2番目の条件ステップは実行されます." #: ../../src/topics/workflows.md:627 9679e32f65e0482a8b083387e4a18c1f -#, fuzzy msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." -msgstr "`--val 2` を使用した場合など、条件を満たさない場合は、ワークフローはpermanentFailを発生させ、失敗となります。" +msgstr "`--val 2` を使用した場合など、条件を満たさない場合は、ワークフローはpermanent" +"Failを発生させ、失敗となります。" #: ../../src/topics/yaml-guide.md:1 4fa76441f95d45fab76ab7eef8d7d4d2 msgid "YAML Guide" diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 8a75ef39..764b1903 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-03-20 01:01+0000\n" +"PO-Revision-Date: 2024-03-27 02:01+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified) \n" @@ -3798,7 +3798,8 @@ msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." -msgstr "" +msgstr "`cwlVersion` 字段指明该文件使用的 CWL 规约版本。`class` " +"字段表明该文件描述的是一个工作流。" #: ../../src/topics/workflows.md:221 d6abec8805f649fca668292412263f78 msgid "" @@ -3807,6 +3808,8 @@ msgid "" "and a data type. These parameters can be used as sources for input to " "specific workflows steps." msgstr "" +"`inputs` 代码段描述的是工作流的输入，即一组输入参数。这里面的每个参数都由标识" +"符和数据类型构成，它们可以用作工作流中某个指定步骤的输入源。" #: ../../src/topics/workflows.md:233 22bf3e4910ef4f86a2e8f6d5a6cf0d42 msgid "" @@ -3816,6 +3819,9 @@ msgid "" "`classfile` of the `compile` step to the workflow output parameter " "`compiled_class`." msgstr "" +"`outputs` 代码段描述的是工作流的输出。这同样是一组由标识符和数据类型构成的参" +"数。`outputSource` 将 `compile`（编译）步骤的输出参数 `classfile` " +"同工作流的输出参数 `compiled_class` 建立联系。" #: ../../src/topics/workflows.md:248 e0429688fce445da8083e69323e5b020 msgid "" @@ -3827,6 +3833,11 @@ msgid "" "`source`). In addition, workflow steps which do not depend on one " "another may run in parallel." msgstr "" +"`steps` 代码段描述的是工作流的实际步骤。这个例子中，第一个步骤是从 tar " +"归档文件中提取一个文件，而第二步是使用 Java 编译器编译来自第一步的文件。工作" +"流的各个步骤不是必须按照在代码中列出的顺序运行，而是由各个步骤之间（由 " +"`source` 决定）的依赖关系确定其先后次序。此外，工作流中没有依赖关系的多个步骤" +"允许并行运行。" #: ../../src/topics/workflows.md:256 980f5eada57c4fadbb783838ded1fa0b msgid "" @@ -3835,6 +3846,9 @@ msgid "" " parameters, `tarfile` and `extractfile` and one output parameter " "`extracted_file`." msgstr "" +"第一个步骤 `untar` 运行 `tar-param.cwl`（此前见于[《参数引用》](parameter-" +"references.md)一节）。该工具有两个输入参数 `tarfile` 和 `extractfile`, " +"以及一个输出参数 `extracted_file`." #: ../../src/topics/workflows.md:261 3532e165842f4ebb8db0c78208071555 msgid "" @@ -3845,12 +3859,16 @@ msgid "" "`name_of_file_to_extract` will be used for the parameters `tarfile` and " "`extractfile` in order to run the tool." msgstr "" +"该工作流步骤下的 ``in`` 这段代码将上述两个输入参数同工作流的输入 `tarball` " +"和 `name_of_file_to_extract` 通过`source` " +"关联起来。这意味着当这个工作流步骤执行时，为了运行其指定的工具，`tarball` 和 " +"`name_of_file_to_extract` 所赋予的值将用于 `tarfile` 和 `extractfile` 参数。" #: ../../src/topics/workflows.md:267 04a4db2f3da94ce29e7999039ee13fde msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." -msgstr "" +msgstr "工作流步骤下的 `out` 代码段列出了预期中从工具应获得的参数。" #: ../../src/topics/workflows.md:278 2651ee113a3d4b79b138854ebe729f48 msgid "" @@ -3861,10 +3879,14 @@ msgid "" "and-parameters.md)). The output of this step `classfile` is connected to " "the `outputs` section for the Workflow, described above." msgstr "" +"第二个步骤 `compile`（编译）依赖于第一步的结果，具体而言它的输入参数 `src` " +"与 `untar` 步骤的输出参数 `untar/extracted_file` 相关联。这一步骤运行 " +"`arguments.cwl`（此前见于[《附加参数》](additional-arguments-and-parameters." +"md)一节）。此步骤的输出 `classfile` 关联的是工作流的 `outputs` 部分（见上）。" #: ../../src/topics/workflows.md:285 177040bf9c0045f2878f42bcdd8cbd2d msgid "Nested Workflows" -msgstr "" +msgstr "嵌套的工作流" #: ../../src/topics/workflows.md:287 e8adc2f7c5ac4464b0711712617b8bbe msgid "" @@ -3873,16 +3895,19 @@ msgid "" " workflow can be used as a step in another CWL workflow, if the workflow " "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" +"工作流的作用在于将多种工具组合起来，进行更大规模的操作。我们还可以将一个工作" +"流整体视为一个工具；如果工作流引擎支持 `SubworkflowFeatureRequirement`, 则 " +"CWL 工作流可以用作另一 CWL 工作流中的单个步骤：" #: ../../src/topics/workflows.md:297 44d281d99cd944478db98446a984c001 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" -msgstr "" +msgstr "下面这个例子里的工作流嵌入了我们的 `1st-workflow.cwl` 工作流：" #: ../../src/topics/workflows.md:300 d7b60ce81ea741ffa08f2c2d9d7cca69 msgid "`nestedworkflows.cwl`" -msgstr "" +msgstr "`nestedworkflows.cwl`" #: ../../src/topics/workflows.md:309 a5b7a1ab16e34bda8744ffadacdda3e8 msgid "" From a24c354e739f2fe6a2984e17dacb29ccc9cc3d95 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Mon, 8 Apr 2024 10:17:34 +0200 Subject: [PATCH 135/179] fix broken link --- src/introduction/basic-concepts.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index 27dc22fe..fd075220 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -179,7 +179,7 @@ vendors. - Semantic Versioning - - The CWL Specification page in the CWL website: -- The Command Line Tool Description Standard: <[https://www.commonwl.org/v1.2/CommandLineTool.html](https://w3id.org/cwl/CommandLineTool.html)> +- The Command Line Tool Description Standard: - The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }} - The list of Implementations in the CWL website: - PROV-O: The PROV Ontology - From 87cfa3204434c5cab6b0dbeabaf257dfafe0d8e8 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Mon, 8 Apr 2024 10:38:27 +0200 Subject: [PATCH 136/179] operations: explain how to make the image locally --- src/topics/operations.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/topics/operations.md b/src/topics/operations.md index c802fbf6..1d601eba 100644 --- a/src/topics/operations.md +++ b/src/topics/operations.md @@ -21,9 +21,8 @@ CWL Viewer or `cwltool`: :working-directory: src/_includes/cwl/operations/ ``` -The output of the command above can be rendered with a Graphviz renderer. The -following image is rendered with the Sphinx `{graphviz}` directive (this user -guide is built with Sphinx): +The output of the command above can be rendered `cwltool --print-dot operations.cwl | dot -Tsvg > +operations.svg ; open operations.svg`. ```{graphviz} From d337f1ec780e3987fd018cd60d83a717025d3923 Mon Sep 17 00:00:00 2001 From: Mohd Hafez Date: Mon, 8 Apr 2024 10:23:55 +0200 Subject: [PATCH 137/179] Translated using Weblate (Ainu (Japan)) Currently translated at 7.3% (44 of 598 strings) Added translation using Weblate (Ainu (Japan)) Co-authored-by: Mohd Hafez Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ain/ Translation: Common Workflow Language/CWL User Guide --- locales/ain/LC_MESSAGES/user_guide.po | 3197 +++++++++++++++++++++++++ 1 file changed, 3197 insertions(+) create mode 100644 locales/ain/LC_MESSAGES/user_guide.po diff --git a/locales/ain/LC_MESSAGES/user_guide.po b/locales/ain/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..78c4bfc6 --- /dev/null +++ b/locales/ain/LC_MESSAGES/user_guide.po @@ -0,0 +1,3197 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: 2024-03-20 01:01+0000\n" +"Last-Translator: Mohd Hafez \n" +"Language-Team: Ainu (Japan) \n" +"Language: ain\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 5.5-dev\n" + +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "Instructional Material" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" +"You do not have to comply with the license for elements of the material in " +"the public domain or where your use is permitted by an applicable exception " +"or limitation." + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" +"No warranties are given. The license may not give you all of the permissions " +"necessary for your intended use. For example, other rights such as " +"publicity, privacy, or moral rights may limit how you use the material." + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "Software" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the " +"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" +"CWL is a way to describe command-line tools and connect them together to " +"create workflows. Because CWL is a specification and not a specific piece of " +"software, tools and workflows described using CWL are portable across a " +"variety of platforms that support the CWL standard." + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" +"This example demonstrates how to change the name of an input file as part of " +"a tool description. This could be useful when you are taking files produced " +"from another step in a workflow, and don't want to work with the default " +"names that these files were given when they were created." + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" +"This example demonstrates how to change the name of an output file from the " +"default name given to it by a tool:" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "Referencing a Local Script" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "There are two ways to reference a local script:" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" +"The first method involves adding the folder containing your scripts to the " +"`PATH` environment variable. This allows you to run the shell script " +"directly without using `sh` or `bash` commands." + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "Start with adding a _shebang_ at the top of your file:" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" +"After that, make the script executable with the command `chmod +x scriptname." +"sh`" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" +"Finally, modify your `PATH` to add the directory where your script is " +"located. (It is good practice to use `$HOME/bin` for storing your own " +"scripts)." + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" +"Now you can use `baseCommand: scriptname.sh` to run the script directly." + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" +"When you wish to share your work later, you can place your script in a " +"software container in the Docker format." + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" +"The second method involves including an input of `type: File` in the script " +"itself:" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "In CWL, everything must be directly stated." + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" +"Currently, `cwltool` can't cope with missing optional inputs if their input " +"binding makes use of `self`. Below is an example workaround for this, " +"pending a more sophisticated fix." + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "Model a \"one-or-the-other\" Parameter" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" +"Below is an example showing how to specify different strings to be added to " +"a command line, based on the value given to a Boolean parameter." + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "Connect a Solo Value to an Input that Expects an Array of that Type" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" +"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" +"The input must be an array consisting of exactly one entry for each input " +"link. If \"merge_nested\" is specified with a single link, the value from " +"the link must be wrapped in a single-item list." + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" +"Or in other words: if the destination is of type `File[]` (an array of " +"`File`s) and the source is a single `File` then add " +"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " +"add `linkMerge: merge_nested` under the appropriate `in` entry of the " +"destination step." + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "Optional Inputs 💯" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" +"To make an input parameter optional, add a question mark to the type " +"declaration." + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "Record Inputs 📀" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" +"For commandline flags that are either **mutually exclusive** or **dependent**" +" a special record type can be defined. You can also specify null here to " +"create optional inputs." + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "Setting Mutually Exclusive Parameters" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" +"To properly set fields in a record input type, you need to pass a dictionary " +"to the input to properly set the parameters. This is done by using inline " +"JavaScript and returning the dictionary with the key of the field you want " +"to set. The source field is set to indicate the input from the workflow to " +"be used as the value." + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "Setting Booleans" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "These can be set by using the default field" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "Concatenating Strings in Inputs" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "The valueFrom field must be used instead of default." + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "`cwltool` does not allow some characters in filenames by default." + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" +"For example, the filename `a space is here.txt` includes 3 space characters." + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" +"If you can not avoid these dangerous characters, then pass `--relax-path-" +"checks` to `cwltool`." + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "CWL Parameter Reference Error due to Hyphen in Input Identifier" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "The file is here" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" +"The CWL standards are built around (optional) Docker format containers. The " +"reference runner and several other CWL implementations support running those " +"Docker format containers using the Singularity engine. Directly specifying a " +"Singularity format container is not part of the CWL standards." + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" +"You can use the --js-console option of cwltool, or " +"you can try creating a JavaScript or TypeScript project for your code, and " +"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool." +"cwl#L6-L8" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 4dee8504a8e5496081dadc386ab45540 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 674c238b25e240eda05e22e399f2f78f +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: b651f80f47b4442fbf29454a233697fc +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: ecf2b9c0b1664afe9c4e180610610021 +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: e24cb13d98014e558b6a6946758359e0 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: 928e3df7ca3e479ca6474a8e72cf36eb +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: d355f035676446c88b028f327aeb4829 +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 339b852df24242189d6efcd2898a3396 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: 3ef57e6862f240bebcf193a52397af0a +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: fae385da16aa443da996fa23ac03d6ae +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: 92430be71ecc40e18bbbb80d5576c613 +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 387d83db81024f65aa9a890c2d07874a +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: d8e2280a75a74916a1630afaa2fe2ae3 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: f1c1340f9745458980e0fbd641738687 +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 5424e5472c3d466fa2a3d2022c6cb475 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: 12f57b2ba76b492abe1816e06bfb1417 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: e1f657a46ce94a0d83671540e2cc2dab +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a5eacdbc9aa142c890b177869da4143d +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: e3bdaceae8784ab0807b2cf356a98580 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: ed521ac365db4a6ba5a1051fbaa2932e +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 67573252cc064b27ab13eebc468ac58a +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 73e68b3af9cf41338d843c0c40e50cdc +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: a999b1acda2641598086648c64aa3831 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: f8c12a58cb0b46a488823c6ae95f25ea +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: f25a63e0926d4932bbe64b2e4bdabf9e +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: d718630a296545f3a989c8c71e9ddc77 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 9a97acd430064710bcdf76edbd9f711c +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: 48deb71f361a43e48a56ed483075bca8 +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 716b56506ca7470299899c5d820a9ea2 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: e3ecac0a8e604f2b98a2a12b0579990a +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 007a345b4bad49cf996c4301b8386473 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: efb5fd14988c4e2a8f834ee5369d4102 +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: 276f688ba7cc471a842f085ca852b1d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 8b70a1ad70514039b97164fa630c12e4 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 2f28ab412d2843ffa5f14acdc01fc732 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: cbec9277b5004e50af2728cbda0df740 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: e259f55f8000479bbd8009e25cf0ca6c +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 8210b36347a749889450529ecdf4ff0e +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 23088850ad02459696f6bbd385109aac +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: f02257a822ad46ac93c5981531cc85d5 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: d289541e460147aa933f7878996f8649 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: f495da32f05a4a5ba9539be0a54c1a59 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: bdb4c68a175047ddbe141ca24960127f +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 97b61352363f47cb890e8937c5613fa3 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: 0bc424ef2ca346099f29b937379908a0 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 29b73e1dd72744f68377f0a38c10f062 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 38a2afaf4a6c4d04909af22c93f2808d +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: cd74f34b21af4de9be96fd897efc469b +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: f12e371f3f1a4b0cb2cff9800352d48c +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 8f0e8f050e334ac08334e9215e1dcf61 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 7a6be0005a6441feb67f036d005d7885 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 06635145b441418aaae84dc804f3d6ac +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 04eaf1f7c630450db318dcd8b7626e15 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: fd4579a3c9844492b314b5c3c1775fc7 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: e024bcb70e04412e90e1838426d1b69a +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: a3db21c0b3114802a8a5b610e252ef13 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 0f5bc8520d6a4dafa37c65343da9702a +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 5cb830da47464a8b9c3950983fa4d56f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: a2ce43b391864e8bbde16328cc19b32b +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 56ee4dcfff6141d5bef80eb96559876d +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 96671c56523c4ea9992fb5dfcfa6490e +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: bcc6246742cb46bfb185e415c4a3431a +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 86dce36de687449c88fb5eb9d64eb045 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 7dc630ea86464b1dba3a4e5079260b3b +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: 651e032007ea4a119d20c820bb61f86b +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 0b056dde9e87428996e47870b12119da +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 628124a1670b4b058bb0fb6e495a099c +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: ec2adb3912bc46e28891229e9e0d9a1c +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: a519be60726a44af9941fdce04735353 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: cb8fc8c4c79e467eac5fab4ca685201e +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: a26cc105716f47cb807174c9003153b0 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: cc159dd5fe5748caac838862f5b8c4d1 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 6812698e9ad84d3385de5e88e9dde0b3 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: d1f02be278754267893dfce5a940997d +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: 75d59e395c66416cae9b352db5081516 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 874c6f19abbf45d7ab7d30a378c4048d +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: dea0d4b681f94e73b13965dcfe75cf7d +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: 750474486a84482292eeba45f118287f +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 1eb0e39bb6d04b8cab300f44a79f3add +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 4b2ab812f62c4f949dd25c8527f2411c +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 2c3b884cb1c54521900cc90782e8a58d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: a1073b6306044dffb414319ae01f68bb +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: 9a1d92334685449386dfa3b3a899ed48 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: fb623af4c480411b8fde28d01c981411 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: e98e165f6bba40809c90473d72f9d592 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 5565c1b2d8a349169a305a9b26b4574d +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: 88160cef4cfa4add9020aa89511a5749 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 730ba1434a1445ae847ec6153b6a3b72 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: a25d0b1e13324b40a6b8fcd227948c4f +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: d661df070e3040869da412d07a71f716 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: a11585474d3849cca5467512ed964743 +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 2682f9ca8e604a0c9986f7746fdec960 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 22447a560f6f4317bf67bd7c4336126c +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 52703d6b7f914097934bfad13663abeb +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 5e1c79df657d4a6e84e055dd6b300a5d +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 329d2809dfae4f90bc638f5f03a47ee3 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 9647019d8c37466886e7aab6f176634d +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: cc067051f22f433bbece08f60933e002 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: dbfe2c1123144316aa026374b0f353d3 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: 074cf5d912854d8c864607cc24b15302 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: b54240bb94f746bba7511633aa969db0 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 8b70a072aa87414c88e89a3e19af0a51 +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: eea20f89c45f424a888178df53713b28 +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7647e0229a924f988cf02b7812a55c06 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 9d663249666045618a0d3acddb85a9a9 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: dbf6153cd02542a6a01c172803122b7f +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: b6250cf6fa8a4a0c94b33302e0decca5 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: fa6ca3bbc6784380a03a950a6f49a180 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: b92b516e537a4773ad67b4af586e7a25 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: 467a701228504d06b971b79a59c69064 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: 2634f989eb304009a8568d70ed42786c +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: fbe0c65b444441f785d0054176d036a6 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 9a710602e00c4934ae3a3b471aa68458 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: 21b5be7270a14f0987240c81d1ec879b +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: cfe9d8241fe84bd5b74042a5625d933f +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 764d933cc4da446abd8dd8f913f05dac +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: c93efc6d4e004859981ee7f5fa28ed03 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: 546601da44cb49bd9611b1c85807fd90 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: e07f33d01b804663a25ffb08aad74821 +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: 7a644506619a4f08958ec7d4540cd557 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: b5195b7d8eaa419fb2b90cb33a57783a +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: 2713594c937d4c528fc8d04d9e9819ed +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: cf94c1424fc2413c85647fd1ee73d951 +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: dc0452107c604e29bdf32bb289fe5db8 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 483181f498fc4d968b5fe6ef427709f7 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 7487485d6aa4458089a4b4bdf107ea64 +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 93188ed43ee949cc98b3ea679ce14feb +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 24aca0bea4d94e3593b844cf0586cffe +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 9c56528acd5f49deb139e034dfbfac7c +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: a2dd833fdca4443181648e41051a5232 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: 7e40cc9f9e1341c195e843c009575b94 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: def35d6021394def80a53ae49a2cdbde +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: c84d4450bc6a475dbf34e0b22cea9130 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: cca9665f6daa44b49233baf34ab9fcc7 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: 547edbf5fa424b8286cc21674ff159b0 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 7ca248888b9d484cb544cd76ba538662 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: ae6b240718104380b08db5552d7355ea +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: e5a8b7f84be64020b191099f3fad30ed +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 12a06d8358534102b202965d4258c18e +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: b7f93705e5b8416696be01850072e8c0 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: e87045829b344089ab59dc27063ddd7a +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: 42ef2f145b824d69b63abc1da175c216 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: c61cedf543664d388183e04b3939cc39 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: 9e39e3f1501c4fcaab3e8962e090f6be +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: 03e2f767c4da461982fc3c0f3ba94762 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 3bea5822b8694e2aa32c446e1c54a045 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: 0d498cd4caf54c15891ca1afe58e2727 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: b2d75045e02741b4850f5ff1243f7858 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: 5fa79c62049a447c8328ebf9db54ebf4 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: d947c54933d64aad90df392a1cedd63f +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 651d35997332404186aa6d5711da4a3d +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: b662c1a5a4424c8d8350a806356acc61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 04d6babfd87343d7a5f13867ea02b65f +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 2eaacf1a90204a2b9bd621344560f2a1 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: e3a7182f00f440b8b5461da91194a64b +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: b5338f39e8c74ff28e139da68089a742 +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: f6d92156d67c4a339bcfd194cff897df +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: d80ab383eec9402faba997b548fe42eb +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: 49217c02f58c43ff9ec00f10da8d4e84 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 8dbd56473f8c40c0bb12a48be06117e3 +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 78d7f3ede2c746d482042adef050b2c4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: cbbf93c70fe04ba7932ba25758ddc611 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: cfa1c1fde4454df283f87cc54a9c59ec +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 1a8be2950cbb475bbb2617e005f0fac9 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: 5d83c56102e141cc978500f678dd0c1c +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: cda73485875d4c8e9464679a20558616 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 98cae24919b74c088a5d89706aec581b +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: b4b0940b4b5743c09637b36b964202d0 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 9ca3554d771d45998e88aaede525b227 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 3fca839cede94cfd8e4f605c73ba699d +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: 3ded0f125249485c921994b6e6b93ac9 +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 53ece35d309a4c8d99f1efb2122a7092 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 87bafb845c714b109874f6137b84462d +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: fcd05b1ef31a4046946a2399c7fc5575 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: 859368c1f25c4a4aad57abfd046c63f5 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" From 2d17e40eb873d6c4fc12629afec8f7ea06287365 Mon Sep 17 00:00:00 2001 From: Languages add-on Date: Mon, 8 Apr 2024 10:23:55 +0200 Subject: [PATCH 138/179] Added translation using Weblate (Ainu (Japan)) Co-authored-by: Languages add-on --- locales/ain/LC_MESSAGES/sphinx.po | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 locales/ain/LC_MESSAGES/sphinx.po diff --git a/locales/ain/LC_MESSAGES/sphinx.po b/locales/ain/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..ebc03a1d --- /dev/null +++ b/locales/ain/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: ain\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "" From 1fb41611fb2bc248df114e5537ddfbe988f24548 Mon Sep 17 00:00:00 2001 From: Michael Crusoe Date: Mon, 8 Apr 2024 10:23:55 +0200 Subject: [PATCH 139/179] Translated using Weblate (Japanese) Currently translated at 75.9% (455 of 599 strings) Deleted translation using Weblate (Ainu (Japan)) Deleted translation using Weblate (Ainu (Japan)) Co-authored-by: Michael Crusoe Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide --- locales/ain/LC_MESSAGES/sphinx.po | 27 - locales/ain/LC_MESSAGES/user_guide.po | 3197 ------------------------- locales/ja/LC_MESSAGES/user_guide.po | 46 +- 3 files changed, 26 insertions(+), 3244 deletions(-) delete mode 100644 locales/ain/LC_MESSAGES/sphinx.po delete mode 100644 locales/ain/LC_MESSAGES/user_guide.po diff --git a/locales/ain/LC_MESSAGES/sphinx.po b/locales/ain/LC_MESSAGES/sphinx.po deleted file mode 100644 index ebc03a1d..00000000 --- a/locales/ain/LC_MESSAGES/sphinx.po +++ /dev/null @@ -1,27 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" -"Language: ain\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" - -#: ../../src/_templates/sidebar-nav-bs.html:1 -#: d65b012160e9455eb4d2628279fffc42 -msgid "Main navigation" -msgstr "" - -#: ../../src/_templates/sidebar-nav-bs.html:3 -#: 4b3441eb77f448daa60718b7bfa862db -msgid "Section Navigation" -msgstr "" diff --git a/locales/ain/LC_MESSAGES/user_guide.po b/locales/ain/LC_MESSAGES/user_guide.po deleted file mode 100644 index 78c4bfc6..00000000 --- a/locales/ain/LC_MESSAGES/user_guide.po +++ /dev/null @@ -1,3197 +0,0 @@ -# SOME DESCRIPTIVE TITLE. -# Copyright (C) 2013, CWL Project Team -# This file is distributed under the same license as the Common Workflow Language User Guide package. -# FIRST AUTHOR , YEAR. -# -msgid "" -msgstr "" -"Project-Id-Version: Common Workflow Language User Guide\n" -"Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2024-03-20 01:01+0000\n" -"Last-Translator: Mohd Hafez \n" -"Language-Team: Ainu (Japan) \n" -"Language: ain\n" -"MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=UTF-8\n" -"Content-Transfer-Encoding: 8bit\n" -"Plural-Forms: nplurals=2; plural=n != 1;\n" -"X-Generator: Weblate 5.5-dev\n" - -#: ../../LICENSE.md:2 -#: 4e203044f0464fd5a3256430391dde12 -msgid "Licenses" -msgstr "" - -#: ../../LICENSE.md:4 -#: 79a9837f877147fa8e3931968aae7fb5 -msgid "Instructional Material" -msgstr "Instructional Material" - -#: ../../LICENSE.md:6 -#: 747f9dd48bc54f44adcd8b18c57f4d9d -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." -msgstr "" - -#: ../../LICENSE.md:12 -#: 98f18f72afa043f9a79aa9b5fc8bdf22 -msgid "You are free:" -msgstr "" - -#: ../../LICENSE.md:14 -#: 466be810dd8d4a838e0edb5869f2c4eb -msgid "to **Share**---copy and redistribute the material in any medium or format" -msgstr "" - -#: ../../LICENSE.md:15 -#: 18a3a0aec35743848c97bc178f9c94ff -msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" - -#: ../../LICENSE.md:17 -#: b746b1e4dca14de1a8e18036b7602a73 -msgid "for any purpose, even commercially." -msgstr "" - -#: ../../LICENSE.md:19 -#: 6021e65292a149d5b15e14491f3eb05e -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" -msgstr "" - -#: ../../LICENSE.md:24 -#: 8fb7a2946c384364814c6ec3910997d3 -msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." -msgstr "" - -#: ../../LICENSE.md:32 -#: 8161753b7526445db319210044566200 -msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" -msgstr "" - -#: ../../LICENSE.md:36 -#: 15314ba527864eaa834cf1185cfcc4e3 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." -msgstr "" -"You do not have to comply with the license for elements of the material in " -"the public domain or where your use is permitted by an applicable exception " -"or limitation." - -#: ../../LICENSE.md:39 -#: b351ddf9847d48b1a2a87fc78eaba4d2 -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." -msgstr "" -"No warranties are given. The license may not give you all of the permissions " -"necessary for your intended use. For example, other rights such as " -"publicity, privacy, or moral rights may limit how you use the material." - -#: ../../LICENSE.md:44 -#: a091addc2dea4830a06bb72ead56c5ea -msgid "Software" -msgstr "Software" - -#: ../../LICENSE.md:46 -#: 84b2c685bbab48449fdc72d2a1e42bf4 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." -msgstr "" -"Except where otherwise noted, the example programs and other software " -"provided by Common Workflow Language project are made available under the " -"[OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." - -#: ../../LICENSE.md:51 -#: 0f68eafafaef4b54accba7e13bfaa702 -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." -msgstr "" - -#: ../../src/_includes/what-is-cwl.md:1 -#: ../../src/_includes/what-is-cwl.md:2 -#: eab02dc13915490bb3c9ba744d78b6a7 -#: d4f35995b0f6494d9771a4be0a82538f -#: d6ccd4b546254f56a597d67dd4fdc5d6 -msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." -msgstr "" -"CWL is a way to describe command-line tools and connect them together to " -"create workflows. Because CWL is a specification and not a specific piece of " -"software, tools and workflows described using CWL are portable across a " -"variety of platforms that support the CWL standard." - -#: ../../src/episodes.md:5 -#: ../../src/setup.md:5 -#: 0d3267f84f4e4aedb1e9fce00b4ea4bc -#: 436cfca6f857469bbff7c652df32160f -msgid "This page has moved" -msgstr "" - -#: ../../src/episodes.md:9 -#: cc11f5d29206492d9f2f0922882b6159 -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." -msgstr "" - -#: ../../src/faq.md:1 -#: e2ed894d325a4f50a5e2dc69da5531a1 -msgid "FAQ" -msgstr "" - -#: ../../src/faq.md:11 -#: 61edb787dab04ca2ad3ed07616d878a0 -msgid "Non \"`File`\" Types Using `evalFrom`" -msgstr "" - -#: ../../src/faq.md:41 -#: d5321589e7ed4f0db3c630cc39800791 -msgid "Rename an Input File" -msgstr "" - -#: ../../src/faq.md:43 -#: fc62427c0a004810b055dee90ec5e2d9 -msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." -msgstr "" -"This example demonstrates how to change the name of an input file as part of " -"a tool description. This could be useful when you are taking files produced " -"from another step in a workflow, and don't want to work with the default " -"names that these files were given when they were created." - -#: ../../src/faq.md:59 -#: 1c6b8a4194a14611b4061b1540c3807f -msgid "Rename an Output File" -msgstr "" - -#: ../../src/faq.md:61 -#: bc7ad10c929848a3a9a240a3c501d299 -msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" -msgstr "" -"This example demonstrates how to change the name of an output file from the " -"default name given to it by a tool:" - -#: ../../src/faq.md:82 -#: 7225a993d281421b95c8e3df2846a0e3 -msgid "Referencing a Local Script" -msgstr "Referencing a Local Script" - -#: ../../src/faq.md:84 -#: 7ef1dbb81993473f948d9c6f3c64b381 -msgid "There are two ways to reference a local script:" -msgstr "There are two ways to reference a local script:" - -#: ../../src/faq.md:86 -#: 450edf800a18423195bea4fe8793a2cb -msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." -msgstr "" -"The first method involves adding the folder containing your scripts to the " -"`PATH` environment variable. This allows you to run the shell script " -"directly without using `sh` or `bash` commands." - -#: ../../src/faq.md:89 -#: 1a8cc75ea6174b9297871b2e58971077 -msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "Start with adding a _shebang_ at the top of your file:" - -#: ../../src/faq.md:95 -#: a7d84f740a714ec588503ee084fbbc34 -msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" -msgstr "" -"After that, make the script executable with the command `chmod +x scriptname." -"sh`" - -#: ../../src/faq.md:97 -#: 569d553abe85450c9d1c37456bf412f4 -msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." -msgstr "" -"Finally, modify your `PATH` to add the directory where your script is " -"located. (It is good practice to use `$HOME/bin` for storing your own " -"scripts)." - -#: ../../src/faq.md:104 -#: 95f5dbbd21084a318413b9528fb867be -msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." -msgstr "" -"Now you can use `baseCommand: scriptname.sh` to run the script directly." - -#: ../../src/faq.md:113 -#: 1b3cae80fa9a40ffb2259b8c1cd2b468 -msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." -msgstr "" -"When you wish to share your work later, you can place your script in a " -"software container in the Docker format." - -#: ../../src/faq.md:115 -#: 8d86baa239364f799d4f9d5ea2b0e314 -msgid "The second method involves including an input of `type: File` in the script itself:" -msgstr "" -"The second method involves including an input of `type: File` in the script " -"itself:" - -#: ../../src/faq.md:135 -#: f2c109998c76434893ff16b17fdb2bd0 -msgid "In CWL, everything must be directly stated." -msgstr "In CWL, everything must be directly stated." - -#: ../../src/faq.md:138 -#: c2c752b86bf94d6fb3751f4dd81bc7a7 -msgid "Setting `self`-based Input Bindings for Optional Inputs" -msgstr "" - -#: ../../src/faq.md:140 -#: 2c38cc58cbb340bc935a5f00e96ba95c -msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." -msgstr "" -"Currently, `cwltool` can't cope with missing optional inputs if their input " -"binding makes use of `self`. Below is an example workaround for this, " -"pending a more sophisticated fix." - -#: ../../src/faq.md:165 -#: ce6db54bd0f54839a5beb948530a21f0 -msgid "Model a \"one-or-the-other\" Parameter" -msgstr "Model a \"one-or-the-other\" Parameter" - -#: ../../src/faq.md:167 -#: d06cbf89028b4638ad54c2529bcbfa25 -msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." -msgstr "" -"Below is an example showing how to specify different strings to be added to " -"a command line, based on the value given to a Boolean parameter." - -#: ../../src/faq.md:188 -#: d53fb28dcad04e7788cba9e280a2343c -msgid "Connect a Solo Value to an Input that Expects an Array of that Type" -msgstr "Connect a Solo Value to an Input that Expects an Array of that Type" - -#: ../../src/faq.md:190 -#: d9e30e11533b4d53a144f5df7041268d -msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" -"Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" -"Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" - -#: ../../src/faq.md:194 -#: 941077158ec54ae19bfa2e2ad6662da1 -msgid "merge_nested" -msgstr "" - -#: ../../src/faq.md:196 -#: 937cb94a370640c788fbc3fe0b19f2e5 -msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." -msgstr "" -"The input must be an array consisting of exactly one entry for each input " -"link. If \"merge_nested\" is specified with a single link, the value from " -"the link must be wrapped in a single-item list." - -#: ../../src/faq.md:199 -#: a1d57e15656548128a76a8b975c564c9 -msgid "Which means \"create a list with exactly these sources as elements\"" -msgstr "" - -#: ../../src/faq.md:201 -#: c8c235a9bf6240628f0b5493ffebf7e0 -msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." -msgstr "" -"Or in other words: if the destination is of type `File[]` (an array of " -"`File`s) and the source is a single `File` then add " -"`MultipleInputFeatureRequirement` to the Workflow level `requirements` and " -"add `linkMerge: merge_nested` under the appropriate `in` entry of the " -"destination step." - -#: ../../src/faq.md:229 -#: 3da4dcb043eb4423a53a14182949d9cd -msgid "Optional Inputs 💯" -msgstr "Optional Inputs 💯" - -#: ../../src/faq.md:231 -#: 89b90d3bf1ea4ebd88482d435241fac5 -msgid "To make an input parameter optional, add a question mark to the type declaration." -msgstr "" -"To make an input parameter optional, add a question mark to the type " -"declaration." - -#: ../../src/faq.md:247 -#: a854006054ce4ffe94bbfa73bdbecbf2 -msgid "" -msgstr "" - -#: ../../src/faq.md:248 -#: f80eb714e9df417fbba555b5dd5f4d8c -msgid "Enum Inputs ⚜️" -msgstr "" - -#: ../../src/faq.md:250 -#: 10af80fa13af4158aec7060550485350 -msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" -msgstr "" - -#: ../../src/faq.md:267 -#: ad1c26711ccd4efd8fdb25f9293d33fd -msgid "" -msgstr "" - -#: ../../src/faq.md:268 -#: 49e2095b51f84f609f5d4bc088ad9745 -msgid "Record Inputs 📀" -msgstr "Record Inputs 📀" - -#: ../../src/faq.md:270 -#: 52b8538177c64090af51f5f6a696c28c -msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." -msgstr "" -"For commandline flags that are either **mutually exclusive** or **dependent**" -" a special record type can be defined. You can also specify null here to " -"create optional inputs." - -#: ../../src/faq.md:322 -#: f96c9257e3734b8aa0cc5e065f74f944 -msgid "Setting Mutually Exclusive Parameters" -msgstr "Setting Mutually Exclusive Parameters" - -#: ../../src/faq.md:324 -#: 7dc0540508084a3495ff3b2ac90fd323 -msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." -msgstr "" -"To properly set fields in a record input type, you need to pass a dictionary " -"to the input to properly set the parameters. This is done by using inline " -"JavaScript and returning the dictionary with the key of the field you want " -"to set. The source field is set to indicate the input from the workflow to " -"be used as the value." - -#: ../../src/faq.md:342 -#: b53dc77466b24a67b52b8aadf4fab724 -msgid "Setting Booleans" -msgstr "Setting Booleans" - -#: ../../src/faq.md:344 -#: cf4e7f3977ae4f9b877072c2b1c4b533 -msgid "These can be set by using the default field" -msgstr "These can be set by using the default field" - -#: ../../src/faq.md:349 -#: 99b37739ef18443ca7c0e715a131e0c7 -msgid "Concatenating Strings in Inputs" -msgstr "Concatenating Strings in Inputs" - -#: ../../src/faq.md:351 -#: 9b00b5a55ee941e1adbfe89e133791e3 -msgid "The valueFrom field must be used instead of default." -msgstr "The valueFrom field must be used instead of default." - -#: ../../src/faq.md:359 -#: 07922147f7ab487ba2a1e7c43c9f410c -msgid "`cwltool` Errors due to Filenames with Space Characters Inside" -msgstr "" - -#: ../../src/faq.md:361 -#: 7a11806f0c7045b48fe58a271f814797 -msgid "`cwltool` does not allow some characters in filenames by default." -msgstr "`cwltool` does not allow some characters in filenames by default." - -#: ../../src/faq.md:363 -#: fdaec25650ab4b0fb1c527610e24ae5a -msgid "For example, the filename `a space is here.txt` includes 3 space characters." -msgstr "" -"For example, the filename `a space is here.txt` includes 3 space characters." - -#: ../../src/faq.md:371 -#: 182959fc9f4746d082994e07d05c8cde -msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." -msgstr "" -"If you can not avoid these dangerous characters, then pass `--relax-path-" -"checks` to `cwltool`." - -#: ../../src/faq.md:373 -#: cc7752e9989e4a6d957682f479d6fc60 -msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" -msgstr "CWL Parameter Reference Error due to Hyphen in Input Identifier" - -#: ../../src/faq.md:375 -#: 6db1ebd2d6c74ceca889662cd7df5cd5 -msgid "If `cwltool --validate` returns valid" -msgstr "" - -#: ../../src/faq.md:384 -#: 3de2513c7d7b4569ba63f7e6d29137b7 -msgid "But executing it causes an error like:" -msgstr "" - -#: ../../src/faq.md:396 -#: ae3a9188706649e28f97bc4ec34c0821 -msgid "The file is here" -msgstr "The file is here" - -#: ../../src/faq.md:410 -#: e1ac97ab6ad3449b8c54933d25257f73 -msgid "Problem caused by `-` (hyphen character)." -msgstr "" - -#: ../../src/faq.md:423 -#: f6c402f7f6974edbbb5582c8e22f3869 -msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" -msgstr "" - -#: ../../src/faq.md:436 -#: 190099a242a645c9b9f8bc3ce89d920d -msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" -msgstr "" - -#: ../../src/faq.md:442 -#: 06a4f6ffc2da4d43b453d4784b42efd3 -msgid "Use CWL and cwltool with Singularity" -msgstr "" - -#: ../../src/faq.md:445 -#: 1901c34201054a9cae199b0dbb8b945e -msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." -msgstr "" -"The CWL standards are built around (optional) Docker format containers. The " -"reference runner and several other CWL implementations support running those " -"Docker format containers using the Singularity engine. Directly specifying a " -"Singularity format container is not part of the CWL standards." - -#: ../../src/faq.md:450 -#: 2d498470524d47f18f9936ace6acebb0 -msgid "Debug JavaScript Expressions" -msgstr "" - -#: ../../src/faq.md:452 -#: d7b044f5224a48eda09bc949cf645193 -msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" -msgstr "" -"You can use the --js-console option of cwltool, or " -"you can try creating a JavaScript or TypeScript project for your code, and " -"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" -"common-workflow-language/blob/master/v1.0/v1.0/template-tool." -"cwl#L6-L8" - -#: ../../src/index.md:1 -#: 2754519265eb426b940bbbd2b8d64e1e -msgid "Common Workflow Language User Guide" -msgstr "" - -#: ../../src/index.md:3 -#: f8d6e4cd54cb42c88182a43171d97bab -msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." -msgstr "" - -#: ../../src/index.md:7 -#: 132d40fee3b84469afa80d5ff613bf77 -msgid "Contributions and Feedback are Welcome!" -msgstr "" - -#: ../../src/index.md:9 -#: 0f47157605a34ea58770ea898deebae4 -msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." -msgstr "" - -#: ../../src/index.md:16 -#: 6d269e8d70184034bcb56385a6ca198f -msgid "Navigating the User Guide" -msgstr "" - -#: ../../src/index.md:18 -#: ed74c9a4b623464480e2c184668fcec0 -msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." -msgstr "" - -#: ../../src/index.md:23 -#: cfa67cf5521b414da6f7d34cbed283f7 -msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." -msgstr "" - -#: ../../src/index.md:28 -#: ee6b82bd86264e4bb1e8e4065b1e6b9c -msgid "Table of Contents" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:1 -#: e208c8a7506e41dcac9a403c5d2850c1 -msgid "Basic Concepts" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:3 -#: ac62d326a68145b695e46b714d4e8156 -msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:10 -#: 984e6676b9d04c7092bc492f195dfb91 -msgid "The CWL Specification" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:21 -#: cbe1d761da5b403d9605fa1fb8e62fdf -msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:25 -#: 3a71b269bd3c49eb913cf69b60373c24 -msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:33 -#: b171b72c48d44050a3416a7a42c4021d -msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:37 -#: b3df1607e9d242d78b22dc44335fbe2d -msgid "Implementations" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:39 -#: 078b58ffc1cc4d25a7c4eea3bb76e025 -msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:44 -#: c3869b4ec5ff47d99e8da79770722e04 -msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:51 -#: 2482c84831fc4dfab629e7bfcfb41cbf -msgid "CWL specification, implementations, and other tools." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:105 -#: a5ebc727fb3443f78e81d6b7ed5ac750 -msgid "Processes and Requirements" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:107 -#: 86e6a06992dc4228bfda7add48e28ca3 -msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:112 -#: 8c9772f96caf4169924d22eb929a4f0f -msgid "A command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:113 -#: 4fac209a62114798b79e4810f7a0148b -msgid "An expression tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:114 -#: b97ba368fd664caab0494e2392795697 -msgid "An operation." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:115 -#: 903a6796e3304a19ad885b2428b0e80f -msgid "A workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:118 -#: 6e352ac1f8e144c392ac5adf18c28298 -msgid "The processing units available in the CWL objects model." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:119 -#: cf2922f645904ac7955428ecddc37b8a -msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:122 -#: 5f47aae608c041aeb4134d59dad314d2 -msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:127 -#: f6f589481d0c4891beaccb63160619ef -msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:131 -#: 73b0c1ccb18c4b74a2c0fdf9706eca85 -msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:137 -#: 4ace6b92f4e04a07aa202840ebe36417 -msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:141 -#: cc6cd8cb81564cadb8e6a4c49423b7f7 -msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:142 -#: 2d9f53b6ed5041dbb6c0b54835897856 -msgid "`SubworkflowFeatureRequirement` - enables nested workflows." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:143 -#: 907674a4ecff4826a2b880e28fc38f33 -msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:145 -#: 037cd0e5ceda482eaeaca03d51745aee -msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:151 -#: e4643938445b48cc80eb8973ceeb126e -msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:155 -#: c4c3315c96714e81b364f8cc003b87e6 -msgid "FAIR Workflows" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:157 -#: 3eb6a013a2a4478ca2ad134661f65c58 -msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:167 -#: 074af9633627470485e5225326d5f20a -msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:171 -#: 847951c055b94a83b1e081594cef22ee -msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:176 -#: 44bde1fae06b4678bcac4f3224601296 -msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." -msgstr "" - -#: ../../src/introduction/basic-concepts.md:178 -#: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 -#: 65c24244713741e196da08cb9ba237b2 -#: f059896039524095b4deb65d693f8ddf -#: 3439764fab0e49d2bcb7c9fbae556e65 -msgid "Learn More" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:180 -#: 9d5100c7d0a040aea1020bf633ad17de -msgid "Semantic Versioning - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:181 -#: 36eb4b3b966640af90faa55db3789cb6 -msgid "The CWL Specification page in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:182 -#: 2ccb956baa6b4376a04ad9fcc4654631 -msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" -msgstr "" - -#: ../../src/introduction/basic-concepts.md:183 -#: 72889b830c514afe9a7cb1e64b5666a0 -msgid "The list of Implementations in the CWL website: " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:184 -#: e29bd7f973544600be589c3b3f84cf63 -msgid "PROV-O: The PROV Ontology - " -msgstr "" - -#: ../../src/introduction/basic-concepts.md:185 -#: c377a7f5dbe645cebbb6c7eccf831a0b -msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." -msgstr "" - -#: ../../src/introduction/index.md:1 -#: 1769a0cbf4de4d77879c1f202cd11af9 -msgid "Introduction" -msgstr "" - -#: ../../src/introduction/index.md:3 -#: 950370f0a36048b38e1bde9b78f80816 -msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." -msgstr "" - -#: ../../src/introduction/prerequisites.md:1 -#: f01faaf1b253407cbbc2f353c24774f3 -msgid "Prerequisites" -msgstr "" - -#: ../../src/introduction/prerequisites.md:6 -#: 353b14f06ee845d0a06a829643e31534 -msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:12 -#: b5a0607096814c0aa577f977c3b57c54 -msgid "CWL Implementations" -msgstr "" - -#: ../../src/introduction/prerequisites.md:14 -#: ff2bb4c6504b456bac7ca9c514414dbf -msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:19 -#: cbbcce4c2a96471b8b0ae3593ad59de4 -msgid "Operating System" -msgstr "" - -#: ../../src/introduction/prerequisites.md:21 -#: 5089fdba8aed4113983fa86e698df98b -msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:24 -#: dbaa4bae22fe4d05b18d7351967ddbc3 -msgid "Linux" -msgstr "" - -#: ../../src/introduction/prerequisites.md:25 -#: c05187af85be41b782678b79627f8fbf -msgid "macOS" -msgstr "" - -#: ../../src/introduction/prerequisites.md:26 -#: beb6cf4d7c154eb9b6d7fe024a318ed7 -msgid "Windows" -msgstr "" - -#: ../../src/introduction/prerequisites.md:29 -#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 -msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." -msgstr "" - -#: ../../src/introduction/prerequisites.md:35 -#: 56d78c95daa54135b6aa9b2bfdc34d01 -msgid "CWL Runner" -msgstr "" - -#: ../../src/introduction/prerequisites.md:41 -#: 0f2704bf1f7148be95e999e312899f11 -msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." -msgstr "" - -#: ../../src/introduction/prerequisites.md:46 -#: 86264c9e56104ecea9146407c379aae2 -msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:51 -#: 0a0f0e5151ab4c498b4f8a12c016f28d -msgid "Installing `cwltool` with `pip` and `venv`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:62 -#: f7aaafeee230400da056464c853582c2 -msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:65 -#: 5eced7e4cd084e8a806b1d3b12d0c000 -msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:67 -#: 040c019b6e844eda8c8c2b210852516b -msgid "`true.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:73 -#: 6391e08e0bde49f4b21286d8fdb97433 -msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:79 -#: cdef47fca304479c9a9df75afc0afb35 -msgid "Validating `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:84 -#: d41c4bc740aa474ea09a7cbd267c8840 -msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:86 -#: 24d7be55d3994f0b82c38da47918e0c9 -msgid "Running `true.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:91 -#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 -msgid "Cwl-runner Python Module" -msgstr "" - -#: ../../src/introduction/prerequisites.md:93 -#: 096d0a50f69e48bd9915238d1b4264c1 -msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." -msgstr "" - -#: ../../src/introduction/prerequisites.md:101 -#: f9df974a8e2645a6918e67466bd1fdc2 -msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:104 -#: 71ebe91d4bda473abe87578929433212 -msgid "Installing `cwl-runner` alias for cwltool with `pip`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:111 -#: 746c6fc9c29d466494458a08d4c96672 -msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." -msgstr "" - -#: ../../src/introduction/prerequisites.md:115 -#: b9cc5a843a0f49daad56e9303657bdd5 -msgid "Validating `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:120 -#: 34ab40437ab646488ba3ee86cd7fe071 -msgid "Running `true.cwl` with `cwl-runner`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:125 -#: 705807fae182425dbf4244dbf2be1226 -msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:129 -#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a -msgid "`true_shebang.cwl`" -msgstr "" - -#: ../../src/introduction/prerequisites.md:135 -#: 164c438baab54ec19bbb4584a10dd411 -msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "" - -#: ../../src/introduction/prerequisites.md:137 -#: bf8be77af6154326b28442c5d2e2b852 -msgid "Making `true.cwl` executable." -msgstr "" - -#: ../../src/introduction/prerequisites.md:144 -#: 695184d1b45a42f393e2da99c3721773 -msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." -msgstr "" - -#: ../../src/introduction/prerequisites.md:148 -#: 7c4f45b3e7b549e186126693aa4a3d4f -msgid "Running `true_shebang.cwl` with a shebang." -msgstr "" - -#: ../../src/introduction/prerequisites.md:154 -#: 3ba23b4ea01c46848e4e43bbeff5f5a1 -msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," -msgstr "" - -#: ../../src/introduction/prerequisites.md:161 -#: eec6c07455384630809ff1c532bfe7d4 -msgid "Text Editor" -msgstr "" - -#: ../../src/introduction/prerequisites.md:163 -#: f6b39b12bd5c495cb53e2795bf9200ed -msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." -msgstr "" - -#: ../../src/introduction/prerequisites.md:167 -#: 2fdb62a13f9447bc89183426260ce781 -msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" -msgstr "" - -#: ../../src/introduction/prerequisites.md:171 -#: 1f07135156254f74a6b043bf33d00cc3 -msgid "Visual Studio Code with the Benten (CWL) plugin - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:172 -#: de344f356b1c466d9131cdbd4d7353a3 -msgid "cwl-plugin for IntelliJ - " -msgstr "" - -#: ../../src/introduction/prerequisites.md:174 -#: 3f9324ede11441f58d93875867034cf0 -msgid "The CWL community also maintains a list of editors and viewers: " -msgstr "" - -#: ../../src/introduction/prerequisites.md:177 -#: 6ce8b81560e341c580d316d69202b268 -msgid "Docker" -msgstr "" - -#: ../../src/introduction/prerequisites.md:181 -#: 40cfd559d6a848d1aae354d3bdaa8e9c -msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." -msgstr "" - -#: ../../src/introduction/prerequisites.md:185 -#: 8a9a50b0ebe847ce90593881ffe0d69c -msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." -msgstr "" - -#: ../../src/introduction/prerequisites.md:191 -#: 923cf9dd6d6c417aabe42f9fa62ffa35 -msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." -msgstr "" - -#: ../../src/introduction/prerequisites.md:198 -#: 9390b03889de44638141d705e0ef8322 -msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." -msgstr "" - -#: ../../src/introduction/prerequisites.md:199 -#: 12042e411482458f8c35a2491f9433e0 -msgid "The Python `venv` module: " -msgstr "" - -#: ../../src/introduction/quick-start.md:1 -#: cdd4196f9aa34beba115901ec97913b6 -msgid "Quick Start" -msgstr "" - -#: ../../src/introduction/quick-start.md:3 -#: c43d9675ed134b78b02acb5a102a764a -msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." -msgstr "" - -#: ../../src/introduction/quick-start.md:7 -#: 280936bb2a22469799b2c9e9ba22adee -msgid "“Hello World”" -msgstr "" - -#: ../../src/introduction/quick-start.md:12 -#: cb203354977d42a58112d09357f62565 -msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:16 -#: 9e51962a7e5c47248f3e20703ae101eb -msgid "`hello_world.cwl`" -msgstr "" - -#: ../../src/introduction/quick-start.md:22 -#: 7e475e3f3c4a4404bb0236124c0f7ce7 -msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." -msgstr "" - -#: ../../src/introduction/quick-start.md:27 -#: 82613ca4e32b4ccab1b7735f5ba2d5a1 -msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." -msgstr "" - -#: ../../src/introduction/quick-start.md:32 -#: 498a43362a4749f3b8b433709d34a1d5 -msgid "Installing a CWL Runner" -msgstr "" - -#: ../../src/introduction/quick-start.md:34 -#: f3e56aedd56b4b93bdc3894273e8c144 -msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" -msgstr "" - -#: ../../src/introduction/quick-start.md:39 -#: 81481f5b82e4488398f87f0a169bd359 -msgid "Installing `cwltool` with `pip`." -msgstr "" - -#: ../../src/introduction/quick-start.md:47 -#: a81342e756d24c40acc15835d0a768f2 -msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." -msgstr "" - -#: ../../src/introduction/quick-start.md:51 -#: c12cf89f8b9a421ebd05330326e219b3 -msgid "Running \"Hello World\"" -msgstr "" - -#: ../../src/introduction/quick-start.md:53 -#: 9b68bcb1a41849dc9601ab47c5bbb0fe -msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" -msgstr "" - -#: ../../src/introduction/quick-start.md:57 -#: ce04027dfcfe4b7b91ea3c2136b18b23 -msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:62 -#: 0d8a788402914ebd8f09a5ca80650011 -msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" -msgstr "" - -#: ../../src/introduction/quick-start.md:65 -#: 6d0b679efab24813a7a3b709ade940d1 -msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "" - -#: ../../src/introduction/quick-start.md:70 -#: 2ea056ab04b6419a9faf350de22a17f2 -msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" -msgstr "" - -#: ../../src/introduction/quick-start.md:74 -#: 1a44a545434b448aa956005deeed90a8 -msgid "`hello_world-job.json`" -msgstr "" - -#: ../../src/introduction/quick-start.md:80 -#: e76bfcc0c9f84bcdb3f6d5277869a88c -msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" -msgstr "" - -#: ../../src/introduction/quick-start.md:82 -#: d4cdbe870a6f4a68b542ca719d989062 -msgid "Passing an Inputs Object file to `cwltool`." -msgstr "" - -#: ../../src/introduction/quick-start.md:88 -#: b6d59e4b9c854abab1b3f7a0fa26f504 -msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." -msgstr "" - -#: ../../src/introduction/quick-start.md:96 -#: 5535b98e8b1342f09f003ec6db2b44b1 -msgid "Continue reading the next sections of this User Guide!" -msgstr "" - -#: ../../src/introduction/quick-start.md:97 -#: 77e43c7117fd4c52b140f0dd52cc3963 -msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." -msgstr "" - -#: ../../src/introduction/quick-start.md:98 -#: 7282abfa7155497ca47c30f9abfb6474 -msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." -msgstr "" - -#: ../../src/introduction/quick-start.md:99 -#: 176d8d47830f4031bb95dc231ebf1303 -msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." -msgstr "" - -#: ../../src/introduction/quick-start.md:100 -#: 82a7ca3703bc4f0daa18942a1ac8943b -msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." -msgstr "" - -#: ../../src/introduction/quick-start.md:101 -#: d039a9d6461c44628d4660c00d9ce6ff -msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." -msgstr "" - -#: ../../src/introduction/quick-start.md:102 -#: fbc3383d9e1c4eaca7931c3cc4f1752b -msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." -msgstr "" - -#: ../../src/setup.md:9 -#: 1330bd38c4b5495f890b98c669f81a9d -msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 9c87c76c690948ac8e18088a0fffe679 -msgid "Additional Arguments and Parameters" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:3 -#: ad00d94d4fb64bbdac356e64dd3803b9 -msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:6 -#: d8110ed19da94ad8a9f56e7006c4a2cf -msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:13 -#: a74935dc31664e979ca8f90a6a4ba53c -msgid "`arguments.cwl`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 -#: 0a8065edd8af4eaea08989a1060ce48f -#: f357755f6dcb4971bade8636064f8dd1 -msgid "`arguments-job.yml`" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 6359191b4f684d5aa3602e4aaf394883 -msgid "Next, create a sample Java file to use with the command-line tool." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:30 -#: 9643449da1da46d7861866dce490cbcb -msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 713666580a0a4466b4ba6e3eb2b54f0a -msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." -msgstr "" - -#: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d50574c8b9694f83aa376d39b9a6fcd6 -msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." -msgstr "" - -#: ../../src/topics/best-practices.md:1 -#: 612c4a66c36a43d4ac5d74c1757d6845 -msgid "Best Practices" -msgstr "" - -#: ../../src/topics/best-practices.md:3 -#: 939cd9e9eaff4e3ab74fe707a5d4eb21 -msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." -msgstr "" - -#: ../../src/topics/best-practices.md:8 -#: 4bcb84707acb40a0bfe2ea0853cb10b7 -msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." -msgstr "" - -#: ../../src/topics/best-practices.md:11 -#: 4dee8504a8e5496081dadc386ab45540 -msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." -msgstr "" - -#: ../../src/topics/best-practices.md:20 -#: 674c238b25e240eda05e22e399f2f78f -msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." -msgstr "" - -#: ../../src/topics/best-practices.md:26 -#: b651f80f47b4442fbf29454a233697fc -msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" -msgstr "" - -#: ../../src/topics/best-practices.md:28 -#: 263a127a77cf4c41af76854f22f1f260 -msgid "_Example of metadata field for license with SPDX identifier:_" -msgstr "" - -#: ../../src/topics/best-practices.md:37 -#: 3a87a0fb2a364e3da5aaa4017e430b19 -msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." -msgstr "" - -#: ../../src/topics/best-practices.md:40 -#: ecf2b9c0b1664afe9c4e180610610021 -msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." -msgstr "" - -#: ../../src/topics/best-practices.md:44 -#: e24cb13d98014e558b6a6946758359e0 -msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:47 -#: f2b14a92374e449d9fb1e8c86ae0dd61 -msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." -msgstr "" - -#: ../../src/topics/best-practices.md:50 -#: 928e3df7ca3e479ca6474a8e72cf36eb -msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." -msgstr "" - -#: ../../src/topics/best-practices.md:55 -#: d355f035676446c88b028f327aeb4829 -msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." -msgstr "" - -#: ../../src/topics/best-practices.md:58 -#: 339b852df24242189d6efcd2898a3396 -msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." -msgstr "" - -#: ../../src/topics/best-practices.md:66 -#: 3ef57e6862f240bebcf193a52397af0a -msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." -msgstr "" - -#: ../../src/topics/best-practices.md:69 -#: f1a7c4f896a04a80b0c5f6a1db61ff8c -msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." -msgstr "" - -#: ../../src/topics/best-practices.md:73 -#: 1ac4c3d8c3e44bd1af3fc5df70051926 -msgid "Custom types should be defined with one external YAML per type definition for re-use." -msgstr "" - -#: ../../src/topics/best-practices.md:76 -#: c858f64e66f048a5b0032ef3e4d83694 -msgid "Include a top-level short `label` summarising the tool/workflow." -msgstr "" - -#: ../../src/topics/best-practices.md:78 -#: fae385da16aa443da996fa23ac03d6ae -msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." -msgstr "" - -#: ../../src/topics/best-practices.md:82 -#: 92430be71ecc40e18bbbb80d5576c613 -msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." -msgstr "" - -#: ../../src/topics/best-practices.md:85 -#: 387d83db81024f65aa9a890c2d07874a -msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." -msgstr "" - -#: ../../src/topics/best-practices.md:90 -#: d8e2280a75a74916a1630afaa2fe2ae3 -msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." -msgstr "" - -#: ../../src/topics/best-practices.md:93 -#: f1c1340f9745458980e0fbd641738687 -msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." -msgstr "" - -#: ../../src/topics/best-practices.md:97 -#: 5424e5472c3d466fa2a3d2022c6cb475 -msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." -msgstr "" - -#: ../../src/topics/command-line-tool.md:1 -#: 3f4e98f6bfa141feba8c4b120e3d03e8 -msgid "Command Line Tool" -msgstr "" - -#: ../../src/topics/command-line-tool.md:3 -#: 12f57b2ba76b492abe1816e06bfb1417 -msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." -msgstr "" - -#: ../../src/topics/command-line-tool.md:8 -#: e1f657a46ce94a0d83671540e2cc2dab -msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." -msgstr "" - -#: ../../src/topics/command-line-tool.md:19 -#: abb83f0097654a43bd78639d3dbb2bc8 -msgid "CWL command-line tool." -msgstr "" - -#: ../../src/topics/command-line-tool.md:50 -#: 3b1a9ae3412f4d6e96a39b9a16934232 -msgid "`echo.cwl`" -msgstr "" - -#: ../../src/topics/command-line-tool.md:57 -#: a5eacdbc9aa142c890b177869da4143d -msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." -msgstr "" - -#: ../../src/topics/command-line-tool.md:68 -#: 1849b8f3ae1c4a84ae59a78ffd6b371e -msgid "Network Access" -msgstr "" - -#: ../../src/topics/command-line-tool.md:69 -#: e3bdaceae8784ab0807b2cf356a98580 -msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." -msgstr "" - -#: ../../src/topics/command-line-tool.md:83 -#: ed521ac365db4a6ba5a1051fbaa2932e -msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:1 -#: a2a0f0eb0f404eb3aaf19cfd3cdb559b -msgid "Creating Files at Runtime" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:3 -#: 0cf51b6da6884065ae42032abc20eb0d -msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:7 -#: 2df3a3a9094d4b79b1d5dd99195f3bff -msgid "To generate such files, we can use the `InitialWorkDirRequirement`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:9 -#: d3f74c3b094a427fbec831afab657d50 -msgid "`createfile.cwl`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:15 -#: cfffc518ba6e4ed1a80762ed6f7d25df -msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:20 -#: 9454a330b9324744b89448f2694b1b03 -msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:27 -#: 7f8d99a30b644457a62ac1523d0c72aa -msgid "To test the above CWL tool, use this job to provide the input value `message`:" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:29 -#: ../../src/topics/environment-variables.md:13 -#: ../../src/topics/outputs.md:77 -#: 2d2ef4769b2347e79db827655f1bcdeb -#: 2699fbc4376148af91b7a5a6cdac467c -#: ca03defa3ad14cf698171cb09e3055c1 -msgid "`echo-job.yml`" -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:35 -#: 10d1373bb14a4a3cacd3b92a2f83382d -msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:40 -#: 70e257091bdb456e8957f90a8fa90e8c -msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:51 -#: 1741804e33aa43ce88b4320c11ae5973 -msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." -msgstr "" - -#: ../../src/topics/creating-files-at-runtime.md:54 -#: ../../src/topics/environment-variables.md:18 -#: ../../src/topics/file-formats.md:52 -#: ../../src/topics/staging-input-files.md:20 -#: ../../src/topics/workflows.md:198 -#: b372f33c65bb4707b2a462a960bb1373 -#: 293fb1d428b849aebccad598a932992d -#: f924d65fed0c4cb5b0a019b084a8b535 -#: d6255506eebe44be94c5ce703c44a513 -#: 7bbd2d738fc54649aeb10f8d2bc38b6f -msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/custom-types.md:1 -#: cb34fd4c8cb04053ada491a227651048 -msgid "Custom Types" -msgstr "" - -#: ../../src/topics/custom-types.md:3 -#: 67573252cc064b27ab13eebc468ac58a -msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." -msgstr "" - -#: ../../src/topics/custom-types.md:9 -#: 73e68b3af9cf41338d843c0c40e50cdc -msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:12 -#: ef5f35acb97f4ddfad7b688712f53484 -msgid "`custom-types.cwl`" -msgstr "" - -#: ../../src/topics/custom-types.md:18 -#: 7015dfa99a6f4cfb87ebf0ed61e8043c -msgid "`custom-types.yml`" -msgstr "" - -#: ../../src/topics/custom-types.md:24 -#: a999b1acda2641598086648c64aa3831 -msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/custom-types.md:30 -#: f8c12a58cb0b46a488823c6ae95f25ea -msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" -msgstr "" - -#: ../../src/topics/custom-types.md:46 -#: f25a63e0926d4932bbe64b2e4bdabf9e -msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." -msgstr "" - -#: ../../src/topics/custom-types.md:53 -#: b0a4df0fd3ca42338cff4689235dcf4e -msgid "The contents of the YAML file describing the custom type are given below:" -msgstr "" - -#: ../../src/topics/custom-types.md:55 -#: fecfbb44456640d8ba05e519bf2ff564 -msgid "`biom-convert-table.yaml`" -msgstr "" - -#: ../../src/topics/custom-types.md:61 -#: d718630a296545f3a989c8c71e9ddc77 -msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" -msgstr "" - -#: ../../src/topics/custom-types.md:76 -#: 9a97acd430064710bcdf76edbd9f711c -msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." -msgstr "" - -#: ../../src/topics/environment-variables.md:1 -#: 59014808cbef4c02aaef03129d8a29b0 -msgid "Environment Variables" -msgstr "" - -#: ../../src/topics/environment-variables.md:3 -#: 3c821c9c46d841ec89b8a5b1018f3af8 -msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." -msgstr "" - -#: ../../src/topics/environment-variables.md:7 -#: bfdebb32440a4034beb42135e38884e8 -msgid "`env.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:1 -#: 777d4a52f7554eff84db2df6d4d0f729 -msgid "Expression Tool" -msgstr "" - -#: ../../src/topics/expression-tool.md:3 -#: 48deb71f361a43e48a56ed483075bca8 -msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." -msgstr "" - -#: ../../src/topics/expression-tool.md:8 -#: 716b56506ca7470299899c5d820a9ea2 -msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." -msgstr "" - -#: ../../src/topics/expression-tool.md:17 -#: b63e6f5a2e89431c8fc7d04f47fd69fe -msgid "CWL expression tool." -msgstr "" - -#: ../../src/topics/expression-tool.md:48 -#: 39727e9058f24b62b8746a46d3f812c2 -msgid "`uppercase.cwl`" -msgstr "" - -#: ../../src/topics/expression-tool.md:67 -#: e3ecac0a8e604f2b98a2a12b0579990a -msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." -msgstr "" - -#: ../../src/topics/expressions.md:1 -#: c8d648b765ec499a8e9c464590838492 -msgid "Expressions" -msgstr "" - -#: ../../src/topics/expressions.md:3 -#: 007a345b4bad49cf996c4301b8386473 -msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." -msgstr "" - -#: ../../src/topics/expressions.md:9 -#: 2edbd398eadb458b8eacd5fa5496f0a2 -msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." -msgstr "" - -#: ../../src/topics/expressions.md:16 -#: 7fdbfd1c937b4991bf4a2fa26ea310e4 -msgid "`expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:22 -#: efb5fd14988c4e2a8f834ee5369d4102 -msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" -msgstr "" - -#: ../../src/topics/expressions.md:25 -#: e833649b951841c49397796f996d29f3 -msgid "`empty.yml`" -msgstr "" - -#: ../../src/topics/expressions.md:31 -#: 276f688ba7cc471a842f085ca852b1d9 -msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." -msgstr "" - -#: ../../src/topics/expressions.md:35 -#: ebf399ea4d5f47b9be03e24f04c69f2d -msgid "We can then run `expression.cwl`:" -msgstr "" - -#: ../../src/topics/expressions.md:37 -#: 65e0cdd505b944caa40f65e612cdddfc -msgid "Running `expression.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:47 -#: 8b70a1ad70514039b97164fa630c12e4 -msgid "Note that requirements can be provided with the map syntax, as in the example above:" -msgstr "" - -#: ../../src/topics/expressions.md:54 -#: 2f28ab412d2843ffa5f14acdc01fc732 -msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." -msgstr "" - -#: ../../src/topics/expressions.md:62 -#: d957f55a6377422c9834f85d45e35009 -msgid "Where are JavaScript expressions allowed?" -msgstr "" - -#: ../../src/topics/expressions.md:64 -#: cbec9277b5004e50af2728cbda0df740 -msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" -msgstr "" - -#: ../../src/topics/expressions.md:66 -#: e259f55f8000479bbd8009e25cf0ca6c -msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 -#: 1acb064f7a4a482aa0174bdc847c6382 -#: 0222780b98ac48e89b1b4f57c9df8590 -msgid "`arguments`" -msgstr "" - -#: ../../src/topics/expressions.md:68 -#: ../../src/topics/expressions.md:76 -#: ../../src/topics/expressions.md:89 -#: ../../src/topics/parameter-references.md:65 -#: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 -#: ef2b8433778a40408f179c3e6f0cf99e -#: 224732683a9c41f3ba1b778851e745a8 -#: 17b10d1e91b24dc582df98fcd2ac850e -#: ffd3ca1f97cf4d3a892ef4f4b04771e4 -#: e4e68011dc5f42e4918c747afa7d764b -#: d44e3cfa661840eb851782e24caf1b68 -msgid "`valueFrom`" -msgstr "" - -#: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 -#: 0bddedfe40e841f7878e09792531e6bf -#: 17ac6d2c703b466f9720b7489209a2ff -msgid "`stdin`" -msgstr "" - -#: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 -#: 58a6510ef69a4c51a4ea348cd98ef0d2 -#: a11d0de5ac6a4a6d9afe0e34823e3b45 -msgid "`stdout`" -msgstr "" - -#: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 -#: 2437656e20354d63bede1b98d5348e2c -#: 37392218309d4baebe62fc38bf50efe9 -msgid "`stderr`" -msgstr "" - -#: ../../src/topics/expressions.md:72 -#: 8210b36347a749889450529ecdf4ff0e -msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:73 -#: ../../src/topics/expressions.md:78 -#: ../../src/topics/expressions.md:85 -#: ../../src/topics/expressions.md:93 -#: ../../src/topics/parameter-references.md:70 -#: ../../src/topics/parameter-references.md:75 -#: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 -#: d0a92a3792b549e9b5ddce4667d168d2 -#: 801729c7c71b4109824b035437e69bf9 -#: 1bc510d525f0414e88692e356e67fbbc -#: d2e246ae56a24e4abdd6b7d9812a86e2 -#: b1446bab2732412e91f721a08067b0bd -#: e89dbeb22f41430ca39c923d9fdf68cb -#: bd61499b71e64164878dea08d6d7141e -#: ed875a006df64f9e8a55fa5e9fa87404 -msgid "`format`" -msgstr "" - -#: ../../src/topics/expressions.md:74 -#: ../../src/topics/expressions.md:79 -#: ../../src/topics/expressions.md:86 -#: ../../src/topics/expressions.md:94 -#: ../../src/topics/parameter-references.md:71 -#: ../../src/topics/parameter-references.md:76 -#: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 -#: 8a1748579de14f0888d5ee9023e37c2d -#: f760465a49d64d4c8468ad9c4fea62b1 -#: 28b6b5ffa7524374aaa9525ebfafb762 -#: d11f6a19ddf34cf19ec856bacf998e29 -#: bcb7cd10cb5947bb9d85c040f57f954f -#: da5188d3bedc4997a35bdf417f2f643c -#: cd7a0190511d4613b09600a3b1e9d55f -#: 47def3b078e2402182039be0227090ae -msgid "`secondaryFiles`" -msgstr "" - -#: ../../src/topics/expressions.md:75 -#: 23088850ad02459696f6bbd385109aac -msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:77 -#: f02257a822ad46ac93c5981531cc85d5 -msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:80 -#: 989a1c4aaa1143be9f53b90cd8b6d500 -msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 -#: 582b03ac742745a89f4dfc86b7404db2 -#: d193ce0123db4535a4f0b11405ad0322 -msgid "`glob`" -msgstr "" - -#: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 -#: d555a3d991e344a5a8e1289168d7c6d1 -#: 44b3f123c9b04a308c1161b742a7b34b -msgid "`outputEval`" -msgstr "" - -#: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 -#: e9fa9430535c424fa3e8be5d460d2ba4 -#: 0e306cc923974d1db83fdfb45105a11c -msgid "From `Workflow`" -msgstr "" - -#: ../../src/topics/expressions.md:84 -#: d289541e460147aa933f7878996f8649 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 -#: b0290d1a477b48119e17cf1fed9d6dff -#: 446f1190af7a40a0913ff04ce7aa938c -msgid "From `steps`" -msgstr "" - -#: ../../src/topics/expressions.md:88 -#: 81b4d1f23a3642bfa9bb395b94260cd1 -msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 -#: e1cde4aa32c041238ed2596173c6d824 -#: 557694f82e314baa9ccafba14d6ff2c9 -msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "" - -#: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 -#: c2a92d3eca7f4ee39cec649170eeea53 -#: 3c939769ede94602a67fc50c435741cf -msgid "`expression`" -msgstr "" - -#: ../../src/topics/expressions.md:92 -#: f495da32f05a4a5ba9539be0a54c1a59 -msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/expressions.md:95 -#: bdb4c68a175047ddbe141ca24960127f -msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 -#: 4b73495cf18a4d908525292b6f23c419 -#: d0eec6969d174b258e0f010800884cc6 -msgid "`coresMin`" -msgstr "" - -#: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 -#: 718ceee9973240ec9c100977bbcc8921 -#: 2b25152f6df5494a8632f3ce631c20d8 -msgid "`coresMax`" -msgstr "" - -#: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 -#: c07ab08eb75d4528949c56a3d7c12b28 -#: 846cd427ae25410eae7c920b237edcb0 -msgid "`ramMin`" -msgstr "" - -#: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 -#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 -#: b885e108dced4981a445e5fa0a044394 -msgid "`ramMax`" -msgstr "" - -#: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 -#: 700c57ccd5e347be86702c83a8af24b3 -#: e9f5306ae6ea49bbb6801dcce9be2d67 -msgid "`tmpdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 -#: 509a5e2ec52d413eb57754d359f133e4 -#: 58bf8016f5f04c26b645025f405e2288 -msgid "`tmpdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 -#: 5a60ab5ee19446f8a6f49ab8583101a9 -#: 7c817029d55b4700ae8e84be4d0f0ca0 -msgid "`outdirMin`" -msgstr "" - -#: ../../src/topics/expressions.md:103 -#: ../../src/topics/parameter-references.md:100 -#: 1f39f016524a459895ed03c72d74932b -#: e3b76f42c924489f9a0bcf5a7b636d23 -msgid "`outdirMax`" -msgstr "" - -#: ../../src/topics/expressions.md:104 -#: 97b61352363f47cb890e8937c5613fa3 -msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/expressions.md:105 -#: ../../src/topics/parameter-references.md:102 -#: 9359ef94c41249ea8e76fe629926054e -#: a258554d462f4f5f83ece28d5b2fc584 -msgid "`listing`" -msgstr "" - -#: ../../src/topics/expressions.md:106 -#: 8d0b142bb7ed4e61b8fb03de197240ce -msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/expressions.md:107 -#: ../../src/topics/parameter-references.md:104 -#: effc0208cf4f4551958db6e526c0528b -#: 9d4889c8cec24351a7a9e3c547e331b6 -msgid "`entry`" -msgstr "" - -#: ../../src/topics/expressions.md:108 -#: ../../src/topics/parameter-references.md:105 -#: be6c1e85c7b6495d8086c262daad20e7 -#: af4f7f232a9d42388c0ba1cfc7c2cdf7 -msgid "`entryname`" -msgstr "" - -#: ../../src/topics/expressions.md:109 -#: ../../src/topics/parameter-references.md:106 -#: 2183ac54ae10428388649daa57b6a7f4 -#: 6abeba392b0444b19f92a19f178a4682 -msgid "From `EnvVarRequirement`" -msgstr "" - -#: ../../src/topics/expressions.md:110 -#: 0bc424ef2ca346099f29b937379908a0 -msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/expressions.md:111 -#: ../../src/topics/parameter-references.md:108 -#: 107b54b832df4d408d1315bdba05b4dd -#: 949c376120d8441796ec9c89364f8851 -msgid "`envValue`" -msgstr "" - -#: ../../src/topics/expressions.md:116 -#: 10d36a1adfd04144b401c993b12b4094 -msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" -msgstr "" - -#: ../../src/topics/expressions.md:118 -#: 29b73e1dd72744f68377f0a38c10f062 -msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." -msgstr "" - -#: ../../src/topics/expressions.md:122 -#: 38a2afaf4a6c4d04909af22c93f2808d -msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:128 -#: cd74f34b21af4de9be96fd897efc469b -msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." -msgstr "" - -#: ../../src/topics/expressions.md:135 -#: f12e371f3f1a4b0cb2cff9800352d48c -msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:139 -#: 49d0fda2fc144e0b8b7c92afc1d8945e -msgid "`hello-world-expressionlib-inline.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:146 -#: 8f0e8f050e334ac08334e9215e1dcf61 -msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" -msgstr "" - -#: ../../src/topics/expressions.md:149 -#: 26c74b11bb1849cea0763bb74ec43e42 -msgid "Running `hello-world-expressionlib-inline.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:155 -#: 7a6be0005a6441feb67f036d005d7885 -msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" -msgstr "" - -#: ../../src/topics/expressions.md:158 -#: ed590f9e6f4f425da886b110295c45db -msgid "`custom-functions.js`" -msgstr "" - -#: ../../src/topics/expressions.md:164 -#: 093235307d6f47d4858e559b780ef5e5 -msgid "`hello-world-expressionlib-external.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:171 -#: 06635145b441418aaae84dc804f3d6ac -msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." -msgstr "" - -#: ../../src/topics/expressions.md:175 -#: 973a9b257b1a4f0dbd4444d4f11dadd7 -msgid "Running `hello-world-expressionlib-external.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:181 -#: 04eaf1f7c630450db318dcd8b7626e15 -msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." -msgstr "" - -#: ../../src/topics/expressions.md:186 -#: c4098489fbb049789f022cd3e5c3d49b -msgid "`hello-world-expressionlib.cwl`" -msgstr "" - -#: ../../src/topics/expressions.md:193 -#: 5979e4ae5c424276bdbc47f69b379d0f -msgid "Running `hello-world-expressionlib.cwl`." -msgstr "" - -#: ../../src/topics/expressions.md:200 -#: fd4579a3c9844492b314b5c3c1775fc7 -msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." -msgstr "" - -#: ../../src/topics/file-formats.md:1 -#: 3f038e7371f84ed9b4547358dfb55a11 -msgid "File Formats" -msgstr "" - -#: ../../src/topics/file-formats.md:3 -#: e024bcb70e04412e90e1838426d1b69a -msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." -msgstr "" - -#: ../../src/topics/file-formats.md:8 -#: a3db21c0b3114802a8a5b610e252ef13 -msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." -msgstr "" - -#: ../../src/topics/file-formats.md:14 -#: 0f5bc8520d6a4dafa37c65343da9702a -msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." -msgstr "" - -#: ../../src/topics/file-formats.md:17 -#: 5cb830da47464a8b9c3950983fa4d56f -msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." -msgstr "" - -#: ../../src/topics/file-formats.md:20 -#: 0535d5de416b4ea3b2f5996583deecc1 -msgid "`metadata_example.cwl`" -msgstr "" - -#: ../../src/topics/file-formats.md:26 -#: ../../src/topics/metadata-and-authorship.md:22 -#: f558bcf2a993482195cd418b37761809 -#: fb47f73c38cf4ec59bd3021866a631f8 -msgid "The equivalent of this CWL description in command line format is:" -msgstr "" - -#: ../../src/topics/file-formats.md:32 -#: 74b28c1b09c6429b82e462e4ec61808e -msgid "Sample Parameter Files" -msgstr "" - -#: ../../src/topics/file-formats.md:34 -#: a2ce43b391864e8bbde16328cc19b32b -msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." -msgstr "" - -#: ../../src/topics/file-formats.md:39 -#: aebee48b742c4145a600fd2daf8c75dc -msgid "`sample.yml`" -msgstr "" - -#: ../../src/topics/file-formats.md:45 -#: 56ee4dcfff6141d5bef80eb96559876d -msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" -msgstr "" - -#: ../../src/topics/index.md:1 -#: 8d3a6d83e2e54c56995893c41590b7ff -msgid "Topics" -msgstr "" - -#: ../../src/topics/inputs.md:1 -#: 5abcdebfa1cb401bb8892553be285fd3 -msgid "Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:3 -#: d3a55f71dc244026a97902de9ed819ea -msgid "Essential Input Parameters" -msgstr "" - -#: ../../src/topics/inputs.md:5 -#: 96671c56523c4ea9992fb5dfcfa6490e -msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/inputs.md:9 -#: bcc6246742cb46bfb185e415c4a3431a -msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." -msgstr "" - -#: ../../src/topics/inputs.md:13 -#: 86dce36de687449c88fb5eb9d64eb045 -msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." -msgstr "" - -#: ../../src/topics/inputs.md:16 -#: cd9cea15f57b492ba4098237cd7c5bed -msgid "First, create a file called `inp.cwl`, containing the following:" -msgstr "" - -#: ../../src/topics/inputs.md:18 -#: 8bdb875b63104f699efe28ea0abb1e3d -msgid "`inp.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:24 -#: c6a0151a68494c0cb0176781e65e252e -msgid "Create a file called `inp-job.yml`:" -msgstr "" - -#: ../../src/topics/inputs.md:26 -#: dc5e6b5e01d64226bd5dbbf3175fe010 -msgid "`inp-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:33 -#: 36ab1d9edafc4831bb1bca5f123b04b0 -msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" -msgstr "" - -#: ../../src/topics/inputs.md:40 -#: 7dc630ea86464b1dba3a4e5079260b3b -msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." -msgstr "" - -#: ../../src/topics/inputs.md:44 -#: ae37901a8dbe48a59e27ab4e2e6e2d30 -msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." -msgstr "" - -#: ../../src/topics/inputs.md:47 -#: 651e032007ea4a119d20c820bb61f86b -msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:53 -#: 0b056dde9e87428996e47870b12119da -msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:64 -#: 628124a1670b4b058bb0fb6e495a099c -msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" -msgstr "" - -#: ../../src/topics/inputs.md:70 -#: 10ca6321ce3e4b08ab6a5bb380b19c11 -msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." -msgstr "" - -#: ../../src/topics/inputs.md:83 -#: ec2adb3912bc46e28891229e9e0d9a1c -msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." -msgstr "" - -#: ../../src/topics/inputs.md:95 -#: a519be60726a44af9941fdce04735353 -msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." -msgstr "" - -#: ../../src/topics/inputs.md:109 -#: cb8fc8c4c79e467eac5fab4ca685201e -msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." -msgstr "" - -#: ../../src/topics/inputs.md:124 -#: a26cc105716f47cb807174c9003153b0 -msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:131 -#: cc159dd5fe5748caac838862f5b8c4d1 -msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." -msgstr "" - -#: ../../src/topics/inputs.md:134 -#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 -msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." -msgstr "" - -#: ../../src/topics/inputs.md:142 -#: 6812698e9ad84d3385de5e88e9dde0b3 -msgid "The `baseCommand` field will always appear in the final command line before the parameters." -msgstr "" - -#: ../../src/topics/inputs.md:146 -#: 9654e65b1c0642dbb5d4f34edb211989 -msgid "Array Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:148 -#: d1f02be278754267893dfce5a940997d -msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." -msgstr "" - -#: ../../src/topics/inputs.md:154 -#: 01f30e38dfdd452dba3a996073936e16 -msgid "`array-inputs.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:160 -#: 787d4bfb093c4ad287b902084706b751 -msgid "`array-inputs-job.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:166 -#: ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 -#: 588f0f7f967f4d69af27c9729d6d3119 -#: 02adef8ee8204842b5b4a0408f3bac33 -#: 9db68837918a4a349f32f15f12697a1d -msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/inputs.md:178 -#: 75d59e395c66416cae9b352db5081516 -msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." -msgstr "" - -#: ../../src/topics/inputs.md:185 -#: 874c6f19abbf45d7ab7d30a378c4048d -msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." -msgstr "" - -#: ../../src/topics/inputs.md:191 -#: 5d7d7a28cc5d4862803032aec78174d9 -msgid "Inclusive and Exclusive Inputs" -msgstr "" - -#: ../../src/topics/inputs.md:193 -#: dea0d4b681f94e73b13965dcfe75cf7d -msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." -msgstr "" - -#: ../../src/topics/inputs.md:198 -#: ddf598abf4f34aca9fffa045860fbf96 -msgid "`record.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:204 -#: d52a8089920e45bd89d582533b50e3a1 -msgid "`record-job1.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:215 -#: 750474486a84482292eeba45f118287f -msgid "In the first example, you can't provide `itemA` without also providing `itemB`." -msgstr "" - -#: ../../src/topics/inputs.md:217 -#: 9a5cf1d76fc84c1f9b0d123a3a2a480b -msgid "`record-job2.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:233 -#: 1eb0e39bb6d04b8cab300f44a79f3add -msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." -msgstr "" - -#: ../../src/topics/inputs.md:236 -#: bc21ee10bff843689cc98ac6630edcea -msgid "`record-job3.yml`" -msgstr "" - -#: ../../src/topics/inputs.md:252 -#: 4b2ab812f62c4f949dd25c8527f2411c -msgid "In the third example, only `itemD` is provided, so it appears on the command line." -msgstr "" - -#: ../../src/topics/inputs.md:255 -#: b771302d1bec4050a9417b080eef76c9 -msgid "Exclusive Input Parameters with Expressions" -msgstr "" - -#: ../../src/topics/inputs.md:257 -#: 2c3b884cb1c54521900cc90782e8a58d -msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." -msgstr "" - -#: ../../src/topics/inputs.md:262 -#: a1073b6306044dffb414319ae01f68bb -msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." -msgstr "" - -#: ../../src/topics/inputs.md:265 -#: 4a31c733092142b1af834eab1747c224 -msgid "`exclusive-parameter-expressions.cwl`" -msgstr "" - -#: ../../src/topics/inputs.md:271 -#: 9a1d92334685449386dfa3b3a899ed48 -msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" -msgstr "" - -#: ../../src/topics/inputs.md:280 -#: fb623af4c480411b8fde28d01c981411 -msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." -msgstr "" - -#: ../../src/topics/inputs.md:289 -#: e98e165f6bba40809c90473d72f9d592 -msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:1 -#: d33aa2353ad44fb885d3a1ee48263dc4 -msgid "Metadata and Authorship" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:3 -#: cd64d2d828834cbbb24ea5358caf5405 -msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:13 -#: 80af387fe3ff4e2da999903385bd602b -msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:16 -#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 -msgid "`metadata_example2.cwl`" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:28 -#: d402bf528c7f4eb69aaaa275be2bf1d4 -msgid "Extended Example" -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:30 -#: cb9980db4e5f4c74b01c2dec6d5e92d0 -msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." -msgstr "" - -#: ../../src/topics/metadata-and-authorship.md:35 -#: 2dfbd4d580044ed083992f3ceb1bc64e -msgid "`metadata_example3.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:1 -#: 8acf361cf77c4d45ba3f2e344146259f -msgid "Operations" -msgstr "" - -#: ../../src/topics/operations.md:3 -#: 83d3b9a0ed3148fda9ce72cd108cb9e1 -msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." -msgstr "" - -#: ../../src/topics/operations.md:7 -#: 5565c1b2d8a349169a305a9b26b4574d -msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" -msgstr "" - -#: ../../src/topics/operations.md:10 -#: 49cf614893d8438299b3bca384eb40cf -msgid "`operations.cwl`" -msgstr "" - -#: ../../src/topics/operations.md:16 -#: 88160cef4cfa4add9020aa89511a5749 -msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" -msgstr "" - -#: ../../src/topics/operations.md:24 -#: 2f73a786b5d94dc0b23ed0cdd185afc8 -msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" -msgstr "" - -#: ../../src/topics/operations.md:55 -#: 730ba1434a1445ae847ec6153b6a3b72 -msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" -msgstr "" - -#: ../../src/topics/operations.md:58 -#: 98d9b8d867594543890af99e77e24edb -msgid "`cwltool` does not know how to run operations" -msgstr "" - -#: ../../src/topics/operations.md:66 -#: a25d0b1e13324b40a6b8fcd227948c4f -msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." -msgstr "" - -#: ../../src/topics/outputs.md:1 -#: da077da5eb8a4ffebfde041fc16300de -msgid "Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:3 -#: 1b3016f0462f42deb42ddaa33f28bf3d -msgid "Returning Output Files" -msgstr "" - -#: ../../src/topics/outputs.md:5 -#: d661df070e3040869da412d07a71f716 -msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." -msgstr "" - -#: ../../src/topics/outputs.md:10 -#: a11585474d3849cca5467512ed964743 -msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." -msgstr "" - -#: ../../src/topics/outputs.md:16 -#: 2682f9ca8e604a0c9986f7746fdec960 -msgid "The following example demonstrates how to return a file that has been extracted from a tar file." -msgstr "" - -#: ../../src/topics/outputs.md:19 -#: 7e3fa7baf0f549ec89457e7004ac9545 -msgid "Passing mandatory arguments to the `baseCommand`" -msgstr "" - -#: ../../src/topics/outputs.md:21 -#: 22447a560f6f4317bf67bd7c4336126c -msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" -msgstr "" - -#: ../../src/topics/outputs.md:26 -#: f1ee2e00b0cc4112b51c9df3a919b73f -msgid "`tar.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:32 -#: ad8e1acb251246d2a47c39b20d4e483a -msgid "`tar-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:38 -#: dc200c6960ae4476a772645d021f14b8 -msgid "Next, create a tar file for the example." -msgstr "" - -#: ../../src/topics/outputs.md:45 -#: 52703d6b7f914097934bfad13663abeb -msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/outputs.md:51 -#: 5e1c79df657d4a6e84e055dd6b300a5d -msgid "The field `outputBinding` describes how to set the value of each output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:62 -#: 329d2809dfae4f90bc638f5f03a47ee3 -msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." -msgstr "" - -#: ../../src/topics/outputs.md:65 -#: 96df2d45e42441d49ce193ccbfab78a3 -msgid "Capturing Standard Output" -msgstr "" - -#: ../../src/topics/outputs.md:67 -#: c6bcf7c6a8774dd6be41cc775848c3b8 -msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." -msgstr "" - -#: ../../src/topics/outputs.md:71 -#: 9d86c03ab44841c785b924cc44727e31 -msgid "`stdout.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:89 -#: 2fb58c2feaa84970bb5274c49f4b5b64 -msgid "Array Outputs" -msgstr "" - -#: ../../src/topics/outputs.md:91 -#: 9647019d8c37466886e7aab6f176634d -msgid "You can also capture multiple output files into an array of files using `glob`." -msgstr "" - -#: ../../src/topics/outputs.md:93 -#: b9eaf21f5e014eefaae301c47dafd144 -msgid "`array-outputs.cwl`" -msgstr "" - -#: ../../src/topics/outputs.md:99 -#: cffff6c43b4945daa3b2a49763bc50ae -msgid "`array-outputs-job.yml`" -msgstr "" - -#: ../../src/topics/outputs.md:112 -#: cc067051f22f433bbece08f60933e002 -msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." -msgstr "" - -#: ../../src/topics/parameter-references.md:1 -#: a190a6440ec34898990cdac05d809f22 -msgid "Parameter References" -msgstr "" - -#: ../../src/topics/parameter-references.md:3 -#: dbfe2c1123144316aa026374b0f353d3 -msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." -msgstr "" - -#: ../../src/topics/parameter-references.md:13 -#: 280f1a07d0ae41d7a4674504f832fcf0 -msgid "`tar-param.cwl`" -msgstr "" - -#: ../../src/topics/parameter-references.md:19 -#: 5c64d938862747cb9fb52515a656ce27 -msgid "`tar-param-job.yml`" -msgstr "" - -#: ../../src/topics/parameter-references.md:25 -#: 074cf5d912854d8c864607cc24b15302 -msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/parameter-references.md:36 -#: 0290af3e3cbb4b32b0450c8771f3bf95 -msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." -msgstr "" - -#: ../../src/topics/parameter-references.md:47 -#: b54240bb94f746bba7511633aa969db0 -msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." -msgstr "" - -#: ../../src/topics/parameter-references.md:51 -#: 8b70a072aa87414c88e89a3e19af0a51 -msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." -msgstr "" - -#: ../../src/topics/parameter-references.md:54 -#: eea20f89c45f424a888178df53713b28 -msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." -msgstr "" - -#: ../../src/topics/parameter-references.md:59 -#: cb4ea13f5db84c0da43df3f7f2478d78 -msgid "Where are parameter references allowed?" -msgstr "" - -#: ../../src/topics/parameter-references.md:61 -#: 6d3fb423e6c4434697cd113fb27e28ad -msgid "You can only use parameter references in certain fields. These are:" -msgstr "" - -#: ../../src/topics/parameter-references.md:63 -#: 7647e0229a924f988cf02b7812a55c06 -msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "" - -#: ../../src/topics/parameter-references.md:69 -#: 9d663249666045618a0d3acddb85a9a9 -msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:72 -#: 5fed4984f6784347b4cbe0630b1dd2c2 -msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:74 -#: dbf6153cd02542a6a01c172803122b7f -msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:77 -#: b6250cf6fa8a4a0c94b33302e0decca5 -msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -msgstr "" - -#: ../../src/topics/parameter-references.md:81 -#: fa6ca3bbc6784380a03a950a6f49a180 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:85 -#: b92b516e537a4773ad67b4af586e7a25 -msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "" - -#: ../../src/topics/parameter-references.md:89 -#: 467a701228504d06b971b79a59c69064 -msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -msgstr "" - -#: ../../src/topics/parameter-references.md:92 -#: 2634f989eb304009a8568d70ed42786c -msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:101 -#: 5d8bed66282c408695292ea92a03b2c4 -msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -msgstr "" - -#: ../../src/topics/parameter-references.md:103 -#: 958178d1fa8843aaa0541e2bb115cfd4 -msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" - -#: ../../src/topics/parameter-references.md:107 -#: 9a6b311ded8d4e43ae635b1b927dbdf2 -msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "" - -#: ../../src/topics/requirements-and-hints.md:5 -#: aac74f957774479a83aab4c6ff1390ae -msgid "Requirements and Hints" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:1 -#: b75d29d1d55d44488338f9689f156855 -msgid "Specifying Software Requirements" -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:3 -#: 574d93d1d592458a985f259519c036cb -msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:13 -#: 82e48b3e3c3f451480cc0b6a529271f6 -msgid "In this example, the software requirement being described is InterProScan version 5.21-60." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:25 -#: 02e40154eac74ecc98d0447d03475b44 -msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." -msgstr "" - -#: ../../src/topics/specifying-software-requirements.md:29 -#: 8cb1c5d9b1a54c40924099494eb766c6 -msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." -msgstr "" - -#: ../../src/topics/staging-input-files.md:1 -#: b85eb83e05e845d7a179f1b1d74db444 -msgid "Staging Input Files" -msgstr "" - -#: ../../src/topics/staging-input-files.md:3 -#: 35f97d37492b4c7ca3ad6cfc1e6fa366 -msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." -msgstr "" - -#: ../../src/topics/staging-input-files.md:9 -#: c8159d0cb2ab452a9ce8e8d2adbaaa94 -msgid "`linkfile.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:1 -#: 0f7508ce59754a7eb230dea6042244c6 -msgid "Troubleshooting" -msgstr "" - -#: ../../src/topics/troubleshooting.md:3 -#: fbe0c65b444441f785d0054176d036a6 -msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." -msgstr "" - -#: ../../src/topics/troubleshooting.md:6 -#: 1b6b7a75cc754775bf9dd80c0941e8da -msgid "Run `cwltool` with `cachedir`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:8 -#: 9a710602e00c4934ae3a3b471aa68458 -msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." -msgstr "" - -#: ../../src/topics/troubleshooting.md:14 -#: 21b5be7270a14f0987240c81d1ec879b -msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." -msgstr "" - -#: ../../src/topics/troubleshooting.md:20 -#: 0490b1fab86749e49b473949c52bbe8b -msgid "`troubleshooting-wf1.cwl`" -msgstr "" - -#: ../../src/topics/troubleshooting.md:27 -#: cfe9d8241fe84bd5b74042a5625d933f -msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" -msgstr "" - -#: ../../src/topics/troubleshooting.md:35 -#: 764d933cc4da446abd8dd8f913f05dac -msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" -msgstr "" - -#: ../../src/topics/troubleshooting.md:44 -#: c93efc6d4e004859981ee7f5fa28ed03 -msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." -msgstr "" - -#: ../../src/topics/troubleshooting.md:48 -#: 546601da44cb49bd9611b1c85807fd90 -msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." -msgstr "" - -#: ../../src/topics/troubleshooting.md:59 -#: 7e0bf00f8ce542b9b009cdcf1945a9e5 -msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." -msgstr "" - -#: ../../src/topics/using-containers.md:1 -#: eff5f28ca83c458a9b07faf7a81f7e91 -msgid "Using Containers" -msgstr "" - -#: ../../src/topics/using-containers.md:3 -#: 2e634f3737d04d279ae78ceee4b0a664 -msgid "Running Tools Inside Docker" -msgstr "" - -#: ../../src/topics/using-containers.md:5 -#: e07f33d01b804663a25ffb08aad74821 -msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." -msgstr "" - -#: ../../src/topics/using-containers.md:15 -#: 7a644506619a4f08958ec7d4540cd557 -msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." -msgstr "" - -#: ../../src/topics/using-containers.md:18 -#: b5195b7d8eaa419fb2b90cb33a57783a -msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." -msgstr "" - -#: ../../src/topics/using-containers.md:21 -#: 7921a837ee744c5aa9a5bda04b0c8db1 -msgid "`docker.cwl`" -msgstr "" - -#: ../../src/topics/using-containers.md:27 -#: 387e9bc9381a4450af54aff77e4df6a2 -msgid "`docker-job.yml`" -msgstr "" - -#: ../../src/topics/using-containers.md:33 -#: 2713594c937d4c528fc8d04d9e9819ed -msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." -msgstr "" - -#: ../../src/topics/using-containers.md:44 -#: cf94c1424fc2413c85647fd1ee73d951 -msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." -msgstr "" - -#: ../../src/topics/using-containers.md:52 -#: dc0452107c604e29bdf32bb289fe5db8 -msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" -msgstr "" - -#: ../../src/topics/using-containers.md:55 -#: 1a5596243cec4c948d9b6bf0bb12fad0 -msgid "`hello.js`" -msgstr "" - -#: ../../src/topics/using-containers.md:69 -#: 483181f498fc4d968b5fe6ef427709f7 -msgid "Notice the CWL runner has constructed a Docker command line to run the script." -msgstr "" - -#: ../../src/topics/using-containers.md:72 -#: 7487485d6aa4458089a4b4bdf107ea64 -msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." -msgstr "" - -#: ../../src/topics/workflows.md:1 -#: 7394e7690f934043af617436b40845f0 -msgid "Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:3 -#: b9ae9e9a896048caad7e6c38a5bc1bd1 -msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." -msgstr "" - -#: ../../src/topics/workflows.md:13 -#: f228fb7953ea48ed99d89880205f4620 -msgid "CWL workflow." -msgstr "" - -#: ../../src/topics/workflows.md:41 -#: 5870ac44e4c24b8daf5f06c49f95ce04 -msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." -msgstr "" - -#: ../../src/topics/workflows.md:51 -#: a913c76d06164fa18718a8a6a7dcf0d6 -msgid "`echo-uppercase.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:81 -#: 93188ed43ee949cc98b3ea679ce14feb -msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" -msgstr "" - -#: ../../src/topics/workflows.md:91 -#: 36618126a4df4326b236ebe2ea42cffa -msgid "`echo-uppercase-single-file.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:150 -#: 1cc17ad26e9c474b895ba5cd20c8b66a -msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." -msgstr "" - -#: ../../src/topics/workflows.md:160 -#: 24aca0bea4d94e3593b844cf0586cffe -msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." -msgstr "" - -#: ../../src/topics/workflows.md:165 -#: 46cc4859856e4367a9e5e68eecd48b73 -msgid "Writing Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:167 -#: 9c56528acd5f49deb139e034dfbfac7c -msgid "This workflow extracts a java source file from a tar file and then compiles it." -msgstr "" - -#: ../../src/topics/workflows.md:170 -#: 55ab007d472f43388e4c77aae8f165e7 -msgid "`1st-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:179 -#: ../../src/topics/workflows.md:180 -#: 23af7bd2facf4043b2b1c4373fce15fa -#: 307b6618a92948fca4203ccb497c77e6 -msgid "Visualization of 1st-workflow.cwl" -msgstr "" - -#: ../../src/topics/workflows.md:180 -#: a2dd833fdca4443181648e41051a5232 -msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" -msgstr "" - -#: ../../src/topics/workflows.md:183 -#: 7e40cc9f9e1341c195e843c009575b94 -msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" -msgstr "" - -#: ../../src/topics/workflows.md:185 -#: 26c51dcb76364ed780376aecb7cbacda -msgid "`1st-workflow-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:191 -#: 6fcf8ad3d1bd49afa4a105622437bd59 -msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." -msgstr "" - -#: ../../src/topics/workflows.md:205 -#: 71cb81fa4511495b80422244849979e4 -msgid "What's going on here? Let's break it down:" -msgstr "" - -#: ../../src/topics/workflows.md:212 -#: def35d6021394def80a53ae49a2cdbde -msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." -msgstr "" - -#: ../../src/topics/workflows.md:221 -#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 -msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." -msgstr "" - -#: ../../src/topics/workflows.md:233 -#: c84d4450bc6a475dbf34e0b22cea9130 -msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." -msgstr "" - -#: ../../src/topics/workflows.md:248 -#: cca9665f6daa44b49233baf34ab9fcc7 -msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:256 -#: 547edbf5fa424b8286cc21674ff159b0 -msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." -msgstr "" - -#: ../../src/topics/workflows.md:261 -#: 7ca248888b9d484cb544cd76ba538662 -msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." -msgstr "" - -#: ../../src/topics/workflows.md:267 -#: ae6b240718104380b08db5552d7355ea -msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." -msgstr "" - -#: ../../src/topics/workflows.md:278 -#: e5a8b7f84be64020b191099f3fad30ed -msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." -msgstr "" - -#: ../../src/topics/workflows.md:285 -#: f0b04849253c4693904512ddd7f9ce84 -msgid "Nested Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:287 -#: 12a06d8358534102b202965d4258c18e -msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" -msgstr "" - -#: ../../src/topics/workflows.md:297 -#: 1658cac0de1b47e9b60f6d4a4ad9bb19 -msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:300 -#: 49ed137fe996452a8534c68d100db941 -msgid "`nestedworkflows.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:309 -#: b7f93705e5b8416696be01850072e8c0 -msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." -msgstr "" - -#: ../../src/topics/workflows.md:314 -#: e87045829b344089ab59dc27063ddd7a -msgid "\"Visualization \"Visualization" -msgstr "" - -#: ../../src/topics/workflows.md:322 -#: 42ef2f145b824d69b63abc1da175c216 -msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." -msgstr "" - -#: ../../src/topics/workflows.md:336 -#: c61cedf543664d388183e04b3939cc39 -msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." -msgstr "" - -#: ../../src/topics/workflows.md:341 -#: 9e39e3f1501c4fcaab3e8962e090f6be -msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." -msgstr "" - -#: ../../src/topics/workflows.md:347 -#: 03e2f767c4da461982fc3c0f3ba94762 -msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." -msgstr "" - -#: ../../src/topics/workflows.md:366 -#: 3bea5822b8694e2aa32c446e1c54a045 -msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" -msgstr "" - -#: ../../src/topics/workflows.md:383 -#: 426023bd6e3a471cbb30dbda3d6f9e57 -msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." -msgstr "" - -#: ../../src/topics/workflows.md:389 -#: 0d498cd4caf54c15891ca1afe58e2727 -msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." -msgstr "" - -#: ../../src/topics/workflows.md:394 -#: b2d75045e02741b4850f5ff1243f7858 -msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." -msgstr "" - -#: ../../src/topics/workflows.md:398 -#: cfa765264a27411ab914de569aa3dac4 -msgid "Scattering Steps" -msgstr "" - -#: ../../src/topics/workflows.md:400 -#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 -msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." -msgstr "" - -#: ../../src/topics/workflows.md:411 -#: 5fa79c62049a447c8328ebf9db54ebf4 -msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" -msgstr "" - -#: ../../src/topics/workflows.md:415 -#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd -msgid "`scatter-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:421 -#: 3a67d77a2e7b4c0bb61cc3585ceae942 -msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" -msgstr "" - -#: ../../src/topics/workflows.md:429 -#: f1cb55fc59824cc18a95fd6dcb32cf4c -msgid "First of all, notice that the main workflow level input here requires an array of strings." -msgstr "" - -#: ../../src/topics/workflows.md:441 -#: d947c54933d64aad90df392a1cedd63f -msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." -msgstr "" - -#: ../../src/topics/workflows.md:445 -#: 651d35997332404186aa6d5711da4a3d -msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" -msgstr "" - -#: ../../src/topics/workflows.md:450 -#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 -msgid "Using the following input file:" -msgstr "" - -#: ../../src/topics/workflows.md:452 -#: 842b926ae34542cb9023021f137b08be -msgid "`scatter-job.yml`" -msgstr "" - -#: ../../src/topics/workflows.md:458 -#: b662c1a5a4424c8d8350a806356acc61 -msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" -msgstr "" - -#: ../../src/topics/workflows.md:466 -#: 04d6babfd87343d7a5f13867ea02b65f -msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" -msgstr "" - -#: ../../src/topics/workflows.md:469 -#: 2eaacf1a90204a2b9bd621344560f2a1 -msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" -msgstr "" - -#: ../../src/topics/workflows.md:472 -#: 242993d42b164ee5abe7ca10d45856de -msgid "`hello_world_to_stdout.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:480 -#: 4a94e5f7e1bc4d628702140e4e51d6d3 -msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" -msgstr "" - -#: ../../src/topics/workflows.md:483 -#: e61d93b848184c8e8e573928427b4d0a -msgid "`wc-tool.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:489 -#: e3a7182f00f440b8b5461da91194a64b -msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" -msgstr "" - -#: ../../src/topics/workflows.md:491 -#: 99fa96caacaa45cb97aded9a24fcac6d -msgid "`scatter-two-steps.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:497 -#: b5338f39e8c74ff28e139da68089a742 -msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." -msgstr "" - -#: ../../src/topics/workflows.md:509 -#: f6d92156d67c4a339bcfd194cff897df -msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" -msgstr "" - -#: ../../src/topics/workflows.md:513 -#: 1c9e386922324ec8a59306572c19fb8b -msgid "`scatter-nested-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:519 -#: d80ab383eec9402faba997b548fe42eb -msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." -msgstr "" - -#: ../../src/topics/workflows.md:522 -#: f7d2827d97db4bf4ab84b5d6621c3b48 -msgid "Conditional Workflows" -msgstr "" - -#: ../../src/topics/workflows.md:524 -#: 49217c02f58c43ff9ec00f10da8d4e84 -msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." -msgstr "" - -#: ../../src/topics/workflows.md:527 -#: 20b9f181420c401d8615c17a10027517 -msgid "`conditional-workflow.cwl`" -msgstr "" - -#: ../../src/topics/workflows.md:566 -#: 8dbd56473f8c40c0bb12a48be06117e3 -msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." -msgstr "" - -#: ../../src/topics/workflows.md:573 -#: 78d7f3ede2c746d482042adef050b2c4 -msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." -msgstr "" - -#: ../../src/topics/workflows.md:587 -#: cbbf93c70fe04ba7932ba25758ddc611 -msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." -msgstr "" - -#: ../../src/topics/workflows.md:607 -#: cfa1c1fde4454df283f87cc54a9c59ec -msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." -msgstr "" - -#: ../../src/topics/workflows.md:627 -#: 1a8be2950cbb475bbb2617e005f0fac9 -msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." -msgstr "" - -#: ../../src/topics/yaml-guide.md:1 -#: 5f09d4d897cf457d80b9a11b8c01747e -msgid "YAML Guide" -msgstr "" - -#: ../../src/topics/yaml-guide.md:6 -#: 5d83c56102e141cc978500f678dd0c1c -msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." -msgstr "" - -#: ../../src/topics/yaml-guide.md:13 -#: c38438fbf9a04e729ec2e3c962435289 -msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" - -#: ../../src/topics/yaml-guide.md:16 -#: fdb9cc750cec43ee962517e637dc5fea -msgid "Contents" -msgstr "" - -#: ../../src/topics/yaml-guide.md:18 -#: 08da9cd8056b4ddd8f5150cc85ba72ee -msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:19 -#: b027fc234ed943bbb00d4c6bc03c040a -msgid "[Comments](#comments)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:20 -#: b8befec0d8684638aaa616a659e0100c -msgid "[Maps](#maps)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:21 -#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc -msgid "[Arrays](#arrays)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:22 -#: 36db4f26b5194e9da5c6a1ed8cb0ad04 -msgid "[JSON Style](#json-style)" -msgstr "" - -#: ../../src/topics/yaml-guide.md:24 -#: 98056c5cfd5640ad9de0679360797cc7 -msgid "Key-Value Pairs" -msgstr "" - -#: ../../src/topics/yaml-guide.md:26 -#: cda73485875d4c8e9464679a20558616 -msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:42 -#: 98cae24919b74c088a5d89706aec581b -msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." -msgstr "" - -#: ../../src/topics/yaml-guide.md:51 -#: b4b0940b4b5743c09637b36b964202d0 -msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." -msgstr "" - -#: ../../src/topics/yaml-guide.md:61 -#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 -msgid "Comments" -msgstr "" - -#: ../../src/topics/yaml-guide.md:63 -#: 9ca3554d771d45998e88aaede525b227 -msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:76 -#: 3fca839cede94cfd8e4f605c73ba699d -msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" -msgstr "" - -#: ../../src/topics/yaml-guide.md:79 -#: da34c635707345b2a5e85a2fcd30bbaf -msgid "Maps" -msgstr "" - -#: ../../src/topics/yaml-guide.md:81 -#: 3ded0f125249485c921994b6e6b93ac9 -msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:104 -#: 53ece35d309a4c8d99f1efb2122a7092 -msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." -msgstr "" - -#: ../../src/topics/yaml-guide.md:127 -#: d74321b111d84ae7a515f2f17dd39e23 -msgid "Arrays" -msgstr "" - -#: ../../src/topics/yaml-guide.md:129 -#: 7fc0bdf2489a44f2a29e71b86f7c0055 -msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:146 -#: fd64dd818ec64bb6aa9a11586a5747f6 -msgid "and a more complex example combining maps and arrays:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:167 -#: 8c06e542dd4144fa83388d8142552c8d -msgid "JSON Style" -msgstr "" - -#: ../../src/topics/yaml-guide.md:169 -#: 87bafb845c714b109874f6137b84462d -msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:177 -#: 5ab9ddf613a540a2b8228e37600cc5dc -msgid "and:" -msgstr "" - -#: ../../src/topics/yaml-guide.md:184 -#: fcd05b1ef31a4046946a2399c7fc5575 -msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." -msgstr "" - -#: ../../src/topics/yaml-guide.md:194 -#: f4b8fc8236044fada420def13a02813d -msgid "Reference" -msgstr "" - -#: ../../src/topics/yaml-guide.md:196 -#: 859368c1f25c4a4aad57abfd046c63f5 -msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." -msgstr "" - -#: ../../src/tutorials.md:1 -#: 2203c93f02ac4514a43508ecb98dfcc5 -msgid "Tutorials" -msgstr "" - -#: ../../src/tutorials.md:5 -#: 5d92464923c245818c070fbef102be89 -msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." -msgstr "" - -#: ../../src/tutorials.md:7 -#: 8a5cd557dab5456bb41cdc24af73b50c -msgid "Beginner Tutorials" -msgstr "" - -#: ../../src/tutorials.md:9 -#: 13d7e2e92e96432787c712cf6a595424 -msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" -msgstr "" - -#: ../../src/tutorials.md:11 -#: 0abdd85c9b964a4e89ba3d80a6c78d6f -msgid "Advanced Tutorials" -msgstr "" - -#: ../../src/tutorials.md:13 -#: 3cbf1f69a5514fd3bee90e68b201190f -msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" - -#: ../../src/tutorials.md:15 -#: 68c97a7065634d02956f3f5c1d4eeb9f -msgid "Bioinformatics Tutorials" -msgstr "" - -#: ../../src/tutorials.md:17 -#: a67c7e0eaf4e4d27b3e5db303333a088 -msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index a55d3d7a..8aa06c13 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,8 +9,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-04-06 01:01+0000\n" -"Last-Translator: Manabu ISHII \n" +"PO-Revision-Date: 2024-04-08 08:23+0000\n" +"Last-Translator: Michael Crusoe \n" "Language-Team: Japanese \n" "Language: ja\n" @@ -1346,7 +1346,7 @@ msgid "" "[OPTIONS] [CWL_DOCUMENT] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -"基本的に `cwltool` の使い方は、`cwltool [OPTIONS] [cwl_document] " +"基本的に `cwltool` の使い方は、`cwltool [OPTIONS] [CWL_DOCUMENT] " "[INPUTS_OBJECT]`です。`hello_world.cwl` " "Workflowは、オプションを指定せずに実行することができます：" @@ -1639,8 +1639,8 @@ msgid "" "In tool descriptions, list dependencies using short name(s) under " "[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "" -"ツール定義では、[`SoftwareRequirement`] (https://w3id.org/cwl/CommandLineTool" -".html#SoftwareRequirement)." +"ツール定義では、[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#SoftwareRequirement)." "の下に、短い名前を使用して依存関係をリストアップします。" #: ../../src/topics/best-practices.md:47 6c9eaae099fa4ca4b0986b1c4146df50 @@ -1669,9 +1669,9 @@ msgid "" "known to work with this description under " "[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." msgstr "" -"ツール定義では、[`SoftwareRequirement`] (https://w3id.org/cwl/CommandLineTool" -".html#SoftwareRequirement)の下に、このツール定義で動作することが確認されてい" -"るツールのバージョンのリストを書きます。" +"ツール定義では、[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#SoftwareRequirement)の下に、このツール定義で動作することが確認されている" +"ツールのバージョンのリストを書きます。" #: ../../src/topics/best-practices.md:58 88806cb0462f4359801c1fa0ff0ebcc0 #, fuzzy @@ -1712,9 +1712,10 @@ msgid "" "(sub)command is capable of more. Don't overcomplicate your tool " "descriptions with options that you don't need or use." msgstr "" -"各`CommandLineTool` の定義は、たとえ（サブ）コマンドがそれ以上の機能を備えて" -"いたとしても、一つの使用方法のみに焦点を当てるべきです。必要ないまたは、使用" -"しないオプションでツールの定義を複雑にし過ぎないようにしましょう。" +"各[`CommandLineTool`](https://w3id.org/cwl/CommandLineTool." +"html#CommandLineTool) の定義は、たとえ（サブ）コマンドがそれ以上の機能を備え" +"ていたとしても、一つの使用方法のみに焦点を当てるべきです。必要ないまたは、使" +"用しないオプションでツールの定義を複雑にし過ぎないようにしましょう。" #: ../../src/topics/best-practices.md:73 ef5a5f9b253c4ca3916802a695fb7c6d msgid "" @@ -2136,15 +2137,16 @@ msgid "Expressions" msgstr "Expressions" #: ../../src/topics/expressions.md:3 24d05cbbab8e460e99f2edc97ab0dcec -#, fuzzy msgid "" "If you need to manipulate input parameters, include the requirement " "[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" " and then anywhere a parameter reference is legal you can provide a " "fragment of Javascript that will be evaluated by the CWL runner." msgstr "" -"入力パラメータを操作する必要がある場合は、`InlineJavascriptRequirement` " -"を含めると、パラメータ参照が合法な場所であれば、CWL runnerによって評価されるJavascriptを使用できます。" +"入力パラメータを操作する必要がある場合は、[`InlineJavascriptRequirement`](htt" +"ps://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement) " +"を含めると、パラメータ参照が合法な場所であれば、CWL " +"runnerによって評価されるJavascriptを使用できます。" #: ../../src/topics/expressions.md:9 3d48d1a8f7f74bc1886e41653cb53a22 #, fuzzy @@ -2623,7 +2625,6 @@ msgid "File Formats" msgstr "ファイルフォーマット" #: ../../src/topics/file-formats.md:3 d99dab4f2f264c68b839b59b80d570e0 -#, fuzzy msgid "" "Tools and workflows can take " "[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types as input " @@ -2632,8 +2633,12 @@ msgid "" "helps document for others how to use your tool while allowing you to do " "some simple type-checking when creating parameter files." msgstr "" -"ToolsやWorkflowsは、`File` 型を入力として受け取り、出力として生成することができます。また、`File` " -"タイプのフォーマットを示すことをお勧めします。これにより、ツールの使用方法を他の人に示すことができ、また、パラメータファイルを作成する際に簡単な型チェックを行うことができるようになります。" +"ToolsやWorkflowsは、[`File`](https://w3id.org/cwl/CommandLineTool.html#File) " +"型を入力として受け取り、出力として生成することができます。また、[`File`](http" +"s://w3id.org/cwl/CommandLineTool.html#File) タイプのフォーマットを示すことを" +"お勧めします。これにより、ツールの使用方法を他の人に示すことができ、また、パ" +"ラメータファイルを作成する際に簡単な型チェックを行うことができるようになりま" +"す。" #: ../../src/topics/file-formats.md:8 23ba3dd26f5543119e2c152105b58e98 msgid "" @@ -3854,7 +3859,6 @@ msgid "`docker-job.yml`" msgstr "`docker-job.yml`" #: ../../src/topics/using-containers.md:33 d766b66de4714a5da0cd87ed886cc32f -#, fuzzy msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " @@ -3862,8 +3866,10 @@ msgid "" "[`dockerRequirement`](https://w3id.org/cwl/CommandLineTool.html#DockerRequirement)" " section." msgstr "" -"これを実行する前に、これを分解して、いくつか細かく何をするのかを見てみましょう。 " -"この大部分は以前のセクションで説明したもので、本当に新しいのは`dockerRequirement` の部分だけです。" +"これを実行する前に、これを分解して、いくつか細かく何をするのかを見てみましょ" +"う。 この大部分は以前のセクションで説明したもので、本当に新しいのは[`dockerR" +"equirement`](https://w3id.org/cwl/CommandLineTool.html#DockerRequirement) " +"の部分だけです。" #: ../../src/topics/using-containers.md:44 1f02618ab6254459ae71f72844e3cc18 #, fuzzy From 5ff279ddffb9781e6327f6ab249a4afe0ba162fa Mon Sep 17 00:00:00 2001 From: Manabu ISHII Date: Mon, 8 Apr 2024 10:23:55 +0200 Subject: [PATCH 140/179] Translated using Weblate (Japanese) Currently translated at 75.9% (455 of 599 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide --- locales/ja/LC_MESSAGES/user_guide.po | 41 +++++++++++++++------------- 1 file changed, 22 insertions(+), 19 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 8aa06c13..5e646410 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -10,7 +10,7 @@ msgstr "" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" "PO-Revision-Date: 2024-04-08 08:23+0000\n" -"Last-Translator: Michael Crusoe \n" +"Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" "Language: ja\n" @@ -872,11 +872,12 @@ msgstr "CWLサイト内の「CWL仕様」ページ：" -msgstr "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)から" +msgstr "" +"<[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)>から" #: ../../src/introduction/basic-concepts.md:183 #: 44af015fa36644b99f07338d241d29c1 @@ -1148,7 +1149,6 @@ msgid "Running `true_shebang.cwl` with a shebang." msgstr "`true_shebang.cwl` をシェバングで実行する。" #: ../../src/introduction/prerequisites.md:141 11fea992c00940d29eb29ccf4b9370e9 -#, fuzzy msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -1157,10 +1157,10 @@ msgid "" " using a hard-coded location, since `/usr/bin/env [executable]` looks for" " the `[executable]` program in the system `PATH`," msgstr "" -"*shebang* は、スクリプトの冒頭の2文字列`#!` のことです。スクリプトが実行可能" -"な場合、オペレーティングシステムは、shebangの後に指定された実行可能ファイルを" -"使用してスクリプトを実行します。`/usr/bin/env ` は` `" -" プログラムを設定されている環境変数`PATH` " +"*shebang* (訳注：発音、シバン、シェバン)は、スクリプトの冒頭の2文字列`#!` の" +"ことです。スクリプトが実行可能な場合、オペレーティングシステムは、shebangの後" +"に指定された実行可能ファイルを使用してスクリプトを実行します。`/usr/bin/env " +"` は` ` プログラムを設定されている環境変数`PATH` " "の中で探すので、ハードコードされた場所を使うよりも`/usr/bin/env `" " を使うことが良い習慣と考えられています" @@ -1297,14 +1297,14 @@ msgstr "" "echo \"Hello World\"`." #: ../../src/introduction/quick-start.md:27 7b2ae93353184faea0ae4f4acdfc3350 -#, fuzzy msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " "“workflow” here. You will learn more about this in the [basic concepts" "](basic-concepts.md) section." msgstr "" -"CWLでは、CommandLineToolとWorkflowは区別されています。しかし、ここでは簡略化のため、「ワークフロー」という用語を使用しています。これについては、[基本概念" +"CWLでは、CommandLineToolとWorkflowは区別されています。しかし、ここでは簡略化" +"のため、「ワークフロー」という用語を使用しています。これについては、[基本概念" "](basic-concepts.md)のセクションで詳しく説明します。" #: ../../src/introduction/quick-start.md:32 1ed30b04073d47a9893774746479fb5d @@ -1782,16 +1782,16 @@ msgid "Command Line Tool" msgstr "コマンドラインツール" #: ../../src/topics/command-line-tool.md:3 cf0f1c00c0b34c94a8e2460a700c303e -#, fuzzy msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " "`tar`, etc. The command-line tool is defined in the `baseCommand` " "attribute of the command-line tool CWL document." msgstr "" -"コマンドラインツールは、Processオブジェクトの一種であり、それ自体またはワークフローのステップとし " -"て実行することができます。`ls`,`echo`,`tar` " -"などのコマンドのラッパーです。コマンドラインツールは、コマンドラインツールCWL文書の`baseCommand` 属性で定義されています。" +"CommandLineToolは、Processオブジェクトの一種であり、それ自体またはワークフロ" +"ーのステップとして実行することができます。`ls`,`echo`,`tar` などの実行したい" +"コマンドのラッパーです。実行したいコマンドは、CommandLineToolについてのCWL定" +"義の`baseCommand` 属性で定義されています。" #: ../../src/topics/command-line-tool.md:8 7a180ba1f2d746a78b79be7e899cbad6 msgid "" @@ -1811,12 +1811,14 @@ msgid "`echo.cwl`" msgstr "`echo.cwl`" #: ../../src/topics/command-line-tool.md:57 e3a06ebe51b64b0183673a8acc04969f -#, fuzzy msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." -msgstr "上記の例では、簡略化した形で入力と出力を定義しています。[Inputs](../topics/inputs.md)と[Outputs](../topics/outputs.md)のセクションで、より詳しく説明する予定です。" +msgstr "" +"上記の例では、簡略化した形で入力と出力を定義しています。[Inputs](../topics/" +"inputs.md)と[Outputs](../topics/outputs." +"md)のセクションで、より詳しく説明する予定です。" #: ../../src/topics/command-line-tool.md:68 2bab464d19d14562a6501373aff13905 msgid "Network Access" @@ -2499,15 +2501,16 @@ msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "`expressionLib` による外部ライブラリの利用とインラインJavaScriptコードの利用" #: ../../src/topics/expressions.md:118 ea6cbaa5dae647538c0bd9a4d5cad3f9 -#, fuzzy msgid "" "The requirement " "[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" " supports an `expressionLib` attribute that allows users to load external" " JavaScript files, or to provide inline JavaScript code." msgstr "" -"`InlineJavascriptRequirement` は、`expressionLib` 属性をサポートし、ユーザーが外部 " -"JavaScript ファイルを読み込んだり、インライン JavaScript コードを提供したりできるようにします。" +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#InlineJavascriptRequirement)は、`expressionLib` 属性をサポートし、" +"ユーザーが外部 JavaScript ファイルを読み込んだり、インライン JavaScript " +"コードを提供したりできるようにします。" #: ../../src/topics/expressions.md:122 484dc17440524cfda4dc486a7c5d5f63 msgid "" From cc6c5631ecb3aee641d20365e40ba92879ba11fb Mon Sep 17 00:00:00 2001 From: Michael Crusoe Date: Mon, 8 Apr 2024 08:27:47 +0000 Subject: [PATCH 141/179] Translated using Weblate (Japanese) Currently translated at 76.1% (456 of 599 strings) Translation: Common Workflow Language/CWL User Guide Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ --- locales/ja/LC_MESSAGES/user_guide.po | 25 ++++++++++++------------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 5e646410..e546154d 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,8 +9,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-04-08 08:23+0000\n" -"Last-Translator: Manabu ISHII \n" +"PO-Revision-Date: 2024-04-08 08:39+0000\n" +"Last-Translator: Michael Crusoe \n" "Language-Team: Japanese \n" "Language: ja\n" @@ -758,7 +758,7 @@ msgid "" " - enables JavaScript in expressions." msgstr "" "[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow." -"html#InlineJavascriptRequirement) - でJavaScriptを有効にします。" +"html#InlineJavascriptRequirement) - でJavaScriptを有効にします。" #: ../../src/introduction/basic-concepts.md:142 #: 6f9854ae1b884ad39f88d2f39d66cb98 @@ -767,7 +767,7 @@ msgid "" " - enables nested workflows." msgstr "" "[`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow." -"html#SubworkflowFeatureRequirement) - ネストしたワークフローを有効にします。" +"html#SubworkflowFeatureRequirement) - ネストしたワークフローを有効にします。" #: ../../src/introduction/basic-concepts.md:143 #: 23fef6de073f4da18118e4d0512670fe @@ -776,7 +776,7 @@ msgid "" " - controls staging files in the input directory." msgstr "" "[`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow." -"html#InitialWorkDirRequirement) - " +"html#InitialWorkDirRequirement) - " "入力ディレクトリのステージングファイルを制御します。" #: ../../src/introduction/basic-concepts.md:145 @@ -876,8 +876,8 @@ msgid "" "The Command Line Tool Description Standard: " "<[https://www.commonwl.org/v1.2/CommandLineTool.html](https://w3id.org/cwl/CommandLineTool.html)>" msgstr "" -"<[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." -"html#CommandLineTool)>から" +"<[https://www.commonwl.org/v1.2/CommandLineTool.html](https://w3id.org/cwl/" +"CommandLineTool.html)>から" #: ../../src/introduction/basic-concepts.md:183 #: 44af015fa36644b99f07338d241d29c1 @@ -3099,7 +3099,6 @@ msgstr "" "に変更すると、コマンドラインやジョブ入力ファイルで何も指定されていない場合にデフォルト値を持つようになります。" #: ../../src/topics/inputs.md:295 b5055c77f85e43609fe3e9b9839778e3 -#, fuzzy msgid "" "Here, the boolean “or” operator `||` in JavaScript is used for its " "_short-circuiting_ property. If `inputs.file_format` is “true” in a " @@ -3110,11 +3109,11 @@ msgid "" "reasonable default can be provided there." msgstr "" "ここでは、JavaScriptのブール値 \"or\"、 \"演算子 `||` は、その_short-" -"circuiting_プロパティに使用されます。`inputs.file_format`がブール値の \"true " -"\"である場合（例えば、列挙された有効な空でない文字列）、式の評価は`||`の最初" -"のオペランドで停止します。しかし、`inputs.file_format`が`null`の場合、式全体" -"の値は2番目のオペランドの値になります。これにより合理的なデフォルト値を提供し" -"ます。" +"circuiting_プロパティに使用されます。`inputs.file_format`がブール値の \"true" +"\"である場合（例えば、列挙された有効な空でない文字列）、式の評価は " +"`||`の最初のオペランドで停止します。しかし、 `inputs.file_format`が`null`の場" +"合、式全体の値は2番目のオペランドの値になります。これにより合理的なデフォルト" +"値を提供します。" #: ../../src/topics/metadata-and-authorship.md:1 #: 723c2232310c4276aeac2bd6728d2912 From d62d67eb586c4c7afefd741fcfbcf770a1efd570 Mon Sep 17 00:00:00 2001 From: Michael Crusoe Date: Mon, 8 Apr 2024 08:39:39 +0000 Subject: [PATCH 142/179] Translated using Weblate (Japanese) Currently translated at 76.7% (460 of 599 strings) Translation: Common Workflow Language/CWL User Guide Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ --- locales/ja/LC_MESSAGES/user_guide.po | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index e546154d..a85945e7 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-04-08 08:39+0000\n" +"PO-Revision-Date: 2024-04-09 09:01+0000\n" "Last-Translator: Michael Crusoe \n" "Language-Team: Japanese \n" @@ -2111,7 +2111,7 @@ msgid "" msgstr "" "CommandLinetToolと同様に、`inputs` と`outputs` " "が必要です。しかし、`baseCommand` の代わりに、[`expression`](https://w3id." -"org/cwl/CommandLineTool.html#Expressions_(Optional)) 属性を必要とします。" +"org/cwl/CommandLineTool.html#Expressions_(Optional)) 属性を必要とします。" #: ../../src/topics/expression-tool.md:17 f172488c19a94d688036197117d30b38 msgid "CWL expression tool." @@ -3301,7 +3301,7 @@ msgid "" msgstr "" "これまでの例では、`baseCommand` " "は単なる文字列で、引数はCWL入力として渡していました。単一の文字列の代わりに、" -"_文字列の配列_ を使用することができます。 配列の最初の要素は実行するコマンド" +"_文字列の配列_ を使用することができます。 配列の最初の要素は実行するコマンド" "で、それ以降の要素は必須のコマンドライン引数です" #: ../../src/topics/outputs.md:28 9b65071222c94951bed12ac53e964ee3 From 060ace8ec39979fd38f52fce4d873a5548d271c2 Mon Sep 17 00:00:00 2001 From: Manabu ISHII Date: Tue, 9 Apr 2024 00:09:37 +0000 Subject: [PATCH 143/179] Translated using Weblate (Japanese) Currently translated at 76.7% (460 of 599 strings) Translation: Common Workflow Language/CWL User Guide Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ --- locales/ja/LC_MESSAGES/user_guide.po | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index a85945e7..c67c3321 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -10,7 +10,7 @@ msgstr "" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" "PO-Revision-Date: 2024-04-09 09:01+0000\n" -"Last-Translator: Michael Crusoe \n" +"Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" "Language: ja\n" @@ -838,13 +838,14 @@ msgstr "" #: ../../src/introduction/basic-concepts.md:171 #: c0f53138bf084939a54b0a576b44199f -#, fuzzy msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" " leverage technologies such as Docker and be used with CWL " "implementations from different vendors." -msgstr "CWLで定義されたツールやワークフローは、Dockerなどの技術を透過的に活用し、異なるベンダーのCWL実装と組み合わせて使用することができるためです。" +msgstr "" +"CWLで定義されたツールやワークフローは、Dockerなどの技術を透過的に活用し、異な" +"るベンダーのCWL実装と組み合わせて使用することができるためです。" #: ../../src/introduction/basic-concepts.md:176 #: 91d6eb4984a6410ba99616b6617ba9af @@ -1590,7 +1591,6 @@ msgstr "" "[Apache 2.0][apache-license]です。" #: ../../src/topics/best-practices.md:20 384eb620dc31468e8c3f5f33a3436200 -#, fuzzy msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1825,7 +1825,6 @@ msgid "Network Access" msgstr "ネットワークアクセス" #: ../../src/topics/command-line-tool.md:69 201712f3ceee4d4ea56ab96d3fef97b0 -#, fuzzy msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. Starting with CWL v1.1, programs are not granted network access " @@ -1842,11 +1841,13 @@ msgstr "" msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 or v1.2 " "will have `networkAccess: true` set automatically." -msgstr "CWL v1.0のコマンドラインツールをv1.1またはv1.2にアップグレードすると、自動的にネットワークアクセスを取得します。" +msgstr "" +"CWL v1.0のコマンドラインツールをv1.1またはv1." +"2にアップグレードすると、自動的に`networkAccess: " +"true`が追加されネットワークアクセスを取得します。" #: ../../src/topics/creating-files-at-runtime.md:1 #: 17c5b4ee43cc4a979676ad27e473d046 -#, fuzzy msgid "Creating Files at Runtime" msgstr "実行時にファイルを作成する" From 73e615408b037b6040979245f93fbddd5e0ca20d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 10 Apr 2024 07:15:33 +0200 Subject: [PATCH 144/179] Bump peaceiris/actions-gh-pages from 3 to 4 (#467) Bumps [peaceiris/actions-gh-pages](https://github.com/peaceiris/actions-gh-pages) from 3 to 4. - [Release notes](https://github.com/peaceiris/actions-gh-pages/releases) - [Changelog](https://github.com/peaceiris/actions-gh-pages/blob/main/CHANGELOG.md) - [Commits](https://github.com/peaceiris/actions-gh-pages/compare/v3...v4) --- updated-dependencies: - dependency-name: peaceiris/actions-gh-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com> --- .github/workflows/gh-pages.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/gh-pages.yaml b/.github/workflows/gh-pages.yaml index 79ebd7ec..2a8dc626 100644 --- a/.github/workflows/gh-pages.yaml +++ b/.github/workflows/gh-pages.yaml @@ -43,7 +43,7 @@ jobs: done - name: Deploy - uses: peaceiris/actions-gh-pages@v3 + uses: peaceiris/actions-gh-pages@v4 with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: ./_build/html/ From 76659c00694787a805e69ea21a0b8cd7ef615279 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 25 Apr 2024 11:24:05 +0200 Subject: [PATCH 145/179] Update myst-parser requirement from ==2.* to ==3.* (#472) Updates the requirements on [myst-parser](https://github.com/executablebooks/MyST-Parser) to permit the latest version. - [Release notes](https://github.com/executablebooks/MyST-Parser/releases) - [Changelog](https://github.com/executablebooks/MyST-Parser/blob/master/CHANGELOG.md) - [Commits](https://github.com/executablebooks/MyST-Parser/compare/v2.0.0...v3.0.0) --- updated-dependencies: - dependency-name: myst-parser dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 748cf83d..4399b149 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,7 @@ dependencies = [ "cwltool", "cwlref-runner", "cwl-utils==0.*", - "myst-parser==2.*", + "myst-parser==3.*", "pydata-sphinx-theme==0.*", "sphinx==7.*", "sphinx-reredirects==0.1.*", From 645512b4fc2ad2aa5fd9276b63cae0a4bab28085 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Thu, 25 Apr 2024 12:16:19 +0300 Subject: [PATCH 146/179] inputs: fix a line emphasis --- src/topics/inputs.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/topics/inputs.md b/src/topics/inputs.md index a5356a7a..e4e162b9 100644 --- a/src/topics/inputs.md +++ b/src/topics/inputs.md @@ -241,7 +241,7 @@ matching item (`itemC`) is added to the command line and remaining item (`itemD` ```{runcmd} cwltool record.cwl record-job3.yml :working-directory: src/_includes/cwl/inputs -:emphasize-lines: 9-10, 22 +:emphasize-lines: 9-10, 21 ``` ```{code-block} console From 3f04d2401fb1146f28b8d79d36b7398544c72f69 Mon Sep 17 00:00:00 2001 From: Kuan-Yi Li Date: Thu, 25 Apr 2024 17:50:58 +0800 Subject: [PATCH 147/179] Fix empty section navigation sidebar and reorganize templates a bit (#471) * fix section navigation sidebar The sidebar generation logic in the PyData Sphinx Theme was altered, causing the navigation sidebar to become consistently displayed but always empty. The `sidebar-nav-bs.html` override was initially added to address a responsive design issue, which has now been effectively resolved by the upstream. Let's remove the override to avoid future breakage. `sidebar_includehidden` is set to `False` to get rid of the sidebar when its content is empty. * reposition the project links Add project-related links in a way that does not override upstream templates. --- src/_templates/layout.html | 26 -------------------------- src/_templates/project-links.html | 15 +++++++++++++++ src/_templates/sidebar-nav-bs.html | 8 -------- src/conf.py | 2 ++ 4 files changed, 17 insertions(+), 34 deletions(-) delete mode 100644 src/_templates/layout.html create mode 100644 src/_templates/project-links.html delete mode 100644 src/_templates/sidebar-nav-bs.html diff --git a/src/_templates/layout.html b/src/_templates/layout.html deleted file mode 100644 index e55cff18..00000000 --- a/src/_templates/layout.html +++ /dev/null @@ -1,26 +0,0 @@ -{% extends '!layout.html' %} - -{% block footer %} -
-
-
- -
-
-
- -{{ super() }} -{% endblock %} diff --git a/src/_templates/project-links.html b/src/_templates/project-links.html new file mode 100644 index 00000000..e842f85b --- /dev/null +++ b/src/_templates/project-links.html @@ -0,0 +1,15 @@ +{# Displays project-related links. #} + diff --git a/src/_templates/sidebar-nav-bs.html b/src/_templates/sidebar-nav-bs.html deleted file mode 100644 index a559969d..00000000 --- a/src/_templates/sidebar-nav-bs.html +++ /dev/null @@ -1,8 +0,0 @@ - diff --git a/src/conf.py b/src/conf.py index 600fcc04..6d1ca68b 100644 --- a/src/conf.py +++ b/src/conf.py @@ -207,6 +207,7 @@ # "json_url": json_url, # "version_match": version_match, # }, + "sidebar_includehidden": False, "use_edit_page_button": True, "navbar_align": "content", "navbar_end": [ @@ -219,6 +220,7 @@ "collapse_navigation": True, "show_prev_next": True, "footer_start": ["copyright", "sphinx-version"], + "footer_center": ["project-links"], "footer_end": ["theme-version"], } From 7e6e66fe3ef07b917e696be09a772e4a0c32c8dd Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Thu, 25 Apr 2024 12:01:52 +0200 Subject: [PATCH 148/179] Translations update from Hosted Weblate (#468) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Translated using Weblate (Chinese (Simplified)) Currently translated at 77.9% (467 of 599 strings) Co-authored-by: Zoë Ma Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Japanese) Currently translated at 84.6% (507 of 599 strings) Translated using Weblate (Japanese) Currently translated at 83.9% (503 of 599 strings) Translated using Weblate (Japanese) Currently translated at 82.3% (493 of 599 strings) Translated using Weblate (Japanese) Currently translated at 81.4% (488 of 599 strings) Translated using Weblate (Japanese) Currently translated at 81.3% (487 of 599 strings) Translated using Weblate (Japanese) Currently translated at 79.1% (474 of 599 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide --------- Co-authored-by: Zoë Ma Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 190 ++++++++++------------ locales/zh_Hans/LC_MESSAGES/user_guide.po | 21 ++- 2 files changed, 104 insertions(+), 107 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index c67c3321..f4d773cf 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-04-09 09:01+0000\n" +"PO-Revision-Date: 2024-04-25 09:24+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -18,7 +18,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.5-dev\n" +"X-Generator: Weblate 5.5.1-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -390,29 +390,27 @@ msgstr "" "は、値として使用するワークフローからの入力を示すものが設定されます。" #: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 -#, fuzzy msgid "How can I set Booleans?" -msgstr "ブール値の設定" +msgstr "ブール値を設定するにはどうしたらよいでしょうか？" #: ../../src/faq.md:344 8dcb88744e5840029de0e1bbf1c4b967 msgid "These can be set by using the default field" msgstr "デフォルトフィールドを使って、これらを設定します" #: ../../src/faq.md:349 972b7a5551bb43e6b9fa30e0cb713ff7 -#, fuzzy msgid "What should I do when concatenating strings in inputs?" -msgstr "入力された文字列を連結する" +msgstr "入力された文字列を連結するにはどうしたら良いでしょうか？" #: ../../src/faq.md:351 68f74afc21d846dd9070d45dec0cc1d8 msgid "The valueFrom field must be used instead of default." msgstr "defaultフィールドの代わりにvalueFromフィールドを使用する必要があります。" #: ../../src/faq.md:359 53b633c6f8644106beb95ae567eb0708 -#, fuzzy msgid "" "I get `cwltool` errors due to filenames with space characters inside. " "What should I do?" -msgstr "`cwltool` ファイル名の中に空白文字があるために起こるエラー" +msgstr "`cwltool` ファイル名の中に空白文字があるために起こるエラーにはどのように対処" +"したらよいでしょうか？" #: ../../src/faq.md:361 7101bb5cb69e4faca4e60eabb4eb258e msgid "`cwltool` does not allow some characters in filenames by default." @@ -431,16 +429,15 @@ msgid "" msgstr "これらの危険な文字を避けられない場合は、`--relax-path-checks` を`cwltool` に渡してください。" #: ../../src/faq.md:373 b7ec33f38ce74ceb890f4379e4c41054 -#, fuzzy msgid "" "What should I do when I get CWL Parameter Reference error due to hyphen " "in an input identifier?" -msgstr "入力識別子の中のハイフンに起因するCWLパラメータリファレンスエラー" +msgstr "入力パラメータ名の中のハイフンがあるため、CWLパラメータリファレンスエラーが起" +"こりました。どのようしたらよいでしょうか？" #: ../../src/faq.md:375 e39b65947b294b20a444f18d780246f4 -#, fuzzy msgid "If `cwltool --validate` returns valid" -msgstr "`cwltool --validate` の結果が問題ない場合" +msgstr "`cwltool --validate` の結果に問題ない場合" #: ../../src/faq.md:384 dcd42c65681b438bb541fb38ddebb536 msgid "But executing it causes an error like:" @@ -451,14 +448,13 @@ msgid "The file is here" msgstr "ファイルはこちらです" #: ../../src/faq.md:410 f59751d2f0014e59af7879a748062cec -#, fuzzy msgid "Problem caused by `-` (hyphen character)." msgstr "`-` (ハイフン文字、引き算の記号)が原因で発生した問題です。" #: ../../src/faq.md:423 7780f461ca4c478b92fca893c0b0894a -#, fuzzy msgid "To fix this error, change `-` (hyphen) to `_` (underscore):" -msgstr "このエラーを修正するには、`-` (ハイフン) を`_` (アンダースコア) に変更してください" +msgstr "このエラーを修正するには、`-` (ハイフン) を`_` (アンダースコア) " +"に変更してください:" #: ../../src/faq.md:436 88df56dfff854fc68fb6ad3835a846e4 msgid "" @@ -2166,19 +2162,17 @@ msgstr "" "のいずれかを代わりに使用できるかどうかを検討してください。[ベストプラクティスのリスト](best-practices.md)を参照してください。" #: ../../src/topics/expressions.md:16 7d444aacd418466bbe588fa964b45179 -#, fuzzy msgid "`expression.cwl`" msgstr "`expression.cwl`" #: ../../src/topics/expressions.md:22 72a0558a83964796a8c1a0eb55fd78e8 -#, fuzzy msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" -msgstr "このツールは`inputs` を必要としないので、（ほとんど）空のジョブファイルで実行することができます：" +msgstr "このツールは`inputs` " +"を必要としないので、（ほとんど）空のジョブファイルで実行することができます：" #: ../../src/topics/expressions.md:25 d679fd1363b24c81979c68e7342159cf -#, fuzzy msgid "`empty.yml`" msgstr "`empty.yml`" @@ -2206,13 +2200,13 @@ msgid "" msgstr "なお、上の例のように、map構文で requirements を指定することも可能です：" #: ../../src/topics/expressions.md:54 052e24e2ad044cc28f04d7f39be871d6 -#, fuzzy msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -"または配列として、各エントリ（この場合、`class: InlineJavascriptRequirement` だけです）に`-` " +"または配列として、各エントリ（この場合、`class: InlineJavascriptRequirement` " +"だけです）に`-` " "を付けます。同じ構文で、追加のコマンドライン引数を定義します。" #: ../../src/topics/expressions.md:62 84b31c076d4b4826aae35e8c23fe6a25 @@ -2229,11 +2223,12 @@ msgstr "" "以下はその例です：" #: ../../src/topics/expressions.md:66 9bf5ca0e769147c6a9705bc40bd1febc -#, fuzzy msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -msgstr "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)から" +msgstr "" +"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool)から" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 7ab0dbd54c1441539673fa12ef96b89e @@ -2271,11 +2266,12 @@ msgid "`stderr`" msgstr "`stderr`" #: ../../src/topics/expressions.md:72 7a2d74aa018f4cab8c68e8775d83dd01 -#, fuzzy msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" -msgstr "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)から" +msgstr "" +"[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandInputParameter)から" #: ../../src/topics/expressions.md:73 ../../src/topics/expressions.md:78 #: ../../src/topics/expressions.md:85 ../../src/topics/expressions.md:93 @@ -2336,44 +2332,43 @@ msgstr "`outputEval`" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 9448462d104b4be5904623c85a9e16b7 #: bf11a7a72147445c9b8e44b541e09f36 -#, fuzzy msgid "From [`Workflow`](https://w3id.org/cwl/Workflow.html)" -msgstr "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)から" +msgstr "[`Workflow`](https://w3id.org/cwl/Workflow.html)から" #: ../../src/topics/expressions.md:84 0d54a777a33d4f17a2f3390384a3c0c5 -#, fuzzy msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" " and " "[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" と " -"[WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)から" +"[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) " +"と [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowOutputParameter)から" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 7918d0661be746faaddf25ad49172f30 #: b8439dbaa949427097e25ccb48fe15ee -#, fuzzy msgid "From `steps`" msgstr "`steps`から" #: ../../src/topics/expressions.md:88 7b37eb600c9b4847a58a7e5077bef4c3 -#, fuzzy msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -msgstr "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)から" +msgstr "" +"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)から" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 368ef005c2ca4b8599f76242f7178375 #: ab1ba7626eae483a8b614ee4cd5bab6f -#, fuzzy msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)から" +msgstr "" +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow." +"html#ExpressionTool)から" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 595b9ddcee734d6595c1b4b2d169dcb8 @@ -2393,11 +2388,12 @@ msgstr "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)から" #: ../../src/topics/expressions.md:95 32b1a39cca1a4402af9bdc0abc4d70c8 -#, fuzzy msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -msgstr "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)から" +msgstr "" +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement)から" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 2518d499801e4bcf82e9e4666280504d @@ -2460,7 +2456,6 @@ msgid "`listing`" msgstr "`listing`" #: ../../src/topics/expressions.md:106 7d8755f05d6541439f72ec9d6806d3fc -#, fuzzy msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "[Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)に" @@ -2479,16 +2474,16 @@ msgstr "`entryname`" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 #: 408f69a2df1343a78f93ff2ac0a994ea d37c78309e8b427f835af4fbd367e643 -#, fuzzy msgid "From `EnvVarRequirement`" msgstr "`EnvVarRequirement`から" #: ../../src/topics/expressions.md:110 53752bdff0974e39b2a86e8f2d96455f -#, fuzzy msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -msgstr "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)から" +msgstr "" +"[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef)から" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 @@ -2497,7 +2492,6 @@ msgid "`envValue`" msgstr "`envValue`" #: ../../src/topics/expressions.md:116 93d6c90b49d8424f9283c384062ce333 -#, fuzzy msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "`expressionLib` による外部ライブラリの利用とインラインJavaScriptコードの利用" @@ -2551,12 +2545,12 @@ msgid "`hello-world-expressionlib-inline.cwl`" msgstr "`hello-world-expressionlib-inline.cwl`" #: ../../src/topics/expressions.md:146 5b5e59fa1688499ea4560ee6f8023227 -#, fuzzy msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" -msgstr "このCWLワークフローを実行すると、JavaScript関数が起動し、`echo` コマンドが入力メッセージを大文字の頭文字で表示します：" +msgstr "このCWLワークフローを実行すると、JavaScript関数が起動し、`echo` " +"コマンドが入力メッセージの頭文字を大文字にして表示します：" #: ../../src/topics/expressions.md:149 a1e57c6833c848d3974cf448493ab924 #, fuzzy @@ -2736,14 +2730,13 @@ msgstr "" "と、そのパラメーターに有効な値の種類を示す`type` があります。" #: ../../src/topics/inputs.md:9 521cb5dead5d4e9ab5ff037fb4b683cb -#, fuzzy msgid "" "Available primitive types are *string*, *boolean*, *int*, *long*, " "*float*, *double*, and *null*; complex types are *array* and *record*; in" " addition there are special types *File*, *Directory* and *Any*." msgstr "" -"利用可能なプリミティブ型は*string*,*int*,*long*,*float*,*double*, *null*; 複合型は*array* " -"and*record*; さらに特殊型*File*,*Directory* ,*Any* があります。" +"利用可能なプリミティブ型は*string*,*int*,*long*,*float*,*double*, *null*; " +"複合型は*array*と*record*; さらに特殊型*File*,*Directory* ,*Any* があります。" #: ../../src/topics/inputs.md:13 fbdf2c1bed3e41d7a41ec6b14d134a98 msgid "" @@ -2768,23 +2761,22 @@ msgid "`inp-job.yml`" msgstr "`inp-job.yml`" #: ../../src/topics/inputs.md:33 9cc4a60d01f945aa9b4c43afcf20098b -#, fuzzy msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in an input object file:" msgstr "" -"`cwltool` " -"を使って、テンプレートとなる入力オブジェクトを作成することができます。これにより、入力オブジェクトファイルにすべての入力パラメータを入力する手間を省くことができます：" +"`cwltool` を使って、テンプレートとなる入力オブジェクトを作成することができま" +"す。これにより、入力オブジェクトファイルにすべての入力パラメータを入力する手" +"間を省くことができます：" #: ../../src/topics/inputs.md:40 5ac6da11d56446de97c251a37d997671 -#, fuzzy msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -"`cwltool --make-template inp.cwl > inp-job.yml` " -"のように、出力をファイルにリダイレクトし、デフォルト値を希望の入力値で修正することができます。" +"`cwltool --make-template inp.cwl > inp-job.yml` のように、出力をファイルにリ" +"ダイレクトします。その後デフォルト値を希望の入力値で修正することができます。" #: ../../src/topics/inputs.md:44 6a3edb0d259d4d7c900dd9811f978d4e msgid "" @@ -2812,13 +2804,15 @@ msgstr "" "を起動します。次のボックステキストは、これら2つのコマンドと、コマンドラインから期待される出力について説明しています：" #: ../../src/topics/inputs.md:64 5c78d7824ef34636ae2ed68d524d79e8 -#, fuzzy msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " "that the tools aren't accidentally accessing files that were not " "explicitly specified" -msgstr "CWLリファレンスランナー（cwltool）と他のランナーは、ツールが明示的に指定されていないファイルに誤ってアクセスしないように、入力ファイルへの（\"ソフト\"）シンボリックリンクを持つ一時ディレクトリを作成します。" +msgstr "" +"CWLリファレンスランナー（cwltool）と他のランナーは、ツールが明示的に指定され" +"ていないファイルに誤ってアクセスしないように、入力ファイルへの（\"ソフト\"" +"）シンボリックリンクを持つ一時ディレクトリを作成します" #: ../../src/topics/inputs.md:70 5bdf77c45346445d8f93353c1e73f768 #, fuzzy @@ -3510,35 +3504,31 @@ msgstr "" " から" #: ../../src/topics/parameter-references.md:74 ea0117748adc4324901024f21eed04ac -#, fuzzy msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" -" から" +"[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputParameter) から" #: ../../src/topics/parameter-references.md:77 3a30e73176cf4e4eb9f26770a176b9c9 -#, fuzzy msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" -" から" +"[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandOutputBinding) から" #: ../../src/topics/parameter-references.md:81 551c199c9a6344fca9bfacfb69fc4e53 -#, fuzzy msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" " and " "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" と " -"[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" -" から" +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) " +"と [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#WorkflowOutputParameter) から" #: ../../src/topics/parameter-references.md:85 7008a1ff1af54fda827637e787e5c7dd msgid "" @@ -3549,52 +3539,46 @@ msgstr "" " から" #: ../../src/topics/parameter-references.md:89 45743e1b261c4195856de0c2e30ea72e -#, fuzzy msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" " and " "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" -" と " -"[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" -" から" +"[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) " +"と [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#ExpressionToolOutputParameter) から" #: ../../src/topics/parameter-references.md:92 0ae32d1db5f9452bbfcbbc4719b0b9f1 -#, fuzzy msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" -"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" -" から" +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#ResourceRequirement) から" #: ../../src/topics/parameter-references.md:101 #: 7e1907ff15c74f488187531de336eccf -#, fuzzy msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" -"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" -" から" +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#InitialWorkDirRequirement) から" #: ../../src/topics/parameter-references.md:103 #: 678874668fed4f4d80a1b0990e183e2f -#, fuzzy msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "[Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent) の中に" #: ../../src/topics/parameter-references.md:107 #: e2882880886046ac88ae1c0d414366d1 -#, fuzzy msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" -"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" -" から" +"[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool." +"html#EnvironmentDef) から" #: ../../src/topics/requirements-and-hints.md:5 #: 05324169d8ae48d4a1abe3a0ac07c891 @@ -3626,7 +3610,6 @@ msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 #: 6f722d6fd54f485fa964076c8d08938b -#, fuzzy msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." @@ -3931,47 +3914,43 @@ msgid "Workflows" msgstr "ワークフロー" #: ../../src/topics/workflows.md:3 325a656f9b8e4c1fa6f699cd8c447d00 -#, fuzzy msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -"Workflowは、CommandLineTool、ExpressionTool、またはWorkflow（サブワークフロー）をステップ " -"として実行する CWL 処理ユニットです。CWLドキュメントには`inputs` 、`outputs` 、`steps` " -"を定義する必要があります。" +"Workflowは、CommandLineTool、ExpressionTool、またはWorkflow（サブワークフロー" +"）をステップ として実行する CWL 処理単位です。CWL定義には`inputs` 、`outputs`" +" 、`steps` を定義する必要があります。" #: ../../src/topics/workflows.md:13 b92275181c9e480da64e660b7aca0745 -#, fuzzy msgid "CWL workflow." -msgstr "CWLのワークフローです。" +msgstr "CWLワークフローです。" #: ../../src/topics/workflows.md:41 be2540315f854b8e9a1d257bcabd78db -#, fuzzy msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -"CWL定義`echo-uppercase.cwl` " -"は、コマンドラインツール、および先の例で示したExpressionToolを実行するワークフローを定義しています。" +"CWL定義`echo-uppercase.cwl` は、CommandLineTool、および先の例で示したExpressi" +"onToolを実行するワークフローを定義しています。" #: ../../src/topics/workflows.md:51 3be900594bb743399854b95baa9ae2f9 msgid "`echo-uppercase.cwl`" msgstr "`echo-uppercase.cwl`" #: ../../src/topics/workflows.md:81 5133c4e062bc4e479ce1dc8abbb08107 -#, fuzzy msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -"コマンドラインツールやExpressionToolは、ワークフローと同じCWLドキュメントに直接記述することも可能です。例えば、`echo-" -"uppercase.cwl` ワークフローを1つのファイルとして書き換えることができます：" +"CommandLineToolやExpressionToolは、Workflowと同じCWL定義に直接記述することも" +"可能です。例えば、`echo-uppercase.cwl` " +"ワークフローを1つのファイルとして書き換えることができます：" #: ../../src/topics/workflows.md:91 83bc2796889f4dccb713764ac1b3c3ad -#, fuzzy msgid "`echo-uppercase-single-file.cwl`" msgstr "`echo-uppercase-single-file.cwl`" @@ -4370,22 +4349,23 @@ msgid "" msgstr "`requirements` セクションの`ScatterFeatureRequirement` などを含めて、ここはどうなっているのでしょうか？" #: ../../src/topics/workflows.md:429 ccbbba3189404241a44736c970249b84 -#, fuzzy msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." -msgstr "まず、ここでのメインワークフローの入力には、文字列の配列が必要であることに注目してください。" +msgstr "まず、ここでのメインワークフローの入力には、文字列の配列が必要であることに注" +"目してください。" #: ../../src/topics/workflows.md:441 31eff13bb8334fc7b6d48ef6c5b1ce33 -#, fuzzy msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" " particular step. Note that the input name listed after scatter is the " "one of the step's input, not a workflow level input." msgstr "" -"ここでは、ステップ`echo` に、`scatter` " -"という新しいフィールドを追加しました。このフィールドは、CWLランナーに、この特定のステップのためにこの入力を分散したいことを伝えます。scatterの後に記載されている入力名は、ワークフローレベルの入力名ではなく、ステップの入力名であることに注意してください。" +"ここでは、ステップ`echo` に、`scatter` という新しいフィールドを追加しました。" +"このフィールドは、CWLランナーに、このステップの入力を分散して実行したいことを" +"伝えます。scatterの後に記載されている入力名は、ワークフローレベルの入力名では" +"なく、ステップの入力名であることに注意してください。" #: ../../src/topics/workflows.md:445 0d5cf8b82dbd47f2abd1ed16b9b3eb61 #, fuzzy @@ -4407,15 +4387,15 @@ msgid "`scatter-job.yml`" msgstr "`scatter-job.yml`" #: ../../src/topics/workflows.md:458 f9fa7046c89c417db51dc7c8a026fd5d -#, fuzzy msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" "注意点として、[`hello_world.cwl`](../introduction/quick-start.md) " -"は単にメッセージに対して`echo` というコマンドを呼び出します。コマンドラインで `cwltool scatter-workflow.cwl " -"scatter-job.yml` を呼び出すとします：" +"は単にメッセージに対して`echo` というコマンドを呼び出します。" +"コマンドラインで `cwltool scatter-workflow.cwl scatter-job.yml` " +"を呼び出します：" #: ../../src/topics/workflows.md:466 b6a33410ee9a45d7bf7b2ba56f786f8f msgid "" @@ -4433,7 +4413,6 @@ msgid "" msgstr "上記のような簡単なエコーを実行します、`outputs: []`の代わりに次の行を追加して`stdout` をキャプチャしてみましょう" #: ../../src/topics/workflows.md:472 97bf58937d3f4e98af702e3c1a418992 -#, fuzzy msgid "`hello_world_to_stdout.cwl`" msgstr "`hello_world_to_stdout.cwl`" @@ -4444,7 +4423,6 @@ msgid "" msgstr "そして、`wc` を使って各ファイルの文字数をカウントする第2ステップを追加します。以下のツールを見てください：" #: ../../src/topics/workflows.md:483 4afccfe982ff4be2be96cbe5889e5014 -#, fuzzy msgid "`wc-tool.cwl`" msgstr "`wc-tool.cwl`" diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 764b1903..76861f20 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-03-27 02:01+0000\n" +"PO-Revision-Date: 2024-04-11 09:01+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified) \n" @@ -3916,8 +3916,12 @@ msgid "" " diagrammed on the right. In purple we see the fixed string " "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" +"这个由两个步骤构成的工作流，起始于 `create-tar` 步骤，进而接入橙色的 " +"`compile` 步骤；如右侧图所示，`compile` 是另一个工作流。" +"由紫色的部分可见字符串常量 `\"Hello.java\"` 赋值给 `name_of_file_to_extract`." #: ../../src/topics/workflows.md:314 8654f2d86b644609aaa5b9b73db30bda +#, fuzzy msgid "" "" msgstr "" +"\"Visualization \"Visualization" #: ../../src/topics/workflows.md:322 7ce847ab54224452b6425de2a55ec893 msgid "" @@ -3938,6 +3952,11 @@ msgid "" "`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " "mapped to become the step's input/outputs." msgstr "" +"CWL `Workflow`（工作流）就和 " +"`CommandLineTool`（命令行工具）一样，可以充当一个步骤。通过 `run` " +"字段可以将其 CWL 文件包含进来。然后，工作流的输入 (`tarball` 和 " +"`name_of_file_to_extract`) 与输出 (`compiled_class`) " +"就可以映射为这一步骤的输入/输出。" #: ../../src/topics/workflows.md:336 d621821d2c1b403cb7415b381dd883f6 msgid "" From 369e14b31cfbad206080d451e3ae452fefcebb1a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 25 Apr 2024 12:19:04 +0200 Subject: [PATCH 149/179] Update sphinx-autobuild requirement from ==2024.2.* to ==2024.4.* (#470) Updates the requirements on [sphinx-autobuild](https://github.com/sphinx-doc/sphinx-autobuild) to permit the latest version. - [Release notes](https://github.com/sphinx-doc/sphinx-autobuild/releases) - [Changelog](https://github.com/sphinx-doc/sphinx-autobuild/blob/main/NEWS.rst) - [Commits](https://github.com/sphinx-doc/sphinx-autobuild/compare/2024.02.04...2024.04.13) --- updated-dependencies: - dependency-name: sphinx-autobuild dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 4399b149..dc36a740 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -53,7 +53,7 @@ test = [ "cwltest==2.*", "cwltool==3.1.*", ] -watch = ["sphinx-autobuild==2024.2.*"] +watch = ["sphinx-autobuild==2024.4.*"] rtd = ["udocker"] all = ["cwl-user-guide[test,watch,rtd]"] From abb640cf7f9aa69c02fdd8e4b2114fa17e5fcb9a Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Thu, 2 May 2024 10:51:54 +0200 Subject: [PATCH 150/179] Translated using Weblate (Japanese) (#473) Currently translated at 87.1% (522 of 599 strings) Translated using Weblate (Japanese) Currently translated at 86.6% (519 of 599 strings) Translated using Weblate (Japanese) Currently translated at 86.3% (517 of 599 strings) Translated using Weblate (Japanese) Currently translated at 85.9% (515 of 599 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 78 ++++++++++++++-------------- 1 file changed, 38 insertions(+), 40 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index f4d773cf..aadae0eb 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-04-25 09:24+0000\n" +"PO-Revision-Date: 2024-05-02 08:07+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -18,7 +18,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.5.1-dev\n" +"X-Generator: Weblate 5.5.3-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -1764,14 +1764,14 @@ msgid "" msgstr "抽象化できる個々のコンポーネントを持つ複雑なワークフローは、ワークフローをモジュール化し、その一部を容易に再利用できるようにするために、[`SubworkflowFeatureRequirement`][subworkflow]を利用します。" #: ../../src/topics/best-practices.md:97 93f6d6b544c24ce780184272f66bacab -#, fuzzy msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -"ソフトウェアのコンテナは、[\"Recommendations for packaging and containerizing of " -"bioinformatics software\"][containers] に準拠するようにします（他の分野でも有用です）。" +"ソフトウェアのコンテナは、[\"Recommendations for packaging and " +"containerizing of bioinformatics software\"][containers] " +"に準拠するようにします（他の分野でも有用です）。" #: ../../src/topics/command-line-tool.md:1 a378a2f7d268401abfbbbe6e5090a952 msgid "Command Line Tool" @@ -1833,14 +1833,13 @@ msgstr "" "にネットワーク・アクセスの要件を含める必要があります。" #: ../../src/topics/command-line-tool.md:84 3282a357799f4a72a6b8bace206144c4 -#, fuzzy msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 or v1.2 " "will have `networkAccess: true` set automatically." msgstr "" "CWL v1.0のコマンドラインツールをv1.1またはv1." "2にアップグレードすると、自動的に`networkAccess: " -"true`が追加されネットワークアクセスを取得します。" +"true`が追加されネットワークアクセスできるようになります。" #: ../../src/topics/creating-files-at-runtime.md:1 #: 17c5b4ee43cc4a979676ad27e473d046 @@ -1859,11 +1858,12 @@ msgstr "コマンドラインパラメーターではなく、ファイルから #: ../../src/topics/creating-files-at-runtime.md:7 #: bf4aea0a22334a1ca75cc20e937e6581 -#, fuzzy msgid "" "To generate such files, we can use the " "[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)." -msgstr "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)から" +msgstr "" +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#InitialWorkDirRequirement)から" #: ../../src/topics/creating-files-at-runtime.md:9 #: 008f768d56b8465bb4e8f4fde15853a7 @@ -2553,7 +2553,6 @@ msgstr "このCWLワークフローを実行すると、JavaScript関数が起 "コマンドが入力メッセージの頭文字を大文字にして表示します：" #: ../../src/topics/expressions.md:149 a1e57c6833c848d3974cf448493ab924 -#, fuzzy msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "`hello-world-expressionlib-inline.cwl` 実行しています。" @@ -2940,11 +2939,11 @@ msgstr "`array-inputs-job.yml`" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:86 #: ../../src/topics/outputs.md:109 015a0f00c2b245e2b0e87735926da736 #: 390384208d7b4771888f164b587c7b9a edb3ae59c48945f29c3086b16a5265d3 -#, fuzzy msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" -msgstr "ここで、コマンドラインにツール定義と入力オブジェクトを指定し `cwltool` を起動します：" +msgstr "ここで、コマンドラインにツール定義と入力オブジェクトを指定し `cwltool` " +"を起動します：" #: ../../src/topics/inputs.md:178 13e59751d43b49f0ac366538a14f9c84 msgid "" @@ -3272,9 +3271,11 @@ msgid "" "output parameters returned by the CWL tool are either the output files " "themselves, or the result of examining the content of those files." msgstr "" -"CWLでツールを実行する場合、開始時の作業ディレクトリは指定された出力ディレクトリになります。 " -"基礎となるツールやスクリプトは、出力ディレクトリに作成されるファイルの形でその結果を記録しなければなりません。 " -"CWLツールによって返される出力パラメータは、出力ファイルそのものであるか、またはそれらのファイルの内容を調べることによって得られるものです。" +"CWLでツールを実行する場合、開始時の作業ディレクトリが出力ディレクトリになりま" +"す。 基礎となるツールやスクリプトは、出力ディレクトリに作成されるファイルの" +"形でその結果を記録しなければなりません。 CWLツールによって返される出力パラメ" +"ータは、出力ファイルそのものであるか、またはそれらのファイルの内容を調べるこ" +"とによって得られるものです。" #: ../../src/topics/outputs.md:16 9845e517f7d848e5b59a97880ca6999f msgid "" @@ -3346,14 +3347,13 @@ msgid "Capturing Standard Output" msgstr "標準出力をキャプチャする" #: ../../src/topics/outputs.md:71 a7c4fdaeda3e411fbeb802c5fa529ce9 -#, fuzzy msgid "" "To capture a tool's standard output stream, add the " "[`stdout`](https://w3id.org/cwl/CommandLineTool.html#stdout) field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -"ツールの標準出力をキャプチャするには、[`stdout`](https://w3id.org/cwl/" +"ツールの標準出力を保存するには、[`stdout`](https://w3id.org/cwl/" "CommandLineTool.html#stdout) " "フィールドに、標準出力を保存したいファイル名を追加します。 " "次に、対応する出力パラメータに`type: stdout` を追加します。" @@ -3381,7 +3381,6 @@ msgid "`array-outputs-job.yml`" msgstr "`array-outputs-job.yml`" #: ../../src/topics/outputs.md:116 9a14271c3180429988aaa14869f783a0 -#, fuzzy msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -3389,9 +3388,11 @@ msgid "" " to mark entries in arrays, as demonstrated in several of the upcoming " "sections." msgstr "" -"[YAML Guide](yaml-guide.md#arrays) で説明されているように、期待される出力の配列は`array-outputs-" -"job.yml` で指定され、それぞれのエントリーは先頭の`-` " -"でマークされています。このフォーマットは、CWL定義で配列のエントリーをマークするために使用することもでき、今後のいくつかのセクションでデモがあります。" +"[YAML Guide](yaml-guide.md#arrays) " +"で説明されているように、期待される出力の配列は`array-outputs-job.yml` " +"で指定され、配列のエントリーはそれぞれ先頭の`-` で示されています。この書き方" +"は、CWL定義で配列のエントリーを示すために使用することもでき、今後のいくつかの" +"セクションでデモがあります。" #: ../../src/topics/parameter-references.md:1 c8a6ea340e6a43398e97b68e03a8bb3b msgid "Parameter References" @@ -3442,15 +3443,14 @@ msgid "" msgstr "`$(...)` で囲まれたパラメータ参照を許可するフィールドもあります。これらは評価され、参照されている値に置き換えられます。" #: ../../src/topics/parameter-references.md:47 384fe8188f414eafbbb8d6b81bdfd779 -#, fuzzy msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -"パラメータリファレンスは、Javascriptの構文のサブセットを使用して記述します。 " -"この例では、`$(inputs.extractfile)` 、`$(inputs[\"extractfile\"])` " -"、`$(inputs['extractfile'])` は同等です。" +"パラメータリファレンスは、Javascriptの構文のサブセットを使用して記述します。" +" この例では、`$(inputs.extractfile)` 、`$(inputs[\"extractfile\"])` " +"、`$(inputs['extractfile'])` は同じです。" #: ../../src/topics/parameter-references.md:51 56ead1c8d45c43bdbcbc6f7cbb8e1e92 msgid "" @@ -3459,33 +3459,32 @@ msgid "" msgstr "変数 \"inputs \"の値は、CWLツールの起動時に提供された入力オブジェクトです。" #: ../../src/topics/parameter-references.md:54 56bca89e314c4223b33d7fe63c9b771d -#, fuzzy msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " "reference the path to the tar file in the above example you would write " "`$(inputs.tarfile.path)`." msgstr "" -"`File` " -"パラメータはオブジェクトであるため、入力ファイルのパスを取得するには、ファイルオブジェクトのpathフィールドを参照する必要があります。上記の例でtarファイルのパスを参照するには、`$(inputs.tarfile.path)`となります。" +"`File` パラメータはオブジェクトであるため、入力ファイルのパスを取得するには、" +"ファイルオブジェクトのpathフィールドを参照する必要があります。上記の例でtarフ" +"ァイルのパスを参照するには、`$(inputs.tarfile.path)`となります。" #: ../../src/topics/parameter-references.md:59 1c1ab240c4114572bb4e42955baad361 msgid "Where are parameter references allowed?" msgstr "パラメータ参照はどこで許されるのですか？" #: ../../src/topics/parameter-references.md:61 055d3268859c46c4b7db5005608bae05 -#, fuzzy msgid "You can only use parameter references in certain fields. These are:" -msgstr "パラメータ参照は、特定のフィールドにのみ使用することができます。 以下はその例です：" +msgstr "パラメータ参照は、特定のフィールドでのみ使用することができます。 " +"以下はその例です：" #: ../../src/topics/parameter-references.md:63 2ed66835bd9044adbfdd0b5097787f22 -#, fuzzy msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" -" から" +"[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool." +"html#CommandLineTool) から" #: ../../src/topics/parameter-references.md:69 f592619e4b2c497e80cd75da0548cf07 msgid "" @@ -3651,7 +3650,6 @@ msgid "Staging Input Files" msgstr "入力ファイルのステージング" #: ../../src/topics/staging-input-files.md:3 ac2ef1fced5f4044861761a11c35e78a -#, fuzzy msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -3727,13 +3725,13 @@ msgid "`troubleshooting-wf1.cwl`" msgstr "`troubleshooting-wf1.cwl`" #: ../../src/topics/troubleshooting.md:27 b777877c88024c9fb06a6614029ef8d6 -#, fuzzy msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -"`--cachedir` に `/tmp/cachedir/` を指定して、このワークフローを実行してみましょう（`cwltool` " +"`--cachedir` に `/tmp/cachedir/` " +"を指定して、このワークフローを実行してみましょう（`cwltool` " "は、ディレクトリがまだ存在しない場合、新規作成します）：" #: ../../src/topics/troubleshooting.md:35 8654b7f2f4464d13be4b47729e1f07e5 @@ -4434,7 +4432,6 @@ msgid "" msgstr "さて、スキャッターはどのように取り入れるのでしょうか？スキャッターフィールドは各ステップの下にあることを思い出してください：" #: ../../src/topics/workflows.md:491 a7f96ec6e4f24c62ac0f5b6edcc9734b -#, fuzzy msgid "`scatter-two-steps.cwl`" msgstr "`scatter-two-steps.cwl`" @@ -4524,8 +4521,10 @@ msgid "" "`in1` from the workflow contains a value `< 1` this step will be " "executed." msgstr "" -"ワークフローの最初のステップ（step1）には2つの入力プロパティがあり、条件を満たしたときにfoo.cwlを実行します。新しいプロパティ`when`" -" は、条件の検証が行われる場所です。この場合、ワークフローから`in1` に値`< 1` が含まれるときのみ、このステップが実行されます。" +"ワークフローの最初のステップ（step1）には2つの入力プロパティがあり、条件を満" +"たしたときにfoo.cwlを実行します。新しいプロパティ`when` " +"は、条件の検証が行われる場所です。この場合、ワークフローから`in1` に値`< 1` " +"が含まれるときのみ、このステップが実行されます。" #: ../../src/topics/workflows.md:587 b33ecd2b8af042feb08687e32d4b6bbf msgid "" @@ -4707,7 +4706,6 @@ msgstr "" "オブジェクトを図式化したものを示します。" #: ../../src/topics/yaml-guide.md:127 965405e2a45a4cbb8f227bc8ceeb05df -#, fuzzy msgid "Arrays" msgstr "配列" From d209c449f929291f8e1e263d122654bdf8abc8b1 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Wed, 8 May 2024 14:30:08 +0200 Subject: [PATCH 151/179] Translated using Weblate (Japanese) (#474) Currently translated at 89.3% (535 of 599 strings) Translated using Weblate (Japanese) Currently translated at 88.9% (533 of 599 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Manabu ISHII --- locales/ja/LC_MESSAGES/user_guide.po | 59 ++++++++++++---------------- 1 file changed, 25 insertions(+), 34 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index aadae0eb..1279724d 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-05-02 08:07+0000\n" +"PO-Revision-Date: 2024-05-08 01:07+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -18,7 +18,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.5.3-dev\n" +"X-Generator: Weblate 5.5.4-rc\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -155,7 +155,7 @@ msgstr "よくある質問" #: ../../src/faq.md:11 370a9659c7904ef6b5e1ae7480f82ef6 msgid "How do I create non \"`File`\" types using `evalFrom`?" -msgstr "\"`File`\" 型をつかわず `evalFrom`を使う方法" +msgstr "\"`File`\" 型をつかわず `evalFrom`を使うにはどうしたらよいですか?" #: ../../src/faq.md:41 8333f51e3f5945fe8963adfc6685bcb1 msgid "How do I rename an input file?" @@ -246,9 +246,9 @@ msgid "" msgstr "2つ目の方法は、`type: File` をスクリプト自体に含める方法です：" #: ../../src/faq.md:138 ba246320fdd94a1aab4736f83718d793 -#, fuzzy msgid "How can I set `self`-based input bindings for optional inputs?" -msgstr "オプショナル入力のために `self`-形式のInput Bindings を設定します" +msgstr "オプショナル入力のために `self`-形式のInput Bindings " +"をどのように設定しますか?" #: ../../src/faq.md:140 6169b7be9af7448abcb57eaf91e1cc91 msgid "" @@ -271,23 +271,22 @@ msgid "" msgstr "以下は、Booleanパラメータの値によって、コマンドラインに追加する文字列を変える例を示しています。" #: ../../src/faq.md:188 5c9980839f404ba6aef92ef23034500f -#, fuzzy msgid "" "How do I connect a solo value to an input that expects an array of that " "type?" -msgstr "ある型の配列を期待する入力に１つの値を与える" +msgstr "ある型の配列を期待する入力に１つの値を与えるにはどうしたらよいでしょうか?" #: ../../src/faq.md:190 2525baf16c1f4725b096f33fd99009cf -#, fuzzy msgid "" "Add a " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" " along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput):" msgstr "" -"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" -" と [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)を一緒に使います" +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow." +"html#MultipleInputFeatureRequirement) と [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput)を一緒に使います:" #: ../../src/faq.md:194 a00d5d96b15048a79ae099d22d63bb42 msgid "merge_nested" @@ -302,9 +301,8 @@ msgid "" msgstr "入力は、各入力リンクに対して正確に1つのエントリで構成される配列でなければなりません。\"merge_nested\"が1つのリンクで指定された場合、リンクからの値は1つのアイテムリストでラップされなければなりません。" #: ../../src/faq.md:199 3af16c07e3f148ddb8849c94a3864158 -#, fuzzy msgid "Which means \"create a list with exactly these sources as elements\"." -msgstr "つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです" +msgstr "つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです。" #: ../../src/faq.md:201 0ea3de393d2f42aeb82658c85a19ec45 #, fuzzy @@ -371,9 +369,8 @@ msgstr "" "のいずれかのコマンドラインフラグについては、特別なレコードタイプを定義することができます。また、ここにnullを指定することで、オプションの入力を作成することができます。" #: ../../src/faq.md:322 6fd3c469d11d4d52b9fbb7a3d443a8db -#, fuzzy msgid "How do I set mutually exclusive parameters?" -msgstr "相互に排他的なパラメータを設定する" +msgstr "相互に排他的なパラメータを設定するにはどうしたらよいでしょうか?" #: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f #, fuzzy @@ -1087,7 +1084,7 @@ msgid "" msgstr "" "CWLコミュニティは、`cwlref-runner` " "という名前のPythonパッケージを公開しており、`cwltool` のエイリアスを`cwl-" -"runner` という名前でインストールします" +"runner` という名前でインストールします。" #: ../../src/introduction/prerequisites.md:91 cc1a9b95508e44a1bf08ae75d990c301 msgid "Installing `cwl-runner` alias for cwltool with `pip`." @@ -1863,7 +1860,7 @@ msgid "" "[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)." msgstr "" "[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool." -"html#InitialWorkDirRequirement)から" +"html#InitialWorkDirRequirement)を使ってそのうようなファイルを生成します。" #: ../../src/topics/creating-files-at-runtime.md:9 #: 008f768d56b8465bb4e8f4fde15853a7 @@ -3747,7 +3744,6 @@ msgstr "" "にキャッシュされました。作成された中間ファイルを確認することができます：" #: ../../src/topics/troubleshooting.md:44 04e80f7ce14d4d73bc5d290dcf01bcdb -#, fuzzy msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -3953,7 +3949,6 @@ msgid "`echo-uppercase-single-file.cwl`" msgstr "`echo-uppercase-single-file.cwl`" #: ../../src/topics/workflows.md:150 5a9a1dd6ed1f4ca6803f1d235c4fd392 -#, fuzzy msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3961,20 +3956,19 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" "ファイルを分けることは、モジュール化やコードの整理に役立ちます。しかし、開発" -"のためにすべてを1つのファイルに書いておくと便利なことがあります。複数のファイ" -"ルを1つのファイルにまとめる方法は他にもあります（例：`cwltool --pack` " +"のためにすべてを1つのファイルに書いておくと便利なことがあります。他にも複数の" +"ファイルを1つのファイルにまとめる方法があり（例：`cwltool --pack` " "）このユーザーガイドの他のセクションで詳しく説明します。" #: ../../src/topics/workflows.md:160 277ed30d4b3a4156a4523e8d10e6ce60 -#, fuzzy msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -"サブワークフローでは、Requirement、`SubworkflowFeatureRequirement` を有効にす" -"る必要があります。このユーザーガイドの別のセクションで、より詳しく説明してい" -"ます。" +"サブワークフロー使うにはRequirementの１つである、`SubworkflowFeatureRequireme" +"nt` を有効にする必要があります。このユーザーガイドの別のセクションで、より詳" +"しく説明しています。" #: ../../src/topics/workflows.md:165 82818ab17aa4403eb982fd81a14a5865 msgid "Writing Workflows" @@ -3987,7 +3981,6 @@ msgid "" msgstr "このワークフローでは、tarファイルからJavaのソースファイルを取り出し、コンパイルします。" #: ../../src/topics/workflows.md:170 c61097c695424f7195e8205a23b6ecff -#, fuzzy msgid "`1st-workflow.cwl`" msgstr "`1st-workflow.cwl`" @@ -4122,11 +4115,11 @@ msgstr "" "のパラメータに使用されることになり ます。" #: ../../src/topics/workflows.md:267 04a4db2f3da94ce29e7999039ee13fde -#, fuzzy msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." -msgstr "ワークフローステップの`out` セクションには、ツールから期待される出力パラメータが記載されています。" +msgstr "ワークフローステップの`out` " +"セクションには、ツールから期待される出力パラメータが記載されています。" #: ../../src/topics/workflows.md:278 2651ee113a3d4b79b138854ebe729f48 #, fuzzy @@ -4205,19 +4198,18 @@ msgstr "" "workflow.cwl\" alt=\"Visualization of 1st-workflow.cwl\" />" #: ../../src/topics/workflows.md:322 7ce847ab54224452b6425de2a55ec893 -#, fuzzy msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " "`name_of_file_to_extract`) and outputs (`compiled_class`) then can be " "mapped to become the step's input/outputs." msgstr "" -"CWL`Workflow` は、`CommandLineTool` を`step` として使用することができ、その CWL ファイルは`run` " -"に記述されます。ワークフローの入力（`tarball` および`name_of_file_to_extract` " -"）と出力（`compiled_class` ）は、ステップの入力/出力になるようにマッピングすることができます。" +"CWL`Workflow` は、`CommandLineTool` を`step` として使用することができ、その " +"CWL ファイルは`run` に記述されます。ワークフローの入力（`tarball` " +"および`name_of_file_to_extract` ）と出力（`compiled_class` " +"）は、ステップの入力/出力になるようにマッピングすることができます。" #: ../../src/topics/workflows.md:336 d621821d2c1b403cb7415b381dd883f6 -#, fuzzy msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -4231,7 +4223,6 @@ msgstr "" "テップで再利用できることを意味するため、一般的にベストプラクティスです。" #: ../../src/topics/workflows.md:341 358c612f175241f7bf148a04d75e00c9 -#, fuzzy msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" From 3f1333f68cd4d472de89df42af8b37ceb20c622b Mon Sep 17 00:00:00 2001 From: Manabu ISHII Date: Fri, 17 May 2024 19:01:58 +0900 Subject: [PATCH 152/179] Fix term (#476) --- src/introduction/basic-concepts.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/introduction/basic-concepts.md b/src/introduction/basic-concepts.md index fd075220..c6013a29 100644 --- a/src/introduction/basic-concepts.md +++ b/src/introduction/basic-concepts.md @@ -138,7 +138,7 @@ The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance: -- [`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement) - enables JavaScript in expressions. +- [`InlineJavascriptRequirement`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement) - enables JavaScript in expressions. - [`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow.html#SubworkflowFeatureRequirement) - enables nested workflows. - [`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow.html#InitialWorkDirRequirement) - controls staging files in the input directory. From 86a2911476c34dd84b84296ce9035ac638ef5ab0 Mon Sep 17 00:00:00 2001 From: Manabu ISHII Date: Sat, 18 May 2024 02:24:34 +0900 Subject: [PATCH 153/179] Add space to syntax highlight correctly (#479) --- src/faq.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/faq.md b/src/faq.md index 70704806..7f57e574 100644 --- a/src/faq.md +++ b/src/faq.md @@ -344,7 +344,7 @@ steps: These can be set by using the default field ```yaml input: - default:true + default: true ``` ## What should I do when concatenating strings in inputs? From 40063bfb97273ebda3f3ca7172584eca0925c65a Mon Sep 17 00:00:00 2001 From: Michael Crusoe Date: Fri, 17 May 2024 19:16:56 +0200 Subject: [PATCH 154/179] Added translation using Weblate (Catalan) Co-authored-by: Michael Crusoe --- locales/ca/LC_MESSAGES/user_guide.po | 3122 ++++++++++++++++++++++++++ 1 file changed, 3122 insertions(+) create mode 100644 locales/ca/LC_MESSAGES/user_guide.po diff --git a/locales/ca/LC_MESSAGES/user_guide.po b/locales/ca/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..a5097d09 --- /dev/null +++ b/locales/ca/LC_MESSAGES/user_guide.po @@ -0,0 +1,3122 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: ca\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 4dee8504a8e5496081dadc386ab45540 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 674c238b25e240eda05e22e399f2f78f +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: b651f80f47b4442fbf29454a233697fc +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: ecf2b9c0b1664afe9c4e180610610021 +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: e24cb13d98014e558b6a6946758359e0 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: 928e3df7ca3e479ca6474a8e72cf36eb +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: d355f035676446c88b028f327aeb4829 +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 339b852df24242189d6efcd2898a3396 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: 3ef57e6862f240bebcf193a52397af0a +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: fae385da16aa443da996fa23ac03d6ae +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: 92430be71ecc40e18bbbb80d5576c613 +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 387d83db81024f65aa9a890c2d07874a +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: d8e2280a75a74916a1630afaa2fe2ae3 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: f1c1340f9745458980e0fbd641738687 +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 5424e5472c3d466fa2a3d2022c6cb475 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: 12f57b2ba76b492abe1816e06bfb1417 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: e1f657a46ce94a0d83671540e2cc2dab +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a5eacdbc9aa142c890b177869da4143d +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: e3bdaceae8784ab0807b2cf356a98580 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: ed521ac365db4a6ba5a1051fbaa2932e +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 67573252cc064b27ab13eebc468ac58a +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 73e68b3af9cf41338d843c0c40e50cdc +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: a999b1acda2641598086648c64aa3831 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: f8c12a58cb0b46a488823c6ae95f25ea +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: f25a63e0926d4932bbe64b2e4bdabf9e +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: d718630a296545f3a989c8c71e9ddc77 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 9a97acd430064710bcdf76edbd9f711c +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: 48deb71f361a43e48a56ed483075bca8 +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 716b56506ca7470299899c5d820a9ea2 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: e3ecac0a8e604f2b98a2a12b0579990a +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 007a345b4bad49cf996c4301b8386473 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: efb5fd14988c4e2a8f834ee5369d4102 +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: 276f688ba7cc471a842f085ca852b1d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 8b70a1ad70514039b97164fa630c12e4 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 2f28ab412d2843ffa5f14acdc01fc732 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: cbec9277b5004e50af2728cbda0df740 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: e259f55f8000479bbd8009e25cf0ca6c +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 8210b36347a749889450529ecdf4ff0e +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 23088850ad02459696f6bbd385109aac +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: f02257a822ad46ac93c5981531cc85d5 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: d289541e460147aa933f7878996f8649 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: f495da32f05a4a5ba9539be0a54c1a59 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: bdb4c68a175047ddbe141ca24960127f +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 97b61352363f47cb890e8937c5613fa3 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: 0bc424ef2ca346099f29b937379908a0 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 29b73e1dd72744f68377f0a38c10f062 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 38a2afaf4a6c4d04909af22c93f2808d +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: cd74f34b21af4de9be96fd897efc469b +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: f12e371f3f1a4b0cb2cff9800352d48c +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 8f0e8f050e334ac08334e9215e1dcf61 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 7a6be0005a6441feb67f036d005d7885 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 06635145b441418aaae84dc804f3d6ac +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 04eaf1f7c630450db318dcd8b7626e15 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: fd4579a3c9844492b314b5c3c1775fc7 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: e024bcb70e04412e90e1838426d1b69a +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: a3db21c0b3114802a8a5b610e252ef13 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 0f5bc8520d6a4dafa37c65343da9702a +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 5cb830da47464a8b9c3950983fa4d56f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: a2ce43b391864e8bbde16328cc19b32b +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 56ee4dcfff6141d5bef80eb96559876d +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 96671c56523c4ea9992fb5dfcfa6490e +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: bcc6246742cb46bfb185e415c4a3431a +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 86dce36de687449c88fb5eb9d64eb045 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 7dc630ea86464b1dba3a4e5079260b3b +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: 651e032007ea4a119d20c820bb61f86b +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 0b056dde9e87428996e47870b12119da +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 628124a1670b4b058bb0fb6e495a099c +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: ec2adb3912bc46e28891229e9e0d9a1c +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: a519be60726a44af9941fdce04735353 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: cb8fc8c4c79e467eac5fab4ca685201e +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: a26cc105716f47cb807174c9003153b0 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: cc159dd5fe5748caac838862f5b8c4d1 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 6812698e9ad84d3385de5e88e9dde0b3 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: d1f02be278754267893dfce5a940997d +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: 75d59e395c66416cae9b352db5081516 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 874c6f19abbf45d7ab7d30a378c4048d +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: dea0d4b681f94e73b13965dcfe75cf7d +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: 750474486a84482292eeba45f118287f +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 1eb0e39bb6d04b8cab300f44a79f3add +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 4b2ab812f62c4f949dd25c8527f2411c +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 2c3b884cb1c54521900cc90782e8a58d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: a1073b6306044dffb414319ae01f68bb +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: 9a1d92334685449386dfa3b3a899ed48 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: fb623af4c480411b8fde28d01c981411 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: e98e165f6bba40809c90473d72f9d592 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 5565c1b2d8a349169a305a9b26b4574d +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: 88160cef4cfa4add9020aa89511a5749 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 730ba1434a1445ae847ec6153b6a3b72 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: a25d0b1e13324b40a6b8fcd227948c4f +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: d661df070e3040869da412d07a71f716 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: a11585474d3849cca5467512ed964743 +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 2682f9ca8e604a0c9986f7746fdec960 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 22447a560f6f4317bf67bd7c4336126c +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 52703d6b7f914097934bfad13663abeb +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 5e1c79df657d4a6e84e055dd6b300a5d +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 329d2809dfae4f90bc638f5f03a47ee3 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 9647019d8c37466886e7aab6f176634d +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: cc067051f22f433bbece08f60933e002 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: dbfe2c1123144316aa026374b0f353d3 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: 074cf5d912854d8c864607cc24b15302 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: b54240bb94f746bba7511633aa969db0 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 8b70a072aa87414c88e89a3e19af0a51 +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: eea20f89c45f424a888178df53713b28 +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7647e0229a924f988cf02b7812a55c06 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 9d663249666045618a0d3acddb85a9a9 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: dbf6153cd02542a6a01c172803122b7f +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: b6250cf6fa8a4a0c94b33302e0decca5 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: fa6ca3bbc6784380a03a950a6f49a180 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: b92b516e537a4773ad67b4af586e7a25 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: 467a701228504d06b971b79a59c69064 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: 2634f989eb304009a8568d70ed42786c +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: fbe0c65b444441f785d0054176d036a6 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 9a710602e00c4934ae3a3b471aa68458 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: 21b5be7270a14f0987240c81d1ec879b +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: cfe9d8241fe84bd5b74042a5625d933f +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 764d933cc4da446abd8dd8f913f05dac +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: c93efc6d4e004859981ee7f5fa28ed03 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: 546601da44cb49bd9611b1c85807fd90 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: e07f33d01b804663a25ffb08aad74821 +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: 7a644506619a4f08958ec7d4540cd557 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: b5195b7d8eaa419fb2b90cb33a57783a +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: 2713594c937d4c528fc8d04d9e9819ed +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: cf94c1424fc2413c85647fd1ee73d951 +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: dc0452107c604e29bdf32bb289fe5db8 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 483181f498fc4d968b5fe6ef427709f7 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 7487485d6aa4458089a4b4bdf107ea64 +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 93188ed43ee949cc98b3ea679ce14feb +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 24aca0bea4d94e3593b844cf0586cffe +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 9c56528acd5f49deb139e034dfbfac7c +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: a2dd833fdca4443181648e41051a5232 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: 7e40cc9f9e1341c195e843c009575b94 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: def35d6021394def80a53ae49a2cdbde +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: c84d4450bc6a475dbf34e0b22cea9130 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: cca9665f6daa44b49233baf34ab9fcc7 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: 547edbf5fa424b8286cc21674ff159b0 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 7ca248888b9d484cb544cd76ba538662 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: ae6b240718104380b08db5552d7355ea +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: e5a8b7f84be64020b191099f3fad30ed +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 12a06d8358534102b202965d4258c18e +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: b7f93705e5b8416696be01850072e8c0 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: e87045829b344089ab59dc27063ddd7a +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: 42ef2f145b824d69b63abc1da175c216 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: c61cedf543664d388183e04b3939cc39 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: 9e39e3f1501c4fcaab3e8962e090f6be +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: 03e2f767c4da461982fc3c0f3ba94762 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 3bea5822b8694e2aa32c446e1c54a045 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: 0d498cd4caf54c15891ca1afe58e2727 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: b2d75045e02741b4850f5ff1243f7858 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: 5fa79c62049a447c8328ebf9db54ebf4 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: d947c54933d64aad90df392a1cedd63f +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 651d35997332404186aa6d5711da4a3d +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: b662c1a5a4424c8d8350a806356acc61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 04d6babfd87343d7a5f13867ea02b65f +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 2eaacf1a90204a2b9bd621344560f2a1 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: e3a7182f00f440b8b5461da91194a64b +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: b5338f39e8c74ff28e139da68089a742 +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: f6d92156d67c4a339bcfd194cff897df +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: d80ab383eec9402faba997b548fe42eb +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: 49217c02f58c43ff9ec00f10da8d4e84 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 8dbd56473f8c40c0bb12a48be06117e3 +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 78d7f3ede2c746d482042adef050b2c4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: cbbf93c70fe04ba7932ba25758ddc611 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: cfa1c1fde4454df283f87cc54a9c59ec +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 1a8be2950cbb475bbb2617e005f0fac9 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: 5d83c56102e141cc978500f678dd0c1c +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: cda73485875d4c8e9464679a20558616 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 98cae24919b74c088a5d89706aec581b +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: b4b0940b4b5743c09637b36b964202d0 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 9ca3554d771d45998e88aaede525b227 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 3fca839cede94cfd8e4f605c73ba699d +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: 3ded0f125249485c921994b6e6b93ac9 +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 53ece35d309a4c8d99f1efb2122a7092 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 87bafb845c714b109874f6137b84462d +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: fcd05b1ef31a4046946a2399c7fc5575 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: 859368c1f25c4a4aad57abfd046c63f5 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" From 1e2a1014b7b3b74e534d9b0c7567237552f5b24a Mon Sep 17 00:00:00 2001 From: Manabu ISHII Date: Fri, 17 May 2024 19:16:57 +0200 Subject: [PATCH 155/179] Translated using Weblate (Japanese) Currently translated at 100.0% (599 of 599 strings) Translated using Weblate (Japanese) Currently translated at 100.0% (599 of 599 strings) Translated using Weblate (Japanese) Currently translated at 96.6% (579 of 599 strings) Translated using Weblate (Japanese) Currently translated at 92.3% (553 of 599 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide --- locales/ja/LC_MESSAGES/user_guide.po | 619 +++++++++++++++------------ 1 file changed, 335 insertions(+), 284 deletions(-) diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 1279724d..ef910682 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-05-08 01:07+0000\n" +"PO-Revision-Date: 2024-05-17 17:16+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -18,7 +18,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.5.4-rc\n" +"X-Generator: Weblate 5.6-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -45,15 +45,19 @@ msgstr "" #: ../../LICENSE.md:12 754f3f54aa4142ef9dac27f508dd0bca msgid "You are free:" -msgstr "" +msgstr "あなたは以下の条件に従う限り、自由に：" #: ../../LICENSE.md:14 d2b1d5e965ef4e71b64c359549919975 msgid "to **Share**---copy and redistribute the material in any medium or format" -msgstr "" +msgstr "**共有** --- " +"どのようなメディアやフォーマットでも資料を複製したり、再配布できます。 " +"営利目的も含め、どのような目的でも。" #: ../../LICENSE.md:15 fe9551ffef8149bf8da50e70318e8de8 msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" +msgstr "**翻案** --- " +"マテリアルをリミックスしたり、改変したり、別の作品のベースにしたりできます。 " +"営利目的も含め、どのような目的でも" #: ../../LICENSE.md:17 247db3bcc7024c44a044886a29ef1414 msgid "for any purpose, even commercially." @@ -63,7 +67,8 @@ msgstr "営利目的であっても、いかなる目的であっても。" msgid "" "The licensor cannot revoke these freedoms as long as you follow the " "license terms:" -msgstr "" +msgstr "あなたがライセンスの条件に従っている限り、許諾者がこれらの自由を取り消すこと" +"はできません。" #: ../../LICENSE.md:24 551cb5ab59dd4737b1042a4ef79ffab7 msgid "" @@ -75,6 +80,13 @@ msgid "" "reasonable manner, but not in any way that suggests the licensor endorses" " you or your use." msgstr "" +"**表示** --- あなたは 適切なクレジット を表示し(あなたの作品が「Copyright © " +"the Common Workflow Language project」の作品から派生していることを明記し、" +"可能であれば https://www.commonwl.org/ " +"へのリンクを提供してください)、[ライセンスへのリンク][cc-by-human]を提供し、 " +"変更があったらその旨を示さ なければなりません。これらは合理的であればどのよう" +"な方法で行っても構いませんが、許諾者があなたやあなたの利用行為を支持している" +"と示唆するような方法は除きます。" #: ../../LICENSE.md:32 f6c3b2ccad494ed6811a35537fc1fb0d msgid "" @@ -82,6 +94,9 @@ msgid "" "technological measures that legally restrict others from doing anything " "the license permits. With the understanding that:" msgstr "" +"**追加的な制約は課せません** --- あなたは、" +"このライセンスが他の者に許諾することを法的に制限するようないかなる法的規定も " +"技術的手段 も適用してはなりません。" #: ../../LICENSE.md:36 91c95248cd7f435c909ee263a9a8bf3f msgid "" @@ -89,6 +104,9 @@ msgid "" "in the public domain or where your use is permitted by an applicable " "exception or limitation." msgstr "" +"あなたは、資料の中でパブリック・ドメインに属している部分に関して、" +"あるいはあなたの利用が著作権法上の 権利制限規定 " +"にもとづく場合には、ライセンスの規定に従う必要はありません。" #: ../../LICENSE.md:39 27f79b0b648b4de4b0eb3172b2dc4ae8 msgid "" @@ -97,6 +115,9 @@ msgid "" "such as publicity, privacy, or moral rights may limit how you use the " "material." msgstr "" +"保証は提供されていません。ライセンスはあなたの利用に必要な全ての許諾を与えな" +"いかも知れません。例えば、 パブリシティ権、肖像権、人格権 などの他の諸権利は" +"あなたがどのように資料を利用するかを制限することがあります。" #: ../../LICENSE.md:44 1e367d07720d4f9fb7ebc3149052e823 msgid "Software" @@ -120,6 +141,11 @@ msgid "" "See the License for the specific language governing permissions and " "limitations under the License." msgstr "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 #: 08aa9181d5304e0fa96b28db15718559 d37fc100eb6948bba8b5e757574b2aaf @@ -131,9 +157,9 @@ msgid "" " a variety of platforms that support the CWL standard." msgstr "" "CWLは、コマンドラインツールを定義し、それらのツールを繋げてワークフローを作成" -"するための方法です。CWLは仕様であり、特定のソフトウェアではないため、CWLを使" -"用して定義されたツールやワークフローは、CWL標準をサポートするさまざまなプラッ" -"トフォームで利用可能です。" +"します。CWLは仕様であり、特定のソフトウェアではないため、CWLを使用して定義さ" +"れたツールやワークフローは、CWL標準をサポートするさまざまなプラットフォームで" +"利用可能です。" #: ../../src/episodes.md:5 ../../src/setup.md:5 #: 1361ff6bf4924efc9ce9a85785a6b381 eb254514301c491e81f72ae19c407261 @@ -206,7 +232,7 @@ msgid "" msgstr "" "最初の方法は、スクリプトの入ったフォルダを " "環境変数`PATH`に追加する方法です。これにより、`sh` や`bash` " -"コマンドを使用せずに、シェルスクリプトを直接実行することができます。" +"コマンドを使用せずに、シェルスクリプトを直接実行できます。" #: ../../src/faq.md:93 34ebca4487a54ceab5d087105820e945 msgid "Start with adding a _shebang_ at the top of your file:" @@ -239,7 +265,6 @@ msgstr "後で作ったものを共有したいときは、スクリプトをDoc "きます。" #: ../../src/faq.md:119 796ce8155e32486d9651f8f13bfa3148 -#, fuzzy msgid "" "The second method involves including an input of `type: File` in the " "script itself:" @@ -293,19 +318,20 @@ msgid "merge_nested" msgstr "merge_nested" #: ../../src/faq.md:196 3a92c6cc5c2b40ffa0d692d03bad5c87 -#, fuzzy msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." -msgstr "入力は、各入力リンクに対して正確に1つのエントリで構成される配列でなければなりません。\"merge_nested\"が1つのリンクで指定された場合、リンクからの値は1つのアイテムリストでラップされなければなりません。" +msgstr "" +"入力は、各入力リンクに対して正確に1つのエントリで構成される配列でなければなり" +"ません。\"merge_nested\"が1つのリンクで指定された場合" +"、リンクからの値は1つのアイテムリストでラップされなければなりません。" #: ../../src/faq.md:199 3af16c07e3f148ddb8849c94a3864158 msgid "Which means \"create a list with exactly these sources as elements\"." msgstr "つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです。" #: ../../src/faq.md:201 0ea3de393d2f42aeb82658c85a19ec45 -#, fuzzy msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -314,8 +340,9 @@ msgid "" " destination step." msgstr "" "`File[]` (`File`の配列) で、ソースが単一の`File` " -"の場合、`MultipleInputFeatureRequirement` をワークフローレベルの`requirements` " -"に追加し、`linkMerge: merge_nested` を目的ステップのエントリの該当`in`に追加します。" +"の場合、`MultipleInputFeatureRequirement` " +"をワークフローレベルの`requirements` に追加し、`linkMerge: merge_nested` " +"を目的ステップのエントリの該当`in`に追加します。" #: ../../src/faq.md:229 2f1bbb611c9c4f80b7ae0566432f2f35 msgid "How do make an input optional? 💯" @@ -339,13 +366,16 @@ msgstr "どうやってあらかじめ定義された値のリストから入力 "でenumを使うにはどうしたらよいですか)?" #: ../../src/faq.md:250 b1934a82553b4da3b7f981e576245dd8 -#, fuzzy msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" " form style. It does the same thing as the question mark on the other " "inputs.**" -msgstr "引数として特定の入力を必要とするコマンドラインフラグについては、CWLで列挙型を宣言することで実現できます。**ここでnullを指定することは、ロングフォーム・スタイルとして知られています。他の入力のクエスチョンマークと同じ働きをします。**" +msgstr "" +"引数として特定の入力を必要とするコマンドラインフラグについては、CWLで列挙型(" +"enum type)を宣言することで実現できます。**ここでnullを指定することは、ロング" +"フォーム・スタイルとして知られています。他の入力のクエスチョンマークと同じ働" +"きをします。**" #: ../../src/faq.md:267 17fc34fad2094f5ea60e963dabd632b8 msgid "" @@ -359,21 +389,20 @@ msgstr "依存的または排他的な入力パラメータはどのように記 "レコード入力をどのように使用すればよいですか）？" #: ../../src/faq.md:270 949ce95c082f4a05891a55fee25d4873 -#, fuzzy msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -"**相互排他的** または**依存的** " -"のいずれかのコマンドラインフラグについては、特別なレコードタイプを定義することができます。また、ここにnullを指定することで、オプションの入力を作成することができます。" +"**相互排他的** または**依存的** のいずれかのコマンドラインフラグについては、" +"特別なレコードタイプを定義できます。また、ここにnullを指定することで、オプシ" +"ョンの入力を作成できます。" #: ../../src/faq.md:322 6fd3c469d11d4d52b9fbb7a3d443a8db msgid "How do I set mutually exclusive parameters?" msgstr "相互に排他的なパラメータを設定するにはどうしたらよいでしょうか?" #: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f -#, fuzzy msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -383,7 +412,7 @@ msgid "" msgstr "" "レコード入力タイプのフィールドを適切に設定するには、入力に辞書を渡してパラメ" "ータを適切に設定する必要があります。これは、インラインJavaScriptを使用し、設" -"定したいフィールドのキーを持つ辞書を返すことで実現します。ソースフィールドに" +"定したいフィールドのキーを持つ辞書を返すことで実現します。sourceフィールドに" "は、値として使用するワークフローからの入力を示すものが設定されます。" #: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 @@ -429,8 +458,8 @@ msgstr "これらの危険な文字を避けられない場合は、`--relax-pat msgid "" "What should I do when I get CWL Parameter Reference error due to hyphen " "in an input identifier?" -msgstr "入力パラメータ名の中のハイフンがあるため、CWLパラメータリファレンスエラーが起" -"こりました。どのようしたらよいでしょうか？" +msgstr "入力パラメータ名の中にハイフンがあるため、CWL Parameter Reference " +"エラーが起こりました。どのようしたらよいでしょうか？" #: ../../src/faq.md:375 e39b65947b294b20a444f18d780246f4 msgid "If `cwltool --validate` returns valid" @@ -457,7 +486,8 @@ msgstr "このエラーを修正するには、`-` (ハイフン) を`_` (アン msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" -msgstr "入力識別子を変更することができない場合は、別のCWLパラメータリファレンス構文を使用することができます：" +msgstr "入力識別子を変更することができない場合は、別のCWLパラメータリファレンス構文を" +"使用できます：" #: ../../src/faq.md:442 fc407a9e8d8c4b699d9cd14b369343b5 msgid "How do I use CWL and cwltool with Singularity?" @@ -481,7 +511,6 @@ msgid "How do I debug the JavaScript in my CWL tool?" msgstr "CWLツールのJavaScriptをデバッグするには?" #: ../../src/faq.md:452 5556d3c323664edea55cfb777f4efb3b -#, fuzzy msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -492,12 +521,13 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" "cwltool の --js-console " -"オプションを使用するか、または、あなたのコードのためのJavaScript または TypeScript " -"プロジェクトを作成し、expressionLib を使用して読み込んでみてください（例： " -"https://github.com/common-workflow-language/common-workflow-" -"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +"オプションを使用するか、または、あなたのコードのためのJavaScript または " +"TypeScript プロジェクトを作成し、expressionLib " +"を使用して読み込んでみてください（例： https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool." +"cwl#L6-L8" #: ../../src/index.md:1 1c9fb72b83c9467a9672943fb47ffe32 msgid "Common Workflow Language User Guide" @@ -524,8 +554,10 @@ msgid "" "Request by clicking the \"Edit this page\" button at the right sidebar of" " each page." msgstr "" -"このガイドに足りないものがある場合、またはその他のフィードバックを提供したい場合は、[このユーザーガイドのプロジェクトリポジトリ][repo]にIssueを作成してください。また、各ページの右サイドバーにある「このページを編集する」ボタンをクリックすると、Pull" -" Requestで直接変更を提案することができます。" +"このガイドに足りないものがある場合、またはその他のフィードバックを提供したい" +"場合は、[このユーザーガイドのプロジェクトリポジトリ][repo]にIssueを作成してく" +"ださい。また、各ページの右サイドバーにある「このページを編集する」ボタンをク" +"リックすると、Pull Requestで直接変更を提案できます。" #: ../../src/index.md:16 35c50bb5c3a345b4a4ae66b2df065376 msgid "Navigating the User Guide" @@ -573,7 +605,7 @@ msgstr "" "YAML に精通し、コマンドラインの指示に従うことに慣れていることが期待されます。" "このユーザーガイドの他のセクションは、同じ概念をカバーしていますが、より詳細" "に説明されています。すでにCWLに精通している場合、またはより高度なコンテンツを" -"探している場合は、このセクションをスキップすることができます。" +"探している場合は、このセクションをスキップできます。" #: ../../src/introduction/basic-concepts.md:10 7a56d394fb244431aefce7ebbb834ecf msgid "The CWL Specification" @@ -692,8 +724,8 @@ msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" -"コマンドラインツールは、`echo` 、`ls` 、`tar` " -"のようなコマンドラインユーティリティのラッパーです。コマンドラインツールは、ワークフローから呼び出せます。" +"CommandLineToolは、`echo` 、`ls` 、`tar` " +"のようなコマンドのラッパーです。CommandLineToolは、Workflowから呼び出せます。" #: ../../src/introduction/basic-concepts.md:122 #: c88ad26efa794cbeb6f0690aa0cad5ea @@ -716,8 +748,8 @@ msgid "" "section](../topics/operations.md) of this user guide." msgstr "" "Operationは、入力を受け、出力を出す抽象的なプロセスでもあり、ワークフローで使" -"用することができます。しかし、あまり一般的に使われていない特別な処理です。こ" -"のユーザーガイドの[Operation編](../topics/operations.md)で説明します。" +"用できます。しかし、あまり一般的に使われていない特別な処理です。このユーザー" +"ガイドの[Operation編](../topics/operations.md)で説明します。" #: ../../src/introduction/basic-concepts.md:131 #: 44aac23f302c4178accf7e431cfbb96c @@ -729,9 +761,9 @@ msgid "" "workflow." msgstr "" "Workflowは、ステップを含むプロセスです。ステップには、他のWorkflow（ネストさ" -"れたWorkflow）、CommandLineTool、ExpressionToolを使用することができます。Work" -"flowの入力は、そのステップのいずれかに渡すことができ、ステップによって生成さ" -"れた出力は、Workflowの最終出力に使用することができます。" +"れたWorkflow）、CommandLineTool、ExpressionToolを使用できます。Workflowの入力" +"は、そのステップのいずれかに渡すことができ、ステップによって生成された出力は" +"、Workflowの最終出力に使用できます。" #: ../../src/introduction/basic-concepts.md:137 #: 5afdb7aaf0bf4c1abf4c22cdbdd58be9 @@ -741,8 +773,9 @@ msgid "" "*requirements*. There are many requirements defined in the CWL " "specification, for instance:" msgstr "" -"CWL 仕様では、*requirements* " -"を通じて、実装が追加機能を提供し、ワークフローの前提条件を指定することができます。CWL仕様には、例えば、以下のような多くの要件が定義されています：" +"CWL 仕様では、*requirements* を通じて、実装が追加機能を提供し、ワークフローの" +"前提条件を指定できます。CWL仕様には、例えば、以下のような多くの要件が定義され" +"ています：" #: ../../src/introduction/basic-concepts.md:141 #: 07c5789c59224ed78a3ecd03cfe872e9 @@ -750,7 +783,7 @@ msgid "" "[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement)" " - enables JavaScript in expressions." msgstr "" -"[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow." +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/Workflow." "html#InlineJavascriptRequirement) - でJavaScriptを有効にします。" #: ../../src/introduction/basic-concepts.md:142 @@ -781,10 +814,10 @@ msgid "" "the {{ cwl_version }} specification and may not be supported by other CWL" " runners." msgstr "" -"いくつかのCWLランナーは、仕様にないrequirementsを提供することがあります。例え" +"いくつかのCWL runnerは、仕様にないrequirementsを提供することがあります。例え" "ば、GPUに関するrequirementsは`cwltool` で`cwltool:CUDARequirement` " -"を通してサポートされていますが、{{ cwl_version }}仕様の一部ではないので、他の" -"CWLランナーではサポートされていないかもしれません。" +"を通してサポートされていますが、{{ cwl_version }}仕様の一部ではないので、" +"他のCWL runnerではサポートされていないかもしれません。" #: ../../src/introduction/basic-concepts.md:151 #: b6a5cd431c324078a9a4e1513a14ee28 @@ -816,6 +849,14 @@ msgid "" "Workflows](https://workflows.community/groups/fair/), Workflows Community" " Initiative." msgstr "" +"FAIR原則は、デジタル資産、特にデータを共有し公開するための基礎を作りました。F" +"AIR原則は、機械可読性を重視し、すべてのデジタル資産は、検索可能（Findable）、" +"アクセス可能（Accessible）、相互運用可能（Interoperable）、再利用可能（Reusab" +"le）であるべきとしています。ワークフローは、科学的プロセスが実施され、データ" +"が作成される方法をコード化します。従って、ワークフローがFAIRデータの作成をサ" +"ポートし、かつワークフロー自身がFAIRの原則を遵守することは重要です。- [FAIR " +"Computational Workflows](https://workflows.community/groups/fair/), " +"Workflows Community Initiative." #: ../../src/introduction/basic-concepts.md:167 #: 4ea1d3bf04dc42f0bc6735a45b9e0dc0 @@ -920,7 +961,6 @@ msgid "Prerequisites" msgstr "前提条件" #: ../../src/introduction/prerequisites.md:6 ab9e21b3e99641d096ba70012b4eb035 -#, fuzzy msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -932,10 +972,10 @@ msgstr "" "このセクションに記載されているソフトウェアと構成は、このユーザーガイドに従う" "ための前提条件となるものです。CWL標準は、多くの異なるワークフローランナー(訳" "注:ワークフローを実行するためのソフトウェア)やプラットフォームによって実装さ" -"れています。この要件のリストは、CWL参照ランナー、`cwltool` に焦点を当てていま" -"す。他のCWL互換ランナーやワークフローシステムを使用することもできますが、結果" -"やインターフェイスは異なるかもしれません（ただし、正確なワークフロー出力は同" -"一でなければなりません）。" +"れています。この要件のリストは、CWL reference runner である`cwltool` " +"に焦点を当てています。他のCWL-compatible runnerやワークフローシステムを使用す" +"ることもできますが、結果やインターフェイスは異なるかもしれません（ただし、正" +"確なワークフロー出力は同一でなければなりません）。" #: ../../src/introduction/prerequisites.md:12 8ed426ebcb744839915e7c414d69b1e9 msgid "CWL Implementations" @@ -1052,7 +1092,7 @@ msgstr "`cwltool` を使って `true.cwl` を検証します。" #: ../../src/introduction/prerequisites.md:71 73f074f47d1449dcb40ff960a84851fd msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "`--validate` オプションを省略することで、CWLツール定義を実行することができます：" +msgstr "`--validate` オプションを省略することで、CWLツール定義を実行できます：" #: ../../src/introduction/prerequisites.md:73 2dd5a67870ca41b48e17c468ba15888b msgid "Running `true.cwl` with `cwltool`." @@ -1072,10 +1112,14 @@ msgid "" " administrator or user to point to the preferred CWL implementation. This" " is convenient for environments with multiple CWL runners." msgstr "" -"`cwl-runner` は、CWL準拠のランナーに対する、実装にとらわれないエイリアスです。これは、`cwl-runner` " -"エイリアスコマンドを独立して呼び出すことができ、特定のCWLランナープログラム名に依存しないことを意味します。ユーザーは、`cwltool` " -"のようなCWLランナーを直接呼び出す代わりに、`cwl-runner` を呼び出すことができます。`cwl-runner` " -"は、システム管理者またはユーザーによってインストールされ、好みのCWL実装を指し示す。これは、複数のCWLランナーがある環境では便利です。" +"`cwl-runner` " +"は、CWL準拠のランナーに対する、実装にとらわれないエイリアスです。これは" +"、`cwl-runner` エイリアスコマンドを独立して呼び出すことができ、特定のCWL " +"runner のプログラム名に依存しないことを意味します。ユーザーは、`cwltool` " +"のようなCWL runnerを直接呼び出す代わりに、`cwl-runner` " +"を呼び出すことができます。`cwl-runner` は、システム管理者またはユーザーによっ" +"てインストールされ、好みのCWL実装を指します。これは、複数のCWL " +"runnerがある環境で便利です。" #: ../../src/introduction/prerequisites.md:88 6dd6aa836099469381fb564d63b84f3d msgid "" @@ -1123,7 +1167,8 @@ msgstr "`true_shebang.cwl`" #: ../../src/introduction/prerequisites.md:122 4f3cb8d1f9ce4e3d852e81aa4e0f60be msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "`chmod u+x` を実行することで、 `true_shebang.cwl` を実行可能なファイルにすることができます。" +msgstr "`chmod u+x` を実行することで、 `true_shebang.cwl` " +"を実行可能なファイルにできます。" #: ../../src/introduction/prerequisites.md:124 27693d62faa045d9b03143d9bd2afcdf msgid "Making `true.cwl` executable." @@ -1135,7 +1180,8 @@ msgid "" "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -"そして最後に、コマンドラインで直接実行することができます。実行時には、shebangで指定されたプログラム(`cwl-" +"そして最後に、コマンドラインで直接実行できます。実行時には、shebangで指定され" +"たプログラム(`cwl-" "runner`)が、ファイルの残りの部分を実行するために使用されます。" #: ../../src/introduction/prerequisites.md:135 abba2e14c4e54252bb75983274663a7a @@ -1215,8 +1261,8 @@ msgid "" msgstr "" "`cwltool` は、ツール、ワークフロー、およびワークフロー " "ステップで指定されたソフトウェアコンテナをDockerを使用して実行します。Docker " -"ドキュメントの指示に従って、お使いのオペレーティングシステム用にインストール" -"してください：." +"ドキュメントの指示に従って、お使いのオペレーティングシステム合わせてインスト" +"ールしてください：." #: ../../src/introduction/prerequisites.md:172 2872503638624b7e904ae407375ac165 msgid "" @@ -1342,7 +1388,7 @@ msgid "" msgstr "" "基本的に `cwltool` の使い方は、`cwltool [OPTIONS] [CWL_DOCUMENT] " "[INPUTS_OBJECT]`です。`hello_world.cwl` " -"Workflowは、オプションを指定せずに実行することができます：" +"Workflowは、オプションを指定せずに実行できます：" #: ../../src/introduction/quick-start.md:57 5b393c69816549b084516dda4d4274f5 msgid "Running `hello_world.cwl` with `cwltool`." @@ -1366,8 +1412,9 @@ msgid "" "YAML. For example:" msgstr "" "ワークフロー入力パラメータに値を渡すもう一つの方法は、*Inputs Object* " -"を介する方法です。これは、入力フィールドとその対応する値を含むファイルです。Inputs Objects ファイルは、JSON または YAML " -"で記述することができます。例えば、以下のようになります：" +"を介する方法です。これは、入力フィールドとその対応する値を含むファイルです。" +"Inputs Objects ファイルは、JSON または YAML " +"で記述できます。例えば、以下のようになります：" #: ../../src/introduction/quick-start.md:74 d05e8e016b1d40c28c4b6091103fe920 msgid "`hello_world-job.json`" @@ -1381,7 +1428,7 @@ msgstr "このInputs Objectファイルを使用して、「Hello World」ワー #: ../../src/introduction/quick-start.md:82 4065124edf3a4678a37c82e3070595cb msgid "Passing an Inputs Object file to `cwltool`." -msgstr "`cwltool` に Inputs Object ファイルをします。" +msgstr "`cwltool` に Inputs Object ファイルを渡します。" #: ../../src/introduction/quick-start.md:88 52b1602b5c8d48db88d0b16f788e7703 msgid "" @@ -1556,7 +1603,6 @@ msgstr "" "Direcotry` を適宜使用します。" #: ../../src/topics/best-practices.md:11 ae127b776eed4894af8cb680377703e0 -#, fuzzy msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1602,7 +1648,9 @@ msgstr "" msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" -msgstr "参考文献：\"[科学者・プログラマーのためのソフトウェアライセンス クイックガイド][sci-license]\"" +msgstr "" +"参考文献：\"[A Quick Guide to Software Licensing for the Scientist-Programmer" +"][sci-license]\"" #: ../../src/topics/best-practices.md:28 5b976a5aec7d44bda55b0a019e955416 msgid "_Example of metadata field for license with SPDX identifier:_" @@ -1614,7 +1662,7 @@ msgid "" " Metadata and Authorship section of this User Guide](../topics/metadata-" "and-authorship.md)." msgstr "" -"CW定義にメタデータを与える例については、 " +"CWL定義にメタデータを与える例については、 " "[このユーザーガイドのメタデータと著者名のセクション](../topics/metadata-and-" "authorship.md)を参照してください。" @@ -1667,7 +1715,6 @@ msgstr "" "ツールのバージョンのリストを書きます。" #: ../../src/topics/best-practices.md:58 88806cb0462f4359801c1fa0ff0ebcc0 -#, fuzzy msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1682,10 +1729,10 @@ msgstr "" "フォマティクスツールは、[EDAM][edam-" "example]のフォーマット識別子を使用するのが良いです。`iana:text/plain`,`iana:" "text/tab-separated-values`、`$namespaces：{ iana: \"https://www.iana.org/" -"assignments/media-types/\" }もご参照ください`.[IANA メディアタイプ一覧][iana-" -"types]（MIME タイプとしても知られています）。バイオインフォマティクス以外のツ" -"ールについては、同様に適切なオントロジー/統制語彙を使用または構築してください" -"。このページを編集して私たちに知らせてください。" +"assignments/media-types/\" }` も参照してください`.[IANA メディアタイプ一覧" +"][iana-types]（MIME タイプとしても知られています）。バイオインフォマティクス" +"以外のツールについては、同様に適切なオントロジー/統制語彙を使用または構築して" +"ください。このページを編集して私たちに知らせてください。" #: ../../src/topics/best-practices.md:66 b178c7296ed5491782a4180c76883c14 msgid "" @@ -1736,16 +1783,16 @@ msgid "" msgstr "有効な値のリストが決まっている要素には、`type: string` の代わりに、`type: enum` を使用してください。" #: ../../src/topics/best-practices.md:85 c100d5192a52497fb6a890b81a388fcf -#, fuzzy msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" " one of the [built in `File` properties][file-prop] like `basename`, " "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -"JavaScriptのすべての使用について、削除または置換の可能性を評価します。よくある例：`File` " -"の名前とパスを操作する方法は？`basename`,`nameroot`,`nameext`, などの [built in`File` " -"properties][file-prop] のいずれかを代わりに使用できないか考えてみてください。" +"JavaScriptのすべての使用について、削除または置換の可能性を評価します。よくあ" +"る例：`File` の名前とパスを操作する方法は？`basename`,`nameroot`,`nameext`, " +"などの [ビルトイン`File` プロパティ][file-prop] " +"のいずれかを代わりに使用できないか考えてみてください。" #: ../../src/topics/best-practices.md:90 e22fbacdb2fb4202b1bd69cfc24af5cd msgid "" @@ -1782,9 +1829,9 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" "CommandLineToolは、Processオブジェクトの一種であり、それ自体またはワークフロ" -"ーのステップとして実行することができます。`ls`,`echo`,`tar` などの実行したい" -"コマンドのラッパーです。実行したいコマンドは、CommandLineToolについてのCWL定" -"義の`baseCommand` 属性で定義されています。" +"ーのステップとして実行できます。`ls`,`echo`,`tar` などの実行したいコマンドの" +"ラッパーです。実行したいコマンドは、CommandLineToolについてのCWL定義の`baseCo" +"mmand` 属性で定義されています。" #: ../../src/topics/command-line-tool.md:8 7a180ba1f2d746a78b79be7e899cbad6 msgid "" @@ -1792,8 +1839,9 @@ msgid "" "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -"CWLコマンドラインツールは、`inputs` と`outputs` も持っていなければなりません。次の例は、Linuxコマンド `echo` " -"のためのCWLコマンドラインツールの最小限の例で、inputsとoutputsを使用します。" +"CWL CommandLineToolは、`inputs` と`outputs` " +"も持っていなければなりません。次の例は、Linuxコマンド `echo` のためのCWL " +"CommandLineToolの最小限の例で、inputsとoutputsを使用します。" #: ../../src/topics/command-line-tool.md:19 128bd8cd6788431da54fa07a8dc87f99 msgid "CWL command-line tool." @@ -1845,13 +1893,15 @@ msgstr "実行時にファイルを作成する" #: ../../src/topics/creating-files-at-runtime.md:3 #: cd0dff10471c4ad2b84e3a0e4d7767ea -#, fuzzy msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " "rather than the command line parameters, or need a small wrapper shell " "script." -msgstr "コマンドラインパラメーターではなく、ファイルから入力設定を読み込むことを期待するツールや、小さなラッパーシェルスクリプトが必要な場合など、入力パラメーターからその場でファイルを作成する必要があることがあります。" +msgstr "" +"コマンドラインパラメーターではなく、ファイルから入力設定を読み込むことを期待" +"するツールや、小さなラッパーシェルスクリプトが必要な場合など、入力パラメータ" +"ーからその場でファイルを作成する必要があることがあります。" #: ../../src/topics/creating-files-at-runtime.md:7 #: bf4aea0a22334a1ca75cc20e937e6581 @@ -1880,7 +1930,6 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 #: aca24b72687c4d4d84bf9de8b71413f7 -#, fuzzy msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1888,9 +1937,11 @@ msgid "" "`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " "be evaluated by the shell script instead of the CWL engine." msgstr "" -"_CWL expressions_ は、コマンドラインツール起動時に使用される_shell variables_ とは無関係です。つまり、`$` " -"という文字が本当に必要な場合は、** ` \\` で** をエスケープする必要があります。例えば，上記の`\\${PREFIX}` " -"は，CWLエンジンの代わりにシェルスクリプトで評価されるように，生成されたファイルでは`${PREFIX}` に展開されます．" +"_CWL expressions_ は、コマンドラインツール起動時に使用される_shell " +"variables_ とは無関係です。つまり、`$` という文字が本当に必要な場合は、`\\` " +"で**エスケープ**する必要があります。例えば，上記の`\\${PREFIX}` は，CWLエンジ" +"ンの代わりにシェルスクリプトで評価されるように，生成されたファイルでは`${PREF" +"IX}` に展開されます。" #: ../../src/topics/creating-files-at-runtime.md:27 #: 750b3232e8754448bc2b5913539495b8 @@ -1918,7 +1969,6 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 #: 9aeea5a6a4244bc7a1626e0cb7351068 -#, fuzzy msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1929,7 +1979,7 @@ msgid "" " write the whole script on one line)." msgstr "" "`InitialWorkDirRequirement` は`listing` を必要とします。`listing` は YAML " -"配列なので、配列の各要素の最初の行に`-` が必要です。この場合、要素は 1 " +"配列なので、配列の各要素の行の最初に`-` が必要です。この場合、要素は 1 " "つだけです。`entryname:` は任意の値を指定できますが、`baseCommand` " "で指定したものと一致していなければなりません。最後の部分は`entry:` " "で、この後に`|-` が続きます。これは YAML の引用構文で、" @@ -2008,7 +2058,6 @@ msgstr "" "で、テーブル変換で使用できるテーブルオプションのリストがカスタムオブジェクトとしてインポートされます：" #: ../../src/topics/custom-types.md:46 c791096f537141e8bd7cc941d711d108 -#, fuzzy msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -2145,7 +2194,6 @@ msgstr "" "runnerによって評価されるJavascriptを使用できます。" #: ../../src/topics/expressions.md:9 3d48d1a8f7f74bc1886e41653cb53a22 -#, fuzzy msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -2153,10 +2201,11 @@ msgid "" "`nameroot`, `nameext`, etc, could be used instead. See the [list of best " "practices](best-practices.md)." msgstr "" -"JavaScript " -"の式は、絶対に必要な場合のみ使用するようにしてください。ファイル名、拡張子、パスなどを操作する場合は、`basename`,`nameroot`,`nameext`," -" などの [`File` のビルトインプロパティ][file-prop] " -"のいずれかを代わりに使用できるかどうかを検討してください。[ベストプラクティスのリスト](best-practices.md)を参照してください。" +"JavaScript の式は、絶対に必要な場合のみ使用するようにしてください。ファイル名" +"、拡張子、パスなどを操作する場合は、`basename`,`nameroot`,`nameext`, などの " +"[`File` のビルトインプロパティ][file-prop] のいずれかを代わりに使用できるかど" +"うかを検討してください。[ベストプラクティスのリスト](best-practices." +"md)を参照してください。" #: ../../src/topics/expressions.md:16 7d444aacd418466bbe588fa964b45179 msgid "`expression.cwl`" @@ -2167,7 +2216,7 @@ msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "このツールは`inputs` " -"を必要としないので、（ほとんど）空のジョブファイルで実行することができます：" +"を必要としないので、（ほとんど）空のジョブファイルで実行できます：" #: ../../src/topics/expressions.md:25 d679fd1363b24c81979c68e7342159cf msgid "`empty.yml`" @@ -2184,7 +2233,7 @@ msgstr "" #: ../../src/topics/expressions.md:35 624e4a270e374b1699b780df508b9184 msgid "We can then run `expression.cwl`:" -msgstr "次に、`expression.cwl` を実行することができます：" +msgstr "次に、`expression.cwl` を実行できます：" #: ../../src/topics/expressions.md:37 c252eac9a35e46aab08bd07bc1cdb57d msgid "Running `expression.cwl`" @@ -2211,13 +2260,12 @@ msgid "Where are JavaScript expressions allowed?" msgstr "JavaScriptはどこで使えますか？" #: ../../src/topics/expressions.md:64 8c3b402c40f64880a4bd42c47b910254 -#, fuzzy msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -"[パラメータ参照](parameter-references.md)と同様に、JavaScript 式は特定のフィールドにのみ使用できます。 " -"以下はその例です：" +"[パラメータ参照](parameter-references.md)と同様に、JavaScript " +"式は特定のフィールドにのみ使用できます。 以下はその例です：" #: ../../src/topics/expressions.md:66 9bf5ca0e769147c6a9705bc40bd1febc msgid "" @@ -2511,8 +2559,9 @@ msgid "" "files or to create JavaScript functions that can be called in other parts" " of the CWL document." msgstr "" -"`expressionLib` " -"属性に追加されたエントリーは、CWLランナーのJavaScriptエンジンで解析されます。これは、外部ファイルをインクルードしたり、CWL定義の他の部分で呼び出すことができるJavaScript関数を作成するために使用することができます。" +"`expressionLib` 属性に追加されたエントリーは、CWL runnerのJavaScriptエンジン" +"で解析されます。これは、外部ファイルをインクルードしたり、CWL定義の他の部分で" +"呼び出すことができるJavaScript関数を作成するために使用できます。" #: ../../src/topics/expressions.md:128 5b2336cae1ef4cae8ed187d3f33cff25 msgid "" @@ -2534,8 +2583,9 @@ msgid "" "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -"例えば、`InlineJavascriptRequirement` を使って、`expressionLib` に JavaScript " -"関数をインラインで記述することができます。その関数は、CWL定義の他の部分で使用することができます：" +"例えば、`InlineJavascriptRequirement` を使って、`expressionLib` に " +"JavaScript " +"関数をインラインで記述できます。その関数は、CWL定義の他の部分で使用できます：" #: ../../src/topics/expressions.md:139 6839a02fb82d45c29ae518f2b00cb9d5 msgid "`hello-world-expressionlib-inline.cwl`" @@ -2610,9 +2660,9 @@ msgid "" "the CWL specification to learn more about it." msgstr "" "`$include` ステートメントを使用すると、ローカルディスクまたはリモートロケーシ" -"ョンからファイルをインクルードすることができます。相対パスと絶対パスの両方で" -"動作します。CWL仕様の[`$include`について](https://www.commonwl.org/v1.0/" -"SchemaSalad.html#Include)を読むと、より詳しく知ることができます。" +"ョンからファイルをインクルードできます。相対パスと絶対パスの両方で動作します" +"。CWL仕様の[`$include`について](https://www.commonwl.org/v1.0/SchemaSalad." +"html#Include)を読むと、より詳しく知ることができます。" #: ../../src/topics/file-formats.md:1 ac906f26116c45d882e1afa42ae38e34 msgid "File Formats" @@ -2628,11 +2678,10 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" "ToolsやWorkflowsは、[`File`](https://w3id.org/cwl/CommandLineTool.html#File) " -"型を入力として受け取り、出力として生成することができます。また、[`File`](http" -"s://w3id.org/cwl/CommandLineTool.html#File) タイプのフォーマットを示すことを" -"お勧めします。これにより、ツールの使用方法を他の人に示すことができ、また、パ" -"ラメータファイルを作成する際に簡単な型チェックを行うことができるようになりま" -"す。" +"型を入力として受け取り、出力として生成できます。また、[`File`](https://w3id." +"org/cwl/CommandLineTool.html#File) タイプのフォーマットを示すことをお勧めしま" +"す。これにより、ツールの使用方法を他の人に示すことができ、パラメータファイル" +"を作成する際に簡単な型チェックを行うことができるようになります。" #: ../../src/topics/file-formats.md:8 23ba3dd26f5543119e2c152105b58e98 msgid "" @@ -2646,7 +2695,7 @@ msgstr "" "）、所属機関のローカルオントロジーを参照すること、またはツールを他者と共有す" "る前に迅速に開発するために最初はファイルフォーマットを追加しないことを推奨し" "ています。既存の[IANAファイルフォーマット一覧][IANA]と[EDAMファイルフォーマッ" -"ト一覧][EDAM]は、それぞれのウェブサイトで参照することができます。" +"ト一覧][EDAM]は、それぞれのウェブサイトで参照できます。" #: ../../src/topics/file-formats.md:14 81c441846fc249c58607bacf97095eb8 msgid "" @@ -2677,20 +2726,21 @@ msgid "Sample Parameter Files" msgstr "サンプルパラメーターファイル" #: ../../src/topics/file-formats.md:34 afd8633db1904897aa3e499354b1c376 -#, fuzzy msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " "This allows others to quickly work with your tool, starting from a " "\"known good\" parameterization." -msgstr "以下は、上記の例のパラメータファイルの例です。あなたのツールのパラメータファイルの実例をチェックすることをお勧めします。これにより、他の人が「既知の良い」パラメータ化から始めて、あなたのツールで素早く作業することができます。" +msgstr "" +"以下は、上記の例のパラメータファイルの例です。あなたのツールのパラメータファ" +"イルの実例をチェックすることをお勧めします。これにより、他の人が「既知の良い" +"」パラメータ化から始めて、あなたのツールで素早く作業できます。" #: ../../src/topics/file-formats.md:39 bb69d6963c174191bf527335c3f665b7 msgid "`sample.yml`" msgstr "`sample.yml`" #: ../../src/topics/file-formats.md:45 ddb4f6f81c7d462b974e98c88dd3f558 -#, fuzzy msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2699,9 +2749,9 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" "___注：___ 以下の例に実行するには、例の入力ファイル、*file-formats.bam* " -"をダウンロードする必要があります。このファイルは から入手可能で、`wget` などでダウンロードすることができます：" +"をダウンロードする必要があります。このファイルは から入手可能で、`wget` などでダウンロードできます：" #: ../../src/topics/index.md:1 2995cd4fb85c423dba021611dac4a137 msgid "Topics" @@ -2716,13 +2766,13 @@ msgid "Essential Input Parameters" msgstr "必須入力パラメータ" #: ../../src/topics/inputs.md:5 17365707f58242369dd6aa73fc8d7242 -#, fuzzy msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -"ツールの`inputs` は、ツールの実行に関わる入力パラメーターのリストです。 各パラメーターには、パラメーター名を示す`id` " +"ツールの`inputs` は、ツールの実行に関わる入力パラメーターのリストです。 " +"各パラメーターには、パラメーター名を示す`id` " "と、そのパラメーターに有効な値の種類を示す`type` があります。" #: ../../src/topics/inputs.md:9 521cb5dead5d4e9ab5ff037fb4b683cb @@ -2761,9 +2811,9 @@ msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in an input object file:" msgstr "" -"`cwltool` を使って、テンプレートとなる入力オブジェクトを作成することができま" -"す。これにより、入力オブジェクトファイルにすべての入力パラメータを入力する手" -"間を省くことができます：" +"`cwltool` を使って、テンプレートとなる入力オブジェクトを作成できます。これに" +"より、入力オブジェクトファイルにすべての入力パラメータを入力する手間を省くこ" +"とができます：" #: ../../src/topics/inputs.md:40 5ac6da11d56446de97c251a37d997671 msgid "" @@ -2772,7 +2822,7 @@ msgid "" "desired input values." msgstr "" "`cwltool --make-template inp.cwl > inp-job.yml` のように、出力をファイルにリ" -"ダイレクトします。その後デフォルト値を希望の入力値で修正することができます。" +"ダイレクトします。その後デフォルト値を希望の入力値で修正できます。" #: ../../src/topics/inputs.md:44 6a3edb0d259d4d7c900dd9811f978d4e msgid "" @@ -2806,12 +2856,11 @@ msgid "" "that the tools aren't accidentally accessing files that were not " "explicitly specified" msgstr "" -"CWLリファレンスランナー（cwltool）と他のランナーは、ツールが明示的に指定され" -"ていないファイルに誤ってアクセスしないように、入力ファイルへの（\"ソフト\"" +"CWL reference runner（cwltool）と他のランナーは、ツールが明示的に指定されてい" +"ないファイルに誤ってアクセスしないように、入力ファイルへの（\"ソフト\"" "）シンボリックリンクを持つ一時ディレクトリを作成します" #: ../../src/topics/inputs.md:70 5bdf77c45346445d8f93353c1e73f768 -#, fuzzy msgid "" "The field " "[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)" @@ -2820,10 +2869,10 @@ msgid "" "parameter does not appear on the command line. Let's look at each " "example in detail." msgstr "" -"フィールド[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_bi" -"nding)はオプションであり、入力パラメータをツールのコマンドラインに表示するか" -"どうか、またどのように表示するかを指定します。`inputBinding`がない場合、パラ" -"メータはコマンドラインに表示されません。 それぞれの例を詳しく見てみましょう。" +"[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)フィ" +"ールドはオプションであり、入力パラメータをツールのコマンドラインに含めるかど" +"うか、またどのように含めるかを指定します。`inputBinding`がない場合、パラメー" +"タはコマンドラインに含まれません。 それぞれの例を詳しく見てみましょう。" #: ../../src/topics/inputs.md:83 d783fe52e86f4feda33ea0eecb622603 msgid "" @@ -2846,7 +2895,6 @@ msgstr "" " hello` と与えられます。" #: ../../src/topics/inputs.md:109 b106eed01c1744a792368f91f547e553 -#, fuzzy msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2855,10 +2903,9 @@ msgid "" msgstr "" "整数型（および浮動小数点型）はコマンドラインに10進数のテキスト表現で表示され" "ます。 `separate`オプションがfalseの場合（デフォルト値はtrue）、prefixと値は1" -"つの引数にまとめられます。 上の例では `-i42` として表示されます。" +"つの引数になるようにまとめられます。 上の例では `-i42` として表示されます。" #: ../../src/topics/inputs.md:124 1c70336741a842a5b16b687642d1d9b4 -#, fuzzy msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2869,8 +2916,8 @@ msgid "" msgstr "" "ファイル型は、コマンドライン上にファイルへのパスとして表示されます。 パラメ" "ータの型の末尾にクエスチョンマーク`?`がある場合、これは、パラメータがオプショ" -"ンであることを表します。 上記の例では、`--file=/tmp/random/path/whale.txt` " -"と表示されます。 ただし、入力パラメータに \"example_file\" " +"ナルであることを表します。 上記の例では、`--file=/tmp/random/path/whale.txt`" +" と表示されます。 ただし、入力パラメータに \"example_file\" " "パラメータを指定しなかった場合、コマンドラインには何も表示されません。" #: ../../src/topics/inputs.md:131 9294c07c672b414f9c3895ed70b9b4ee @@ -2910,7 +2957,6 @@ msgid "Array Inputs" msgstr "配列入力" #: ../../src/topics/inputs.md:148 b11a5c7a13b345939e4ae15e1e2c0786 -#, fuzzy msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2919,11 +2965,11 @@ msgid "" " be added after the type name to indicate that input parameter is array " "of that type." msgstr "" -"コマンドラインに表現される入力パラメータの配列を簡単に追加することができます" -"。配列パラメータを指定するには、2つの方法があります。1つ目の方法は、`type` " -"に`type: array` と`items` を指定して、配列に現れる可能性のある有効なデータ型" -"を定義する方法です。2つ目の方法は、入力パラメータがその型の配列であることを示" -"すために、型名の後に`[]` という括弧を付けることもできます。" +"コマンドラインに含まれる入力パラメータの配列は簡単に追加できます。配列パラメ" +"ータを指定するには、2つの方法があります。1つ目の方法は、`type` に`type: " +"array` と`items` を指定して、配列に現れる可能性のある有効なデータ型を定義する" +"方法です。2つ目の方法は、入力パラメータがその型の配列であることを示すために、" +"型名の後に`[]` という括弧を付けることもできます。" #: ../../src/topics/inputs.md:154 aa00bcfc6c0f4085ae52621a2f4ae8d9 msgid "`array-inputs.cwl`" @@ -2952,9 +2998,9 @@ msgid "" "item separator string." msgstr "" "`inputBinding` は、外側の配列パラメータ定義と内側の配列要素定義のいずれかに記" -"述することができ、上図のようにコマンドラインを構築する際に異なる挙動を示しま" -"す。また、`itemSeparator` フィールドがあれば、配列の値を項目区切り文字列で区" -"切って1つの引数に連結することを指定することができます。" +"述でき、上図のようにコマンドラインを構築する際に異なる挙動を示します。また、`" +"itemSeparator` フィールドがあれば、配列の値を項目区切り文字列で区切って1つの" +"引数に連結することを指定できます。" #: ../../src/topics/inputs.md:185 bb31c6784ea843ec88f185523cfa25df msgid "" @@ -2970,7 +3016,7 @@ msgstr "" "列は複数行に渡って表現することも可能で、関連するキーで定義されていない配列の" "値は、先頭の`-` でマークされます。これは次のレッスンで実際に確認し、[YAML " "Guide](yaml-guide.md#arrays) でより詳細に説明されています。配列の配列、レコー" -"ドの配列、その他の複雑な型を指定することができます。" +"ドの配列、その他の複雑な型を指定できます。" #: ../../src/topics/inputs.md:191 53817379078548b2aeb6195cae9cbab7 msgid "Inclusive and Exclusive Inputs" @@ -2985,8 +3031,7 @@ msgid "" msgstr "" "基本的なツールには、一緒に提供しなければならない複数の引数（依存関係あり）や" "、一緒に提供できない複数の引数（排他関係あり）があることがあります。 record" -"とユニオン型を使ってパラメータをグループ化し、この2つの条件を定義することがで" -"きます。" +"とユニオン型を使ってパラメータをグループ化し、この2つの条件を定義できます。" #: ../../src/topics/inputs.md:198 84e1ab25511c49d1baabb1f80f247b49 msgid "`record.cwl`" @@ -3039,8 +3084,9 @@ msgid "" msgstr "" "排他的入力パラメータを式と組み合わせて使用する場合、JavaScript " "オブジェクトの`inputs` に排他的入力値のいずれかが含まれることを意識する必要が" -"あります。つまり、**or** のブーリアン演算子を使用して、`inputs`にどの値が存在" -"するかをチェックする必要がある場合があります。" +"あります。つまり、これらの排他的な値の型は異なる可能性があるので、`input` オ" +"ブジェクトのプロパティを参照するときに、どの型が使用されているかを確認する必" +"要があるかもしれません。" #: ../../src/topics/inputs.md:263 0fecb128b19b44d796b6c1b6de4f7166 msgid "" @@ -3067,7 +3113,6 @@ msgstr "" "すると、コマンドは正常に実行されるはずです：" #: ../../src/topics/inputs.md:281 11fdeb057d674f118830f431ff019c15 -#, fuzzy msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to `null`, which does not match the expected type for the " @@ -3075,19 +3120,21 @@ msgid "" "workflow." msgstr "" "しかし、入力値を提供しない場合、`file_format` は、`null` " -"の値として評価されます。これは、出力フィールドが期待する型（`string` ）と一致しないため、ワークフロー実行時に失敗することになります。" +"の値として評価されます。これは、出力フィールドが期待する型（`string` " +"）と一致しないため、ワークフロー実行時に失敗することになります。" #: ../../src/topics/inputs.md:290 8594cca9d93b4280b6cfee64c8a7c578 -#, fuzzy msgid "" "To correct it, you should explicitly handle the possibility of a `null` " "value. For example, the expression could be changed to " "`$(inputs.file_format || 'auto')`, to have a default value `\"auto\"` if " "none was provided in the command line or job input file." msgstr "" -"これを修正するには、排他的パラメータ、または`null` を許可するパラメータを使用する場合、JavaScript 式で or " -"演算子を使用することを忘れてはなりません。たとえば、式を`$(inputs.file_format || 'auto')` " -"に変更すると、コマンドラインやジョブ入力ファイルで何も指定されていない場合にデフォルト値を持つようになります。" +"これを修正するには、排他的パラメータ、または`null` " +"を許可するパラメータを使用する場合、JavaScript 式で or " +"演算子を使用することを忘れてはなりません。たとえば、式を`$(" +"inputs.file_format || 'auto')` に変更すると、コマンドラインやジョブ入力ファイ" +"ルで何も指定されていない場合にデフォルト値`\"auto\"`を持つようになります。" #: ../../src/topics/inputs.md:295 b5055c77f85e43609fe3e9b9839778e3 msgid "" @@ -3099,12 +3146,12 @@ msgid "" "expression’s value becomes that of the second operand, which is why a " "reasonable default can be provided there." msgstr "" -"ここでは、JavaScriptのブール値 \"or\"、 \"演算子 `||` は、その_short-" -"circuiting_プロパティに使用されます。`inputs.file_format`がブール値の \"true" -"\"である場合（例えば、列挙された有効な空でない文字列）、式の評価は " -"`||`の最初のオペランドで停止します。しかし、 `inputs.file_format`が`null`の場" -"合、式全体の値は2番目のオペランドの値になります。これにより合理的なデフォルト" -"値を提供します。" +"ここでは、JavaScriptのブール値 \"or\"、 演算子 `||` は、その _short-" +"circuiting_ プロパティに使用されます。`inputs.file_format`がブール値の \"true" +"\"である場合（例えば、列挙された有効な空でない文字列）、式の評価は `||`" +"の最初のオペランド\"short-circuits\"で停止します。しかし、 `inputs.file_forma" +"t`が`null`の場合、式全体の値は2番目のオペランドの値になります。これにより合理" +"的なデフォルト値を提供します。" #: ../../src/topics/metadata-and-authorship.md:1 #: 723c2232310c4276aeac2bd6728d2912 @@ -3150,20 +3197,22 @@ msgstr "`metadata_example2.cwl`" #: ../../src/topics/metadata-and-authorship.md:28 #: 37b07ea9b7124842b8ba3040f70308e9 -#, fuzzy msgid "Extended Example" msgstr "拡張された例" #: ../../src/topics/metadata-and-authorship.md:30 #: 1cd5989ade6741aabe625c13bed3c8ed -#, fuzzy msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " "ontology tags as keywords (allowing the grouping of related tools), hints" " at hardware requirements in order to use the tool, and a few more " "metadata fields." -msgstr "高いモチベーションを持つ人であれば、ツールにもっと多くのメタデータを付与することも可能です。この例では、EDAMオントロジーのタグをキーワードとして含み（関連するツールのグループ化が可能）、ツールを使用するために必要なハードウェアのヒントや、さらにいくつかのメタデータフィールドがあります。" +msgstr "" +"高いモチベーションを持つ人であれば、ツールにもっと多くのメタデータを付与する" +"ことも可能です。この例では、EDAMオントロジーのタグをキーワードとして含み（関" +"連するツールのグループ化が可能）、ツールを使用するために必要なハードウェアの" +"ヒントや、さらにいくつかのメタデータフィールドがあります。" #: ../../src/topics/metadata-and-authorship.md:35 #: ae7369ba14404d23b72d1ef30dcd4153 @@ -3189,7 +3238,8 @@ msgstr "" msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" -msgstr "CWLランナーにワークフローを送信する前に、開発中のワークフローを可視化することができます：" +msgstr "CWL " +"runnerでワークフローを実行する前に、開発中のワークフローを可視化できます：" #: ../../src/topics/operations.md:10 e9b2b97f3059460b867577a49934a338 msgid "`operations.cwl`" @@ -3202,8 +3252,8 @@ msgid "" "with the CWL Viewer or `cwltool`:" msgstr "" "ワークフローの`uppercase` ステップは Operation " -"です。CommandLineToolやExpressionToolのように使用することができます。また、" -"CWL Viewerや`cwltool` を使って可視化することもできます：" +"です。CommandLineToolやExpressionToolのように使用できます。また、CWL " +"Viewerや`cwltool` を使って可視化できます：" #: ../../src/topics/operations.md:24 61e4ae6ed18e41708270eb358cd55277 msgid "" @@ -3211,9 +3261,9 @@ msgid "" " The following image is rendered with the Sphinx `{graphviz}` directive " "(this user guide is built with Sphinx):" msgstr "" -"上記のコマンドの出力は、Graphvizを使ってレンダリングすることができます。以下" -"の画像は、SphinxのGraphvizディレクティブでレンダリングしたものです（このユー" -"ザーガイドはSphinxで構築されています）：" +"上記のコマンドの出力は、Graphvizを使ってレンダリングできます。以下の画像は、S" +"phinxの`{graphviz}`ディレクティブでレンダリングしたものです（このユーザーガイ" +"ドはSphinxで構築されています）：" #: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd msgid "" @@ -3228,16 +3278,15 @@ msgid "`cwltool` does not know how to run operations" msgstr "`cwltool` は、どうやってoperationsを実行するかを知りません" #: ../../src/topics/operations.md:67 3b90445d3428444cafd7d5c0e5884980 -#, fuzzy msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" "CWL runnerは、operations " -"を具体的なステップにバインドする見出すかもしれません。例えば、CWL runnerは、" +"を具体的なステップに結びつけるかもしれません。例えば、CWL runnerは、" "ワークフローエンジンで実行される異なるステップに対応するIDを持つ抽象的な " -"operation を使用することができます。" +"operation を使用できます。" #: ../../src/topics/outputs.md:1 35e7bad6fdc04bcf9bbfbb2d8d42cfa5 msgid "Outputs" @@ -3260,7 +3309,6 @@ msgstr "" "と、そのパラメーターに有効な値の型を示す`type` があります。" #: ../../src/topics/outputs.md:10 a229d8d983344e51a231edb5f667d84b -#, fuzzy msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -3268,11 +3316,11 @@ msgid "" "output parameters returned by the CWL tool are either the output files " "themselves, or the result of examining the content of those files." msgstr "" -"CWLでツールを実行する場合、開始時の作業ディレクトリが出力ディレクトリになりま" -"す。 基礎となるツールやスクリプトは、出力ディレクトリに作成されるファイルの" -"形でその結果を記録しなければなりません。 CWLツールによって返される出力パラメ" -"ータは、出力ファイルそのものであるか、またはそれらのファイルの内容を調べるこ" -"とによって得られるものです。" +"CWLでツールを実行する場合、実行を開始したディレクトリが出力ディレクトリになり" +"ます。 基礎となるツールやスクリプトは、出力ディレクトリに作成されるファイル" +"の形でその結果を記録しなければなりません。 CWLツールによって返される出力パラ" +"メータは、出力ファイルそのものであるか、またはそれらのファイルの内容を調べる" +"ことによって得られるものです。" #: ../../src/topics/outputs.md:16 9845e517f7d848e5b59a97880ca6999f msgid "" @@ -3294,8 +3342,8 @@ msgid "" msgstr "" "これまでの例では、`baseCommand` " "は単なる文字列で、引数はCWL入力として渡していました。単一の文字列の代わりに、" -"_文字列の配列_ を使用することができます。 配列の最初の要素は実行するコマンド" -"で、それ以降の要素は必須のコマンドライン引数です" +"_文字列の配列_ を使用できます。 配列の最初の要素は実行するコマンドで、それ以" +"降の要素は必須のコマンドライン引数です" #: ../../src/topics/outputs.md:28 9b65071222c94951bed12ac53e964ee3 msgid "`tar.cwl`" @@ -3337,7 +3385,7 @@ msgstr "" "[`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) フィ" "ールドは、出力ディレクトリ内のファイル名で構成されます。前もって出力ファイル" "名が分からない場合は、`glob: '*.txt'` " -"のようにワイルドカードパターンを使用することができます。" +"のようにワイルドカードパターンを使用できます。" #: ../../src/topics/outputs.md:69 8a6e9173198241429effd911c3a7c4d7 msgid "Capturing Standard Output" @@ -3414,8 +3462,8 @@ msgstr "" "ん。なぜなら、\"hello.txt \"というファイル名は" "、使用する入力ファイルによって異なるか、または依存する可能性があるからです。" " これを避けるために、ジョブパラメーターファイル(`.yml`)で必要なファイル名を" -"指定することができます。この例では、入力パラメーターの値を他のフィールドから" -"動的に参照して、抽出するファイル名を指定する方法を説明します。" +"指定できます。この例では、入力パラメーターの値を他のフィールドから動的に参照" +"して、抽出するファイル名を指定する方法を説明します。" #: ../../src/topics/parameter-references.md:13 50db8add9b1942d986e581b8d21c2ee4 msgid "`tar-param.cwl`" @@ -3433,11 +3481,11 @@ msgstr "入力ファイル(入力オブジェクト)を作成し、コマンド "ジェクトを指定して`cwltool` を呼び出します：" #: ../../src/topics/parameter-references.md:36 06926a516ae6432d96e3eaa62202cd86 -#, fuzzy msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." -msgstr "`$(...)` で囲まれたパラメータ参照を許可するフィールドもあります。これらは評価され、参照されている値に置き換えられます。" +msgstr "`$(...)` で囲まれたパラメータ参照を許可するフィールドもあります。これらは評価" +"され、参照されている値に置き換えられます。" #: ../../src/topics/parameter-references.md:47 384fe8188f414eafbbb8d6b81bdfd779 msgid "" @@ -3472,8 +3520,7 @@ msgstr "パラメータ参照はどこで許されるのですか？" #: ../../src/topics/parameter-references.md:61 055d3268859c46c4b7db5005608bae05 msgid "You can only use parameter references in certain fields. These are:" -msgstr "パラメータ参照は、特定のフィールドでのみ使用することができます。 " -"以下はその例です：" +msgstr "パラメータ参照は、特定のフィールドでのみ使用できます。 以下はその例です：" #: ../../src/topics/parameter-references.md:63 2ed66835bd9044adbfdd0b5097787f22 msgid "" @@ -3588,7 +3635,6 @@ msgstr "ソフトウェア要求事項の指定" #: ../../src/topics/specifying-software-requirements.md:3 #: e708866921ea49d69d3c2a32d63ea468 -#, fuzzy msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -3619,10 +3665,10 @@ msgid "" "enable these checks with the reference implementation, use the " "[dependency resolvers configuration][dependencies]." msgstr "" -"CWLランナーによっては、これらのヒントを使用して、ジョブの実行前に必要なソフト" -"ウェアがインストールされ、利用可能であることをチェックすることができます。リ" -"ファレンス実装でこれらのチェックを有効にするには、[依存性解決のための設定][de" -"pendencies] を使用します。" +"CWL runnerによっては、これらのヒントを使用して、ジョブの実行前に必要なソフト" +"ウェアがインストールされ、利用可能であることをチェックできます。リファレンス" +"実装でこれらのチェックを有効にするには、[依存性解決のための設定][dependencies" +"] を使用します。" #: ../../src/topics/specifying-software-requirements.md:29 #: 1a8b8aadf1c64e87b8b670e288bc14bc @@ -3641,6 +3687,17 @@ msgid "" "preference, are to include the DOI for the main tool citation and the URL" " to the tool." msgstr "" +"バージョン番号だけでなく、ツールの一意なリソース識別子（URI）が[RRID][rrid]の" +"形で与えられます。RRIDを持つリソースは[SciCrunch][scicrunch]レジストリで検索" +"することができ、科学リソースを一貫して検索、追跡、参照するためのポータルを提" +"供します。ツールを [`SoftwareRequirement`](https://w3id.org/cwl/" +"CommandLineTool.html#SoftwareRequirement) として指定したい場合は、SciCrunch " +"でツールを検索し、レジストリで割り当てられた RRID を使用してください。(" +"ツールを SciCrunch に追加するには [リソースの追加チュートリアル][scicrunch-" +"add-tool] を参照してください)。この RRID を使って、（[identifiers." +"org][identifiers] 経由で）要件説明の `specs` フィールドでツールを参照できます" +"。他の良い選択としては、優先順位の高い順に、メインのツールの引用のためのDOIと" +"ツールのURLを含めることです。" #: ../../src/topics/staging-input-files.md:1 d10c792550e8498c8ee384d3093da306 msgid "Staging Input Files" @@ -3679,8 +3736,9 @@ msgid "" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -"このセクションでは、CWLの実行に問題がある場合にトラブルシューティングを行う方法を説明します。ここでは、`cwltool` " -"に焦点を当てますが、これらのテクニックのいくつかは他のCWLランナーにも適用されるかもしれません。" +"このセクションでは、CWLの実行に問題がある場合にトラブルシューティングを行う方" +"法を説明します。ここでは、`cwltool` に焦点を当てますが、" +"いくつかのテクニックは他のCWL runnerでも使えるかもしれません。" #: ../../src/topics/troubleshooting.md:6 1d47f4ce04554cabb1ccf40a13ee42ec msgid "Run `cwltool` with `cachedir`" @@ -3696,9 +3754,9 @@ msgid "" msgstr "" "ワークフロー実行時に`--cachedir` オプションを使用すると、`cwltool` に中間ファ" "イル（入力ファイルでも出力ファイルでもないが、ワークフロー実行中に作成される" -"ファイル）をキャッシュするよう指示することができます。デフォルトでは、これら" -"のファイルは一時ディレクトリに作成されますが、別のディレクトリに書き込むこと" -"でアクセスが容易になります。" +"ファイル）をキャッシュするよう指示できます。デフォルトでは、これらのファイル" +"は一時ディレクトリに作成されますが、別のディレクトリに書き込むことでアクセス" +"が容易になります。" #: ../../src/topics/troubleshooting.md:14 36ec60b80c714357a4274217274136ff msgid "" @@ -3741,7 +3799,7 @@ msgstr "" "`step_b` が存在しない `revv` コマンドの実行に失敗したため、ワークフローは " "`permanentFail` ステータスになっています。`step_a` は正常に実行され、" "その出力は `cachedir` " -"にキャッシュされました。作成された中間ファイルを確認することができます：" +"にキャッシュされました。作成された中間ファイルを確認できます：" #: ../../src/topics/troubleshooting.md:44 04e80f7ce14d4d73bc5d290dcf01bcdb msgid "" @@ -3811,18 +3869,17 @@ msgstr "" "いランタイムを提供することによって、ソフトウェアのインストールを簡素化します" "。 しかし、コンテナはホストシステムから意図的に隔離されているため、Dockerコ" "ンテナ内でツールを実行するには、入力ファイルがコンテナ内で利用可能で、出力フ" -"ァイルがコンテナから回収できることを確認するための追加作業が必要です。 CWLラ" -"ンナーはこの作業を自動的に行うことができるため、Dockerコンテナの呼び出しや管" -"理の複雑さを回避しながら、Dockerを使用してソフトウェア管理を簡素化することが" -"できます。" +"ァイルがコンテナから回収できることを確認するための追加作業が必要です。 CWL r" +"unnerはこの作業を自動的に行うことができるため、Dockerコンテナの呼び出しや管理" +"の複雑さを回避しながら、Dockerを使用してソフトウェア管理を簡素化できます。" #: ../../src/topics/using-containers.md:15 4b0f6cfc8a774c77bfbc99e568af2ece msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." -msgstr "CWLランナーの役割のひとつに、入力ファイルのパスをコンテナ内のでの配置位置に合" -"わせることがあります。" +msgstr "CWL runnerの役割のひとつに、入力ファイルのパスをコンテナ内のでのパスに合わせ" +"ることがあります。" #: ../../src/topics/using-containers.md:18 27c02a5d479a420eab7d14888d9fb288 msgid "" @@ -3852,7 +3909,6 @@ msgstr "" "の部分だけです。" #: ../../src/topics/using-containers.md:44 1f02618ab6254459ae71f72844e3cc18 -#, fuzzy msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3890,7 +3946,8 @@ msgstr "`hello.js`" msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." -msgstr "CWLランナーがスクリプトを実行するためにDockerコマンドラインを構築していることに注目してください。" +msgstr "CWL runnerがスクリプトを実行するためにDockerコマンドラインを構築していること" +"に注目してください。" #: ../../src/topics/using-containers.md:72 d2dd89a5edde4f2eab4c2baf0cc78745 msgid "" @@ -3990,7 +4047,6 @@ msgid "Visualization of 1st-workflow.cwl" msgstr "1st-workflow.cwlの可視化" #: ../../src/topics/workflows.md:180 f0831481a43548039fbc4fd17555af57 -#, fuzzy msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -4002,15 +4058,13 @@ msgid "" "language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" "-1st-workflow/1st-workflow.cwl)" msgstr "" -"[[1st-" -"workflow.cwlを可視化したもの]](https://view.commonwl.org/graph/png/github.com" -"/common-workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-" -"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-workflow.cwl)" +"[![1st-workflow.cwlを可視化したもの](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/" +"common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)" #: ../../src/topics/workflows.md:183 5ff059fc8ae6471c8ea86dab7e5a93f5 msgid "" @@ -4066,7 +4120,6 @@ msgstr "" "を、ワークフロー出力パラメータ`compiled_class` とします。" #: ../../src/topics/workflows.md:248 e0429688fce445da8083e69323e5b020 -#, fuzzy msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -4085,19 +4138,18 @@ msgstr "" "されることがあります。" #: ../../src/topics/workflows.md:256 980f5eada57c4fadbb783838ded1fa0b -#, fuzzy msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" " parameters, `tarfile` and `extractfile` and one output parameter " "`extracted_file`." msgstr "" -"最初のステップである`untar` は、`tar-param.cwl` を実行します（[パラメータ参照](parameter-" -"references.md)で以前説明しました）。このツールは、2つの入力パラメータ、`tarfile` と`extractfile` " -"と1つの出力パラメータ`extracted_file` を持ちます。" +"最初のステップである`untar` は、`tar-param.cwl` を実行します（[パラメータ参照" +"](parameter-references." +"md)で以前説明しました）。このツールは、2つの入力パラメータ、`tarfile` " +"と`extractfile` と1つの出力パラメータ`extracted_file` を持ちます。" #: ../../src/topics/workflows.md:261 3532e165842f4ebb8db0c78208071555 -#, fuzzy msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -4122,7 +4174,6 @@ msgstr "ワークフローステップの`out` " "セクションには、ツールから期待される出力パラメータが記載されています。" #: ../../src/topics/workflows.md:278 2651ee113a3d4b79b138854ebe729f48 -#, fuzzy msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -4134,7 +4185,7 @@ msgstr "" "第2ステップ `compile` は、第1ステップの結果に依存し、入力パラメータ`src` " "を`untar` の出力パラメータに接続し、`untar/extracted_file` を使用します。 " "これは、`arguments.cwl` (以前に [追加の引数とパラメータ](additional-" -"arguments-and-parameters.md)で説明) " +"arguments-and-parameters.md)で説明したものです) " "を実行します。このステップの出力`classfile` は、前述のワークフローの`outputs`" " セクションに接続されています。" @@ -4149,8 +4200,10 @@ msgid "" " workflow can be used as a step in another CWL workflow, if the workflow " "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -"ワークフローは、複数のツールを組み合わせてより大きな処理を実行するための方法です。ワークフローエンジンが`SubworkflowFeatureRequirement`" -" をサポートしている場合、CWL ワークフローを別の CWL ワークフローのステップとすることができます ：" +"ワークフローは、複数のツールを組み合わせてより大きな処理を実行するための方法" +"です。ワークフローエンジンが`SubworkflowFeatureRequirement` " +"をサポートしている場合、CWL ワークフローを別の CWL " +"ワークフローのステップにできます ：" #: ../../src/topics/workflows.md:297 44d281d99cd944478db98446a984c001 msgid "" @@ -4207,7 +4260,7 @@ msgstr "" "CWL`Workflow` は、`CommandLineTool` を`step` として使用することができ、その " "CWL ファイルは`run` に記述されます。ワークフローの入力（`tarball` " "および`name_of_file_to_extract` ）と出力（`compiled_class` " -"）は、ステップの入力/出力になるようにマッピングすることができます。" +"）は、ステップの入力/出力になるようにマッピングできます。" #: ../../src/topics/workflows.md:336 d621821d2c1b403cb7415b381dd883f6 msgid "" @@ -4238,28 +4291,28 @@ msgstr "" "るのがよいでしょう。これらは、ツールとしての使用法にも現れるからです。" #: ../../src/topics/workflows.md:347 c6297c120e004ae8b52d5b519fbc04d2 -#, fuzzy msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" "coded `Hello.java` file using the previously mentioned " "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -"また、あまり一般的でない方法で、ジョブファイルの外部依存を回避することも可能です。そこで、このワークフローでは、先に述べた`InitialWorkDirRequirement`" -" の要件を使用して、ハードコードされた`Hello.java` ファイルを生成してから、それを tar ファイルに追加することができます。" +"また、あまり一般的でない方法で、ジョブファイルの外部依存を回避することも可能" +"です。そこで、このワークフローでは、先に述べた`InitialWorkDirRequirement` " +"の要件を使用して、ハードコードされた`Hello.java` ファイルを生成してから、" +"それを tar ファイルに追加できます。" #: ../../src/topics/workflows.md:366 66f76677f4ce42baa8a8813410ea5aee -#, fuzzy msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -"この場合、ステップではパラメータ化するのではなく、`Hello.java` を想定することができるので、`baseCommand` " -"で直接書かれた値`hello.tar` と`Hello.java` を使用でき、結果として`outputs` が得られます：" +"この場合、ステップではパラメータ化するのではなく、`Hello.java` " +"を想定することができるので、`baseCommand` に直接書かれた値`hello.tar` " +"と`Hello.java` を使用でき、結果として`outputs` が得られます：" #: ../../src/topics/workflows.md:383 a8ccb9f9ab4448e087ea8448d620d33c -#, fuzzy msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -4267,8 +4320,11 @@ msgid "" "reason for doing it in this case is because the command line is hard-" "coded with filenames that only make sense within this workflow." msgstr "" -"`tar --create` ツールを別のファイルに分割せず、CWL Workflow " -"定義の中に埋め込んだことにお気づきでしょうか。これは一般的にベストプラクティスではありません。なぜなら、そのツールを再利用できないからです。このケースでそれを行う理由は、コマンドラインに、このワークフロー定義内でしか意味をなさないファイル名がハードコーディングされているためです。" +"`tar --create` ツールを別のファイルに分割せず、CWL Workflow 定義の中に埋め込" +"んだことにお気づきでしょうか。これは一般的にベストプラクティスではありません" +"。なぜなら、そのツールを再利用できないからです。このケースでそれを行う理由は" +"、コマンドラインに、このワークフロー定義内でしか意味をなさないファイル名がハ" +"ードコーディングされているためです。" #: ../../src/topics/workflows.md:389 afe43b9e92e949a589f493293eff2903 msgid "" @@ -4300,7 +4356,6 @@ msgid "Scattering Steps" msgstr "Scatter ステップ" #: ../../src/topics/workflows.md:400 eab4437bf9994b649954221375e3dd6d -#, fuzzy msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -4312,10 +4367,10 @@ msgid "" msgstr "" "ワークフローの書き方がわかったので、`ScatterFeatureRequirement` を利用し始め" "ることができます。この機能は、ツールやワークフローを入力のリストに対して複数" -"回実行したいことをランナーに伝えます。ワークフローは、入力を配列として受け取" -"り、配列の各要素に対して、あたかも1つの入力であるかのように、指定されたステッ" -"プを実行します。これにより、多くの異なるコマンドや入力 yaml ファイルを生成す" -"ることなく、複数の入力に対して同じワークフローを実行することができます。" +"回実行したいことをrunnerに伝えます。ワークフローは、入力を配列として受け取り" +"、配列の各要素をあたかも1つの入力であるかのように、指定されたステップを実行し" +"ます。これにより、多くの異なるコマンドや入力 yaml ファイルを生成することなく" +"、複数の入力に対して同じワークフローを実行できます。" #: ../../src/topics/workflows.md:411 c245ba0ae2074fa388ad6c35695033c8 msgid "" @@ -4351,21 +4406,23 @@ msgid "" " particular step. Note that the input name listed after scatter is the " "one of the step's input, not a workflow level input." msgstr "" -"ここでは、ステップ`echo` に、`scatter` という新しいフィールドを追加しました。" -"このフィールドは、CWLランナーに、このステップの入力を分散して実行したいことを" -"伝えます。scatterの後に記載されている入力名は、ワークフローレベルの入力名では" -"なく、ステップの入力名であることに注意してください。" +"ここでは、ステップ`echo` に、`scatter` " +"という新しいフィールドを追加しました。このフィールドは、CWL runnerに、このス" +"テップの入力を分散して実行したいことを伝えます。scatterの後に記載されている入" +"力名は、ワークフローレベルの入力名ではなく、ステップの入力名であることに注意" +"してください。" #: ../../src/topics/workflows.md:445 0d5cf8b82dbd47f2abd1ed16b9b3eb61 -#, fuzzy msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " "you expect that the final output of your workflow will now have multiple " "outputs to collect, be sure to update that to an array type as well!" msgstr "" -"最初のスキャッターでは、これと同じくらい簡単です！このツールは出力を回収しないので、`outputs: []` " -"を使います。しかし、ワークフローの最終出力に収集する複数の出力があることが予想される場合、それを配列型に更新するようにしてください！" +"最初のスキャッターでは、これと同じくらい簡単です！このツールは出力を回収しな" +"いので、`outputs: []` を使います。しかし、ワークフローの最終出力に収集する複" +"数の出力があることが予想される場合、それを配列型に更新するようにしてください" +"！" #: ../../src/topics/workflows.md:450 38b7042a270043ba82c11cf2e758f0c8 msgid "Using the following input file:" @@ -4416,18 +4473,17 @@ msgid "`wc-tool.cwl`" msgstr "`wc-tool.cwl`" #: ../../src/topics/workflows.md:489 63595d35dded4911aab0be3a165eec0c -#, fuzzy msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" -msgstr "さて、スキャッターはどのように取り入れるのでしょうか？スキャッターフィールドは各ステップの下にあることを思い出してください：" +msgstr "さて、scatterはどのように取り入れるのでしょうか？scatterフィールドは各ステッ" +"プの下にあることを思い出してください：" #: ../../src/topics/workflows.md:491 a7f96ec6e4f24c62ac0f5b6edcc9734b msgid "`scatter-two-steps.cwl`" msgstr "`scatter-two-steps.cwl`" #: ../../src/topics/workflows.md:497 122452b7d7114c3fa53cbea286703023 -#, fuzzy msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -4490,7 +4546,7 @@ msgid "" msgstr "" "このワークフローは、条件付きステップを含み、入力に基づき実行されます。これに" "より、ワークフローは、プログラムの開始時に与えられた入力パラメータや以前のス" -"テップによって、追加のステップをスキップすることができます。" +"テップによって、追加のステップをスキップできます。" #: ../../src/topics/workflows.md:527 9ac7b4f71621411da9a4ca3bc277dcb0 msgid "`conditional-workflow.cwl`" @@ -4504,7 +4560,6 @@ msgstr "まず、このワークフローはCWL仕様のバージョン1." "2以降から対応しているがわかります。" #: ../../src/topics/workflows.md:573 4742fe09a4264fb8be6f092519de5d72 -#, fuzzy msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -4614,7 +4669,7 @@ msgstr "" "上記のYAMLは4つのキー -`first_name`,`last_name`,`age_years`, `home` - 及びそ" "れぞれの値を定義しています。値は、文字列、数値（整数、浮動小数点、科学的表現" "）、ブール値（`true` または`false` " -"）、またはより複雑な入れ子型（下記参照）にすることができます。" +"）、またはより複雑な入れ子型（下記参照）にできます。" #: ../../src/topics/yaml-guide.md:51 6939eb7e783744d7bcf75ea0a7cae129 msgid "" @@ -4641,8 +4696,8 @@ msgid "" "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -"`#` を使うと、CWL定義や入力パラメータファイルにコメントを追加することができま" -"す。` #` の右側にある文字は、YAML " +"`#` を使うと、CWL定義や入力パラメータファイルにコメントを追加できます。` #` " +"の右側にある文字は、YAML " "を解釈するプログラムによって無視されます。たとえば、次のようになります：" #: ../../src/topics/yaml-guide.md:76 13da997c82c04023a4b7bb36b76e969d @@ -4657,7 +4712,6 @@ msgid "Maps" msgstr "マップ" #: ../../src/topics/yaml-guide.md:81 aedf8c4f615845ad91a7947217005d6e -#, fuzzy msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -4667,15 +4721,14 @@ msgid "" "the key to which they belong (the \"parent\"), and should be indented " "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -"CWLでツールやワークフローを定義する場合、通常、より複雑で入れ子の表現を構築す" -"る必要があります。_maps_ と呼ばれるこれらの階層構造は、キーの値として追加のキ" -"ーと値のペアを提供することでYAMLで記述されます。これらのペア（「子」と呼ばれ" -"ることもあります）は、属するキー（「親」）の下の新しい行に書かれ、2つのスペー" -"スでインデントされます（⇥タブ文字は許可されていません）。例えば、次のようにな" -"ります：" +"CWLでツールやワークフローを定義する場合、通常、より複雑で入れ子構造の表現を構" +"築する必要があります。_maps_ と呼ばれるこれらの階層構造は、キーの値として追加" +"のキーと値のペアを提供することによりYAMLで記述されます。これらのペア（「子」" +"と呼ばれることもあります）は、属するキー（「親」）の下の新しい行に書かれ、2つ" +"のスペースでインデントされます（⇥タブ文字は許可されていません）。例えば、次の" +"ようになります：" #: ../../src/topics/yaml-guide.md:104 f0f1f414f74342a89065ba5ded8668e5 -#, fuzzy msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -4688,8 +4741,8 @@ msgid "" "object it describes." msgstr "" "上記のYAMLは、複雑なネストされたオブジェクトの記述を比較的素早く構築する方法" -"を示しています。`inputs` マップは単一のキー、`example_flag` " -"を含み、それ自体が2つのキー、`type` と`inputBinding` " +"を示しています。`inputs` マップはキー`example_flag` " +"だけを含み、それ自体が2つのキー、`type` と`inputBinding` " "を含み、これらの子の1つ、`inputBinding` はさらに2つのキーと値のペア " "(`position` と`prefix`) を含みます。1つのキーに対して複数の値/キーバリューペ" "アを提供することについての詳細は、以下の[配列](#arrays)のセクションを参照して" @@ -4701,7 +4754,6 @@ msgid "Arrays" msgstr "配列" #: ../../src/topics/yaml-guide.md:129 5aca9a90fb6149529ed717992746a2f3 -#, fuzzy msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -4713,13 +4765,12 @@ msgid "" msgstr "" "ある状況下では、1つのキーに対して複数の値やオブジェクトを提供する必要がありま" "す。上記の[Maps](#maps)のセクションですでに見たように、1つのキーに複数のキー" -"と値のペアをマッピングすることができます。しかし、各値にユニークなキーを用意" -"しなくても、キーに対して複数の値を定義することも可能です。この場合、_array_ " +"と値のペアをマッピングできます。しかし、各値にユニークなキーを用意しなくても" +"、キーに対して複数の値を定義することも可能です。この場合、_array_ " "を用いて、各値を独自の行で定義し、その前に`-` " "を置くことで実現できます。例えば、次のようになります：" #: ../../src/topics/yaml-guide.md:146 d1c9e72e004b4fb4a6efb7748a15ab6f -#, fuzzy msgid "and a more complex example combining maps and arrays:" msgstr "と、マップと配列を組み合わせたより複雑な例です：" @@ -4737,12 +4788,10 @@ msgstr "" "(JSON)][json]に基づいています。マップと配列は、JSON構文を使ってYAMLで定義することもできます。例えば:" #: ../../src/topics/yaml-guide.md:177 d8feed2d36d04fe283b9de9784d91941 -#, fuzzy msgid "and:" msgstr "と：" #: ../../src/topics/yaml-guide.md:184 5156ad32791048f8ace51475d7689575 -#, fuzzy msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -4751,23 +4800,25 @@ msgid "" "However, as the second example above shows, it can severely affect the " "readability of a YAML file, and should be used sparingly." msgstr "" -"ネイティブ JSON は、フィールドが意図的に空のままになっている場所 (空の配列を表す`[]` など) " -"や、値が同じ行にあることがより理にかなっている場所 (たとえば、シェルコマンドでオプションフラグとその値を提供する場合) " -"を示すのに便利なことがあります。しかし、上の2番目の例が示すように、YAMLファイルの可読性に深刻な影響を与える可能性があるので、控えめに使用する必要があります。" +"ネイティブ JSON は、フィールドが意図的に空のままになっている場所 " +"(空の配列を表す`[]` など) や、値が同じ行にあることがより理にかなっている場所 " +"(たとえば、シェルコマンドでオプションフラグとその値を提供する場合) を示すのに" +"便利なことがあります。しかし、上の2番目の例が示すように、YAMLファイルの可読性" +"に深刻な影響を与える可能性があるので、控えめに使用する必要があります。" #: ../../src/topics/yaml-guide.md:194 ce49f80e6fc0498b8ad298fb1f0268f3 msgid "Reference" msgstr "リファレンス" #: ../../src/topics/yaml-guide.md:196 180d261392a644fcb8ff47d7a4a160c0 -#, fuzzy msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -"[Learn YAML in Y Minutes][yaml-y-mins] " -"リファレンスは、CWLでは有効でない機能もカバーしていますが、このガイドを書く間、私たちにとって非常に役に立ちました。" +"[Learn YAML in Y Minutes][yaml-y-mins] リファレンスは、CWLでは有効でない機能" +"もカバーしていますが、このガイドを書く間、私たちにとって非常に役に立ちました" +"。" #: ../../src/tutorials.md:1 d682035afebf4c128755bd4e58780dd2 msgid "Tutorials" From feb369ed19565cad8af1006f4ca032e2dd1de979 Mon Sep 17 00:00:00 2001 From: Languages add-on Date: Fri, 17 May 2024 19:16:57 +0200 Subject: [PATCH 156/179] Added translation using Weblate (Catalan) Co-authored-by: Languages add-on --- locales/ca/LC_MESSAGES/sphinx.po | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 locales/ca/LC_MESSAGES/sphinx.po diff --git a/locales/ca/LC_MESSAGES/sphinx.po b/locales/ca/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..b13b0b9a --- /dev/null +++ b/locales/ca/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: ca\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "" From 596257942853e5331d8a361b2ea784059d855950 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?N=C3=BAria=20Queralt=20Rosinach?= Date: Fri, 17 May 2024 19:16:57 +0200 Subject: [PATCH 157/179] Translated using Weblate (Catalan) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Currently translated at 1.0% (6 of 598 strings) Translated using Weblate (Catalan) Currently translated at 0.1% (1 of 598 strings) Translated using Weblate (Spanish) Currently translated at 4.5% (27 of 599 strings) Co-authored-by: Núria Queralt Rosinach Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ca/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/es/ Translation: Common Workflow Language/CWL User Guide --- locales/ca/LC_MESSAGES/user_guide.po | 27 +++++++++++++++++++-------- locales/es/LC_MESSAGES/user_guide.po | 28 ++++++++++++++++++---------- 2 files changed, 37 insertions(+), 18 deletions(-) diff --git a/locales/ca/LC_MESSAGES/user_guide.po b/locales/ca/LC_MESSAGES/user_guide.po index a5097d09..70ee8d30 100644 --- a/locales/ca/LC_MESSAGES/user_guide.po +++ b/locales/ca/LC_MESSAGES/user_guide.po @@ -8,48 +8,59 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" +"PO-Revision-Date: 2024-05-17 10:02+0000\n" +"Last-Translator: Núria Queralt Rosinach \n" +"Language-Team: Catalan \n" "Language: ca\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 5.6-dev\n" #: ../../LICENSE.md:2 #: 4e203044f0464fd5a3256430391dde12 +#, fuzzy msgid "Licenses" -msgstr "" +msgstr "Llicències" #: ../../LICENSE.md:4 #: 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" -msgstr "" +msgstr "Material Didàctic" #: ../../LICENSE.md:6 #: 747f9dd48bc54f44adcd8b18c57f4d9d msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." msgstr "" +"Tot el material didàctic del projecte Common Workflow Language i els canvis " +"de l’estructura estan disponibles sota la llicència [Creative Commons " +"Attribution License][cc-by-human]. El següent és un resum (i no un substitut)" +" en format llegible per persones del [text legal complet de la llicència CC " +"BY 4.0][cc-by-legal]." #: ../../LICENSE.md:12 #: 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" -msgstr "" +msgstr "Vostè és lliure de:" #: ../../LICENSE.md:14 #: 466be810dd8d4a838e0edb5869f2c4eb msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" +"a **Compartir**---còpia i redistribueix el material en qualsevol medi o " +"format" #: ../../LICENSE.md:15 #: 18a3a0aec35743848c97bc178f9c94ff msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" +msgstr "a **Adaptar**---remescla, transforma i construeix segons el material" #: ../../LICENSE.md:17 #: b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." -msgstr "" +msgstr "per qualsevol propòsit, fins i tot comercial." #: ../../LICENSE.md:19 #: 6021e65292a149d5b15e14491f3eb05e diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index 6f69499c..b0b2e427 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,15 +9,16 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2023-01-27 14:27+0000\n" -"Last-Translator: Michael Crusoe \n" +"PO-Revision-Date: 2024-05-16 13:22+0000\n" +"Last-Translator: Núria Queralt Rosinach \n" +"Language-Team: Spanish \n" "Language: es\n" -"Language-Team: Spanish \n" -"Plural-Forms: nplurals=2; plural=n != 1;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 5.6-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -156,11 +157,16 @@ msgid "" " of software, tools and workflows described using CWL are portable across" " a variety of platforms that support the CWL standard." msgstr "" +"CWL es una manera de describir herramientas de línea de comandos y " +"conectarlas para crear flujos de trabajo. Puesto que CWL es una " +"especificación y no un software concreto, las herramientas y flujos de " +"trabajo descritos usando CWL son portables en múltiples plataformas que " +"soporten el estándar CWL." #: ../../src/episodes.md:5 ../../src/setup.md:5 #: 1361ff6bf4924efc9ce9a85785a6b381 eb254514301c491e81f72ae19c407261 msgid "This page has moved" -msgstr "" +msgstr "Esta página se ha trasladado" #: ../../src/episodes.md:9 f03d7cbe6670451db0896f1b674d56c7 msgid "" @@ -168,10 +174,13 @@ msgid "" "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" +"Esta página es obsoleta y la mantenemos aquí para preservar los enlaces de " +"la Guía del Usuario antigua. Por favor utilice la nueva [Tabla de " +"Contenidos](index.md#table-of-contents) para navegar por la Guía del Usuario." #: ../../src/faq.md:1 d65ad48ac6314bf0a74c34a6766561fc msgid "FAQ" -msgstr "" +msgstr "Preguntas frecuentes" #: ../../src/faq.md:11 370a9659c7904ef6b5e1ae7480f82ef6 msgid "How do I create non \"`File`\" types using `evalFrom`?" @@ -208,11 +217,11 @@ msgstr "" #: ../../src/faq.md:86 8641f105131b4ac1bca7e0a46756ef79 msgid "How do I reference a local script?" -msgstr "" +msgstr "¿Cómo hago referencia a un script local?" #: ../../src/faq.md:88 d3e43b40d6994b32bc37067ee116418e msgid "There are two ways to reference a local script:" -msgstr "" +msgstr "Hay dos maneras de referenciar un script local:" #: ../../src/faq.md:90 64b140a321ca4087945339c523cc24dd msgid "" @@ -4368,4 +4377,3 @@ msgstr "" #~ " only part that is really new " #~ "is the `dockerRequirement` section." #~ msgstr "" - From f615b239bbddfaf01b40e2ec0e75c787558c7705 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jos=C3=A9=20Ra=C3=BAl=20Romero?= Date: Fri, 17 May 2024 19:16:57 +0200 Subject: [PATCH 158/179] Translated using Weblate (Spanish) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Currently translated at 10.1% (61 of 599 strings) Translated using Weblate (Spanish) Currently translated at 4.5% (27 of 599 strings) Co-authored-by: José Raúl Romero Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/es/ Translation: Common Workflow Language/CWL User Guide --- locales/es/LC_MESSAGES/user_guide.po | 106 +++++++++++++++++++++++---- 1 file changed, 91 insertions(+), 15 deletions(-) diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index b0b2e427..aadfd529 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,8 +9,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-05-16 13:22+0000\n" -"Last-Translator: Núria Queralt Rosinach \n" +"PO-Revision-Date: 2024-05-17 10:02+0000\n" +"Last-Translator: José Raúl Romero \n" "Language-Team: Spanish \n" "Language: es\n" @@ -184,11 +184,11 @@ msgstr "Preguntas frecuentes" #: ../../src/faq.md:11 370a9659c7904ef6b5e1ae7480f82ef6 msgid "How do I create non \"`File`\" types using `evalFrom`?" -msgstr "" +msgstr "¿Cómo creo tipos que no sean \"`File`\" utilizando `evalFrom`?" #: ../../src/faq.md:41 8333f51e3f5945fe8963adfc6685bcb1 msgid "How do I rename an input file?" -msgstr "" +msgstr "¿Cómo renombro un fichero de entrada?" #: ../../src/faq.md:43 f6b88d9154d049d7807afa9bb0f1ac98 msgid "" @@ -197,16 +197,23 @@ msgid "" "produced from another step in a workflow, and don't want to work with the" " default names that these files were given when they were created." msgstr "" +"Este ejemplo muestra como cambiar el nombre de un fichero de entrada como " +"parte de la descripción de una herramienta. Esto podría ser útil cuando se " +"están tomando archivos producidos por otro paso del flujo de trabajo y no se " +"desea trabajar con los nombres predeterminados que se les asignó cuando " +"fueron creados." #: ../../src/faq.md:59 833510f5896b4a6eb5875d25eca5b047 msgid "How do I rename an output file?" -msgstr "" +msgstr "¿Cómo renombro un fichero de salida?" #: ../../src/faq.md:61 207e2f97d1c44233ae3f109c5a6ec944 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" +"Este ejemplo muestra cómo cambiar el nombre de un fichero de salida a partir " +"del nombre por defecto asignado por una herramienta:" #: ../../src/faq.md:83 d66acc583da24273980a52be03e79e91 msgid "" @@ -214,6 +221,9 @@ msgid "" " engines will rename the file using the new name for subsequent steps or " "as a workflow-level output." msgstr "" +"Cambiando el campo `basename` en `outputEval`, los motores de flujo de " +"trabajo CWL renombrarán el fichero utilizando el nuevo nombre para los pasos " +"posteriores o como salida a nivel de flujo de trabajo." #: ../../src/faq.md:86 8641f105131b4ac1bca7e0a46756ef79 msgid "How do I reference a local script?" @@ -230,16 +240,21 @@ msgid "" "the shell script directly (without explicitly using the `sh` or `bash` " "commands)." msgstr "" +"El primer método implica añadir la ruta al directorio donde se alojan los " +"scripts a la variable de entorno `PATH`. Esto permite ejecutar directamente " +"el script de shell (sin necesidad de utilizar explícitamente comandos `sh` o " +"`bash`)." #: ../../src/faq.md:93 34ebca4487a54ceab5d087105820e945 msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" +msgstr "Se empieza añadiendo _shebang_ en la parte superior del fichero:" #: ../../src/faq.md:99 6b04a4dcdada4515b28d74aacff3537a msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" +"Después, se hace el script ejecutable con el comando `chmod +x scriptname.sh`" #: ../../src/faq.md:101 756ab4f7edcf42d3872bb86818e088c3 msgid "" @@ -247,26 +262,37 @@ msgid "" "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" +"Finalmente, se modifica el `PATH` para añadir el directorio en el que se " +"aloja el script. (Es buena práctica utilizar `$HOME/bin` para alojar los " +"scripts propios.)" #: ../../src/faq.md:108 efb46b3a2d7c4c51b65998602bfa6f18 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" +"Ahora se puede utilizar `baseCommand: scriptname.sh` para ejecutar el script " +"directamente." #: ../../src/faq.md:117 844938d5d2304c6cb03184b4b4b0b024 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" +"Cuando se desee compartir el trabajo más tarde, se puede colocar su script " +"en un contenedor de software en formato Docker." #: ../../src/faq.md:119 796ce8155e32486d9651f8f13bfa3148 msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" +"El segundo método consiste en incluir una entrada con `type: File` en el " +"propio script:" #: ../../src/faq.md:138 ba246320fdd94a1aab4736f83718d793 msgid "How can I set `self`-based input bindings for optional inputs?" msgstr "" +"¿Cómo puedo configurar enlaces de entrada basados en `self` para entradas " +"opcionales?" #: ../../src/faq.md:140 6169b7be9af7448abcb57eaf91e1cc91 msgid "" @@ -274,6 +300,10 @@ msgid "" "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" +"Actualmente, `cwltool` no puede hacer frente a la falta de entradas " +"opcionales si su enlace de entrada hace uso de `self`. A continuación se " +"muestra un ejemplo de solución para esto, a la espera de una solución más " +"sofisticada." #: ../../src/faq.md:165 6c98b7948059411b8e09cf03a552c5ab msgid "How can I model a \"one-or-the-other\" parameter?" @@ -284,12 +314,17 @@ msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" +"A continuación se muestra un ejemplo de cómo especificar diferentes cadenas " +"que se añadirán a una línea de comandos, en función del valor dado a un " +"parámetro booleano." #: ../../src/faq.md:188 5c9980839f404ba6aef92ef23034500f msgid "" "How do I connect a solo value to an input that expects an array of that " "type?" msgstr "" +"¿Cómo puedo conectar un valor aislado a una entrada que espera un array de " +"ese tipo?" #: ../../src/faq.md:190 2525baf16c1f4725b096f33fd99009cf msgid "" @@ -298,10 +333,14 @@ msgid "" " along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput):" msgstr "" +"Añade un [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) junto con [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput):" #: ../../src/faq.md:194 a00d5d96b15048a79ae099d22d63bb42 msgid "merge_nested" -msgstr "" +msgstr "merge_nested" #: ../../src/faq.md:196 3a92c6cc5c2b40ffa0d692d03bad5c87 msgid "" @@ -309,10 +348,15 @@ msgid "" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" +"La entrada debe ser una matriz que conste exactamente de una entrada por " +"cada enlace de entrada. Si se especifica \"merge_nested\" con un solo " +"enlace, el valor del enlace debe envolverse en una lista de un solo elemento." #: ../../src/faq.md:199 3af16c07e3f148ddb8849c94a3864158 msgid "Which means \"create a list with exactly these sources as elements\"." msgstr "" +"¿Qué significa \"crear una lista con exactamente estas fuentes como " +"elementos\"?" #: ../../src/faq.md:201 0ea3de393d2f42aeb82658c85a19ec45 msgid "" @@ -322,26 +366,35 @@ msgid "" "and add `linkMerge: merge_nested` under the appropriate `in` entry of the" " destination step." msgstr "" +"O en otras palabras: si el destino es de tipo `File[]` (un array de `File`s) " +"y el origen es un único `File`, entonces se añade " +"`MultipleInputFeatureRequirement` al `requirements` a nivel de flujo de " +"trabajo y se añade `linkMerge: merge_nested` bajo la entrada `in` apropiada " +"del paso de destino." #: ../../src/faq.md:229 2f1bbb611c9c4f80b7ae0566432f2f35 msgid "How do make an input optional? 💯" -msgstr "" +msgstr "¿Cómo hago una entrada opcional? 💯" #: ../../src/faq.md:231 08a226efe5d141e68215ac77725033db msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" +"Para crear un parámetro de entrada opcional, se añade un símbolo de " +"interrogación a la declaración del tipo." #: ../../src/faq.md:247 06e70a855a8f455ca0536eead77073c2 msgid "" -msgstr "" +msgstr "" #: ../../src/faq.md:248 7fda8eeb6a7f4689993ed0118c77f023 msgid "" "How do I specify an input that must come from a list of predefined values" " (i.e. How do I use enum inputs) ?" msgstr "" +"¿Cómo especifico una entrada que debe proceder de una lista de valores " +"predeterminados (esto es, cómo utilizar entradas \"enum\")?" #: ../../src/faq.md:250 b1934a82553b4da3b7f981e576245dd8 msgid "" @@ -350,16 +403,22 @@ msgid "" " form style. It does the same thing as the question mark on the other " "inputs.**" msgstr "" +"Para los indicadores de línea de comandos que requieren una entrada " +"específica como argumento, se puede declarar un tipo enum en CWL. **" +"Especificar null aquí se conoce como estilo de forma larga. Hace lo mismo " +"que el signo de interrogación en las otras entradas.**" #: ../../src/faq.md:267 17fc34fad2094f5ea60e963dabd632b8 msgid "" -msgstr "" +msgstr "" #: ../../src/faq.md:268 4d7acfbeba5b4e9cb31f08ef4b280447 msgid "" "How do I describe dependent or exclusive input parameters(e.g. How do I " "use record inputs)?" msgstr "" +"¿Cómo describo los parámetros de entrada dependientes o exclusivos (por " +"ejemplo, cómo utilizo las entradas de registro)?" #: ../../src/faq.md:270 949ce95c082f4a05891a55fee25d4873 msgid "" @@ -367,10 +426,13 @@ msgid "" "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" +"Para los indicadores de línea de comandos que son mutuamente excluyentes ****" +" o dependientes **** se puede definir un tipo de registro especial. También " +"se puede especificar null aquí para crear entradas opcionales." #: ../../src/faq.md:322 6fd3c469d11d4d52b9fbb7a3d443a8db msgid "How do I set mutually exclusive parameters?" -msgstr "" +msgstr "¿Cómo configuro parámetros mutuamente excluyentes?" #: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f msgid "" @@ -380,44 +442,58 @@ msgid "" "field you want to set. The source field is set to indicate the input from" " the workflow to be used as the value." msgstr "" +"Para establecer correctamente los campos en un tipo de entrada de registro, " +"es necesario pasar un diccionario a la entrada para establecer correctamente " +"los parámetros. Esto se hace utilizando JavaScript en línea y devolviendo el " +"diccionario con la clave del campo que desea establecer. El campo fuente se " +"establece para indicar la entrada del flujo de trabajo que se utilizará como " +"valor." #: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 msgid "How can I set Booleans?" -msgstr "" +msgstr "¿Cómo puedo establecer valores de tipo Boolean?" #: ../../src/faq.md:344 8dcb88744e5840029de0e1bbf1c4b967 msgid "These can be set by using the default field" -msgstr "" +msgstr "Se pueden asignar utilizando valores \"default\"" #: ../../src/faq.md:349 972b7a5551bb43e6b9fa30e0cb713ff7 msgid "What should I do when concatenating strings in inputs?" -msgstr "" +msgstr "¿Qué debería hacer para concatenar cadenas en las entradas?" #: ../../src/faq.md:351 68f74afc21d846dd9070d45dec0cc1d8 msgid "The valueFrom field must be used instead of default." -msgstr "" +msgstr "El campo `valueFrom` debe ser utilizado en lugar de `default`." #: ../../src/faq.md:359 53b633c6f8644106beb95ae567eb0708 msgid "" "I get `cwltool` errors due to filenames with space characters inside. " "What should I do?" msgstr "" +"Obtengo errores en `cwltool` debido a nombres de fichero con caracteres de " +"espacio. ¿Qué debo hacer?" #: ../../src/faq.md:361 7101bb5cb69e4faca4e60eabb4eb258e msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" +"`cwltool` no me permite algunos caracteres en los nombres de fichero por " +"defecto." #: ../../src/faq.md:363 0eaf834b0ca847cca6736794895f5f81 msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" +"Por ejemplo, el nombre de fichero `aqui hay un espacio.txt` incluye 3 " +"caracteres de espacio." #: ../../src/faq.md:371 7dabd8aab7a5423b842433616640bac0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" +"Si no puede evitar estos caracteres peligrosos, pase `--relax-path-checks` a " +"`cwltool`." #: ../../src/faq.md:373 b7ec33f38ce74ceb890f4379e4c41054 msgid "" From 92c1a5d2631432a588a0132a00717218a779dd46 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Fri, 17 May 2024 19:34:03 +0200 Subject: [PATCH 159/179] Translations update from Hosted Weblate (#475) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Added translation using Weblate (Catalan) Co-authored-by: Michael Crusoe * Translated using Weblate (Japanese) Currently translated at 100.0% (599 of 599 strings) Translated using Weblate (Japanese) Currently translated at 100.0% (599 of 599 strings) Translated using Weblate (Japanese) Currently translated at 96.6% (579 of 599 strings) Translated using Weblate (Japanese) Currently translated at 92.3% (553 of 599 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Added translation using Weblate (Catalan) Co-authored-by: Languages add-on * Translated using Weblate (Catalan) Currently translated at 1.0% (6 of 598 strings) Translated using Weblate (Catalan) Currently translated at 0.1% (1 of 598 strings) Translated using Weblate (Spanish) Currently translated at 4.5% (27 of 599 strings) Co-authored-by: Núria Queralt Rosinach Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ca/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/es/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Spanish) Currently translated at 10.1% (61 of 599 strings) Translated using Weblate (Spanish) Currently translated at 4.5% (27 of 599 strings) Co-authored-by: José Raúl Romero Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/es/ Translation: Common Workflow Language/CWL User Guide --------- Co-authored-by: Michael Crusoe Co-authored-by: Manabu ISHII Co-authored-by: Languages add-on Co-authored-by: Núria Queralt Rosinach Co-authored-by: José Raúl Romero --- locales/ca/LC_MESSAGES/sphinx.po | 27 + locales/ca/LC_MESSAGES/user_guide.po | 3133 ++++++++++++++++++++++++++ locales/es/LC_MESSAGES/user_guide.po | 130 +- locales/ja/LC_MESSAGES/user_guide.po | 619 ++--- 4 files changed, 3602 insertions(+), 307 deletions(-) create mode 100644 locales/ca/LC_MESSAGES/sphinx.po create mode 100644 locales/ca/LC_MESSAGES/user_guide.po diff --git a/locales/ca/LC_MESSAGES/sphinx.po b/locales/ca/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..b13b0b9a --- /dev/null +++ b/locales/ca/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: ca\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "" diff --git a/locales/ca/LC_MESSAGES/user_guide.po b/locales/ca/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..70ee8d30 --- /dev/null +++ b/locales/ca/LC_MESSAGES/user_guide.po @@ -0,0 +1,3133 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: 2024-05-17 10:02+0000\n" +"Last-Translator: Núria Queralt Rosinach \n" +"Language-Team: Catalan \n" +"Language: ca\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 5.6-dev\n" + +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +#, fuzzy +msgid "Licenses" +msgstr "Llicències" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "Material Didàctic" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" +"Tot el material didàctic del projecte Common Workflow Language i els canvis " +"de l’estructura estan disponibles sota la llicència [Creative Commons " +"Attribution License][cc-by-human]. El següent és un resum (i no un substitut)" +" en format llegible per persones del [text legal complet de la llicència CC " +"BY 4.0][cc-by-legal]." + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "Vostè és lliure de:" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" +"a **Compartir**---còpia i redistribueix el material en qualsevol medi o " +"format" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "a **Adaptar**---remescla, transforma i construeix segons el material" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "per qualsevol propòsit, fins i tot comercial." + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" + +#: ../../src/topics/best-practices.md:1 +#: 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../src/topics/best-practices.md:3 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" + +#: ../../src/topics/best-practices.md:8 +#: 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" + +#: ../../src/topics/best-practices.md:11 +#: 4dee8504a8e5496081dadc386ab45540 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" + +#: ../../src/topics/best-practices.md:20 +#: 674c238b25e240eda05e22e399f2f78f +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" + +#: ../../src/topics/best-practices.md:26 +#: b651f80f47b4442fbf29454a233697fc +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../src/topics/best-practices.md:37 +#: 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" + +#: ../../src/topics/best-practices.md:40 +#: ecf2b9c0b1664afe9c4e180610610021 +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" + +#: ../../src/topics/best-practices.md:44 +#: e24cb13d98014e558b6a6946758359e0 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:47 +#: f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" + +#: ../../src/topics/best-practices.md:50 +#: 928e3df7ca3e479ca6474a8e72cf36eb +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" + +#: ../../src/topics/best-practices.md:55 +#: d355f035676446c88b028f327aeb4829 +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" + +#: ../../src/topics/best-practices.md:58 +#: 339b852df24242189d6efcd2898a3396 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" + +#: ../../src/topics/best-practices.md:66 +#: 3ef57e6862f240bebcf193a52397af0a +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" + +#: ../../src/topics/best-practices.md:69 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" + +#: ../../src/topics/best-practices.md:73 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../src/topics/best-practices.md:76 +#: c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" + +#: ../../src/topics/best-practices.md:78 +#: fae385da16aa443da996fa23ac03d6ae +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" + +#: ../../src/topics/best-practices.md:82 +#: 92430be71ecc40e18bbbb80d5576c613 +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" + +#: ../../src/topics/best-practices.md:85 +#: 387d83db81024f65aa9a890c2d07874a +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" + +#: ../../src/topics/best-practices.md:90 +#: d8e2280a75a74916a1630afaa2fe2ae3 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" + +#: ../../src/topics/best-practices.md:93 +#: f1c1340f9745458980e0fbd641738687 +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" + +#: ../../src/topics/best-practices.md:97 +#: 5424e5472c3d466fa2a3d2022c6cb475 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" + +#: ../../src/topics/command-line-tool.md:1 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../src/topics/command-line-tool.md:3 +#: 12f57b2ba76b492abe1816e06bfb1417 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" + +#: ../../src/topics/command-line-tool.md:8 +#: e1f657a46ce94a0d83671540e2cc2dab +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" + +#: ../../src/topics/command-line-tool.md:19 +#: abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../src/topics/command-line-tool.md:57 +#: a5eacdbc9aa142c890b177869da4143d +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" + +#: ../../src/topics/command-line-tool.md:68 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../src/topics/command-line-tool.md:69 +#: e3bdaceae8784ab0807b2cf356a98580 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" + +#: ../../src/topics/command-line-tool.md:83 +#: ed521ac365db4a6ba5a1051fbaa2932e +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/custom-types.md:1 +#: cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../src/topics/custom-types.md:3 +#: 67573252cc064b27ab13eebc468ac58a +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" + +#: ../../src/topics/custom-types.md:9 +#: 73e68b3af9cf41338d843c0c40e50cdc +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:12 +#: ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../src/topics/custom-types.md:24 +#: a999b1acda2641598086648c64aa3831 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/custom-types.md:30 +#: f8c12a58cb0b46a488823c6ae95f25ea +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" + +#: ../../src/topics/custom-types.md:46 +#: f25a63e0926d4932bbe64b2e4bdabf9e +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" + +#: ../../src/topics/custom-types.md:53 +#: b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../src/topics/custom-types.md:61 +#: d718630a296545f3a989c8c71e9ddc77 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../src/topics/custom-types.md:76 +#: 9a97acd430064710bcdf76edbd9f711c +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" + +#: ../../src/topics/environment-variables.md:1 +#: 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../src/topics/environment-variables.md:3 +#: 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" + +#: ../../src/topics/environment-variables.md:7 +#: bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../src/topics/expression-tool.md:3 +#: 48deb71f361a43e48a56ed483075bca8 +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" + +#: ../../src/topics/expression-tool.md:8 +#: 716b56506ca7470299899c5d820a9ea2 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" + +#: ../../src/topics/expression-tool.md:17 +#: b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:67 +#: e3ecac0a8e604f2b98a2a12b0579990a +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" + +#: ../../src/topics/expressions.md:1 +#: c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../src/topics/expressions.md:3 +#: 007a345b4bad49cf996c4301b8386473 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../src/topics/expressions.md:9 +#: 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" + +#: ../../src/topics/expressions.md:16 +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:22 +#: efb5fd14988c4e2a8f834ee5369d4102 +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" + +#: ../../src/topics/expressions.md:25 +#: e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../src/topics/expressions.md:31 +#: 276f688ba7cc471a842f085ca852b1d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" + +#: ../../src/topics/expressions.md:35 +#: ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:47 +#: 8b70a1ad70514039b97164fa630c12e4 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" + +#: ../../src/topics/expressions.md:54 +#: 2f28ab412d2843ffa5f14acdc01fc732 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" + +#: ../../src/topics/expressions.md:62 +#: d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../src/topics/expressions.md:64 +#: cbec9277b5004e50af2728cbda0df740 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" + +#: ../../src/topics/expressions.md:66 +#: e259f55f8000479bbd8009e25cf0ca6c +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 8210b36347a749889450529ecdf4ff0e +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 23088850ad02459696f6bbd385109aac +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: f02257a822ad46ac93c5981531cc85d5 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:80 +#: 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: d289541e460147aa933f7878996f8649 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c +msgid "From `steps`" +msgstr "" + +#: ../../src/topics/expressions.md:88 +#: 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: f495da32f05a4a5ba9539be0a54c1a59 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:95 +#: bdb4c68a175047ddbe141ca24960127f +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 97b61352363f47cb890e8937c5613fa3 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../src/topics/expressions.md:106 +#: 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: 0bc424ef2ca346099f29b937379908a0 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../src/topics/expressions.md:118 +#: 29b73e1dd72744f68377f0a38c10f062 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" + +#: ../../src/topics/expressions.md:122 +#: 38a2afaf4a6c4d04909af22c93f2808d +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:128 +#: cd74f34b21af4de9be96fd897efc469b +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" + +#: ../../src/topics/expressions.md:135 +#: f12e371f3f1a4b0cb2cff9800352d48c +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:139 +#: 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:146 +#: 8f0e8f050e334ac08334e9215e1dcf61 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" + +#: ../../src/topics/expressions.md:149 +#: 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:155 +#: 7a6be0005a6441feb67f036d005d7885 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" + +#: ../../src/topics/expressions.md:158 +#: ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:171 +#: 06635145b441418aaae84dc804f3d6ac +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" + +#: ../../src/topics/expressions.md:175 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:181 +#: 04eaf1f7c630450db318dcd8b7626e15 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" + +#: ../../src/topics/expressions.md:186 +#: c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: fd4579a3c9844492b314b5c3c1775fc7 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" + +#: ../../src/topics/file-formats.md:1 +#: 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../src/topics/file-formats.md:3 +#: e024bcb70e04412e90e1838426d1b69a +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" + +#: ../../src/topics/file-formats.md:8 +#: a3db21c0b3114802a8a5b610e252ef13 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" + +#: ../../src/topics/file-formats.md:14 +#: 0f5bc8520d6a4dafa37c65343da9702a +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" + +#: ../../src/topics/file-formats.md:17 +#: 5cb830da47464a8b9c3950983fa4d56f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" + +#: ../../src/topics/file-formats.md:20 +#: 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../src/topics/file-formats.md:34 +#: a2ce43b391864e8bbde16328cc19b32b +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../src/topics/file-formats.md:45 +#: 56ee4dcfff6141d5bef80eb96559876d +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../src/topics/inputs.md:5 +#: 96671c56523c4ea9992fb5dfcfa6490e +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/inputs.md:9 +#: bcc6246742cb46bfb185e415c4a3431a +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" + +#: ../../src/topics/inputs.md:13 +#: 86dce36de687449c88fb5eb9d64eb045 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" + +#: ../../src/topics/inputs.md:16 +#: cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:33 +#: 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" + +#: ../../src/topics/inputs.md:40 +#: 7dc630ea86464b1dba3a4e5079260b3b +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" + +#: ../../src/topics/inputs.md:44 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" + +#: ../../src/topics/inputs.md:47 +#: 651e032007ea4a119d20c820bb61f86b +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:53 +#: 0b056dde9e87428996e47870b12119da +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:64 +#: 628124a1670b4b058bb0fb6e495a099c +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../src/topics/inputs.md:70 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" + +#: ../../src/topics/inputs.md:83 +#: ec2adb3912bc46e28891229e9e0d9a1c +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" + +#: ../../src/topics/inputs.md:95 +#: a519be60726a44af9941fdce04735353 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" + +#: ../../src/topics/inputs.md:109 +#: cb8fc8c4c79e467eac5fab4ca685201e +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" + +#: ../../src/topics/inputs.md:124 +#: a26cc105716f47cb807174c9003153b0 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:131 +#: cc159dd5fe5748caac838862f5b8c4d1 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" + +#: ../../src/topics/inputs.md:134 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" + +#: ../../src/topics/inputs.md:142 +#: 6812698e9ad84d3385de5e88e9dde0b3 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:148 +#: d1f02be278754267893dfce5a940997d +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" + +#: ../../src/topics/inputs.md:154 +#: 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:160 +#: 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/inputs.md:178 +#: 75d59e395c66416cae9b352db5081516 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" + +#: ../../src/topics/inputs.md:185 +#: 874c6f19abbf45d7ab7d30a378c4048d +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" + +#: ../../src/topics/inputs.md:191 +#: 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:193 +#: dea0d4b681f94e73b13965dcfe75cf7d +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" + +#: ../../src/topics/inputs.md:198 +#: ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:215 +#: 750474486a84482292eeba45f118287f +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" + +#: ../../src/topics/inputs.md:217 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:233 +#: 1eb0e39bb6d04b8cab300f44a79f3add +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" + +#: ../../src/topics/inputs.md:236 +#: bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../src/topics/inputs.md:252 +#: 4b2ab812f62c4f949dd25c8527f2411c +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" + +#: ../../src/topics/inputs.md:255 +#: b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../src/topics/inputs.md:257 +#: 2c3b884cb1c54521900cc90782e8a58d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" + +#: ../../src/topics/inputs.md:262 +#: a1073b6306044dffb414319ae01f68bb +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" + +#: ../../src/topics/inputs.md:265 +#: 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:271 +#: 9a1d92334685449386dfa3b3a899ed48 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" + +#: ../../src/topics/inputs.md:280 +#: fb623af4c480411b8fde28d01c981411 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" + +#: ../../src/topics/inputs.md:289 +#: e98e165f6bba40809c90473d72f9d592 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../src/topics/operations.md:3 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../src/topics/operations.md:7 +#: 5565c1b2d8a349169a305a9b26b4574d +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" + +#: ../../src/topics/operations.md:10 +#: 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:16 +#: 88160cef4cfa4add9020aa89511a5749 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" + +#: ../../src/topics/operations.md:24 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" + +#: ../../src/topics/operations.md:55 +#: 730ba1434a1445ae847ec6153b6a3b72 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" + +#: ../../src/topics/operations.md:58 +#: 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../src/topics/operations.md:66 +#: a25d0b1e13324b40a6b8fcd227948c4f +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" + +#: ../../src/topics/outputs.md:1 +#: da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../src/topics/outputs.md:5 +#: d661df070e3040869da412d07a71f716 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../src/topics/outputs.md:10 +#: a11585474d3849cca5467512ed964743 +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" + +#: ../../src/topics/outputs.md:16 +#: 2682f9ca8e604a0c9986f7746fdec960 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" + +#: ../../src/topics/outputs.md:19 +#: 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../src/topics/outputs.md:21 +#: 22447a560f6f4317bf67bd7c4336126c +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" + +#: ../../src/topics/outputs.md:26 +#: f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../src/topics/outputs.md:45 +#: 52703d6b7f914097934bfad13663abeb +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/outputs.md:51 +#: 5e1c79df657d4a6e84e055dd6b300a5d +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:62 +#: 329d2809dfae4f90bc638f5f03a47ee3 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" + +#: ../../src/topics/outputs.md:65 +#: 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../src/topics/outputs.md:67 +#: c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" + +#: ../../src/topics/outputs.md:71 +#: 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:91 +#: 9647019d8c37466886e7aab6f176634d +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" + +#: ../../src/topics/outputs.md:93 +#: b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:112 +#: cc067051f22f433bbece08f60933e002 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" + +#: ../../src/topics/parameter-references.md:1 +#: a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../src/topics/parameter-references.md:3 +#: dbfe2c1123144316aa026374b0f353d3 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" + +#: ../../src/topics/parameter-references.md:13 +#: 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../src/topics/parameter-references.md:25 +#: 074cf5d912854d8c864607cc24b15302 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/parameter-references.md:36 +#: 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: b54240bb94f746bba7511633aa969db0 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 8b70a072aa87414c88e89a3e19af0a51 +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" + +#: ../../src/topics/parameter-references.md:54 +#: eea20f89c45f424a888178df53713b28 +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" + +#: ../../src/topics/parameter-references.md:59 +#: cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../src/topics/parameter-references.md:61 +#: 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" + +#: ../../src/topics/parameter-references.md:63 +#: 7647e0229a924f988cf02b7812a55c06 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../src/topics/parameter-references.md:69 +#: 9d663249666045618a0d3acddb85a9a9 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:72 +#: 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:74 +#: dbf6153cd02542a6a01c172803122b7f +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:77 +#: b6250cf6fa8a4a0c94b33302e0decca5 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: fa6ca3bbc6784380a03a950a6f49a180 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:85 +#: b92b516e537a4773ad67b4af586e7a25 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: 467a701228504d06b971b79a59c69064 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" + +#: ../../src/topics/parameter-references.md:92 +#: 2634f989eb304009a8568d70ed42786c +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" + +#: ../../src/topics/staging-input-files.md:1 +#: b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../src/topics/staging-input-files.md:3 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" + +#: ../../src/topics/staging-input-files.md:9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../src/topics/troubleshooting.md:3 +#: fbe0c65b444441f785d0054176d036a6 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" + +#: ../../src/topics/troubleshooting.md:6 +#: 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:8 +#: 9a710602e00c4934ae3a3b471aa68458 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" + +#: ../../src/topics/troubleshooting.md:14 +#: 21b5be7270a14f0987240c81d1ec879b +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" + +#: ../../src/topics/troubleshooting.md:20 +#: 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:27 +#: cfe9d8241fe84bd5b74042a5625d933f +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" + +#: ../../src/topics/troubleshooting.md:35 +#: 764d933cc4da446abd8dd8f913f05dac +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" + +#: ../../src/topics/troubleshooting.md:44 +#: c93efc6d4e004859981ee7f5fa28ed03 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" + +#: ../../src/topics/troubleshooting.md:48 +#: 546601da44cb49bd9611b1c85807fd90 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" + +#: ../../src/topics/troubleshooting.md:59 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" + +#: ../../src/topics/using-containers.md:1 +#: eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../src/topics/using-containers.md:5 +#: e07f33d01b804663a25ffb08aad74821 +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" + +#: ../../src/topics/using-containers.md:15 +#: 7a644506619a4f08958ec7d4540cd557 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" + +#: ../../src/topics/using-containers.md:18 +#: b5195b7d8eaa419fb2b90cb33a57783a +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" + +#: ../../src/topics/using-containers.md:21 +#: 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../src/topics/using-containers.md:33 +#: 2713594c937d4c528fc8d04d9e9819ed +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" + +#: ../../src/topics/using-containers.md:44 +#: cf94c1424fc2413c85647fd1ee73d951 +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" + +#: ../../src/topics/using-containers.md:52 +#: dc0452107c604e29bdf32bb289fe5db8 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" + +#: ../../src/topics/using-containers.md:55 +#: 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../src/topics/using-containers.md:69 +#: 483181f498fc4d968b5fe6ef427709f7 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" + +#: ../../src/topics/using-containers.md:72 +#: 7487485d6aa4458089a4b4bdf107ea64 +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" + +#: ../../src/topics/workflows.md:1 +#: 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:3 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" + +#: ../../src/topics/workflows.md:13 +#: f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../src/topics/workflows.md:41 +#: 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" + +#: ../../src/topics/workflows.md:51 +#: a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:81 +#: 93188ed43ee949cc98b3ea679ce14feb +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" + +#: ../../src/topics/workflows.md:91 +#: 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:150 +#: 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" + +#: ../../src/topics/workflows.md:160 +#: 24aca0bea4d94e3593b844cf0586cffe +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" + +#: ../../src/topics/workflows.md:165 +#: 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:167 +#: 9c56528acd5f49deb139e034dfbfac7c +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" + +#: ../../src/topics/workflows.md:170 +#: 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: a2dd833fdca4443181648e41051a5232 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" + +#: ../../src/topics/workflows.md:183 +#: 7e40cc9f9e1341c195e843c009575b94 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" + +#: ../../src/topics/workflows.md:185 +#: 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:191 +#: 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/workflows.md:205 +#: 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../src/topics/workflows.md:212 +#: def35d6021394def80a53ae49a2cdbde +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" + +#: ../../src/topics/workflows.md:221 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" + +#: ../../src/topics/workflows.md:233 +#: c84d4450bc6a475dbf34e0b22cea9130 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" + +#: ../../src/topics/workflows.md:248 +#: cca9665f6daa44b49233baf34ab9fcc7 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:256 +#: 547edbf5fa424b8286cc21674ff159b0 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" + +#: ../../src/topics/workflows.md:261 +#: 7ca248888b9d484cb544cd76ba538662 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" + +#: ../../src/topics/workflows.md:267 +#: ae6b240718104380b08db5552d7355ea +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" + +#: ../../src/topics/workflows.md:278 +#: e5a8b7f84be64020b191099f3fad30ed +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" + +#: ../../src/topics/workflows.md:285 +#: f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:287 +#: 12a06d8358534102b202965d4258c18e +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../src/topics/workflows.md:297 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:300 +#: 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:309 +#: b7f93705e5b8416696be01850072e8c0 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" + +#: ../../src/topics/workflows.md:314 +#: e87045829b344089ab59dc27063ddd7a +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../src/topics/workflows.md:322 +#: 42ef2f145b824d69b63abc1da175c216 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" + +#: ../../src/topics/workflows.md:336 +#: c61cedf543664d388183e04b3939cc39 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" + +#: ../../src/topics/workflows.md:341 +#: 9e39e3f1501c4fcaab3e8962e090f6be +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" + +#: ../../src/topics/workflows.md:347 +#: 03e2f767c4da461982fc3c0f3ba94762 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" + +#: ../../src/topics/workflows.md:366 +#: 3bea5822b8694e2aa32c446e1c54a045 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" + +#: ../../src/topics/workflows.md:383 +#: 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" + +#: ../../src/topics/workflows.md:389 +#: 0d498cd4caf54c15891ca1afe58e2727 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" + +#: ../../src/topics/workflows.md:394 +#: b2d75045e02741b4850f5ff1243f7858 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" + +#: ../../src/topics/workflows.md:398 +#: cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../src/topics/workflows.md:400 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" + +#: ../../src/topics/workflows.md:411 +#: 5fa79c62049a447c8328ebf9db54ebf4 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" + +#: ../../src/topics/workflows.md:415 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:421 +#: 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" + +#: ../../src/topics/workflows.md:429 +#: f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../src/topics/workflows.md:441 +#: d947c54933d64aad90df392a1cedd63f +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" + +#: ../../src/topics/workflows.md:445 +#: 651d35997332404186aa6d5711da4a3d +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" + +#: ../../src/topics/workflows.md:450 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../src/topics/workflows.md:458 +#: b662c1a5a4424c8d8350a806356acc61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" + +#: ../../src/topics/workflows.md:466 +#: 04d6babfd87343d7a5f13867ea02b65f +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" + +#: ../../src/topics/workflows.md:469 +#: 2eaacf1a90204a2b9bd621344560f2a1 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" + +#: ../../src/topics/workflows.md:472 +#: 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:480 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" + +#: ../../src/topics/workflows.md:483 +#: e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:489 +#: e3a7182f00f440b8b5461da91194a64b +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" + +#: ../../src/topics/workflows.md:491 +#: 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:497 +#: b5338f39e8c74ff28e139da68089a742 +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" + +#: ../../src/topics/workflows.md:509 +#: f6d92156d67c4a339bcfd194cff897df +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" + +#: ../../src/topics/workflows.md:513 +#: 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:519 +#: d80ab383eec9402faba997b548fe42eb +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" + +#: ../../src/topics/workflows.md:522 +#: f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../src/topics/workflows.md:524 +#: 49217c02f58c43ff9ec00f10da8d4e84 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" + +#: ../../src/topics/workflows.md:527 +#: 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:566 +#: 8dbd56473f8c40c0bb12a48be06117e3 +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" + +#: ../../src/topics/workflows.md:573 +#: 78d7f3ede2c746d482042adef050b2c4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" + +#: ../../src/topics/workflows.md:587 +#: cbbf93c70fe04ba7932ba25758ddc611 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" + +#: ../../src/topics/workflows.md:607 +#: cfa1c1fde4454df283f87cc54a9c59ec +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" + +#: ../../src/topics/workflows.md:627 +#: 1a8be2950cbb475bbb2617e005f0fac9 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" + +#: ../../src/topics/yaml-guide.md:1 +#: 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../src/topics/yaml-guide.md:6 +#: 5d83c56102e141cc978500f678dd0c1c +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" + +#: ../../src/topics/yaml-guide.md:13 +#: c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: cda73485875d4c8e9464679a20558616 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 98cae24919b74c088a5d89706aec581b +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: b4b0940b4b5743c09637b36b964202d0 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 9ca3554d771d45998e88aaede525b227 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 3fca839cede94cfd8e4f605c73ba699d +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: 3ded0f125249485c921994b6e6b93ac9 +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 53ece35d309a4c8d99f1efb2122a7092 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 87bafb845c714b109874f6137b84462d +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: fcd05b1ef31a4046946a2399c7fc5575 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: 859368c1f25c4a4aad57abfd046c63f5 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index 6f69499c..aadfd529 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,15 +9,16 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2023-01-27 14:27+0000\n" -"Last-Translator: Michael Crusoe \n" +"PO-Revision-Date: 2024-05-17 10:02+0000\n" +"Last-Translator: José Raúl Romero \n" +"Language-Team: Spanish \n" "Language: es\n" -"Language-Team: Spanish \n" -"Plural-Forms: nplurals=2; plural=n != 1;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 5.6-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -156,11 +157,16 @@ msgid "" " of software, tools and workflows described using CWL are portable across" " a variety of platforms that support the CWL standard." msgstr "" +"CWL es una manera de describir herramientas de línea de comandos y " +"conectarlas para crear flujos de trabajo. Puesto que CWL es una " +"especificación y no un software concreto, las herramientas y flujos de " +"trabajo descritos usando CWL son portables en múltiples plataformas que " +"soporten el estándar CWL." #: ../../src/episodes.md:5 ../../src/setup.md:5 #: 1361ff6bf4924efc9ce9a85785a6b381 eb254514301c491e81f72ae19c407261 msgid "This page has moved" -msgstr "" +msgstr "Esta página se ha trasladado" #: ../../src/episodes.md:9 f03d7cbe6670451db0896f1b674d56c7 msgid "" @@ -168,18 +174,21 @@ msgid "" "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" +"Esta página es obsoleta y la mantenemos aquí para preservar los enlaces de " +"la Guía del Usuario antigua. Por favor utilice la nueva [Tabla de " +"Contenidos](index.md#table-of-contents) para navegar por la Guía del Usuario." #: ../../src/faq.md:1 d65ad48ac6314bf0a74c34a6766561fc msgid "FAQ" -msgstr "" +msgstr "Preguntas frecuentes" #: ../../src/faq.md:11 370a9659c7904ef6b5e1ae7480f82ef6 msgid "How do I create non \"`File`\" types using `evalFrom`?" -msgstr "" +msgstr "¿Cómo creo tipos que no sean \"`File`\" utilizando `evalFrom`?" #: ../../src/faq.md:41 8333f51e3f5945fe8963adfc6685bcb1 msgid "How do I rename an input file?" -msgstr "" +msgstr "¿Cómo renombro un fichero de entrada?" #: ../../src/faq.md:43 f6b88d9154d049d7807afa9bb0f1ac98 msgid "" @@ -188,16 +197,23 @@ msgid "" "produced from another step in a workflow, and don't want to work with the" " default names that these files were given when they were created." msgstr "" +"Este ejemplo muestra como cambiar el nombre de un fichero de entrada como " +"parte de la descripción de una herramienta. Esto podría ser útil cuando se " +"están tomando archivos producidos por otro paso del flujo de trabajo y no se " +"desea trabajar con los nombres predeterminados que se les asignó cuando " +"fueron creados." #: ../../src/faq.md:59 833510f5896b4a6eb5875d25eca5b047 msgid "How do I rename an output file?" -msgstr "" +msgstr "¿Cómo renombro un fichero de salida?" #: ../../src/faq.md:61 207e2f97d1c44233ae3f109c5a6ec944 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" +"Este ejemplo muestra cómo cambiar el nombre de un fichero de salida a partir " +"del nombre por defecto asignado por una herramienta:" #: ../../src/faq.md:83 d66acc583da24273980a52be03e79e91 msgid "" @@ -205,14 +221,17 @@ msgid "" " engines will rename the file using the new name for subsequent steps or " "as a workflow-level output." msgstr "" +"Cambiando el campo `basename` en `outputEval`, los motores de flujo de " +"trabajo CWL renombrarán el fichero utilizando el nuevo nombre para los pasos " +"posteriores o como salida a nivel de flujo de trabajo." #: ../../src/faq.md:86 8641f105131b4ac1bca7e0a46756ef79 msgid "How do I reference a local script?" -msgstr "" +msgstr "¿Cómo hago referencia a un script local?" #: ../../src/faq.md:88 d3e43b40d6994b32bc37067ee116418e msgid "There are two ways to reference a local script:" -msgstr "" +msgstr "Hay dos maneras de referenciar un script local:" #: ../../src/faq.md:90 64b140a321ca4087945339c523cc24dd msgid "" @@ -221,16 +240,21 @@ msgid "" "the shell script directly (without explicitly using the `sh` or `bash` " "commands)." msgstr "" +"El primer método implica añadir la ruta al directorio donde se alojan los " +"scripts a la variable de entorno `PATH`. Esto permite ejecutar directamente " +"el script de shell (sin necesidad de utilizar explícitamente comandos `sh` o " +"`bash`)." #: ../../src/faq.md:93 34ebca4487a54ceab5d087105820e945 msgid "Start with adding a _shebang_ at the top of your file:" -msgstr "" +msgstr "Se empieza añadiendo _shebang_ en la parte superior del fichero:" #: ../../src/faq.md:99 6b04a4dcdada4515b28d74aacff3537a msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" +"Después, se hace el script ejecutable con el comando `chmod +x scriptname.sh`" #: ../../src/faq.md:101 756ab4f7edcf42d3872bb86818e088c3 msgid "" @@ -238,26 +262,37 @@ msgid "" "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" +"Finalmente, se modifica el `PATH` para añadir el directorio en el que se " +"aloja el script. (Es buena práctica utilizar `$HOME/bin` para alojar los " +"scripts propios.)" #: ../../src/faq.md:108 efb46b3a2d7c4c51b65998602bfa6f18 msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" +"Ahora se puede utilizar `baseCommand: scriptname.sh` para ejecutar el script " +"directamente." #: ../../src/faq.md:117 844938d5d2304c6cb03184b4b4b0b024 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" +"Cuando se desee compartir el trabajo más tarde, se puede colocar su script " +"en un contenedor de software en formato Docker." #: ../../src/faq.md:119 796ce8155e32486d9651f8f13bfa3148 msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" +"El segundo método consiste en incluir una entrada con `type: File` en el " +"propio script:" #: ../../src/faq.md:138 ba246320fdd94a1aab4736f83718d793 msgid "How can I set `self`-based input bindings for optional inputs?" msgstr "" +"¿Cómo puedo configurar enlaces de entrada basados en `self` para entradas " +"opcionales?" #: ../../src/faq.md:140 6169b7be9af7448abcb57eaf91e1cc91 msgid "" @@ -265,6 +300,10 @@ msgid "" "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" +"Actualmente, `cwltool` no puede hacer frente a la falta de entradas " +"opcionales si su enlace de entrada hace uso de `self`. A continuación se " +"muestra un ejemplo de solución para esto, a la espera de una solución más " +"sofisticada." #: ../../src/faq.md:165 6c98b7948059411b8e09cf03a552c5ab msgid "How can I model a \"one-or-the-other\" parameter?" @@ -275,12 +314,17 @@ msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" +"A continuación se muestra un ejemplo de cómo especificar diferentes cadenas " +"que se añadirán a una línea de comandos, en función del valor dado a un " +"parámetro booleano." #: ../../src/faq.md:188 5c9980839f404ba6aef92ef23034500f msgid "" "How do I connect a solo value to an input that expects an array of that " "type?" msgstr "" +"¿Cómo puedo conectar un valor aislado a una entrada que espera un array de " +"ese tipo?" #: ../../src/faq.md:190 2525baf16c1f4725b096f33fd99009cf msgid "" @@ -289,10 +333,14 @@ msgid "" " along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput):" msgstr "" +"Añade un [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) junto con [`linkMerge: " +"merge_nested`](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput):" #: ../../src/faq.md:194 a00d5d96b15048a79ae099d22d63bb42 msgid "merge_nested" -msgstr "" +msgstr "merge_nested" #: ../../src/faq.md:196 3a92c6cc5c2b40ffa0d692d03bad5c87 msgid "" @@ -300,10 +348,15 @@ msgid "" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" +"La entrada debe ser una matriz que conste exactamente de una entrada por " +"cada enlace de entrada. Si se especifica \"merge_nested\" con un solo " +"enlace, el valor del enlace debe envolverse en una lista de un solo elemento." #: ../../src/faq.md:199 3af16c07e3f148ddb8849c94a3864158 msgid "Which means \"create a list with exactly these sources as elements\"." msgstr "" +"¿Qué significa \"crear una lista con exactamente estas fuentes como " +"elementos\"?" #: ../../src/faq.md:201 0ea3de393d2f42aeb82658c85a19ec45 msgid "" @@ -313,26 +366,35 @@ msgid "" "and add `linkMerge: merge_nested` under the appropriate `in` entry of the" " destination step." msgstr "" +"O en otras palabras: si el destino es de tipo `File[]` (un array de `File`s) " +"y el origen es un único `File`, entonces se añade " +"`MultipleInputFeatureRequirement` al `requirements` a nivel de flujo de " +"trabajo y se añade `linkMerge: merge_nested` bajo la entrada `in` apropiada " +"del paso de destino." #: ../../src/faq.md:229 2f1bbb611c9c4f80b7ae0566432f2f35 msgid "How do make an input optional? 💯" -msgstr "" +msgstr "¿Cómo hago una entrada opcional? 💯" #: ../../src/faq.md:231 08a226efe5d141e68215ac77725033db msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" +"Para crear un parámetro de entrada opcional, se añade un símbolo de " +"interrogación a la declaración del tipo." #: ../../src/faq.md:247 06e70a855a8f455ca0536eead77073c2 msgid "" -msgstr "" +msgstr "" #: ../../src/faq.md:248 7fda8eeb6a7f4689993ed0118c77f023 msgid "" "How do I specify an input that must come from a list of predefined values" " (i.e. How do I use enum inputs) ?" msgstr "" +"¿Cómo especifico una entrada que debe proceder de una lista de valores " +"predeterminados (esto es, cómo utilizar entradas \"enum\")?" #: ../../src/faq.md:250 b1934a82553b4da3b7f981e576245dd8 msgid "" @@ -341,16 +403,22 @@ msgid "" " form style. It does the same thing as the question mark on the other " "inputs.**" msgstr "" +"Para los indicadores de línea de comandos que requieren una entrada " +"específica como argumento, se puede declarar un tipo enum en CWL. **" +"Especificar null aquí se conoce como estilo de forma larga. Hace lo mismo " +"que el signo de interrogación en las otras entradas.**" #: ../../src/faq.md:267 17fc34fad2094f5ea60e963dabd632b8 msgid "" -msgstr "" +msgstr "" #: ../../src/faq.md:268 4d7acfbeba5b4e9cb31f08ef4b280447 msgid "" "How do I describe dependent or exclusive input parameters(e.g. How do I " "use record inputs)?" msgstr "" +"¿Cómo describo los parámetros de entrada dependientes o exclusivos (por " +"ejemplo, cómo utilizo las entradas de registro)?" #: ../../src/faq.md:270 949ce95c082f4a05891a55fee25d4873 msgid "" @@ -358,10 +426,13 @@ msgid "" "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" +"Para los indicadores de línea de comandos que son mutuamente excluyentes ****" +" o dependientes **** se puede definir un tipo de registro especial. También " +"se puede especificar null aquí para crear entradas opcionales." #: ../../src/faq.md:322 6fd3c469d11d4d52b9fbb7a3d443a8db msgid "How do I set mutually exclusive parameters?" -msgstr "" +msgstr "¿Cómo configuro parámetros mutuamente excluyentes?" #: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f msgid "" @@ -371,44 +442,58 @@ msgid "" "field you want to set. The source field is set to indicate the input from" " the workflow to be used as the value." msgstr "" +"Para establecer correctamente los campos en un tipo de entrada de registro, " +"es necesario pasar un diccionario a la entrada para establecer correctamente " +"los parámetros. Esto se hace utilizando JavaScript en línea y devolviendo el " +"diccionario con la clave del campo que desea establecer. El campo fuente se " +"establece para indicar la entrada del flujo de trabajo que se utilizará como " +"valor." #: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 msgid "How can I set Booleans?" -msgstr "" +msgstr "¿Cómo puedo establecer valores de tipo Boolean?" #: ../../src/faq.md:344 8dcb88744e5840029de0e1bbf1c4b967 msgid "These can be set by using the default field" -msgstr "" +msgstr "Se pueden asignar utilizando valores \"default\"" #: ../../src/faq.md:349 972b7a5551bb43e6b9fa30e0cb713ff7 msgid "What should I do when concatenating strings in inputs?" -msgstr "" +msgstr "¿Qué debería hacer para concatenar cadenas en las entradas?" #: ../../src/faq.md:351 68f74afc21d846dd9070d45dec0cc1d8 msgid "The valueFrom field must be used instead of default." -msgstr "" +msgstr "El campo `valueFrom` debe ser utilizado en lugar de `default`." #: ../../src/faq.md:359 53b633c6f8644106beb95ae567eb0708 msgid "" "I get `cwltool` errors due to filenames with space characters inside. " "What should I do?" msgstr "" +"Obtengo errores en `cwltool` debido a nombres de fichero con caracteres de " +"espacio. ¿Qué debo hacer?" #: ../../src/faq.md:361 7101bb5cb69e4faca4e60eabb4eb258e msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" +"`cwltool` no me permite algunos caracteres en los nombres de fichero por " +"defecto." #: ../../src/faq.md:363 0eaf834b0ca847cca6736794895f5f81 msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" +"Por ejemplo, el nombre de fichero `aqui hay un espacio.txt` incluye 3 " +"caracteres de espacio." #: ../../src/faq.md:371 7dabd8aab7a5423b842433616640bac0 msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" +"Si no puede evitar estos caracteres peligrosos, pase `--relax-path-checks` a " +"`cwltool`." #: ../../src/faq.md:373 b7ec33f38ce74ceb890f4379e4c41054 msgid "" @@ -4368,4 +4453,3 @@ msgstr "" #~ " only part that is really new " #~ "is the `dockerRequirement` section." #~ msgstr "" - diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index 1279724d..ef910682 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-05-08 01:07+0000\n" +"PO-Revision-Date: 2024-05-17 17:16+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -18,7 +18,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.5.4-rc\n" +"X-Generator: Weblate 5.6-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -45,15 +45,19 @@ msgstr "" #: ../../LICENSE.md:12 754f3f54aa4142ef9dac27f508dd0bca msgid "You are free:" -msgstr "" +msgstr "あなたは以下の条件に従う限り、自由に：" #: ../../LICENSE.md:14 d2b1d5e965ef4e71b64c359549919975 msgid "to **Share**---copy and redistribute the material in any medium or format" -msgstr "" +msgstr "**共有** --- " +"どのようなメディアやフォーマットでも資料を複製したり、再配布できます。 " +"営利目的も含め、どのような目的でも。" #: ../../LICENSE.md:15 fe9551ffef8149bf8da50e70318e8de8 msgid "to **Adapt**---remix, transform, and build upon the material" -msgstr "" +msgstr "**翻案** --- " +"マテリアルをリミックスしたり、改変したり、別の作品のベースにしたりできます。 " +"営利目的も含め、どのような目的でも" #: ../../LICENSE.md:17 247db3bcc7024c44a044886a29ef1414 msgid "for any purpose, even commercially." @@ -63,7 +67,8 @@ msgstr "営利目的であっても、いかなる目的であっても。" msgid "" "The licensor cannot revoke these freedoms as long as you follow the " "license terms:" -msgstr "" +msgstr "あなたがライセンスの条件に従っている限り、許諾者がこれらの自由を取り消すこと" +"はできません。" #: ../../LICENSE.md:24 551cb5ab59dd4737b1042a4ef79ffab7 msgid "" @@ -75,6 +80,13 @@ msgid "" "reasonable manner, but not in any way that suggests the licensor endorses" " you or your use." msgstr "" +"**表示** --- あなたは 適切なクレジット を表示し(あなたの作品が「Copyright © " +"the Common Workflow Language project」の作品から派生していることを明記し、" +"可能であれば https://www.commonwl.org/ " +"へのリンクを提供してください)、[ライセンスへのリンク][cc-by-human]を提供し、 " +"変更があったらその旨を示さ なければなりません。これらは合理的であればどのよう" +"な方法で行っても構いませんが、許諾者があなたやあなたの利用行為を支持している" +"と示唆するような方法は除きます。" #: ../../LICENSE.md:32 f6c3b2ccad494ed6811a35537fc1fb0d msgid "" @@ -82,6 +94,9 @@ msgid "" "technological measures that legally restrict others from doing anything " "the license permits. With the understanding that:" msgstr "" +"**追加的な制約は課せません** --- あなたは、" +"このライセンスが他の者に許諾することを法的に制限するようないかなる法的規定も " +"技術的手段 も適用してはなりません。" #: ../../LICENSE.md:36 91c95248cd7f435c909ee263a9a8bf3f msgid "" @@ -89,6 +104,9 @@ msgid "" "in the public domain or where your use is permitted by an applicable " "exception or limitation." msgstr "" +"あなたは、資料の中でパブリック・ドメインに属している部分に関して、" +"あるいはあなたの利用が著作権法上の 権利制限規定 " +"にもとづく場合には、ライセンスの規定に従う必要はありません。" #: ../../LICENSE.md:39 27f79b0b648b4de4b0eb3172b2dc4ae8 msgid "" @@ -97,6 +115,9 @@ msgid "" "such as publicity, privacy, or moral rights may limit how you use the " "material." msgstr "" +"保証は提供されていません。ライセンスはあなたの利用に必要な全ての許諾を与えな" +"いかも知れません。例えば、 パブリシティ権、肖像権、人格権 などの他の諸権利は" +"あなたがどのように資料を利用するかを制限することがあります。" #: ../../LICENSE.md:44 1e367d07720d4f9fb7ebc3149052e823 msgid "Software" @@ -120,6 +141,11 @@ msgid "" "See the License for the specific language governing permissions and " "limitations under the License." msgstr "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 #: 08aa9181d5304e0fa96b28db15718559 d37fc100eb6948bba8b5e757574b2aaf @@ -131,9 +157,9 @@ msgid "" " a variety of platforms that support the CWL standard." msgstr "" "CWLは、コマンドラインツールを定義し、それらのツールを繋げてワークフローを作成" -"するための方法です。CWLは仕様であり、特定のソフトウェアではないため、CWLを使" -"用して定義されたツールやワークフローは、CWL標準をサポートするさまざまなプラッ" -"トフォームで利用可能です。" +"します。CWLは仕様であり、特定のソフトウェアではないため、CWLを使用して定義さ" +"れたツールやワークフローは、CWL標準をサポートするさまざまなプラットフォームで" +"利用可能です。" #: ../../src/episodes.md:5 ../../src/setup.md:5 #: 1361ff6bf4924efc9ce9a85785a6b381 eb254514301c491e81f72ae19c407261 @@ -206,7 +232,7 @@ msgid "" msgstr "" "最初の方法は、スクリプトの入ったフォルダを " "環境変数`PATH`に追加する方法です。これにより、`sh` や`bash` " -"コマンドを使用せずに、シェルスクリプトを直接実行することができます。" +"コマンドを使用せずに、シェルスクリプトを直接実行できます。" #: ../../src/faq.md:93 34ebca4487a54ceab5d087105820e945 msgid "Start with adding a _shebang_ at the top of your file:" @@ -239,7 +265,6 @@ msgstr "後で作ったものを共有したいときは、スクリプトをDoc "きます。" #: ../../src/faq.md:119 796ce8155e32486d9651f8f13bfa3148 -#, fuzzy msgid "" "The second method involves including an input of `type: File` in the " "script itself:" @@ -293,19 +318,20 @@ msgid "merge_nested" msgstr "merge_nested" #: ../../src/faq.md:196 3a92c6cc5c2b40ffa0d692d03bad5c87 -#, fuzzy msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." -msgstr "入力は、各入力リンクに対して正確に1つのエントリで構成される配列でなければなりません。\"merge_nested\"が1つのリンクで指定された場合、リンクからの値は1つのアイテムリストでラップされなければなりません。" +msgstr "" +"入力は、各入力リンクに対して正確に1つのエントリで構成される配列でなければなり" +"ません。\"merge_nested\"が1つのリンクで指定された場合" +"、リンクからの値は1つのアイテムリストでラップされなければなりません。" #: ../../src/faq.md:199 3af16c07e3f148ddb8849c94a3864158 msgid "Which means \"create a list with exactly these sources as elements\"." msgstr "つまり、\"まさにこれらのソースを要素とするリストを作成する\" ということです。" #: ../../src/faq.md:201 0ea3de393d2f42aeb82658c85a19ec45 -#, fuzzy msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -314,8 +340,9 @@ msgid "" " destination step." msgstr "" "`File[]` (`File`の配列) で、ソースが単一の`File` " -"の場合、`MultipleInputFeatureRequirement` をワークフローレベルの`requirements` " -"に追加し、`linkMerge: merge_nested` を目的ステップのエントリの該当`in`に追加します。" +"の場合、`MultipleInputFeatureRequirement` " +"をワークフローレベルの`requirements` に追加し、`linkMerge: merge_nested` " +"を目的ステップのエントリの該当`in`に追加します。" #: ../../src/faq.md:229 2f1bbb611c9c4f80b7ae0566432f2f35 msgid "How do make an input optional? 💯" @@ -339,13 +366,16 @@ msgstr "どうやってあらかじめ定義された値のリストから入力 "でenumを使うにはどうしたらよいですか)?" #: ../../src/faq.md:250 b1934a82553b4da3b7f981e576245dd8 -#, fuzzy msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" " form style. It does the same thing as the question mark on the other " "inputs.**" -msgstr "引数として特定の入力を必要とするコマンドラインフラグについては、CWLで列挙型を宣言することで実現できます。**ここでnullを指定することは、ロングフォーム・スタイルとして知られています。他の入力のクエスチョンマークと同じ働きをします。**" +msgstr "" +"引数として特定の入力を必要とするコマンドラインフラグについては、CWLで列挙型(" +"enum type)を宣言することで実現できます。**ここでnullを指定することは、ロング" +"フォーム・スタイルとして知られています。他の入力のクエスチョンマークと同じ働" +"きをします。**" #: ../../src/faq.md:267 17fc34fad2094f5ea60e963dabd632b8 msgid "" @@ -359,21 +389,20 @@ msgstr "依存的または排他的な入力パラメータはどのように記 "レコード入力をどのように使用すればよいですか）？" #: ../../src/faq.md:270 949ce95c082f4a05891a55fee25d4873 -#, fuzzy msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -"**相互排他的** または**依存的** " -"のいずれかのコマンドラインフラグについては、特別なレコードタイプを定義することができます。また、ここにnullを指定することで、オプションの入力を作成することができます。" +"**相互排他的** または**依存的** のいずれかのコマンドラインフラグについては、" +"特別なレコードタイプを定義できます。また、ここにnullを指定することで、オプシ" +"ョンの入力を作成できます。" #: ../../src/faq.md:322 6fd3c469d11d4d52b9fbb7a3d443a8db msgid "How do I set mutually exclusive parameters?" msgstr "相互に排他的なパラメータを設定するにはどうしたらよいでしょうか?" #: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f -#, fuzzy msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -383,7 +412,7 @@ msgid "" msgstr "" "レコード入力タイプのフィールドを適切に設定するには、入力に辞書を渡してパラメ" "ータを適切に設定する必要があります。これは、インラインJavaScriptを使用し、設" -"定したいフィールドのキーを持つ辞書を返すことで実現します。ソースフィールドに" +"定したいフィールドのキーを持つ辞書を返すことで実現します。sourceフィールドに" "は、値として使用するワークフローからの入力を示すものが設定されます。" #: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 @@ -429,8 +458,8 @@ msgstr "これらの危険な文字を避けられない場合は、`--relax-pat msgid "" "What should I do when I get CWL Parameter Reference error due to hyphen " "in an input identifier?" -msgstr "入力パラメータ名の中のハイフンがあるため、CWLパラメータリファレンスエラーが起" -"こりました。どのようしたらよいでしょうか？" +msgstr "入力パラメータ名の中にハイフンがあるため、CWL Parameter Reference " +"エラーが起こりました。どのようしたらよいでしょうか？" #: ../../src/faq.md:375 e39b65947b294b20a444f18d780246f4 msgid "If `cwltool --validate` returns valid" @@ -457,7 +486,8 @@ msgstr "このエラーを修正するには、`-` (ハイフン) を`_` (アン msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" -msgstr "入力識別子を変更することができない場合は、別のCWLパラメータリファレンス構文を使用することができます：" +msgstr "入力識別子を変更することができない場合は、別のCWLパラメータリファレンス構文を" +"使用できます：" #: ../../src/faq.md:442 fc407a9e8d8c4b699d9cd14b369343b5 msgid "How do I use CWL and cwltool with Singularity?" @@ -481,7 +511,6 @@ msgid "How do I debug the JavaScript in my CWL tool?" msgstr "CWLツールのJavaScriptをデバッグするには?" #: ../../src/faq.md:452 5556d3c323664edea55cfb777f4efb3b -#, fuzzy msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -492,12 +521,13 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" "cwltool の --js-console " -"オプションを使用するか、または、あなたのコードのためのJavaScript または TypeScript " -"プロジェクトを作成し、expressionLib を使用して読み込んでみてください（例： " -"https://github.com/common-workflow-language/common-workflow-" -"language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +"オプションを使用するか、または、あなたのコードのためのJavaScript または " +"TypeScript プロジェクトを作成し、expressionLib " +"を使用して読み込んでみてください（例： https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool." +"cwl#L6-L8" #: ../../src/index.md:1 1c9fb72b83c9467a9672943fb47ffe32 msgid "Common Workflow Language User Guide" @@ -524,8 +554,10 @@ msgid "" "Request by clicking the \"Edit this page\" button at the right sidebar of" " each page." msgstr "" -"このガイドに足りないものがある場合、またはその他のフィードバックを提供したい場合は、[このユーザーガイドのプロジェクトリポジトリ][repo]にIssueを作成してください。また、各ページの右サイドバーにある「このページを編集する」ボタンをクリックすると、Pull" -" Requestで直接変更を提案することができます。" +"このガイドに足りないものがある場合、またはその他のフィードバックを提供したい" +"場合は、[このユーザーガイドのプロジェクトリポジトリ][repo]にIssueを作成してく" +"ださい。また、各ページの右サイドバーにある「このページを編集する」ボタンをク" +"リックすると、Pull Requestで直接変更を提案できます。" #: ../../src/index.md:16 35c50bb5c3a345b4a4ae66b2df065376 msgid "Navigating the User Guide" @@ -573,7 +605,7 @@ msgstr "" "YAML に精通し、コマンドラインの指示に従うことに慣れていることが期待されます。" "このユーザーガイドの他のセクションは、同じ概念をカバーしていますが、より詳細" "に説明されています。すでにCWLに精通している場合、またはより高度なコンテンツを" -"探している場合は、このセクションをスキップすることができます。" +"探している場合は、このセクションをスキップできます。" #: ../../src/introduction/basic-concepts.md:10 7a56d394fb244431aefce7ebbb834ecf msgid "The CWL Specification" @@ -692,8 +724,8 @@ msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" -"コマンドラインツールは、`echo` 、`ls` 、`tar` " -"のようなコマンドラインユーティリティのラッパーです。コマンドラインツールは、ワークフローから呼び出せます。" +"CommandLineToolは、`echo` 、`ls` 、`tar` " +"のようなコマンドのラッパーです。CommandLineToolは、Workflowから呼び出せます。" #: ../../src/introduction/basic-concepts.md:122 #: c88ad26efa794cbeb6f0690aa0cad5ea @@ -716,8 +748,8 @@ msgid "" "section](../topics/operations.md) of this user guide." msgstr "" "Operationは、入力を受け、出力を出す抽象的なプロセスでもあり、ワークフローで使" -"用することができます。しかし、あまり一般的に使われていない特別な処理です。こ" -"のユーザーガイドの[Operation編](../topics/operations.md)で説明します。" +"用できます。しかし、あまり一般的に使われていない特別な処理です。このユーザー" +"ガイドの[Operation編](../topics/operations.md)で説明します。" #: ../../src/introduction/basic-concepts.md:131 #: 44aac23f302c4178accf7e431cfbb96c @@ -729,9 +761,9 @@ msgid "" "workflow." msgstr "" "Workflowは、ステップを含むプロセスです。ステップには、他のWorkflow（ネストさ" -"れたWorkflow）、CommandLineTool、ExpressionToolを使用することができます。Work" -"flowの入力は、そのステップのいずれかに渡すことができ、ステップによって生成さ" -"れた出力は、Workflowの最終出力に使用することができます。" +"れたWorkflow）、CommandLineTool、ExpressionToolを使用できます。Workflowの入力" +"は、そのステップのいずれかに渡すことができ、ステップによって生成された出力は" +"、Workflowの最終出力に使用できます。" #: ../../src/introduction/basic-concepts.md:137 #: 5afdb7aaf0bf4c1abf4c22cdbdd58be9 @@ -741,8 +773,9 @@ msgid "" "*requirements*. There are many requirements defined in the CWL " "specification, for instance:" msgstr "" -"CWL 仕様では、*requirements* " -"を通じて、実装が追加機能を提供し、ワークフローの前提条件を指定することができます。CWL仕様には、例えば、以下のような多くの要件が定義されています：" +"CWL 仕様では、*requirements* を通じて、実装が追加機能を提供し、ワークフローの" +"前提条件を指定できます。CWL仕様には、例えば、以下のような多くの要件が定義され" +"ています：" #: ../../src/introduction/basic-concepts.md:141 #: 07c5789c59224ed78a3ecd03cfe872e9 @@ -750,7 +783,7 @@ msgid "" "[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement)" " - enables JavaScript in expressions." msgstr "" -"[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow." +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/Workflow." "html#InlineJavascriptRequirement) - でJavaScriptを有効にします。" #: ../../src/introduction/basic-concepts.md:142 @@ -781,10 +814,10 @@ msgid "" "the {{ cwl_version }} specification and may not be supported by other CWL" " runners." msgstr "" -"いくつかのCWLランナーは、仕様にないrequirementsを提供することがあります。例え" +"いくつかのCWL runnerは、仕様にないrequirementsを提供することがあります。例え" "ば、GPUに関するrequirementsは`cwltool` で`cwltool:CUDARequirement` " -"を通してサポートされていますが、{{ cwl_version }}仕様の一部ではないので、他の" -"CWLランナーではサポートされていないかもしれません。" +"を通してサポートされていますが、{{ cwl_version }}仕様の一部ではないので、" +"他のCWL runnerではサポートされていないかもしれません。" #: ../../src/introduction/basic-concepts.md:151 #: b6a5cd431c324078a9a4e1513a14ee28 @@ -816,6 +849,14 @@ msgid "" "Workflows](https://workflows.community/groups/fair/), Workflows Community" " Initiative." msgstr "" +"FAIR原則は、デジタル資産、特にデータを共有し公開するための基礎を作りました。F" +"AIR原則は、機械可読性を重視し、すべてのデジタル資産は、検索可能（Findable）、" +"アクセス可能（Accessible）、相互運用可能（Interoperable）、再利用可能（Reusab" +"le）であるべきとしています。ワークフローは、科学的プロセスが実施され、データ" +"が作成される方法をコード化します。従って、ワークフローがFAIRデータの作成をサ" +"ポートし、かつワークフロー自身がFAIRの原則を遵守することは重要です。- [FAIR " +"Computational Workflows](https://workflows.community/groups/fair/), " +"Workflows Community Initiative." #: ../../src/introduction/basic-concepts.md:167 #: 4ea1d3bf04dc42f0bc6735a45b9e0dc0 @@ -920,7 +961,6 @@ msgid "Prerequisites" msgstr "前提条件" #: ../../src/introduction/prerequisites.md:6 ab9e21b3e99641d096ba70012b4eb035 -#, fuzzy msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -932,10 +972,10 @@ msgstr "" "このセクションに記載されているソフトウェアと構成は、このユーザーガイドに従う" "ための前提条件となるものです。CWL標準は、多くの異なるワークフローランナー(訳" "注:ワークフローを実行するためのソフトウェア)やプラットフォームによって実装さ" -"れています。この要件のリストは、CWL参照ランナー、`cwltool` に焦点を当てていま" -"す。他のCWL互換ランナーやワークフローシステムを使用することもできますが、結果" -"やインターフェイスは異なるかもしれません（ただし、正確なワークフロー出力は同" -"一でなければなりません）。" +"れています。この要件のリストは、CWL reference runner である`cwltool` " +"に焦点を当てています。他のCWL-compatible runnerやワークフローシステムを使用す" +"ることもできますが、結果やインターフェイスは異なるかもしれません（ただし、正" +"確なワークフロー出力は同一でなければなりません）。" #: ../../src/introduction/prerequisites.md:12 8ed426ebcb744839915e7c414d69b1e9 msgid "CWL Implementations" @@ -1052,7 +1092,7 @@ msgstr "`cwltool` を使って `true.cwl` を検証します。" #: ../../src/introduction/prerequisites.md:71 73f074f47d1449dcb40ff960a84851fd msgid "You can run the CWL tool description by omitting the `--validate` option:" -msgstr "`--validate` オプションを省略することで、CWLツール定義を実行することができます：" +msgstr "`--validate` オプションを省略することで、CWLツール定義を実行できます：" #: ../../src/introduction/prerequisites.md:73 2dd5a67870ca41b48e17c468ba15888b msgid "Running `true.cwl` with `cwltool`." @@ -1072,10 +1112,14 @@ msgid "" " administrator or user to point to the preferred CWL implementation. This" " is convenient for environments with multiple CWL runners." msgstr "" -"`cwl-runner` は、CWL準拠のランナーに対する、実装にとらわれないエイリアスです。これは、`cwl-runner` " -"エイリアスコマンドを独立して呼び出すことができ、特定のCWLランナープログラム名に依存しないことを意味します。ユーザーは、`cwltool` " -"のようなCWLランナーを直接呼び出す代わりに、`cwl-runner` を呼び出すことができます。`cwl-runner` " -"は、システム管理者またはユーザーによってインストールされ、好みのCWL実装を指し示す。これは、複数のCWLランナーがある環境では便利です。" +"`cwl-runner` " +"は、CWL準拠のランナーに対する、実装にとらわれないエイリアスです。これは" +"、`cwl-runner` エイリアスコマンドを独立して呼び出すことができ、特定のCWL " +"runner のプログラム名に依存しないことを意味します。ユーザーは、`cwltool` " +"のようなCWL runnerを直接呼び出す代わりに、`cwl-runner` " +"を呼び出すことができます。`cwl-runner` は、システム管理者またはユーザーによっ" +"てインストールされ、好みのCWL実装を指します。これは、複数のCWL " +"runnerがある環境で便利です。" #: ../../src/introduction/prerequisites.md:88 6dd6aa836099469381fb564d63b84f3d msgid "" @@ -1123,7 +1167,8 @@ msgstr "`true_shebang.cwl`" #: ../../src/introduction/prerequisites.md:122 4f3cb8d1f9ce4e3d852e81aa4e0f60be msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." -msgstr "`chmod u+x` を実行することで、 `true_shebang.cwl` を実行可能なファイルにすることができます。" +msgstr "`chmod u+x` を実行することで、 `true_shebang.cwl` " +"を実行可能なファイルにできます。" #: ../../src/introduction/prerequisites.md:124 27693d62faa045d9b03143d9bd2afcdf msgid "Making `true.cwl` executable." @@ -1135,7 +1180,8 @@ msgid "" "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -"そして最後に、コマンドラインで直接実行することができます。実行時には、shebangで指定されたプログラム(`cwl-" +"そして最後に、コマンドラインで直接実行できます。実行時には、shebangで指定され" +"たプログラム(`cwl-" "runner`)が、ファイルの残りの部分を実行するために使用されます。" #: ../../src/introduction/prerequisites.md:135 abba2e14c4e54252bb75983274663a7a @@ -1215,8 +1261,8 @@ msgid "" msgstr "" "`cwltool` は、ツール、ワークフロー、およびワークフロー " "ステップで指定されたソフトウェアコンテナをDockerを使用して実行します。Docker " -"ドキュメントの指示に従って、お使いのオペレーティングシステム用にインストール" -"してください：." +"ドキュメントの指示に従って、お使いのオペレーティングシステム合わせてインスト" +"ールしてください：." #: ../../src/introduction/prerequisites.md:172 2872503638624b7e904ae407375ac165 msgid "" @@ -1342,7 +1388,7 @@ msgid "" msgstr "" "基本的に `cwltool` の使い方は、`cwltool [OPTIONS] [CWL_DOCUMENT] " "[INPUTS_OBJECT]`です。`hello_world.cwl` " -"Workflowは、オプションを指定せずに実行することができます：" +"Workflowは、オプションを指定せずに実行できます：" #: ../../src/introduction/quick-start.md:57 5b393c69816549b084516dda4d4274f5 msgid "Running `hello_world.cwl` with `cwltool`." @@ -1366,8 +1412,9 @@ msgid "" "YAML. For example:" msgstr "" "ワークフロー入力パラメータに値を渡すもう一つの方法は、*Inputs Object* " -"を介する方法です。これは、入力フィールドとその対応する値を含むファイルです。Inputs Objects ファイルは、JSON または YAML " -"で記述することができます。例えば、以下のようになります：" +"を介する方法です。これは、入力フィールドとその対応する値を含むファイルです。" +"Inputs Objects ファイルは、JSON または YAML " +"で記述できます。例えば、以下のようになります：" #: ../../src/introduction/quick-start.md:74 d05e8e016b1d40c28c4b6091103fe920 msgid "`hello_world-job.json`" @@ -1381,7 +1428,7 @@ msgstr "このInputs Objectファイルを使用して、「Hello World」ワー #: ../../src/introduction/quick-start.md:82 4065124edf3a4678a37c82e3070595cb msgid "Passing an Inputs Object file to `cwltool`." -msgstr "`cwltool` に Inputs Object ファイルをします。" +msgstr "`cwltool` に Inputs Object ファイルを渡します。" #: ../../src/introduction/quick-start.md:88 52b1602b5c8d48db88d0b16f788e7703 msgid "" @@ -1556,7 +1603,6 @@ msgstr "" "Direcotry` を適宜使用します。" #: ../../src/topics/best-practices.md:11 ae127b776eed4894af8cb680377703e0 -#, fuzzy msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1602,7 +1648,9 @@ msgstr "" msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" -msgstr "参考文献：\"[科学者・プログラマーのためのソフトウェアライセンス クイックガイド][sci-license]\"" +msgstr "" +"参考文献：\"[A Quick Guide to Software Licensing for the Scientist-Programmer" +"][sci-license]\"" #: ../../src/topics/best-practices.md:28 5b976a5aec7d44bda55b0a019e955416 msgid "_Example of metadata field for license with SPDX identifier:_" @@ -1614,7 +1662,7 @@ msgid "" " Metadata and Authorship section of this User Guide](../topics/metadata-" "and-authorship.md)." msgstr "" -"CW定義にメタデータを与える例については、 " +"CWL定義にメタデータを与える例については、 " "[このユーザーガイドのメタデータと著者名のセクション](../topics/metadata-and-" "authorship.md)を参照してください。" @@ -1667,7 +1715,6 @@ msgstr "" "ツールのバージョンのリストを書きます。" #: ../../src/topics/best-practices.md:58 88806cb0462f4359801c1fa0ff0ebcc0 -#, fuzzy msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1682,10 +1729,10 @@ msgstr "" "フォマティクスツールは、[EDAM][edam-" "example]のフォーマット識別子を使用するのが良いです。`iana:text/plain`,`iana:" "text/tab-separated-values`、`$namespaces：{ iana: \"https://www.iana.org/" -"assignments/media-types/\" }もご参照ください`.[IANA メディアタイプ一覧][iana-" -"types]（MIME タイプとしても知られています）。バイオインフォマティクス以外のツ" -"ールについては、同様に適切なオントロジー/統制語彙を使用または構築してください" -"。このページを編集して私たちに知らせてください。" +"assignments/media-types/\" }` も参照してください`.[IANA メディアタイプ一覧" +"][iana-types]（MIME タイプとしても知られています）。バイオインフォマティクス" +"以外のツールについては、同様に適切なオントロジー/統制語彙を使用または構築して" +"ください。このページを編集して私たちに知らせてください。" #: ../../src/topics/best-practices.md:66 b178c7296ed5491782a4180c76883c14 msgid "" @@ -1736,16 +1783,16 @@ msgid "" msgstr "有効な値のリストが決まっている要素には、`type: string` の代わりに、`type: enum` を使用してください。" #: ../../src/topics/best-practices.md:85 c100d5192a52497fb6a890b81a388fcf -#, fuzzy msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" " one of the [built in `File` properties][file-prop] like `basename`, " "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -"JavaScriptのすべての使用について、削除または置換の可能性を評価します。よくある例：`File` " -"の名前とパスを操作する方法は？`basename`,`nameroot`,`nameext`, などの [built in`File` " -"properties][file-prop] のいずれかを代わりに使用できないか考えてみてください。" +"JavaScriptのすべての使用について、削除または置換の可能性を評価します。よくあ" +"る例：`File` の名前とパスを操作する方法は？`basename`,`nameroot`,`nameext`, " +"などの [ビルトイン`File` プロパティ][file-prop] " +"のいずれかを代わりに使用できないか考えてみてください。" #: ../../src/topics/best-practices.md:90 e22fbacdb2fb4202b1bd69cfc24af5cd msgid "" @@ -1782,9 +1829,9 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" "CommandLineToolは、Processオブジェクトの一種であり、それ自体またはワークフロ" -"ーのステップとして実行することができます。`ls`,`echo`,`tar` などの実行したい" -"コマンドのラッパーです。実行したいコマンドは、CommandLineToolについてのCWL定" -"義の`baseCommand` 属性で定義されています。" +"ーのステップとして実行できます。`ls`,`echo`,`tar` などの実行したいコマンドの" +"ラッパーです。実行したいコマンドは、CommandLineToolについてのCWL定義の`baseCo" +"mmand` 属性で定義されています。" #: ../../src/topics/command-line-tool.md:8 7a180ba1f2d746a78b79be7e899cbad6 msgid "" @@ -1792,8 +1839,9 @@ msgid "" "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -"CWLコマンドラインツールは、`inputs` と`outputs` も持っていなければなりません。次の例は、Linuxコマンド `echo` " -"のためのCWLコマンドラインツールの最小限の例で、inputsとoutputsを使用します。" +"CWL CommandLineToolは、`inputs` と`outputs` " +"も持っていなければなりません。次の例は、Linuxコマンド `echo` のためのCWL " +"CommandLineToolの最小限の例で、inputsとoutputsを使用します。" #: ../../src/topics/command-line-tool.md:19 128bd8cd6788431da54fa07a8dc87f99 msgid "CWL command-line tool." @@ -1845,13 +1893,15 @@ msgstr "実行時にファイルを作成する" #: ../../src/topics/creating-files-at-runtime.md:3 #: cd0dff10471c4ad2b84e3a0e4d7767ea -#, fuzzy msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " "rather than the command line parameters, or need a small wrapper shell " "script." -msgstr "コマンドラインパラメーターではなく、ファイルから入力設定を読み込むことを期待するツールや、小さなラッパーシェルスクリプトが必要な場合など、入力パラメーターからその場でファイルを作成する必要があることがあります。" +msgstr "" +"コマンドラインパラメーターではなく、ファイルから入力設定を読み込むことを期待" +"するツールや、小さなラッパーシェルスクリプトが必要な場合など、入力パラメータ" +"ーからその場でファイルを作成する必要があることがあります。" #: ../../src/topics/creating-files-at-runtime.md:7 #: bf4aea0a22334a1ca75cc20e937e6581 @@ -1880,7 +1930,6 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 #: aca24b72687c4d4d84bf9de8b71413f7 -#, fuzzy msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1888,9 +1937,11 @@ msgid "" "`\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to " "be evaluated by the shell script instead of the CWL engine." msgstr "" -"_CWL expressions_ は、コマンドラインツール起動時に使用される_shell variables_ とは無関係です。つまり、`$` " -"という文字が本当に必要な場合は、** ` \\` で** をエスケープする必要があります。例えば，上記の`\\${PREFIX}` " -"は，CWLエンジンの代わりにシェルスクリプトで評価されるように，生成されたファイルでは`${PREFIX}` に展開されます．" +"_CWL expressions_ は、コマンドラインツール起動時に使用される_shell " +"variables_ とは無関係です。つまり、`$` という文字が本当に必要な場合は、`\\` " +"で**エスケープ**する必要があります。例えば，上記の`\\${PREFIX}` は，CWLエンジ" +"ンの代わりにシェルスクリプトで評価されるように，生成されたファイルでは`${PREF" +"IX}` に展開されます。" #: ../../src/topics/creating-files-at-runtime.md:27 #: 750b3232e8754448bc2b5913539495b8 @@ -1918,7 +1969,6 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 #: 9aeea5a6a4244bc7a1626e0cb7351068 -#, fuzzy msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1929,7 +1979,7 @@ msgid "" " write the whole script on one line)." msgstr "" "`InitialWorkDirRequirement` は`listing` を必要とします。`listing` は YAML " -"配列なので、配列の各要素の最初の行に`-` が必要です。この場合、要素は 1 " +"配列なので、配列の各要素の行の最初に`-` が必要です。この場合、要素は 1 " "つだけです。`entryname:` は任意の値を指定できますが、`baseCommand` " "で指定したものと一致していなければなりません。最後の部分は`entry:` " "で、この後に`|-` が続きます。これは YAML の引用構文で、" @@ -2008,7 +2058,6 @@ msgstr "" "で、テーブル変換で使用できるテーブルオプションのリストがカスタムオブジェクトとしてインポートされます：" #: ../../src/topics/custom-types.md:46 c791096f537141e8bd7cc941d711d108 -#, fuzzy msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -2145,7 +2194,6 @@ msgstr "" "runnerによって評価されるJavascriptを使用できます。" #: ../../src/topics/expressions.md:9 3d48d1a8f7f74bc1886e41653cb53a22 -#, fuzzy msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -2153,10 +2201,11 @@ msgid "" "`nameroot`, `nameext`, etc, could be used instead. See the [list of best " "practices](best-practices.md)." msgstr "" -"JavaScript " -"の式は、絶対に必要な場合のみ使用するようにしてください。ファイル名、拡張子、パスなどを操作する場合は、`basename`,`nameroot`,`nameext`," -" などの [`File` のビルトインプロパティ][file-prop] " -"のいずれかを代わりに使用できるかどうかを検討してください。[ベストプラクティスのリスト](best-practices.md)を参照してください。" +"JavaScript の式は、絶対に必要な場合のみ使用するようにしてください。ファイル名" +"、拡張子、パスなどを操作する場合は、`basename`,`nameroot`,`nameext`, などの " +"[`File` のビルトインプロパティ][file-prop] のいずれかを代わりに使用できるかど" +"うかを検討してください。[ベストプラクティスのリスト](best-practices." +"md)を参照してください。" #: ../../src/topics/expressions.md:16 7d444aacd418466bbe588fa964b45179 msgid "`expression.cwl`" @@ -2167,7 +2216,7 @@ msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "このツールは`inputs` " -"を必要としないので、（ほとんど）空のジョブファイルで実行することができます：" +"を必要としないので、（ほとんど）空のジョブファイルで実行できます：" #: ../../src/topics/expressions.md:25 d679fd1363b24c81979c68e7342159cf msgid "`empty.yml`" @@ -2184,7 +2233,7 @@ msgstr "" #: ../../src/topics/expressions.md:35 624e4a270e374b1699b780df508b9184 msgid "We can then run `expression.cwl`:" -msgstr "次に、`expression.cwl` を実行することができます：" +msgstr "次に、`expression.cwl` を実行できます：" #: ../../src/topics/expressions.md:37 c252eac9a35e46aab08bd07bc1cdb57d msgid "Running `expression.cwl`" @@ -2211,13 +2260,12 @@ msgid "Where are JavaScript expressions allowed?" msgstr "JavaScriptはどこで使えますか？" #: ../../src/topics/expressions.md:64 8c3b402c40f64880a4bd42c47b910254 -#, fuzzy msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -"[パラメータ参照](parameter-references.md)と同様に、JavaScript 式は特定のフィールドにのみ使用できます。 " -"以下はその例です：" +"[パラメータ参照](parameter-references.md)と同様に、JavaScript " +"式は特定のフィールドにのみ使用できます。 以下はその例です：" #: ../../src/topics/expressions.md:66 9bf5ca0e769147c6a9705bc40bd1febc msgid "" @@ -2511,8 +2559,9 @@ msgid "" "files or to create JavaScript functions that can be called in other parts" " of the CWL document." msgstr "" -"`expressionLib` " -"属性に追加されたエントリーは、CWLランナーのJavaScriptエンジンで解析されます。これは、外部ファイルをインクルードしたり、CWL定義の他の部分で呼び出すことができるJavaScript関数を作成するために使用することができます。" +"`expressionLib` 属性に追加されたエントリーは、CWL runnerのJavaScriptエンジン" +"で解析されます。これは、外部ファイルをインクルードしたり、CWL定義の他の部分で" +"呼び出すことができるJavaScript関数を作成するために使用できます。" #: ../../src/topics/expressions.md:128 5b2336cae1ef4cae8ed187d3f33cff25 msgid "" @@ -2534,8 +2583,9 @@ msgid "" "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -"例えば、`InlineJavascriptRequirement` を使って、`expressionLib` に JavaScript " -"関数をインラインで記述することができます。その関数は、CWL定義の他の部分で使用することができます：" +"例えば、`InlineJavascriptRequirement` を使って、`expressionLib` に " +"JavaScript " +"関数をインラインで記述できます。その関数は、CWL定義の他の部分で使用できます：" #: ../../src/topics/expressions.md:139 6839a02fb82d45c29ae518f2b00cb9d5 msgid "`hello-world-expressionlib-inline.cwl`" @@ -2610,9 +2660,9 @@ msgid "" "the CWL specification to learn more about it." msgstr "" "`$include` ステートメントを使用すると、ローカルディスクまたはリモートロケーシ" -"ョンからファイルをインクルードすることができます。相対パスと絶対パスの両方で" -"動作します。CWL仕様の[`$include`について](https://www.commonwl.org/v1.0/" -"SchemaSalad.html#Include)を読むと、より詳しく知ることができます。" +"ョンからファイルをインクルードできます。相対パスと絶対パスの両方で動作します" +"。CWL仕様の[`$include`について](https://www.commonwl.org/v1.0/SchemaSalad." +"html#Include)を読むと、より詳しく知ることができます。" #: ../../src/topics/file-formats.md:1 ac906f26116c45d882e1afa42ae38e34 msgid "File Formats" @@ -2628,11 +2678,10 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" "ToolsやWorkflowsは、[`File`](https://w3id.org/cwl/CommandLineTool.html#File) " -"型を入力として受け取り、出力として生成することができます。また、[`File`](http" -"s://w3id.org/cwl/CommandLineTool.html#File) タイプのフォーマットを示すことを" -"お勧めします。これにより、ツールの使用方法を他の人に示すことができ、また、パ" -"ラメータファイルを作成する際に簡単な型チェックを行うことができるようになりま" -"す。" +"型を入力として受け取り、出力として生成できます。また、[`File`](https://w3id." +"org/cwl/CommandLineTool.html#File) タイプのフォーマットを示すことをお勧めしま" +"す。これにより、ツールの使用方法を他の人に示すことができ、パラメータファイル" +"を作成する際に簡単な型チェックを行うことができるようになります。" #: ../../src/topics/file-formats.md:8 23ba3dd26f5543119e2c152105b58e98 msgid "" @@ -2646,7 +2695,7 @@ msgstr "" "）、所属機関のローカルオントロジーを参照すること、またはツールを他者と共有す" "る前に迅速に開発するために最初はファイルフォーマットを追加しないことを推奨し" "ています。既存の[IANAファイルフォーマット一覧][IANA]と[EDAMファイルフォーマッ" -"ト一覧][EDAM]は、それぞれのウェブサイトで参照することができます。" +"ト一覧][EDAM]は、それぞれのウェブサイトで参照できます。" #: ../../src/topics/file-formats.md:14 81c441846fc249c58607bacf97095eb8 msgid "" @@ -2677,20 +2726,21 @@ msgid "Sample Parameter Files" msgstr "サンプルパラメーターファイル" #: ../../src/topics/file-formats.md:34 afd8633db1904897aa3e499354b1c376 -#, fuzzy msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " "This allows others to quickly work with your tool, starting from a " "\"known good\" parameterization." -msgstr "以下は、上記の例のパラメータファイルの例です。あなたのツールのパラメータファイルの実例をチェックすることをお勧めします。これにより、他の人が「既知の良い」パラメータ化から始めて、あなたのツールで素早く作業することができます。" +msgstr "" +"以下は、上記の例のパラメータファイルの例です。あなたのツールのパラメータファ" +"イルの実例をチェックすることをお勧めします。これにより、他の人が「既知の良い" +"」パラメータ化から始めて、あなたのツールで素早く作業できます。" #: ../../src/topics/file-formats.md:39 bb69d6963c174191bf527335c3f665b7 msgid "`sample.yml`" msgstr "`sample.yml`" #: ../../src/topics/file-formats.md:45 ddb4f6f81c7d462b974e98c88dd3f558 -#, fuzzy msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2699,9 +2749,9 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" "___注：___ 以下の例に実行するには、例の入力ファイル、*file-formats.bam* " -"をダウンロードする必要があります。このファイルは から入手可能で、`wget` などでダウンロードすることができます：" +"をダウンロードする必要があります。このファイルは から入手可能で、`wget` などでダウンロードできます：" #: ../../src/topics/index.md:1 2995cd4fb85c423dba021611dac4a137 msgid "Topics" @@ -2716,13 +2766,13 @@ msgid "Essential Input Parameters" msgstr "必須入力パラメータ" #: ../../src/topics/inputs.md:5 17365707f58242369dd6aa73fc8d7242 -#, fuzzy msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -"ツールの`inputs` は、ツールの実行に関わる入力パラメーターのリストです。 各パラメーターには、パラメーター名を示す`id` " +"ツールの`inputs` は、ツールの実行に関わる入力パラメーターのリストです。 " +"各パラメーターには、パラメーター名を示す`id` " "と、そのパラメーターに有効な値の種類を示す`type` があります。" #: ../../src/topics/inputs.md:9 521cb5dead5d4e9ab5ff037fb4b683cb @@ -2761,9 +2811,9 @@ msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in an input object file:" msgstr "" -"`cwltool` を使って、テンプレートとなる入力オブジェクトを作成することができま" -"す。これにより、入力オブジェクトファイルにすべての入力パラメータを入力する手" -"間を省くことができます：" +"`cwltool` を使って、テンプレートとなる入力オブジェクトを作成できます。これに" +"より、入力オブジェクトファイルにすべての入力パラメータを入力する手間を省くこ" +"とができます：" #: ../../src/topics/inputs.md:40 5ac6da11d56446de97c251a37d997671 msgid "" @@ -2772,7 +2822,7 @@ msgid "" "desired input values." msgstr "" "`cwltool --make-template inp.cwl > inp-job.yml` のように、出力をファイルにリ" -"ダイレクトします。その後デフォルト値を希望の入力値で修正することができます。" +"ダイレクトします。その後デフォルト値を希望の入力値で修正できます。" #: ../../src/topics/inputs.md:44 6a3edb0d259d4d7c900dd9811f978d4e msgid "" @@ -2806,12 +2856,11 @@ msgid "" "that the tools aren't accidentally accessing files that were not " "explicitly specified" msgstr "" -"CWLリファレンスランナー（cwltool）と他のランナーは、ツールが明示的に指定され" -"ていないファイルに誤ってアクセスしないように、入力ファイルへの（\"ソフト\"" +"CWL reference runner（cwltool）と他のランナーは、ツールが明示的に指定されてい" +"ないファイルに誤ってアクセスしないように、入力ファイルへの（\"ソフト\"" "）シンボリックリンクを持つ一時ディレクトリを作成します" #: ../../src/topics/inputs.md:70 5bdf77c45346445d8f93353c1e73f768 -#, fuzzy msgid "" "The field " "[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)" @@ -2820,10 +2869,10 @@ msgid "" "parameter does not appear on the command line. Let's look at each " "example in detail." msgstr "" -"フィールド[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_bi" -"nding)はオプションであり、入力パラメータをツールのコマンドラインに表示するか" -"どうか、またどのように表示するかを指定します。`inputBinding`がない場合、パラ" -"メータはコマンドラインに表示されません。 それぞれの例を詳しく見てみましょう。" +"[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)フィ" +"ールドはオプションであり、入力パラメータをツールのコマンドラインに含めるかど" +"うか、またどのように含めるかを指定します。`inputBinding`がない場合、パラメー" +"タはコマンドラインに含まれません。 それぞれの例を詳しく見てみましょう。" #: ../../src/topics/inputs.md:83 d783fe52e86f4feda33ea0eecb622603 msgid "" @@ -2846,7 +2895,6 @@ msgstr "" " hello` と与えられます。" #: ../../src/topics/inputs.md:109 b106eed01c1744a792368f91f547e553 -#, fuzzy msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2855,10 +2903,9 @@ msgid "" msgstr "" "整数型（および浮動小数点型）はコマンドラインに10進数のテキスト表現で表示され" "ます。 `separate`オプションがfalseの場合（デフォルト値はtrue）、prefixと値は1" -"つの引数にまとめられます。 上の例では `-i42` として表示されます。" +"つの引数になるようにまとめられます。 上の例では `-i42` として表示されます。" #: ../../src/topics/inputs.md:124 1c70336741a842a5b16b687642d1d9b4 -#, fuzzy msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2869,8 +2916,8 @@ msgid "" msgstr "" "ファイル型は、コマンドライン上にファイルへのパスとして表示されます。 パラメ" "ータの型の末尾にクエスチョンマーク`?`がある場合、これは、パラメータがオプショ" -"ンであることを表します。 上記の例では、`--file=/tmp/random/path/whale.txt` " -"と表示されます。 ただし、入力パラメータに \"example_file\" " +"ナルであることを表します。 上記の例では、`--file=/tmp/random/path/whale.txt`" +" と表示されます。 ただし、入力パラメータに \"example_file\" " "パラメータを指定しなかった場合、コマンドラインには何も表示されません。" #: ../../src/topics/inputs.md:131 9294c07c672b414f9c3895ed70b9b4ee @@ -2910,7 +2957,6 @@ msgid "Array Inputs" msgstr "配列入力" #: ../../src/topics/inputs.md:148 b11a5c7a13b345939e4ae15e1e2c0786 -#, fuzzy msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2919,11 +2965,11 @@ msgid "" " be added after the type name to indicate that input parameter is array " "of that type." msgstr "" -"コマンドラインに表現される入力パラメータの配列を簡単に追加することができます" -"。配列パラメータを指定するには、2つの方法があります。1つ目の方法は、`type` " -"に`type: array` と`items` を指定して、配列に現れる可能性のある有効なデータ型" -"を定義する方法です。2つ目の方法は、入力パラメータがその型の配列であることを示" -"すために、型名の後に`[]` という括弧を付けることもできます。" +"コマンドラインに含まれる入力パラメータの配列は簡単に追加できます。配列パラメ" +"ータを指定するには、2つの方法があります。1つ目の方法は、`type` に`type: " +"array` と`items` を指定して、配列に現れる可能性のある有効なデータ型を定義する" +"方法です。2つ目の方法は、入力パラメータがその型の配列であることを示すために、" +"型名の後に`[]` という括弧を付けることもできます。" #: ../../src/topics/inputs.md:154 aa00bcfc6c0f4085ae52621a2f4ae8d9 msgid "`array-inputs.cwl`" @@ -2952,9 +2998,9 @@ msgid "" "item separator string." msgstr "" "`inputBinding` は、外側の配列パラメータ定義と内側の配列要素定義のいずれかに記" -"述することができ、上図のようにコマンドラインを構築する際に異なる挙動を示しま" -"す。また、`itemSeparator` フィールドがあれば、配列の値を項目区切り文字列で区" -"切って1つの引数に連結することを指定することができます。" +"述でき、上図のようにコマンドラインを構築する際に異なる挙動を示します。また、`" +"itemSeparator` フィールドがあれば、配列の値を項目区切り文字列で区切って1つの" +"引数に連結することを指定できます。" #: ../../src/topics/inputs.md:185 bb31c6784ea843ec88f185523cfa25df msgid "" @@ -2970,7 +3016,7 @@ msgstr "" "列は複数行に渡って表現することも可能で、関連するキーで定義されていない配列の" "値は、先頭の`-` でマークされます。これは次のレッスンで実際に確認し、[YAML " "Guide](yaml-guide.md#arrays) でより詳細に説明されています。配列の配列、レコー" -"ドの配列、その他の複雑な型を指定することができます。" +"ドの配列、その他の複雑な型を指定できます。" #: ../../src/topics/inputs.md:191 53817379078548b2aeb6195cae9cbab7 msgid "Inclusive and Exclusive Inputs" @@ -2985,8 +3031,7 @@ msgid "" msgstr "" "基本的なツールには、一緒に提供しなければならない複数の引数（依存関係あり）や" "、一緒に提供できない複数の引数（排他関係あり）があることがあります。 record" -"とユニオン型を使ってパラメータをグループ化し、この2つの条件を定義することがで" -"きます。" +"とユニオン型を使ってパラメータをグループ化し、この2つの条件を定義できます。" #: ../../src/topics/inputs.md:198 84e1ab25511c49d1baabb1f80f247b49 msgid "`record.cwl`" @@ -3039,8 +3084,9 @@ msgid "" msgstr "" "排他的入力パラメータを式と組み合わせて使用する場合、JavaScript " "オブジェクトの`inputs` に排他的入力値のいずれかが含まれることを意識する必要が" -"あります。つまり、**or** のブーリアン演算子を使用して、`inputs`にどの値が存在" -"するかをチェックする必要がある場合があります。" +"あります。つまり、これらの排他的な値の型は異なる可能性があるので、`input` オ" +"ブジェクトのプロパティを参照するときに、どの型が使用されているかを確認する必" +"要があるかもしれません。" #: ../../src/topics/inputs.md:263 0fecb128b19b44d796b6c1b6de4f7166 msgid "" @@ -3067,7 +3113,6 @@ msgstr "" "すると、コマンドは正常に実行されるはずです：" #: ../../src/topics/inputs.md:281 11fdeb057d674f118830f431ff019c15 -#, fuzzy msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to `null`, which does not match the expected type for the " @@ -3075,19 +3120,21 @@ msgid "" "workflow." msgstr "" "しかし、入力値を提供しない場合、`file_format` は、`null` " -"の値として評価されます。これは、出力フィールドが期待する型（`string` ）と一致しないため、ワークフロー実行時に失敗することになります。" +"の値として評価されます。これは、出力フィールドが期待する型（`string` " +"）と一致しないため、ワークフロー実行時に失敗することになります。" #: ../../src/topics/inputs.md:290 8594cca9d93b4280b6cfee64c8a7c578 -#, fuzzy msgid "" "To correct it, you should explicitly handle the possibility of a `null` " "value. For example, the expression could be changed to " "`$(inputs.file_format || 'auto')`, to have a default value `\"auto\"` if " "none was provided in the command line or job input file." msgstr "" -"これを修正するには、排他的パラメータ、または`null` を許可するパラメータを使用する場合、JavaScript 式で or " -"演算子を使用することを忘れてはなりません。たとえば、式を`$(inputs.file_format || 'auto')` " -"に変更すると、コマンドラインやジョブ入力ファイルで何も指定されていない場合にデフォルト値を持つようになります。" +"これを修正するには、排他的パラメータ、または`null` " +"を許可するパラメータを使用する場合、JavaScript 式で or " +"演算子を使用することを忘れてはなりません。たとえば、式を`$(" +"inputs.file_format || 'auto')` に変更すると、コマンドラインやジョブ入力ファイ" +"ルで何も指定されていない場合にデフォルト値`\"auto\"`を持つようになります。" #: ../../src/topics/inputs.md:295 b5055c77f85e43609fe3e9b9839778e3 msgid "" @@ -3099,12 +3146,12 @@ msgid "" "expression’s value becomes that of the second operand, which is why a " "reasonable default can be provided there." msgstr "" -"ここでは、JavaScriptのブール値 \"or\"、 \"演算子 `||` は、その_short-" -"circuiting_プロパティに使用されます。`inputs.file_format`がブール値の \"true" -"\"である場合（例えば、列挙された有効な空でない文字列）、式の評価は " -"`||`の最初のオペランドで停止します。しかし、 `inputs.file_format`が`null`の場" -"合、式全体の値は2番目のオペランドの値になります。これにより合理的なデフォルト" -"値を提供します。" +"ここでは、JavaScriptのブール値 \"or\"、 演算子 `||` は、その _short-" +"circuiting_ プロパティに使用されます。`inputs.file_format`がブール値の \"true" +"\"である場合（例えば、列挙された有効な空でない文字列）、式の評価は `||`" +"の最初のオペランド\"short-circuits\"で停止します。しかし、 `inputs.file_forma" +"t`が`null`の場合、式全体の値は2番目のオペランドの値になります。これにより合理" +"的なデフォルト値を提供します。" #: ../../src/topics/metadata-and-authorship.md:1 #: 723c2232310c4276aeac2bd6728d2912 @@ -3150,20 +3197,22 @@ msgstr "`metadata_example2.cwl`" #: ../../src/topics/metadata-and-authorship.md:28 #: 37b07ea9b7124842b8ba3040f70308e9 -#, fuzzy msgid "Extended Example" msgstr "拡張された例" #: ../../src/topics/metadata-and-authorship.md:30 #: 1cd5989ade6741aabe625c13bed3c8ed -#, fuzzy msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " "ontology tags as keywords (allowing the grouping of related tools), hints" " at hardware requirements in order to use the tool, and a few more " "metadata fields." -msgstr "高いモチベーションを持つ人であれば、ツールにもっと多くのメタデータを付与することも可能です。この例では、EDAMオントロジーのタグをキーワードとして含み（関連するツールのグループ化が可能）、ツールを使用するために必要なハードウェアのヒントや、さらにいくつかのメタデータフィールドがあります。" +msgstr "" +"高いモチベーションを持つ人であれば、ツールにもっと多くのメタデータを付与する" +"ことも可能です。この例では、EDAMオントロジーのタグをキーワードとして含み（関" +"連するツールのグループ化が可能）、ツールを使用するために必要なハードウェアの" +"ヒントや、さらにいくつかのメタデータフィールドがあります。" #: ../../src/topics/metadata-and-authorship.md:35 #: ae7369ba14404d23b72d1ef30dcd4153 @@ -3189,7 +3238,8 @@ msgstr "" msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" -msgstr "CWLランナーにワークフローを送信する前に、開発中のワークフローを可視化することができます：" +msgstr "CWL " +"runnerでワークフローを実行する前に、開発中のワークフローを可視化できます：" #: ../../src/topics/operations.md:10 e9b2b97f3059460b867577a49934a338 msgid "`operations.cwl`" @@ -3202,8 +3252,8 @@ msgid "" "with the CWL Viewer or `cwltool`:" msgstr "" "ワークフローの`uppercase` ステップは Operation " -"です。CommandLineToolやExpressionToolのように使用することができます。また、" -"CWL Viewerや`cwltool` を使って可視化することもできます：" +"です。CommandLineToolやExpressionToolのように使用できます。また、CWL " +"Viewerや`cwltool` を使って可視化できます：" #: ../../src/topics/operations.md:24 61e4ae6ed18e41708270eb358cd55277 msgid "" @@ -3211,9 +3261,9 @@ msgid "" " The following image is rendered with the Sphinx `{graphviz}` directive " "(this user guide is built with Sphinx):" msgstr "" -"上記のコマンドの出力は、Graphvizを使ってレンダリングすることができます。以下" -"の画像は、SphinxのGraphvizディレクティブでレンダリングしたものです（このユー" -"ザーガイドはSphinxで構築されています）：" +"上記のコマンドの出力は、Graphvizを使ってレンダリングできます。以下の画像は、S" +"phinxの`{graphviz}`ディレクティブでレンダリングしたものです（このユーザーガイ" +"ドはSphinxで構築されています）：" #: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd msgid "" @@ -3228,16 +3278,15 @@ msgid "`cwltool` does not know how to run operations" msgstr "`cwltool` は、どうやってoperationsを実行するかを知りません" #: ../../src/topics/operations.md:67 3b90445d3428444cafd7d5c0e5884980 -#, fuzzy msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" "CWL runnerは、operations " -"を具体的なステップにバインドする見出すかもしれません。例えば、CWL runnerは、" +"を具体的なステップに結びつけるかもしれません。例えば、CWL runnerは、" "ワークフローエンジンで実行される異なるステップに対応するIDを持つ抽象的な " -"operation を使用することができます。" +"operation を使用できます。" #: ../../src/topics/outputs.md:1 35e7bad6fdc04bcf9bbfbb2d8d42cfa5 msgid "Outputs" @@ -3260,7 +3309,6 @@ msgstr "" "と、そのパラメーターに有効な値の型を示す`type` があります。" #: ../../src/topics/outputs.md:10 a229d8d983344e51a231edb5f667d84b -#, fuzzy msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -3268,11 +3316,11 @@ msgid "" "output parameters returned by the CWL tool are either the output files " "themselves, or the result of examining the content of those files." msgstr "" -"CWLでツールを実行する場合、開始時の作業ディレクトリが出力ディレクトリになりま" -"す。 基礎となるツールやスクリプトは、出力ディレクトリに作成されるファイルの" -"形でその結果を記録しなければなりません。 CWLツールによって返される出力パラメ" -"ータは、出力ファイルそのものであるか、またはそれらのファイルの内容を調べるこ" -"とによって得られるものです。" +"CWLでツールを実行する場合、実行を開始したディレクトリが出力ディレクトリになり" +"ます。 基礎となるツールやスクリプトは、出力ディレクトリに作成されるファイル" +"の形でその結果を記録しなければなりません。 CWLツールによって返される出力パラ" +"メータは、出力ファイルそのものであるか、またはそれらのファイルの内容を調べる" +"ことによって得られるものです。" #: ../../src/topics/outputs.md:16 9845e517f7d848e5b59a97880ca6999f msgid "" @@ -3294,8 +3342,8 @@ msgid "" msgstr "" "これまでの例では、`baseCommand` " "は単なる文字列で、引数はCWL入力として渡していました。単一の文字列の代わりに、" -"_文字列の配列_ を使用することができます。 配列の最初の要素は実行するコマンド" -"で、それ以降の要素は必須のコマンドライン引数です" +"_文字列の配列_ を使用できます。 配列の最初の要素は実行するコマンドで、それ以" +"降の要素は必須のコマンドライン引数です" #: ../../src/topics/outputs.md:28 9b65071222c94951bed12ac53e964ee3 msgid "`tar.cwl`" @@ -3337,7 +3385,7 @@ msgstr "" "[`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) フィ" "ールドは、出力ディレクトリ内のファイル名で構成されます。前もって出力ファイル" "名が分からない場合は、`glob: '*.txt'` " -"のようにワイルドカードパターンを使用することができます。" +"のようにワイルドカードパターンを使用できます。" #: ../../src/topics/outputs.md:69 8a6e9173198241429effd911c3a7c4d7 msgid "Capturing Standard Output" @@ -3414,8 +3462,8 @@ msgstr "" "ん。なぜなら、\"hello.txt \"というファイル名は" "、使用する入力ファイルによって異なるか、または依存する可能性があるからです。" " これを避けるために、ジョブパラメーターファイル(`.yml`)で必要なファイル名を" -"指定することができます。この例では、入力パラメーターの値を他のフィールドから" -"動的に参照して、抽出するファイル名を指定する方法を説明します。" +"指定できます。この例では、入力パラメーターの値を他のフィールドから動的に参照" +"して、抽出するファイル名を指定する方法を説明します。" #: ../../src/topics/parameter-references.md:13 50db8add9b1942d986e581b8d21c2ee4 msgid "`tar-param.cwl`" @@ -3433,11 +3481,11 @@ msgstr "入力ファイル(入力オブジェクト)を作成し、コマンド "ジェクトを指定して`cwltool` を呼び出します：" #: ../../src/topics/parameter-references.md:36 06926a516ae6432d96e3eaa62202cd86 -#, fuzzy msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." -msgstr "`$(...)` で囲まれたパラメータ参照を許可するフィールドもあります。これらは評価され、参照されている値に置き換えられます。" +msgstr "`$(...)` で囲まれたパラメータ参照を許可するフィールドもあります。これらは評価" +"され、参照されている値に置き換えられます。" #: ../../src/topics/parameter-references.md:47 384fe8188f414eafbbb8d6b81bdfd779 msgid "" @@ -3472,8 +3520,7 @@ msgstr "パラメータ参照はどこで許されるのですか？" #: ../../src/topics/parameter-references.md:61 055d3268859c46c4b7db5005608bae05 msgid "You can only use parameter references in certain fields. These are:" -msgstr "パラメータ参照は、特定のフィールドでのみ使用することができます。 " -"以下はその例です：" +msgstr "パラメータ参照は、特定のフィールドでのみ使用できます。 以下はその例です：" #: ../../src/topics/parameter-references.md:63 2ed66835bd9044adbfdd0b5097787f22 msgid "" @@ -3588,7 +3635,6 @@ msgstr "ソフトウェア要求事項の指定" #: ../../src/topics/specifying-software-requirements.md:3 #: e708866921ea49d69d3c2a32d63ea468 -#, fuzzy msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -3619,10 +3665,10 @@ msgid "" "enable these checks with the reference implementation, use the " "[dependency resolvers configuration][dependencies]." msgstr "" -"CWLランナーによっては、これらのヒントを使用して、ジョブの実行前に必要なソフト" -"ウェアがインストールされ、利用可能であることをチェックすることができます。リ" -"ファレンス実装でこれらのチェックを有効にするには、[依存性解決のための設定][de" -"pendencies] を使用します。" +"CWL runnerによっては、これらのヒントを使用して、ジョブの実行前に必要なソフト" +"ウェアがインストールされ、利用可能であることをチェックできます。リファレンス" +"実装でこれらのチェックを有効にするには、[依存性解決のための設定][dependencies" +"] を使用します。" #: ../../src/topics/specifying-software-requirements.md:29 #: 1a8b8aadf1c64e87b8b670e288bc14bc @@ -3641,6 +3687,17 @@ msgid "" "preference, are to include the DOI for the main tool citation and the URL" " to the tool." msgstr "" +"バージョン番号だけでなく、ツールの一意なリソース識別子（URI）が[RRID][rrid]の" +"形で与えられます。RRIDを持つリソースは[SciCrunch][scicrunch]レジストリで検索" +"することができ、科学リソースを一貫して検索、追跡、参照するためのポータルを提" +"供します。ツールを [`SoftwareRequirement`](https://w3id.org/cwl/" +"CommandLineTool.html#SoftwareRequirement) として指定したい場合は、SciCrunch " +"でツールを検索し、レジストリで割り当てられた RRID を使用してください。(" +"ツールを SciCrunch に追加するには [リソースの追加チュートリアル][scicrunch-" +"add-tool] を参照してください)。この RRID を使って、（[identifiers." +"org][identifiers] 経由で）要件説明の `specs` フィールドでツールを参照できます" +"。他の良い選択としては、優先順位の高い順に、メインのツールの引用のためのDOIと" +"ツールのURLを含めることです。" #: ../../src/topics/staging-input-files.md:1 d10c792550e8498c8ee384d3093da306 msgid "Staging Input Files" @@ -3679,8 +3736,9 @@ msgid "" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -"このセクションでは、CWLの実行に問題がある場合にトラブルシューティングを行う方法を説明します。ここでは、`cwltool` " -"に焦点を当てますが、これらのテクニックのいくつかは他のCWLランナーにも適用されるかもしれません。" +"このセクションでは、CWLの実行に問題がある場合にトラブルシューティングを行う方" +"法を説明します。ここでは、`cwltool` に焦点を当てますが、" +"いくつかのテクニックは他のCWL runnerでも使えるかもしれません。" #: ../../src/topics/troubleshooting.md:6 1d47f4ce04554cabb1ccf40a13ee42ec msgid "Run `cwltool` with `cachedir`" @@ -3696,9 +3754,9 @@ msgid "" msgstr "" "ワークフロー実行時に`--cachedir` オプションを使用すると、`cwltool` に中間ファ" "イル（入力ファイルでも出力ファイルでもないが、ワークフロー実行中に作成される" -"ファイル）をキャッシュするよう指示することができます。デフォルトでは、これら" -"のファイルは一時ディレクトリに作成されますが、別のディレクトリに書き込むこと" -"でアクセスが容易になります。" +"ファイル）をキャッシュするよう指示できます。デフォルトでは、これらのファイル" +"は一時ディレクトリに作成されますが、別のディレクトリに書き込むことでアクセス" +"が容易になります。" #: ../../src/topics/troubleshooting.md:14 36ec60b80c714357a4274217274136ff msgid "" @@ -3741,7 +3799,7 @@ msgstr "" "`step_b` が存在しない `revv` コマンドの実行に失敗したため、ワークフローは " "`permanentFail` ステータスになっています。`step_a` は正常に実行され、" "その出力は `cachedir` " -"にキャッシュされました。作成された中間ファイルを確認することができます：" +"にキャッシュされました。作成された中間ファイルを確認できます：" #: ../../src/topics/troubleshooting.md:44 04e80f7ce14d4d73bc5d290dcf01bcdb msgid "" @@ -3811,18 +3869,17 @@ msgstr "" "いランタイムを提供することによって、ソフトウェアのインストールを簡素化します" "。 しかし、コンテナはホストシステムから意図的に隔離されているため、Dockerコ" "ンテナ内でツールを実行するには、入力ファイルがコンテナ内で利用可能で、出力フ" -"ァイルがコンテナから回収できることを確認するための追加作業が必要です。 CWLラ" -"ンナーはこの作業を自動的に行うことができるため、Dockerコンテナの呼び出しや管" -"理の複雑さを回避しながら、Dockerを使用してソフトウェア管理を簡素化することが" -"できます。" +"ァイルがコンテナから回収できることを確認するための追加作業が必要です。 CWL r" +"unnerはこの作業を自動的に行うことができるため、Dockerコンテナの呼び出しや管理" +"の複雑さを回避しながら、Dockerを使用してソフトウェア管理を簡素化できます。" #: ../../src/topics/using-containers.md:15 4b0f6cfc8a774c77bfbc99e568af2ece msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." -msgstr "CWLランナーの役割のひとつに、入力ファイルのパスをコンテナ内のでの配置位置に合" -"わせることがあります。" +msgstr "CWL runnerの役割のひとつに、入力ファイルのパスをコンテナ内のでのパスに合わせ" +"ることがあります。" #: ../../src/topics/using-containers.md:18 27c02a5d479a420eab7d14888d9fb288 msgid "" @@ -3852,7 +3909,6 @@ msgstr "" "の部分だけです。" #: ../../src/topics/using-containers.md:44 1f02618ab6254459ae71f72844e3cc18 -#, fuzzy msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3890,7 +3946,8 @@ msgstr "`hello.js`" msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." -msgstr "CWLランナーがスクリプトを実行するためにDockerコマンドラインを構築していることに注目してください。" +msgstr "CWL runnerがスクリプトを実行するためにDockerコマンドラインを構築していること" +"に注目してください。" #: ../../src/topics/using-containers.md:72 d2dd89a5edde4f2eab4c2baf0cc78745 msgid "" @@ -3990,7 +4047,6 @@ msgid "Visualization of 1st-workflow.cwl" msgstr "1st-workflow.cwlの可視化" #: ../../src/topics/workflows.md:180 f0831481a43548039fbc4fd17555af57 -#, fuzzy msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -4002,15 +4058,13 @@ msgid "" "language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" "-1st-workflow/1st-workflow.cwl)" msgstr "" -"[[1st-" -"workflow.cwlを可視化したもの]](https://view.commonwl.org/graph/png/github.com" -"/common-workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-" -"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-" -"workflow-" -"language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21" -"-1st-workflow/1st-workflow.cwl)" +"[![1st-workflow.cwlを可視化したもの](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/" +"common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)" #: ../../src/topics/workflows.md:183 5ff059fc8ae6471c8ea86dab7e5a93f5 msgid "" @@ -4066,7 +4120,6 @@ msgstr "" "を、ワークフロー出力パラメータ`compiled_class` とします。" #: ../../src/topics/workflows.md:248 e0429688fce445da8083e69323e5b020 -#, fuzzy msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -4085,19 +4138,18 @@ msgstr "" "されることがあります。" #: ../../src/topics/workflows.md:256 980f5eada57c4fadbb783838ded1fa0b -#, fuzzy msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" " parameters, `tarfile` and `extractfile` and one output parameter " "`extracted_file`." msgstr "" -"最初のステップである`untar` は、`tar-param.cwl` を実行します（[パラメータ参照](parameter-" -"references.md)で以前説明しました）。このツールは、2つの入力パラメータ、`tarfile` と`extractfile` " -"と1つの出力パラメータ`extracted_file` を持ちます。" +"最初のステップである`untar` は、`tar-param.cwl` を実行します（[パラメータ参照" +"](parameter-references." +"md)で以前説明しました）。このツールは、2つの入力パラメータ、`tarfile` " +"と`extractfile` と1つの出力パラメータ`extracted_file` を持ちます。" #: ../../src/topics/workflows.md:261 3532e165842f4ebb8db0c78208071555 -#, fuzzy msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -4122,7 +4174,6 @@ msgstr "ワークフローステップの`out` " "セクションには、ツールから期待される出力パラメータが記載されています。" #: ../../src/topics/workflows.md:278 2651ee113a3d4b79b138854ebe729f48 -#, fuzzy msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -4134,7 +4185,7 @@ msgstr "" "第2ステップ `compile` は、第1ステップの結果に依存し、入力パラメータ`src` " "を`untar` の出力パラメータに接続し、`untar/extracted_file` を使用します。 " "これは、`arguments.cwl` (以前に [追加の引数とパラメータ](additional-" -"arguments-and-parameters.md)で説明) " +"arguments-and-parameters.md)で説明したものです) " "を実行します。このステップの出力`classfile` は、前述のワークフローの`outputs`" " セクションに接続されています。" @@ -4149,8 +4200,10 @@ msgid "" " workflow can be used as a step in another CWL workflow, if the workflow " "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -"ワークフローは、複数のツールを組み合わせてより大きな処理を実行するための方法です。ワークフローエンジンが`SubworkflowFeatureRequirement`" -" をサポートしている場合、CWL ワークフローを別の CWL ワークフローのステップとすることができます ：" +"ワークフローは、複数のツールを組み合わせてより大きな処理を実行するための方法" +"です。ワークフローエンジンが`SubworkflowFeatureRequirement` " +"をサポートしている場合、CWL ワークフローを別の CWL " +"ワークフローのステップにできます ：" #: ../../src/topics/workflows.md:297 44d281d99cd944478db98446a984c001 msgid "" @@ -4207,7 +4260,7 @@ msgstr "" "CWL`Workflow` は、`CommandLineTool` を`step` として使用することができ、その " "CWL ファイルは`run` に記述されます。ワークフローの入力（`tarball` " "および`name_of_file_to_extract` ）と出力（`compiled_class` " -"）は、ステップの入力/出力になるようにマッピングすることができます。" +"）は、ステップの入力/出力になるようにマッピングできます。" #: ../../src/topics/workflows.md:336 d621821d2c1b403cb7415b381dd883f6 msgid "" @@ -4238,28 +4291,28 @@ msgstr "" "るのがよいでしょう。これらは、ツールとしての使用法にも現れるからです。" #: ../../src/topics/workflows.md:347 c6297c120e004ae8b52d5b519fbc04d2 -#, fuzzy msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" "coded `Hello.java` file using the previously mentioned " "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -"また、あまり一般的でない方法で、ジョブファイルの外部依存を回避することも可能です。そこで、このワークフローでは、先に述べた`InitialWorkDirRequirement`" -" の要件を使用して、ハードコードされた`Hello.java` ファイルを生成してから、それを tar ファイルに追加することができます。" +"また、あまり一般的でない方法で、ジョブファイルの外部依存を回避することも可能" +"です。そこで、このワークフローでは、先に述べた`InitialWorkDirRequirement` " +"の要件を使用して、ハードコードされた`Hello.java` ファイルを生成してから、" +"それを tar ファイルに追加できます。" #: ../../src/topics/workflows.md:366 66f76677f4ce42baa8a8813410ea5aee -#, fuzzy msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -"この場合、ステップではパラメータ化するのではなく、`Hello.java` を想定することができるので、`baseCommand` " -"で直接書かれた値`hello.tar` と`Hello.java` を使用でき、結果として`outputs` が得られます：" +"この場合、ステップではパラメータ化するのではなく、`Hello.java` " +"を想定することができるので、`baseCommand` に直接書かれた値`hello.tar` " +"と`Hello.java` を使用でき、結果として`outputs` が得られます：" #: ../../src/topics/workflows.md:383 a8ccb9f9ab4448e087ea8448d620d33c -#, fuzzy msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -4267,8 +4320,11 @@ msgid "" "reason for doing it in this case is because the command line is hard-" "coded with filenames that only make sense within this workflow." msgstr "" -"`tar --create` ツールを別のファイルに分割せず、CWL Workflow " -"定義の中に埋め込んだことにお気づきでしょうか。これは一般的にベストプラクティスではありません。なぜなら、そのツールを再利用できないからです。このケースでそれを行う理由は、コマンドラインに、このワークフロー定義内でしか意味をなさないファイル名がハードコーディングされているためです。" +"`tar --create` ツールを別のファイルに分割せず、CWL Workflow 定義の中に埋め込" +"んだことにお気づきでしょうか。これは一般的にベストプラクティスではありません" +"。なぜなら、そのツールを再利用できないからです。このケースでそれを行う理由は" +"、コマンドラインに、このワークフロー定義内でしか意味をなさないファイル名がハ" +"ードコーディングされているためです。" #: ../../src/topics/workflows.md:389 afe43b9e92e949a589f493293eff2903 msgid "" @@ -4300,7 +4356,6 @@ msgid "Scattering Steps" msgstr "Scatter ステップ" #: ../../src/topics/workflows.md:400 eab4437bf9994b649954221375e3dd6d -#, fuzzy msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -4312,10 +4367,10 @@ msgid "" msgstr "" "ワークフローの書き方がわかったので、`ScatterFeatureRequirement` を利用し始め" "ることができます。この機能は、ツールやワークフローを入力のリストに対して複数" -"回実行したいことをランナーに伝えます。ワークフローは、入力を配列として受け取" -"り、配列の各要素に対して、あたかも1つの入力であるかのように、指定されたステッ" -"プを実行します。これにより、多くの異なるコマンドや入力 yaml ファイルを生成す" -"ることなく、複数の入力に対して同じワークフローを実行することができます。" +"回実行したいことをrunnerに伝えます。ワークフローは、入力を配列として受け取り" +"、配列の各要素をあたかも1つの入力であるかのように、指定されたステップを実行し" +"ます。これにより、多くの異なるコマンドや入力 yaml ファイルを生成することなく" +"、複数の入力に対して同じワークフローを実行できます。" #: ../../src/topics/workflows.md:411 c245ba0ae2074fa388ad6c35695033c8 msgid "" @@ -4351,21 +4406,23 @@ msgid "" " particular step. Note that the input name listed after scatter is the " "one of the step's input, not a workflow level input." msgstr "" -"ここでは、ステップ`echo` に、`scatter` という新しいフィールドを追加しました。" -"このフィールドは、CWLランナーに、このステップの入力を分散して実行したいことを" -"伝えます。scatterの後に記載されている入力名は、ワークフローレベルの入力名では" -"なく、ステップの入力名であることに注意してください。" +"ここでは、ステップ`echo` に、`scatter` " +"という新しいフィールドを追加しました。このフィールドは、CWL runnerに、このス" +"テップの入力を分散して実行したいことを伝えます。scatterの後に記載されている入" +"力名は、ワークフローレベルの入力名ではなく、ステップの入力名であることに注意" +"してください。" #: ../../src/topics/workflows.md:445 0d5cf8b82dbd47f2abd1ed16b9b3eb61 -#, fuzzy msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " "you expect that the final output of your workflow will now have multiple " "outputs to collect, be sure to update that to an array type as well!" msgstr "" -"最初のスキャッターでは、これと同じくらい簡単です！このツールは出力を回収しないので、`outputs: []` " -"を使います。しかし、ワークフローの最終出力に収集する複数の出力があることが予想される場合、それを配列型に更新するようにしてください！" +"最初のスキャッターでは、これと同じくらい簡単です！このツールは出力を回収しな" +"いので、`outputs: []` を使います。しかし、ワークフローの最終出力に収集する複" +"数の出力があることが予想される場合、それを配列型に更新するようにしてください" +"！" #: ../../src/topics/workflows.md:450 38b7042a270043ba82c11cf2e758f0c8 msgid "Using the following input file:" @@ -4416,18 +4473,17 @@ msgid "`wc-tool.cwl`" msgstr "`wc-tool.cwl`" #: ../../src/topics/workflows.md:489 63595d35dded4911aab0be3a165eec0c -#, fuzzy msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" -msgstr "さて、スキャッターはどのように取り入れるのでしょうか？スキャッターフィールドは各ステップの下にあることを思い出してください：" +msgstr "さて、scatterはどのように取り入れるのでしょうか？scatterフィールドは各ステッ" +"プの下にあることを思い出してください：" #: ../../src/topics/workflows.md:491 a7f96ec6e4f24c62ac0f5b6edcc9734b msgid "`scatter-two-steps.cwl`" msgstr "`scatter-two-steps.cwl`" #: ../../src/topics/workflows.md:497 122452b7d7114c3fa53cbea286703023 -#, fuzzy msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -4490,7 +4546,7 @@ msgid "" msgstr "" "このワークフローは、条件付きステップを含み、入力に基づき実行されます。これに" "より、ワークフローは、プログラムの開始時に与えられた入力パラメータや以前のス" -"テップによって、追加のステップをスキップすることができます。" +"テップによって、追加のステップをスキップできます。" #: ../../src/topics/workflows.md:527 9ac7b4f71621411da9a4ca3bc277dcb0 msgid "`conditional-workflow.cwl`" @@ -4504,7 +4560,6 @@ msgstr "まず、このワークフローはCWL仕様のバージョン1." "2以降から対応しているがわかります。" #: ../../src/topics/workflows.md:573 4742fe09a4264fb8be6f092519de5d72 -#, fuzzy msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -4614,7 +4669,7 @@ msgstr "" "上記のYAMLは4つのキー -`first_name`,`last_name`,`age_years`, `home` - 及びそ" "れぞれの値を定義しています。値は、文字列、数値（整数、浮動小数点、科学的表現" "）、ブール値（`true` または`false` " -"）、またはより複雑な入れ子型（下記参照）にすることができます。" +"）、またはより複雑な入れ子型（下記参照）にできます。" #: ../../src/topics/yaml-guide.md:51 6939eb7e783744d7bcf75ea0a7cae129 msgid "" @@ -4641,8 +4696,8 @@ msgid "" "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -"`#` を使うと、CWL定義や入力パラメータファイルにコメントを追加することができま" -"す。` #` の右側にある文字は、YAML " +"`#` を使うと、CWL定義や入力パラメータファイルにコメントを追加できます。` #` " +"の右側にある文字は、YAML " "を解釈するプログラムによって無視されます。たとえば、次のようになります：" #: ../../src/topics/yaml-guide.md:76 13da997c82c04023a4b7bb36b76e969d @@ -4657,7 +4712,6 @@ msgid "Maps" msgstr "マップ" #: ../../src/topics/yaml-guide.md:81 aedf8c4f615845ad91a7947217005d6e -#, fuzzy msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -4667,15 +4721,14 @@ msgid "" "the key to which they belong (the \"parent\"), and should be indented " "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -"CWLでツールやワークフローを定義する場合、通常、より複雑で入れ子の表現を構築す" -"る必要があります。_maps_ と呼ばれるこれらの階層構造は、キーの値として追加のキ" -"ーと値のペアを提供することでYAMLで記述されます。これらのペア（「子」と呼ばれ" -"ることもあります）は、属するキー（「親」）の下の新しい行に書かれ、2つのスペー" -"スでインデントされます（⇥タブ文字は許可されていません）。例えば、次のようにな" -"ります：" +"CWLでツールやワークフローを定義する場合、通常、より複雑で入れ子構造の表現を構" +"築する必要があります。_maps_ と呼ばれるこれらの階層構造は、キーの値として追加" +"のキーと値のペアを提供することによりYAMLで記述されます。これらのペア（「子」" +"と呼ばれることもあります）は、属するキー（「親」）の下の新しい行に書かれ、2つ" +"のスペースでインデントされます（⇥タブ文字は許可されていません）。例えば、次の" +"ようになります：" #: ../../src/topics/yaml-guide.md:104 f0f1f414f74342a89065ba5ded8668e5 -#, fuzzy msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -4688,8 +4741,8 @@ msgid "" "object it describes." msgstr "" "上記のYAMLは、複雑なネストされたオブジェクトの記述を比較的素早く構築する方法" -"を示しています。`inputs` マップは単一のキー、`example_flag` " -"を含み、それ自体が2つのキー、`type` と`inputBinding` " +"を示しています。`inputs` マップはキー`example_flag` " +"だけを含み、それ自体が2つのキー、`type` と`inputBinding` " "を含み、これらの子の1つ、`inputBinding` はさらに2つのキーと値のペア " "(`position` と`prefix`) を含みます。1つのキーに対して複数の値/キーバリューペ" "アを提供することについての詳細は、以下の[配列](#arrays)のセクションを参照して" @@ -4701,7 +4754,6 @@ msgid "Arrays" msgstr "配列" #: ../../src/topics/yaml-guide.md:129 5aca9a90fb6149529ed717992746a2f3 -#, fuzzy msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -4713,13 +4765,12 @@ msgid "" msgstr "" "ある状況下では、1つのキーに対して複数の値やオブジェクトを提供する必要がありま" "す。上記の[Maps](#maps)のセクションですでに見たように、1つのキーに複数のキー" -"と値のペアをマッピングすることができます。しかし、各値にユニークなキーを用意" -"しなくても、キーに対して複数の値を定義することも可能です。この場合、_array_ " +"と値のペアをマッピングできます。しかし、各値にユニークなキーを用意しなくても" +"、キーに対して複数の値を定義することも可能です。この場合、_array_ " "を用いて、各値を独自の行で定義し、その前に`-` " "を置くことで実現できます。例えば、次のようになります：" #: ../../src/topics/yaml-guide.md:146 d1c9e72e004b4fb4a6efb7748a15ab6f -#, fuzzy msgid "and a more complex example combining maps and arrays:" msgstr "と、マップと配列を組み合わせたより複雑な例です：" @@ -4737,12 +4788,10 @@ msgstr "" "(JSON)][json]に基づいています。マップと配列は、JSON構文を使ってYAMLで定義することもできます。例えば:" #: ../../src/topics/yaml-guide.md:177 d8feed2d36d04fe283b9de9784d91941 -#, fuzzy msgid "and:" msgstr "と：" #: ../../src/topics/yaml-guide.md:184 5156ad32791048f8ace51475d7689575 -#, fuzzy msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -4751,23 +4800,25 @@ msgid "" "However, as the second example above shows, it can severely affect the " "readability of a YAML file, and should be used sparingly." msgstr "" -"ネイティブ JSON は、フィールドが意図的に空のままになっている場所 (空の配列を表す`[]` など) " -"や、値が同じ行にあることがより理にかなっている場所 (たとえば、シェルコマンドでオプションフラグとその値を提供する場合) " -"を示すのに便利なことがあります。しかし、上の2番目の例が示すように、YAMLファイルの可読性に深刻な影響を与える可能性があるので、控えめに使用する必要があります。" +"ネイティブ JSON は、フィールドが意図的に空のままになっている場所 " +"(空の配列を表す`[]` など) や、値が同じ行にあることがより理にかなっている場所 " +"(たとえば、シェルコマンドでオプションフラグとその値を提供する場合) を示すのに" +"便利なことがあります。しかし、上の2番目の例が示すように、YAMLファイルの可読性" +"に深刻な影響を与える可能性があるので、控えめに使用する必要があります。" #: ../../src/topics/yaml-guide.md:194 ce49f80e6fc0498b8ad298fb1f0268f3 msgid "Reference" msgstr "リファレンス" #: ../../src/topics/yaml-guide.md:196 180d261392a644fcb8ff47d7a4a160c0 -#, fuzzy msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -"[Learn YAML in Y Minutes][yaml-y-mins] " -"リファレンスは、CWLでは有効でない機能もカバーしていますが、このガイドを書く間、私たちにとって非常に役に立ちました。" +"[Learn YAML in Y Minutes][yaml-y-mins] リファレンスは、CWLでは有効でない機能" +"もカバーしていますが、このガイドを書く間、私たちにとって非常に役に立ちました" +"。" #: ../../src/tutorials.md:1 d682035afebf4c128755bd4e58780dd2 msgid "Tutorials" From aee2d52a8f853b20dca3dbaceae8d0350de7f921 Mon Sep 17 00:00:00 2001 From: Manabu ISHII Date: Sat, 18 May 2024 02:37:12 +0900 Subject: [PATCH 160/179] Update workflows.md (#478) --- src/topics/workflows.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/topics/workflows.md b/src/topics/workflows.md index 505d6191..ff7c02d5 100644 --- a/src/topics/workflows.md +++ b/src/topics/workflows.md @@ -311,11 +311,11 @@ the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `"Hello.java"` being supplied as the `name_of_file_to_extract`. -Visualization of nestedworkflows.cwl -Visualization of 1st-workflow.cwl ``` From 588a8d368e90449f111d9b2581d4ba57039836d4 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Sun, 14 Jul 2024 15:42:26 +0200 Subject: [PATCH 161/179] Translations update from Hosted Weblate (#482) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Translated using Weblate (Japanese) Currently translated at 100.0% (599 of 599 strings) Co-authored-by: Manabu ISHII Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ja/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Spanish) Currently translated at 11.5% (69 of 599 strings) Co-authored-by: Benjamin Esteban González Morales Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/es/ Translation: Common Workflow Language/CWL User Guide * Translated using Weblate (Portuguese (Portugal)) Currently translated at 50.0% (1 of 2 strings) Co-authored-by: ssantos Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-sphinx/pt_PT/ Translation: Common Workflow Language/CWL User Guide: Sphinx --------- Co-authored-by: Manabu ISHII Co-authored-by: Benjamin Esteban González Morales Co-authored-by: ssantos --- locales/es/LC_MESSAGES/user_guide.po | 31 ++++++++++++++++++---------- locales/ja/LC_MESSAGES/user_guide.po | 9 ++++---- locales/pt_PT/LC_MESSAGES/sphinx.po | 11 ++++++---- 3 files changed, 32 insertions(+), 19 deletions(-) diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index aadfd529..00d7f57d 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,8 +9,9 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-05-17 10:02+0000\n" -"Last-Translator: José Raúl Romero \n" +"PO-Revision-Date: 2024-07-10 21:09+0000\n" +"Last-Translator: Benjamin Esteban González Morales \n" "Language-Team: Spanish \n" "Language: es\n" @@ -18,7 +19,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=2; plural=n != 1;\n" -"X-Generator: Weblate 5.6-dev\n" +"X-Generator: Weblate 5.7-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -503,29 +504,32 @@ msgstr "" #: ../../src/faq.md:375 e39b65947b294b20a444f18d780246f4 msgid "If `cwltool --validate` returns valid" -msgstr "" +msgstr "Sí `cwltool --validate` devuelve válido" #: ../../src/faq.md:384 dcd42c65681b438bb541fb38ddebb536 msgid "But executing it causes an error like:" -msgstr "" +msgstr "Pero ejecutarlo causa un error como:" #: ../../src/faq.md:396 2b96665acac449758b852bbe7600e007 +#, fuzzy msgid "The file is here" -msgstr "" +msgstr "El documento está aquí" #: ../../src/faq.md:410 f59751d2f0014e59af7879a748062cec msgid "Problem caused by `-` (hyphen character)." -msgstr "" +msgstr "Problema causado por `-` (guión)." #: ../../src/faq.md:423 7780f461ca4c478b92fca893c0b0894a msgid "To fix this error, change `-` (hyphen) to `_` (underscore):" -msgstr "" +msgstr "Para arreglar este error, cambie el `-` (guión) por `_` (barra baja):" #: ../../src/faq.md:436 88df56dfff854fc68fb6ad3835a846e4 msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" +"Si no es posible cambiar el indentificador del input, entonces puedes usar " +"una sintaxis alternativa para referencias de parámetros CWL:" #: ../../src/faq.md:442 fc407a9e8d8c4b699d9cd14b369343b5 msgid "How do I use CWL and cwltool with Singularity?" @@ -541,8 +545,9 @@ msgid "" msgstr "" #: ../../src/faq.md:450 61641314d82b43e982e54c64c73232c5 +#, fuzzy msgid "How do I debug the JavaScript in my CWL tool?" -msgstr "" +msgstr "¿Como corrijo (debug) el Javascript en mi herramienta CLW?" #: ../../src/faq.md:452 5556d3c323664edea55cfb777f4efb3b msgid "" @@ -568,7 +573,7 @@ msgstr "" #: ../../src/index.md:7 0adfc2adb0c74372b25d197dd3a73b8b msgid "Contributions and Feedback are Welcome!" -msgstr "" +msgstr "¡Aceptamos feedback y contribuciones!" #: ../../src/index.md:9 96c8dca812f1415db7c5c006b0c0e022 msgid "" @@ -581,7 +586,7 @@ msgstr "" #: ../../src/index.md:16 35c50bb5c3a345b4a4ae66b2df065376 msgid "Navigating the User Guide" -msgstr "" +msgstr "Navegando la Guia de Usuario" #: ../../src/index.md:18 9431edcf4e344fb89b6a251e627279d2 msgid "" @@ -590,6 +595,10 @@ msgid "" "subsections of the [Topics](/topics/index.md) have detailed information " "about the most common topics for CWL." msgstr "" +"Si eres un principiante comienza con la sección de [Introduction](/" +"introduction/index.md). Para usuarios avanzados las subsecciones de " +"[Topics](/topics/index.md) tienen información detallada sobre los temas mas " +"comunes para CWL." #: ../../src/index.md:23 61cf57e61a9f46e5a1bff6368c5ad5e3 msgid "" diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index ef910682..3d1c2e1c 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-05-17 17:16+0000\n" +"PO-Revision-Date: 2024-05-30 05:09+0000\n" "Last-Translator: Manabu ISHII \n" "Language-Team: Japanese \n" @@ -1149,7 +1149,7 @@ msgstr "検証`true.cwl` with`cwl-runner`." #: ../../src/introduction/prerequisites.md:107 4890bf20bc3842d3a7421b555bcda94a msgid "Running `true.cwl` with `cwl-runner`." -msgstr "`true.cwl` を `cwl-runner` で実行します。" +msgstr "`cwl-runner` で `true.cwl` を 実行します。" #: ../../src/introduction/prerequisites.md:112 2475a83cf6ed4389bb680fa37e8fe69c msgid "" @@ -1392,7 +1392,7 @@ msgstr "" #: ../../src/introduction/quick-start.md:57 5b393c69816549b084516dda4d4274f5 msgid "Running `hello_world.cwl` with `cwltool`." -msgstr "`hello_world.cwl` を `cwltool` で実行します。" +msgstr "`cwltool` で`hello_world.cwl` を 実行します。" #: ../../src/introduction/quick-start.md:62 4306d8ad802f45c18487d932d04492fa msgid "" @@ -1402,7 +1402,8 @@ msgstr "また、`echo` base コマンドの引数を変更するのと同様に #: ../../src/introduction/quick-start.md:65 8339ec411ad04c70ab8d795eb154fc38 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." -msgstr "`hello_world.cwl` を`cwltool` で入力パラメータを渡して実行する。" +msgstr "`cwltool` で`hello_world.cwl` " +"と、それに対する入力パラメータを渡して実行します。" #: ../../src/introduction/quick-start.md:70 3ecca6985e754951aee00c93effe9517 msgid "" diff --git a/locales/pt_PT/LC_MESSAGES/sphinx.po b/locales/pt_PT/LC_MESSAGES/sphinx.po index cbb0bd34..d03d2b21 100644 --- a/locales/pt_PT/LC_MESSAGES/sphinx.po +++ b/locales/pt_PT/LC_MESSAGES/sphinx.po @@ -8,18 +8,21 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" +"PO-Revision-Date: 2024-07-14 10:09+0000\n" +"Last-Translator: ssantos \n" +"Language-Team: Portuguese (Portugal) \n" "Language: pt_PT\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 5.7-dev\n" #: ../../src/_templates/sidebar-nav-bs.html:1 #: d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" -msgstr "" +msgstr "Navegação principal" #: ../../src/_templates/sidebar-nav-bs.html:3 #: 4b3441eb77f448daa60718b7bfa862db From 4fb1d07185ac044b66ecacc1897f0bc7d55a3046 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 3 Oct 2024 01:20:08 +0200 Subject: [PATCH 162/179] Update sphinx-autobuild requirement from ==2024.4.* to ==2024.10.* (#489) Updates the requirements on [sphinx-autobuild](https://github.com/sphinx-doc/sphinx-autobuild) to permit the latest version. - [Release notes](https://github.com/sphinx-doc/sphinx-autobuild/releases) - [Changelog](https://github.com/sphinx-doc/sphinx-autobuild/blob/main/NEWS.rst) - [Commits](https://github.com/sphinx-doc/sphinx-autobuild/compare/2024.04.13...2024.10.02) --- updated-dependencies: - dependency-name: sphinx-autobuild dependency-type: direct:production ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index dc36a740..fd76251b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -53,7 +53,7 @@ test = [ "cwltest==2.*", "cwltool==3.1.*", ] -watch = ["sphinx-autobuild==2024.4.*"] +watch = ["sphinx-autobuild==2024.10.*"] rtd = ["udocker"] all = ["cwl-user-guide[test,watch,rtd]"] From cefa152900d499d84f1764a72ad20f8f32a38dfb Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Sun, 6 Oct 2024 12:20:14 +0200 Subject: [PATCH 163/179] Translated using Weblate (Chinese (Simplified Han script)) (#490) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Currently translated at 89.3% (535 of 599 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Zoë Ma --- locales/zh_Hans/LC_MESSAGES/user_guide.po | 329 +++++++++++----------- 1 file changed, 167 insertions(+), 162 deletions(-) diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 76861f20..57cdc83f 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -9,16 +9,16 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-04-11 09:01+0000\n" +"PO-Revision-Date: 2024-10-06 10:16+0000\n" "Last-Translator: Zoë Ma \n" -"Language-Team: Chinese (Simplified) \n" +"Language-Team: Chinese (Simplified Han script) \n" "Language: zh_Hans\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.5-dev\n" +"X-Generator: Weblate 5.8-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -152,14 +152,12 @@ msgid "FAQ" msgstr "常见问题" #: ../../src/faq.md:11 370a9659c7904ef6b5e1ae7480f82ef6 -#, fuzzy msgid "How do I create non \"`File`\" types using `evalFrom`?" -msgstr "使用 `evalFrom` 的非“`File`”类型" +msgstr "如何用 `evalFrom` 创建非“`File`”类型？" #: ../../src/faq.md:41 8333f51e3f5945fe8963adfc6685bcb1 -#, fuzzy msgid "How do I rename an input file?" -msgstr "重命名输入文件" +msgstr "如何重命名输入文件？" #: ../../src/faq.md:43 f6b88d9154d049d7807afa9bb0f1ac98 msgid "" @@ -172,9 +170,8 @@ msgstr "" "中更改输入文件名称。如果要使用工作流中其它步骤产生的文件，但又不想使用这些文件创建时的默认名称，这时候更名操作可以派上用场。" #: ../../src/faq.md:59 833510f5896b4a6eb5875d25eca5b047 -#, fuzzy msgid "How do I rename an output file?" -msgstr "重命名输出文件" +msgstr "如何重命名输出文件？" #: ../../src/faq.md:61 207e2f97d1c44233ae3f109c5a6ec944 msgid "" @@ -188,26 +185,26 @@ msgid "" " engines will rename the file using the new name for subsequent steps or " "as a workflow-level output." msgstr "" +"通过修改 `outputEval` 字段下的 `basename` 字段，可让 CWL " +"工作流引擎为后续步骤或工作流级别的输出重命名该文件，使用新文件名。" #: ../../src/faq.md:86 8641f105131b4ac1bca7e0a46756ef79 -#, fuzzy msgid "How do I reference a local script?" -msgstr "引用本地脚本" +msgstr "如何引用本地脚本？" #: ../../src/faq.md:88 d3e43b40d6994b32bc37067ee116418e msgid "There are two ways to reference a local script:" msgstr "引用本地脚本有两种方法：" #: ../../src/faq.md:90 64b140a321ca4087945339c523cc24dd -#, fuzzy msgid "" "The first method involves adding the path to a folder containing your " "scripts to the `PATH` environment variable. This allows you to execute " "the shell script directly (without explicitly using the `sh` or `bash` " "commands)." msgstr "" -"第一种方法是将包含相关脚本的文件夹添加至`PATH`（路径）环境变量。这样可以直接运行 shell 脚本，无需使用 `sh` 或 `bash` " -"命令。" +"第一种方法是将包含相关脚本的文件夹添加至`PATH`（路径）环境变量。" +"这样可以直接运行 shell 脚本，无需直接使用 `sh` 或 `bash` 命令。" #: ../../src/faq.md:93 34ebca4487a54ceab5d087105820e945 msgid "Start with adding a _shebang_ at the top of your file:" @@ -243,9 +240,8 @@ msgid "" msgstr "第二种方法是将 `type: File` 输入内容编写进脚本：" #: ../../src/faq.md:138 ba246320fdd94a1aab4736f83718d793 -#, fuzzy msgid "How can I set `self`-based input bindings for optional inputs?" -msgstr "为可选输入项设置用到 `self` 变量的输入绑定" +msgstr "如何为可选输入项设置用到 `self` 变量的输入绑定？" #: ../../src/faq.md:140 6169b7be9af7448abcb57eaf91e1cc91 msgid "" @@ -255,9 +251,8 @@ msgid "" msgstr "目前，如果缺失的可选输入项用到了 `self`, `cwltool` 将无法处理。在更高明的解决办法出现前，下面的例子可作为临时变通一用。" #: ../../src/faq.md:165 6c98b7948059411b8e09cf03a552c5ab -#, fuzzy msgid "How can I model a \"one-or-the-other\" parameter?" -msgstr "构建“非此即彼”参数的模型" +msgstr "如何构建“非此即彼”的参数？" #: ../../src/faq.md:167 d1424da3f43c4519a4c4735f4a720341 msgid "" @@ -266,25 +261,22 @@ msgid "" msgstr "以下示例演示的，是根据某个布尔参数的取值，来指定添加到命令行的字符串。" #: ../../src/faq.md:188 5c9980839f404ba6aef92ef23034500f -#, fuzzy msgid "" "How do I connect a solo value to an input that expects an array of that " "type?" -msgstr "将某个元素值与期待该值类型的数组关联起来" +msgstr "如何将某个元素值与期待同一类型的数组关联起来？" #: ../../src/faq.md:190 2525baf16c1f4725b096f33fd99009cf -#, fuzzy msgid "" "Add a " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" " along with [`linkMerge: " "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput):" msgstr "" -"将 " -"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" -" 与 [`linkMerge: " -"merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" -" 联合使用" +"将 [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow" +".html#MultipleInputFeatureRequirement) 与 " +"[`linkMerge:merge_nested`](https://www.commonwl.org/v1.0/Workflow." +"html#WorkflowStepInput) 联合使用：" #: ../../src/faq.md:194 a00d5d96b15048a79ae099d22d63bb42 msgid "merge_nested" @@ -298,9 +290,8 @@ msgid "" msgstr "输入必须是一个数组，每个输入链接只包含一个条目。如果使用单个链接指定“merge_nested”，则链接中的值必须包含在单项列表中。" #: ../../src/faq.md:199 3af16c07e3f148ddb8849c94a3864158 -#, fuzzy msgid "Which means \"create a list with exactly these sources as elements\"." -msgstr "这段话意思是，“创建一个列表，其中的元素正是这些源”" +msgstr "这段话意思是，“创建一个列表，令其中的元素正是这些源”。" #: ../../src/faq.md:201 0ea3de393d2f42aeb82658c85a19ec45 msgid "" @@ -316,7 +307,7 @@ msgstr "" #: ../../src/faq.md:229 2f1bbb611c9c4f80b7ae0566432f2f35 msgid "How do make an input optional? 💯" -msgstr "" +msgstr "如何使某个输入称为可选的？💯" #: ../../src/faq.md:231 08a226efe5d141e68215ac77725033db msgid "" @@ -332,7 +323,7 @@ msgstr "" msgid "" "How do I specify an input that must come from a list of predefined values" " (i.e. How do I use enum inputs) ?" -msgstr "" +msgstr "如何让某个输入只能从一组固定的值中取一（即：如何使用枚举类型输入）？" #: ../../src/faq.md:250 b1934a82553b4da3b7f981e576245dd8 msgid "" @@ -352,7 +343,7 @@ msgstr "" msgid "" "How do I describe dependent or exclusive input parameters(e.g. How do I " "use record inputs)?" -msgstr "" +msgstr "如何描述彼此依存或互斥的输入参数（即：如何使用记录类型输入）？" #: ../../src/faq.md:270 949ce95c082f4a05891a55fee25d4873 msgid "" @@ -364,9 +355,8 @@ msgstr "" "null 创建可选输入。" #: ../../src/faq.md:322 6fd3c469d11d4d52b9fbb7a3d443a8db -#, fuzzy msgid "How do I set mutually exclusive parameters?" -msgstr "设定互斥参数" +msgstr "如何设定互斥参数？" #: ../../src/faq.md:324 a0687ce5c1f940538abc977cad83138f msgid "" @@ -380,29 +370,26 @@ msgstr "" "返回以待设置字段为主键的字典。此处设定了 source （源）字段，以指示工作流中要充当其键值的输入。" #: ../../src/faq.md:342 12869ce2cdab4c858f3232c6158514f1 -#, fuzzy msgid "How can I set Booleans?" -msgstr "设置布尔参数" +msgstr "如何设置布尔参数？" #: ../../src/faq.md:344 8dcb88744e5840029de0e1bbf1c4b967 msgid "These can be set by using the default field" msgstr "可使用 default（默认）字段设置" #: ../../src/faq.md:349 972b7a5551bb43e6b9fa30e0cb713ff7 -#, fuzzy msgid "What should I do when concatenating strings in inputs?" -msgstr "在输入中串联字符串" +msgstr "在输入中串联多个字符串时该如何操作？" #: ../../src/faq.md:351 68f74afc21d846dd9070d45dec0cc1d8 msgid "The valueFrom field must be used instead of default." msgstr "为此必须使用 valueFrom 而非 default 字段。" #: ../../src/faq.md:359 53b633c6f8644106beb95ae567eb0708 -#, fuzzy msgid "" "I get `cwltool` errors due to filenames with space characters inside. " "What should I do?" -msgstr "因文件名含有空格字符，`cwltool`报错" +msgstr "因文件名含有空格字符，`cwltool`报错，该怎么解决？" #: ../../src/faq.md:361 7101bb5cb69e4faca4e60eabb4eb258e msgid "`cwltool` does not allow some characters in filenames by default." @@ -421,11 +408,10 @@ msgid "" msgstr "如果不能避开这些危险的字符，您可以为 `cwltool` 传递 `--relax-path-checks` 选项。" #: ../../src/faq.md:373 b7ec33f38ce74ceb890f4379e4c41054 -#, fuzzy msgid "" "What should I do when I get CWL Parameter Reference error due to hyphen " "in an input identifier?" -msgstr "输入标识符中包含连字符导致 CWL 参数引用错误" +msgstr "输入标识符中包含连字符造成 CWL 参数引用错误，如何解决？" #: ../../src/faq.md:375 e39b65947b294b20a444f18d780246f4 msgid "If `cwltool --validate` returns valid" @@ -444,9 +430,8 @@ msgid "Problem caused by `-` (hyphen character)." msgstr "问题由 `-`（连字符）引发。" #: ../../src/faq.md:423 7780f461ca4c478b92fca893c0b0894a -#, fuzzy msgid "To fix this error, change `-` (hyphen) to `_` (underscore):" -msgstr "修复方法是将 `-`（连字符）更改为 `_`（下划线）" +msgstr "修复方法是将 `-`（连字符）更改为 `_`（下划线）：" #: ../../src/faq.md:436 88df56dfff854fc68fb6ad3835a846e4 msgid "" @@ -455,9 +440,8 @@ msgid "" msgstr "如果不能改动输入标识符，您可使用另一种 CWL 参数引用句法：" #: ../../src/faq.md:442 fc407a9e8d8c4b699d9cd14b369343b5 -#, fuzzy msgid "How do I use CWL and cwltool with Singularity?" -msgstr "在 Singularity 下使用 CWL 和 cwltool" +msgstr "如何在 Singularity 下使用 CWL 和 cwltool?" #: ../../src/faq.md:445 239f5f81cef042b08fb8015c36b3ecad msgid "" @@ -472,7 +456,7 @@ msgstr "" #: ../../src/faq.md:450 61641314d82b43e982e54c64c73232c5 msgid "How do I debug the JavaScript in my CWL tool?" -msgstr "" +msgstr "如何调试 CWL 工具中的 JavaScript 代码？" #: ../../src/faq.md:452 5556d3c323664edea55cfb777f4efb3b msgid "" @@ -710,27 +694,30 @@ msgstr "CWL 规约允许其实现提供额外功能，或通过 *requirements* #: ../../src/introduction/basic-concepts.md:141 #: 07c5789c59224ed78a3ecd03cfe872e9 -#, fuzzy msgid "" "[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow.html#InlineJavascriptRequirement)" " - enables JavaScript in expressions." -msgstr "`InlineJavascriptWorkflow` —— 在表达式中启用 JavaScript。" +msgstr "" +"[`InlineJavascriptWorkflow`](https://w3id.org/cwl/Workflow." +"html#InlineJavascriptRequirement) —— 在表达式中启用 JavaScript." #: ../../src/introduction/basic-concepts.md:142 #: 6f9854ae1b884ad39f88d2f39d66cb98 -#, fuzzy msgid "" "[`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow.html#SubworkflowFeatureRequirement)" " - enables nested workflows." -msgstr "`SubworkflowFeatureRequirement` —— 启用嵌套工作流。" +msgstr "" +"[`SubworkflowFeatureRequirement`](https://w3id.org/cwl/Workflow." +"html#SubworkflowFeatureRequirement) —— 启用嵌套工作流。" #: ../../src/introduction/basic-concepts.md:143 #: 23fef6de073f4da18118e4d0512670fe -#, fuzzy msgid "" "[`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow.html#InitialWorkDirRequirement)" " - controls staging files in the input directory." -msgstr "`InitialWorkDirRequirement` —— 控制输入目录中的暂存文件。" +msgstr "" +"[`InitialWorkDirRequirement`](https://w3id.org/cwl/Workflow." +"html#InitialWorkDirRequirement) —— 控制输入目录中的暂存文件。" #: ../../src/introduction/basic-concepts.md:145 #: fb3762f91177401ea624d1e716d67ae6 @@ -762,7 +749,6 @@ msgstr "FAIR 工作流" #: ../../src/introduction/basic-concepts.md:157 #: bcbf5d76cf5f47b2a9691b7d2d8ef891 -#, fuzzy msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -775,10 +761,11 @@ msgid "" " Initiative." msgstr "" "FAIR 为数字资源（尤其是数据）的共享和发布提供了一组基本原则。FAIR " -"四项原则强调了“机器可读”的重要性，进而提出应使所有数字资源可发现、可访问、可互操作以及可重用 (Findable, Accessible, " -"Interoperable, and " -"Reusable)。工作流通过代码所描述的，正是科学工作得以开展、数据得以创建的过程。因此，应强调工作流须支持创建 FAIR 数据，遵从 FAIR" -" 原则。—— 工作流社群行动之[FAIR 计算工作流](https://workflows.community/groups/fair/)。" +"四项原则强调“机器可读”的重要性，进而提出应使所有数字资源可发现、可访问、" +"可互操作以及可重用 (Findable, Accessible, Interoperable, and Reusable)。工作" +"流通过代码所描述的，正是让科学工作得以开展、数据得以创建的过程。因此，" +"应强调工作流须支持创建 FAIR 数据，并且其自身也遵从 FAIR 原则。—— " +"工作流社群行动之[FAIR 计算工作流](https://workflows.community/groups/fair/)。" #: ../../src/introduction/basic-concepts.md:167 #: 4ea1d3bf04dc42f0bc6735a45b9e0dc0 @@ -828,13 +815,12 @@ msgstr "CWL网站上的规约页面： #: ../../src/introduction/basic-concepts.md:182 #: a5b37924c7d04ab984ff2542847afc4a -#, fuzzy msgid "" "The Command Line Tool Description Standard: " "<[https://www.commonwl.org/v1.2/CommandLineTool.html](https://w3id.org/cwl/CommandLineTool.html)>" msgstr "" -"来自 " -"[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +"命令行工具描述标准：<[https://www.commonwl.org/v1.2/CommandLineTool." +"html](https://w3id.org/cwl/CommandLineTool.html)>" #: ../../src/introduction/basic-concepts.md:183 #: 44af015fa36644b99f07338d241d29c1 @@ -929,7 +915,6 @@ msgid "Windows" msgstr "Windows" #: ../../src/introduction/prerequisites.md:29 aeeb990abbbd42cca122c342054be29c -#, fuzzy msgid "" "If you are using Windows, you will have to install the Windows Subsystem " "for Linux 2 as documented in the [`cwltool` documentation for Microsoft " @@ -937,11 +922,11 @@ msgid "" "language/cwltool/blob/main/README.rst#ms-windows-users). Your operating " "system also needs internet access and a recent version of Python (3.6+)." msgstr "" -"如使用 Windows 操作系统，须首先安装[适用于 Linux 的 Windows 子系统 " -"2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2)。请参阅 " -"`cwltool` [说明文件](https://github.com/common-workflow-" -"language/cwltool/blob/main/README.rst#ms-windows-users) ，了解关于安装 WSL2 " -"的细节。同时，您的操作系统还需能接入互联网，以及运行较新版本（3.6 以上）的 Python." +"如使用 Windows 操作系统，须首先安装适用于 Linux 的 Windows 子系统 2 (WSL2)，" +"详请参阅 [`cwltool` 说明文件针对微软 Windows 用户的部分](https://github.com/" +"common-workflow-language/cwltool/blob/main/README.rst#ms-windows-" +"users)。同时，您的操作系统还需能接入互联网，以及运行较新版本（3.6 以上）的 " +"Python." #: ../../src/introduction/prerequisites.md:34 21d1f29fb15745c480194eae6acdd031 msgid "CWL Runner" @@ -961,17 +946,17 @@ msgstr "" msgid "" "`cwltool` can be installed with `pip`, `apt`, or `conda`. We recommend " "using a virtual environment like `venv` or `conda`." -msgstr "" +msgstr "`cwltool` 可通过 `pip`, `apt`, " +"或者`conda`安装。我们推荐使用`venv`或`conda`等虚拟环境。" #: ../../src/introduction/prerequisites.md:48 1edf8b8438334ae29dc406dbfd711228 -#, fuzzy msgid "" "Visit the `cwltool` " "[documentation](https://cwltool.readthedocs.io/en/latest/#install) for " "details on installing `cwltool`." msgstr "" -"请参阅 `cwltool` [说明文件](https://github.com/common-workflow-" -"language/cwltool#install)查看其他安装方法，包括用 `apt` 或 `conda`." +"关于安装`cwltoom`的详情，请参阅 `cwltool` [说明文件](https://cwltool." +"readthedocs.io/en/latest/#install)." #: ../../src/introduction/prerequisites.md:52 5e300141ce43435f9437507374987213 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." @@ -1009,7 +994,7 @@ msgstr "用 `cwltool` 运行 `true.cwl`." #: ../../src/introduction/prerequisites.md:78 d2dc809318be49cc996d892e93ad84ac msgid "Generic ``cwl-runner`` alias" -msgstr "" +msgstr "通用别名``cwl-runner``" #: ../../src/introduction/prerequisites.md:80 9809c2e262924ef286b0bd62e0b00995 msgid "" @@ -1027,11 +1012,12 @@ msgstr "" "CWL 运行程序共存的环境。" #: ../../src/introduction/prerequisites.md:88 6dd6aa836099469381fb564d63b84f3d -#, fuzzy msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`." -msgstr "CWL 社群发布有名为 `cwlref-runner` 的 Python 包，以安装 `cwl-runner` 作为 `cwltool` 的别名" +msgstr "" +"CWL 社群发布有名为 `cwlref-runner` 的 Python 包，以安装 `cwl-runner` 作为 " +"`cwltool` 的别名。" #: ../../src/introduction/prerequisites.md:91 cc1a9b95508e44a1bf08ae75d990c301 msgid "Installing `cwl-runner` alias for cwltool with `pip`." @@ -1088,7 +1074,6 @@ msgid "Running `true_shebang.cwl` with a shebang." msgstr "使用 shebang 运行 `true_shebang.cwl`." #: ../../src/introduction/prerequisites.md:141 11fea992c00940d29eb29ccf4b9370e9 -#, fuzzy msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -1097,10 +1082,11 @@ msgid "" " using a hard-coded location, since `/usr/bin/env [executable]` looks for" " the `[executable]` program in the system `PATH`," msgstr "" -"所谓 *shebang* 是指脚本起始处的 `#!` 两个连续字符。如果脚本可执行，操作系统将用紧跟在 shebang " -"之后写明的可执行程序来执行此脚本。一个好习惯是用 `/usr/bin/env <可执行程序名>`， 而不是硬性编码其所在路径，理由是 " -"`/usr/bin/env <可执行程序名>` 进行的，是在系统 `PATH`（命令路径环境变量）中查找 " -"`<可执行程序名>` 的实际路径" +"所谓 *shebang* 是指脚本起始处 `#!` 这两个连续字符。如果脚本可执行，" +"操作系统将用紧跟在 shebang 之后写明的可执行程序来执行此脚本。一个好习惯是用 " +"`/usr/bin/env [可执行程序名]`，而不是硬性编码其所在路径。这是因为 `/usr/bin/" +"env [可执行程序名]` 所做的事情，是在系统 `PATH`（命令路径环境变量）下查找 " +"`[可执行程序名]` 的实际位置，" #: ../../src/introduction/prerequisites.md:148 854736eef2ac4b63b187a4cea9660ae4 msgid "Text Editor" @@ -1263,14 +1249,13 @@ msgid "Running \"Hello World\"" msgstr "运行“Hello World”" #: ../../src/introduction/quick-start.md:53 0595e96912dc40e5a09f2ced2d2b7bcd -#, fuzzy msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [CWL_DOCUMENT] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -"`cwltool` 命令行程序的基本用法是 `cwltool [选项] <CWL 文件名> [输入对象]`. " -"您可以不指定任何选项，直接运行 `hello_world.cwl` 工作流：" +"`cwltool` 命令行程序的基本用法是 `cwltool [选项] [CWL 文件] [输入对象]`. " +"运行 `hello_world.cwl` 工作流，您无需指定任何选项：" #: ../../src/introduction/quick-start.md:57 5b393c69816549b084516dda4d4274f5 msgid "Running `hello_world.cwl` with `cwltool`." @@ -1515,14 +1500,14 @@ msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "_用 SPDX 标识符指定许可协议的元数据字段示例：_" #: ../../src/topics/best-practices.md:37 924b8df24deb4c82b32732f491c9a246 -#, fuzzy msgid "" "For more examples of providing metadata within CWL descriptions, see [the" " Metadata and Authorship section of this User Guide](../topics/metadata-" "and-authorship.md)." msgstr "" -"关于在 CWL 描述中提供元数据的更多示例，请参见[《用户指南》的“元数据和著作权”一节](../topics/metadata-and-" -"authorship.md)。" +"关于在 CWL " +"描述中提供元数据的更多示例，请参见[本《用户指南》中“元数据和著作权”一节](../" +"topics/metadata-and-authorship.md)。" #: ../../src/topics/best-practices.md:40 9e64a9fc89cb45cfbff0e925cc91b1be msgid "" @@ -1532,11 +1517,12 @@ msgid "" msgstr "为 CWL 工具或工作流描述的作者添加[署名信息][license-example]。请使用明确、独一无二的标识符，如[ORCID][orcid]." #: ../../src/topics/best-practices.md:44 87030aef02044b8283c76debab4772bf -#, fuzzy msgid "" "In tool descriptions, list dependencies using short name(s) under " "[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." -msgstr "在工具描述中，将所依赖的软件在 `SoftwareRequirement` 下以简短的名称列出。" +msgstr "" +"在工具描述中，将所依赖的软件在 [`SoftwareRequirement`](https://w3id.org/cwl/" +"CommandLineTool.html#SoftwareRequirement) 下以简短的名称列出。" #: ../../src/topics/best-practices.md:47 6c9eaae099fa4ca4b0986b1c4146df50 msgid "" @@ -1559,12 +1545,13 @@ msgstr "" "`foo_input`、`foo_file`、`result`、`input`、`output` 等缺乏明确内涵的名称。" #: ../../src/topics/best-practices.md:55 b0493895105e43849bff2026763e472a -#, fuzzy msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under " "[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool.html#SoftwareRequirement)." -msgstr "在工具描述中 `SoftwareRequirement` 下，请列出已知能与该描述兼容的工具版本。" +msgstr "" +"在工具描述中 [`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#SoftwareRequirement) 下，请列出已知能与该描述兼容的工具版本。" #: ../../src/topics/best-practices.md:58 88806cb0462f4359801c1fa0ff0ebcc0 msgid "" @@ -1592,7 +1579,6 @@ msgid "" msgstr "将所有能作为流读写（即单次、非随机访问）的输入和输出 `File`（文件）标记为 `streamable: true`." #: ../../src/topics/best-practices.md:69 886d15c1972243acadccff5760f842f1 -#, fuzzy msgid "" "Each " "[`CommandLineTool`](https://w3id.org/cwl/CommandLineTool.html#CommandLineTool)" @@ -1600,8 +1586,9 @@ msgid "" "(sub)command is capable of more. Don't overcomplicate your tool " "descriptions with options that you don't need or use." msgstr "" -"即使某个命令或其子命令能够执行更多操作，每个 " -"`CommandLineTool`（命令行工具）描述也应侧重于单个操作。请勿添加非必需或用不到的选项，以免工作描述过于复杂。" +"即使某个命令或其子命令有多种功能，每个 [`CommandLineTool`](https://w3id.org/" +"cwl/CommandLineTool.html#CommandLineTool)（命令行工具）描述也应侧重于单个操作" +"。请勿添加非必需或用不到的选项，以免工作描述过度复杂。" #: ../../src/topics/best-practices.md:73 ef5a5f9b253c4ca3916802a695fb7c6d msgid "" @@ -1713,13 +1700,15 @@ msgid "" "by default, so you must include the requirement for network access in the" " specification of your tool." msgstr "" +"这用来指明某个进程是否需要对外 IPv4/IPv6 网络连接。从 CWL v1.1 " +"版本起，程序不再默认有权访问网络，因此您需要在工具描述中加入网络访问需求。" #: ../../src/topics/command-line-tool.md:84 3282a357799f4a72a6b8bace206144c4 -#, fuzzy msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 or v1.2 " "will have `networkAccess: true` set automatically." -msgstr "从 CWL v1.0 版本升级到 1.1 或 1.2 版的命令行工具将自动获取网络访问权限。" +msgstr "从 CWL v1.0 版本升级到 1.1 或 1.2 版的命令行工具将自动加入 `networkAccess: " +"true` 设置。" #: ../../src/topics/creating-files-at-runtime.md:1 #: 17c5b4ee43cc4a979676ad27e473d046 @@ -1739,13 +1728,12 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 #: bf4aea0a22334a1ca75cc20e937e6581 -#, fuzzy msgid "" "To generate such files, we can use the " "[`InitialWorkDirRequirement`](https://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)." msgstr "" -"来自 " -"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +"要生成这样的文件，我们可以使用 [`InitialWorkDirRequirement`](https://w3id." +"org/cwl/CommandLineTool.html#InitialWorkDirRequirement)." #: ../../src/topics/creating-files-at-runtime.md:9 #: 008f768d56b8465bb4e8f4fde15853a7 @@ -1917,7 +1905,6 @@ msgstr "" "项，如下例 `custom-types.cwl` 所示：" #: ../../src/topics/custom-types.md:76 dce43b138ba24b22bfa9fa5692a17009 -#, fuzzy msgid "" "Note also that the author of this CWL description has also included " "[`ResourceRequirement`](https://w3id.org/cwl/CommandLineTool.html#ResourceRequirement)s," @@ -1927,8 +1914,10 @@ msgid "" "These features are discussed further in other chapters of this user " "guide." msgstr "" -"另请注意，作者还在此 CWL 描述中加入了 `ResourceRequirement`, " -"指定了工具正常运行所需的最低内存容量和内核数、该描述针对的软件具体版本、以及其他有用的元数据。这些功能将在《用户指南》其他章节中进一步讨论。" +"另请注意，作者还在此 CWL 描述中加入了 [`ResourceRequirement`](https://w3id." +"org/cwl/CommandLineTool.html#ResourceRequirement), 指定了工具正常运行所需的最" +"低内存容量和内核数、该描述针对的软件具体版本、以及其他有用的元数据。这些功能" +"将在《用户指南》其他章节中进一步讨论。" #: ../../src/topics/environment-variables.md:1 19737f89f2994815969fa4a88346f49a msgid "Environment Variables" @@ -1960,15 +1949,16 @@ msgstr "" "JavaScript 表达式，以对输入数据进行运算，并生成结果作为输出。" #: ../../src/topics/expression-tool.md:8 7e930144163e4d6e9f0bcaa764497ccf -#, fuzzy msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an " "[`expression`](https://w3id.org/cwl/CommandLineTool.html#Expressions_(Optional))" " attribute." msgstr "" -"与命令行工具一样，它需要 `inputs`（输入）和 `outputs`（输出），但与之不同的是，它需要的是 `expression` 属性，而非" -" `baseCommand`." +"与命令行工具一样，它需要 `inputs`（输入）和 " +"`outputs`（输出），但与之不同的是，它需要的是 [`expression`](https://w3id." +"org/cwl/CommandLineTool.html#Expressions_(Optional)) 属性，而非 " +"`baseCommand`." #: ../../src/topics/expression-tool.md:17 f172488c19a94d688036197117d30b38 msgid "CWL expression tool." @@ -1979,7 +1969,6 @@ msgid "`uppercase.cwl`" msgstr "`uppercase.cwl`" #: ../../src/topics/expression-tool.md:67 0b63da31bc274b3cad798b07149592ab -#, fuzzy msgid "" "We had to use an " "[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" @@ -1988,22 +1977,25 @@ msgid "" "requirement." msgstr "" "因为我们的表达式在 `.toUpperCase()` 处含有一个 JavaScript 调用，所以必须使用 " -"`InlineJavascriptRequirements`. 这向使用表达式工具的其他工具表明 JavaScript 是必备条件。" +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#InlineJavascriptRequirement). 这向使用表达式工具的其他工具表明 " +"JavaScript 是必备条件。" #: ../../src/topics/expressions.md:1 b0e567a985f748538552bdb486a47998 msgid "Expressions" msgstr "表达式" #: ../../src/topics/expressions.md:3 24d05cbbab8e460e99f2edc97ab0dcec -#, fuzzy msgid "" "If you need to manipulate input parameters, include the requirement " "[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" " and then anywhere a parameter reference is legal you can provide a " "fragment of Javascript that will be evaluated by the CWL runner." msgstr "" -"如果需要对输入参数进行处理，请添加需求 `InlineJavascriptRequirement`. " -"然后，在可以合法引用参数的任何地方，您都可以提供一 JavaScript 片段，让 CWL 运行程序计算其值。" +"如果需要对输入参数进行处理，请添加需求 " +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#InlineJavascriptRequirement). 然后，在任何可以合法引用参数的地方，" +"您都可以提供一 JavaScript 片段，让 CWL 运行程序计算其值。" #: ../../src/topics/expressions.md:9 3d48d1a8f7f74bc1886e41653cb53a22 msgid "" @@ -2189,11 +2181,8 @@ msgstr "`outputEval`" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 9448462d104b4be5904623c85a9e16b7 #: bf11a7a72147445c9b8e44b541e09f36 -#, fuzzy msgid "From [`Workflow`](https://w3id.org/cwl/Workflow.html)" -msgstr "" -"来自 " -"[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "来自 [`Workflow`](https://w3id.org/cwl/Workflow.html)" #: ../../src/topics/expressions.md:84 0d54a777a33d4f17a2f3390384a3c0c5 msgid "" @@ -2360,15 +2349,15 @@ msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "通过 `expressionLib` 使用外部库和内联 JavaScript 代码" #: ../../src/topics/expressions.md:118 ea6cbaa5dae647538c0bd9a4d5cad3f9 -#, fuzzy msgid "" "The requirement " "[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool.html#InlineJavascriptRequirement)" " supports an `expressionLib` attribute that allows users to load external" " JavaScript files, or to provide inline JavaScript code." msgstr "" -"`InlineJavascriptRequirements` 这一需求支持 `expressionLib` 属性，可以让用户加载外部 " -"JavaScript 文件或提供内联 JavaScript 代码。" +"[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#InlineJavascriptRequirement) 这一需求支持 `expressionLib` 属性，" +"可以让用户加载外部 JavaScript 文件或提供内联 JavaScript 代码。" #: ../../src/topics/expressions.md:122 484dc17440524cfda4dc486a7c5d5f63 msgid "" @@ -2481,7 +2470,6 @@ msgid "File Formats" msgstr "文件格式" #: ../../src/topics/file-formats.md:3 d99dab4f2f264c68b839b59b80d570e0 -#, fuzzy msgid "" "Tools and workflows can take " "[`File`](https://w3id.org/cwl/CommandLineTool.html#File) types as input " @@ -2490,8 +2478,10 @@ msgid "" "helps document for others how to use your tool while allowing you to do " "some simple type-checking when creating parameter files." msgstr "" -"`File` 类型既可作为工具和工作流的输入，也可以成为它们生成的输出。另外，我们建议指明 `File` " -"类型的格式，以便向他人说明您的工具如何使用，同时还能让您在创建参数文件时进行简单的类型检验。" +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) " +"类型既可作为工具和工作流的输入，也可以成为它们生成的输出。另外，我们建议指明 " +"[`File`](https://w3id.org/cwl/CommandLineTool.html#File) 类型的格式，以便向他" +"人说明您的工具如何使用，同时还能让您在创建参数文件时进行简单的类型检验。" #: ../../src/topics/file-formats.md:8 23ba3dd26f5543119e2c152105b58e98 msgid "" @@ -2579,15 +2569,16 @@ msgstr "" "字段描述有效参数值的类型。" #: ../../src/topics/inputs.md:9 521cb5dead5d4e9ab5ff037fb4b683cb -#, fuzzy msgid "" "Available primitive types are *string*, *boolean*, *int*, *long*, " "*float*, *double*, and *null*; complex types are *array* and *record*; in" " addition there are special types *File*, *Directory* and *Any*." msgstr "" -"可用的原始类型有 *string*（字符串）、 *int*（整型）、*long*（长整型）、 " -"*float*（浮点数）、*double*（双精度浮点数）以及 *null*（空）等；复合类型指的是 *array*（数组）和 " -"*record*（记录）；此外还有特殊类型 *File*（文件）、*Directory*（目录）以及 *Any*（任意）等。" +"可用的原始类型有 " +"*string*（字符串）、*boolean*（布尔变量）、*int*（整型）、*long*（长整型）、 " +"*float*（浮点数）、*double*（双精度浮点数）以及 *null*（空）等；" +"复合类型指的是 *array*（数组）和 *record*（记录）；此外还有特殊类型 " +"*File*（文件）、*Directory*（目录）以及 *Any*（任意）等。" #: ../../src/topics/inputs.md:13 fbdf2c1bed3e41d7a41ec6b14d134a98 msgid "" @@ -2612,11 +2603,10 @@ msgid "`inp-job.yml`" msgstr "`inp-job.yml`" #: ../../src/topics/inputs.md:33 9cc4a60d01f945aa9b4c43afcf20098b -#, fuzzy msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in an input object file:" -msgstr "您可以用 `cwltool` 创建模板输入对象，以省去在输入对象文件中一一键入输入参数：" +msgstr "您可以用 `cwltool` 创建模板输入对象，以免在输入对象文件中写入全部输入参数：" #: ../../src/topics/inputs.md:40 5ac6da11d56446de97c251a37d997671 msgid "" @@ -2660,7 +2650,6 @@ msgstr "" "和其他运行程序会建立临时目录，在其中创建指向您文件的符号链接（又称“软”链接），以防工具意外访问未经明文指定的文件" #: ../../src/topics/inputs.md:70 5bdf77c45346445d8f93353c1e73f768 -#, fuzzy msgid "" "The field " "[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)" @@ -2669,8 +2658,11 @@ msgid "" "parameter does not appear on the command line. Let's look at each " "example in detail." msgstr "" -"字段 `inputBinding` 为可选项，用来说明该输入参数是否应出现在工具的命令行上、以何种方式出现。 如果没有 " -"`inputBinding`, 则该参数不会出现在命令行上。 我们来仔细看看每个示例。" +"字段 [`inputBinding`](https://w3id.org/cwl/CommandLineTool." +"html#Input_binding) " +"为可选项，用来说明该输入参数是否应出现在工具的命令行上、以何种方式出现。 " +"如果没有 `inputBinding`, 则该参数不会出现在命令行上。 " +"我们来仔细看看每个示例。" #: ../../src/topics/inputs.md:83 d783fe52e86f4feda33ea0eecb622603 msgid "" @@ -2855,7 +2847,6 @@ msgid "Exclusive Input Parameters with Expressions" msgstr "互斥输入参数与表达式" #: ../../src/topics/inputs.md:257 cf22f21ec44c483986979316544a7c3b -#, fuzzy msgid "" "If you use exclusive input parameters and reference them in expressions, " "you need to be aware that the `inputs` JavaScript object will contain one" @@ -2864,7 +2855,8 @@ msgid "" " use when you reference the properties of the `input` object." msgstr "" "将互斥的输入参数与表达式结合使用时，需要注意 `inputs` 这个 JavaScript " -"对象可能包含互斥输入值中的任何一个。这意味着你可能需要用逻辑“**或**”运算符来检查哪些值是存在的。" +"对象可能包含互斥输入值中的任何一个。因为这些互斥值可能属于不同类型，" +"您可能需要在引用 `input` 对象的属性时检查实际出现的是哪一类型。" #: ../../src/topics/inputs.md:263 0fecb128b19b44d796b6c1b6de4f7166 msgid "" @@ -2880,38 +2872,36 @@ msgid "`exclusive-parameter-expressions.cwl`" msgstr "`exclusive-parameter-expressions.cwl`" #: ../../src/topics/inputs.md:272 60b585142f06489d9f48090b664b6d32 -#, fuzzy msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " "provide a valid value, such as `fasta` (one of the possible values of the" " enum), your command should execute successfully:" msgstr "" -"请注意，这里的 JavaScript 表达式用到了互斥输入参数的值，但没有考虑到空值 `null` 的情况。如果提供的值有效，比如 “fasta”" -" （枚举中的一个值），命令将会成功执行：" +"请注意，这里的 JavaScript 表达式用到了互斥输入参数的值，但没有考虑到出现空值 " +"`null` 的情况。如果提供的值有效，比如 " +"`fasta`（枚举中的一个值），命令将会成功执行：" #: ../../src/topics/inputs.md:281 11fdeb057d674f118830f431ff019c15 -#, fuzzy msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to `null`, which does not match the expected type for the " "output field (a `string`), resulting in failure when running your " "workflow." msgstr "" -"但是，如果未提供任何输入值，则 `file_format` 的值为 `null`, 从而不符合输出字段的预期类型（字符串 " -"`string`），导致工作流运行失败。" +"但是，如果未提供任何输入值，则 `file_format` 的值为 `null`, " +"从而不符合输出字段的预期类型（字符串 `string`），导致工作流运行失败。" #: ../../src/topics/inputs.md:290 8594cca9d93b4280b6cfee64c8a7c578 -#, fuzzy msgid "" "To correct it, you should explicitly handle the possibility of a `null` " "value. For example, the expression could be changed to " "`$(inputs.file_format || 'auto')`, to have a default value `\"auto\"` if " "none was provided in the command line or job input file." msgstr "" -"为了修正这个问题，需要记住的，是在 JavaScript 表达式中使用互斥参数或任何允许为空 (`null`) " -"的参数时，应使用逻辑“或”运算符。例如，表达式可以修改为 `$(inputs.file_format || 'auto')`, " -"从而在命令行或作业输入文件未提供值的情况下有默认值可用。" +"为了修正这个问题，需要专门处理出现 `null` 空值的情形。例如，表达式可以修改为 " +"`$(inputs.file_format || 'auto')`, " +"从而在命令行或作业输入文件未提供值的情况下有默认值 `\"auto\"` 可用。" #: ../../src/topics/inputs.md:295 b5055c77f85e43609fe3e9b9839778e3 msgid "" @@ -2923,6 +2913,11 @@ msgid "" "expression’s value becomes that of the second operand, which is why a " "reasonable default can be provided there." msgstr "" +"这里，我们要使用的是 JavaScript 中布尔“或”运算符 `||` 的_短路_特点。如果 " +"`inputs.file_format` 为布尔意义上的“真值”（例如来自枚举的有效、非空字符串），" +"这个表达式的计值过程到 `||` 运算符前的操作数就终止，也就是“短路”了。反之，" +"如果 `inputs.file_format` 为 `null`, " +"则该表达式整体的值就等于后一个操作数，因此这里可以用来安放合理的默认值。" #: ../../src/topics/metadata-and-authorship.md:1 #: 723c2232310c4276aeac2bd6728d2912 @@ -3009,30 +3004,29 @@ msgid "`operations.cwl`" msgstr "`operations.cwl`" #: ../../src/topics/operations.md:16 d21e9444182d4e27bae934db4573ae99 -#, fuzzy msgid "" "The `uppercase` step of the workflow is an operation. It can appear where" " a command line tool or an expression is expected. You can also plot it " "with the CWL Viewer or `cwltool`:" msgstr "" -"工作流中的 `uppercase` 步骤是一个抽象操作，可以充当命令行工具或表达式使用。您可以用 CWL Viewer 或 `cwltool` " -"将它绘制出来：" +"工作流中的 `uppercase` " +"步骤是一个操作，可以出现在命令行工具或表达式能出现的任何位置。您还可以用 CWL " +"Viewer 或 `cwltool` 将它绘制出来：" #: ../../src/topics/operations.md:24 61e4ae6ed18e41708270eb358cd55277 -#, fuzzy msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx `{graphviz}` directive " "(this user guide is built with Sphinx):" msgstr "" -"以上命令的输出可用 Graphviz 渲染出来。下面的图片是使用 Sphinx Graphviz 指令来渲染的（本《用户指南》是以 Sphinx " -"编译）：" +"以上命令的输出可用 Graphviz 渲染出来。下面的图片是使用 Sphinx 的 `{graphviz}`" +" 指令来渲染的（本《用户指南》就是用 Sphinx 编译的）：" #: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd msgid "" "The operation file will fail to run with `cwltool` because `cwltool` " "lacks the necessary information to execute it:" -msgstr "" +msgstr "用 `cwltool` 运行该操作文件将会失败，因为 `cwltool` 缺少执行所需的必要信息：" #: ../../src/topics/operations.md:59 e184470550e645f6b9ce658af7e65ecf msgid "`cwltool` does not know how to run operations" @@ -3064,7 +3058,6 @@ msgstr "" "`id`字段，以及描述其有效值类型的 `type` 字段。" #: ../../src/topics/outputs.md:10 a229d8d983344e51a231edb5f667d84b -#, fuzzy msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -3072,7 +3065,8 @@ msgid "" "output parameters returned by the CWL tool are either the output files " "themselves, or the result of examining the content of those files." msgstr "" -"工具在 CWL 下运行时，起始工作目录即指定输出目录。 基础工具或脚本记录运行结果，必须以输出目录下文件的形式实现。 CWL " +"工具在 CWL 下运行时，起始工作目录即指定输出目录。 " +"基础工具或脚本要记录运行结果，必须以输出目录下文件的形式实现。 CWL " "工具返回的输出参数要么是输出文件本身，要么是分析这些文件的内容而得出的信息。" #: ../../src/topics/outputs.md:16 9845e517f7d848e5b59a97880ca6999f @@ -3086,7 +3080,6 @@ msgid "Passing mandatory arguments to the `baseCommand`" msgstr "将必要参数传递给 `baseCommand`" #: ../../src/topics/outputs.md:21 553d535b023e4d69a888fe5b24bb8c5b -#, fuzzy msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string, we can use an" @@ -3094,8 +3087,9 @@ msgid "" "the array is the command to run, and any subsequent elements are " "mandatory command line arguments" msgstr "" -"在此前的例子里，`baseCommand` 命令不过是一个字符串，命令的参数都由 CWL " -"输入传递而来。不过，我们也可以用字符串数组构建命令。为此，只需要让待运行的命令成为数组的第一个元素，这样所有后续元素均成为命令行的必要参数" +"在此前的例子里，`baseCommand` 命令只是一个字符串，命令的参数都由 CWL " +"输入传递而来。不过，我们也可以用_字符串数组_作为 `baseCommand` " +"的值。数组的第一个元素是将要运行的命令，其后的元素均为命令行的必要参数" #: ../../src/topics/outputs.md:28 9b65071222c94951bed12ac53e964ee3 msgid "`tar.cwl`" @@ -3116,15 +3110,15 @@ msgid "" msgstr "现在，在命令行上结合工具描述和输入对象运行 `cwltool`:" #: ../../src/topics/outputs.md:53 707803bec0cb42919905c7c321bd9d30 -#, fuzzy msgid "" "The field " "[`outputBinding`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding)" " describes how to set the value of each output parameter." -msgstr "`outputBinding` 字段描述如何设置每个输出参数的值。" +msgstr "" +"[`outputBinding`](https://w3id.org/cwl/CommandLineTool." +"html#CommandOutputBinding) 字段描述如何设置每个输出参数的值。" #: ../../src/topics/outputs.md:64 cbaec50871e04718883c8c91ff475d20 -#, fuzzy msgid "" "The " "[`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) " @@ -3132,22 +3126,25 @@ msgid "" "directory. This can simply be the file's exact name. But if you don't " "know the name of the file in advance, you can use a wildcard pattern like" " `glob: '*.txt'`." -msgstr "`glob` 字段由输出目录中的文件名组成。如果事先不知道文件名，可以使用通配符，例如 `glob: '*.txt'`." +msgstr "" +"[`glob`](https://w3id.org/cwl/CommandLineTool.html#CommandOutputBinding) 字段" +"包含可匹配输出目录中文件名的模式。这可以是确切的文件名，不过如果事先不知道文" +"件名，还可以使用通配符，如 `glob: '*.txt'`." #: ../../src/topics/outputs.md:69 8a6e9173198241429effd911c3a7c4d7 msgid "Capturing Standard Output" msgstr "捕获标准输出" #: ../../src/topics/outputs.md:71 a7c4fdaeda3e411fbeb802c5fa529ce9 -#, fuzzy msgid "" "To capture a tool's standard output stream, add the " "[`stdout`](https://w3id.org/cwl/CommandLineTool.html#stdout) field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -"要捕获工具的标准输出流，请添加 `stdout` 字段，配上输出流应定向到的文件名。 然后，给相应的输出参数添加 `type: stdout` " -"字段。" +"要捕获工具的标准输出流，请添加 [`stdout`](https://w3id.org/cwl/" +"CommandLineTool.html#stdout) 字段，配上输出流应定向到的文件名。 然后，" +"给相应的输出参数添加 `type: stdout` 字段。" #: ../../src/topics/outputs.md:75 cf2ef8dc7fda49308c09efe4f4ef5d7b msgid "`stdout.cwl`" @@ -3371,7 +3368,6 @@ msgstr "指定软件需求" #: ../../src/topics/specifying-software-requirements.md:3 #: e708866921ea49d69d3c2a32d63ea468 -#, fuzzy msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -3380,8 +3376,10 @@ msgid "" " field in the `hints` section. This may also help to avoid confusion " "about which version of a tool the description was written for." msgstr "" -"工具描述往往是针对特定版本的软件而编写。为了方便他人使用您的工具描述，您可以在 `hints` 部分添加`SoftwareRequirement`" -" 字段，用来指明该描述适用于哪些版本的工具。" +"工具描述往往是针对特定版本的软件而编写。为了方便他人使用您的工具描述，" +"您可以在 `hints` 部分添加[`SoftwareRequirement`](https://w3id.org/cwl/" +"CommandLineTool.html#SoftwareRequirement) " +"字段，用来指明该描述适用于哪个工具版本。" #: ../../src/topics/specifying-software-requirements.md:13 #: 6f722d6fd54f485fa964076c8d08938b @@ -3921,7 +3919,6 @@ msgstr "" "由紫色的部分可见字符串常量 `\"Hello.java\"` 赋值给 `name_of_file_to_extract`." #: ../../src/topics/workflows.md:314 8654f2d86b644609aaa5b9b73db30bda -#, fuzzy msgid "" " Date: Tue, 8 Oct 2024 09:37:05 +0200 Subject: [PATCH 164/179] Translated using Weblate (Chinese (Simplified Han script)) (#491) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Currently translated at 92.4% (554 of 599 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Zoë Ma --- locales/zh_Hans/LC_MESSAGES/user_guide.po | 61 ++++++++++++++++++++--- 1 file changed, 54 insertions(+), 7 deletions(-) diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 57cdc83f..8e1875ff 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-10-06 10:16+0000\n" +"PO-Revision-Date: 2024-10-08 03:26+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified Han script) \n" @@ -3989,6 +3989,9 @@ msgid "" "coded `Hello.java` file using the previously mentioned " "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" +"另一种可能是采用更加特殊化的办法，避免作业文件中的外部依赖。在这个工作流中， " +"我们可以利用前述 `InitialWorkDirRequirement` 需求，生成一个硬性编码的 `Hello." +"java` 文件，然后将它添加到 tar 文件。" #: ../../src/topics/workflows.md:366 66f76677f4ce42baa8a8813410ea5aee msgid "" @@ -3996,6 +3999,9 @@ msgid "" "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" +"这种情况下，我们的步骤中可以直接以 `Hello.java` 为前提假定，无需参数化，" +"从而在 `baseCommand` 以及产出的 `outputs` 中使用硬性编码的值 `hello.tar` 和 " +"`Hello.java`:" #: ../../src/topics/workflows.md:383 a8ccb9f9ab4448e087ea8448d620d33c msgid "" @@ -4005,6 +4011,10 @@ msgid "" "reason for doing it in this case is because the command line is hard-" "coded with filenames that only make sense within this workflow." msgstr "" +"您是否注意到，我们并没有将 `tar --create` 工具划分到一个独立的文件，" +"而是嵌入到 CWL 工作流文件中？一般而言这样做并不是最合适的，将导致工具无法重复" +"使用。在这个特例中，如此操作的原因是命令行已是硬性编码的，其中的文件名仅对这" +"一个工作流有效。" #: ../../src/topics/workflows.md:389 afe43b9e92e949a589f493293eff2903 msgid "" @@ -4014,6 +4024,9 @@ msgid "" "to compile, which would simplify its usage as a tool step in other " "workflows." msgstr "" +"这个例子里我们不得不在外部创制 tar 文件，但这无非是因为我们将内部工作流设计成" +"以该文件为输入。内部工作流更好的重整方式，可以是令其接受一个待编译 Java " +"文件的列表，使之作为工具步骤用于其它工作流中时的用法得以简化。" #: ../../src/topics/workflows.md:394 239eef3a740d42a69208a8f4e716d2b3 msgid "" @@ -4022,10 +4035,12 @@ msgid "" " Tool description, care must be taken to improve its usability in " "multiple workflows." msgstr "" +"嵌套的工作流作为一种强大的功能，可以用于生成高阶函数和可复用的工作流单元——然" +"而，正如创建 CWL 工具描述时一样，我们必须用心于提高它在多个工作流间的可用性。" #: ../../src/topics/workflows.md:398 96d1ca78cc324f40b61c4b7330447db2 msgid "Scattering Steps" -msgstr "" +msgstr "分散步骤" #: ../../src/topics/workflows.md:400 eab4437bf9994b649954221375e3dd6d msgid "" @@ -4037,6 +4052,11 @@ msgid "" "allows you to run the same workflow on multiple inputs without having to " "generate many different commands or input yaml files." msgstr "" +"了解了如何编写工作流，我们可以准备使用 `ScatterFeatureRequirement`. 该功能用" +"于告诉运行程序，您打算对列表中的多个输入重复运行某个工具或者工作流。这样，工" +"作流可以将输入作为数组，并对每个数组元素运行指定的步骤，如同单个输入一样。这" +"样， 我们可以让同一工作流对多个输入运行，而无需生成多个不同的命令或者 YAML " +"输入文件。" #: ../../src/topics/workflows.md:411 c245ba0ae2074fa388ad6c35695033c8 msgid "" @@ -4045,6 +4065,9 @@ msgid "" "workflow that calls our first example (`hello_world.cwl`) and takes an " "array of strings as input to the workflow:" msgstr "" +"用户第一次接触分散 (scatter) 功能，最主要的原因一般是为了对多个不同的样本进行" +"同一分析。我们从一个简单的工作流出发，调用我们的第一个示例 (`hello_world." +"cwl`), 并以一个字符串数组作为工作流的输入：" #: ../../src/topics/workflows.md:415 83537938ce1244709f9b72269b048d63 msgid "`scatter-workflow.cwl`" @@ -4054,13 +4077,14 @@ msgstr "`scatter-workflow.cwl`" msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" -msgstr "" +msgstr "除了 `requirements` 代码段加入了 `ScatterFeatureRequirement` " +"以外，还有什么新情况？" #: ../../src/topics/workflows.md:429 ccbbba3189404241a44736c970249b84 msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." -msgstr "" +msgstr "首先，请注意，主工作流级别的输入这时需要字符串数组。" #: ../../src/topics/workflows.md:441 31eff13bb8334fc7b6d48ef6c5b1ce33 msgid "" @@ -4069,6 +4093,9 @@ msgid "" " particular step. Note that the input name listed after scatter is the " "one of the step's input, not a workflow level input." msgstr "" +"这里，我们在 `echo` 步骤下添加了名为 `scatter` " +"的新字段。该字段告诉运行程序，我们希望让这一特定步骤对输入分散运行。请注意，" +"\"scatter\" 后列出的输入名是该步骤的输入之一，而非工作流层面的输入。" #: ../../src/topics/workflows.md:445 0d5cf8b82dbd47f2abd1ed16b9b3eb61 msgid "" @@ -4077,10 +4104,13 @@ msgid "" "you expect that the final output of your workflow will now have multiple " "outputs to collect, be sure to update that to an array type as well!" msgstr "" +"我们第一次做分散，就是这么简单。因为我们的工具并不收集任何输出，" +"我们仍然可以在工作流中写上 `outputs: []`. 但是，如果你知道工作流的最终输出需" +"要归集多个输出，请记得这里同样要更改为数组类型！" #: ../../src/topics/workflows.md:450 38b7042a270043ba82c11cf2e758f0c8 msgid "Using the following input file:" -msgstr "" +msgstr "使用如下输入文件：" #: ../../src/topics/workflows.md:452 b3fc75c262fe4a3a8e8bfba1abb07b3d msgid "`scatter-job.yml`" @@ -4092,6 +4122,9 @@ msgid "" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" +"提醒一下，[`hello_world.cwl`](../introduction/quick-start.md) " +"仅仅是对某段文字调用 `echo` 这个命令。如果我们在命令行调用 `cwltool scatter-" +"workflow.cwl scatter-job.yml`:" #: ../../src/topics/workflows.md:466 b6a33410ee9a45d7bf7b2ba56f786f8f msgid "" @@ -4099,12 +4132,16 @@ msgid "" "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" +"可以看到，这个工作流分多次对 `message_array` 数组的每个元素一一调用 \"echo\"" +". 好的，那么如果我们想要让工作流中两个步骤进行分散，该怎么办？" #: ../../src/topics/workflows.md:469 99b5c8a845ab4beb8524a69c051e2d42 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" +"和之前一样，我们来做一个简单的回显 (echo), 但这次将捕获 " +"`stdout`（标准输出）。为此，我们用以下数行代码取代 `outputs: []`" #: ../../src/topics/workflows.md:472 97bf58937d3f4e98af702e3c1a418992 msgid "`hello_world_to_stdout.cwl`" @@ -4114,7 +4151,7 @@ msgstr "`hello_world_to_stdout.cwl`" msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" -msgstr "" +msgstr "进而添加第二个步骤，用 `wc` 命令计算每个文件中的字符数量。请见如下工具：" #: ../../src/topics/workflows.md:483 4afccfe982ff4be2be96cbe5889e5014 msgid "`wc-tool.cwl`" @@ -4124,7 +4161,7 @@ msgstr "`wc-tool.cwl`" msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" -msgstr "" +msgstr "现在，该如何加入分散操作呢？请记住，\"scatter\"（分散）字段出现在每个步骤下：" #: ../../src/topics/workflows.md:491 a7f96ec6e4f24c62ac0f5b6edcc9734b msgid "`scatter-two-steps.cwl`" @@ -4147,6 +4184,16 @@ msgid "" "the first step must wait on `echo Hallo welt!`. You can see how this " "might not scale well." msgstr "" +"这里，我们在每一步骤下加入了 \"scatter\" 字段。对这个具体的示例而言这样做无妨" +"，因为这段程序运行得很快。但是，如果要对较多样本运行更复杂的工作流，您可能得" +"另寻途径。这里，我们在每个步骤中独立地进行分散，但既然第二个步骤并不实际依赖" +"第一个步骤对所有语种（即输入数组中的一个元素）全部完成操作，我们并没有高效地" +"运用分散功能。第二个步骤期待从第一个步骤得来的数组作为其输入，因此将一直等待" +"到第一步骤完全结束才会开始运行。打个比方，假设运行 `echo Hello World!` " +"需要花1分钟，对其输出运行 `wc -c` 需要3分钟，然后 `echo Hallo welt!` " +"需要5分钟来运行，最后对其输出运行 `wc` 需要3分钟。即使 `echo Hello World!` " +"本可以在4分钟内完成，它也要实际花费8分钟，因为第一个步骤必须等待 `echo Hallo " +"welt!` 完成。很显然，运算量大时这样的表现会很差劲。" #: ../../src/topics/workflows.md:509 85dd63daf04546b78bdcb68c1d985fa9 msgid "" From 028b6909019e590c5f98b26d0d4782530afb4cc7 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Fri, 11 Oct 2024 13:44:02 +0200 Subject: [PATCH 165/179] Translated using Weblate (Chinese (Simplified Han script)) (#492) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Currently translated at 95.8% (574 of 599 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Zoë Ma --- locales/zh_Hans/LC_MESSAGES/user_guide.po | 53 ++++++++++++++++------- 1 file changed, 37 insertions(+), 16 deletions(-) diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 8e1875ff..33ed0caf 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-10-08 03:26+0000\n" +"PO-Revision-Date: 2024-10-11 11:16+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified Han script) \n" @@ -4202,6 +4202,9 @@ msgid "" " make an entire workflow a single step in another workflow! Convert our " "two-step workflow to a single step subworkflow:" msgstr "" +"好的，那么，我们对不依赖其它样本、可以独立进行的步骤，该如何分散？请回想[嵌套" +"的工作流](#nested-workflows)部分，其中写道，我们可以让整个工作流称为另一个工" +"作流中的一个步骤！我们将两步骤的工作流改写为单一步骤的子工作流：" #: ../../src/topics/workflows.md:513 fac138ba275745898b763a7d719a8235 msgid "`scatter-nested-workflow.cwl`" @@ -4211,18 +4214,20 @@ msgstr "`scatter-nested-workflow.cwl`" msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." -msgstr "" +msgstr "这样，分散就可以针对一个单独的步骤进行，不过该步骤本身分为两个子步骤。这就让" +"每个分散的步骤并行进行。" #: ../../src/topics/workflows.md:522 b0bf01dad1234a1db3c87b10953e42ef msgid "Conditional Workflows" -msgstr "" +msgstr "条件性工作流" #: ../../src/topics/workflows.md:524 8d933ed1ec6e408589f781e3a425b869 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." -msgstr "" +msgstr "这个工作流包含一个取决于输入的有条件步骤，可以根据程序起始或先前步骤给出的输" +"入参数决定是否跳过某些额外步骤。" #: ../../src/topics/workflows.md:527 9ac7b4f71621411da9a4ca3bc277dcb0 msgid "`conditional-workflow.cwl`" @@ -4232,7 +4237,7 @@ msgstr "`conditional-workflow.cwl`" msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." -msgstr "" +msgstr "首先要注意，这个工作流只能兼容于版本1.2或以上的 CWL 标准。" #: ../../src/topics/workflows.md:573 4742fe09a4264fb8be6f092519de5d72 msgid "" @@ -4242,6 +4247,9 @@ msgid "" "`in1` from the workflow contains a value `< 1` this step will be " "executed." msgstr "" +"工作流的第一个步骤 (step1) 包含两个输入字段，它将在条件满足时执行 foo.cwl. " +"这里新出现的字段 `when` 就是进行条件检验的地方。这个例子里，只有当 `in1` " +"从工作流获取的值小于1 (`< 1`) 时，此步骤才会执行。" #: ../../src/topics/workflows.md:587 b33ecd2b8af042feb08687e32d4b6bbf msgid "" @@ -4250,61 +4258,69 @@ msgid "" "is shown in the log by `INFO [step step1] start` whereas the second step " "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" +"使用命令如 `cwltool cond-wf-003.1.cwl --val 0`, 则输入参数值 (0) " +"将满足第一个步骤的条件，从而使之得到执行，并且在日志中以 `INFO [step step1] " +"start` 出现。相反，第二个步骤则跳过了，即日志中 `INFO [step step2] will be " +"skipped` 所记。" #: ../../src/topics/workflows.md:607 7cd80b31a94543358ece7a2d413adce9 msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" +"当参数值为3, 如命令 `cwltool cond-wf-003.1.cwl --val 3` " +"所给出，则第一个条件行步骤不会执行，反之第二个会。" #: ../../src/topics/workflows.md:627 9679e32f65e0482a8b083387e4a18c1f msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." -msgstr "" +msgstr "如果条件都不成立，如用 `--val 2` 所导致的，则工作流将发起 permanentFail " +"异常。" #: ../../src/topics/yaml-guide.md:1 4fa76441f95d45fab76ab7eef8d7d4d2 msgid "YAML Guide" -msgstr "" +msgstr "YAML 语言指南" #: ../../src/topics/yaml-guide.md:6 705765787eb84ecaae004194225924cb msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." -msgstr "" +msgstr "[YAML][yaml] 是一种让计算机和人都能读懂的文件格式。这部分指南主要针对编写 " +"CWL 描述和输入参数文件，介绍 YAML 的特性。" #: ../../src/topics/yaml-guide.md:13 cb243f6ab11f48ffb5c91945c4e0d101 msgid "You can skip this section if you are already comfortable with YAML." -msgstr "" +msgstr "如果你已经能够得心应手地运用 YAML, 这一部分可以跳过。" #: ../../src/topics/yaml-guide.md:16 cfc95d15e33a492f842649f92ced941d msgid "Contents" -msgstr "" +msgstr "目录" #: ../../src/topics/yaml-guide.md:18 f618d44d202f4c2ea6ff72a1dca2c659 msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "" +msgstr "[键值对](#key-value-pairs)" #: ../../src/topics/yaml-guide.md:19 36bfa6ed40c54bd99826bedff12c759d msgid "[Comments](#comments)" -msgstr "" +msgstr "[注释](#comments)" #: ../../src/topics/yaml-guide.md:20 61913753eb0c4c728889b47f1110be24 msgid "[Maps](#maps)" -msgstr "" +msgstr "[映射](#maps)" #: ../../src/topics/yaml-guide.md:21 0de824a05eea46209aafa6f9e2e8623c msgid "[Arrays](#arrays)" -msgstr "" +msgstr "[数组](#arrays)" #: ../../src/topics/yaml-guide.md:22 95627bc476b3415ca4d77246125137d2 msgid "[JSON Style](#json-style)" -msgstr "" +msgstr "[JSON 样式](#json-style)" #: ../../src/topics/yaml-guide.md:24 3f64a6d33d9a4c22a8a839a8def82686 msgid "Key-Value Pairs" -msgstr "" +msgstr "键值对" #: ../../src/topics/yaml-guide.md:26 2f74f6eaa8d84dc9b4d0a166844dedbe msgid "" @@ -4315,6 +4331,11 @@ msgid "" "special meaning in the CWL specification and underscored key names " "otherwise. For example:" msgstr "" +"根本而言，YAML 格式的文件是一组形如 `key: value`（即“键: 值”）的_键值对_ " +"(key-value pair). 这里，冒号 `:` 后的空白字符是不可少的。CWL " +"文件中的键名不得包含空白字符——CWL 规约中有特殊含义的词组键名写为 " +"[_camelCase_][camelCase]（“驼峰”大小写），无特殊含义者用下划线 (_) " +"分隔键名中的词。例如：" #: ../../src/topics/yaml-guide.md:42 514365e59d9648deb896e2068d967a64 msgid "" From 06a8eeaccbc71f2261df593142fa3a8b962457a0 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Wed, 16 Oct 2024 16:19:23 +0200 Subject: [PATCH 166/179] Translated using Weblate (Chinese (Simplified Han script)) (#493) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Currently translated at 100.0% (599 of 599 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Zoë Ma --- locales/zh_Hans/LC_MESSAGES/user_guide.po | 72 +++++++++++++++++------ 1 file changed, 54 insertions(+), 18 deletions(-) diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 33ed0caf..16ae112b 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-10-11 11:16+0000\n" +"PO-Revision-Date: 2024-10-16 10:15+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified Han script) \n" @@ -18,7 +18,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=1; plural=0;\n" -"X-Generator: Weblate 5.8-dev\n" +"X-Generator: Weblate 5.8-rc\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -4345,6 +4345,9 @@ msgid "" "representation), Boolean (`true` or `false`), or more complex nested " "types (see below)." msgstr "" +"上面这一段 YAML 包含4个键——`first_name`, `last_name`, `age_years`, 以及 `home" +"`——及其对应的值。值可以是字符串，数值（整数，浮点数，或者科学记数法），布尔值" +"（真值 `true` 或非真值 `false`），或者更复杂的嵌套类型（见下）。" #: ../../src/topics/yaml-guide.md:51 6939eb7e783744d7bcf75ea0a7cae129 msgid "" @@ -4356,27 +4359,34 @@ msgid "" "want to specify a fixed numeric value to a command, make sure that you " "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" +"值可以用括号包围起来，但要当心这样做可能改变其理解：`\"1234\"` " +"会被当作字符串，而 `1234` " +"为整数。有的时候，这之间的区别会很重要，例如描述命令的参数时：CWL " +"语言中，`baseCommand` 的所有部分都必须为字符串；因此，如果你打算给命令传递一" +"个数值常数作为参数值，那就必须将该数值用括号包围起来：`baseCommand: [echo, " +"\"42\"]`." #: ../../src/topics/yaml-guide.md:61 96e1776b09e840ebbc9b4b7e01da0e43 msgid "Comments" -msgstr "" +msgstr "注释" #: ../../src/topics/yaml-guide.md:63 8b17f7557c3540b2b0d0beca0fe4ebc7 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" -msgstr "" +msgstr "在 CWL 和参数文件中，可以用 `#` 符号引入注释。每行中 ` #` " +"之后的全部字符都会被 YAML 解释程序忽略。例如：" #: ../../src/topics/yaml-guide.md:76 13da997c82c04023a4b7bb36b76e969d msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" -msgstr "" +msgstr "如果在某行里，注释之前有任何内容，记得 `#` 前需要至少一个空白字符！" #: ../../src/topics/yaml-guide.md:79 b9fc191166a64450b64a8182adabad75 msgid "Maps" -msgstr "" +msgstr "映射" #: ../../src/topics/yaml-guide.md:81 aedf8c4f615845ad91a7947217005d6e msgid "" @@ -4388,6 +4398,10 @@ msgid "" "the key to which they belong (the \"parent\"), and should be indented " "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" +"用 CWL 描述工具或工作流时，通常需要构造更加复杂、多级嵌套的表示。这样的层级结" +"构称为“映射”；用 YAML 表示映射，是用一组键值对作为某个键的值。这样（作为值）" +"的键值对有时称为“子”键值对，写为其所属键（“母”键）下另起的新行，且应该用两个" +"空格字符增加一级缩进（制表符⇥不允许用作此目的）。例如：" #: ../../src/topics/yaml-guide.md:104 f0f1f414f74342a89065ba5ded8668e5 msgid "" @@ -4401,10 +4415,16 @@ msgid "" " example YAML above, here is a graphical representation of the `inputs` " "object it describes." msgstr "" +"上面的 YAML 样本展示了快速构建复杂嵌套对象描述的办法。`inputs` " +"这个映射包含单独一个键 `example_flag`, 而后者本身又包含两个键 `type` 和 " +"`inputBinding`; 其中，`inputBinding` 这个子键又包含另外两个键值对 (`position`" +" 和 `prefix`). 如果要为某一个键提供多个单值或子键值对值，请参见后面的[数组](#" +"arrays)部分。这里，我们用如下图形表示它所描述的 `inputs` 这个对象，" +"以供与上面的 YAML 对照。" #: ../../src/topics/yaml-guide.md:127 965405e2a45a4cbb8f227bc8ceeb05df msgid "Arrays" -msgstr "" +msgstr "数组" #: ../../src/topics/yaml-guide.md:129 5aca9a90fb6149529ed717992746a2f3 msgid "" @@ -4416,14 +4436,18 @@ msgid "" "this with an _array_, where each value is defined on its own line and " "preceded by `-`. For example:" msgstr "" +"有些情况下，我们需要为某个键提供多个值或对象。如前面的[映射](#maps)部分所述，" +"一个键下可以映射多个键值对。不过，我们还可以为某个键指定多个值，同时无需为每" +"个值都添加一个独特的子键。这可以通过“数组”实现；数组中的每个元素值出现在 " +"`-`（短线）符号后的新行上。例如：" #: ../../src/topics/yaml-guide.md:146 d1c9e72e004b4fb4a6efb7748a15ab6f msgid "and a more complex example combining maps and arrays:" -msgstr "" +msgstr "以及将映射与数组结合的一个较复杂例子：" #: ../../src/topics/yaml-guide.md:167 9a3d6879404745a48cd394bf86865dbc msgid "JSON Style" -msgstr "" +msgstr "JSON 样式" #: ../../src/topics/yaml-guide.md:169 6a7cca0339794e679329b00d89e29d2b msgid "" @@ -4431,10 +4455,12 @@ msgid "" "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" +"YAML 的基础是 [JavaScript Object Notation (JSON)][json]. YAML " +"映射与数组都可以用 JSON 原生的语法表达。例如：" #: ../../src/topics/yaml-guide.md:177 d8feed2d36d04fe283b9de9784d91941 msgid "and:" -msgstr "" +msgstr "以及：" #: ../../src/topics/yaml-guide.md:184 5156ad32791048f8ace51475d7689575 msgid "" @@ -4445,10 +4471,14 @@ msgid "" "However, as the second example above shows, it can severely affect the " "readability of a YAML file, and should be used sparingly." msgstr "" +"原生 JSON 可以用于表达某字段值有意为空（如使用 `[]` " +"代表空数组），以及多个值适合出现在同一行内的情况（如为 shell " +"命令行提供选项和参数值的时候）。不过，如上第二个例子所示，这种格式可能让 " +"YAML 文件的可读性大打折扣，因此应慎用。" #: ../../src/topics/yaml-guide.md:194 ce49f80e6fc0498b8ad298fb1f0268f3 msgid "Reference" -msgstr "" +msgstr "参考资料" #: ../../src/topics/yaml-guide.md:196 180d261392a644fcb8ff47d7a4a160c0 msgid "" @@ -4456,21 +4486,25 @@ msgid "" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" +"[Learn YAML in Y Minutes][yaml-y-mins] " +"作为参考资料在我们写作本《指南》的过程中起到了很大的帮助，" +"不过其中介绍的部分语言特性不适用于 CWL." #: ../../src/tutorials.md:1 d682035afebf4c128755bd4e58780dd2 msgid "Tutorials" -msgstr "" +msgstr "教程" #: ../../src/tutorials.md:5 d9adeab63ec54084bc41fb90f264d3ae msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." -msgstr "" +msgstr "这里是 CWL 社区提供的一份教程列表。如果您想添加新的教程，请使用菜单栏中的 `" +"Edit this page`（编辑此页面）链接。" #: ../../src/tutorials.md:7 23c81edb650b4f86a60c5e0bcedeac1d msgid "Beginner Tutorials" -msgstr "" +msgstr "入门教程" #: ../../src/tutorials.md:9 87ddaa1e5f57445c8f13803722aa146e msgid "" @@ -4478,22 +4512,24 @@ msgid "" "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" +"[Introduction to Workflows with Common Workflow Language: For " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" #: ../../src/tutorials.md:11 b8ee193ba533498db6263e0f5f4ec45f msgid "Advanced Tutorials" -msgstr "" +msgstr "进阶教程" #: ../../src/tutorials.md:13 67c4b3923fce46fdab025495125c91d4 msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" +msgstr "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" #: ../../src/tutorials.md:15 e640316669104239970794191b6da38b msgid "Bioinformatics Tutorials" -msgstr "" +msgstr "生物信息学相关教程" #: ../../src/tutorials.md:17 efe94af44b874f9b81b245fbdee43f7f msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" +msgstr "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" #~ msgid "In CWL, everything must be directly stated." #~ msgstr "在CWL中，一切都必须直接说明。" From 3bfa62397cece91175f3652e2df7d8b43beb0c15 Mon Sep 17 00:00:00 2001 From: "Weblate (bot)" Date: Sun, 20 Oct 2024 15:58:44 +0200 Subject: [PATCH 167/179] Translated using Weblate (Chinese (Simplified Han script)) (#494) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Currently translated at 100.0% (599 of 599 strings) Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/zh_Hans/ Translation: Common Workflow Language/CWL User Guide Co-authored-by: Zoë Ma --- locales/zh_Hans/LC_MESSAGES/user_guide.po | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index 16ae112b..50854ec7 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -9,7 +9,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-10-16 10:15+0000\n" +"PO-Revision-Date: 2024-10-19 09:16+0000\n" "Last-Translator: Zoë Ma \n" "Language-Team: Chinese (Simplified Han script) \n" @@ -1992,7 +1992,7 @@ msgid "" " and then anywhere a parameter reference is legal you can provide a " "fragment of Javascript that will be evaluated by the CWL runner." msgstr "" -"如果需要对输入参数进行处理，请添加需求 " +"如果需要对输入参数进行处理，请添加需求 " "[`InlineJavascriptRequirement`](https://w3id.org/cwl/CommandLineTool." "html#InlineJavascriptRequirement). 然后，在任何可以合法引用参数的地方，" "您都可以提供一 JavaScript 片段，让 CWL 运行程序计算其值。" @@ -2913,7 +2913,7 @@ msgid "" "expression’s value becomes that of the second operand, which is why a " "reasonable default can be provided there." msgstr "" -"这里，我们要使用的是 JavaScript 中布尔“或”运算符 `||` 的_短路_特点。如果 " +"这里，我们要使用的是 JavaScript 中布尔“或”运算符 `||` 的“短路”特点。如果 " "`inputs.file_format` 为布尔意义上的“真值”（例如来自枚举的有效、非空字符串），" "这个表达式的计值过程到 `||` 运算符前的操作数就终止，也就是“短路”了。反之，" "如果 `inputs.file_format` 为 `null`, " @@ -3088,7 +3088,7 @@ msgid "" "mandatory command line arguments" msgstr "" "在此前的例子里，`baseCommand` 命令只是一个字符串，命令的参数都由 CWL " -"输入传递而来。不过，我们也可以用_字符串数组_作为 `baseCommand` " +"输入传递而来。不过，我们也可以用“字符串数组”作为 `baseCommand` " "的值。数组的第一个元素是将要运行的命令，其后的元素均为命令行的必要参数" #: ../../src/topics/outputs.md:28 9b65071222c94951bed12ac53e964ee3 @@ -3378,7 +3378,7 @@ msgid "" msgstr "" "工具描述往往是针对特定版本的软件而编写。为了方便他人使用您的工具描述，" "您可以在 `hints` 部分添加[`SoftwareRequirement`](https://w3id.org/cwl/" -"CommandLineTool.html#SoftwareRequirement) " +"CommandLineTool.html#SoftwareRequirement) " "字段，用来指明该描述适用于哪个工具版本。" #: ../../src/topics/specifying-software-requirements.md:13 From 16549813f1ac99002608dbc37a2c30d8e863f81b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 12 Aug 2025 10:24:24 +0200 Subject: [PATCH 168/179] Bump actions/checkout from 4 to 5 (#496) Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/ci-tests.yml | 2 +- .github/workflows/codeql.yml | 2 +- .github/workflows/gh-pages.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml index e7c0d108..5c992d18 100644 --- a/.github/workflows/ci-tests.yml +++ b/.github/workflows/ci-tests.yml @@ -28,7 +28,7 @@ jobs: py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }} steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 - name: Set up Python uses: actions/setup-python@v5 diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index c4095636..a3602998 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -24,7 +24,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v4 + uses: actions/checkout@v5 - name: Initialize CodeQL uses: github/codeql-action/init@v3 diff --git a/.github/workflows/gh-pages.yaml b/.github/workflows/gh-pages.yaml index 2a8dc626..cb5c4da1 100644 --- a/.github/workflows/gh-pages.yaml +++ b/.github/workflows/gh-pages.yaml @@ -15,7 +15,7 @@ jobs: permissions: contents: write steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 - name: Install apt packages run: | From 7865c7d188aeb4c04416b171e4621c1474345012 Mon Sep 17 00:00:00 2001 From: gfbdrgng Date: Tue, 12 Aug 2025 12:26:19 +0200 Subject: [PATCH 169/179] Translated using Weblate (Russian) Currently translated at 80.7% (483 of 598 strings) Added translation using Weblate (Russian) Co-authored-by: gfbdrgng Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ru/ Translation: Common Workflow Language/CWL User Guide --- locales/ru/LC_MESSAGES/user_guide.po | 4423 ++++++++++++++++++++++++++ 1 file changed, 4423 insertions(+) create mode 100644 locales/ru/LC_MESSAGES/user_guide.po diff --git a/locales/ru/LC_MESSAGES/user_guide.po b/locales/ru/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..a5098347 --- /dev/null +++ b/locales/ru/LC_MESSAGES/user_guide.po @@ -0,0 +1,4423 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: 2025-01-06 04:00+0000\n" +"Last-Translator: gfbdrgng \n" +"Language-Team: Russian \n" +"Language: ru\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=3; plural=n%10==1 && n%100!=11 ? 0 : n%10>=2 && " +"n%10<=4 && (n%100<10 || n%100>=20) ? 1 : 2;\n" +"X-Generator: Weblate 5.10-dev\n" + +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "Лицензии" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "Инструкционные материалы" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" +"Все учебные материалы проекта Common Workflow Language и изменения в " +"структуре также доступны по лицензии [Creative Commons Attribution]" +"[cc-by-human]. Нижеследующее является человекочитаемым кратким изложением " +"[полного юридического текста лицензии CC BY 4.0][cc-by-legal] (но не " +"заменяет его)." + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "Вы свободны:" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" +"**Пользоваться** - копировать и распространять материал на любом носителе " +"или в любом формате" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Адаптировать** - смешивать, преобразовывать и развивать материал" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "для любых целей, даже коммерчески." + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" +"Лицензиар не может лишить вас этих свобод, если вы соблюдаете условия " +"лицензии:" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" +"**Атрибуция**---Вы должны отдать должное (упомянуть, что ваша работа " +"получена из работы, которая является Copyright © проекта Common Workflow " +"Language, и, где это возможно, дать ссылку на https://www.commonwl.org/ ), " +"предоставить [ссылку на лицензию][cc-by-human], и указать, были ли внесены " +"изменения. Вы можете сделать это любым разумным способом, но не таким, " +"который предполагает, что лицензиар одобряет вас или ваше использование." + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" +"**Нет дополнительных ограничений**---Вы не имеете права применять " +"юридические условия или технологические меры, которые законно ограничивают " +"других от выполнения действий, разрешенных лицензией. При понимании того, " +"что:" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" +"Вы не обязаны соблюдать лицензию в отношении элементов материала, " +"находящихся в общественном достоянии, или если их использование допускается " +"в соответствии с применимыми исключениями или ограничениями." + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" +"Гарантии не предоставляются. Лицензия может не предоставлять вам всех " +"разрешений, необходимых для предполагаемого использования. Например, другие " +"права, такие как публичность, неприкосновенность частной жизни или моральные " +"права, могут ограничивать использование материала." + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "Программное обеспечение" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" +"Если не указано иное, примеры программ и другое программное обеспечение, " +"предоставляемое проектом Common Workflow Language, доступно на условиях [OSI]" +"[osi]-одобренной [Apache 2.0 license][apache-2.0-license]." + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" +"За исключением случаев, предусмотренных действующим законодательством или " +"оговоренных в письменном виде, программное обеспечение, распространяемое в " +"рамках Лицензии, распространяется на условиях \"КАК ЕСТЬ\", БЕЗ КАКИХ-ЛИБО " +"ГАРАНТИЙ И УСЛОВИЙ, как явных, так и подразумеваемых. Конкретные " +"формулировки, регулирующие разрешения и ограничения в рамках Лицензии, см. в " +"Лицензии." + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" +"CWL - это способ описания инструментов командной строки и их соединения для " +"создания рабочих процессов. Поскольку CWL - это спецификация, а не " +"конкретный программный продукт, инструменты и рабочие процессы, описанные с " +"помощью CWL, переносятся на различные платформы, поддерживающие стандарт CWL." + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "Эта страница переехала" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" +"Эта страница устарела и была оставлена здесь, чтобы сохранить ссылки на " +"старое Руководство пользователя. Пожалуйста, используйте новое [Оглавление]" +"(index.md#table-of-contents) для просмотра Руководства пользователя." + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "Часто задаваемые вопросы" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "Не \"`Файл`\" Типы, использующие `evalFrom`" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "Переименование входного файла" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" +"Этот пример демонстрирует, как изменить имя входного файла в описании " +"инструмента. Это может быть полезно, когда вы берете файлы, созданные на " +"другом этапе рабочего процесса, и не хотите работать с именами по умолчанию, " +"которые были присвоены этим файлам при их создании." + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "Переименование выходного файла" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" +"В этом примере показано, как изменить имя выходного файла по сравнению с " +"именем по умолчанию, присвоенным ему инструментом:" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "Ссылка на локальный сценарий" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "Существует два способа сослаться на локальный скрипт:" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" +"Первый способ заключается в добавлении папки с вашими скриптами в переменную " +"окружения `PATH`. Это позволит вам запускать сценарий оболочки напрямую, без " +"использования команд `sh` или `bash`." + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "Начните с добавления _shebang_ в начало файла:" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" +"После этого сделайте скрипт исполняемым с помощью команды `chmod +x " +"scriptname.sh`" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" +"Наконец, измените `PATH`, чтобы добавить каталог, в котором находится ваш " +"скрипт. (Хорошей практикой является использование `$HOME/bin` для хранения " +"собственных скриптов)." + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" +"Теперь вы можете использовать `baseCommand: scriptname.sh`, чтобы запустить " +"скрипт напрямую." + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" +"Если вы захотите поделиться своей работой позже, вы можете поместить свой " +"скрипт в программный контейнер в формате Docker." + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" +"Второй способ предполагает включение входных данных типа `type: File` в " +"самом скрипте:" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "В CWL все должно быть прямо указано." + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "Установка привязок ввода на основе `self` для необязательных входов" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" +"В настоящее время `cwltool` не может справиться с отсутствующими " +"необязательными входами, если их привязка к входу использует `self`. Ниже " +"приведен пример обходного пути для этого, в ожидании более сложного " +"исправления." + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "Моделирование параметра \"один-другой\"" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" +"Ниже приведен пример, показывающий, как указать различные строки для " +"добавления в командную строку в зависимости от значения булевого параметра." + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "Подключите значение Solo к входу, который ожидает массив этого типа" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" +"Использование [`MultipleInputFeatureRequirement`](https://www.commonwl.org/" +"v1.0/Workflow.html#MultipleInputFeatureRequirement) вместе с " +"[`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/" +"Workflow.html#WorkflowStepInput)" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +#, fuzzy +msgid "merge_nested" +msgstr "merge_nested" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" +"Входные данные должны представлять собой массив, состоящий ровно из одной " +"записи для каждой входной ссылки. Если для одной ссылки указано " +"\"merge_nested\", то значение из ссылки должно быть обернуто в список из " +"одного элемента." + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" +"Что означает " +"\"создать список, элементами которого являются именно эти источники\"" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" +"Или другими словами: если пункт назначения имеет тип `File[]` (массив `File`)" +", а источник - один `File`, то добавьте `MultipleInputFeatureRequirement` в " +"`требования` уровня Workflow и добавьте `linkMerge: merge_nested` в " +"соответствующую запись `in` шага назначения." + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "Дополнительные входы 💯" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" +"Чтобы сделать входной параметр необязательным, добавьте вопросительный знак " +"в объявление типа." + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +#, fuzzy +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "Входы Enum ⚜️" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" +"Для флагов командной строки, которые требуют определенного ввода в качестве " +"аргумента, в CWL может быть объявлен тип enum. **Указание здесь null " +"известно как стиль длинной формы. Он делает то же самое, что и " +"вопросительный знак на других входах**" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +#, fuzzy +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "Запись входов 📀" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" +"Для флагов командной строки, которые являются **взаимоисключающими** или " +"**зависимыми**, может быть определен специальный тип записи. Вы также можете " +"указать здесь null для создания необязательных входов." + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "Установка взаимоисключающих параметров" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" +"Чтобы правильно задать поля в типе ввода записи, необходимо передать словарь " +"в input для правильной установки параметров. Для этого используется " +"встроенный JavaScript и возвращается словарь с ключом поля, которое вы " +"хотите установить. Поле источника задается для указания ввода из рабочего " +"процесса, который будет использоваться в качестве значения." + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "Настройка булевых значений" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "Их можно задать с помощью поля по умолчанию" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "Конкатенация строк во входных данных" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "Поле valueFrom должно использоваться вместо default." + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "Ошибки `cwltool` из-за имен файлов с пробельными символами внутри" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" +"По умолчанию `cwltool` не разрешает использовать некоторые символы в именах " +"файлов." + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "Например, имя файла `a space is here.txt` содержит 3 символа пробела." + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" +"Если вы не можете избежать этих опасных символов, то передайте `--relax-path-" +"checks` в `cwltool`." + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "Ошибка ссылки на параметр CWL из-за дефиса в входном идентификаторе" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "Если `cwltool --validate` возвращает действительный" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "Но его выполнение приводит к ошибке типа:" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "Файл находится здесь" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "Проблема, вызванная `-` (символом дефиса)." + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" +"Чтобы исправить эту ошибку, замените `-` (дефис) на `_` (знак подчеркивания)" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" +"Если изменить входной идентификатор невозможно, можно использовать " +"альтернативный синтаксис справочника параметров CWL:" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "Использование CWL и cwltool с Singularity" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" +"Стандарты CWL построены на основе контейнеров формата Docker (по желанию). " +"Эталонный runner и некоторые другие реализации CWL поддерживают запуск " +"контейнеров формата Docker с помощью движка Singularity. Прямое указание " +"контейнера формата Singularity не является частью стандартов CWL." + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "Отладка выражений JavaScript" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +#, fuzzy +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" +"You can use the --js-console option of cwltool, or " +"you can try creating a JavaScript or TypeScript project for your code, and " +"load it using expressionLib, e.g.: https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-" +"tool.cwl#L6-L8" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "Руководство пользователя Common Workflow Language" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" +"Это руководство познакомит вас с написанием рабочих процессов с " +"использованием открытых стандартов [Common Workflow Language](https://" +"www.commonwl.org/) (CWL). В этом руководстве описывается последняя " +"спецификация {{ cwl_version }}." + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "Вклад и отзывы приветствуются!" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" +"Если вы обнаружили, что в этом руководстве чего-то не хватает, или хотите " +"дать другие отзывы, оформите проблему в " +"[репозитории проекта для этого руководства][repo]. Вы также можете " +"предложить изменения непосредственно в Pull Request, нажав кнопку " +"\"Редактировать эту страницу\" в правой боковой панели каждой страницы." + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "Навигация по руководству пользователя" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" +"Если вы начинающий пользователь, начните с раздела [Введение](/introduction/" +"index.md). Для опытных пользователей в подразделах раздела [Topics](/topics/" +"index.md) содержится подробная информация о наиболее распространенных темах " +"для CWL." + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" +"Оглавление отображается в верхнем меню, а также на левой боковой панели. Оно " +"также отображается далее на этой странице, но со ссылками на подразделы. " +"Правая боковая панель содержит ссылки на разделы каждой страницы, а форма " +"поиска находится на левой боковой панели." + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "Оглавление" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "Основные концепции" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" +"В этом разделе описаны основные понятия, с помощью которых пользователи " +"смогут начать работу с рабочими процессами на Common Workflow Language (CWL)" +". Предполагается, что читатели знакомы с менеджерами рабочих процессов, YAML " +"и умеют выполнять инструкции в командной строке. В других разделах " +"руководства пользователя рассматриваются те же концепции, но более подробно. " +"Если вы уже знакомы с CWL или ищете более продвинутое содержание, вы можете " +"пропустить этот раздел." + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "Спецификация CWL" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" +"Спецификация CWL - это документ, написанный и поддерживаемый сообществом " +"CWL. У спецификации есть разные версии. В данном руководстве пользователя " +"рассматривается версия {{ cwl_version }}." + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" +"Версия спецификации может содержать до трех чисел, разделенных `.` (точками)" +". Первый номер - это основной выпуск, используемый для изменений, " +"несовместимых с прошлым, например, для удаления устаревших функций. Второй " +"номер - это минорный релиз, который используется для новых функций или " +"небольших изменений, совместимых с предыдущими версиями. Последний номер " +"используется для исправления ошибок, например, опечаток и других исправлений " +"в спецификации." + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" +"Модель, используемая для создания версии спецификации, называется Semantic " +"Versioning. См. конец этого раздела, чтобы [узнать больше](#learn-more) о " +"ней." + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "Осуществление" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" +"Реализация спецификации CWL - это любое программное обеспечение, написанное " +"в соответствии с тем, что определено в той или иной версии документа " +"спецификации. Однако реализации могут не реализовывать все аспекты " +"спецификации. Реализации CWL лицензируются как под Open Source, так и под " +"коммерческими лицензиями." + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" +"CWL хорошо подходит для описания крупномасштабных рабочих процессов в " +"кластерных, облачных и высокопроизводительных вычислительных средах, где " +"задачи планируются параллельно на многих узлах." + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "Спецификация CWL, реализации и другие инструменты." + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "Процессы и требования" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" +"Процесс - это вычислительная единица, которая принимает входные данные и " +"производит выходные. На поведение процесса могут влиять входы, требования и " +"подсказки. В спецификации CWL {{ cwl_version }} определены четыре типа " +"процессов:" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "Инструмент командной строки." + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "Инструмент выражения." + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "Операция." + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "Рабочий процесс." + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "Блоки обработки, доступные в модели объектов CWL." + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" +"Инструмент командной строки - это обертка для утилит командной строки, таких " +"как `echo`, `ls` и `tar`. Инструмент командной строки может быть вызван из " +"рабочего процесса." + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" +"Инструмент выражения - это обертка для выражения JavaScript. Он может " +"использоваться для упрощения рабочих процессов и инструментов командной " +"строки, перенося общие части выполнения рабочего процесса в многократно " +"используемый код JavaScript, который принимает входные данные и выдает " +"выходные, как инструмент командной строки." + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" +"Операция - это абстрактный процесс, который также принимает входные данные, " +"производит выходные и может быть использован в рабочем процессе. Но это " +"особая операция, которая используется не так часто. Она рассматривается в " +"разделе [Операции](../topics/operations.md) этого руководства пользователя." + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" +"Рабочий процесс - это процесс, содержащий шаги. Шаги могут быть другими " +"рабочими процессами (вложенными рабочими процессами), инструментами " +"командной строки или средствами выражения. Входные данные рабочего процесса " +"могут быть переданы любому из его этапов, а выходные данные, созданные его " +"этапами, могут быть использованы в конечном результате рабочего процесса." + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" +"Спецификация CWL позволяет реализациям предоставлять дополнительную " +"функциональность и указывать необходимые условия для рабочих процессов с " +"помощью *требований*. В спецификации CWL определено множество требований, " +"например:" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "`InlineJavascriptWorkflow` - включает JavaScript в выражениях." + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "`SubworkflowFeatureRequirement` - включает вложенные рабочие процессы." + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" +"`InitialWorkDirRequirement` - контролирует размещение файлов во входном " +"каталоге." + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" +"Некоторые прогоны CWL могут предоставлять требования, которых нет в " +"спецификации. Например, требования к GPU поддерживаются в `cwltool` с " +"помощью требования `cwltool:CUDARequirement`, но оно не является частью " +"спецификации {{ cwl_version }} и может не поддерживаться другими " +"CWL-прогонами." + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" +"Подсказки похожи на требования, но если в требованиях перечислены " +"обязательные функции, то в подсказках - необязательные. Требования подробно " +"описаны в разделе [Требования](../topics/requirements-and-hints.md)." + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "Рабочие процессы FAIR" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" +"Принципы FAIR заложили основу для обмена и публикации цифровых активов, в " +"частности данных. Принципы FAIR подчеркивают доступность машин и то, что все " +"цифровые активы должны быть находимыми, доступными, взаимодействующими и " +"многократно используемыми. Рабочие процессы кодируют методы, с помощью " +"которых осуществляется научный процесс и создаются данные. Поэтому важно, " +"чтобы рабочие процессы поддерживали создание данных FAIR и соответствовали " +"принципам FAIR. - [FAIR Computational Workflows](https://workflows.community/" +"groups/fair/), Workflows Community Initiative." + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" +"CWL уходит корнями в \"make\" и многие другие подобные инструменты, которые " +"определяют порядок выполнения, основываясь на зависимостях между задачами. " +"Однако, в отличие от \"make\", задачи CWL изолированы, и вы должны явно " +"указывать свои входы и выходы." + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" +"Преимуществами явности и изолированности являются гибкость, переносимость и " +"масштабируемость; инструменты и рабочие процессы, описанные с помощью CWL, " +"могут прозрачно использовать такие технологии, как Docker, и применяться с " +"реализациями CWL от разных производителей." + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" +"`cwltool` также использует стандартную онтологию PROV-O для проверки " +"достоверности данных." + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "Узнать больше" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "Семантическое версионирование - " + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" +"Страница спецификации CWL на сайте CWL: " + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" +"Текущая спецификация CWL на GitHub: {{ ''.format(cwl_version_text) }}" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" +"Список реализаций на сайте CWL: " + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "PROV-O: Онтология PROV - " + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" +"Операции CWL рассматриваются в разделе [Операции](../topics/operations.md) " +"данного руководства пользователя." + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "Введение" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" +"В этом разделе мы расскажем вам о кратком введении в CWL, предпосылках для " +"изучения данного руководства пользователя и некоторых основных понятиях, " +"которые полезно знать перед прочтением остальной части руководства " +"пользователя." + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "Пререквизиты" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" +"Программное обеспечение и конфигурации, перечисленные в этом разделе, " +"являются необходимыми условиями для выполнения данного руководства " +"пользователя. Стандарты CWL реализуются множеством различных программ и " +"платформ для запуска рабочих процессов. В этом списке требований основное " +"внимание уделено эталонному исполнителю CWL, `cwltool`. Вы можете " +"использовать другой CWL-совместимый прогон или систему документооборота, но " +"результаты и интерфейс могут выглядеть иначе (хотя точные результаты " +"документооборота должны быть идентичными)." + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "Реализации CWL" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" +"Существует множество реализаций стандартов CWL. Некоторые из них " +"представляют собой полноценные CWL-программы, в то время как другие могут " +"быть плагинами или расширениями для движков рабочих процессов. Более " +"подробное описание приведено в разделе [Реализации](basic-" +"concepts.md#implementations)." + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "Операционная система" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" +"Мы рекомендуем использовать современную операционную систему. Вы можете " +"выбрать любой из следующих вариантов операционной системы:" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +#, fuzzy +msgid "Linux" +msgstr "Linux" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +#, fuzzy +msgid "macOS" +msgstr "macOS" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +#, fuzzy +msgid "Windows" +msgstr "Windows" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" +"Если вы используете Windows, вам придется установить " +"[Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/" +"wsl/install) (WSL2). Подробную информацию об установке WSL2 можно найти в " +"`cwltool` [документации](https://github.com/common-workflow-language/cwltool/" +"blob/main/README.rst#ms-windows-users). Вашей операционной системе также " +"необходим доступ в Интернет и последняя версия Python (3.6+)." + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "Бегун CWL" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" +"Первое, что вам понадобится для запуска рабочих процессов CWL, - это CWL " +"runner. `cwltool` - это проект с открытым исходным кодом на Python, " +"поддерживаемый сообществом CWL. Он также является эталонным бегуном CWL, что " +"означает, что он должен поддерживать все, что есть в текущей спецификации " +"CWL, {{ cwl_version }}." + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" +"`cwltool` может быть установлен с помощью `pip`. Мы рекомендуем использовать " +"виртуальную среду, например `venv` или `conda`. Следующие команды создадут и " +"активируют виртуальную среду Python с помощью модуля `venv`, а также " +"установят `cwltool` в эту среду:" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "Установка `cwltool` с помощью `pip` и `venv`." + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" +"О других способах установки `cwltool` с помощью `apt` и `conda` читайте в " +"разделе `cwltool` [документация](https://github.com/common-workflow-language/" +"cwltool#install)." + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" +"Давайте воспользуемся простым описанием CWL-инструмента `true.cwl` с помощью " +"`cwltool`." + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +#, fuzzy +msgid "`true.cwl`" +msgstr "`true.cwl`" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" +"Команда `cwltool` имеет опцию для проверки описаний инструментов и рабочих " +"процессов CWL. Эта опция будет разбирать документ CWL, искать синтаксические " +"ошибки и проверять соответствие описаний рабочих процессов стандартам CWL. " +"Однако эти действия будут выполнены без запуска документа. Чтобы проверить " +"рабочие процессы CWL (или даже описание отдельного инструмента командной " +"строки, как показано выше), передайте опцию `--validate` команде `cwltool`:" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "Проверка `true.cwl` с помощью `cwltool`." + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" +"Вы можете запустить описание инструмента CWL, опустив опцию `--validate`:" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "Запуск `true.cwl` с помощью `cwltool`." + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "Модуль Cwl-runner Python" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" +"`cwl-runner` - это псевдоним для любого CWL-совместимого бегуна, не " +"зависящий от реализации. Это просто означает, что команда псевдонима `cwl-" +"runner` может быть вызвана независимо и не зависит от имени конкретной " +"программы CWL runner. Пользователи могут вызывать `cwl-runner` вместо того, " +"чтобы напрямую вызывать CWL-бегунок, например `cwltool`. Программа `cwl-" +"runner` устанавливается системным администратором или пользователем, чтобы " +"указать на предпочтительную реализацию CWL. Это удобно для сред с " +"несколькими CWL-бегунами." + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" +"Сообщество CWL публикует пакет Python с именем `cwlref-runner`, который " +"устанавливает псевдоним для `cwltool` под именем `cwl-runner`" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "Установка псевдонима `cwl-runner` для cwltool с помощью `pip`." + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" +"Теперь вы можете проверить и запустить свой рабочий процесс с помощью " +"исполняемого файла `cwl-runner`, который вызовет `cwltool`. Вы должны " +"получить те же результаты и вывод, что и в предыдущем разделе." + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "Проверка `true.cwl` с помощью `cwl-runner`." + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "Запуск `true.cwl` с помощью `cwl-runner`." + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" +"Другой способ выполнить `cwl-runner` - вызвать файл напрямую. Для этого вам " +"нужно скопировать рабочий процесс `true.cwl` в новый файл: `true_shebang.cwl`" +", и включить в него специальную первую строку, *shebang*:" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +#, fuzzy +msgid "`true_shebang.cwl`" +msgstr "`true_shebang.cwl`" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "" +"Теперь вы можете сделать файл `true_shebang.cwl` исполняемым с помощью `" +"chmod u+x`." + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "Создание исполняемого файла `true.cwl`." + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" +"И, наконец, вы можете выполнить его непосредственно в командной строке. При " +"выполнении программа, указанная в shebang (`cwl-runner`), будет использована " +"для выполнения остальной части файла." + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "Запуск `true_shebang.cwl` с шебангом." + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" +"*Шебанг* - это двухсимвольная последовательность `#!` в начале сценария. " +"Если сценарий является исполняемым, операционная система выполнит его с " +"помощью исполняемого файла, указанного после shebang. Считается хорошей " +"практикой использовать `/usr/bin/env `, а не жестко заданное " +"местоположение, поскольку `/usr/bin/env ` ищет программу " +"`` в системном `PATH`," + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "Текстовый редактор" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" +"Вы можете использовать любой текстовый редактор с CWL, но для подсветки " +"синтаксиса мы рекомендуем редактор с поддержкой YAML. Популярными " +"редакторами являются Visual Studio Code, Sublime, WebStorm, vim/neovim и " +"Emacs." + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" +"Существуют расширения для Visual Studio Code и WebStorm, обеспечивающие " +"интеграцию с CWL, а также такие функции, как настраиваемая подсветка " +"синтаксиса и улучшенное автозаполнение:" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" +"Visual Studio Code с плагином Benten (CWL) - " + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" +"cwl-плагин для IntelliJ - " + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" +"Сообщество CWL также поддерживает список редакторов и зрителей: " + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" +"`cwltool` использует Docker для запуска инструментов, рабочих процессов и " +"шагов рабочего процесса, которые определяют программный контейнер. Следуйте " +"инструкциям в документации Docker, чтобы установить его для вашей " +"операционной системы: ." + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" +"Вам не нужно знать, как писать и собирать контейнеры Docker. В остальной " +"части руководства мы будем использовать существующие образы Docker для " +"запуска примеров, а также для пояснения различий между моделями выполнения с " +"контейнерами и без них." + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" +"`cwltool` поддерживает запуск контейнеров с помощью Docker, Podman, udocker " +"и Singularity. Вы также можете использовать альтернативные реестры " +"контейнеров для получения образов." + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" +"Тема [Реализации](basic-concepts.md#implementations) в следующем разделе, " +"Основные концепции." + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "Модуль Python `venv`: " + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "Быстрый старт" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" +"В этом разделе вы найдете краткий обзор того, что такое CWL, и узнаете, где " +"можно узнать о нем больше. Никаких предварительных знаний о CWL не " +"требуется, но вам должно быть удобно выполнять инструкции для командной " +"строки." + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "\"Здравствуй, мир\"" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" +"Документы CWL записываются в формате [YAML](../topics/index.md) (и/или JSON)" +". В примере ниже показан простой CWL-документ \"Hello World\", снабженный " +"комментариями. Обратите внимание, что комментарии начинаются с `#`:" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +#, fuzzy +msgid "`hello_world.cwl`" +msgstr "`hello_world.cwl`" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" +"Приведенный выше пример - это просто обертка для инструмента командной " +"строки `echo`. Запуск приведенного выше рабочего процесса с входными " +"значениями по умолчанию даст тот же результат, что и командная строка `echo " +"\"Hello World\"`." + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" +"В CWL существует различие между инструментом командной строки и рабочим " +"процессом. Но для простоты мы используем здесь термин \"рабочий процесс\". " +"Подробнее об этом вы узнаете в разделе [основные понятия](basic-concepts.md)." + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "Установка программы CWL Runner" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" +"`cwltool` - это реализация спецификации CWL. Он также является CWL *" +"Reference Runner* для этой спецификации и совместим с последней версией " +"спецификации: {{ cwl_version }}. Вы можете установить `cwltool` с помощью " +"`pip`:" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "Установка `cwltool` с `pip`." + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" +"Если установка cwltool с помощью команды pip вам не подходит, в разделе " +"[prerequisites](prerequisites.md) приведены другие способы установки " +"`cwltool` и более подробный список программного обеспечения и библиотек, " +"используемых в остальной части этого руководства пользователя." + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "Запуск \"Hello World\"" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" +"Исполняемый модуль командной строки `cwltool` используется в основном как `" +"cwltool [OPTIONS] [INPUTS_OBJECT]`. Вы можете запустить " +"рабочий процесс `hello_world.cwl`, не указывая никаких опций:" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "Запуск `hello_world.cwl` с помощью `cwltool`." + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" +"Или вы можете переопределить значение по умолчанию входного параметра " +"`message`, подобно тому, как вы изменяете аргумент базовой команды `echo`:" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" +"Запуск `hello_world.cwl` с помощью `cwltool` с передачей входного параметра." + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" +"Другой способ передачи значений входным параметрам рабочего процесса - через " +"объект *Inputs Object*. Это файл, содержащий поля ввода с соответствующими " +"значениями. Файл Inputs Objects может быть записан в формате JSON или YAML. " +"Например:" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +#, fuzzy +msgid "`hello_world-job.json`" +msgstr "`hello_world-job.json`" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" +"Теперь вы можете использовать этот файл Inputs Object для выполнения " +"рабочего процесса \"Hello World\":" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "Передача файла Inputs Object в `cwltool`." + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" +"Мы использовали одинаковые имена файлов для рабочего процесса и для файлов " +"объектов ввода. Суффикс *-job.json* очень часто встречается в файлах Inputs " +"Object, но это не обязательное условие. Вы можете выбрать любое имя для " +"своих рабочих процессов и файлов Inputs Object." + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "Продолжайте читать следующие разделы этого руководства пользователя!" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "[Список реализаций CWL](https://www.commonwl.org/implementations)." + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" +"Организация [`common-workflow-language`](https://github.com/common-workflow-" +"language) на GitHub." + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +#, fuzzy +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" +"[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" +"[YAML.org](http://yaml.org/) и [YAML at Wikipedia](https://en.wikipedia.org/" +"wiki/YAML)." + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" +"В качестве источника информации используется {{'[ВЕРСИЯ спецификации CWL]" +"(https://www.commonwl.org/VERSION)'.replace('ВЕРСИЯ', cwl_version_text)}}." + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" +"[Система управления рабочими процессами в Википедии](https://" +"en.wikipedia.org/wiki/Workflow_management_system)." + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" +"Эта страница устарела и была оставлена здесь, чтобы сохранить ссылки на " +"старое руководство пользователя. Информация на этой странице была перенесена " +"в раздел [FAQ](/faq.md) нового руководства пользователя." + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "Дополнительные аргументы и параметры" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" +"Иногда инструменты требуют дополнительных опций командной строки, которые не " +"совсем соответствуют входным параметрам." + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" +"В этом примере мы обернем компилятор Java, чтобы скомпилировать исходный " +"файл java в файл класса. По умолчанию \"javac\" создаст файлы классов в том " +"же каталоге, что и исходный файл. Однако входные файлы CWL (и каталоги, в " +"которых они находятся) могут быть доступны только для чтения, поэтому нам " +"нужно указать \"javac\" записать файл класса в указанный выходной каталог." + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +#, fuzzy +msgid "`arguments.cwl`" +msgstr "`arguments.cwl`" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +#, fuzzy +msgid "`arguments-job.yml`" +msgstr "`arguments-job.yml`" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" +"Далее создайте пример Java-файла для использования с инструментом командной " +"строки." + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" +"А теперь вызовите `cwltool`, указав в командной строке описание инструмента " +"и объект ввода:" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" +"Здесь мы используем поле `arguments`, чтобы добавить в командную строку " +"дополнительный аргумент, который не привязан к конкретному входному " +"параметру." + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" +"Этот пример ссылается на параметр времени выполнения. Параметры времени " +"выполнения предоставляют информацию об аппаратном или программном окружении, " +"когда инструмент фактически выполняется. Параметр `$(runtime.outdir)` - это " +"путь к указанному каталогу вывода. Другие параметры включают " +"`$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, " +"`$(runtime.outdirSize)` и `$(runtime.tmpdirSize)`. Подробности см. в " +"разделе [Runtime Environment][runtime] спецификации CWL." + +#: ../../src/topics/best-practices.md:1 +#: 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "Передовая практика" + +#: ../../src/topics/best-practices.md:3 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" +"Ниже приведен набор рекомендуемых передовых методов, которые следует иметь в " +"виду при написании описания инструмента или рабочего процесса на языке " +"Common Workflow Language. Эти рекомендации представлены для рассмотрения по " +"шкале полезности: хотя больше - значит лучше, не все из них обязательны." + +#: ../../src/topics/best-practices.md:8 +#: 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" +"Нет параметров `type: string` для имен входных или справочных " +"файлов/директорий; используйте `type: File` или `type: Directory` в " +"зависимости от ситуации." + +#: ../../src/topics/best-practices.md:11 +#: 4dee8504a8e5496081dadc386ab45540 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" +"Документ CWL (в сочетании с любыми внешними компонентами, такими как " +"`Dockerfile`) является программным кодом. Разработчики рабочих процессов " +"должны знать, что к этому документу применяются обычные правила " +"лицензирования программного обеспечения. Например, если рабочий процесс " +"выкладывается в открытый доступ, условия лицензирования должны быть понятны, " +"чтобы будущий пользователь понимал, при каких условиях он может запускать " +"рабочий процесс, изменять его и/или комбинировать с другими рабочими " +"процессами. По этой причине рассмотрите возможность включения в документ " +"поля лицензии. Авторы этого руководства настоятельно рекомендуют вам выбрать " +"уже существующую лицензию, а не пытаться написать свою собственную (см. " +"ссылку ниже, чтобы узнать больше о выборе лицензии). Мы рекомендуем выбирать " +"лицензию, которая позволяет повторное использование любым пользователем, " +"например [Apache 2.0][apache-license]." + +#: ../../src/topics/best-practices.md:20 +#: 674c238b25e240eda05e22e399f2f78f +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" +"Если возможно, лицензия должна быть указана с соответствующим " +"[SPDX-идентификатором][spdx]. Создайте поле метаданных для лицензии, указав " +"URL вида `https://spdx.org/licenses/[SPDX-ID]`, где `SPDX-ID` берется из " +"списка идентификаторов, приведенного выше. См. пример фрагмента ниже. Для " +"нестандартных лицензий без идентификатора SPDX укажите URL-адрес лицензии." + +#: ../../src/topics/best-practices.md:26 +#: b651f80f47b4442fbf29454a233697fc +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" +"Полезное чтение: \"[Краткое руководство по лицензированию программного " +"обеспечения для ученого-программиста][sci-license]\"" + +#: ../../src/topics/best-practices.md:28 +#: 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "_Пример поля метаданных для лицензии с идентификатором SPDX:_" + +#: ../../src/topics/best-practices.md:37 +#: 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" +"Другие примеры предоставления метаданных в описаниях CWL см. в " +"[разделе \"Метаданные и авторство\" данного руководства пользователя](../" +"topics/metadata-and-authorship.md)." + +#: ../../src/topics/best-practices.md:40 +#: ecf2b9c0b1664afe9c4e180610610021 +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" +"Включите [информацию об авторстве][пример лицензии] для автора(ов) описания " +"инструмента CWL или рабочего процесса. Используйте однозначные " +"идентификаторы, например [ORCID][orcid]." + +#: ../../src/topics/best-practices.md:44 +#: e24cb13d98014e558b6a6946758359e0 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" +"В описаниях инструментов перечисляйте зависимости, используя краткое " +"название (названия) в разделе `SoftwareRequirement`." + +#: ../../src/topics/best-practices.md:47 +#: f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" +"Включите идентификаторы [SciCrunch][scicrunch] для зависимостей в формате " +"`https://identifiers.org/rrid/RRID:SCR_NNNNNN`." + +#: ../../src/topics/best-practices.md:50 +#: 928e3df7ca3e479ca6474a8e72cf36eb +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" +"Все идентификаторы `ввода` и `вывода` должны отражать их концептуальную " +"идентичность. Используйте информативные имена типа `unaligned_sequences`, " +"`reference_genome`, `phylogeny` или `aligned_sequences` вместо `foo_input`, " +"`foo_file`, `result`, `input`, `output` и так далее." + +#: ../../src/topics/best-practices.md:55 +#: d355f035676446c88b028f327aeb4829 +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" +"В описаниях инструментов в разделе `SoftwareRequirement` указывайте список " +"версий инструмента, которые, как известно, работают с данным описанием." + +#: ../../src/topics/best-practices.md:58 +#: 339b852df24242189d6efcd2898a3396 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" +"`Формат` должен быть указан для всех входных и выходных `файлов`. " +"Инструменты биоинформатики должны использовать идентификаторы формата из " +"[EDAM][edam-example]. См. также `iana:text/plain`, `iana:text/tab-separated-" +"values` с `$namespaces: { iana: " +"\"https://www.iana.org/assignments/media-types//" }`. " +"[Полный список медиатипов IANA][iana-types] (также известные как типы MIME). " +"Для инструментов, не относящихся к биоинформатике, используйте или создайте " +"соответствующую онтологию/контролируемый словарь таким же образом. " +"Пожалуйста, отредактируйте эту страницу, чтобы сообщить нам об этом." + +#: ../../src/topics/best-practices.md:66 +#: 3ef57e6862f240bebcf193a52397af0a +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" +"Пометьте все входные и выходные `файлы`, которые считываются или " +"записываются совместимым с потоковой передачей способом (только один раз, " +"без случайного доступа), как `streamable: true`." + +#: ../../src/topics/best-practices.md:69 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" +"Описание каждого инструмента `CommandLineTool` должно быть сфокусировано " +"только на одной операции, даже если (под)команда способна на большее. Не " +"усложняйте описание инструментов опциями, которые вам не нужны или не " +"используются." + +#: ../../src/topics/best-practices.md:73 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" +"Пользовательские типы должны быть определены с помощью одного внешнего YAML " +"для каждого определения типа для повторного использования." + +#: ../../src/topics/best-practices.md:76 +#: c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" +"Включите краткую `метку` верхнего уровня, кратко описывающую инструмент/" +"рабочий процесс." + +#: ../../src/topics/best-practices.md:78 +#: fae385da16aa443da996fa23ac03d6ae +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" +"Если это полезно, включите также верхнеуровневый `doc`. Он должен содержать " +"более длинное и подробное описание, чем то, которое было представлено в " +"`label` верхнего уровня (см. выше)." + +#: ../../src/topics/best-practices.md:82 +#: 92430be71ecc40e18bbbb80d5576c613 +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" +"Используйте `type: enum` вместо `type: string` для элементов с фиксированным " +"списком допустимых значений." + +#: ../../src/topics/best-practices.md:85 +#: 387d83db81024f65aa9a890c2d07874a +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" +"Проанализируйте все случаи использования JavaScript на предмет возможного " +"исключения или замены. Один из распространенных примеров: манипулирование " +"именами и путями к `файлам`? Подумайте, можно ли вместо этого использовать " +"одно из [встроенных свойств `File`][file-prop], например `basename`, " +"`nameroot`, `nameext` и т. д." + +#: ../../src/topics/best-practices.md:90 +#: d8e2280a75a74916a1630afaa2fe2ae3 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" +"Дайте описание инструмента коллеге (желательно в другом учреждении), чтобы " +"он протестировал его и предоставил отзывы." + +#: ../../src/topics/best-practices.md:93 +#: f1c1340f9745458980e0fbd641738687 +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" +"Сложные рабочие процессы с отдельными компонентами, которые могут быть " +"абстрагированы, должны использовать [`SubworkflowFeatureRequirement`]" +"[subworkflow], чтобы сделать их модульными и позволить легко использовать их " +"части повторно." + +#: ../../src/topics/best-practices.md:97 +#: 5424e5472c3d466fa2a3d2022c6cb475 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" +"Контейнеры для программного обеспечения должны соответствовать [" +"\"Рекомендациям по упаковке и контейнеризации программного обеспечения для " +"биоинформатики\"][контейнеры] (также полезны для других дисциплин)." + +#: ../../src/topics/command-line-tool.md:1 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "Инструмент командной строки" + +#: ../../src/topics/command-line-tool.md:3 +#: 12f57b2ba76b492abe1816e06bfb1417 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" +"Инструмент командной строки - это тип объекта Process, который можно " +"запускать самостоятельно или в качестве шага Workflow. Он представляет собой " +"обертку для таких команд, как `ls`, `echo`, `tar` и т. д. Инструмент " +"командной строки определяется в атрибуте `baseCommand` документа CWL " +"инструмента командной строки." + +#: ../../src/topics/command-line-tool.md:8 +#: e1f657a46ce94a0d83671540e2cc2dab +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" +"Инструмент командной строки CWL также должен иметь `входы` и `выходы`. " +"Следующий пример содержит минимальный пример инструмента командной строки " +"CWL для команды `echo` Linux, использующий входы и выходы." + +#: ../../src/topics/command-line-tool.md:19 +#: abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "Инструмент командной строки CWL." + +#: ../../src/topics/command-line-tool.md:50 +#: 3b1a9ae3412f4d6e96a39b9a16934232 +#, fuzzy +msgid "`echo.cwl`" +msgstr "`echo.cwl`" + +#: ../../src/topics/command-line-tool.md:57 +#: a5eacdbc9aa142c890b177869da4143d +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" +"В приведенном примере используется упрощенная форма для определения входов и " +"выходов. Подробнее об этом вы узнаете в разделах [Inputs](../topics/" +"inputs.md) и [Outputs](../topics/outputs.md)." + +#: ../../src/topics/command-line-tool.md:68 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "Доступ к сети" + +#: ../../src/topics/command-line-tool.md:69 +#: e3bdaceae8784ab0807b2cf356a98580 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" +"Указывает, требуется ли процессу исходящий доступ к сети IPv4/IPv6. Если " +"инструмент командной строки написан вручную в CWL v1.1+, необходимо указать, " +"когда требуется доступ к сети." + +#: ../../src/topics/command-line-tool.md:83 +#: ed521ac365db4a6ba5a1051fbaa2932e +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" +"Инструменты командной строки CWL v1.0, обновленные до v1.1 или v1.2, " +"получают доступ к сети автоматически." + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "Создание файлов во время выполнения" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" +"Иногда требуется создать файл на лету из входных параметров, например, для " +"инструментов, которые ожидают, что их входная конфигурация будет считана из " +"файла, а не из параметров командной строки, или для небольших сценариев " +"оболочки-обертки." + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" +"Для генерации таких файлов мы можем использовать `InitialWorkDirRequirement`." + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +#, fuzzy +msgid "`createfile.cwl`" +msgstr "`createfile.cwl`" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" +"Любые [выражения](../topics/expressions.md) типа `$(inputs.message)` " +"расширяются движком CWL перед созданием файла. Здесь вставьте значение во " +"входной `message`." + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" +"Выражения _CWL_ не зависят от переменных оболочки, используемых в дальнейшем " +"при вызове инструментов командной строки. Это означает, что любая реальная " +"потребность в символе `$` должна быть **эскейпирована** с помощью `\\`. " +"Например, `\\${PREFIX}` выше расширено до `${PREFIX}` в сгенерированном " +"файле, чтобы быть оцененным сценарием оболочки, а не движком CWL." + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" +"Чтобы протестировать вышеупомянутый инструмент CWL, используйте это задание " +"для предоставления входного значения `message`:" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 +#, fuzzy +msgid "`echo-job.yml`" +msgstr "`echo-job.yml`" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" +"Прежде чем приступить к выполнению, давайте рассмотрим каждый шаг немного " +"подробнее. Базовая команда `baseCommand: [\"sh\", \"example.sh\"]` выполнит " +"команду `sh example.sh`. Это приведет к запуску файла, который мы создали в " +"оболочке." + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" +"Для `InitialWorkDirRequirement` требуется `список`. Поскольку `список` - это " +"массив YAML, нам нужен `-` в первой строке каждого элемента массива, в " +"данном случае у нас только один элемент. `Имя входа:` может иметь любое " +"значение, но оно должно совпадать с тем, что было указано в `базовой команде`" +". Последняя часть - `entry:`, за ней следует `|-`, что является синтаксисом " +"кавычек YAML и означает, что вы используете многострочную строку (без этого " +"нам пришлось бы писать весь скрипт в одну строку)." + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" +"Подробнее о форматировании см. в [Руководстве по YAML](../topics/yaml-" +"guide.md#maps)." + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" +"Теперь вызовите `cwltool` с описанием инструмента и входным объектом в " +"командной строке:" + +#: ../../src/topics/custom-types.md:1 +#: cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "Пользовательские типы" + +#: ../../src/topics/custom-types.md:3 +#: 67573252cc064b27ab13eebc468ac58a +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" +"Иногда вы можете захотеть написать собственные пользовательские типы для " +"использования в описаниях CWL. Использование таких пользовательских типов " +"может уменьшить избыточность между несколькими описаниями, использующими " +"один и тот же тип, а также позволяет дополнительно настраивать/" +"конфигурировать инструмент/анализ, не прибегая к непосредственной работе с " +"описанием CWL." + +#: ../../src/topics/custom-types.md:9 +#: 73e68b3af9cf41338d843c0c40e50cdc +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" +"Ниже приведен пример CWL-описания инструмента [biom convert format][biom] " +"для преобразования стандартного файла таблицы biom в формат hdf5." + +#: ../../src/topics/custom-types.md:12 +#: ef5f35acb97f4ddfad7b688712f53484 +#, fuzzy +msgid "`custom-types.cwl`" +msgstr "`custom-types.cwl`" + +#: ../../src/topics/custom-types.md:18 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c +#, fuzzy +msgid "`custom-types.yml`" +msgstr "`custom-types.yml`" + +#: ../../src/topics/custom-types.md:24 +#: a999b1acda2641598086648c64aa3831 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" +"___Примечание:___Чтобы следовать приведенному ниже примеру, вам необходимо " +"[скачать входной файл примера](https://github.com/common-workflow-language/" +"user_guide/blob/main/src/_includes/cwl/custom-types/" +"rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom*, например, с " +"помощью `wget`:" + +#: ../../src/topics/custom-types.md:30 +#: f8c12a58cb0b46a488823c6ae95f25ea +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" +"В строке 29 в `inputs:table_type` в качестве пользовательского объекта " +"импортируется список допустимых параметров таблицы, которые будут " +"использоваться при преобразовании таблицы:" + +#: ../../src/topics/custom-types.md:46 +#: f25a63e0926d4932bbe64b2e4bdabf9e +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" +"Ссылка на пользовательский тип представляет собой комбинацию имени файла, в " +"котором определен объект (`biom-convert-table.yaml`), и имени объекта в этом " +"файле (`table_type`), определяющего пользовательский тип. В этом случае " +"массив `символов` из импортированного файла `biom-convert-table.yaml` " +"определяет допустимые опции таблицы. Например, в `custom-types.yml` мы " +"передаем `OTU table` в качестве `входа`, который указывает инструменту " +"создать таблицу OTU в формате hdf5." + +#: ../../src/topics/custom-types.md:53 +#: b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" +"Ниже приведено содержимое YAML-файла, описывающего пользовательский тип:" + +#: ../../src/topics/custom-types.md:55 +#: fecfbb44456640d8ba05e519bf2ff564 +#, fuzzy +msgid "`biom-convert-table.yaml`" +msgstr "`biom-convert-table.yaml`" + +#: ../../src/topics/custom-types.md:61 +#: d718630a296545f3a989c8c71e9ddc77 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" +"Чтобы пользовательский тип мог использоваться в описании CWL, он должен быть " +"импортирован. Импорт описывается в `requirements:SchemaDefRequirement`, как " +"показано ниже в примере описания `custom-types.cwl`:" + +#: ../../src/topics/custom-types.md:76 +#: 9a97acd430064710bcdf76edbd9f711c +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" +"Обратите внимание, что автор описания CWL также включил в него " +"`ResourceRequirement`, указав минимальный объем оперативной памяти и " +"количество ядер, необходимых для успешной работы инструмента, а также " +"сведения о версии программного обеспечения, для которого было написано " +"описание, и другие полезные метаданные. Более подробно эти функции " +"рассматриваются в других главах данного руководства пользователя." + +#: ../../src/topics/environment-variables.md:1 +#: 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "Переменные среды" + +#: ../../src/topics/environment-variables.md:3 +#: 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" +"Инструменты работают в ограниченном окружении и не наследуют большинство " +"переменных окружения от родительского процесса. Вы можете задать переменные " +"окружения для инструмента с помощью `EnvVarRequirement`." + +#: ../../src/topics/environment-variables.md:7 +#: bfdebb32440a4034beb42135e38884e8 +#, fuzzy +msgid "`env.cwl`" +msgstr "`env.cwl`" + +#: ../../src/topics/expression-tool.md:1 +#: 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "Экспресс-инструмент" + +#: ../../src/topics/expression-tool.md:3 +#: 48deb71f361a43e48a56ed483075bca8 +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" +"Инструмент выражения - это тип процесса, который можно запускать " +"самостоятельно или в качестве шага рабочего процесса. Он выполняет чистое " +"выражение JavaScript. Его можно использовать как способ изолировать сложные " +"выражения JavaScript, которые должны оперировать входными данными и выдавать " +"на выходе некоторый результат." + +#: ../../src/topics/expression-tool.md:8 +#: 716b56506ca7470299899c5d820a9ea2 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" +"Как и инструмент командной строки, он требует `входов` и `выходов`. Но " +"вместо `baseCommand` ему требуется атрибут `expression`." + +#: ../../src/topics/expression-tool.md:17 +#: b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "Средство выражения CWL." + +#: ../../src/topics/expression-tool.md:48 +#: 39727e9058f24b62b8746a46d3f812c2 +#, fuzzy +msgid "`uppercase.cwl`" +msgstr "`uppercase.cwl`" + +#: ../../src/topics/expression-tool.md:67 +#: e3ecac0a8e604f2b98a2a12b0579990a +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" +"Мы должны были использовать `InlineJavascriptRequirement`, поскольку наше " +"выражение содержит вызов JavaScript в `.toUpperCase()`. Это означает для " +"инструментов, использующих инструмент выражения, что JavaScript является " +"требованием." + +#: ../../src/topics/expressions.md:1 +#: c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "Выражения" + +#: ../../src/topics/expressions.md:3 +#: 007a345b4bad49cf996c4301b8386473 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" +"Если вам нужно манипулировать входными параметрами, включите требование " +"`InlineJavascriptRequirement`, а затем везде, где ссылка на параметр " +"является законной, вы можете предоставить фрагмент Javascript, который будет " +"оценен CWL runner'ом." + +#: ../../src/topics/expressions.md:9 +#: 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" +"Выражения JavaScript следует использовать только в случае крайней " +"необходимости. При манипуляциях с именами файлов, расширениями, путями и т. " +"д. подумайте, нельзя ли вместо этого использовать одно из " +"[встроенных свойств `File`][file-prop], например `basename`, `nameroot`, " +"`nameext` и т. д. См. [список лучших практик](best-practices.md)." + +#: ../../src/topics/expressions.md:16 +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +#, fuzzy +msgid "`expression.cwl`" +msgstr "`expression.cwl`" + +#: ../../src/topics/expressions.md:22 +#: efb5fd14988c4e2a8f834ee5369d4102 +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" +"Поскольку этот инструмент не требует никаких `входных данных`, мы можем " +"запустить его с (почти) пустым файлом задания:" + +#: ../../src/topics/expressions.md:25 +#: e833649b951841c49397796f996d29f3 +#, fuzzy +msgid "`empty.yml`" +msgstr "`empty.yml`" + +#: ../../src/topics/expressions.md:31 +#: 276f688ba7cc471a842f085ca852b1d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" +"`empty.yml` содержит описание пустого JSON-объекта. Описания JSON-объектов " +"содержатся внутри фигурных скобок `{}`, поэтому пустой объект представляется " +"просто набором пустых скобок." + +#: ../../src/topics/expressions.md:35 +#: ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "Затем мы можем запустить `expression.cwl`:" + +#: ../../src/topics/expressions.md:37 +#: 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "Запуск `expression.cwl`" + +#: ../../src/topics/expressions.md:47 +#: 8b70a1ad70514039b97164fa630c12e4 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" +"Обратите внимание, что требования могут быть представлены с помощью " +"синтаксиса map, как в примере выше:" + +#: ../../src/topics/expressions.md:54 +#: 2f28ab412d2843ffa5f14acdc01fc732 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" +"Или в виде массива, в котором каждая запись (в данном случае только `class: " +"InlineJavascriptRequirement`) отмечена символом `-`. Тот же синтаксис " +"используется для описания дополнительных аргументов командной строки." + +#: ../../src/topics/expressions.md:62 +#: d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "Где разрешены выражения JavaScript?" + +#: ../../src/topics/expressions.md:64 +#: cbec9277b5004e50af2728cbda0df740 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" +"Так же, как и [ссылки на параметры](parameter-references.md), вы можете " +"использовать выражения JavaScript только в определенных полях. К ним " +"относятся:" + +#: ../../src/topics/expressions.md:66 +#: e259f55f8000479bbd8009e25cf0ca6c +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" +"Из [`CommandLineTool`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandLineTool)" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 +msgid "`arguments`" +msgstr "`аргументы`" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 +#, fuzzy +msgid "`valueFrom`" +msgstr "`valueFrom`" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +#, fuzzy +msgid "`stdin`" +msgstr "`stdin`" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +#, fuzzy +msgid "`stdout`" +msgstr "`stdout`" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +#, fuzzy +msgid "`stderr`" +msgstr "`stderr`" + +#: ../../src/topics/expressions.md:72 +#: 8210b36347a749889450529ecdf4ff0e +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" +"Из [CommandInputParameter](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandInputParameter)" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "`формат`" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae +#, fuzzy +msgid "`secondaryFiles`" +msgstr "`secondaryFiles`" + +#: ../../src/topics/expressions.md:75 +#: 23088850ad02459696f6bbd385109aac +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" +"Из [`inputBinding`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandLineBinding)" + +#: ../../src/topics/expressions.md:77 +#: f02257a822ad46ac93c5981531cc85d5 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" +"Из [CommandOutputParamater](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandOutputParameter)" + +#: ../../src/topics/expressions.md:80 +#: 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" +"Из [CommandOutputBinding](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandOutputBinding)" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +#, fuzzy +msgid "`glob`" +msgstr "`glob`" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b +#, fuzzy +msgid "`outputEval`" +msgstr "`outputEval`" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c +msgid "From `Workflow`" +msgstr "Из `Рабочего процесса`" + +#: ../../src/topics/expressions.md:84 +#: d289541e460147aa933f7878996f8649 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" +"Из [InputParameter](https://www.commonwl.org/v1.0/" +"Workflow.html#InputParameter) и [WorkflowOutputParameter](https://" +"www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c +msgid "From `steps`" +msgstr "От `шагов`" + +#: ../../src/topics/expressions.md:88 +#: 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" +"Из [WorkflowStepInput](https://www.commonwl.org/v1.0/" +"Workflow.html#WorkflowStepInput)" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "" +"Из [ExpressionTool](https://www.commonwl.org/v1.0/" +"Workflow.html#ExpressionTool)" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf +msgid "`expression`" +msgstr "`выражение`" + +#: ../../src/topics/expressions.md:92 +#: f495da32f05a4a5ba9539be0a54c1a59 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" +"Из [InputParameter](https://www.commonwl.org/v1.0/" +"Workflow.html#InputParameter) и [ExpressionToolOutputParameter](https://" +"www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" + +#: ../../src/topics/expressions.md:95 +#: bdb4c68a175047ddbe141ca24960127f +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" +"Из [`ResourceRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#ResourceRequirement)" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +#, fuzzy +msgid "`coresMin`" +msgstr "`coresMin`" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 +#, fuzzy +msgid "`coresMax`" +msgstr "`coresMax`" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 +#, fuzzy +msgid "`ramMin`" +msgstr "`ramMin`" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +#, fuzzy +msgid "`ramMax`" +msgstr "`ramMax`" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +#, fuzzy +msgid "`tmpdirMin`" +msgstr "`tmpdirMin`" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +#, fuzzy +msgid "`tmpdirMax`" +msgstr "`tmpdirMax`" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +#, fuzzy +msgid "`outdirMin`" +msgstr "`outdirMin`" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 +#, fuzzy +msgid "`outdirMax`" +msgstr "`outdirMax`" + +#: ../../src/topics/expressions.md:104 +#: 97b61352363f47cb890e8937c5613fa3 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" +"Из [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "`список`" + +#: ../../src/topics/expressions.md:106 +#: 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "в [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 +msgid "`entry`" +msgstr "`вход`" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +#, fuzzy +msgid "`entryname`" +msgstr "`entryname`" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "Из `EnvVarRequirement`" + +#: ../../src/topics/expressions.md:110 +#: 0bc424ef2ca346099f29b937379908a0 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" +"Из [EnvironmentDef](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#EnvironmentDef)" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 +#, fuzzy +msgid "`envValue`" +msgstr "`envValue`" + +#: ../../src/topics/expressions.md:116 +#: 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" +"Использование внешних библиотек и встроенного кода JavaScript с помощью " +"`expressionLib`" + +#: ../../src/topics/expressions.md:118 +#: 29b73e1dd72744f68377f0a38c10f062 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" +"Требование `InlineJavascriptRequirement` поддерживает атрибут `expressionLib`" +", который позволяет пользователям загружать внешние файлы JavaScript или " +"предоставлять встроенный код JavaScript." + +#: ../../src/topics/expressions.md:122 +#: 38a2afaf4a6c4d04909af22c93f2808d +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" +"Записи, добавленные в атрибут `expressionLib`, анализируются JavaScript-" +"движком программы запуска CWL. Это может быть использовано для включения " +"внешних файлов или создания функций JavaScript, которые могут быть вызваны в " +"других частях документа CWL." + +#: ../../src/topics/expressions.md:128 +#: cd74f34b21af4de9be96fd897efc469b +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" +"В стандартах CWL (версии 1.0 - 1.2) [указано](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#Expressions), что единственной версией JavaScript, " +"допустимой в выражениях CWL, является [ECMAScript 5.1](https://" +"262.ecma-international.org/5.1/). Это означает, что любой код, который вы " +"включаете или пишете в документе CWL, должен соответствовать ECMAScript 5.1." + +#: ../../src/topics/expressions.md:135 +#: f12e371f3f1a4b0cb2cff9800352d48c +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" +"Например, мы можем использовать `InlineJavascriptRequirement` и записать " +"функцию JavaScript в строку в `expressionLib`. Затем эта функция может быть " +"использована в других частях документа CWL:" + +#: ../../src/topics/expressions.md:139 +#: 49d0fda2fc144e0b8b7c92afc1d8945e +#, fuzzy +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "`hello-world-expressionlib-inline.cwl`" + +#: ../../src/topics/expressions.md:146 +#: 8f0e8f050e334ac08334e9215e1dcf61 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" +"Запуск этого рабочего процесса CWL вызовет функцию JavaScript и приведет к " +"тому, что команда `echo` напечатает входное сообщение с заглавными буквами:" + +#: ../../src/topics/expressions.md:149 +#: 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "Запуск `hello-world-expressionlib-inline.cwl`." + +#: ../../src/topics/expressions.md:155 +#: 7a6be0005a6441feb67f036d005d7885 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" +"Давайте перенесем функцию `capitalizeWords` во внешний файл, `custom-" +"functions.js`, и импортируем ее в наш CWL-документ:" + +#: ../../src/topics/expressions.md:158 +#: ed590f9e6f4f425da886b110295c45db +#, fuzzy +msgid "`custom-functions.js`" +msgstr "`custom-functions.js`" + +#: ../../src/topics/expressions.md:164 +#: 093235307d6f47d4858e559b780ef5e5 +#, fuzzy +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "`hello-world-expressionlib-external.cwl`" + +#: ../../src/topics/expressions.md:171 +#: 06635145b441418aaae84dc804f3d6ac +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" +"Файл `custom-functions.js` включается в документ CWL с помощью оператора " +"`$include: custom-functions.js`. Это делает функции и переменные доступными " +"для использования в других частях документа CWL." + +#: ../../src/topics/expressions.md:175 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "Запускаем `hello-world-expressionlib-external.cwl`." + +#: ../../src/topics/expressions.md:181 +#: 04eaf1f7c630450db318dcd8b7626e15 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" +"Наконец, обратите внимание, что в документе CWL может присутствовать как " +"встроенный, так и внешний код JavaScript. В этом последнем примере мы " +"добавили еще одну запись в атрибут `expressionLib` с новой функцией " +"`createHelloWorldMessage`, которая вызывает функцию `capitalizeWords` из " +"внешнего файла `custom-functions.js`." + +#: ../../src/topics/expressions.md:186 +#: c4098489fbb049789f022cd3e5c3d49b +#, fuzzy +msgid "`hello-world-expressionlib.cwl`" +msgstr "`hello-world-expressionlib.cwl`" + +#: ../../src/topics/expressions.md:193 +#: 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "Запуск `hello-world-expressionlib.cwl`." + +#: ../../src/topics/expressions.md:200 +#: fd4579a3c9844492b314b5c3c1775fc7 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" +"Оператор `$include` можно использовать для включения файла с локального " +"диска или из удаленного места. Он работает как с относительными, так и с " +"абсолютными путями. Прочитайте [текст о `$include`](https://www.commonwl.org/" +"v1.0/SchemaSalad.html#Include) из спецификации CWL, чтобы узнать о нем " +"больше." + +#: ../../src/topics/file-formats.md:1 +#: 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "Форматы файлов" + +#: ../../src/topics/file-formats.md:3 +#: e024bcb70e04412e90e1838426d1b69a +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" +"Инструменты и рабочие процессы могут принимать типы `File` на вход и " +"выдавать их на выход. Мы также рекомендуем указывать формат типов `File`. " +"Это поможет задокументировать другим, как использовать ваш инструмент, а вам " +"позволит выполнить простую проверку типов при создании файлов параметров." + +#: ../../src/topics/file-formats.md:8 +#: a3db21c0b3114802a8a5b610e252ef13 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" +"В отношении форматов файлов мы рекомендуем ссылаться на существующие " +"онтологии (например, EDAM в нашем примере), ссылаться на локальную онтологию " +"вашего учреждения или не добавлять формат файла изначально, чтобы быстро " +"разработать его, прежде чем предоставлять свой инструмент другим. Вы можете " +"просмотреть существующие списки [IANA file format listings][IANA] и " +"[EDAM file format listings][EDAM] на их веб-сайтах." + +#: ../../src/topics/file-formats.md:14 +#: 0f5bc8520d6a4dafa37c65343da9702a +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" +"В следующем уроке мы более подробно расскажем о разделах `$namespaces` и " +"`$schemas`, так что пока не беспокойтесь об этом." + +#: ../../src/topics/file-formats.md:17 +#: 5cb830da47464a8b9c3950983fa4d56f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" +"Обратите внимание, что для дополнительной пользы `cwltool` может выполнять " +"некоторые базовые рассуждения на основе форматов файлов и предупреждать вас, " +"если есть очевидные несоответствия." + +#: ../../src/topics/file-formats.md:20 +#: 0535d5de416b4ea3b2f5996583deecc1 +#, fuzzy +msgid "`metadata_example.cwl`" +msgstr "`metadata_example.cwl`" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "Эквивалентом этого описания CWL в формате командной строки является:" + +#: ../../src/topics/file-formats.md:32 +#: 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "Образцы файлов параметров" + +#: ../../src/topics/file-formats.md:34 +#: a2ce43b391864e8bbde16328cc19b32b +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" +"Ниже приведен пример файла параметров для приведенного выше примера. Мы " +"рекомендуем присылать рабочие примеры файлов параметров для вашего " +"инструмента. Это позволит другим быстро работать с вашим инструментом, " +"начиная с \"заведомо хорошей\" параметризации." + +#: ../../src/topics/file-formats.md:39 +#: aebee48b742c4145a600fd2daf8c75dc +#, fuzzy +msgid "`sample.yml`" +msgstr "`sample.yml`" + +#: ../../src/topics/file-formats.md:45 +#: 56ee4dcfff6141d5bef80eb96559876d +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" +"___Примечание:___ Чтобы выполнить приведенный ниже пример, необходимо " +"загрузить входной файл примера, *file-formats.bam*. Этот файл доступен по " +"адресу и может быть загружен, " +"например, с помощью `wget`:" + +#: ../../src/topics/index.md:1 +#: 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "Темы" + +#: ../../src/topics/inputs.md:1 +#: 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "Входы" + +#: ../../src/topics/inputs.md:3 +#: d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "Основные входные параметры" + +#: ../../src/topics/inputs.md:5 +#: 96671c56523c4ea9992fb5dfcfa6490e +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" +"В `входах` инструмента содержится список входных параметров, которые " +"определяют, как запустить инструмент. Каждый параметр имеет `id` для " +"названия параметра и `type`, описывающий, какие типы значений допустимы для " +"этого параметра." + +#: ../../src/topics/inputs.md:9 +#: bcc6246742cb46bfb185e415c4a3431a +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" +"Доступные примитивные типы - *string*, *int*, *long*, *float*, *double* и " +"*null*; сложные типы - *array* и *record*; кроме того, есть специальные типы " +"*File*, *Directory* и *Any*." + +#: ../../src/topics/inputs.md:13 +#: 86dce36de687449c88fb5eb9d64eb045 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" +"Следующий пример демонстрирует некоторые входные параметры, имеющие " +"различные типы и по-разному отображающиеся в командной строке." + +#: ../../src/topics/inputs.md:16 +#: cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "Сначала создайте файл `inp.cwl`, содержащий следующее:" + +#: ../../src/topics/inputs.md:18 +#: 8bdb875b63104f699efe28ea0abb1e3d +#, fuzzy +msgid "`inp.cwl`" +msgstr "`inp.cwl`" + +#: ../../src/topics/inputs.md:24 +#: c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "Создайте файл с именем `inp-job.yml`:" + +#: ../../src/topics/inputs.md:26 +#: dc5e6b5e01d64226bd5dbbf3175fe010 +#, fuzzy +msgid "`inp-job.yml`" +msgstr "`inp-job.yml`" + +#: ../../src/topics/inputs.md:33 +#: 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" +"Вы можете использовать `cwltool` для создания шаблонного объекта ввода. Это " +"избавит вас от необходимости вводить все входные параметры в файл объекта " +"ввода:" + +#: ../../src/topics/inputs.md:40 +#: 7dc630ea86464b1dba3a4e5079260b3b +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" +"Вы можете перенаправить вывод в файл, например, `cwltool --make-template " +"inp.cwl > inp-job.yml`, а затем изменить значения по умолчанию на нужные вам " +"входные значения." + +#: ../../src/topics/inputs.md:44 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" +"Обратите внимание, что \"example_file\", как тип `File`, должен быть " +"предоставлен в виде объекта с полями `class: File` и `path`." + +#: ../../src/topics/inputs.md:47 +#: 651e032007ea4a119d20c820bb61f86b +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" +"Затем создайте файл whale.txt с помощью [touch], набрав в командной строке `" +"touch whale.txt`." + +#: ../../src/topics/inputs.md:53 +#: 0b056dde9e87428996e47870b12119da +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" +"Теперь вызовите `cwltool` с описанием инструмента и входным объектом в " +"командной строке, используя команду `cwltool inp.cwl inp-job.yml`. В " +"следующем тексте в рамке описаны эти две команды и ожидаемый вывод из " +"командной строки:" + +#: ../../src/topics/inputs.md:64 +#: 628124a1670b4b058bb0fb6e495a099c +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" +"Программа запуска ссылок на CWL (cwltool) и другие программы создают " +"временные каталоги с символическими (\"мягкими\") ссылками на ваши входные " +"файлы, чтобы гарантировать, что инструменты не получат случайный доступ к " +"файлам, которые не были явно указаны" + +#: ../../src/topics/inputs.md:70 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" +"Поле `inputBinding` является необязательным и указывает, должен ли входной " +"параметр отображаться в командной строке инструмента. Если `inputBinding` " +"отсутствует, параметр не отображается в командной строке. Давайте " +"рассмотрим каждый пример подробнее." + +#: ../../src/topics/inputs.md:83 +#: ec2adb3912bc46e28891229e9e0d9a1c +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" +"Булевы типы рассматриваются как флаг. Если входной параметр \"example_flag\"" +" равен \"true\", то в командную строку будет добавлен `prefix`. Если false, " +"то флаг не добавляется." + +#: ../../src/topics/inputs.md:95 +#: a519be60726a44af9941fdce04735353 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" +"Строковые типы отображаются в командной строке как литеральные значения. " +"Префикс ` необязателен, если он указан, то отображается как отдельный " +"аргумент в командной строке перед параметром . В приведенном выше примере " +"это выглядит как `--пример строки hello`." + +#: ../../src/topics/inputs.md:109 +#: cb8fc8c4c79e467eac5fab4ca685201e +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" +"Целочисленные типы (и типы с плавающей точкой) отображаются в командной " +"строке в десятичном текстовом представлении. Когда опция `separate` равна " +"false (по умолчанию значение true), префикс и значение объединяются в один " +"аргумент. В приведенном выше примере это выглядит как `-i42`." + +#: ../../src/topics/inputs.md:124 +#: a26cc105716f47cb807174c9003153b0 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" +"Типы файлов отображаются в командной строке в виде пути к файлу. Если тип " +"параметра заканчивается вопросительным знаком `?`, это означает, что " +"параметр необязателен. В приведенном выше примере это выглядит как `--file=/" +"tmp/random/path/whale.txt`. Однако если бы параметр \"example_file\" не был " +"указан во входных данных, в командной строке ничего бы не появилось." + +#: ../../src/topics/inputs.md:131 +#: cc159dd5fe5748caac838862f5b8c4d1 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" +"Входные файлы доступны только для чтения. Если вы хотите обновить входной " +"файл, вы должны [сначала скопировать его в выходной каталог](staging-input-" +"files.md)." + +#: ../../src/topics/inputs.md:134 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" +"Значение `position` используется для определения места появления параметра в " +"командной строке. Позиции являются относительными друг к другу, а не " +"абсолютными. В результате, позиции не обязательно должны быть " +"последовательными, три параметра с позициями 1, 3, 5 приведут к той же " +"командной строке, что и 1, 2, 3. Более одного параметра могут иметь " +"одинаковую позицию (связи разрываются с помощью имени параметра), а само " +"поле позиции является необязательным. Позиция по умолчанию равна 0." + +#: ../../src/topics/inputs.md:142 +#: 6812698e9ad84d3385de5e88e9dde0b3 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" +"Поле `baseCommand` всегда будет отображаться в конечной командной строке " +"перед параметрами." + +#: ../../src/topics/inputs.md:146 +#: 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "Входы массива" + +#: ../../src/topics/inputs.md:148 +#: d1f02be278754267893dfce5a940997d +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" +"В командную строку легко добавлять массивы входных параметров, " +"представленных в виде массива. Существует два способа указать параметр " +"массива. Первый - указать поле `type` с `type: array` и `items`, " +"определяющими допустимые типы данных, которые могут присутствовать в " +"массиве. В качестве альтернативы после имени типа можно добавить скобки `[]`" +", чтобы указать, что входной параметр является массивом данного типа." + +#: ../../src/topics/inputs.md:154 +#: 01f30e38dfdd452dba3a996073936e16 +#, fuzzy +msgid "`array-inputs.cwl`" +msgstr "`array-inputs.cwl`" + +#: ../../src/topics/inputs.md:160 +#: 787d4bfb093c4ad287b902084706b751 +#, fuzzy +msgid "`array-inputs-job.yml`" +msgstr "`array-inputs-job.yml`" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" +"Теперь вызовите `cwltool`, указав в командной строке описание инструмента и " +"входной объект:" + +#: ../../src/topics/inputs.md:178 +#: 75d59e395c66416cae9b352db5081516 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" +"Поле `inputBinding` может находиться как в определении внешнего параметра " +"массива, так и в определении внутреннего элемента массива, что приводит к " +"различному поведению при построении командной строки, как показано выше. " +"Кроме того, поле `itemSeparator`, если оно задано, указывает, что значения " +"массива должны быть объединены в один аргумент, разделенный строкой-" +"разделителем элементов." + +#: ../../src/topics/inputs.md:185 +#: 874c6f19abbf45d7ab7d30a378c4048d +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" +"Обратите внимание, что массивы входных данных указываются внутри квадратных " +"скобок `[]` в файле `array-inputs-job.yml`. Массивы также могут быть " +"выражены в нескольких строках, при этом значения массива, которые не " +"определены с соответствующим ключом, помечаются ведущим `-`. Это будет " +"продемонстрировано в следующем уроке и более подробно рассмотрено в " +"[Руководстве по YAML](yaml-guide.md#arrays). Вы можете указывать массивы " +"массивов, массивы записей и другие сложные типы." + +#: ../../src/topics/inputs.md:191 +#: 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "Инклюзивные и эксклюзивные входы" + +#: ../../src/topics/inputs.md:193 +#: dea0d4b681f94e73b13965dcfe75cf7d +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" +"Иногда базовый инструмент имеет несколько аргументов, которые должны быть " +"предоставлены вместе (они зависимы) или несколько аргументов, которые не " +"могут быть предоставлены вместе (они исключительны). Для описания этих двух " +"условий можно использовать записи и объединения типов, чтобы сгруппировать " +"параметры." + +#: ../../src/topics/inputs.md:198 +#: ddf598abf4f34aca9fffa045860fbf96 +#, fuzzy +msgid "`record.cwl`" +msgstr "`record.cwl`" + +#: ../../src/topics/inputs.md:204 +#: d52a8089920e45bd89d582533b50e3a1 +#, fuzzy +msgid "`record-job1.yml`" +msgstr "`record-job1.yml`" + +#: ../../src/topics/inputs.md:215 +#: 750474486a84482292eeba45f118287f +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" +"В первом примере вы не можете предоставить `пунктА`, не предоставив также " +"`пунктВ`." + +#: ../../src/topics/inputs.md:217 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +#, fuzzy +msgid "`record-job2.yml`" +msgstr "`record-job2.yml`" + +#: ../../src/topics/inputs.md:233 +#: 1eb0e39bb6d04b8cab300f44a79f3add +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" +"Во втором примере `itemC` и `itemD` являются эксклюзивными, поэтому только " +"первый совпадающий элемент (`itemC`) будет добавлен в командную строку, а " +"оставшийся элемент (`itemD`) будет проигнорирован." + +#: ../../src/topics/inputs.md:236 +#: bc21ee10bff843689cc98ac6630edcea +#, fuzzy +msgid "`record-job3.yml`" +msgstr "`record-job3.yml`" + +#: ../../src/topics/inputs.md:252 +#: 4b2ab812f62c4f949dd25c8527f2411c +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" +"В третьем примере указан только `itemD`, поэтому он появляется в командной " +"строке." + +#: ../../src/topics/inputs.md:255 +#: b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "Исключение входных параметров с помощью выражений" + +#: ../../src/topics/inputs.md:257 +#: 2c3b884cb1c54521900cc90782e8a58d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" +"Если вы используете эксклюзивные входные параметры в сочетании с " +"выражениями, вы должны знать, что объект JavaScript `inputs` будет содержать " +"одно из эксклюзивных входных значений. Это означает, что вам может " +"понадобиться использовать булевый оператор **or**, чтобы проверить, какие " +"значения присутствуют." + +#: ../../src/topics/inputs.md:262 +#: a1073b6306044dffb414319ae01f68bb +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" +"Рассмотрим пример, содержащий эксклюзивный входной параметр `file_format`, " +"который принимает значение `null` (т.е. значение не предоставляется) или " +"любое значение из перечисления." + +#: ../../src/topics/inputs.md:265 +#: 4a31c733092142b1af834eab1747c224 +#, fuzzy +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "`exclusive-parameter-expressions.cwl`" + +#: ../../src/topics/inputs.md:271 +#: 9a1d92334685449386dfa3b3a899ed48 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" +"Обратите внимание, что выражение JavaScript использует значение " +"исключительного входного параметра, не принимая во внимание значение `null`. " +"Если вы предоставите корректное значение, например \"fasta\" (одно из " +"значений перечисления), ваша команда будет выполнена успешно:" + +#: ../../src/topics/inputs.md:280 +#: fb623af4c480411b8fde28d01c981411 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" +"Однако если вы не предоставите никакого входного значения, то `file_format` " +"будет оценен как `null`, что не соответствует ожидаемому типу выходного поля " +"(`string`), что приведет к неудаче при запуске рабочего процесса." + +#: ../../src/topics/inputs.md:289 +#: e98e165f6bba40809c90473d72f9d592 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" +"Чтобы исправить это, нужно не забывать использовать оператор or в выражении " +"JavaScript при использовании эксклюзивных параметров или любых параметров, " +"допускающих `null`. Например, выражение можно изменить на `$(" +"inputs.file_format || 'auto')`, чтобы иметь значение по умолчанию, если оно " +"не было указано в командной строке или входном файле задания." + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "Метаданные и авторство" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" +"Расширения реализации, не требуемые для корректного выполнения (например, " +"поля, связанные с представлением графического интерфейса), и метаданные о " +"самом инструменте или рабочем процессе (например, авторство для " +"использования в цитировании) могут быть предоставлены в качестве " +"дополнительных полей любого объекта. Такие поля расширения (например, " +"`format: edam:format_2572`) могут использовать префикс пространства имен, " +"перечисленный в разделе `$namespaces` документа (например, edam: http://" +"edamontology.org/), как описано в [Schema Salad specification][schema-salad]" +". После добавления префикса пространства имен вы можете обращаться к нему в " +"любом месте документа, как показано ниже. В противном случае необходимо " +"использовать полные URL: `формат: http://edamontology.org/format_2572`." + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" +"Для всех разработчиков мы рекомендуем следующие минимальные метаданные для " +"вашего инструмента и рабочих процессов. Этот пример включает метаданные, " +"позволяющие другим пользователям ссылаться на ваш инструмент." + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +#, fuzzy +msgid "`metadata_example2.cwl`" +msgstr "`metadata_example2.cwl`" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "Расширенный пример" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" +"Для тех, кто очень мотивирован, есть возможность аннотировать свой " +"инструмент гораздо большим количеством метаданных. Этот пример включает теги " +"онтологии EDAM в качестве ключевых слов (что позволяет группировать " +"связанные инструменты), намеки на требования к аппаратному обеспечению для " +"использования инструмента и еще несколько полей метаданных." + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +#, fuzzy +msgid "`metadata_example3.cwl`" +msgstr "`metadata_example3.cwl`" + +#: ../../src/topics/operations.md:1 +#: 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "Операции" + +#: ../../src/topics/operations.md:3 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" +"Операция - это тип процесса CWL, такой же, как рабочий процесс, инструмент " +"командной строки или инструмент выражений. Это шаг рабочего процесса, " +"который определяет входы и выходы, но не предоставляет достаточно информации " +"для выполнения." + +#: ../../src/topics/operations.md:7 +#: 5565c1b2d8a349169a305a9b26b4574d +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" +"Вы можете создавать операции для визуализации рабочего процесса во время " +"разработки, прежде чем вы будете готовы отправить рабочий процесс в CWL " +"runner:" + +#: ../../src/topics/operations.md:10 +#: 49cf614893d8438299b3bca384eb40cf +#, fuzzy +msgid "`operations.cwl`" +msgstr "`operations.cwl`" + +#: ../../src/topics/operations.md:16 +#: 88160cef4cfa4add9020aa89511a5749 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" +"Шаг `uppercase` рабочего процесса - это операция. Ее можно использовать как " +"инструмент командной строки или выражение. Вы также можете построить график " +"с помощью CWL Viewer или `cwltool`:" + +#: ../../src/topics/operations.md:24 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" +"Вывод команды выше может быть отображен с помощью рендерера Graphviz. " +"Следующее изображение отображается с помощью директивы Sphinx Graphviz (это " +"руководство пользователя построено с помощью Sphinx):" + +#: ../../src/topics/operations.md:55 +#: 730ba1434a1445ae847ec6153b6a3b72 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" +"Если вы попытаетесь запустить ее с помощью `cwltool`, команда завершится " +"неудачей, поскольку `cwltool` не имеет достаточно информации, чтобы понять, " +"как ее выполнить:" + +#: ../../src/topics/operations.md:58 +#: 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "`cwltool` не знает, как выполнять операции" + +#: ../../src/topics/operations.md:66 +#: a25d0b1e13324b40a6b8fcd227948c4f +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" +"Исполнители CWL могут придумать способы привязки операций к конкретным " +"шагам. Например, CWL-прогонщик может использовать абстрактные операции с " +"идентификаторами, которые соответствуют шагам, выполняемым другим механизмом " +"рабочего процесса." + +#: ../../src/topics/outputs.md:1 +#: da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "Выходы" + +#: ../../src/topics/outputs.md:3 +#: 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "Возвращение выходных файлов" + +#: ../../src/topics/outputs.md:5 +#: d661df070e3040869da412d07a71f716 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" +"Выходные данные\" инструмента - это список выходных параметров, которые " +"должны быть возвращены после выполнения инструмента. Каждый параметр имеет " +"`id` для имени параметра и `type`, описывающий, какие типы значений " +"допустимы для этого параметра." + +#: ../../src/topics/outputs.md:10 +#: a11585474d3849cca5467512ed964743 +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" +"Когда инструмент запускается под управлением CWL, начальным рабочим " +"каталогом является назначенный выходной каталог. Инструмент или сценарий " +"должен записывать свои результаты в виде файлов, созданных в выходном " +"каталоге. Выходные параметры, возвращаемые инструментом CWL, являются либо " +"самими выходными файлами, либо получены в результате изучения содержимого " +"этих файлов." + +#: ../../src/topics/outputs.md:16 +#: 2682f9ca8e604a0c9986f7746fdec960 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" +"В следующем примере показано, как вернуть файл, извлеченный из tar-файла." + +#: ../../src/topics/outputs.md:19 +#: 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "Передача обязательных аргументов в `baseCommand`" + +#: ../../src/topics/outputs.md:21 +#: 22447a560f6f4317bf67bd7c4336126c +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" +"В предыдущих примерах `базовая команда` была просто строкой, а все аргументы " +"передавались как CWL-входы. Вместо одной строки мы можем использовать " +"_массив строк_. Первый элемент - это команда, которую нужно выполнить, а " +"все последующие элементы - обязательные аргументы командной строки" + +#: ../../src/topics/outputs.md:26 +#: f1ee2e00b0cc4112b51c9df3a919b73f +#, fuzzy +msgid "`tar.cwl`" +msgstr "`tar.cwl`" + +#: ../../src/topics/outputs.md:32 +#: ad8e1acb251246d2a47c39b20d4e483a +#, fuzzy +msgid "`tar-job.yml`" +msgstr "`tar-job.yml`" + +#: ../../src/topics/outputs.md:38 +#: dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "Затем создайте tar-файл для примера." + +#: ../../src/topics/outputs.md:45 +#: 52703d6b7f914097934bfad13663abeb +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" +"А теперь вызовите `cwltool` с описанием инструмента и входным объектом в " +"командной строке:" + +#: ../../src/topics/outputs.md:51 +#: 5e1c79df657d4a6e84e055dd6b300a5d +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" +"Поле `outputBinding` описывает, как установить значение каждого выходного " +"параметра." + +#: ../../src/topics/outputs.md:62 +#: 329d2809dfae4f90bc638f5f03a47ee3 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" +"Поле `glob` состоит из имени файла в выходном каталоге. Если вы не знаете " +"имя файла заранее, вы можете использовать подстановочный шаблон, например " +"`glob: '*.txt'`." + +#: ../../src/topics/outputs.md:65 +#: 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "Захват стандартного вывода" + +#: ../../src/topics/outputs.md:67 +#: c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" +"Чтобы захватить стандартный поток вывода инструмента, добавьте поле `stdout` " +"с именем файла, в который должен попасть поток вывода. Затем добавьте `type:" +" stdout` в соответствующий параметр вывода." + +#: ../../src/topics/outputs.md:71 +#: 9d86c03ab44841c785b924cc44727e31 +#, fuzzy +msgid "`stdout.cwl`" +msgstr "`stdout.cwl`" + +#: ../../src/topics/outputs.md:89 +#: 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "Выходы массивов" + +#: ../../src/topics/outputs.md:91 +#: 9647019d8c37466886e7aab6f176634d +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" +"Вы также можете объединить несколько выходных файлов в массив файлов с " +"помощью `glob`." + +#: ../../src/topics/outputs.md:93 +#: b9eaf21f5e014eefaae301c47dafd144 +#, fuzzy +msgid "`array-outputs.cwl`" +msgstr "`array-outputs.cwl`" + +#: ../../src/topics/outputs.md:99 +#: cffff6c43b4945daa3b2a49763bc50ae +#, fuzzy +msgid "`array-outputs-job.yml`" +msgstr "`array-outputs-job.yml`" + +#: ../../src/topics/outputs.md:112 +#: cc067051f22f433bbece08f60933e002 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" +"Как описано в [YAML Guide](yaml-guide.md#arrays), массив ожидаемых " +"результатов задается в `array-outputs-job.yml` с каждой записью, помеченной " +"ведущим `-`. Этот формат также может использоваться в описаниях CWL для " +"маркировки записей в массивах, как будет показано в нескольких последующих " +"разделах." + +#: ../../src/topics/parameter-references.md:1 +#: a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "Ссылки на параметры" + +#: ../../src/topics/parameter-references.md:3 +#: dbfe2c1123144316aa026374b0f353d3 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" +"В предыдущем примере мы извлекли файл с помощью программы \"tar\". Однако " +"этот пример был очень ограниченным, поскольку предполагалось, что " +"интересующий нас файл называется \"hello.txt\", и он был записан в файл " +"`.cwl`. Это не самый лучший способ, поскольку имя файла \"hello.txt\" может " +"меняться или зависеть от используемого входного файла (файлов). Чтобы " +"избежать этого, мы можем указать имя нужного нам файла в файле параметров " +"задания (`.yml`). В этом примере вы увидите, как динамически ссылаться на " +"значение входных параметров из других полей, что позволит нам затем указать " +"имя файла для извлечения." + +#: ../../src/topics/parameter-references.md:13 +#: 280f1a07d0ae41d7a4674504f832fcf0 +#, fuzzy +msgid "`tar-param.cwl`" +msgstr "`tar-param.cwl`" + +#: ../../src/topics/parameter-references.md:19 +#: 5c64d938862747cb9fb52515a656ce27 +#, fuzzy +msgid "`tar-param-job.yml`" +msgstr "`tar-param-job.yml`" + +#: ../../src/topics/parameter-references.md:25 +#: 074cf5d912854d8c864607cc24b15302 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" +"Создайте входные файлы и вызовите `cwltool` с описанием инструмента и " +"входным объектом в командной строке:" + +#: ../../src/topics/parameter-references.md:36 +#: 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" +"Некоторые поля допускают ссылки на параметры, заключенные в `$(...)`. Они " +"оцениваются и заменяются значением, на которое ссылаются." + +#: ../../src/topics/parameter-references.md:47 +#: b54240bb94f746bba7511633aa969db0 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" +"Ссылки записываются с использованием подмножества синтаксиса Javascript. В " +"данном примере `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])` и " +"`$(inputs['extractfile'])` эквивалентны." + +#: ../../src/topics/parameter-references.md:51 +#: 8b70a072aa87414c88e89a3e19af0a51 +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" +"Значением переменной \"inputs\" является объект ввода, предоставленный при " +"вызове инструмента CWL." + +#: ../../src/topics/parameter-references.md:54 +#: eea20f89c45f424a888178df53713b28 +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" +"Обратите внимание, что поскольку параметры `File` являются объектами, для " +"получения пути к входному файлу необходимо сослаться на поле path в файловом " +"объекте; чтобы сослаться на путь к tar-файлу в приведенном выше примере, " +"нужно написать `$(inputs.tarfile.path)`." + +#: ../../src/topics/parameter-references.md:59 +#: cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "Где разрешены ссылки на параметры?" + +#: ../../src/topics/parameter-references.md:61 +#: 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" +"Ссылки на параметры можно использовать только в определенных полях. К ним " +"относятся:" + +#: ../../src/topics/parameter-references.md:63 +#: 7647e0229a924f988cf02b7812a55c06 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" +"Из [`CommandLineTool`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandLineTool)" + +#: ../../src/topics/parameter-references.md:69 +#: 9d663249666045618a0d3acddb85a9a9 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" +"Из [CommandInputParameter](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandInputParameter)" + +#: ../../src/topics/parameter-references.md:72 +#: 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" +"Из [`inputBinding`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandLineBinding)" + +#: ../../src/topics/parameter-references.md:74 +#: dbf6153cd02542a6a01c172803122b7f +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" +"Из [CommandOutputParamater](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandOutputParameter)" + +#: ../../src/topics/parameter-references.md:77 +#: b6250cf6fa8a4a0c94b33302e0decca5 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" +"Из [CommandOutputBinding](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandOutputBinding)" + +#: ../../src/topics/parameter-references.md:81 +#: fa6ca3bbc6784380a03a950a6f49a180 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" +"Из [InputParameter](http://www.commonwl.org/v1.0/" +"Workflow.html#InputParameter) и [WorkflowOutputParameter](http://" +"www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" + +#: ../../src/topics/parameter-references.md:85 +#: b92b516e537a4773ad67b4af586e7a25 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" +"Из [WorkflowStepInput](http://www.commonwl.org/v1.0/" +"Workflow.html#WorkflowStepInput)" + +#: ../../src/topics/parameter-references.md:89 +#: 467a701228504d06b971b79a59c69064 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" +"Из [InputParameter](http://www.commonwl.org/v1.0/" +"Workflow.html#InputParameter) и [ExpressionToolOutputParameter](http://" +"www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" + +#: ../../src/topics/parameter-references.md:92 +#: 2634f989eb304009a8568d70ed42786c +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" +"Из [`ResourceRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#ResourceRequirement)" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" +"Из [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement)" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "в [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" +"Из [EnvironmentDef](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#EnvironmentDef)" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "Требования и советы" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "Определение требований к программному обеспечению" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" +"Часто описания инструментов пишутся для определенной версии программного " +"обеспечения. Чтобы другим было проще использовать ваши описания, вы можете " +"включить поле `SoftwareRequirement` в раздел `hints`. Это также поможет " +"избежать путаницы в вопросе о том, для какой версии инструмента было " +"написано описание." + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" +"В данном примере описываемое программное обеспечение - это InterProScan " +"версии 5.21-60." + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" +"В зависимости от используемой программы запуска CWL, эти подсказки могут " +"использоваться для проверки того, что необходимое программное обеспечение " +"установлено и доступно до запуска задания. Чтобы включить эти проверки в " +"эталонной реализации, воспользуйтесь параметром " +"[dependency resolvers configuration][dependencies]." + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" +"Помимо номера версии, для инструмента указывается уникальный идентификатор " +"ресурса (URI) в виде [RRID][rrid]. Ресурсы с RRID могут быть найдены в " +"реестре [SciCrunch][scicrunch], который предоставляет портал для поиска, " +"отслеживания и последовательного обращения к научным ресурсам. Если вы " +"хотите указать инструмент в качестве `SoftwareRequirement`, найдите его на " +"SciCrunch и используйте RRID, присвоенный ему в реестре. (Следуйте этому " +"[Adding a Resource Tutorial][scicrunch-add-tool], чтобы добавить инструмент " +"в SciCrunch). Вы можете использовать этот RRID для ссылки на инструмент (" +"через [identifiers.org][identifiers]) в поле `specs` вашего описания " +"требований. Другими хорошими вариантами, в порядке предпочтения, являются " +"включение DOI для основного цитирования инструмента и URL-адреса инструмента." + +#: ../../src/topics/staging-input-files.md:1 +#: b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "Постановка входных файлов" + +#: ../../src/topics/staging-input-files.md:3 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" +"Обычно входные файлы располагаются в каталоге, доступном только для чтения, " +"отдельно от выходного каталога. Это приводит к проблемам, если базовый " +"инструмент ожидает записи своих выходных файлов рядом с входным файлом в том " +"же каталоге. Вы используете `InitialWorkDirRequirement`, чтобы поместить " +"входные файлы в выходной каталог. В этом примере мы используем выражение " +"JavaScript для извлечения базового имени входного файла из его ведущего пути " +"к каталогу." + +#: ../../src/topics/staging-input-files.md:9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +#, fuzzy +msgid "`linkfile.cwl`" +msgstr "`linkfile.cwl`" + +#: ../../src/topics/troubleshooting.md:1 +#: 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "Устранение неполадок" + +#: ../../src/topics/troubleshooting.md:3 +#: fbe0c65b444441f785d0054176d036a6 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" +"В этом разделе вы найдете способы устранения неполадок, когда возникают " +"проблемы при выполнении CWL. Здесь мы сосредоточимся на `cwltool`, но " +"некоторые из этих методов могут быть применимы и к другим CWL Runners." + +#: ../../src/topics/troubleshooting.md:6 +#: 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "Запустите `cwltool` с `cachedir`" + +#: ../../src/topics/troubleshooting.md:8 +#: 9a710602e00c4934ae3a3b471aa68458 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" +"Вы можете использовать опцию `--cachedir` при запуске рабочего процесса, " +"чтобы указать `cwltool` кэшировать промежуточные файлы (файлы, которые не " +"являются ни входными, ни выходными, но создаются во время выполнения " +"рабочего процесса). По умолчанию эти файлы создаются во временном каталоге, " +"но их запись в отдельный каталог упрощает доступ к ним." + +#: ../../src/topics/troubleshooting.md:14 +#: 21b5be7270a14f0987240c81d1ec879b +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" +"В следующем примере `troubleshooting-wf1.cwl` у нас есть два шага, `step_a` " +"и `step_b`. Этот шаг эквивалентен команде `echo \"Hello World\" | rev`, " +"которая выведет сообщение \"Hello World\" в обратном порядке, т. е. " +"\"dlroW olleH\". Однако второй шаг, `step_b`, **содержит опечатку**, когда " +"вместо команды `rev` он пытается выполнить `revv`, что не удается." + +#: ../../src/topics/troubleshooting.md:20 +#: 0490b1fab86749e49b473949c52bbe8b +#, fuzzy +msgid "`troubleshooting-wf1.cwl`" +msgstr "`troubleshooting-wf1.cwl`" + +#: ../../src/topics/troubleshooting.md:27 +#: cfe9d8241fe84bd5b74042a5625d933f +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" +"Давайте выполним этот рабочий процесс с `/tmp/cachedir/` в качестве значения " +"`--cachedir` (`cwltool` создаст каталог, если он еще не существует):" + +#: ../../src/topics/troubleshooting.md:35 +#: 764d933cc4da446abd8dd8f913f05dac +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" +"Рабочий процесс находится в состоянии `постоянного отказа` из-за того, что " +"`шаг_b` не смог выполнить несуществующую команду `revv`. Шаг `step_a` был " +"выполнен успешно, и его результаты были кэшированы в вашем расположении " +"`cachedir`. Вы можете просмотреть созданные промежуточные файлы:" + +#: ../../src/topics/troubleshooting.md:44 +#: c93efc6d4e004859981ee7f5fa28ed03 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" +"Каждый шаг рабочего процесса получил уникальный ID (длинное значение, " +"похожее на хэш). Файлы `${HASH}.status` отображают статус каждого шага, " +"выполняемого рабочим процессом. А выходной файл `stdout.txt` шага `step_a` " +"виден в выводе команды выше." + +#: ../../src/topics/troubleshooting.md:48 +#: 546601da44cb49bd9611b1c85807fd90 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" +"Теперь исправьте опечатку, чтобы `step_b` выполнял `rev` (т.е. замените " +"`revv` на `rev` в `step_b`). После исправления опечатки, когда вы выполните " +"`cwltool` с теми же аргументами, что и в предыдущий раз, обратите внимание, " +"что теперь вывод `cwltool` содержит информацию о предварительно кэшированных " +"выводах для `step_a`, а также о новой записи в кэше для вывода `step_b`. " +"Также обратите внимание, что статус `step_b` теперь успешный." + +#: ../../src/topics/troubleshooting.md:59 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" +"В этом примере шаг рабочего процесса `step_a` не был переоценен, поскольку " +"он был кэширован, и никаких изменений в его выполнении или выходе не " +"произошло. Более того, `cwltool` смог распознать, когда ему нужно было " +"повторно оценить `step_b` после того, как мы исправили имя исполняемого " +"файла. Эта техника полезна для устранения неполадок в документах CWL, а " +"также как способ предотвратить ненужную переоценку шагов программой " +"`cwltool`." + +#: ../../src/topics/using-containers.md:1 +#: eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "Использование контейнеров" + +#: ../../src/topics/using-containers.md:3 +#: 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "Запуск инструментов внутри Docker" + +#: ../../src/topics/using-containers.md:5 +#: e07f33d01b804663a25ffb08aad74821 +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" +"Контейнеры [Docker][docker] упрощают установку программного обеспечения, " +"предоставляя полное известное время выполнения для программ и их " +"зависимостей. Однако контейнеры также специально изолированы от хост-" +"системы, поэтому для запуска инструмента в контейнере Docker необходимо " +"выполнить дополнительную работу, чтобы убедиться, что входные файлы доступны " +"внутри контейнера, а выходные файлы могут быть восстановлены из контейнера. " +"CWL runner может выполнять эту работу автоматически, позволяя вам " +"использовать Docker для упрощения управления программным обеспечением, " +"избегая при этом сложностей, связанных с вызовом и управлением контейнерами " +"Docker." + +#: ../../src/topics/using-containers.md:15 +#: 7a644506619a4f08958ec7d4540cd557 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" +"Одной из обязанностей программы запуска CWL является корректировка путей к " +"входным файлам с учетом их расположения внутри контейнера." + +#: ../../src/topics/using-containers.md:18 +#: b5195b7d8eaa419fb2b90cb33a57783a +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" +"Этот пример запускает простой скрипт Node.js внутри контейнера Docker, " +"который затем выводит \"Hello World\" на стандартный вывод." + +#: ../../src/topics/using-containers.md:21 +#: 7921a837ee744c5aa9a5bda04b0c8db1 +#, fuzzy +msgid "`docker.cwl`" +msgstr "`docker.cwl`" + +#: ../../src/topics/using-containers.md:27 +#: 387e9bc9381a4450af54aff77e4df6a2 +#, fuzzy +msgid "`docker-job.yml`" +msgstr "`docker-job.yml`" + +#: ../../src/topics/using-containers.md:33 +#: 2713594c937d4c528fc8d04d9e9819ed +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" +"Прежде чем мы запустим эту программу, давайте разберем ее на части и " +"посмотрим, что делают некоторые элементы. Большая часть этого уже " +"объяснялась в предыдущих разделах, единственная часть, которая действительно " +"является новой, - это раздел `dockerRequirement`." + +#: ../../src/topics/using-containers.md:44 +#: cf94c1424fc2413c85647fd1ee73d951 +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" +"`Базовая команда: node` сообщает CWL, что мы будем выполнять эту команду, " +"используя среду выполнения Node Js, предназначенную для файлов Javascript. " +"Затем нам нужно указать несколько `подсказок` для поиска нужного нам " +"контейнера. В данном случае мы перечислим только наши требования к " +"контейнеру docker в `DockerRequirements`. Параметр `dockerPull:` принимает " +"то же значение, которое вы бы передали команде `docker pull`. То есть имя " +"образа контейнера (можно даже указать тег, что является хорошей идеей для " +"лучших практик использования контейнеров для воспроизводимых исследований). " +"В данном случае мы использовали контейнер под названием `node:slim`." + +#: ../../src/topics/using-containers.md:52 +#: dc0452107c604e29bdf32bb289fe5db8 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" +"Создайте Javascript-файл с именем \"hello.js\" и вызовите `cwltool`, указав " +"в командной строке описание инструмента и объект ввода:" + +#: ../../src/topics/using-containers.md:55 +#: 1a5596243cec4c948d9b6bf0bb12fad0 +#, fuzzy +msgid "`hello.js`" +msgstr "`hello.js`" + +#: ../../src/topics/using-containers.md:69 +#: 483181f498fc4d968b5fe6ef427709f7 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" +"Обратите внимание, что программа запуска CWL создала командную строку Docker " +"для запуска сценария." + +#: ../../src/topics/using-containers.md:72 +#: 7487485d6aa4458089a4b4bdf107ea64 +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" +"В этом примере путь к скрипту `hello.js` - это `/home/me/cwl/user_guide/" +"hello.js` вне контейнера, но `/var/lib/cwl/job369354770_examples/hello.js` " +"внутри контейнера, что отражено в вызове команды `node`." + +#: ../../src/topics/workflows.md:1 +#: 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "Рабочие процессы" + +#: ../../src/topics/workflows.md:3 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" +"Рабочий процесс - это блок обработки CWL, который выполняет инструменты " +"командной строки, средства выражения или рабочие процессы (подрабочие " +"процессы) в качестве шагов. Он должен иметь `входы`, `выходы` и `шаги`, " +"определенные в документе CWL." + +#: ../../src/topics/workflows.md:13 +#: f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "Рабочий процесс CWL." + +#: ../../src/topics/workflows.md:41 +#: 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" +"CWL-документ `echo-uppercase.cwl` определяет рабочий процесс, который " +"запускает инструмент командной строки и инструмент для работы с выражениями, " +"показанный в предыдущих примерах." + +#: ../../src/topics/workflows.md:51 +#: a913c76d06164fa18718a8a6a7dcf0d6 +#, fuzzy +msgid "`echo-uppercase.cwl`" +msgstr "`echo-uppercase.cwl`" + +#: ../../src/topics/workflows.md:81 +#: 93188ed43ee949cc98b3ea679ce14feb +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" +"Инструмент командной строки или инструмент выражения также может быть " +"записан непосредственно в том же документе CWL, что и рабочий процесс. " +"Например, мы можем переписать рабочий процесс `echo-uppercase.cwl` в виде " +"одного файла:" + +#: ../../src/topics/workflows.md:91 +#: 36618126a4df4326b236ebe2ea42cffa +#, fuzzy +msgid "`echo-uppercase-single-file.cwl`" +msgstr "`echo-uppercase-single-file.cwl`" + +#: ../../src/topics/workflows.md:150 +#: 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" +"Наличие отдельных файлов помогает в обеспечении модульности и организации " +"кода. Но для разработки может быть полезно писать все в одном файле. " +"Существуют и другие способы объединения нескольких файлов в один файл (" +"например, `cwltool --pack`), о которых мы поговорим в других разделах этого " +"руководства пользователя." + +#: ../../src/topics/workflows.md:160 +#: 24aca0bea4d94e3593b844cf0586cffe +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" +"Для субрабочих процессов необходимо включить требование " +"`SubworkflowFeatureRequirement`. Более подробно об этом говорится в другом " +"разделе данного руководства пользователя." + +#: ../../src/topics/workflows.md:165 +#: 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "Написание рабочих процессов" + +#: ../../src/topics/workflows.md:167 +#: 9c56528acd5f49deb139e034dfbfac7c +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" +"Этот рабочий процесс извлекает исходный файл java из tar-файла, а затем " +"компилирует его." + +#: ../../src/topics/workflows.md:170 +#: 55ab007d472f43388e4c77aae8f165e7 +#, fuzzy +msgid "`1st-workflow.cwl`" +msgstr "`1st-workflow.cwl`" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 +#, fuzzy +msgid "Visualization of 1st-workflow.cwl" +msgstr "Visualization of 1st-workflow.cwl" + +#: ../../src/topics/workflows.md:180 +#: a2dd833fdca4443181648e41051a5232 +#, fuzzy +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr "" +"[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/" +"common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)" + +#: ../../src/topics/workflows.md:183 +#: 7e40cc9f9e1341c195e843c009575b94 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" +"Используйте YAML или JSON-объект в отдельном файле для описания входных " +"данных для запуска:" + +#: ../../src/topics/workflows.md:185 +#: 26c51dcb76364ed780376aecb7cbacda +#, fuzzy +msgid "`1st-workflow-job.yml`" +msgstr "`1st-workflow-job.yml`" + +#: ../../src/topics/workflows.md:191 +#: 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" +"Далее создайте пример Java-файла и добавьте его в tar-файл для использования " +"с инструментом командной строки." + +#: ../../src/topics/workflows.md:205 +#: 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "Что здесь происходит? Давайте разберемся:" + +#: ../../src/topics/workflows.md:212 +#: def35d6021394def80a53ae49a2cdbde +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" +"Поле `cwlVersion` указывает на версию спецификации CWL, используемую в " +"документе. Поле `class` указывает, что этот документ описывает рабочий " +"процесс." + +#: ../../src/topics/workflows.md:221 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" +"Раздел `входы` описывает входы рабочего процесса. Это список входных " +"параметров, где каждый параметр состоит из идентификатора и типа данных. " +"Эти параметры могут быть использованы в качестве источников входных данных " +"для определенных этапов рабочего процесса." + +#: ../../src/topics/workflows.md:233 +#: c84d4450bc6a475dbf34e0b22cea9130 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" +"Раздел `outputs` описывает выходные данные рабочего процесса. Это список " +"выходных параметров, где каждый параметр состоит из идентификатора и типа " +"данных. Параметр `outputSource` соединяет выходной параметр `classfile` " +"шага `compile` с выходным параметром рабочего процесса `compiled_class`." + +#: ../../src/topics/workflows.md:248 +#: cca9665f6daa44b49233baf34ab9fcc7 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" +"Раздел `steps` описывает фактические шаги рабочего процесса. В этом примере " +"первый шаг извлекает файл из tar-файла, а второй шаг компилирует файл, " +"полученный на первом шаге, с помощью java-компилятора. Шаги рабочего " +"процесса не обязательно выполняются в том порядке, в котором они " +"перечислены, вместо этого порядок определяется зависимостями между шагами (с " +"помощью `source`). Кроме того, шаги рабочего процесса, которые не зависят " +"друг от друга, могут выполняться параллельно." + +#: ../../src/topics/workflows.md:256 +#: 547edbf5fa424b8286cc21674ff159b0 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" +"Первый шаг, `untar`, запускает `tar-param.cwl` (описанный ранее в " +"[Parameter References](parameter-references.md)). Этот инструмент имеет два " +"входных параметра, `tarfile` и `extractfile`, и один выходной параметр " +"`extracted_file`." + +#: ../../src/topics/workflows.md:261 +#: 7ca248888b9d484cb544cd76ba538662 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" +"Секция ``in`` шага рабочего процесса соединяет эти два входных параметра с " +"входами рабочего процесса, `tarball` и `name_of_file_to_extract`, используя " +"`source`. Это означает, что при выполнении шага рабочего процесса значения, " +"присвоенные параметрам `tarball` и `name_of_file_to_extract`, будут " +"использоваться для параметров `tarfile` и `extractfile` для запуска " +"инструмента." + +#: ../../src/topics/workflows.md:267 +#: ae6b240718104380b08db5552d7355ea +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" +"В разделе `out` шага рабочего процесса перечислены выходные параметры, " +"которые ожидаются от инструмента." + +#: ../../src/topics/workflows.md:278 +#: e5a8b7f84be64020b191099f3fad30ed +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" +"Второй шаг `compile` зависит от результатов первого шага, соединяя входной " +"параметр `src` с выходным параметром `untar` с помощью `untar/extracted_file`" +". Он запускает `arguments.cwl` (описанный ранее в " +"[Additional Arguments and Parameters](additional-arguments-and-" +"parameters.md)). Выход этого шага `classfile` подключается к секции `outputs`" +" для рабочего процесса, описанного выше." + +#: ../../src/topics/workflows.md:285 +#: f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "Вложенные рабочие процессы" + +#: ../../src/topics/workflows.md:287 +#: 12a06d8358534102b202965d4258c18e +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" +"Рабочие процессы - это способы объединения нескольких инструментов для " +"выполнения более крупных операций. Можно также считать, что рабочий процесс " +"сам по себе является инструментом; рабочий процесс CWL может использоваться " +"в качестве шага в другом рабочем процессе CWL, если механизм рабочего " +"процесса поддерживает `SubworkflowFeatureRequirement`:" + +#: ../../src/topics/workflows.md:297 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" +"Вот пример рабочего процесса, который использует наш `1st-workflow.cwl` в " +"качестве вложенного рабочего процесса:" + +#: ../../src/topics/workflows.md:300 +#: 49ed137fe996452a8534c68d100db941 +#, fuzzy +msgid "`nestedworkflows.cwl`" +msgstr "`nestedworkflows.cwl`" + +#: ../../src/topics/workflows.md:309 +#: b7f93705e5b8416696be01850072e8c0 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" +"Этот двухэтапный рабочий процесс начинается с шага `create-tar`, который " +"связан с шагом `compile` оранжевым цветом; `compile` - это другой рабочий " +"процесс, показанный на диаграмме справа. В фиолетовом цвете мы видим " +"фиксированную строку `\"Hello.java\"`, предоставляемую в качестве " +"`имени_файла_для_извлечения`." + +#: ../../src/topics/workflows.md:314 +#: e87045829b344089ab59dc27063ddd7a +msgid "\"Visualization \"Visualization" +msgstr "" +" + +" + +#: ../../src/topics/workflows.md:322 +#: 42ef2f145b824d69b63abc1da175c216 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" +"CWL `Workflow` может быть использован в качестве `шага`, как и " +"`CommandLineTool`, его CWL-файл включается в `run`. Входы рабочего процесса " +"(`tarball` и `name_of_file_to_extract`) и выходы (`compiled_class`) затем " +"могут быть сопоставлены, чтобы стать входами/выходами шага." + +#: ../../src/topics/workflows.md:336 +#: c61cedf543664d388183e04b3939cc39 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" +"Наш `1st-workflow.cwl` был параметризован входами рабочего процесса, поэтому " +"при его запуске мы должны были указать файл задания, чтобы обозначить tar-" +"файл и имя файла `*.java`. Это, как правило, лучшая практика, так как это " +"означает, что его можно повторно использовать в нескольких родительских " +"рабочих процессах или даже в нескольких шагах в рамках одного рабочего " +"процесса." + +#: ../../src/topics/workflows.md:341 +#: 9e39e3f1501c4fcaab3e8962e090f6be +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" +"Здесь мы используем `default:` для жесткого кодирования `\"Hello.java\"` в " +"качестве входного `имени_файла_к_извлечению`, однако наш рабочий процесс " +"также требует tar-файл в `tarball`, который мы подготовим на шаге `create-" +"tar`. На данном этапе, вероятно, стоит рефакторить `1st-workflow.cwl`, чтобы " +"иметь более конкретные имена входов/выходов, так как они также появляются " +"при его использовании в качестве инструмента." + +#: ../../src/topics/workflows.md:347 +#: 03e2f767c4da461982fc3c0f3ba94762 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" +"Также можно использовать менее общий подход и избежать внешних зависимостей " +"в файле задания. Так, в этом рабочем процессе мы можем сгенерировать жестко " +"закодированный файл `Hello.java`, используя ранее упомянутое требование " +"`InitialWorkDirRequirement`, прежде чем добавить его в tar-файл." + +#: ../../src/topics/workflows.md:366 +#: 3bea5822b8694e2aa32c446e1c54a045 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" +"В этом случае наш шаг может предполагать `Hello.java`, а не быть " +"параметризованным, поэтому мы можем использовать жестко заданные значения " +"`hello.tar` и `Hello.java` в `baseCommand` и получаемых `выводах`:" + +#: ../../src/topics/workflows.md:383 +#: 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" +"Вы заметили, что мы не выделили инструмент `tar --create` в отдельный файл, " +"а встроили его в файл CWL Workflow? Как правило, это не лучшая практика, " +"поскольку инструмент нельзя использовать повторно. В данном случае причина в " +"том, что в командной строке жестко заданы имена файлов, которые имеют смысл " +"только в рамках данного рабочего процесса." + +#: ../../src/topics/workflows.md:389 +#: 0d498cd4caf54c15891ca1afe58e2727 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" +"В этом примере мы должны были подготовить tar-файл снаружи, но только " +"потому, что наш внутренний рабочий процесс был разработан так, чтобы " +"принимать его в качестве входных данных. Лучшим рефакторингом внутреннего " +"рабочего процесса было бы получение списка Java-файлов для компиляции, что " +"упростило бы его использование в качестве инструментального шага в других " +"рабочих процессах." + +#: ../../src/topics/workflows.md:394 +#: b2d75045e02741b4850f5ff1243f7858 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" +"Вложенные рабочие процессы могут быть мощной функцией для создания " +"функциональных и многократно используемых единиц рабочего процесса более " +"высокого уровня - но, как и при создании описания инструмента CWL, " +"необходимо позаботиться о том, чтобы повысить удобство его использования в " +"нескольких рабочих процессах." + +#: ../../src/topics/workflows.md:398 +#: cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "Шаги рассеивания" + +#: ../../src/topics/workflows.md:400 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" +"Теперь, когда мы знаем, как писать рабочие процессы, мы можем начать " +"использовать `ScatterFeatureRequirement`. Эта функция сообщает исполнителю, " +"что вы хотите запустить инструмент или рабочий процесс несколько раз над " +"списком входных данных. Тогда рабочий процесс принимает входные данные в " +"виде массива и выполняет указанные шаги на каждом элементе массива, как если " +"бы это был один вход. Это позволяет запускать один и тот же рабочий процесс " +"на нескольких входах без необходимости генерировать множество различных " +"команд или входных yaml-файлов." + +#: ../../src/topics/workflows.md:411 +#: 5fa79c62049a447c8328ebf9db54ebf4 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" +"Наиболее распространенная причина, по которой новый пользователь может " +"захотеть использовать scatter, - это проведение одного и того же анализа для " +"разных образцов. Давайте начнем с простого рабочего процесса, который " +"вызывает наш первый пример (`hello_world.cwl`) и принимает массив строк в " +"качестве входных данных для рабочего процесса:" + +#: ../../src/topics/workflows.md:415 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +#, fuzzy +msgid "`scatter-workflow.cwl`" +msgstr "`scatter-workflow.cwl`" + +#: ../../src/topics/workflows.md:421 +#: 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" +"Помимо раздела `requirements`, включающего `ScatterFeatureRequirement`, что " +"здесь происходит?" + +#: ../../src/topics/workflows.md:429 +#: f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" +"Прежде всего, обратите внимание, что для ввода основного уровня рабочего " +"процесса здесь требуется массив строк." + +#: ../../src/topics/workflows.md:441 +#: d947c54933d64aad90df392a1cedd63f +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" +"Здесь мы добавили новое поле в шаг `echo` под названием `scatter`. Это поле " +"сообщает бегуну, что мы хотим разбросать данные по входу для этого " +"конкретного шага. Обратите внимание, что имя входа, указанное после scatter, " +"- это имя входа шага, а не входа уровня рабочего процесса." + +#: ../../src/topics/workflows.md:445 +#: 651d35997332404186aa6d5711da4a3d +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" +"Для нашего первого скаттера все просто! Поскольку наш инструмент не собирает " +"никаких выходов, мы по-прежнему используем `outputs: []` в нашем рабочем " +"процессе, но если вы ожидаете, что конечный результат вашего рабочего " +"процесса теперь будет иметь несколько выходов для сбора, не забудьте " +"обновить этот тип до массива!" + +#: ../../src/topics/workflows.md:450 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "Используя следующий входной файл:" + +#: ../../src/topics/workflows.md:452 +#: 842b926ae34542cb9023021f137b08be +#, fuzzy +msgid "`scatter-job.yml`" +msgstr "`scatter-job.yml`" + +#: ../../src/topics/workflows.md:458 +#: b662c1a5a4424c8d8350a806356acc61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" +"Напомним, что [`hello_world.cwl`](../introduction/quick-start.md) просто " +"вызывает команду `echo` для сообщения. Если мы вызовем `cwltool scatter-" +"workflow.cwl scatter-job.yml` в командной строке:" + +#: ../../src/topics/workflows.md:466 +#: 04d6babfd87343d7a5f13867ea02b65f +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" +"Вы видите, что рабочий процесс вызывает echo несколько раз для каждого " +"элемента нашего `message_array`. Хорошо, а как быть, если мы хотим " +"разбросать данные по двум шагам рабочего процесса?" + +#: ../../src/topics/workflows.md:469 +#: 2eaacf1a90204a2b9bd621344560f2a1 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" +"Давайте выполним простое эхо, как описано выше, но перехватим `stdout`, " +"добавив следующие строки вместо `outputs: []`" + +#: ../../src/topics/workflows.md:472 +#: 242993d42b164ee5abe7ca10d45856de +#, fuzzy +msgid "`hello_world_to_stdout.cwl`" +msgstr "`hello_world_to_stdout.cwl`" + +#: ../../src/topics/workflows.md:480 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" +"И добавьте второй шаг, который использует `wc` для подсчета символов в " +"каждом файле. Смотрите инструмент ниже:" + +#: ../../src/topics/workflows.md:483 +#: e61d93b848184c8e8e573928427b4d0a +#, fuzzy +msgid "`wc-tool.cwl`" +msgstr "`wc-tool.cwl`" + +#: ../../src/topics/workflows.md:489 +#: e3a7182f00f440b8b5461da91194a64b +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" +"Итак, как нам включить рассеивание? Помните, что поле разброса находится под " +"каждым шагом:" + +#: ../../src/topics/workflows.md:491 +#: 99fa96caacaa45cb97aded9a24fcac6d +#, fuzzy +msgid "`scatter-two-steps.cwl`" +msgstr "`scatter-two-steps.cwl`" + +#: ../../src/topics/workflows.md:497 +#: b5338f39e8c74ff28e139da68089a742 +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" +"Здесь мы поместили поле разброса под каждым шагом. Это подходит для данного " +"примера, поскольку он выполняется быстро, но если вы выполняете много " +"образцов для более сложного рабочего процесса, возможно, вам стоит " +"рассмотреть альтернативный вариант. Здесь мы запускаем scatter на каждом " +"шаге независимо, но поскольку второй шаг не зависит от первого, заполняя все " +"языки, мы не используем функциональность scatter эффективно. Второй шаг " +"ожидает массив в качестве входных данных от первого шага, поэтому он будет " +"ждать, пока все на первом шаге не будет завершено, прежде чем что-то делать. " +"Представьте, что выполнение `echo Hello World!` занимает 1 минуту, а вывод `" +"wc -c` - 3 минуты, а выполнение `echo Hallo welt!` занимает 5 минут, а вывод " +"`wc` - 3 минуты. Даже если `echo Hello World!` может завершиться за 4 " +"минуты, на самом деле он завершится за 8 минут, потому что первый шаг должен " +"ждать `echo Hallo welt!`. Вы можете видеть, как это может не очень хорошо " +"масштабироваться." + +#: ../../src/topics/workflows.md:509 +#: f6d92156d67c4a339bcfd194cff897df +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" +"Итак, как нам разбросать шаги, которые могут выполняться независимо от " +"других проб? Помните из [Nested Workflows](#nested-workflows), что мы можем " +"сделать весь рабочий процесс одним шагом в другом рабочем процессе! " +"Преобразуйте наш двухэтапный рабочий процесс в одноэтапный подпроцесс:" + +#: ../../src/topics/workflows.md:513 +#: 1c9e386922324ec8a59306572c19fb8b +#, fuzzy +msgid "`scatter-nested-workflow.cwl`" +msgstr "`scatter-nested-workflow.cwl`" + +#: ../../src/topics/workflows.md:519 +#: d80ab383eec9402faba997b548fe42eb +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" +"Теперь рассеиватель действует на один шаг, но этот шаг состоит из двух " +"шагов, поэтому каждый шаг выполняется параллельно." + +#: ../../src/topics/workflows.md:522 +#: f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "Условные рабочие процессы" + +#: ../../src/topics/workflows.md:524 +#: 49217c02f58c43ff9ec00f10da8d4e84 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" +"Этот рабочий процесс содержит условный шаг и выполняется на основе входных " +"данных. Это позволяет рабочим процессам пропускать дополнительные шаги на " +"основе входных параметров, заданных в начале программы или на предыдущих " +"шагах." + +#: ../../src/topics/workflows.md:527 +#: 20b9f181420c401d8615c17a10027517 +#, fuzzy +msgid "`conditional-workflow.cwl`" +msgstr "`conditional-workflow.cwl`" + +#: ../../src/topics/workflows.md:566 +#: 8dbd56473f8c40c0bb12a48be06117e3 +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" +"Первое, что вы заметите, это то, что этот рабочий процесс совместим только с " +"версией 1.2 или более поздней версией стандартов CWL." + +#: ../../src/topics/workflows.md:573 +#: 78d7f3ede2c746d482042adef050b2c4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" +"Первый шаг рабочего процесса (step1) содержит два входных свойства и будет " +"выполнять foo.cwl при выполнении условий. Новое свойство `when` - это место, " +"где происходит проверка условия. В данном случае только когда `in1` из " +"рабочего процесса содержит значение `<1`, этот шаг будет выполнен." + +#: ../../src/topics/workflows.md:587 +#: cbbf93c70fe04ba7932ba25758ddc611 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" +"При использовании следующей команды `cwltool cond-wf-003.1.cwl --val 0` " +"значение пройдет первый условный шаг и, следовательно, будет выполнено, что " +"отображается в журнале командой `INFO [step step1] start`, тогда как второй " +"шаг будет пропущен, о чем свидетельствует `INFO [step step2] will be " +"skipped`." + +#: ../../src/topics/workflows.md:607 +#: cfa1c1fde4454df283f87cc54a9c59ec +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" +"Если задано значение 3, первый условный шаг не будет выполнен, но второй шаг " +"будет выполнен `cwltool cond-wf-003.1.cwl --val 3`." + +#: ../../src/topics/workflows.md:627 +#: 1a8be2950cbb475bbb2617e005f0fac9 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" +"Если ни одно из условий не выполнено, например, при использовании `--val 2`, " +"рабочий процесс выдаст ошибку permanentFail." + +#: ../../src/topics/yaml-guide.md:1 +#: 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "Руководство по YAML" + +#: ../../src/topics/yaml-guide.md:6 +#: 5d83c56102e141cc978500f678dd0c1c +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" +"[YAML][yaml] - это формат файлов, предназначенный для чтения как " +"компьютером, так и человеком. В этом руководстве представлены особенности " +"YAML, которые важны при написании описаний CWL и файлов входных параметров." + +#: ../../src/topics/yaml-guide.md:13 +#: c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "Вы можете пропустить этот раздел, если вы уже знакомы с YAML." + +#: ../../src/topics/yaml-guide.md:16 +#: fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "Содержание" + +#: ../../src/topics/yaml-guide.md:18 +#: 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "[Пары ключ-значение](#key-value-pairs)" + +#: ../../src/topics/yaml-guide.md:19 +#: b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "[Комментарии](#comments)" + +#: ../../src/topics/yaml-guide.md:20 +#: b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../src/topics/yaml-guide.md:26 +#: cda73485875d4c8e9464679a20558616 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:42 +#: 98cae24919b74c088a5d89706aec581b +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" + +#: ../../src/topics/yaml-guide.md:51 +#: b4b0940b4b5743c09637b36b964202d0 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" + +#: ../../src/topics/yaml-guide.md:61 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../src/topics/yaml-guide.md:63 +#: 9ca3554d771d45998e88aaede525b227 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:76 +#: 3fca839cede94cfd8e4f605c73ba699d +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" + +#: ../../src/topics/yaml-guide.md:79 +#: da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../src/topics/yaml-guide.md:81 +#: 3ded0f125249485c921994b6e6b93ac9 +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:104 +#: 53ece35d309a4c8d99f1efb2122a7092 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" + +#: ../../src/topics/yaml-guide.md:127 +#: d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../src/topics/yaml-guide.md:129 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:146 +#: fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../src/topics/yaml-guide.md:169 +#: 87bafb845c714b109874f6137b84462d +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:177 +#: 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:184 +#: fcd05b1ef31a4046946a2399c7fc5575 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" + +#: ../../src/topics/yaml-guide.md:194 +#: f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../src/topics/yaml-guide.md:196 +#: 859368c1f25c4a4aad57abfd046c63f5 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" From 253fc19c0abac866003b91b4c89d7bf38cf2682c Mon Sep 17 00:00:00 2001 From: Languages add-on Date: Tue, 12 Aug 2025 12:26:20 +0200 Subject: [PATCH 170/179] Added translation using Weblate (Tamil) Added translation using Weblate (Russian) Co-authored-by: Languages add-on --- locales/ru/LC_MESSAGES/sphinx.po | 27 +++++++++++++++++++++++++++ locales/ta/LC_MESSAGES/sphinx.po | 27 +++++++++++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 locales/ru/LC_MESSAGES/sphinx.po create mode 100644 locales/ta/LC_MESSAGES/sphinx.po diff --git a/locales/ru/LC_MESSAGES/sphinx.po b/locales/ru/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..13426aa9 --- /dev/null +++ b/locales/ru/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: ru\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "" diff --git a/locales/ta/LC_MESSAGES/sphinx.po b/locales/ta/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..af786eba --- /dev/null +++ b/locales/ta/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: ta\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "" From 0bbce9eb289a4941dd1314eac790c421782e6017 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E0=AE=A4=E0=AE=AE=E0=AE=BF=E0=AE=B4=E0=AF=8D=E0=AE=A8?= =?UTF-8?q?=E0=AF=87=E0=AE=B0=E0=AE=AE=E0=AF=8D?= Date: Tue, 12 Aug 2025 12:26:20 +0200 Subject: [PATCH 171/179] Translated using Weblate (Tamil) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Currently translated at 100.0% (2 of 2 strings) Translated using Weblate (Tamil) Currently translated at 100.0% (598 of 598 strings) Translated using Weblate (Tamil) Currently translated at 100.0% (2 of 2 strings) Translated using Weblate (Tamil) Currently translated at 100.0% (598 of 598 strings) Added translation using Weblate (Tamil) Co-authored-by: தமிழ்நேரம் Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-sphinx/ta/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ta/ Translation: Common Workflow Language/CWL User Guide Translation: Common Workflow Language/CWL User Guide: Sphinx --- locales/ta/LC_MESSAGES/sphinx.po | 13 +- locales/ta/LC_MESSAGES/user_guide.po | 4260 ++++++++++++++++++++++++++ 2 files changed, 4268 insertions(+), 5 deletions(-) create mode 100644 locales/ta/LC_MESSAGES/user_guide.po diff --git a/locales/ta/LC_MESSAGES/sphinx.po b/locales/ta/LC_MESSAGES/sphinx.po index af786eba..e424842e 100644 --- a/locales/ta/LC_MESSAGES/sphinx.po +++ b/locales/ta/LC_MESSAGES/sphinx.po @@ -8,20 +8,23 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" +"PO-Revision-Date: 2024-12-20 20:00+0000\n" +"Last-Translator: தமிழ்நேரம் \n" +"Language-Team: Tamil \n" "Language: ta\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 5.10-dev\n" #: ../../src/_templates/sidebar-nav-bs.html:1 #: d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" -msgstr "" +msgstr "முதன்மை வழிசெலுத்தல்" #: ../../src/_templates/sidebar-nav-bs.html:3 #: 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" -msgstr "" +msgstr "பிரிவு வழிசெலுத்தல்" diff --git a/locales/ta/LC_MESSAGES/user_guide.po b/locales/ta/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..c1aa9a0b --- /dev/null +++ b/locales/ta/LC_MESSAGES/user_guide.po @@ -0,0 +1,4260 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: 2024-12-17 12:00+0000\n" +"Last-Translator: தமிழ்நேரம் \n" +"Language-Team: Tamil \n" +"Language: ta\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 5.9\n" + +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "உரிமங்கள்" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "அறிவுறுத்தல் பொருள்" + +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." +msgstr "" +"அனைத்து பொதுவான பணிப்பாய்வு மொழி திட்ட அறிவுறுத்தல் பொருள் மற்றும் கட்டமைப்பில் மாற்றங்கள் [" +"Creative Commons Attribution license][cc-by-human] இன் கீழ் கிடைக்கின்றன. " +"பின்வருபவை மனிதனால் படிக்கக்கூடிய சுருக்கமாகும் (மற்றும் இதற்கான மாற்று அல்ல)[full " +"legal text of the CC BY 4.0 license][cc-by-legal]." + +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "நீங்கள் இலவசம்:" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" +"** பகிர ** --- எந்த நடுத்தரத்திலும் அல்லது வடிவத்திலும் பொருளை நகலெடுத்து மறுபகிர்வு " +"செய்யுங்கள்" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "** மாற்றியமைக்க ** --- ரீமிக்ச், மாற்ற மற்றும் பொருள் மீது உருவாக்க" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "எந்தவொரு நோக்கத்திற்காகவும், வணிக ரீதியாக கூட." + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" +"உரிம விதிமுறைகளைப் பின்பற்றும் வரை உரிமதாரர் இந்த சுதந்திரங்களை ரத்து செய்ய முடியாது:" + +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +msgstr "" +"** பண்புக்கூறு ** --- நீங்கள் பொருத்தமான கடன் கொடுக்க வேண்டும் (உங்கள் பணி பதிப்புரிமை பெற்" +"ற வேலையிலிருந்து பெறப்பட்டது என்பதைக் குறிப்பிடுவது பொதுவான பணிப்பாய்வு மொழி திட்டம், " +"மற்றும், நடைமுறையில், https://www.commonwl.org/ உடன் இணைகிறது) . நீங்கள் எந்தவொரு " +"நியாயமான முறையில் அவ்வாறு செய்யலாம், ஆனால் உரிமதாரர் உங்களை அல்லது உங்கள் பயன்பாட்டை " +"ஒப்புக் கொள்ள பரிந்துரைக்கும் எந்த வகையிலும் அல்ல." + +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +msgstr "" +"** கூடுதல் கட்டுப்பாடுகள் எதுவும் இல்லை ** --- உரிமம் அனுமதிக்கும் எதையும் " +"செய்வதிலிருந்து மற்றவர்களை சட்டப்பூர்வமாக கட்டுப்படுத்தும் சட்ட விதிமுறைகள் அல்லது தொழில்நுட்" +"ப நடவடிக்கைகளை நீங்கள் பயன்படுத்தக்கூடாது. அதைப் புரிந்துகொள்வதன் மூலம்:" + +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 +msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +msgstr "" +"பொது களத்தில் உள்ள பொருளின் கூறுகளுக்கான உரிமத்திற்கு நீங்கள் இணங்க வேண்டியதில்லை அல்லது " +"பொருந்தக்கூடிய விதிவிலக்கு அல்லது வரம்பால் உங்கள் பயன்பாடு அனுமதிக்கப்படுகிறது." + +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +msgstr "" +"உத்தரவாதங்கள் எதுவும் கொடுக்கப்படவில்லை. நீங்கள் விரும்பிய பயன்பாட்டிற்கு தேவையான அனைத்து " +"அனுமதிகளையும் உரிமம் உங்களுக்கு வழங்காது. எடுத்துக்காட்டாக, விளம்பரம், தனியுரிமை அல்லது " +"தார்மீக உரிமைகள் போன்ற பிற உரிமைகள் நீங்கள் பொருளை எவ்வாறு பயன்படுத்துகிறீர்கள் என்பதைக் " +"கட்டுப்படுத்தலாம்." + +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "மென்பொருள்" + +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." +msgstr "" +"வேறுவிதமாகக் குறிப்பிடப்பட்ட இடத்தைத் தவிர, பொதுவான பணிப்பாய்வு மொழி திட்டத்தால் வழங்கப்பட்" +"ட எடுத்துக்காட்டு நிரல்கள் மற்றும் பிற மென்பொருள் [OSI] [OSI]-அங்கீகரிக்கப்பட்ட [அப்பாச்சி " +"2.0 உரிமம்] [அப்பாச்சி -2.0-உரிமம்] இன் கீழ் கிடைக்கின்றன." + +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +msgstr "" +"பொருந்தக்கூடிய சட்டத்தால் தேவைப்படாவிட்டால் அல்லது எழுத்துப்பூர்வமாக ஒப்புக் கொள்ளப்படாவிட்டால்" +", உரிமத்தின் கீழ் விநியோகிக்கப்படும் மென்பொருள் ஒரு \"அப்படியே\" அடிப்படையில், எந்தவொரு " +"உத்தரவாதங்களும் நிபந்தனைகளும் இல்லாமல், வெளிப்படையான அல்லது மறைமுகமாக " +"விநியோகிக்கப்படுகிறது. உரிமத்தின் கீழ் குறிப்பிட்ட மொழி ஆளும் அனுமதிகள் மற்றும் " +"வரம்புகளுக்கான உரிமத்தைப் பார்க்கவும்." + +#: ../../src/_includes/what-is-cwl.md:1 +#: ../../src/_includes/what-is-cwl.md:2 +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 +msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." +msgstr "" +"CWL என்பது கட்டளை-வரி கருவிகளை விவரிப்பதற்கும் அவற்றை ஒன்றாக இணைக்கவும் ஒரு வழியாகும். " +"சி.டபிள்யூ.எல் ஒரு விவரக்குறிப்பு மற்றும் ஒரு குறிப்பிட்ட மென்பொருள் அல்ல, சி.டபிள்யூ.எல் " +"ஐப் பயன்படுத்தி விவரிக்கப்பட்ட கருவிகள் மற்றும் பணிப்பாய்வுகள் சி.டபிள்யூ.எல் தரத்தை " +"ஆதரிக்கும் பல்வேறு தளங்களில் சிறியவை." + +#: ../../src/episodes.md:5 +#: ../../src/setup.md:5 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "இந்த பக்கம் நகர்ந்தது" + +#: ../../src/episodes.md:9 +#: cc11f5d29206492d9f2f0922882b6159 +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." +msgstr "" +"இந்த பக்கம் காலாவதியானது மற்றும் பழைய பயனர் வழிகாட்டியின் இணைப்புகளைப் பாதுகாக்க இங்கே " +"வைக்கப்பட்டது. பயனர் வழிகாட்டியை உலவ புதிய [உள்ளடக்க அட்டவணை] (Index." +"MD#அட்டவணை-இன்-உள்ளடக்கங்கள்) ஐப் பயன்படுத்தவும்." + +#: ../../src/faq.md:1 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "கேள்விகள்" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "`எவல்ஃப்ரோம்` ஐப் பயன்படுத்தி\" `கோப்பு`\" வகைகள்" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "உள்ளீட்டு கோப்பை மறுபெயரிடுங்கள்" + +#: ../../src/faq.md:43 +#: fc62427c0a004810b055dee90ec5e2d9 +msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." +msgstr "" +"கருவி விளக்கத்தின் ஒரு பகுதியாக உள்ளீட்டு கோப்பின் பெயரை எவ்வாறு மாற்றுவது என்பதை இந்த " +"எடுத்துக்காட்டு நிரூபிக்கிறது. பணிப்பாய்வுகளின் மற்றொரு படியிலிருந்து தயாரிக்கப்பட்ட " +"கோப்புகளை நீங்கள் எடுக்கும்போது இது பயனுள்ளதாக இருக்கும், மேலும் இந்த கோப்புகள் " +"உருவாக்கப்பட்டபோது வழங்கப்பட்ட இயல்புநிலை பெயர்களுடன் வேலை செய்ய விரும்பவில்லை." + +#: ../../src/faq.md:59 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "வெளியீட்டு கோப்பை மறுபெயரிடுங்கள்" + +#: ../../src/faq.md:61 +#: bc7ad10c929848a3a9a240a3c501d299 +msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" +msgstr "" +"ஒரு கருவி மூலம் வழங்கப்பட்ட இயல்புநிலை பெயரிலிருந்து வெளியீட்டு கோப்பின் பெயரை எவ்வாறு " +"மாற்றுவது என்பதை இந்த எடுத்துக்காட்டு நிரூபிக்கிறது:" + +#: ../../src/faq.md:82 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "உள்ளக ச்கிரிப்டைக் குறிப்பிடுகிறது" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "உள்ளக ச்கிரிப்டைக் குறிப்பிட இரண்டு வழிகள் உள்ளன:" + +#: ../../src/faq.md:86 +#: 450edf800a18423195bea4fe8793a2cb +msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." +msgstr "" +"முதல் முறை உங்கள் ச்கிரிப்ட்களைக் கொண்ட கோப்புறையை `பாதை` சுற்றுச்சூழல் மாறியில் சேர்ப்பது " +"அடங்கும். `Sh` அல்லது` பாச்` கட்டளைகளைப் பயன்படுத்தாமல் செல் ச்கிரிப்டை நேரடியாக இயக்க இது" +" உங்களை அனுமதிக்கிறது." + +#: ../../src/faq.md:89 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" +"உங்கள் கோப்பின் மேற்புறத்தில் _shebang_ ஐச் சேர்ப்பதன் மூலம் தொடங்கவும்:" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "அதன்பிறகு, `chmod +x scriptname.sh` கட்டளையுடன் ச்கிரிப்டை இயக்கவும்" + +#: ../../src/faq.md:97 +#: 569d553abe85450c9d1c37456bf412f4 +msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." +msgstr "" +"இறுதியாக, உங்கள் ச்கிரிப்ட் அமைந்துள்ள கோப்பகத்தைச் சேர்க்க உங்கள் `பாதையை` மாற்றவும். (உங்கள் " +"சொந்த ச்கிரிப்ட்களை சேமிக்க `$ home/bin` ஐப் பயன்படுத்துவது நல்ல நடைமுறை)." + +#: ../../src/faq.md:104 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" +"இப்போது நீங்கள் ச்கிரிப்டை நேரடியாக இயக்க `BasCommand: scriptname.sh` ஐப் " +"பயன்படுத்தலாம்." + +#: ../../src/faq.md:113 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 +msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." +msgstr "" +"உங்கள் வேலையை பின்னர் பகிர்ந்து கொள்ள விரும்பினால், உங்கள் ச்கிரிப்டை மென்பொருள் கொள்கலனில் " +"கப்பல்துறை வடிவத்தில் வைக்கலாம்." + +#: ../../src/faq.md:115 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "இரண்டாவது முறை ச்கிரிப்டில் `வகை: கோப்பு` உள்ளீட்டை உள்ளடக்கியது:" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "சி.டபிள்யூ.எல் இல், எல்லாவற்றையும் நேரடியாகக் கூற வேண்டும்." + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" +"விருப்ப உள்ளீடுகளுக்கு `சுய அடிப்படையிலான உள்ளீட்டு பிணைப்புகளை அமைத்தல்" + +#: ../../src/faq.md:140 +#: 2c38cc58cbb340bc935a5f00e96ba95c +msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." +msgstr "" +"தற்போது, `cwltool` அவர்களின் உள்ளீட்டு பிணைப்பு` சுயத்தை 'பயன்படுத்தினால், காணாமல் போன " +"விருப்ப உள்ளீடுகளை சமாளிக்க முடியாது. இதற்கான ஒரு எடுத்துக்காட்டு பணித்தொகுப்பு கீழே " +"உள்ளது, இது மிகவும் அதிநவீன பிழைத்திருத்தம் நிலுவையில் உள்ளது." + +#: ../../src/faq.md:165 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "மாதிரி A \"ஒன்று அல்லது பிற\" அளவுரு" + +#: ../../src/faq.md:167 +#: d06cbf89028b4638ad54c2529bcbfa25 +msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." +msgstr "" +"பூலியன் அளவுருவுக்கு கொடுக்கப்பட்ட மதிப்பின் அடிப்படையில், கட்டளை வரியில் சேர்க்கப்பட வேண்டி" +"ய வெவ்வேறு சரங்களை எவ்வாறு குறிப்பிடுவது என்பதைக் காட்டும் ஒரு எடுத்துக்காட்டு கீழே." + +#: ../../src/faq.md:188 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" +"அந்த வகையின் வரிசையை எதிர்பார்க்கும் உள்ளீட்டுடன் ஒரு தனி மதிப்பை இணைக்கவும்" + +#: ../../src/faq.md:190 +#: d9e30e11533b4d53a144f5df7041268d +msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" +"[`மல்டிபிள்இன் பியூட்ஃபீட்டர்ரெக்மென்ட்`] (https://www.commonwl.org/v1.0/workflow." +"html#multifulutfeatureerequirement) உடன் [` linkerge: mergerge: merge_nested`]" +" (https://wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww" +"wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww" +" /Workflow.html#workflowstepinput)" + +#: ../../src/faq.md:194 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "merge_nested" + +#: ../../src/faq.md:196 +#: 937cb94a370640c788fbc3fe0b19f2e5 +msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." +msgstr "" +"உள்ளீடு ஒவ்வொரு உள்ளீட்டு இணைப்பிற்கும் சரியாக ஒரு உள்ளீட்டைக் கொண்ட ஒரு வரிசையாக இருக்க " +"வேண்டும். \"Merge_nested\" ஒற்றை இணைப்புடன் குறிப்பிடப்பட்டால், இணைப்பிலிருந்து வரும் " +"மதிப்பு ஒற்றை-உருப்படி பட்டியலில் மூடப்பட வேண்டும்." + +#: ../../src/faq.md:199 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "அதாவது \"இந்த ஆதாரங்களைக் கொண்ட ஒரு பட்டியலை கூறுகளாக உருவாக்கவும்\"" + +#: ../../src/faq.md:201 +#: c8c235a9bf6240628f0b5493ffebf7e0 +msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." +msgstr "" +"அல்லது வேறுவிதமாகக் கூறினால்: இலக்கு `கோப்பு []` (`கோப்பின் வரிசையின்) வகை மற்றும் " +"மூலமானது ஒற்றை` கோப்பு` என்றால், பின்னர் `மல்டிபுட்ஃபியூட்யூர்ரெக்யூமென்ட் 'ஐச் சேர்த்து` " +"தேவைகள்` மற்றும் `லிங்க்மர்ச் சேர்க்கவும் ." + +#: ../../src/faq.md:229 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "விருப்ப உள்ளீடுகள்" + +#: ../../src/faq.md:231 +#: 89b90d3bf1ea4ebd88482d435241fac5 +msgid "To make an input parameter optional, add a question mark to the type declaration." +msgstr "" +"உள்ளீட்டு அளவுருவை விருப்பமாக மாற்ற, வகை அறிவிப்பில் கேள்விக்குறியைச் சேர்க்கவும்." + +#: ../../src/faq.md:247 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr " " + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "Enum உள்ளீடுகள்" + +#: ../../src/faq.md:250 +#: 10af80fa13af4158aec7060550485350 +msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" +"ஒரு குறிப்பிட்ட உள்ளீடு தேவைப்படும் கட்டளை வரி கொடிகளுக்கு CWL இல் ஒரு enum வகையை " +"அறிவிக்க முடியும். ** இங்கே NULL ஐக் குறிப்பிடுவது நீண்ட வடிவ பாணி என்று " +"அழைக்கப்படுகிறது. இது மற்ற உள்ளீடுகளில் கேள்விக்குறியைப் போலவே செய்கிறது. **" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr " " + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "உள்ளீடுகளை பதிவு செய்யுங்கள்" + +#: ../../src/faq.md:270 +#: 52b8538177c64090af51f5f6a696c28c +msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." +msgstr "" +"** பரச்பர பிரத்தியேக ** அல்லது ** சார்பு ** ஒரு சிறப்பு பதிவு வகையை வரையறுக்கலாம். " +"விருப்ப உள்ளீடுகளை உருவாக்க நீங்கள் இங்கே NULL ஐ குறிப்பிடலாம்." + +#: ../../src/faq.md:322 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "பரச்பர பிரத்தியேக அளவுருக்களை அமைத்தல்" + +#: ../../src/faq.md:324 +#: 7dc0540508084a3495ff3b2ac90fd323 +msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." +msgstr "" +"பதிவு உள்ளீட்டு வகையில் புலங்களை சரியாக அமைக்க, அளவுருக்களை சரியாக அமைக்க நீங்கள் ஒரு " +"அகராதியை உள்ளீட்டிற்கு அனுப்ப வேண்டும். இன்லைன் சாவாச்கிரிப்டைப் பயன்படுத்துவதன் மூலமும், " +"நீங்கள் அமைக்க விரும்பும் புலத்தின் விசையுடன் அகராதியைத் திருப்புவதன் மூலமும் இது " +"செய்யப்படுகிறது. பணிப்பாய்வுகளிலிருந்து உள்ளீடு மதிப்பாக பயன்படுத்தப்படுவதைக் குறிக்க மூல " +"புலம் அமைக்கப்பட்டுள்ளது." + +#: ../../src/faq.md:342 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "பூலியன்சை அமைத்தல்" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "இயல்புநிலை புலத்தைப் பயன்படுத்தி இவற்றை அமைக்கலாம்" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "உள்ளீடுகளில் சரங்களை இணைத்தல்" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "இயல்புநிலைக்கு பதிலாக மதிப்பு முதல் புலம் பயன்படுத்தப்பட வேண்டும்." + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" +"`cwltool` பிழைகள் உள்ளே உள்ள விண்வெளி எழுத்துக்களைக் கொண்ட கோப்பு பெயர்கள் காரணமாக" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" +"`cwltool` இயல்புநிலையாக கோப்பு பெயர்களில் சில எழுத்துக்களை அனுமதிக்காது." + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" +"எடுத்துக்காட்டாக, `ஒரு இடம் இங்கே உள்ளது. TXT` 3 விண்வெளி எழுத்துக்களை உள்ளடக்கியது." + +#: ../../src/faq.md:371 +#: 182959fc9f4746d082994e07d05c8cde +msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." +msgstr "" +"இந்த ஆபத்தான கதாபாத்திரங்களை நீங்கள் தவிர்க்க முடியாவிட்டால், `--ரெலாக்ச்-பாத்-செக்ச்` ஐ` " +"cwltool` க்கு அனுப்பவும்." + +#: ../../src/faq.md:373 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" +"உள்ளீட்டு அடையாளங்காட்டியில் ஐபன் காரணமாக சி.டபிள்யூ.எல் அளவுரு குறிப்பு பிழை" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "`Cwltool -வாலிடேட்` வருவது செல்லுபடியாகும்" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "ஆனால் அதை செயல்படுத்துவது போன்ற பிழையை ஏற்படுத்துகிறது:" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "கோப்பு இங்கே உள்ளது" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "`-` (ஐபன் எழுத்து) காரணமாக ஏற்படும் சிக்கல்." + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "இந்த பிழையை சரிசெய்ய, `-` (ஐபன்)" + +#: ../../src/faq.md:436 +#: 190099a242a645c9b9f8bc3ce89d920d +msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" +msgstr "" +"உள்ளீட்டு அடையாளங்காட்டியை மாற்ற முடியாவிட்டால், நீங்கள் ஒரு மாற்று CWL அளவுரு குறிப்பு " +"தொடரியல் பயன்படுத்தலாம்:" + +#: ../../src/faq.md:442 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" +"சி.டபிள்யூ.எல் மற்றும் சி.டபிள்யூ.எல்.டூலை ஒருமைப்பாட்டுடன் பயன்படுத்தவும்" + +#: ../../src/faq.md:445 +#: 1901c34201054a9cae199b0dbb8b945e +msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." +msgstr "" +"சி.டபிள்யூ.எல் தரநிலைகள் (விருப்ப) கப்பல்துறை வடிவமைப்பு கொள்கலன்களைச் சுற்றி கட்டப்பட்டுள்" +"ளன. குறிப்பு ரன்னர் மற்றும் பல சி.டபிள்யூ.எல் செயலாக்கங்கள் அந்த கப்பல்துறை வடிவமைப்பு " +"கொள்கலன்களை ஒருமைப்பாட்டு இயந்திரத்தைப் பயன்படுத்தி இயக்குகின்றன. ஒரு ஒருமை வடிவமைப்பு " +"கொள்கலனை நேரடியாகக் குறிப்பிடுவது CWL தரங்களின் ஒரு பகுதியாக இல்லை." + +#: ../../src/faq.md:450 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "சாவாச்கிரிப்ட் வெளிப்பாடுகள் பிழைத்திருத்த" + +#: ../../src/faq.md:452 +#: d7b044f5224a48eda09bc949cf645193 +msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" +msgstr "" +"நீங்கள் -JS-CONSOLE cwltool இன் விருப்பத்தைப் " +"பயன்படுத்தலாம், அல்லது உங்கள் குறியீட்டிற்கான சாவாச்கிரிப்ட் அல்லது டைப்ச்கிரிப்ட் திட்டத்தை " +"உருவாக்க முயற்சி செய்யலாம், மேலும் <குறியீடு> எக்ச்பிரசன் லிப் <ஐப் பயன்படுத்தி அதை ஏற்றலாம்" +" /குறியீடு>, எ.கா. -L8 \"> https://github.com/common-workflow-language/" +"common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#-l8 < /dd>" + +#: ../../src/index.md:1 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "பொதுவான பணிப்பாய்வு மொழி பயனர் வழிகாட்டி" + +#: ../../src/index.md:3 +#: f8d6e4cd54cb42c88182a43171d97bab +msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." +msgstr "" +"[பொதுவான பணிப்பாய்வு மொழி] (https://www.commonwl.org/) (சி.டபிள்யூ.எல்) திறந்த " +"தரங்களைப் பயன்படுத்தி பணிப்பாய்வுகளை எழுதுவதற்கு இந்த வழிகாட்டி உங்களை அறிமுகப்படுத்தும். " +"இந்த வழிகாட்டி அண்மைக் கால விவரக்குறிப்பை விவரிக்கிறது {{ cwl_version }}." + +#: ../../src/index.md:7 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "பங்களிப்புகள் மற்றும் பின்னூட்டங்கள் வரவேற்கப்படுகின்றன!" + +#: ../../src/index.md:9 +#: 0f47157605a34ea58770ea898deebae4 +msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." +msgstr "" +"இந்த வழிகாட்டியிலிருந்து ஏதேனும் காணவில்லை என்று நீங்கள் கண்டால், அல்லது பிற கருத்துக்களை " +"வழங்க விரும்பினால், [இந்த வழிகாட்டிக்கான திட்ட களஞ்சியத்தில்] [ரெப்போ] இல் சிக்கலை தாக்கல் " +"செய்யுங்கள். ஒவ்வொரு பக்கத்தின் வலது பக்கப்பட்டியில் \"இந்த பக்கத்தைத் திருத்து\" பொத்தானைக் " +"சொடுக்கு செய்வதன் மூலம் இழுக்கும் கோரிக்கையில் நேரடியாக மாற்றங்களை நீங்கள் பரிந்துரைக்கலாம்." + +#: ../../src/index.md:16 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "பயனர் வழிகாட்டியை வழிநடத்துதல்" + +#: ../../src/index.md:18 +#: ed74c9a4b623464480e2c184668fcec0 +msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" +"நீங்கள் ஒரு தொடக்க பயனராக இருந்தால் [அறிமுகம்] (/அறிமுகம்/INDEX.MD) பிரிவில் தொடங்கலாம்" +". மேம்பட்ட பயனர்களுக்கு [தலைப்புகள்] (/தலைப்புகள்/குறியீட்டு." + +#: ../../src/index.md:23 +#: cfa67cf5521b414da6f7d34cbed283f7 +msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." +msgstr "" +"உள்ளடக்க அட்டவணை மேல் மெனுவிலும் இடது பக்கப்பட்டியிலும் காட்டப்படும். இது இந்த பக்கத்தின் " +"மேலும் கீழே தோன்றுகிறது, ஆனால் துணைப்பிரிவுகளுக்கான இணைப்புகளுடன். வலது பக்கப்பட்டியில் " +"ஒவ்வொரு பக்கத்தின் பிரிவுகளுக்கான இணைப்புகள் உள்ளன, மேலும் தேடல் படிவம் இடது பக்கப்பட்டியில்" +" உள்ளது." + +#: ../../src/index.md:28 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "உள்ளடக்க அட்டவணை" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "அடிப்படை கருத்துக்கள்" + +#: ../../src/introduction/basic-concepts.md:3 +#: ac62d326a68145b695e46b714d4e8156 +msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." +msgstr "" +"இந்த பிரிவு பயனர்கள் பொதுவான பணிப்பாய்வு மொழி (சி.டபிள்யூ.எல்) பணிப்பாய்வுகளுடன் " +"பணிபுரியத் தொடங்குவதற்கான அடிப்படைக் கருத்துக்களை விவரிக்கிறது. வாசகர்கள் பணிப்பாய்வு " +"மேலாளர்கள், YAML உடன் நன்கு அறிந்திருப்பார்கள், மேலும் கட்டளை வரிக்கான பின்வரும் " +"வழிமுறைகளுடன் வசதியாக இருப்பார்கள். பயனர் வழிகாட்டியின் பிற பிரிவுகள் அதே கருத்துக்களை " +"உள்ளடக்கியது, ஆனால் இன்னும் விரிவாக. நீங்கள் ஏற்கனவே சி.டபிள்யூ.எல் உடன் தெரிந்திருந்தால் " +"அல்லது நீங்கள் இன்னும் மேம்பட்ட உள்ளடக்கத்தைத் தேடுகிறீர்களானால், இந்த பகுதியைத் தவிர்க்க " +"விரும்பலாம்." + +#: ../../src/introduction/basic-concepts.md:10 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "CWL விவரக்குறிப்பு" + +#: ../../src/introduction/basic-concepts.md:21 +#: cbe1d761da5b403d9605fa1fb8e62fdf +msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." +msgstr "" +"சி.டபிள்யூ.எல் விவரக்குறிப்பு என்பது சி.டபிள்யூ.எல் சமூகத்தால் எழுதப்பட்ட மற்றும் " +"பராமரிக்கப்படும் ஒரு ஆவணமாகும். விவரக்குறிப்பில் வெவ்வேறு பதிப்புகள் உள்ளன. இந்த பயனர் " +"வழிகாட்டியில் உள்ள பதிப்பு {{ cwl_version }} ஆகும்." + +#: ../../src/introduction/basic-concepts.md:25 +#: 3a71b269bd3c49eb913cf69b60373c24 +msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." +msgstr "" +"விவரக்குறிப்பு பதிப்பில் `. கள் (புள்ளிகள்) பிரிக்கப்பட்ட மூன்று எண்கள் வரை இருக்கலாம். முதல்" +" எண் முக்கிய வெளியீடு ஆகும், இது நீக்கப்பட்ட அம்சங்களை அகற்றுவது போன்ற பின்தங்கிய-இணக்கமான " +"மாற்றங்களுக்கு பயன்படுத்தப்படுகிறது. இரண்டாவது எண் சிறிய வெளியீடு ஆகும், இது புதிய " +"நற்பொருத்தங்கள் அல்லது பின்தங்கிய-இணக்கமான சிறிய மாற்றங்களுக்குப் பயன்படுத்தப்படுகிறது. " +"எழுத்துப்பிழைகள் மற்றும் விவரக்குறிப்புக்கான பிற திருத்தங்கள் போன்ற பிழை திருத்தங்களுக்கு " +"கடைசி எண் பயன்படுத்தப்படுகிறது." + +#: ../../src/introduction/basic-concepts.md:33 +#: b171b72c48d44050a3416a7a42c4021d +msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." +msgstr "" +"விவரக்குறிப்பு பதிப்பிற்கு பயன்படுத்தப்படும் மாதிரி சொற்பொருள் பதிப்பு என்று " +"அழைக்கப்படுகிறது. இதைப் பற்றி [மேலும் அறிக] (#கற்றுக்கொள்ள) இந்த பிரிவின் முடிவைக் காண்க." + +#: ../../src/introduction/basic-concepts.md:37 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "செயல்படுத்தல்கள்" + +#: ../../src/introduction/basic-concepts.md:39 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 +msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." +msgstr "" +"சி.டபிள்யூ.எல் விவரக்குறிப்பின் செயல்படுத்தல் என்பது விவரக்குறிப்பு ஆவணத்தின் பதிப்பில் " +"வரையறுக்கப்பட்டுள்ளதைத் தொடர்ந்து எழுதப்பட்ட எந்தவொரு மென்பொருளாகும். இருப்பினும், " +"செயலாக்கங்கள் விவரக்குறிப்பின் ஒவ்வொரு அம்சத்தையும் செயல்படுத்தாது. சி.டபிள்யூ.எல் " +"செயலாக்கங்கள் திறந்த மூல மற்றும் வணிக உரிமங்களின் கீழ் உரிமம் பெற்றுள்ளன." + +#: ../../src/introduction/basic-concepts.md:44 +#: c3869b4ec5ff47d99e8da79770722e04 +msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." +msgstr "" +"பல முனைகளில் இணையாக பணிகள் திட்டமிடப்பட்டுள்ள கொத்து, முகில் மற்றும் உயர் செயல்திறன் கொண்ட " +"கணினி சூழல்களில் பெரிய அளவிலான பணிப்பாய்வுகளை விவரிக்க சி.டபிள்யூ.எல் மிகவும் " +"பொருத்தமானது." + +#: ../../src/introduction/basic-concepts.md:51 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "சி.டபிள்யூ.எல் விவரக்குறிப்பு, செயலாக்கங்கள் மற்றும் பிற கருவிகள்." + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "செயல்முறைகள் மற்றும் தேவைகள்" + +#: ../../src/introduction/basic-concepts.md:107 +#: 86e6a06992dc4228bfda7add48e28ca3 +msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" +msgstr "" +"ஒரு செயல்முறை என்பது ஒரு கணினி அலகு ஆகும், இது உள்ளீடுகளை எடுத்து வெளியீடுகளை " +"உருவாக்குகிறது. ஒரு செயல்முறையின் நடத்தை உள்ளீடுகள், தேவைகள் மற்றும் குறிப்புகளால் " +"பாதிக்கப்படலாம். CWL விவரக்குறிப்பில் நான்கு வகையான செயல்முறைகள் வரையறுக்கப்பட்டுள்ளன {{ " +"cwl_version }}:" + +#: ../../src/introduction/basic-concepts.md:112 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "ஒரு கட்டளை-வரி கருவி." + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "ஒரு வெளிப்பாடு கருவி." + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "ஒரு செயல்பாடு." + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "ஒரு பணிப்பாய்வு." + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "CWL பொருள்களின் மாதிரியில் கிடைக்கும் செயலாக்க அலகுகள்." + +#: ../../src/introduction/basic-concepts.md:119 +#: cf2922f645904ac7955428ecddc37b8a +msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." +msgstr "" +"ஒரு கட்டளை-வரி கருவி `எதிரொலி`,` எல்.எச்`, மற்றும் `தார்` போன்ற கட்டளை-வரி " +"பயன்பாட்டிற்கான ஒரு ரேப்பர். ஒரு பணிப்பாய்விலிருந்து கட்டளை-வரி கருவியை அழைக்கலாம்." + +#: ../../src/introduction/basic-concepts.md:122 +#: 5f47aae608c041aeb4134d59dad314d2 +msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." +msgstr "" +"ஒரு வெளிப்பாடு கருவி என்பது சாவாச்கிரிப்ட் வெளிப்பாட்டிற்கான ஒரு ரேப்பர். பணிப்பாய்வு " +"மற்றும் கட்டளை-வரி கருவிகளை எளிதாக்குவதற்கு இதைப் பயன்படுத்தலாம், பணிப்பாய்வு " +"செயலாக்கத்தின் பொதுவான பகுதிகளை மீண்டும் பயன்படுத்தக்கூடிய சாவாச்கிரிப்ட் குறியீட்டிற்கு " +"நகர்த்தும், இது உள்ளீடுகளை எடுத்து கட்டளை-வரி கருவி போன்ற வெளியீடுகளை உருவாக்குகிறது." + +#: ../../src/introduction/basic-concepts.md:127 +#: f6f589481d0c4891beaccb63160619ef +msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." +msgstr "" +"செயல்பாடு என்பது ஒரு சுருக்க செயல்முறையாகும், இது உள்ளீடுகளை எடுக்கும், வெளியீடுகளை " +"உருவாக்குகிறது மற்றும் பணிப்பாய்வுகளில் பயன்படுத்தப்படலாம். ஆனால் இது பொதுவாகப் " +"பயன்படுத்தப்படாத ஒரு சிறப்பு செயல்பாடு. இது இந்த பயனர் வழிகாட்டியின் [செயல்பாட்டு " +"பிரிவு] (../ தலைப்புகள்/செயல்பாடுகள். எம்.டி) இல் விவாதிக்கப்படுகிறது." + +#: ../../src/introduction/basic-concepts.md:131 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 +msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." +msgstr "" +"பணிப்பாய்வு என்பது படிகளைக் கொண்ட ஒரு செயல்முறையாகும். படிகள் பிற பணிப்பாய்வு " +"(உள்ளமைக்கப்பட்ட பணிப்பாய்வுகள்), கட்டளை-வரி கருவிகள் அல்லது வெளிப்பாடு கருவிகளாக " +"இருக்கலாம். ஒரு பணிப்பாய்வுகளின் உள்ளீடுகளை அதன் எந்த படிகளுக்கும் அனுப்ப முடியும், அதே " +"நேரத்தில் அதன் படிகளால் விளைவாக்கம் செய்யப்படும் வெளியீடுகள் பணிப்பாய்வுகளின் இறுதி " +"வெளியீட்டில் பயன்படுத்தப்படலாம்." + +#: ../../src/introduction/basic-concepts.md:137 +#: 4ace6b92f4e04a07aa202840ebe36417 +msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" +msgstr "" +"சி.டபிள்யூ.எல் விவரக்குறிப்பு செயலாக்கங்களை கூடுதல் செயல்பாட்டை வழங்க அனுமதிக்கிறது " +"மற்றும் *தேவைகள் *மூலம் பணிப்பாய்வுகளுக்கு முன்நிபந்தனைகளை குறிப்பிடுகிறது. உதாரணமாக, " +"சி.டபிள்யூ.எல் விவரக்குறிப்பில் பல தேவைகள் வரையறுக்கப்பட்டுள்ளன:" + +#: ../../src/introduction/basic-concepts.md:141 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" +"`இன்லைன் சாவாச்கிரிப்ட் பணிப்பாய்வு` - வெளிப்பாடுகளில் சாவாச்கிரிப்ட் இயக்கப்பட்டது." + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" +"`Subworkflowfeaturerequirement` - உள்ளமைக்கப்பட்ட பணிப்பாய்வுகளை இயக்குகிறது." + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" +"`SiteritWorkDirRequirement` - உள்ளீட்டு கோப்பகத்தில் ச்டேசிங் கோப்புகளை " +"கட்டுப்படுத்துகிறது." + +#: ../../src/introduction/basic-concepts.md:145 +#: 037cd0e5ceda482eaeaca03d51745aee +msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." +msgstr "" +"சில சி.டபிள்யூ.எல் ஓட்டப்பந்தய வீரர்கள் விவரக்குறிப்பில் இல்லாத தேவைகளை வழங்கலாம். " +"எடுத்துக்காட்டாக, சி.பீ.யூ தேவைகள் `சி.டபிள்யு.எல்.டி.ஓ.எல்` இல்` சி.டபிள்யூ.எல்.டி.ஓ." +"எல்: குடர் க்யூரமென்ட்` தேவை மூலம் ஆதரிக்கப்படுகின்றன, ஆனால் இது {{ cwl_version }} " +"விவரக்குறிப்பின் ஒரு பகுதியாக இல்லை, மற்ற சி.டபிள்யூ.எல் ஓட்டப்பந்தய வீரர்களால் " +"ஆதரிக்கப்படாது." + +#: ../../src/introduction/basic-concepts.md:151 +#: e4643938445b48cc80eb8973ceeb126e +msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." +msgstr "" +"குறிப்புகள் தேவைகளுக்கு ஒத்தவை, ஆனால் தேவைகள் தேவைப்படும் அம்சங்களை பட்டியலிடுகையில், " +"குறிப்புகள் விருப்ப அம்சங்களை பட்டியலிடுகின்றன. [தேவைகள்] (../ " +"தலைப்புகள்/தேவைகள்-மற்றும்-இன்ட்ச். எம்.டி) பிரிவில் தேவைகள் விரிவாக விளக்கப்பட்டுள்ளன." + +#: ../../src/introduction/basic-concepts.md:155 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "நியாயமான பணிப்பாய்வு" + +#: ../../src/introduction/basic-concepts.md:157 +#: 3eb6a013a2a4478ca2ad134661f65c58 +msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." +msgstr "" +"நியாயமான கொள்கைகள் டிசிட்டல் சொத்துக்களைப் பகிர்வதற்கும் வெளியிடுவதற்கும் ஒரு அடித்தளத்தை " +"அமைத்துள்ளன, குறிப்பாக தரவுகள். நியாயமான கொள்கைகள் இயந்திர அணுகலை வலியுறுத்துகின்றன, " +"மேலும் அனைத்து டிசிட்டல் சொத்துக்களும் கண்டுபிடிக்கப்படக்கூடியவை, அணுகக்கூடியவை, " +"இயங்கக்கூடியவை மற்றும் மீண்டும் பயன்படுத்தக்கூடியவை. பணிப்பாய்வுகள் விஞ்ஞான செயல்முறை " +"நடத்தப்படும் முறைகள் மற்றும் எந்த தரவு உருவாக்கப்படுகின்றன என்பதை குறியாக்குகின்றன. " +"நியாயமான தரவை உருவாக்குவதை பணிப்பாய்வு ஆதரிப்பது முதன்மை மற்றும் நியாயமான கொள்கைகளை " +"பின்பற்றுகிறது. -." + +#: ../../src/introduction/basic-concepts.md:167 +#: 074af9633627470485e5225326d5f20a +msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." +msgstr "" +"சி.டபிள்யூ.எல் \"மேக்\" இல் வேர்களைக் கொண்டுள்ளது மற்றும் பணிகளுக்கு இடையிலான சார்புகளை " +"அடிப்படையாகக் கொண்டு செயல்படுத்தும் வரிசையை நிர்ணயிக்கும் பல ஒத்த கருவிகள் உள்ளன. " +"இருப்பினும், \"மேக்\" போலல்லாமல், சி.டபிள்யூ.எல் பணிகள் தனிமைப்படுத்தப்பட்டுள்ளன, மேலும் " +"உங்கள் உள்ளீடுகள் மற்றும் வெளியீடுகள் குறித்து நீங்கள் வெளிப்படையாக இருக்க வேண்டும்." + +#: ../../src/introduction/basic-concepts.md:171 +#: 847951c055b94a83b1e081594cef22ee +msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." +msgstr "" +"வெளிப்படையான தன்மை மற்றும் தனிமைப்படுத்தலின் நன்மை நெகிழ்வுத்தன்மை, பெயர்வுத்திறன் மற்றும் " +"அளவிடுதல்; சி.டபிள்யூ.எல் உடன் விவரிக்கப்பட்ட கருவிகள் மற்றும் பணிப்பாய்வுகள் கப்பல்துறை போன்" +"ற தொழில்நுட்பங்களை வெளிப்படையாக மேம்படுத்தலாம் மற்றும் வெவ்வேறு விற்பனையாளர்களிடமிருந்து " +"சி.டபிள்யூ.எல் செயலாக்கங்களுடன் பயன்படுத்தப்படலாம்." + +#: ../../src/introduction/basic-concepts.md:176 +#: 44bde1fae06b4678bcac4f3224601296 +msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." +msgstr "" +"`CWLTool` தரவு ஆதாரத்திற்காக Prov-O நிலையான ஆன்டாலசியையும் பயன்படுத்துகிறது." + +#: ../../src/introduction/basic-concepts.md:178 +#: ../../src/introduction/prerequisites.md:196 +#: ../../src/introduction/quick-start.md:94 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "மேலும் அறிக" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "சொற்பொருள் பதிப்பு - " + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" +"CWL இணையதளத்தில் உள்ள CWL விவரக்குறிப்பு பக்கம்: " + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" +"Github இல் தற்போதைய CWL விவரக்குறிப்பு: {{'' .format (cwl_version_text)}}" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" +"CWL இணையதளத்தில் செயலாக்கங்களின் பட்டியல்: " + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "Prov-o: prov ontology-" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" +"சி.டபிள்யூ.எல் செயல்பாடுகள் இந்த பயனர் வழிகாட்டியின் [செயல்பாடுகள்] (../ " +"தலைப்புகள்/செயல்பாடுகள். எம்.டி) பிரிவில் உள்ளன." + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "அறிமுகம்" + +#: ../../src/introduction/index.md:3 +#: 950370f0a36048b38e1bde9b78f80816 +msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." +msgstr "" +"சி.டபிள்யூ.எல் -க்கு ஒரு குறுகிய அறிமுகம், இந்த பயனர் வழிகாட்டியைப் பின்பற்றுவதற்கான " +"முன்நிபந்தனைகள் மற்றும் மீதமுள்ள பயனர் வழிகாட்டியைப் படிப்பதற்கு முன் தெரிந்து கொள்ள பயனுள்ள " +"சில அடிப்படைக் கருத்துகள் மூலம் இந்த பிரிவு உங்களுக்கு வழிகாட்டும்." + +#: ../../src/introduction/prerequisites.md:1 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "முன்நிபந்தனைகள்" + +#: ../../src/introduction/prerequisites.md:6 +#: 353b14f06ee845d0a06a829643e31534 +msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." +msgstr "" +"இந்த பிரிவில் பட்டியலிடப்பட்டுள்ள மென்பொருள் மற்றும் உள்ளமைவுகள் இந்த பயனர் வழிகாட்டியைப் " +"பின்பற்றுவதற்கான முன்நிபந்தனைகள். சி.டபிள்யூ.எல் தரநிலைகள் பல்வேறு பணிப்பாய்வு ஓட்டப்பந்தய " +"வீரர்கள் மற்றும் தளங்களால் செயல்படுத்தப்படுகின்றன. தேவைகளின் இந்த பட்டியல் CWL குறிப்பு ரன்னர்" +", `CWLTOOL` இல் கவனம் செலுத்துகிறது. நீங்கள் மற்றொரு சி.டபிள்யூ.எல்-இணக்கமான ரன்னர் அல்லது" +" பணிப்பாய்வு முறையைப் பயன்படுத்தலாம், ஆனால் முடிவுகள் மற்றும் இடைமுகம் வித்தியாசமாகத் " +"தோன்றலாம் (சரியான பணிப்பாய்வு வெளியீடுகள் ஒரே மாதிரியாக இருக்க வேண்டும் என்றாலும்)." + +#: ../../src/introduction/prerequisites.md:12 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "சி.டபிள்யூ.எல் செயலாக்கங்கள்" + +#: ../../src/introduction/prerequisites.md:14 +#: ff2bb4c6504b456bac7ca9c514414dbf +msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" +"சி.டபிள்யூ.எல் தரநிலைகளில் பல செயலாக்கங்கள் உள்ளன. சில முழுமையான சி.டபிள்யூ.எல் ஓட்டப்பந்" +"தய வீரர்கள், மற்றவர்கள் பணிப்பாய்வு இயந்திரங்களுக்கு செருகுநிரல்கள் அல்லது நீட்டிப்புகளாக " +"இருக்கலாம். [செயலாக்கங்கள்] (அடிப்படை-கருத்துக்கள். எம்.டி#செயலாக்கங்கள்) பிரிவில் எங்களுக்கு" +" சிறந்த விளக்கம் உள்ளது." + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "இயக்க முறைமை" + +#: ../../src/introduction/prerequisites.md:21 +#: 5089fdba8aed4113983fa86e698df98b +msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" +msgstr "" +"புதுப்பித்த இயக்க முறைமையைப் பயன்படுத்த பரிந்துரைக்கிறோம். உங்கள் இயக்க முறைமைக்கு பின்வரும்" +" விருப்பங்களில் ஏதேனும் ஒன்றை நீங்கள் தேர்வு செய்யலாம்:" + +#: ../../src/introduction/prerequisites.md:24 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "லினக்ச்" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "மேகோச்" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "சாளரங்கள்" + +#: ../../src/introduction/prerequisites.md:29 +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 +msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." +msgstr "" +"நீங்கள் விண்டோசைப் பயன்படுத்துகிறீர்கள் என்றால், நீங்கள் [லினக்ச் 2 க்கான சாளரங்கள் துணை அமைப்பு] " +"(https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2) ஐ நிறுவ வேண்டும்" +". WSL2 ஐ நிறுவுவது குறித்த விவரங்களுக்கு `cwltool` [ஆவணம்] (https://github.com/" +"common-workflow-language/cwltool/blob/readme.rst#ms-mys-windows-users) ஐப் " +"பார்வையிடவும். உங்கள் இயக்க முறைமைக்கு இணைய அணுகல் மற்றும் பைதானின் அண்மைக் கால பதிப்பு (3" +".6+) தேவை." + +#: ../../src/introduction/prerequisites.md:35 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "கூல் ரன்னர்" + +#: ../../src/introduction/prerequisites.md:41 +#: 0f2704bf1f7148be95e999e312899f11 +msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." +msgstr "" +"சி.டபிள்யூ.எல் பணிப்பாய்வுகளை இயக்குவதற்கு உங்களுக்கு முதல் சேதி சி.டபிள்யூ.எல் ரன்னர். " +"`CWLTool` என்பது CWL சமூகத்தால் பராமரிக்கப்படும் பைதான் திறந்த மூல திட்டமாகும். இது " +"CWL குறிப்பு ரன்னர் ஆகும், அதாவது தற்போதைய CWL விவரக்குறிப்பில் உள்ள அனைத்தையும் இது " +"ஆதரிக்க வேண்டும், {{ cwl_version }}." + +#: ../../src/introduction/prerequisites.md:46 +#: 86264c9e56104ecea9146407c379aae2 +msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" +msgstr "" +"`cwltool` உடன்` பிப்` உடன் நிறுவலாம். `Vev` அல்லது` Conda` போன்ற மெய்நிகர் சூழலைப் " +"பயன்படுத்த பரிந்துரைக்கிறோம். பின்வரும் கட்டளைகள் `VENV` தொகுதியைப் பயன்படுத்தி பைதான் " +"மெய்நிகர் சூழலை உருவாக்கி செயல்படுத்தும், மேலும் அந்த சூழலில்` CWLTool` ஐ நிறுவும்:" + +#: ../../src/introduction/prerequisites.md:51 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "`PIP` மற்றும்` vev` உடன் `cwltool` ஐ நிறுவுகிறது." + +#: ../../src/introduction/prerequisites.md:62 +#: f7aaafeee230400da056464c853582c2 +msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." +msgstr "" +"`Cwltool` உடன்` apt` மற்றும் `கான்டா` உடன் நிறுவ பிற வழிகளில்` cwltool` [ஆவணம்] " +"(https://github.com/common-workflow-language/cwltool#install) ஐப் பார்வையிடவும்." + +#: ../../src/introduction/prerequisites.md:65 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" +"`Cwltool` உடன் எளிய CWL கருவி விளக்கத்தை` true.cwl` ஐப் பயன்படுத்துவோம்." + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "`True.cwl`" + +#: ../../src/introduction/prerequisites.md:73 +#: 6391e08e0bde49f4b21286d8fdb97433 +msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" +msgstr "" +"சி.டபிள்யூ.எல் கருவி மற்றும் பணிப்பாய்வு விளக்கங்களை சரிபார்க்க `CWLTOOL` கட்டளைக்கு ஒரு " +"விருப்பம் உள்ளது. இந்த விருப்பம் சி.டபிள்யூ.எல் ஆவணத்தை அலச, தொடரியல் பிழைகளைத் தேடும், " +"மற்றும் பணிப்பாய்வு விளக்கங்கள் சி.டபிள்யூ.எல் தரங்களுக்கு இணங்குகின்றன என்பதை சரிபார்க்கவும்" +". இருப்பினும், இந்த நடவடிக்கைகள் ஆவணத்தை இயக்காமல் செய்யப்படும். சி.டபிள்யூ.எல் " +"பணிப்பாய்வுகளை சரிபார்க்க (அல்லது மேலே உள்ளதைப் போன்ற ஒரு முழுமையான கட்டளை வரி கருவி " +"விளக்கம் கூட) `-வாலிடேட்` விருப்பத்தை` cwltool` கட்டளைக்கு அனுப்பவும்:" + +#: ../../src/introduction/prerequisites.md:79 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "`Cwltool` உடன்` true.cwl` ஐ சரிபார்க்கிறது." + +#: ../../src/introduction/prerequisites.md:84 +#: d41c4bc740aa474ea09a7cbd267c8840 +msgid "You can run the CWL tool description by omitting the `--validate` option:" +msgstr "" +"`-வாலிடேட்` விருப்பத்தைத் தவிர்ப்பதன் மூலம் நீங்கள் CWL கருவி விளக்கத்தை இயக்கலாம்:" + +#: ../../src/introduction/prerequisites.md:86 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "`Cwltool` உடன்` true.cwl` ஐ இயக்குகிறது." + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "கூல்-ரன்னர் பைதான் தொகுதி" + +#: ../../src/introduction/prerequisites.md:93 +#: 096d0a50f69e48bd9915238d1b4264c1 +msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." +msgstr "" +"`சி.டபிள்யூ.எல்-ரன்னர்` என்பது எந்தவொரு சி.டபிள்யூ.எல் இணக்கமான ஓட்டப்பந்தய வீரருக்கும் ஒரு " +"செயல்படுத்தல்-அஞ்ஞான மாற்றாகும். இதன் பொருள் என்னவென்றால், `சி.டபிள்யூ.எல்-ரன்னர்` மாற்று " +"கட்டளை சுயாதீனமாக செயல்படுத்தப்படலாம், மேலும் ஒரு குறிப்பிட்ட சி.டபிள்யூ.எல் ரன்னர் நிரல் " +"பெயரை நம்பவில்லை. `CWLTool` போன்ற CWL ரன்னரை நேரடியாகப் பயன்படுத்துவதற்குப் பதிலாக " +"பயனர்கள்` CWL- ரன்னர்` ஐ அழைக்கலாம். விருப்பமான சி.டபிள்யூ.எல் செயல்படுத்தலை சுட்டிக்காட்ட " +"கணினி நிர்வாகி அல்லது பயனரால் `சி.டபிள்யூ.எல்-ரன்னர்` நிறுவப்பட்டுள்ளது. பல சி.டபிள்யூ." +"எல் ஓட்டப்பந்தய வீரர்களைக் கொண்ட சூழல்களுக்கு இது வசதியானது." + +#: ../../src/introduction/prerequisites.md:101 +#: f9df974a8e2645a6918e67466bd1fdc2 +msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" +msgstr "" +"சி.டபிள்யூ.எல் சமூகம் `cwlref- ரன்னர்` என்ற பெயருடன் ஒரு பைதான் தொகுப்பை வெளியிடுகிறது" +", இது` cwltool` க்கான மாற்றுப்பெயரை `CWL-RUNNER` என்ற பெயரில் நிறுவுகிறது" + +#: ../../src/introduction/prerequisites.md:104 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" +"Cwltool க்கு `பிப்` உடன்` சி.டபிள்யூ.எல்-ரன்னர்` மாற்றுப்பெயரை நிறுவுகிறது." + +#: ../../src/introduction/prerequisites.md:111 +#: 746c6fc9c29d466494458a08d4c96672 +msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." +msgstr "" +"இப்போது நீங்கள் உங்கள் பணிப்பாய்வுகளை `சி.டபிள்யூ.எல்-ரன்னர்` இயங்கக்கூடியதாக சரிபார்த்து " +"இயக்கலாம், இது` cwltool` ஐ அழைக்கும். முந்தைய பிரிவில் உள்ள அதே முடிவுகள் மற்றும் " +"வெளியீட்டை நீங்கள் கொண்டிருக்க வேண்டும்." + +#: ../../src/introduction/prerequisites.md:115 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "`Cwl-runner` உடன்` true.cwl` ஐ சரிபார்க்கிறது." + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "`Cwl-runner` உடன்` true.cwl` ஐ இயக்குகிறது." + +#: ../../src/introduction/prerequisites.md:125 +#: 705807fae182425dbf4244dbf2be1226 +msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" +"`சி.டபிள்யூ.எல்-ரன்னர் 'ஐ இயக்க மற்றொரு வழி கோப்பை நேரடியாக அழைப்பதன் மூலம். அதற்காக, " +"நீங்கள் செய்ய வேண்டிய முதல் சேதி `true.cwl` பணிப்பாய்வுகளை ஒரு புதிய கோப்பில் நகலெடுக்க " +"வேண்டும்:` true_shebang.cwl`, மற்றும் ஒரு சிறப்பு முதல் வரியான ஒரு *செபாங் *:" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "`true_shebang.cwl`" + +#: ../../src/introduction/prerequisites.md:135 +#: 164c438baab54ec19bbb4584a10dd411 +msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." +msgstr "இப்போது நீங்கள் `chmod u+x` உடன் இயங்கக்கூடிய கோப்பை உருவாக்கலாம்." + +#: ../../src/introduction/prerequisites.md:137 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "`True.cwl` இயங்கக்கூடியது." + +#: ../../src/introduction/prerequisites.md:144 +#: 695184d1b45a42f393e2da99c3721773 +msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." +msgstr "" +"இறுதியாக, நீங்கள் அதை நேரடியாக கட்டளை வரிசையில் இயக்கலாம். செயல்படுத்தும்போது, செபாங்கில்" +" குறிப்பிடப்பட்டுள்ள நிரல் (`சி.டபிள்யூ.எல்-ரன்னர்`) மீதமுள்ள கோப்பை இயக்க பயன்படுத்தப்படும்." + +#: ../../src/introduction/prerequisites.md:148 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "ஒரு செபாங்குடன் `true_shebang.cwl` ஐ இயக்குகிறது." + +#: ../../src/introduction/prerequisites.md:154 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 +msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," +msgstr "" +"* செபாங் * என்பது ஒரு ச்கிரிப்ட்டின் தொடக்கத்தில் `#!` என்பது இரண்டு-எழுத்து வரிசை. " +"ச்கிரிப்ட் இயங்கக்கூடியதாக இருக்கும்போது, செபாங்குக்குப் பிறகு குறிப்பிடப்பட்ட " +"இயங்கக்கூடியதைப் பயன்படுத்தி இயக்க முறைமை ச்கிரிப்டை இயக்கும். `/Usr/bin/env " +"` `<இயங்கக்கூடிய>` நிரலைத் தேடுவதால், கடினமான குறியிடப்பட்ட " +"இருப்பிடத்தைப் பயன்படுத்துவதை விட `/usr/bin/env <இயங்கக்கூடிய>` பயன்படுத்துவது ஒரு நல்" +"ல நடைமுறையாகக் கருதப்படுகிறது கணினி `பாதை`," + +#: ../../src/introduction/prerequisites.md:161 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "உரை ஆசிரியர்" + +#: ../../src/introduction/prerequisites.md:163 +#: f6b39b12bd5c495cb53e2795bf9200ed +msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." +msgstr "" +"நீங்கள் சி.டபிள்யூ.எல் உடன் எந்த உரை திருத்தியையும் பயன்படுத்தலாம், ஆனால் தொடரியல் " +"சிறப்பம்சமாக நாங்கள் YAML ஆதரவுடன் ஒரு எடிட்டரை பரிந்துரைக்கிறோம். பிரபலமான ஆசிரியர்கள் " +"விசுவல் ச்டுடியோ குறியீடு, கம்பீரமான, வெப்ச்டார்ம், விஐஎம்/நியோவிம் மற்றும் ஈமாக்ச்." + +#: ../../src/introduction/prerequisites.md:167 +#: 2fdb62a13f9447bc89183426260ce781 +msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" +msgstr "" +"சி.டபிள்யூ.எல் உடன் ஒருங்கிணைப்பை வழங்கும் விசுவல் ச்டுடியோ குறியீடு மற்றும் வெப்ச்டார்ம் " +"ஆகியவற்றிற்கான நீட்டிப்புகள் உள்ளன, மேலும் தனிப்பயனாக்கப்பட்ட தொடரியல் சிறப்பம்சமாக மற்றும் " +"சிறந்த ஆட்டோ-முழுமையானவை போன்ற நற்பொருத்தங்கள் உள்ளன:" + +#: ../../src/introduction/prerequisites.md:171 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" +"பென்டென் (சி.டபிள்யூ.எல்) சொருகி கொண்ட விசுவல் ச்டுடியோ குறியீடு-" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" +"இன்டெல்லினுக்கான சி.டபிள்யூ.எல் சொருகி-" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" +"சி.டபிள்யூ.எல் சமூகம் ஆசிரியர்கள் மற்றும் பார்வையாளர்களின் பட்டியலையும் பராமரிக்கிறது: " +"" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "கப்பல்துறை" + +#: ../../src/introduction/prerequisites.md:181 +#: 40cfd559d6a848d1aae354d3bdaa8e9c +msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." +msgstr "" +"`CWLTool` ஒரு மென்பொருள் கொள்கலனைக் குறிப்பிடும் கருவிகள், பணிப்பாய்வு மற்றும் பணிப்பாய்வு" +" படிகளை இயக்க டோக்கரைப் பயன்படுத்துகிறது. உங்கள் இயக்க முறைமைக்கு அதை நிறுவ கப்பல்துறை " +"ஆவணத்தில் உள்ள வழிமுறைகளைப் பின்பற்றவும்: ." + +#: ../../src/introduction/prerequisites.md:185 +#: 8a9a50b0ebe847ce90593881ffe0d69c +msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." +msgstr "" +"கப்பல்துறை கொள்கலன்களை எவ்வாறு எழுதுவது மற்றும் உருவாக்குவது என்பதை நீங்கள் அறிய " +"தேவையில்லை. மீதமுள்ள பயனர் வழிகாட்டியில், இயங்கும் எடுத்துக்காட்டுகளுக்கு ஏற்கனவே இருக்கும் " +"கப்பல்துறை படங்களைப் பயன்படுத்துவோம், மேலும் கொள்கலன்களுடன் மற்றும் இல்லாமல் செயல்பாட்டு " +"மாதிரிகள் இடையிலான வேறுபாடுகளை தெளிவுபடுத்துவோம்." + +#: ../../src/introduction/prerequisites.md:191 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 +msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." +msgstr "" +"`Cwltool` கப்பல்துறை, போட்மேன், உடோக்கர் மற்றும் ஒருமைப்பாட்டுடன் இயங்கும் கொள்கலன்களை " +"ஆதரிக்கிறது. படங்களை இழுக்க மாற்று கொள்கலன் பதிவுகளையும் பயன்படுத்தலாம்." + +#: ../../src/introduction/prerequisites.md:198 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" +"[செயலாக்கங்கள்] (அடிப்படை-கருத்துக்கள். எம்.டி#செயலாக்கங்கள்) தலைப்பு அடுத்த பிரிவில், " +"அடிப்படை கருத்துக்கள்." + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "பைதான் `வெர்வ்` தொகுதி: " + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "விரைவான தொடக்க" + +#: ../../src/introduction/quick-start.md:3 +#: c43d9675ed134b78b02acb5a102a764a +msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." +msgstr "" +"இந்த பிரிவு சி.டபிள்யூ.எல் என்றால் என்ன என்பதற்கான சுருக்கமான கண்ணோட்டத்தைக் காண்பிக்கும், " +"மேலும் அதைப் பற்றி மேலும் அறியலாம். சி.டபிள்யூ.எல் பற்றிய முந்தைய அறிவு தேவையில்லை, " +"ஆனால் கட்டளை-வரிக்கான வழிமுறைகளைப் பின்பற்றி நீங்கள் வசதியாக இருக்க வேண்டும்." + +#: ../../src/introduction/quick-start.md:7 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "“அலோ வேர்ல்ட்”" + +#: ../../src/introduction/quick-start.md:12 +#: cb203354977d42a58112d09357f62565 +msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" +msgstr "" +"சி.டபிள்யூ.எல் ஆவணங்கள் [YAML] (../ தலைப்புகள்/Index.MD) (மற்றும்/அல்லது JSON) இல் " +"எழுதப்பட்டுள்ளன. கீழேயுள்ள எடுத்துக்காட்டு கருத்துகளுடன் சிறுகுறிப்பு செய்யப்பட்ட ஒரு எளிய " +"சி.டபிள்யூ.எல் “அலோ வேர்ல்ட்” பணிப்பாய்வுகளைக் காட்டுகிறது. கருத்துகள் `#` உடன் தொடங்குகின்" +"றன என்பதை நினைவில் கொள்க:" + +#: ../../src/introduction/quick-start.md:16 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "`Hello_world.cwl`" + +#: ../../src/introduction/quick-start.md:22 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 +msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." +msgstr "" +"மேலே உள்ள எடுத்துக்காட்டு `எதிரொலி` கட்டளை-வரி கருவிக்கான ஒரு ரேப்பர் மட்டுமே. " +"இயல்புநிலை உள்ளீட்டு மதிப்புகளுடன் மேலே உள்ள பணிப்பாய்வுகளை இயக்குவது கட்டளை-வரி " +"`எதிரொலி\" அலோ வேர்ல்ட் \"` போன்ற அதே முடிவை உருவாக்கும்." + +#: ../../src/introduction/quick-start.md:27 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 +msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." +msgstr "" +"சி.டபிள்யூ.எல் இல், ஒரு கட்டளை-வரி கருவி மற்றும் பணிப்பாய்வு இடையே வேறுபாடு உள்ளது. " +"ஆனால் எளிமைக்காக, நாங்கள் இங்கே “பணிப்பாய்வு” என்ற வார்த்தையைப் பயன்படுத்துகிறோம். இதைப் " +"பற்றி [அடிப்படை கருத்துக்கள்] (அடிப்படை-கருத்துக்கள். எம்.டி) பிரிவில் மேலும் அறிந்து " +"கொள்வீர்கள்." + +#: ../../src/introduction/quick-start.md:32 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "CWL ரன்னரை நிறுவுதல்" + +#: ../../src/introduction/quick-start.md:34 +#: f3e56aedd56b4b93bdc3894273e8c144 +msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" +"`CWLTOOL` என்பது CWL விவரக்குறிப்பின் செயல்படுத்தல் ஆகும். இது விவரக்குறிப்பிற்கான CWL *" +" குறிப்பு ரன்னர் * ஆகும், மேலும் இது விவரக்குறிப்பின் அண்மைக் கால பதிப்போடு இணங்குகிறது: " +"{{ cwl_version }}. `பிப்` ஐப் பயன்படுத்தி` cwltool` ஐ நிறுவலாம்:" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "`பிப்` உடன்` cwltool` ஐ நிறுவுகிறது." + +#: ../../src/introduction/quick-start.md:47 +#: a81342e756d24c40acc15835d0a768f2 +msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." +msgstr "" +"PIP கட்டளையைப் பயன்படுத்தி CWLTool ஐ நிறுவுவது உங்களுக்காக வேலை செய்யாது என்றால், " +"[முன்நிபந்தனைகள்] (முன்நிபந்தனைகள். MD) பிரிவில் `CWLTool` ஐ நிறுவ பிற வழிகள் உள்ளன, " +"மேலும் இந்த பயனரின் மீதமுள்ளவற்றை பின்பற்ற பயன்படுத்தப்படும் மென்பொருள் மற்றும் நூலகங்களின் " +"விரிவான பட்டியலையும் கொண்டுள்ளது வழிகாட்டி." + +#: ../../src/introduction/quick-start.md:51 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "\"அலோ வேர்ல்ட்\"" + +#: ../../src/introduction/quick-start.md:53 +#: 9b68bcb1a41849dc9601ab47c5bbb0fe +msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" +msgstr "" +"`Cwltool` கட்டளை-வரி இயங்கக்கூடிய பயன்பாடு அடிப்படையில்` cwltool [விருப்பங்கள்] " +" [inputs_object] `. எந்தவொரு விருப்பத்தையும் குறிப்பிடாமல் " +"`Hello_world.cwl` பணிப்பாய்வுகளை இயக்கலாம்:" + +#: ../../src/introduction/quick-start.md:57 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "`Cwltool` உடன்` Hello_world.cwl` ஐ இயக்குகிறது." + +#: ../../src/introduction/quick-start.md:62 +#: 0d8a788402914ebd8f09a5ca80650011 +msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" +msgstr "" +"அல்லது `எதிரொலி` அடிப்படை கட்டளையின் வாதத்தை நீங்கள் எவ்வாறு மாற்றுவீர்கள் என்பதைப் போலவே, " +"உள்ளீட்டு அளவுருவின் இயல்புநிலை மதிப்பை` செய்தியின் 'மேலெழுதலாம்:" + +#: ../../src/introduction/quick-start.md:65 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" +"`Cwltool` உடன் உள்ளீட்டு அளவுருவைக் கடந்து` hello_world.cwl` ஐ இயக்குகிறது." + +#: ../../src/introduction/quick-start.md:70 +#: 2ea056ab04b6419a9faf350de22a17f2 +msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" +"உங்கள் பணிப்பாய்வு உள்ளீட்டு அளவுருக்களுக்கு மதிப்புகளை அனுப்ப மற்றொரு வழி *உள்ளீடுகள் பொருள்" +" *வழியாகும். இது உள்ளீட்டு புலங்களைக் கொண்ட ஒரு கோப்பு, அவற்றின் தொடர்புடைய மதிப்புகளுடன்" +". உள்ளீட்டு பொருள்கள் கோப்பை சாதொபொகு அல்லது YAML இல் எழுதலாம். உதாரணமாக:" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "`Hello_world-job.json`" + +#: ../../src/introduction/quick-start.md:80 +#: e76bfcc0c9f84bcdb3f6d5277869a88c +msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" +msgstr "" +"“அலோ வேர்ல்ட்” பணிப்பாய்வுகளை இயக்க இந்த உள்ளீடுகள் பொருள் கோப்பை இப்போது பயன்படுத்தலாம்:" + +#: ../../src/introduction/quick-start.md:82 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "உள்ளீட்டு பொருள் கோப்பை `cwltool` க்கு அனுப்புகிறது." + +#: ../../src/introduction/quick-start.md:88 +#: b6d59e4b9c854abab1b3f7a0fa26f504 +msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" +"பணிப்பாய்வு மற்றும் உள்ளீடுகள் பொருள் கோப்புகளுக்கு இதே போன்ற கோப்பு பெயரைப் பயன்படுத்தினோம்" +". உள்ளீடுகள் பொருள் கோப்புகளில் * -job.json * பின்னொட்டு மிகவும் பொதுவானது, ஆனால் அது " +"தேவையில்லை. உங்கள் பணிப்பாய்வு மற்றும் உள்ளீடுகள் பொருள் கோப்புகளுக்கான எந்த பெயரையும் நீங்கள் " +"தேர்வு செய்யலாம்." + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "இந்த பயனர் வழிகாட்டியின் அடுத்த பகுதிகளைப் படிக்கவும்!" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" +"[List of CWL Implementations](https://www.commonwl.org/implementations)." + +#: ../../src/introduction/quick-start.md:98 +#: 7282abfa7155497ca47c30f9abfb6474 +msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." +msgstr "" +"கிதுபில் [`பொதுவான-வேலை-மொழி-மொழி` அமைப்பு] (https://github.com/common-" +"workflow-language)." + +#: ../../src/introduction/quick-start.md:99 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" +"[Common Workflow மொழி at Wikipedia](https://en.wikipedia.org/wiki/" +"Common_Workflow_Language)." + +#: ../../src/introduction/quick-start.md:100 +#: 82a7ca3703bc4f0daa18942a1ac8943b +msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." +msgstr "" +"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." +"org/wiki/YAML)." + +#: ../../src/introduction/quick-start.md:101 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" +"{{'[CWL விவரக்குறிப்பு பதிப்பு] (https://www.commonwl.org/version)' .replace " +"('பதிப்பு', cwl_version_text)}}." + +#: ../../src/introduction/quick-start.md:102 +#: fbc3383d9e1c4eaca7931c3cc4f1752b +msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." +msgstr "" +"[Workflow management மண்டலம் at Wikipedia](https://en.wikipedia.org/wiki/" +"Workflow_management_system)." + +#: ../../src/setup.md:9 +#: 1330bd38c4b5495f890b98c669f81a9d +msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." +msgstr "" +"இந்த பக்கம் காலாவதியானது மற்றும் பழைய பயனர் வழிகாட்டியின் இணைப்புகளைப் பாதுகாக்க இங்கே " +"வைக்கப்பட்டது. இந்த பக்கத்தில் உள்ள தகவல்கள் புதிய பயனர் வழிகாட்டியின் [கேள்விகள்] " +"(/கேள்விகள்) பகுதிக்கு இடம்பெயர்ந்துள்ளன." + +#: ../../src/topics/additional-arguments-and-parameters.md:1 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "கூடுதல் வாதங்கள் மற்றும் அளவுருக்கள்" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: ad00d94d4fb64bbdac356e64dd3803b9 +msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." +msgstr "" +"சில நேரங்களில் கருவிகளுக்கு கூடுதல் கட்டளை வரி விருப்பங்கள் தேவைப்படுகின்றன, அவை உள்ளீட்டு" +" அளவுருக்களுடன் சரியாக ஒத்துப்போகின்றன." + +#: ../../src/topics/additional-arguments-and-parameters.md:6 +#: d8110ed19da94ad8a9f56e7006c4a2cf +msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." +msgstr "" +"இந்த எடுத்துக்காட்டில், சாவா மூல கோப்பை ஒரு வகுப்பு கோப்பில் தொகுக்க சாவா கம்பைலரை " +"மடிக்கவும். இயல்பாக, \"சாவாக்\" வகுப்பு கோப்புகளை மூல கோப்பின் அதே கோப்பகத்தில் " +"உருவாக்கும். இருப்பினும், சி.டபிள்யூ.எல் உள்ளீட்டு கோப்புகள் (மற்றும் அவை தோன்றும் கோப்பகங்கள்)" +" படிக்க மட்டுமே இருக்கலாம், எனவே அதற்கு பதிலாக நியமிக்கப்பட்ட வெளியீட்டு கோப்பகத்திற்கு " +"வகுப்பு கோப்பை எழுத \"சாவாக்\" அறிவுறுத்த வேண்டும்." + +#: ../../src/topics/additional-arguments-and-parameters.md:13 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "`வாதங்கள். CWL`" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "`வாதங்கள்-job.yml`" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" +"அடுத்து, கட்டளை-வரி கருவியுடன் பயன்படுத்த மாதிரி சாவா கோப்பை உருவாக்கவும்." + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 9643449da1da46d7861866dce490cbcb +msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" +"இப்போது கட்டளை வரியில் கருவி விளக்கத்தையும் உள்ளீட்டு பொருளையும் வழங்கும் `cwltool` ஐ " +"அழைக்கவும்:" + +#: ../../src/topics/additional-arguments-and-parameters.md:36 +#: 713666580a0a4466b4ba6e3eb2b54f0a +msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." +msgstr "" +"ஒரு குறிப்பிட்ட உள்ளீட்டு அளவுருவுடன் பிணைக்கப்படாத கட்டளை வரியில் கூடுதல் வாதத்தை சேர்க்க " +"இங்கே `வாதங்கள்` புலத்தைப் பயன்படுத்துகிறோம்." + +#: ../../src/topics/additional-arguments-and-parameters.md:43 +#: d50574c8b9694f83aa376d39b9a6fcd6 +msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." +msgstr "" +"இந்த எடுத்துக்காட்டு ஒரு இயக்க நேர அளவுருவைக் குறிக்கிறது. கருவி உண்மையில் " +"செயல்படுத்தப்படும்போது இயக்க நேர அளவுருக்கள் வன்பொருள் அல்லது மென்பொருள் சூழல் பற்றிய " +"தகவல்களை வழங்குகின்றன. `$ (Runtime.outdir)` அளவுரு என்பது நியமிக்கப்பட்ட வெளியீட்டு " +"கோப்பகத்திற்கான பாதை. பிற அளவுருக்களில் `$ (runtime.tmpdir)`, `$ (இயக்க நேரம். " +"விவரங்களுக்கு CWL விவரக்குறிப்பின் [இயக்க நேர சூழல்] [இயக்க நேரம்] பகுதியைப் பார்க்கவும்." + +#: ../../src/topics/best-practices.md:1 +#: 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "சிறந்த நடைமுறைகள்" + +#: ../../src/topics/best-practices.md:3 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 +msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." +msgstr "" +"ஒரு கருவி அல்லது பணிப்பாய்வுக்கான பொதுவான பணிப்பாய்வு மொழி விளக்கத்தை எழுதும் போது " +"மனதில் கொள்ள பரிந்துரைக்கப்பட்ட நல்ல நடைமுறைகளின் தொகுப்பாகும். இந்த வழிகாட்டுதல்கள் பயனற்ற " +"அளவில் பரிசீலிக்க வழங்கப்படுகின்றன: மேலும் சிறந்தது என்றாலும், அனைத்தும் தேவையில்லை." + +#: ../../src/topics/best-practices.md:8 +#: 4bcb84707acb40a0bfe2ea0853cb10b7 +msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." +msgstr "" +"இல்லை `வகை: உள்ளீடு அல்லது குறிப்பு கோப்புகள்/கோப்பகங்களின் பெயர்களுக்கான சரம்` அளவுருக்கள்;" +" `வகை: கோப்பு` அல்லது` வகை: அடைவு` பொருத்தமானதாகப் பயன்படுத்தவும்." + +#: ../../src/topics/best-practices.md:11 +#: 4dee8504a8e5496081dadc386ab45540 +msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." +msgstr "" +"ஒரு சி.டபிள்யூ.எல் ஆவணம் (`டோக்கர்ஃபைல்'ச் போன்ற எந்தவொரு வெளிப்புற கூறுகளுடனும் இணைந்து)" +" மென்பொருள் குறியீடு. மென்பொருள் உரிமத்தின் வழக்கமான விதிகள் இந்த ஆவணத்திற்கு பொருந்தும் " +"என்பதை பணிப்பாய்வு உருவாக்குபவர்கள் அறிந்திருக்க வேண்டும். எடுத்துக்காட்டாக, பணிப்பாய்வு " +"பகிரங்கமாக பகிரப்பட்டால், உரிம விதிமுறைகள் தெளிவாக இருக்க வேண்டும், இதனால் எதிர்கால " +"பயனர் எந்த நிலைமைகளை அவர்கள் பணிப்பாய்வுகளை இயக்கலாம், அதை மாற்றலாம் மற்றும்/அல்லது பிற " +"பணிப்பாய்வுகளுடன் இணைக்க முடியும் என்பதைப் புரிந்துகொள்கிறார். இந்த காரணத்திற்காக, ஆவணத்தில்" +" உரிமம் புலத்தை சேர்ப்பதைக் கவனியுங்கள். இந்த வழிகாட்டியின் ஆசிரியர்கள் உங்கள் சொந்தமாக எழு" +"த முயற்சிப்பதை விட முன்பே இருக்கும் உரிமத்தைத் தேர்வுசெய்யும்படி கேட்டுக்கொள்கிறார்கள் " +"(உரிமத்தைத் தேர்ந்தெடுப்பது பற்றி மேலும் அறிய கீழேயுள்ள இணைப்பைக் காண்க), மேலும் எங்கள் " +"பரிந்துரைக்கப்பட்ட நடைமுறை மீண்டும் பயன்படுத்த அனுமதிக்கும் உரிமத்தைத் தேர்ந்தெடுப்பதாகும் " +"யாராலும், எ.கா. [அப்பாச்சி 2.0] [அப்பாச்சி-லிசென்ச்]." + +#: ../../src/topics/best-practices.md:20 +#: 674c238b25e240eda05e22e399f2f78f +msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." +msgstr "" +"முடிந்தால், உரிமம் அதனுடன் தொடர்புடைய [SPDX அடையாளங்காட்டி] [SPDX] உடன் குறிப்பிடப்பட " +"வேண்டும். `Https://spdx.org/licenses/ [spdx-id]` `SPDX-ID` படிவத்தின் முகவரி ஐ " +"வழங்குவதன் மூலம் உரிமத்திற்கான மேனிலை தரவு புலத்தை உருவாக்குங்கள், அங்கு மேலே இணைக்கப்பட்" +"ட அடையாளங்காட்டிகளின் பட்டியலிலிருந்து எடுக்கப்படுகிறது. வழிகாட்டுதலுக்கு கீழே உள்ள " +"எடுத்துக்காட்டு துணுக்கைக் காண்க. SPDX அடையாளங்காட்டி இல்லாமல் தரமற்ற உரிமங்களுக்கு, " +"உரிமத்திற்கு முகவரி ஐ வழங்கவும்." + +#: ../../src/topics/best-practices.md:26 +#: b651f80f47b4442fbf29454a233697fc +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" +"பயனுள்ள வாசிப்பு: \"[விஞ்ஞானி-புரோகிராமருக்கான மென்பொருள் உரிமத்திற்கான விரைவான " +"வழிகாட்டி] [அறிவியல்-உரிமம்]\"" + +#: ../../src/topics/best-practices.md:28 +#: 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" +"எச்பி SPDX அடையாளங்காட்டியுடன் உரிமத்திற்கான மேனிலை தரவு புலத்தின் மாதிரி: _" + +#: ../../src/topics/best-practices.md:37 +#: 3a87a0fb2a364e3da5aaa4017e430b19 +msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." +msgstr "" +"சி.டபிள்யூ.எல் விளக்கங்களுக்குள் மெட்டாடேட்டாவை வழங்குவதற்கான கூடுதல் எடுத்துக்காட்டுகளுக்கு" +", [இந்த பயனர் வழிகாட்டியின் மேனிலை தரவு மற்றும் எழுத்தாளர் பிரிவு] (../ " +"தலைப்புகள்/மெட்டாடேட்டா-மற்றும்-அணுகல். எம்.டி) ஐப் பார்க்கவும்." + +#: ../../src/topics/best-practices.md:40 +#: ecf2b9c0b1664afe9c4e180610610021 +msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." +msgstr "" +"சி.டபிள்யூ.எல் கருவி அல்லது பணிப்பாய்வு விளக்கத்தின் ஆசிரியர் (கள்) க்கான [பண்புக்கூறு " +"தகவல்] [உரிமம்-எடுத்துக்காட்டுக்கு] சேர்க்கவும். [ORCID] [ORCID] போன்ற தெளிவற்ற " +"அடையாளங்காட்டிகளைப் பயன்படுத்தவும்." + +#: ../../src/topics/best-practices.md:44 +#: e24cb13d98014e558b6a6946758359e0 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" +"கருவி விளக்கங்களில், `சாப்ட்வேர் ரெகுரிகேமென்ட்` இன் கீழ் குறுகிய பெயர் (களை) பயன்படுத்தி " +"சார்புகளை பட்டியலிடுங்கள்." + +#: ../../src/topics/best-practices.md:47 +#: f2b14a92374e449d9fb1e8c86ae0dd61 +msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." +msgstr "" +"`Https: //identifiers.org/rrid/rrid: scr_nnnnnn` வடிவத்தில் சார்புகளுக்கான " +"[SCICRUNCH] [SCICRUNCH] அடையாளங்காட்டிகளைச் சேர்க்கவும்." + +#: ../../src/topics/best-practices.md:50 +#: 928e3df7ca3e479ca6474a8e72cf36eb +msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." +msgstr "" +"அனைத்து `உள்ளீடு` மற்றும்` வெளியீடு` அடையாளங்காட்டிகள் அவற்றின் கருத்தியல் அடையாளத்தை " +"பிரதிபலிக்க வேண்டும். `Foo_Input`,` foo_file`, `முடிவு`,` உள்ளீடு`, `வெளியீடு` " +"மற்றும் பலவற்றிற்கு பதிலாக` Knaligned_uckences`, `resopt_genome`,` பைலோசெனி`, " +"`சீரமைக்கப்பட்ட_ வரிசைமுறைகள்` போன்ற தகவலறிந்த பெயர்களைப் பயன்படுத்தவும்." + +#: ../../src/topics/best-practices.md:55 +#: d355f035676446c88b028f327aeb4829 +msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." +msgstr "" +"கருவி விளக்கங்களில், `சாப்ட்வேர் ரெக்வைமென்ட்` இன் கீழ் இந்த விளக்கத்துடன் வேலை செய்ய அறியப்பட்" +"ட கருவியின் பதிப்பு (கள்) பட்டியலைச் சேர்க்கவும்." + +#: ../../src/topics/best-practices.md:58 +#: 339b852df24242189d6efcd2898a3396 +msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." +msgstr "" +"அனைத்து உள்ளீடு மற்றும் வெளியீடு `கோப்பு'க்கு` வடிவமைப்பு` குறிப்பிடப்பட வேண்டும். " +"பயோ-இன்ஃபர்மேடிக்ச் கருவிகள் [எடாம்] [எடாம்-எடுத்துக்காட்டாக] இருந்து வடிவமைப்பு " +"அடையாளங்காட்டிகளைப் பயன்படுத்த வேண்டும். `Iana: உரை/வெற்று`,` iana: உரை/தாவலால் " +"பிரிக்கப்பட்ட-மதிப்புகள்` `$ பெயர்வெளிகளுடன்: {iana:\" https://www.iana.org/" +"assignments/media-types/ \". [முழு ஐஏஎன்ஏ மீடியா வகை பட்டியல்] [ஐஏஎன்ஏ வகைகள்] (மைம்" +" வகைகள் என்றும் அழைக்கப்படுகிறது). பயோஇன்ஃபர்மேடிக்ச் அல்லாத கருவிகளுக்கு, அதே வழியில் " +"பொருத்தமான ஆன்டாலசி/கட்டுப்படுத்தப்பட்ட சொற்களஞ்சியத்தைப் பயன்படுத்தவும் அல்லது உருவாக்கவும். " +"இதைப் பற்றி எங்களுக்குத் தெரியப்படுத்த இந்தப் பக்கத்தைத் திருத்தவும்." + +#: ../../src/topics/best-practices.md:66 +#: 3ef57e6862f240bebcf193a52397af0a +msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." +msgstr "" +"ச்ட்ரீமிங் இணக்கமான வழியில் (ஒரு முறை மட்டுமே, சீரற்ற-அணுகல் இல்லை), `ச்ட்ரீம் செய்யக்கூடியது:" +" உண்மை` போன்ற அனைத்து உள்ளீடு மற்றும் வெளியீட்டைக் குறிக்கவும்." + +#: ../../src/topics/best-practices.md:69 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c +msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." +msgstr "" +"(துணை) கட்டளை அதிக திறன் கொண்டிருந்தாலும், ஒவ்வொரு `கட்டளை லைனெட்டூல்` விளக்கமும் ஒரு " +"செயல்பாட்டில் மட்டுமே கவனம் செலுத்த வேண்டும். உங்களுக்குத் தேவையில்லாத அல்லது பயன்படுத்தாத " +"விருப்பங்களுடன் உங்கள் கருவி விளக்கங்களை மிகைப்படுத்த வேண்டாம்." + +#: ../../src/topics/best-practices.md:73 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" +"தனிப்பயன் வகைகள் மறு பயன்பாட்டிற்கான ஒரு வகை வரையறைக்கு ஒரு வெளிப்புற YAML உடன் " +"வரையறுக்கப்பட வேண்டும்." + +#: ../../src/topics/best-practices.md:76 +#: c858f64e66f048a5b0032ef3e4d83694 +msgid "Include a top-level short `label` summarising the tool/workflow." +msgstr "" +"கருவி/பணிப்பாய்வுகளை சுருக்கமாகக் கூறி ஒரு உயர்மட்ட குறுகிய `லேபிள்` சேர்க்கவும்." + +#: ../../src/topics/best-practices.md:78 +#: fae385da16aa443da996fa23ac03d6ae +msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." +msgstr "" +"பயனுள்ளதாக இருந்தால், ஒரு உயர்மட்ட `டாக் 'ஐயும் சேர்க்கவும். இது உயர்மட்ட `லேபிளில் " +"'வழங்கப்பட்டதை விட நீண்ட, விரிவான விளக்கத்தை வழங்க வேண்டும் (மேலே காண்க)." + +#: ../../src/topics/best-practices.md:82 +#: 92430be71ecc40e18bbbb80d5576c613 +msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." +msgstr "" +"செல்லுபடியாகும் மதிப்புகளின் நிலையான பட்டியலைக் கொண்ட உறுப்புகளுக்கு `வகை: சரம்` க்கு " +"பதிலாக` வகை: enum` ஐப் பயன்படுத்தவும்." + +#: ../../src/topics/best-practices.md:85 +#: 387d83db81024f65aa9a890c2d07874a +msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." +msgstr "" +"சாத்தியமான நீக்குதல் அல்லது மாற்றுவதற்கு சாவாச்கிரிப்டின் அனைத்து பயன்பாடுகளையும் மதிப்பீடு " +"செய்யுங்கள். ஒரு பொதுவான எடுத்துக்காட்டு: `கோப்பு` பெயர்கள் மற்றும் பாதைகளை " +"கையாளுகிறீர்களா? [`கோப்பு` பண்புகள்] [கோப்பு-முன்மாதிரிகளில்]` பேச்நேம்`, `நமெரூட்`,` " +"நேமெக்ச்ட்` போன்றவற்றில் ஒன்றைப் பயன்படுத்த முடியுமா என்பதைக் கவனியுங்கள்." + +#: ../../src/topics/best-practices.md:90 +#: d8e2280a75a74916a1630afaa2fe2ae3 +msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." +msgstr "" +"கருவி விளக்கத்தை ஒரு தம ஊழியருக்கு (முன்னுரிமை வேறு நிறுவனத்தில்) சோதிக்கவும் " +"கருத்துக்களை வழங்கவும் கொடுங்கள்." + +#: ../../src/topics/best-practices.md:93 +#: f1c1340f9745458980e0fbd641738687 +msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." +msgstr "" +"சுருக்கமாக இருக்கக்கூடிய தனிப்பட்ட கூறுகளைக் கொண்ட சிக்கலான பணிப்பாய்வுகள் " +"[`subworkflowfeaturerequirement`] [subworkflow] ஐப் பயன்படுத்த வேண்டும், அவற்றின் " +"பணிப்பாய்வுகளை மட்டுப்படுத்தவும், அவற்றின் பிரிவுகளை எளிதில் மீண்டும் பயன்படுத்த " +"அனுமதிக்கவும்." + +#: ../../src/topics/best-practices.md:97 +#: 5424e5472c3d466fa2a3d2022c6cb475 +msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." +msgstr "" +"மென்பொருள் கொள்கலன்கள் [\"பயோ -இன்ஃபர்மேடிக்ச் மென்பொருளை பேக்கேசிங் மற்றும் கொள்கலனுக்கான " +"பரிந்துரைகளுக்கு\" இணக்கமாக இருக்க வேண்டும் [கொள்கலன்கள்] (பிற துறைகளுக்கும் பயனுள்ளதாக " +"இருக்கும்)." + +#: ../../src/topics/command-line-tool.md:1 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "கட்டளை வரி கருவி" + +#: ../../src/topics/command-line-tool.md:3 +#: 12f57b2ba76b492abe1816e06bfb1417 +msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." +msgstr "" +"ஒரு கட்டளை-வரி கருவி என்பது ஒரு வகை செயல்முறை பொருளாகும், இது தானாகவே அல்லது " +"பணிப்பாய்வு படியாக இயக்கப்படலாம். இது `ls`,` எதிரொலி`, `தார்` போன்ற ஒரு கட்டளைக்கான " +"ஒரு ரேப்பர் ஆகும். கட்டளை-வரி கருவி CWL ஆவணத்தின்` பேச் கமாண்ட்` பண்புக்கூறில் கட்டளை-வரி " +"கருவி வரையறுக்கப்பட்டுள்ளது." + +#: ../../src/topics/command-line-tool.md:8 +#: e1f657a46ce94a0d83671540e2cc2dab +msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." +msgstr "" +"ஒரு சி.டபிள்யூ.எல் கட்டளை-வரி கருவி `உள்ளீடுகள்` மற்றும்` வெளியீடுகள்` கொண்டிருக்க வேண்டும்" +". உள்ளீடுகள் மற்றும் வெளியீடுகளைப் பயன்படுத்தி `எதிரொலி` லினக்ச் கட்டளைக்கான CWL கட்டளை-வரி" +" கருவியின் குறைந்தபட்ச எடுத்துக்காட்டு பின்வரும் எடுத்துக்காட்டில் உள்ளது." + +#: ../../src/topics/command-line-tool.md:19 +#: abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "CWL கட்டளை-வரி கருவி." + +#: ../../src/topics/command-line-tool.md:50 +#: 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "`echo.cwl`" + +#: ../../src/topics/command-line-tool.md:57 +#: a5eacdbc9aa142c890b177869da4143d +msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." +msgstr "" +"உள்ளீடுகள் மற்றும் வெளியீடுகளை வரையறுக்க மேலே உள்ள எடுத்துக்காட்டு எளிமையான படிவத்தைப் " +"பயன்படுத்துகிறது. [உள்ளீடுகள்] (../ தலைப்புகள்/உள்ளீடுகள். எம்.டி) மற்றும் [வெளியீடுகள்] " +"(../ தலைப்புகள்/வெளியீடுகள்) பிரிவுகளில் நீங்கள் மேலும் அறிந்து கொள்வீர்கள்." + +#: ../../src/topics/command-line-tool.md:68 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "பிணைய அணுகல்" + +#: ../../src/topics/command-line-tool.md:69 +#: e3bdaceae8784ab0807b2cf356a98580 +msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." +msgstr "" +"ஒரு செயல்முறைக்கு வெளிச்செல்லும் ஐபிவி 4/ஐபிவி 6 பிணைய அணுகல் தேவையா என்பதை இது " +"குறிக்கிறது. CWL V1.1+இல் ஒரு கட்டளை-வரி கருவி கைமுறையாக எழுதப்பட்டிருந்தால், பிணைய " +"அணுகல் தேவைப்படும்போது குறிப்பிட வேண்டிய தேவை உள்ளது." + +#: ../../src/topics/command-line-tool.md:83 +#: ed521ac365db4a6ba5a1051fbaa2932e +msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." +msgstr "" +"CWL V1.0 கட்டளை-வரி கருவிகள் V1.1 அல்லது V1.2 க்கு மேம்படுத்தப்படுகின்றன. பிணைய " +"அணுகலை தானாகவே பெறுங்கள்." + +#: ../../src/topics/creating-files-at-runtime.md:1 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "இயக்க நேரத்தில் கோப்புகளை உருவாக்குதல்" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 0cf51b6da6884065ae42032abc20eb0d +msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." +msgstr "" +"சில நேரங்களில் நீங்கள் உள்ளீட்டு அளவுருக்களிலிருந்து பறக்க ஒரு கோப்பை உருவாக்க வேண்டும், " +"அதாவது கட்டளை வரி அளவுருக்களைக் காட்டிலும் ஒரு கோப்பிலிருந்து அவற்றின் உள்ளீட்டு உள்ளமைவைப்" +" படிக்க எதிர்பார்க்கும் கருவிகள் அல்லது சிறிய ரேப்பர் செல் ச்கிரிப்ட் தேவை." + +#: ../../src/topics/creating-files-at-runtime.md:7 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" +"அத்தகைய கோப்புகளை உருவாக்க, நாம் `SiteritWorkDirRequirement` ஐப் பயன்படுத்தலாம்." + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "`criatefile.cwl`" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" +"`$ (உள்ளீடுகள். மெசேச்)` போன்ற எந்த [வெளிப்பாடுகள்] (../ தலைப்புகள்/வெளிப்பாடுகள். இங்கே, " +"`செய்தி` உள்ளீட்டில் மதிப்பை செருகவும்." + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." +msgstr "" +"_CWL வெளிப்பாடுகள்_ கட்டளை வரி கருவி அழைப்பின் போது பின்னர் பயன்படுத்தப்படும் எந்த " +"_shell மாறிகள்_ இலிருந்து சுயாதீனமாக உள்ளன. அதாவது `$` கதாபாத்திரத்தின் உண்மையான " +"தேவையும் `\\` உடன் ** தப்பிக்க வேண்டும் **. உதாரணமாக, மேலே உள்ள `\\ $ {PREFIX}` சி." +"டபிள்யூ.எல் எஞ்சினுக்கு பதிலாக செல் ச்கிரிப்ட் மூலம் மதிப்பீடு செய்ய உருவாக்கப்பட்ட கோப்பில் " +"`$ {PREFIX}` என விரிவுபடுத்தப்படுகிறது." + +#: ../../src/topics/creating-files-at-runtime.md:27 +#: 7f8d99a30b644457a62ac1523d0c72aa +msgid "To test the above CWL tool, use this job to provide the input value `message`:" +msgstr "" +"மேலே உள்ள CWL கருவியைச் சோதிக்க, உள்ளீட்டு மதிப்பை `செய்தி` வழங்க இந்த வேலையைப் " +"பயன்படுத்தவும்:" + +#: ../../src/topics/creating-files-at-runtime.md:29 +#: ../../src/topics/environment-variables.md:13 +#: ../../src/topics/outputs.md:77 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "`Echo-job.yml`" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 10d1373bb14a4a3cacd3b92a2f83382d +msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." +msgstr "" +"இதை இயக்குவதற்கு முன், ஒவ்வொரு அடியையும் இன்னும் கொஞ்சம் விரிவாகப் பார்ப்போம். அடிப்படை " +"கட்டளை `பேச் கமாண்ட்: [\" எச்.எச் \",\" எடுத்துக்காட்டு. இது செல்லில் நாம் உருவாக்கும் " +"கோப்பை இயக்கும்." + +#: ../../src/topics/creating-files-at-runtime.md:40 +#: 70e257091bdb456e8957f90a8fa90e8c +msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." +msgstr "" +"`SiturtWorkDirRequirement க்கு` பட்டியல்` தேவை. `பட்டியல்` ஒரு YAML வரிசை என்பதால், " +"வரிசையின் ஒவ்வொரு உறுப்பின் முதல் வரியில் எங்களுக்கு`-'தேவை, இந்த விசயத்தில் எங்களிடம் ஒரு" +" உறுப்பு மட்டுமே உள்ளது. `நுழைவு பெயர்:` எந்த மதிப்பும் இருக்க முடியும், ஆனால் அது `பேச்" +" கமாண்டில்` குறிப்பிடப்பட்டவற்றுடன் பொருந்த வேண்டும். இறுதி பகுதி `நுழைவு:`, இதைத் " +"தொடர்ந்து `| --` இது யேம்ல் தொடரியல் மேற்கோள் காட்டுகிறது, மேலும் நீங்கள் ஒரு மல்டிலைன் சரம்" +" பயன்படுத்துகிறீர்கள் என்று பொருள் (அது இல்லாமல், முழு ச்கிரிப்டையும் ஒரு வரியில் எழுத " +"வேண்டும்)." + +#: ../../src/topics/creating-files-at-runtime.md:51 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" +"வடிவமைப்பைப் பற்றி மேலும் அறிய [YAML வழிகாட்டி] (../ தலைப்புகள்/yaml-quide.md#maps) " +"ஐப் பார்க்கவும்." + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f +msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" +"இப்போது கருவி விளக்கம் மற்றும் கட்டளை வரியில் உள்ளீட்டு பொருளுடன் `CWLTool` ஐ அழைக்கவும்:" + +#: ../../src/topics/custom-types.md:1 +#: cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "தனிப்பயன் வகைகள்" + +#: ../../src/topics/custom-types.md:3 +#: 67573252cc064b27ab13eebc468ac58a +msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." +msgstr "" +"சில நேரங்களில் நீங்கள் சி.டபிள்யூ.எல் விளக்கங்களில் பயன்பாட்டிற்காகவும் மறுபயன்பாட்டுக்காகவும் " +"உங்கள் சொந்த தனிப்பயன் வகைகளை எழுத விரும்பலாம். இத்தகைய தனிப்பயன் வகைகளைப் பயன்படுத்துவது " +"அனைத்தும் ஒரே வகையைப் பயன்படுத்தும் பல விளக்கங்களுக்கிடையில் பணிநீக்கத்தைக் குறைக்கும், மேலும்" +" சி.டபிள்யூ.எல் விளக்கத்துடன் நேரடியாக ஃபிடில் செய்ய வேண்டிய அவசியமின்றி ஒரு " +"கருவி/பகுப்பாய்வின் கூடுதல் தனிப்பயனாக்கம்/உள்ளமைவை அனுமதிக்கும்." + +#: ../../src/topics/custom-types.md:9 +#: 73e68b3af9cf41338d843c0c40e50cdc +msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." +msgstr "" +"ஒரு நிலையான பயோம் அட்டவணை கோப்பை HDF5 வடிவமாக மாற்றுவதற்கான [பயோம் மாற்றும் வடிவம்] " +"[பயோம்] கருவியின் CWL விளக்கம் கீழே உள்ள எடுத்துக்காட்டு." + +#: ../../src/topics/custom-types.md:12 +#: ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "`Custom-types.cwl`" + +#: ../../src/topics/custom-types.md:18 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "`Custom-types.yml`" + +#: ../../src/topics/custom-types.md:24 +#: a999b1acda2641598086648c64aa3831 +msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" +msgstr "" +"___ குறிப்பு. rod_sparse_otu_table.biom), * rol_sparse_otu_table.biom * எ.கா. " +"`wget` வழியாக:" + +#: ../../src/topics/custom-types.md:30 +#: f8c12a58cb0b46a488823c6ae95f25ea +msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" +msgstr "" +"29 வது வரியில், `உள்ளீடுகள்: அட்டவணை_ வகை` இல், அட்டவணை மாற்றத்தில் பயன்படுத்த " +"அனுமதிக்கக்கூடிய அட்டவணை விருப்பங்களின் பட்டியல் தனிப்பயன் பொருளாக இறக்குமதி " +"செய்யப்படுகிறது:" + +#: ../../src/topics/custom-types.md:46 +#: f25a63e0926d4932bbe64b2e4bdabf9e +msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." +msgstr "" +"தனிப்பயன் வகைக்கான குறிப்பு என்பது பொருள் வரையறுக்கப்பட்ட (`பயோம்-கோன்வர்ட்-டேபிள்.யம்ல்`) " +"மற்றும் அந்த கோப்பில் உள்ள பொருளின் பெயர் (` டேபிள்_ டைப்`) தனிப்பயனை வரையறுக்கும் கோப்பின் " +"பெயரின் கலவையாகும் தட்டச்சு செய்க. இந்த வழக்கில் இறக்குமதி செய்யப்பட்ட `பயோம்-கான்வர்ட்-டேபிள்" +".யம்ல்` கோப்பிலிருந்து` சின்னங்கள்` வரிசை அனுமதிக்கக்கூடிய அட்டவணை விருப்பங்களை " +"வரையறுக்கவும். எடுத்துக்காட்டாக, `Custom-types.yml` இல், HDF5 வடிவத்தில் OTU அட்டவணையை" +" உருவாக்க கருவியைச் சொல்லும்` உள்ளீட்டாக '`OTU அட்டவணையை` கடந்து செல்கிறோம்." + +#: ../../src/topics/custom-types.md:53 +#: b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" +"தனிப்பயன் வகையை விவரிக்கும் YAML கோப்பின் உள்ளடக்கங்கள் கீழே கொடுக்கப்பட்டுள்ளன:" + +#: ../../src/topics/custom-types.md:55 +#: fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "`பயோம்-கான்ப்-டேபிள்.யம்ல்`" + +#: ../../src/topics/custom-types.md:61 +#: d718630a296545f3a989c8c71e9ddc77 +msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" +"CWL விளக்கத்தில் தனிப்பயன் வகை பயன்படுத்தப்படுவதற்கு, அது இறக்குமதி செய்யப்பட வேண்டும். " +"இறக்குமதிகள் `தேவைகள்: ச்கெமேட்ஃப்ரெக்விரெமென்ட்` இல் விவரிக்கப்பட்டுள்ளன, எடுத்துக்காட்டாக` " +"தனிப்பயன்-வகை. சி.டபிள்யூ.எல்` விளக்கம்:" + +#: ../../src/topics/custom-types.md:76 +#: 9a97acd430064710bcdf76edbd9f711c +msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." +msgstr "" +"இந்த சி.டபிள்யூ.எல் விளக்கத்தின் ஆசிரியருக்கு `ரிசோர்ச் ரெக்விரெமென்ட்'ச் ஆகியவை அடங்கும் " +"என்பதையும் நினைவில் கொள்க, கருவிக்கு வெற்றிகரமாக இயங்க தேவையான குறைந்தபட்ச ரேம் மற்றும் " +"கோரின் எண்ணிக்கையையும், விளக்கம் எழுதப்பட்ட மென்பொருளின் பதிப்பின் விவரங்களையும் " +"குறிப்பிடுகிறது என்பதையும் நினைவில் கொள்க மற்றும் பிற பயனுள்ள மேனிலை தரவு. இந்த பயனர் " +"வழிகாட்டியின் பிற அத்தியாயங்களில் இந்த நற்பொருத்தங்கள் மேலும் விவாதிக்கப்படுகின்றன." + +#: ../../src/topics/environment-variables.md:1 +#: 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "சுற்றுச்சூழல் மாறிகள்" + +#: ../../src/topics/environment-variables.md:3 +#: 3c821c9c46d841ec89b8a5b1018f3af8 +msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." +msgstr "" +"கருவிகள் தடைசெய்யப்பட்ட சூழலில் இயங்குகின்றன மற்றும் பெற்றோர் செயல்முறையிலிருந்து " +"பெரும்பாலான சுற்றுச்சூழல் மாறிகள் பெறவில்லை. `Envvarrequirement` ஐப் பயன்படுத்தி " +"கருவிக்கான சூழல் மாறிகள் அமைக்கலாம்." + +#: ../../src/topics/environment-variables.md:7 +#: bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "`Env.cwl`" + +#: ../../src/topics/expression-tool.md:1 +#: 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "வெளிப்பாடு கருவி" + +#: ../../src/topics/expression-tool.md:3 +#: 48deb71f361a43e48a56ed483075bca8 +msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." +msgstr "" +"ஒரு வெளிப்பாடு கருவி என்பது ஒரு வகை செயல்முறையாகும், இது தானாகவே அல்லது பணிப்பாய்வு " +"படியாக இயக்கப்படலாம். இது ஒரு தூய சாவாச்கிரிப்ட் வெளிப்பாட்டை செயல்படுத்துகிறது. உள்ளீட்டு" +" தரவுகளில் செயல்பட வேண்டிய மற்றும் சில முடிவுகளை வெளியீடாக உருவாக்க வேண்டிய சிக்கலான " +"சாவாச்கிரிப்ட் வெளிப்பாடுகளை தனிமைப்படுத்துவதற்கான ஒரு வழியாக இது பயன்படுத்தப்பட " +"வேண்டும்." + +#: ../../src/topics/expression-tool.md:8 +#: 716b56506ca7470299899c5d820a9ea2 +msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." +msgstr "" +"கட்டளை-வரி கருவியைப் போலவே இதற்கு `உள்ளீடுகள்` மற்றும்` வெளியீடுகள்` தேவைப்படுகிறது. " +"ஆனால் `பேச் கமாண்டிற்கு` பதிலாக, அதற்கு ஒரு` வெளிப்பாடு` பண்புக்கூறு தேவைப்படுகிறது." + +#: ../../src/topics/expression-tool.md:17 +#: b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "சி.டபிள்யூ.எல் வெளிப்பாடு கருவி." + +#: ../../src/topics/expression-tool.md:48 +#: 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "`Worpercase.cwl`" + +#: ../../src/topics/expression-tool.md:67 +#: e3ecac0a8e604f2b98a2a12b0579990a +msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." +msgstr "" +"எங்கள் வெளிப்பாடு `.touppercase ()` இல் சாவாச்கிரிப்ட் அழைப்பைக் கொண்டிருப்பதால், `" +"inlinejavascriptrequirement 'ஐப் பயன்படுத்த வேண்டியிருந்தது. சாவாச்கிரிப்ட் ஒரு தேவை " +"என்று வெளிப்பாடு கருவியைப் பயன்படுத்தும் கருவிகளுக்கு இதன் பொருள்." + +#: ../../src/topics/expressions.md:1 +#: c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "வெளிப்பாடுகள்" + +#: ../../src/topics/expressions.md:3 +#: 007a345b4bad49cf996c4301b8386473 +msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" +"நீங்கள் உள்ளீட்டு அளவுருக்களைக் கையாள வேண்டும் என்றால், `inlinejavascriptrequirement` " +"தேவையைச் சேர்க்கவும், பின்னர் எங்கும் ஒரு அளவுரு குறிப்பு சட்டப்பூர்வமானது, நீங்கள் CWL " +"ரன்னரால் மதிப்பீடு செய்யப்படும் சாவாச்கிரிப்ட்டின் ஒரு பகுதியை வழங்க முடியும்." + +#: ../../src/topics/expressions.md:9 +#: 2edbd398eadb458b8eacd5fa5496f0a2 +msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." +msgstr "" +"சாவாச்கிரிப்ட் வெளிப்பாடுகள் முற்றிலும் தேவைப்படும்போது மட்டுமே பயன்படுத்தப்பட வேண்டும். " +"கோப்பு பெயர்கள், நீட்டிப்புகள், பாதைகள் போன்றவற்றைக் கையாளும் போது, `பேச்இன் பெயர்`,` " +"நமெரூட்`, `நேமெக்ச்ட்` போன்றவற்றைப் போன்ற [` கோப்பு` பண்புகளில்] [கோப்பு-ப்ராப்] ஒன்றைப் " +"பயன்படுத்த முடியுமா என்பதைக் கவனியுங்கள். [சிறந்த நடைமுறைகளின் பட்டியல்] (சிறந்த " +"நடைமுறைகள். எம்.டி) ஐப் பார்க்கவும்." + +#: ../../src/topics/expressions.md:16 +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "`Expression.cwl`" + +#: ../../src/topics/expressions.md:22 +#: efb5fd14988c4e2a8f834ee5369d4102 +msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" +msgstr "" +"இந்த கருவிக்கு `உள்ளீடுகள் 'தேவையில்லை என்பதால், அதை (கிட்டத்தட்ட) வெற்று வேலை கோப்புடன் " +"இயக்க முடியும்:" + +#: ../../src/topics/expressions.md:25 +#: e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "`gaing.yml`" + +#: ../../src/topics/expressions.md:31 +#: 276f688ba7cc471a842f085ca852b1d9 +msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." +msgstr "" +"`gall.yml` வெற்று சாதொபொகு பொருளின் விளக்கத்தைக் கொண்டுள்ளது. சாதொபொகு பொருள்களின் " +"விளக்கங்கள் சுருள் அடைப்புக்குறிக்குள் உள்ளன `{}`, எனவே ஒரு வெற்று பொருள் வெறுமனே வெற்று " +"அடைப்புக்குறிகளால் குறிப்பிடப்படுகிறது." + +#: ../../src/topics/expressions.md:35 +#: ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "நாம் `Expression.cwl` ஐ இயக்கலாம்:" + +#: ../../src/topics/expressions.md:37 +#: 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "`Expression.cwl` ஐ இயக்குகிறது" + +#: ../../src/topics/expressions.md:47 +#: 8b70a1ad70514039b97164fa630c12e4 +msgid "Note that requirements can be provided with the map syntax, as in the example above:" +msgstr "" +"மேலே உள்ள எடுத்துக்காட்டில் உள்ளதைப் போல, வரைபடத் தொடரியல் மூலம் தேவைகளை வழங்க முடியும் " +"என்பதை நினைவில் கொள்க:" + +#: ../../src/topics/expressions.md:54 +#: 2f28ab412d2843ffa5f14acdc01fc732 +msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." +msgstr "" +"அல்லது ஒரு வரிசையாக, ஒவ்வொரு நுழைவுடனும் (இந்த விசயத்தில், `வகுப்பு: " +"inlinejavascriptrequirement`) ஒரு` -` ஆல் குறிக்கப்பட்டுள்ளது. கூடுதல் கட்டளை வரி " +"வாதங்களை விவரிக்க அதே தொடரியல் பயன்படுத்தப்படுகிறது." + +#: ../../src/topics/expressions.md:62 +#: d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "சாவாச்கிரிப்ட் வெளிப்பாடுகள் எங்கே அனுமதிக்கப்படுகின்றன?" + +#: ../../src/topics/expressions.md:64 +#: cbec9277b5004e50af2728cbda0df740 +msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" +msgstr "" +"[அளவுரு குறிப்புகள்] (அளவுரு-குறிப்புகள். எம்.டி) போலவே, நீங்கள் சில துறைகளில் மட்டுமே " +"சாவாச்கிரிப்ட் வெளிப்பாடுகளைப் பயன்படுத்தலாம். அவை:" + +#: ../../src/topics/expressions.md:66 +#: e259f55f8000479bbd8009e25cf0ca6c +msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" +"[`கட்டளை லைனெட்டூல்`] (https://www.commonwl.org/v1.0/commandlinetool." +"html#commandlinetool) இலிருந்து)" + +#: ../../src/topics/expressions.md:67 +#: ../../src/topics/parameter-references.md:64 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 +msgid "`arguments`" +msgstr "`வாதங்கள்`" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 +msgid "`valueFrom`" +msgstr "`மதிப்பு`" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "`stdin`" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "`stdout`" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "`ச்டைடர்`" + +#: ../../src/topics/expressions.md:72 +#: 8210b36347a749889450529ecdf4ff0e +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" +"[CommandInputParameter] (https://www.commonwl.org/v1.0/commandlinetool." +"html#commandinputarameter) இலிருந்து)" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "`வடிவமைப்பு`" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae +msgid "`secondaryFiles`" +msgstr "`இரண்டாம் நிலை கோப்புகள்`" + +#: ../../src/topics/expressions.md:75 +#: 23088850ad02459696f6bbd385109aac +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" +"[`InputBinding`] (https://www.commonwl.org/v1.0/commandlinetool.html#" +"commandlinebinding இலிருந்து)" + +#: ../../src/topics/expressions.md:77 +#: f02257a822ad46ac93c5981531cc85d5 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" +"[CommandOutPutputParamater] (https://www.commonwl.org/v1.0/commandlinetool." +"html#commandoutputparameter) இலிருந்து)" + +#: ../../src/topics/expressions.md:80 +#: 989a1c4aaa1143be9f53b90cd8b6d500 +msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" +"[CommandOutPutpunding] (https://www.commonwl.org/v1.0/commandlinetool." +"html#commandoutputpinting) இலிருந்து)" + +#: ../../src/topics/expressions.md:81 +#: ../../src/topics/parameter-references.md:78 +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "`குளோப்`" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b +msgid "`outputEval`" +msgstr "`வெளிச்செல்லும்" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c +msgid "From `Workflow`" +msgstr "`பணிப்பாய்வு` இலிருந்து" + +#: ../../src/topics/expressions.md:84 +#: d289541e460147aa933f7878996f8649 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" +"இருந்து [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/" +"v1.0/Workflow.html#WorkflowOutputParameter)" + +#: ../../src/topics/expressions.md:87 +#: ../../src/topics/parameter-references.md:84 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c +msgid "From `steps`" +msgstr "`படிகள்` இலிருந்து" + +#: ../../src/topics/expressions.md:88 +#: 81b4d1f23a3642bfa9bb395b94260cd1 +msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" +"[Workflowstepinput] (https://www.commonwl.org/v1.0/workflow.html#" +"workflowstepinput இலிருந்து)" + +#: ../../src/topics/expressions.md:90 +#: ../../src/topics/parameter-references.md:87 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 +msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" +msgstr "[வெளிப்பாடு)" + +#: ../../src/topics/expressions.md:91 +#: ../../src/topics/parameter-references.md:88 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf +msgid "`expression`" +msgstr "`வெளிப்பாடு`" + +#: ../../src/topics/expressions.md:92 +#: f495da32f05a4a5ba9539be0a54c1a59 +msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" +"இருந்து [InputParameter](https://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl" +".org/v1.0/Workflow.html#ExpressionToolOutputParameter)" + +#: ../../src/topics/expressions.md:95 +#: bdb4c68a175047ddbe141ca24960127f +msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" +"[`Resourcerequirement`] இலிருந்து (https://www.commonwl.org/v1.0/" +"commandlinetool.html#resourcerequirement)" + +#: ../../src/topics/expressions.md:96 +#: ../../src/topics/parameter-references.md:93 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "`colorsmin`" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 +msgid "`coresMax`" +msgstr "`colorsmax`" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 +msgid "`ramMin`" +msgstr "`ராம்மின் '" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "`rammax`" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "`tmpdirmin '" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "`tmpdirmax`" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "`வெளிப்புறம்`" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "`outtirmax`" + +#: ../../src/topics/expressions.md:104 +#: 97b61352363f47cb890e8937c5613fa3 +msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" +"[`SiturtWorkDirRequirement`] (https://www.commonwl.org/v1.0/commandlinetool." +"html#initialworkdirrequirement இலிருந்து)" + +#: ../../src/topics/expressions.md:105 +#: ../../src/topics/parameter-references.md:102 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "`பட்டியல்`" + +#: ../../src/topics/expressions.md:106 +#: 8d0b142bb7ed4e61b8fb03de197240ce +msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" +"[dirent] (https://www.commonwl.org/v1.0/commandlinetool.html#dirent இல்)" + +#: ../../src/topics/expressions.md:107 +#: ../../src/topics/parameter-references.md:104 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 +msgid "`entry`" +msgstr "`நுழைவு`" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +msgid "`entryname`" +msgstr "`entryName`" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "`Envvarrequirement` இலிருந்து" + +#: ../../src/topics/expressions.md:110 +#: 0bc424ef2ca346099f29b937379908a0 +msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" +"[சுற்றுச்சூழல் டெஃப்] (https://www.commonwl.org/v1.0/commandlinetool.html#" +"enveronmentdef இலிருந்து)" + +#: ../../src/topics/expressions.md:111 +#: ../../src/topics/parameter-references.md:108 +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "`envValue`" + +#: ../../src/topics/expressions.md:116 +#: 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" +"வெளிப்புற நூலகங்கள் மற்றும் இன்லைன் சாவாச்கிரிப்ட் குறியீட்டை `எக்ச்பிரசன் லிப்` உடன் " +"பயன்படுத்துதல்" + +#: ../../src/topics/expressions.md:118 +#: 29b73e1dd72744f68377f0a38c10f062 +msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." +msgstr "" +"`Inlinejavascriptrequirement` தேவை ஒரு` எக்ச்பிரசன் லிப்` பண்புகளை ஆதரிக்கிறது, இது" +" பயனர்களை வெளிப்புற சாவாச்கிரிப்ட் கோப்புகளை ஏற்ற அனுமதிக்கிறது அல்லது இன்லைன் " +"சாவாச்கிரிப்ட் குறியீட்டை வழங்குகிறது." + +#: ../../src/topics/expressions.md:122 +#: 38a2afaf4a6c4d04909af22c93f2808d +msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." +msgstr "" +"`எக்ச்பிரசன் லிப்` பண்புக்கூறில் சேர்க்கப்பட்ட உள்ளீடுகள் ஒரு சி.டபிள்யூ.எல் ரன்னரின் " +"சாவாச்கிரிப்ட் எஞ்சினுடன் பாகுபடுத்தப்படுகின்றன. வெளிப்புற கோப்புகளைச் சேர்க்க அல்லது சி." +"டபிள்யூ.எல் ஆவணத்தின் பிற பகுதிகளில் அழைக்கக்கூடிய சாவாச்கிரிப்ட் செயல்பாடுகளை உருவாக்க " +"இதைப் பயன்படுத்தலாம்." + +#: ../../src/topics/expressions.md:128 +#: cd74f34b21af4de9be96fd897efc469b +msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." +msgstr "" +"CWL தரநிலைகள் (https://www.commonwl.org/v1.0/commandlinetool.html#expressions)" +" சி.டபிள்யூ.எல். : //262.ecma-international.org/5.1/). இதன் பொருள் உங்கள் சி.டபிள்யூ" +".எல் ஆவணத்தில் நீங்கள் உள்ளடக்கிய அல்லது எழுதும் எந்த குறியீடும் எக்மாச்கிரிப்ட் 5.1 உடன் " +"இணக்கமாக இருக்க வேண்டும்." + +#: ../../src/topics/expressions.md:135 +#: f12e371f3f1a4b0cb2cff9800352d48c +msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" +msgstr "" +"எடுத்துக்காட்டாக, நாம் `inlinejavascriptrequirement` ஐப் பயன்படுத்தலாம் மற்றும்` " +"எக்ச்பிரசன் லிப்` இல் சாவாச்கிரிப்ட் செயல்பாட்டை எழுதலாம். அந்த செயல்பாட்டை சி.டபிள்யூ.எல் " +"ஆவணத்தின் பிற பகுதிகளில் பயன்படுத்தலாம்:" + +#: ../../src/topics/expressions.md:139 +#: 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "`அலோ-வேர்ல்ட்-எக்ச்பிரசன் லிப்-இன்லைன்.ச்விஎல்`" + +#: ../../src/topics/expressions.md:146 +#: 8f0e8f050e334ac08334e9215e1dcf61 +msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" +msgstr "" +"இந்த சி.டபிள்யூ.எல் பணிப்பாய்வுகளை இயக்குவது சாவாச்கிரிப்ட் செயல்பாட்டைக் கோரும், இதன் " +"விளைவாக `எதிரொலி` கட்டளை மூலதன ஆரம்ப எழுத்துக்களுடன் உள்ளீட்டு செய்தியை அச்சிடுகிறது:" + +#: ../../src/topics/expressions.md:149 +#: 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "`அலோ-வேர்ல்ட்-எக்ச்பிரசன் லிப்-இன்லைன்.ச்விஎல்` இயக்குகிறது." + +#: ../../src/topics/expressions.md:155 +#: 7a6be0005a6441feb67f036d005d7885 +msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" +msgstr "" +"`மூலதன சொற்கள்` செயல்பாட்டை வெளிப்புறக் கோப்பிற்கு,` தனிப்பயன்-செயல்பாடுகள். Js` க்கு " +"நகர்த்துவோம், அதை எங்கள் CWL ஆவணத்தில் இறக்குமதி செய்வோம்:" + +#: ../../src/topics/expressions.md:158 +#: ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "`தனிப்பயன்-செயல்பாடுகள். js`" + +#: ../../src/topics/expressions.md:164 +#: 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "`அலோ-வேர்ல்ட்-எக்ச்பிரசன் லிப்-எக்ச்டெர்னல்.ச்விஎல்`" + +#: ../../src/topics/expressions.md:171 +#: 06635145b441418aaae84dc804f3d6ac +msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." +msgstr "" +"`Custom-functions.js` கோப்பு CWL ஆவணத்தில்` $ உடன் சேர்க்கப்பட்டுள்ளது: " +"தனிப்பயன்-செயல்பாடுகள். JS` அறிக்கை. இது சி.டபிள்யூ.எல் ஆவணத்தின் பிற பகுதிகளில் " +"பயன்படுத்த செயல்பாடுகள் மற்றும் மாறிகள் கிடைக்கச் செய்கிறது." + +#: ../../src/topics/expressions.md:175 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "இயங்கும் `அலோ-வேர்ல்ட்-எக்ச்பிரசன் லிப்-எக்ச்டெர்னல்.ச்விஎல்`." + +#: ../../src/topics/expressions.md:181 +#: 04eaf1f7c630450db318dcd8b7626e15 +msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." +msgstr "" +"இறுதியாக, உங்கள் CWL ஆவணத்தில் இன்லைன் மற்றும் வெளிப்புற சாவாச்கிரிப்ட் குறியீடு இரண்டையும் " +"வைத்திருக்க முடியும் என்பதை நினைவில் கொள்க. இந்த இறுதி எடுத்துக்காட்டில், `எக்ச்பிரசன் லிப்`" +" பண்புக்கூறுக்கு புதிய செயல்பாடு` கிரியேட்டிவெல்லோஆர்ல்ட்மெசேச்` உடன் மற்றொரு நுழைவைச் " +"சேர்த்துள்ளோம், இது வெளிப்புறக் கோப்பிலிருந்து `தனிப்பயன்-செயல்பாடுகள். சே.எச்." + +#: ../../src/topics/expressions.md:186 +#: c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "`அலோ-வேர்ல்ட்-எக்ச்பிரசன் லிப்.ச்விஎல்`" + +#: ../../src/topics/expressions.md:193 +#: 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "`அலோ-வேர்ல்ட்-எக்ச்பிரசன் லிப்.ச்விஎல்` இயங்கும்." + +#: ../../src/topics/expressions.md:200 +#: fd4579a3c9844492b314b5c3c1775fc7 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." +msgstr "" +"உள்ளக வட்டில் இருந்து அல்லது தொலைதூர இடத்திலிருந்து ஒரு கோப்பைச் சேர்க்க `$ சேர்க்கவும்` " +"அறிக்கை பயன்படுத்தப்படலாம். இது உறவினர் மற்றும் முழுமையான பாதைகளுடன் செயல்படுகிறது. சி." +"டபிள்யூ.எல் விவரக்குறிப்பிலிருந்து அதைப் பற்றி மேலும் அறிய CWL விவரக்குறிப்பிலிருந்து " +"[`$ incllion அடங்கும்." + +#: ../../src/topics/file-formats.md:1 +#: 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "கோப்பு வடிவங்கள்" + +#: ../../src/topics/file-formats.md:3 +#: e024bcb70e04412e90e1838426d1b69a +msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." +msgstr "" +"கருவிகள் மற்றும் பணிப்பாய்வுகள் `கோப்பு` வகைகளை உள்ளீடாக எடுத்து அவற்றை வெளியீடாக " +"உருவாக்கலாம். `கோப்பு` வகைகளுக்கான வடிவமைப்பைக் குறிக்க பரிந்துரைக்கிறோம். அளவுரு " +"கோப்புகளை உருவாக்கும்போது சில எளிய வகை சரிபார்ப்பைச் செய்ய உங்களை அனுமதிக்கும் போது " +"உங்கள் கருவியை எவ்வாறு பயன்படுத்துவது என்பது மற்றவர்களுக்கு ஆவணப்படுத்த உதவுகிறது." + +#: ../../src/topics/file-formats.md:8 +#: a3db21c0b3114802a8a5b610e252ef13 +msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." +msgstr "" +"கோப்பு வடிவங்களுக்கு, ஏற்கனவே உள்ள ஆன்டாலசிகளைக் குறிப்பிட பரிந்துரைக்கிறோம் (எங்கள் " +"எடுத்துக்காட்டில் எடாம் போன்றவை), உங்கள் நிறுவனத்திற்கான உள்ளக ஆன்டாலசியைக் குறிப்பிடவும் " +"அல்லது உங்கள் கருவியை மற்றவர்களுடன் பகிர்வதற்கு முன்பு விரைவான மேம்பாட்டிற்காக ஆரம்பத்தில் " +"ஒரு கோப்பு வடிவமைப்பைச் சேர்க்க வேண்டாம். ஏற்கனவே உள்ள [IANA கோப்பு வடிவமைப்பு பட்டியல்கள்]" +" [IANA] மற்றும் [EDAM கோப்பு வடிவமைப்பு] [EDAM] ஆகியவற்றை அவர்களின் வலைத்தளங்களில் " +"உலாவலாம்." + +#: ../../src/topics/file-formats.md:14 +#: 0f5bc8520d6a4dafa37c65343da9702a +msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." +msgstr "" +"அடுத்த டுடோரியலில், ஆவணத்தின் `$ பெயர்வெளிகள்` மற்றும்` $ ச்கேமாச்` பகுதியை இன்னும் " +"விரிவாக விளக்குகிறோம், எனவே இப்போதைக்கு இதைப் பற்றி கவலைப்பட வேண்டாம்." + +#: ../../src/topics/file-formats.md:17 +#: 5cb830da47464a8b9c3950983fa4d56f +msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." +msgstr "" +"கூடுதல் மதிப்புக்கு `cwltool` கோப்பு வடிவங்களின் அடிப்படையில் சில அடிப்படை " +"பகுத்தறிவுகளைச் செய்யலாம் மற்றும் சில வெளிப்படையான பொருந்தாத தன்மைகள் இருப்பதாகத் " +"தோன்றினால் உங்களை எச்சரிக்கலாம்." + +#: ../../src/topics/file-formats.md:20 +#: 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "`metadata_example.cwl`" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "கட்டளை வரி வடிவத்தில் இந்த சி.டபிள்யூ.எல் விளக்கத்திற்கு சமம்:" + +#: ../../src/topics/file-formats.md:32 +#: 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "மாதிரி அளவுரு கோப்புகள்" + +#: ../../src/topics/file-formats.md:34 +#: a2ce43b391864e8bbde16328cc19b32b +msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" +"மேலே உள்ள எடுத்துக்காட்டுக்கு ஒரு அளவுரு கோப்பின் எடுத்துக்காட்டு கீழே. உங்கள் கருவிக்கான " +"அளவுரு கோப்புகளின் வேலை எடுத்துக்காட்டுகளைச் சரிபார்க்க நாங்கள் ஊக்குவிக்கிறோம். இது \"அற" +"ியப்பட்ட நல்ல\" அளவுருவாக்கத்திலிருந்து தொடங்கி, உங்கள் கருவியுடன் விரைவாக வேலை செய்ய " +"மற்றவர்கள் அனுமதிக்கிறது." + +#: ../../src/topics/file-formats.md:39 +#: aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "`மாதிரி.ஒய்எம்எல்`" + +#: ../../src/topics/file-formats.md:45 +#: 56ee4dcfff6141d5bef80eb96559876d +msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" +msgstr "" +"___ குறிப்பு: ___ கீழே உள்ள எடுத்துக்காட்டைப் பின்பற்ற, நீங்கள் எடுத்துக்காட்டு உள்ளீட்டு கோப்பை" +" பதிவிறக்கம் செய்ய வேண்டும், *கோப்பு-வடிவங்கள் .பாம் *. கோப்பு இலிருந்து கிடைக்கிறது, மேலும் பதிவிறக்கம் செய்யலாம் எ.கா. `wget` " +"வழியாக:" + +#: ../../src/topics/index.md:1 +#: 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "தலைப்புகள்" + +#: ../../src/topics/inputs.md:1 +#: 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "உள்ளீடுகள்" + +#: ../../src/topics/inputs.md:3 +#: d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "அத்தியாவசிய உள்ளீட்டு அளவுருக்கள்" + +#: ../../src/topics/inputs.md:5 +#: 96671c56523c4ea9992fb5dfcfa6490e +msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" +"ஒரு கருவியின் `உள்ளீடுகள்` கருவியை எவ்வாறு இயக்குவது என்பதைக் கட்டுப்படுத்தும் உள்ளீட்டு " +"அளவுருக்களின் பட்டியல். ஒவ்வொரு அளவுருவிலும் அளவுருவின் பெயருக்கு `ஐடி` உள்ளது, மேலும் " +"அந்த அளவுருவுக்கு எந்த வகையான மதிப்புகள் செல்லுபடியாகும் என்பதை விவரிக்கிறது." + +#: ../../src/topics/inputs.md:9 +#: bcc6246742cb46bfb185e415c4a3431a +msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." +msgstr "" +"கிடைக்கக்கூடிய பழமையான வகைகள் *சரம் *, *எண்ணாக *, *நீண்ட *, *மிதவை *, *இரட்டை *, " +"மற்றும் *பூச்ய *; சிக்கலான வகைகள் *வரிசை *மற்றும் *பதிவு *; கூடுதலாக சிறப்பு வகைகள் " +"*கோப்பு *, *அடைவு *மற்றும் *ஏதேனும் *உள்ளன." + +#: ../../src/topics/inputs.md:13 +#: 86dce36de687449c88fb5eb9d64eb045 +msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." +msgstr "" +"பின்வரும் எடுத்துக்காட்டு வெவ்வேறு வகைகளுடன் சில உள்ளீட்டு அளவுருக்களை நிரூபிக்கிறது " +"மற்றும் கட்டளை வரியில் வெவ்வேறு வழிகளில் தோன்றும்." + +#: ../../src/topics/inputs.md:16 +#: cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "முதலில், பின்வருவனவற்றைக் கொண்ட `inp.cwl` என்ற கோப்பை உருவாக்கவும்:" + +#: ../../src/topics/inputs.md:18 +#: 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "`Inp.cwl`" + +#: ../../src/topics/inputs.md:24 +#: c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "`Inp-job.yml` என்ற கோப்பை உருவாக்கவும்:" + +#: ../../src/topics/inputs.md:26 +#: dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "`inp-job.yml`" + +#: ../../src/topics/inputs.md:33 +#: 36ab1d9edafc4831bb1bca5f123b04b0 +msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" +msgstr "" +"வார்ப்புரு உள்ளீட்டு பொருளை உருவாக்க நீங்கள் `CWLTool` ஐப் பயன்படுத்தலாம். உள்ளீட்டு பொருள் " +"கோப்பில் அனைத்து உள்ளீட்டு அளவுருக்களையும் தட்டச்சு செய்வதிலிருந்து உங்களை காப்பாற்றுகிறது:" + +#: ../../src/topics/inputs.md:40 +#: 7dc630ea86464b1dba3a4e5079260b3b +msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." +msgstr "" +"நீங்கள் வெளியீட்டை ஒரு கோப்பிற்கு திருப்பி விடலாம், அதாவது `cwltool --make-template " +"inp.cwl> inp-job.yml`, பின்னர் இயல்புநிலை மதிப்புகளை நீங்கள் விரும்பிய உள்ளீட்டு " +"மதிப்புகளுடன் மாற்றலாம்." + +#: ../../src/topics/inputs.md:44 +#: ae37901a8dbe48a59e27ab4e2e6e2d30 +msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." +msgstr "" +"`கோப்பு` வகையாக\" எடுத்துக்காட்டு_பீல் \",` வகுப்பு: கோப்பு` மற்றும் `பாதை` ஆகிய " +"புலங்களுடன் ஒரு பொருளாக வழங்கப்பட வேண்டும் என்பதைக் கவனியுங்கள்." + +#: ../../src/topics/inputs.md:47 +#: 651e032007ea4a119d20c820bb61f86b +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "அடுத்து, கட்டளை வரியில் `டச் திமிங்கலம்." + +#: ../../src/topics/inputs.md:53 +#: 0b056dde9e87428996e47870b12119da +msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" +msgstr "" +"`CWLTOOL INP.CWL INP-JOB.YML` என்ற கட்டளையைப் பயன்படுத்தி, கருவி விளக்கம் மற்றும் " +"கட்டளை வரியில் உள்ளீட்டு பொருளுடன்` CWLTool` ஐ இப்போது அழைக்கவும். பின்வரும் பெட்டி உரை " +"இந்த இரண்டு கட்டளைகளையும், கட்டளை வரியிலிருந்து எதிர்பார்க்கப்படும் வெளியீட்டையும் " +"விவரிக்கிறது:" + +#: ../../src/topics/inputs.md:64 +#: 628124a1670b4b058bb0fb6e495a099c +msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" +"சி.டபிள்யூ.எல் குறிப்பு ரன்னர் (சி.டபிள்யூ.எல்.டூல்) மற்றும் பிற ஓட்டப்பந்தய வீரர்கள் உங்கள் " +"உள்ளீட்டு கோப்புகளுக்கு குறியீட்டு (\"மென்மையான\") இணைப்புகளுடன் தற்காலிக கோப்பகங்களை " +"உருவாக்குகிறார்கள், கருவிகள் தற்செயலாக குறிப்பிடப்படாத கோப்புகளை அணுகவில்லை என்பதை " +"உறுதிப்படுத்தவும்" + +#: ../../src/topics/inputs.md:70 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 +msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." +msgstr "" +"புலம் `inputBinding` விருப்பமானது மற்றும் கருவியின் கட்டளை வரியில் உள்ளீட்டு அளவுரு " +"எவ்வாறு தோன்ற வேண்டும் என்பதைக் குறிக்கிறது. `InputBinding` காணவில்லை என்றால், அளவுரு " +"கட்டளை வரியில் தோன்றாது. ஒவ்வொரு உதாரணத்தையும் விரிவாகப் பார்ப்போம்." + +#: ../../src/topics/inputs.md:83 +#: ec2adb3912bc46e28891229e9e0d9a1c +msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." +msgstr "" +"பூலியன் வகைகள் ஒரு கொடியாக கருதப்படுகின்றன. உள்ளீட்டு அளவுரு \"example_flag\" \"உண்மை" +"\" என்றால், `முன்னொட்டு` கட்டளை வரியில் சேர்க்கப்படும். தவறு என்றால், கொடி எதுவும் " +"சேர்க்கப்படவில்லை." + +#: ../../src/topics/inputs.md:95 +#: a519be60726a44af9941fdce04735353 +msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." +msgstr "" +"சரம் வகைகள் கட்டளை வரியில் நேரடி மதிப்புகளாக தோன்றும். `முன்னொட்டு` விருப்பமானது, " +"வழங்கப்பட்டால், அது அளவுருவுக்கு முன் கட்டளை வரியில் ஒரு தனி வாதமாகத் தோன்றுகிறது. மேலே" +" உள்ள எடுத்துக்காட்டில், இது `-எடுத்துக்காட்டாக-சரம் அலோ` என வழங்கப்படுகிறது." + +#: ../../src/topics/inputs.md:109 +#: cb8fc8c4c79e467eac5fab4ca685201e +msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." +msgstr "" +"தசம உரை பிரதிநிதித்துவத்துடன் கட்டளை வரியில் முழு எண் (மற்றும் மிதக்கும் புள்ளி) வகைகள் " +"தோன்றும். `தனித்தனியாக` விருப்பம் தவறானது (இயல்புநிலை மதிப்பு உண்மை), முன்னொட்டு மற்றும் " +"மதிப்பு ஒற்றை வாதமாக இணைக்கப்படுகின்றன. மேலே உள்ள எடுத்துக்காட்டில், இது `-i42` என " +"வழங்கப்படுகிறது." + +#: ../../src/topics/inputs.md:124 +#: a26cc105716f47cb807174c9003153b0 +msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." +msgstr "" +"கோப்பு வகைகள் கட்டளை வரியில் கோப்பின் பாதையாக தோன்றும். அளவுரு வகை ஒரு கேள்விக்குறியுடன்" +" முடிவடையும் போது `?` இது அளவுரு விருப்பமானது என்பதை இது குறிக்கிறது. மேலே உள்ள " +"எடுத்துக்காட்டில், இது `--file =/tmp/சீரற்ற/பாதை/திமிங்கலம். Txt` என வழங்கப்படுகிறது. " +"இருப்பினும், உள்ளீட்டில் \"எடுத்துக்காட்டு_பீல்\" அளவுரு வழங்கப்படவில்லை என்றால், கட்டளை " +"வரியில் எதுவும் தோன்றாது." + +#: ../../src/topics/inputs.md:131 +#: cc159dd5fe5748caac838862f5b8c4d1 +msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." +msgstr "" +"உள்ளீட்டு கோப்புகள் படிக்க மட்டுமே. உள்ளீட்டு கோப்பை நீங்கள் புதுப்பிக்க விரும்பினால், நீங்கள் " +"[முதலில் அதை வெளியீட்டு கோப்பகத்திற்கு நகலெடுக்க வேண்டும்] (ச்டேசிங்-இன்ட்-ஃபைல்ச்.எம்டி)." + +#: ../../src/topics/inputs.md:134 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 +msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." +msgstr "" +"கட்டளை வரியில் அளவுரு எங்கு தோன்ற வேண்டும் என்பதை தீர்மானிக்க `நிலை` இன் மதிப்பு " +"பயன்படுத்தப்படுகிறது. நிலைகள் ஒருவருக்கொருவர் தொடர்புடையவை, முழுமையானவை அல்ல. இதன் " +"விளைவாக, நிலைகள் தொடர்ச்சியாக இருக்க வேண்டியதில்லை, 1, 3, 5 நிலைகளைக் கொண்ட மூன்று " +"அளவுருக்கள் 1, 2, 3 ஆக அதே கட்டளை வரியை ஏற்படுத்தும். ஒன்றுக்கு மேற்பட்ட அளவுருவுகள் ஒரே" +" நிலையை கொண்டிருக்கலாம் (உறவுகளைப் பயன்படுத்தி உறவுகள் உடைக்கப்படுகின்றன அளவுரு பெயர்), " +"மற்றும் நிலை புலம் விருப்பமானது. இயல்புநிலை நிலை 0." + +#: ../../src/topics/inputs.md:142 +#: 6812698e9ad84d3385de5e88e9dde0b3 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" +"`பேச் கமாண்ட்` புலம் எப்போதும் அளவுருக்களுக்கு முன் இறுதி கட்டளை வரியில் தோன்றும்." + +#: ../../src/topics/inputs.md:146 +#: 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "வரிசை உள்ளீடுகள்" + +#: ../../src/topics/inputs.md:148 +#: d1f02be278754267893dfce5a940997d +msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." +msgstr "" +"கட்டளை வரியில் குறிப்பிடப்படும் உள்ளீட்டு அளவுருக்களின் வரிசைகளைச் சேர்ப்பது எளிது. வரிசை " +"அளவுருவைக் குறிப்பிட இரண்டு வழிகள் உள்ளன. முதலாவது `வகை` புலத்துடன்` வகை: வரிசை` " +"மற்றும் `உருப்படிகள்` வரிசையில் தோன்றக்கூடிய செல்லுபடியாகும் தரவு வகைகளை வரையறுத்தல். " +"மாற்றாக, உள்ளீட்டு அளவுரு அந்த வகையின் வரிசை என்பதைக் குறிக்க வகை பெயருக்குப் பிறகு " +"அடைப்புக்குறிகள் `[]` சேர்க்கப்படலாம்." + +#: ../../src/topics/inputs.md:154 +#: 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "`வரிசை-inputs.cwl`" + +#: ../../src/topics/inputs.md:160 +#: 787d4bfb093c4ad287b902084706b751 +msgid "`array-inputs-job.yml`" +msgstr "`array-inputs-job.yml`" + +#: ../../src/topics/inputs.md:166 +#: ../../src/topics/outputs.md:82 +#: ../../src/topics/outputs.md:105 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d +msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" +"இப்போது கட்டளை வரியில் கருவி விளக்கத்தையும் உள்ளீட்டு பொருளையும் வழங்கும் `cwltool` ஐ " +"அழைக்கவும்:" + +#: ../../src/topics/inputs.md:178 +#: 75d59e395c66416cae9b352db5081516 +msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." +msgstr "" +"`InputBinding` வெளிப்புற வரிசை அளவுரு வரையறை அல்லது உள் வரிசை உறுப்பு வரையறை " +"ஆகியவற்றில் தோன்றக்கூடும், மேலும் இவை மேலே காட்டப்பட்டுள்ளபடி கட்டளை வரியை உருவாக்கும் " +"போது வெவ்வேறு நடத்தைகளை உருவாக்குகின்றன. கூடுதலாக, `உருப்படி சிப்பி` புலம், " +"வழங்கப்பட்டால், வரிசை மதிப்புகள் உருப்படி பிரிப்பான் சரத்தால் பிரிக்கப்பட்ட ஒற்றை வாதமாக " +"இணைக்கப்பட வேண்டும் என்பதைக் குறிப்பிடுகிறது." + +#: ../../src/topics/inputs.md:185 +#: 874c6f19abbf45d7ab7d30a378c4048d +msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." +msgstr "" +"உள்ளீடுகளின் வரிசைகள் சதுர அடைப்புக்குறிக்குள் குறிப்பிடப்பட்டுள்ளன `[]` " +"வரிசை-உள்ளீடுகள்-JOB.YML` இல். பல வரிகளிலும் வரிசைகளையும் வெளிப்படுத்தலாம், அங்கு " +"தொடர்புடைய விசையுடன் வரையறுக்கப்படாத வரிசை மதிப்புகள் ஒரு முன்னணி `-` ஆல் " +"குறிக்கப்படுகின்றன. இது அடுத்த பாடத்தில் நிரூபிக்கப்படும் மற்றும் [YAML வழிகாட்டி] (YAML-" +"Quide.MD#வரிசைகள்) இல் விரிவாக விவாதிக்கப்படுகிறது. வரிசைகளின் வரிசைகள், பதிவுகளின் " +"வரிசைகள் மற்றும் பிற சிக்கலான வகைகளை நீங்கள் குறிப்பிடலாம்." + +#: ../../src/topics/inputs.md:191 +#: 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "உள்ளடக்கிய மற்றும் பிரத்யேக உள்ளீடுகள்" + +#: ../../src/topics/inputs.md:193 +#: dea0d4b681f94e73b13965dcfe75cf7d +msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." +msgstr "" +"சில நேரங்களில் ஒரு அடிப்படை கருவியில் பல வாதங்கள் உள்ளன, அவை ஒன்றாக வழங்கப்பட வேண்டும் " +"(அவை சார்புடையவை) அல்லது ஒன்றாக வழங்க முடியாத பல வாதங்கள் (அவை பிரத்தியேகமானவை). இந்" +"த இரண்டு நிபந்தனைகளையும் விவரிக்க நீங்கள் பதிவுகள் மற்றும் குழு அளவுருக்களை ஒன்றாக " +"இணைக்கலாம்." + +#: ../../src/topics/inputs.md:198 +#: ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "`Record.cwl`" + +#: ../../src/topics/inputs.md:204 +#: d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "`Record-job1.yml`" + +#: ../../src/topics/inputs.md:215 +#: 750474486a84482292eeba45f118287f +msgid "In the first example, you can't provide `itemA` without also providing `itemB`." +msgstr "" +"முதல் எடுத்துக்காட்டில், `itemb` ஐ வழங்காமல்` உருப்படி` ஐ வழங்க முடியாது." + +#: ../../src/topics/inputs.md:217 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "`Record-job2.yml`" + +#: ../../src/topics/inputs.md:233 +#: 1eb0e39bb6d04b8cab300f44a79f3add +msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." +msgstr "" +"இரண்டாவது எடுத்துக்காட்டில், `உருப்படிகள்` மற்றும்` உருப்படிகள்` பிரத்தியேகமானவை, எனவே " +"முதல் பொருந்தக்கூடிய உருப்படி (`itemc`) கட்டளை வரியில் சேர்க்கப்பட்டு மீதமுள்ள உருப்படி (`" +" உருப்படிகள்`) புறக்கணிக்கப்படுகிறது." + +#: ../../src/topics/inputs.md:236 +#: bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "`Record-job3.yml`" + +#: ../../src/topics/inputs.md:252 +#: 4b2ab812f62c4f949dd25c8527f2411c +msgid "In the third example, only `itemD` is provided, so it appears on the command line." +msgstr "" +"மூன்றாவது எடுத்துக்காட்டில், `itemd` மட்டுமே வழங்கப்படுகிறது, எனவே இது கட்டளை வரியில் " +"தோன்றும்." + +#: ../../src/topics/inputs.md:255 +#: b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "வெளிப்பாடுகளுடன் பிரத்யேக உள்ளீட்டு அளவுருக்கள்" + +#: ../../src/topics/inputs.md:257 +#: 2c3b884cb1c54521900cc90782e8a58d +msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." +msgstr "" +"வெளிப்பாடுகளுடன் இணைந்து பிரத்யேக உள்ளீட்டு அளவுருக்களைப் பயன்படுத்தினால், `உள்ளீடுகள்` " +"சாவாச்கிரிப்ட் பொருளில் பிரத்யேக உள்ளீட்டு மதிப்புகளில் ஒன்று இருக்கும் என்பதை நீங்கள் " +"அறிந்திருக்க வேண்டும். இதன் பொருள் எந்த மதிப்புகள் உள்ளன என்பதைச் சரிபார்க்க நீங்கள் ** அல்லது " +"** பூலியன் ஆபரேட்டரைப் பயன்படுத்த வேண்டியிருக்கும்." + +#: ../../src/topics/inputs.md:262 +#: a1073b6306044dffb414319ae01f68bb +msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." +msgstr "" +"`NULL` (அதாவது மதிப்பு எதுவும் வழங்கப்படவில்லை) அல்லது ஒரு ENUM இலிருந்து எந்த " +"மதிப்பையும் ஏற்றுக்கொள்ளும் பிரத்யேக` file_format` உள்ளீட்டு அளவுருவைக் கொண்ட ஒரு " +"உதாரணத்தைப் பயன்படுத்துவோம்." + +#: ../../src/topics/inputs.md:265 +#: 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "`பிரத்யேக-அளவுரு-வெளிப்பாடுகள். cwl`" + +#: ../../src/topics/inputs.md:271 +#: 9a1d92334685449386dfa3b3a899ed48 +msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" +msgstr "" +"`பூச்ய` மதிப்பைக் கருத்தில் கொள்ளாமல் சாவாச்கிரிப்ட் வெளிப்பாடு பிரத்யேக உள்ளீட்டு அளவுருவின்" +" மதிப்பை எவ்வாறு பயன்படுத்துகிறது என்பதைக் கவனியுங்கள். “ஃபாச்டா” (ENUM இன் மதிப்புகளில் " +"ஒன்று) போன்ற சரியான மதிப்பை நீங்கள் வழங்கினால், உங்கள் கட்டளை வெற்றிகரமாக செயல்படுத்த " +"வேண்டும்:" + +#: ../../src/topics/inputs.md:280 +#: fb623af4c480411b8fde28d01c981411 +msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." +msgstr "" +"இருப்பினும், நீங்கள் எந்த உள்ளீட்டு மதிப்பையும் வழங்கவில்லை என்றால், `file_format` ஒரு` " +"பூச்ய` மதிப்புக்கு மதிப்பீடு செய்யப்படும், இது வெளியீட்டு புலத்திற்கான எதிர்பார்க்கப்படும் " +"வகையுடன் பொருந்தாது (ஒரு `சரம்`), இதன் விளைவாக உங்கள் பணிப்பாய்வுகளை இயக்கும் போது " +"தோல்வி ஏற்படும் ." + +#: ../../src/topics/inputs.md:289 +#: e98e165f6bba40809c90473d72f9d592 +msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" +"அதை சரிசெய்ய, பிரத்யேக அளவுருக்களைப் பயன்படுத்தும் போது அல்லது `NULL` ஐ அனுமதிக்கும் எந்" +"த அளவுருவையும் பயன்படுத்தும் போது உங்கள் சாவாச்கிரிப்ட் வெளிப்பாட்டில் ஒரு அல்லது " +"ஆபரேட்டரைப் பயன்படுத்த நினைவில் கொள்ள வேண்டும். எடுத்துக்காட்டாக, வெளிப்பாட்டை கட்டளை வரி " +"அல்லது வேலை உள்ளீட்டு கோப்பில் எதுவும் வழங்கப்படாவிட்டால் இயல்புநிலை மதிப்பைக் கொண்டிருக்க `$" +" (உள்ளீடுகள்." + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "மேனிலை தரவு மற்றும் படைப்புரிமை" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." +msgstr "" +"சரியான செயலாக்கத்திற்கு அமலாக்க நீட்டிப்புகள் தேவையில்லை (எடுத்துக்காட்டாக, GUI " +"விளக்கக்காட்சி தொடர்பான புலங்கள்) மற்றும் கருவி அல்லது பணிப்பாய்வு பற்றிய மேனிலை தரவு " +"(எடுத்துக்காட்டாக, மேற்கோள்களில் பயன்படுத்துவதற்கான படைப்புரிமை) எந்தவொரு பொருளிலும் " +"கூடுதல் புலங்களாக வழங்கப்படலாம். [SCAMEAL SALAD EXPLICATION இல் விவரிக்கப்பட்டுள்ளபடி, " +"ஆவணத்தின் `$ பெயர்வெளிகள்` பிரிவில் (எ.கா. EDAM: http://edamontology.org/) " +"பட்டியலிடப்பட்டுள்ள பெயர்வெளி முன்னொட்டை இத்தகைய நீட்டிப்பு புலங்கள் (எ.கா. ] [ச்கீமா-சலாத்]" +". பெயர்வெளி முன்னொட்டை நீங்கள் சேர்த்தவுடன், கீழே காட்டப்பட்டுள்ளபடி ஆவணத்தில் எங்கும் அதை " +"அணுகலாம். இல்லையெனில், ஒருவர் முழு முகவரி களைப் பயன்படுத்த வேண்டும்: `வடிவம்: http: // " +"edamontology.org/format_2572`." + +#: ../../src/topics/metadata-and-authorship.md:13 +#: 80af387fe3ff4e2da999903385bd602b +msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." +msgstr "" +"அனைத்து டெவலப்பர்களுக்கும், உங்கள் கருவி மற்றும் பணிப்பாய்வுகளுக்கான பின்வரும் குறைந்தபட்ச " +"மெட்டாடேட்டாவை நாங்கள் பரிந்துரைக்கிறோம். இந்த எடுத்துக்காட்டில் மேனிலை தரவு உங்கள் கருவியை" +" மேற்கோள் காட்ட அனுமதிக்கிறது." + +#: ../../src/topics/metadata-and-authorship.md:16 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "`metadata_example2.cwl`" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "நீட்டிக்கப்பட்ட எடுத்துக்காட்டு" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 +msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." +msgstr "" +"அதிக உந்துதல் கொண்டவர்களுக்கு, உங்கள் கருவியை மிகப் பெரிய அளவிலான மேனிலை தரவு மூலம் " +"சிறுகுறிப்பு செய்ய முடியும். இந்த எடுத்துக்காட்டில் EDAM ஆன்டாலசி குறிச்சொற்களை முக்கிய " +"வார்த்தைகளாக (தொடர்புடைய கருவிகளின் தொகுப்பை அனுமதிக்கிறது), கருவியைப் " +"பயன்படுத்துவதற்கு வன்பொருள் தேவைகள் மற்றும் இன்னும் சில மேனிலை தரவு புலங்கள் ஆகியவை " +"அடங்கும்." + +#: ../../src/topics/metadata-and-authorship.md:35 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "`டிரான்ச்மிட்டர்_எக்ச்." + +#: ../../src/topics/operations.md:1 +#: 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "செயல்பாடுகள்" + +#: ../../src/topics/operations.md:3 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 +msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" +"ஒரு செயல்பாடு என்பது ஒரு வகை சி.டபிள்யூ.எல் செயல்முறையாகும், இது ஒரு பணிப்பாய்வு, " +"கட்டளை-வரி கருவி அல்லது வெளிப்பாடு கருவி போன்றது. இது உள்ளீடுகள் மற்றும் வெளியீடுகளைக் " +"குறிப்பிடும் பணிப்பாய்வுகளின் ஒரு படியாகும், ஆனால் இது செயல்படுத்த போதுமான தகவல்களை " +"வழங்காது." + +#: ../../src/topics/operations.md:7 +#: 5565c1b2d8a349169a305a9b26b4574d +msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" +msgstr "" +"ஒரு சி.டபிள்யூ.எல் ரன்னருக்கு பணிப்பாய்வுகளை சமர்ப்பிக்க நீங்கள் தயாராக இருப்பதற்கு முன்பு, " +"வளர்ச்சியின் போது ஒரு பணிப்பாய்வுகளை காட்சிப்படுத்த நீங்கள் செயல்பாடுகளை உருவாக்கலாம்:" + +#: ../../src/topics/operations.md:10 +#: 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "`செயல்பாடுகள். CWL`" + +#: ../../src/topics/operations.md:16 +#: 88160cef4cfa4add9020aa89511a5749 +msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" +msgstr "" +"The `uppercase` படி of the workflow is an operation. இது ஒரு கட்டளை வரி கருவி " +"அல்லது வெளிப்பாடு போல பயன்படுத்தப்படலாம். நீங்கள் அதை CWL பார்வையாளர் அல்லது `CWLTool` " +"உடன் சூழ்ச்சி செய்யலாம்:" + +#: ../../src/topics/operations.md:24 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 +msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" +msgstr "" +"மேலே உள்ள கட்டளையின் வெளியீட்டை ஒரு கிராப்விச் ரெண்டரர் மூலம் வழங்கலாம். பின்வரும் படம் " +"சூரரிமாச்சிலை Craffviz உத்தரவுடன் வழங்கப்படுகிறது (இந்த பயனர் வழிகாட்டி சூரரிமாச்சிலை " +"உடன் கட்டப்பட்டுள்ளது):" + +#: ../../src/topics/operations.md:55 +#: 730ba1434a1445ae847ec6153b6a3b72 +msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" +msgstr "" +"`Cwltool` உடன் அதை இயக்க முயற்சித்தால்,` cwltool` ஐ எவ்வாறு செயல்படுத்துவது என்பதை அறி" +"ய போதுமான தகவல்கள் இல்லை என்பதால் கட்டளை தோல்வியடையும்:" + +#: ../../src/topics/operations.md:58 +#: 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "`cwltool` செயல்பாடுகளை எவ்வாறு இயக்குவது என்று தெரியவில்லை" + +#: ../../src/topics/operations.md:66 +#: a25d0b1e13324b40a6b8fcd227948c4f +msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." +msgstr "" +"சி.டபிள்யூ.எல் ஓட்டப்பந்தய வீரர்கள் செயல்பாடுகளை உறுதியான படிகளுடன் பிணைப்பதற்கான வழிகளைக்" +" கொண்டு வரக்கூடும். ஒரு சி.டபிள்யூ.எல் ரன்னர், உதாரணமாக, ஐடியுடன் சுருக்க செயல்பாடுகளைப்" +" பயன்படுத்தலாம், இது வேறு பணிப்பாய்வு இயந்திரத்தால் செயல்படுத்தப்படும் படிகளுக்கு " +"ஒத்திருக்கிறது." + +#: ../../src/topics/outputs.md:1 +#: da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "வெளியீடுகள்" + +#: ../../src/topics/outputs.md:3 +#: 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "வெளியீட்டு கோப்புகளைத் தருகிறது" + +#: ../../src/topics/outputs.md:5 +#: d661df070e3040869da412d07a71f716 +msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" +"ஒரு கருவியின் `வெளியீடுகள்` கருவியை இயக்கிய பின் திருப்பித் தர வேண்டிய வெளியீட்டு " +"அளவுருக்களின் பட்டியல். ஒவ்வொரு அளவுருவிலும் அளவுருவின் பெயருக்கு `ஐடி` உள்ளது, மேலும் " +"அந்த அளவுருவுக்கு எந்த வகையான மதிப்புகள் செல்லுபடியாகும் என்பதை விவரிக்கிறது." + +#: ../../src/topics/outputs.md:10 +#: a11585474d3849cca5467512ed964743 +msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." +msgstr "" +"CWL இன் கீழ் ஒரு கருவி இயங்கும்போது, தொடக்க வேலை அடைவு என்பது நியமிக்கப்பட்ட வெளியீட்டு " +"அடைவு ஆகும். அடிப்படை கருவி அல்லது ச்கிரிப்ட் அதன் முடிவுகளை வெளியீட்டு கோப்பகத்தில் " +"உருவாக்கிய கோப்புகளின் வடிவத்தில் பதிவு செய்ய வேண்டும். சி.டபிள்யூ.எல் கருவியால் திரும்பி" +"ய வெளியீட்டு அளவுருக்கள் வெளியீட்டு கோப்புகள் அல்லது அந்த கோப்புகளின் உள்ளடக்கத்தை " +"ஆராய்வதிலிருந்து வந்தவை." + +#: ../../src/topics/outputs.md:16 +#: 2682f9ca8e604a0c9986f7746fdec960 +msgid "The following example demonstrates how to return a file that has been extracted from a tar file." +msgstr "" +"தார் கோப்பிலிருந்து பிரித்தெடுக்கப்பட்ட கோப்பை எவ்வாறு திருப்பித் தருவது என்பதை பின்வரும் " +"எடுத்துக்காட்டு நிரூபிக்கிறது." + +#: ../../src/topics/outputs.md:19 +#: 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "கட்டாய வாதங்களை `பேச் கமாண்டிற்கு` அனுப்புதல்" + +#: ../../src/topics/outputs.md:21 +#: 22447a560f6f4317bf67bd7c4336126c +msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" +msgstr "" +"முந்தைய எடுத்துக்காட்டுகளில், `பேச் கமாண்ட்` ஒரு சரம் மட்டுமே, எந்தவொரு வாதங்களும் சி." +"டபிள்யூ.எல் உள்ளீடுகளாக நிறைவேற்றப்பட்டன. ஒற்றை சரத்திற்கு பதிலாக நாம் _array இன் _array " +"ஐப் பயன்படுத்தலாம். முதல் உறுப்பு இயக்க கட்டளை, மற்றும் அடுத்தடுத்த கூறுகள் கட்டாய கட்டளை " +"வரி வாதங்கள்" + +#: ../../src/topics/outputs.md:26 +#: f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "'tar.cwl`" + +#: ../../src/topics/outputs.md:32 +#: ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "`tar-job.yml`" + +#: ../../src/topics/outputs.md:38 +#: dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "அடுத்து, எடுத்துக்காட்டுக்கு ஒரு தார் கோப்பை உருவாக்கவும்." + +#: ../../src/topics/outputs.md:45 +#: 52703d6b7f914097934bfad13663abeb +msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" +"இப்போது கருவி விளக்கம் மற்றும் கட்டளை வரியில் உள்ளீட்டு பொருளுடன் `cwltool` ஐ அழைக்கவும்:" + +#: ../../src/topics/outputs.md:51 +#: 5e1c79df657d4a6e84e055dd6b300a5d +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" +"ஒவ்வொரு வெளியீட்டு அளவுருவின் மதிப்பை எவ்வாறு அமைப்பது என்பதை புலம் `வெளியீடு பைண்டிங்` " +"விவரிக்கிறது." + +#: ../../src/topics/outputs.md:62 +#: 329d2809dfae4f90bc638f5f03a47ee3 +msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." +msgstr "" +"`குளோப்` புலம் வெளியீட்டு கோப்பகத்தில் ஒரு கோப்பின் பெயரைக் கொண்டுள்ளது. முன்கூட்டியே " +"கோப்பின் பெயர் உங்களுக்குத் தெரியாவிட்டால், நீங்கள் `குளோப்: '*.txt'` போன்ற வைல்டு அட்டை " +"வடிவத்தைப் பயன்படுத்தலாம்." + +#: ../../src/topics/outputs.md:65 +#: 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "நிலையான வெளியீட்டைக் கைப்பற்றுதல்" + +#: ../../src/topics/outputs.md:67 +#: c6bcf7c6a8774dd6be41cc775848c3b8 +msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." +msgstr "" +"ஒரு கருவியின் நிலையான வெளியீட்டு ச்ட்ரீமைப் பிடிக்க, வெளியீட்டு ச்ட்ரீம் செல்ல வேண்டிய கோப்பின்" +" பெயருடன் `stdout` புலத்தைச் சேர்க்கவும். தொடர்புடைய வெளியீட்டு அளவுருவில் `வகை: " +"stdout` ஐச் சேர்க்கவும்." + +#: ../../src/topics/outputs.md:71 +#: 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "`stdout.cwl`" + +#: ../../src/topics/outputs.md:89 +#: 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "வரிசை வெளியீடுகள்" + +#: ../../src/topics/outputs.md:91 +#: 9647019d8c37466886e7aab6f176634d +msgid "You can also capture multiple output files into an array of files using `glob`." +msgstr "" +"`குளோப்` ஐப் பயன்படுத்தி பல வெளியீட்டு கோப்புகளையும் கோப்புகளின் வரிசையில் கைப்பற்றலாம்." + +#: ../../src/topics/outputs.md:93 +#: b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "`array-outputs.cwl`" + +#: ../../src/topics/outputs.md:99 +#: cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "`array-outputs-job.yml`" + +#: ../../src/topics/outputs.md:112 +#: cc067051f22f433bbece08f60933e002 +msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." +msgstr "" +"[YAML வழிகாட்டி] (yaml-quide.md#வரிசைகள்) இல் விவரிக்கப்பட்டுள்ளபடி, எதிர்பார்க்கப்படும் " +"வெளியீடுகளின் வரிசை `array-outputs-job.yml` இல் குறிப்பிடப்பட்டுள்ளது. வரவிருக்கும் " +"பல பிரிவுகளில் நிரூபிக்கப்பட்டபடி, வரிசைகளில் உள்ளீடுகளைக் குறிக்க CWL விளக்கங்களில் இந்த " +"வடிவத்தைப் பயன்படுத்தலாம்." + +#: ../../src/topics/parameter-references.md:1 +#: a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "அளவுரு குறிப்புகள்" + +#: ../../src/topics/parameter-references.md:3 +#: dbfe2c1123144316aa026374b0f353d3 +msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." +msgstr "" +"முந்தைய எடுத்துக்காட்டில், \"தார்\" நிரலைப் பயன்படுத்தி ஒரு கோப்பைப் பிரித்தெடுத்தோம். " +"எவ்வாறாயினும், அந்த எடுத்துக்காட்டு மிகவும் குறைவாகவே இருந்தது, ஏனெனில் நாங்கள் ஆர்வமாக " +"இருந்த கோப்பு \"அலோ.டெக்ச்டி\" என்று அழைக்கப்பட்டது, இது `.cwl` கோப்பில் எழுதப்பட்டது. " +"இதைச் செய்வதற்கான சிறந்த வழி இதுவல்ல, ஏனெனில் \"அலோ.டெக்ச்டி\" கோப்பு பெயர் மாறுபடலாம் " +"அல்லது பயன்படுத்தப்படும் உள்ளீட்டு கோப்பு (களை) சார்ந்துள்ளது. இதைத் தவிர்க்க, வேலை " +"அளவுருக்கள் கோப்பில் (`.yml`) நாம் விரும்பும் கோப்பின் பெயரை குறிப்பிடலாம். இந்த " +"எடுத்துக்காட்டில், உள்ளீட்டு அளவுருக்களின் மதிப்பை மற்ற புலங்களிலிருந்து மாறும் வகையில் " +"எவ்வாறு குறிப்பிடுவது என்பதை நீங்கள் காண்பீர்கள், இது பிரித்தெடுக்க கோப்பின் பெயரைக் குறிப்பி" +"ட அனுமதிக்கும்." + +#: ../../src/topics/parameter-references.md:13 +#: 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "`tar-param.cwl`" + +#: ../../src/topics/parameter-references.md:19 +#: 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "`tar-param-job.yml`" + +#: ../../src/topics/parameter-references.md:25 +#: 074cf5d912854d8c864607cc24b15302 +msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" +msgstr "" +"உங்கள் உள்ளீட்டு கோப்புகளை உருவாக்கி, கருவி விளக்கம் மற்றும் கட்டளை வரியில் உள்ளீட்டு " +"பொருளுடன் `CWLTool` ஐ அழைக்கவும்:" + +#: ../../src/topics/parameter-references.md:36 +#: 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" +"சில புலங்கள் `$ (...)` இல் இணைக்கப்பட்டுள்ள அளவுரு குறிப்புகளை அனுமதிக்கின்றன. இவை " +"மதிப்பீடு செய்யப்பட்டு குறிப்பிடப்படும் மதிப்பு மூலம் மாற்றப்படுகின்றன." + +#: ../../src/topics/parameter-references.md:47 +#: b54240bb94f746bba7511633aa969db0 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" +"சாவாச்கிரிப்ட் தொடரியல் துணைக்குழுவைப் பயன்படுத்தி குறிப்புகள் எழுதப்பட்டுள்ளன. இந்த " +"எடுத்துக்காட்டில், `$ (உள்ளீடுகள்." + +#: ../../src/topics/parameter-references.md:51 +#: 8b70a072aa87414c88e89a3e19af0a51 +msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." +msgstr "" +"\"உள்ளீடுகள்\" மாறியின் மதிப்பு CWL கருவி செயல்படுத்தப்பட்டபோது வழங்கப்பட்ட உள்ளீட்டு பொருள்." + +#: ../../src/topics/parameter-references.md:54 +#: eea20f89c45f424a888178df53713b28 +msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." +msgstr "" +"`கோப்பு` அளவுருக்கள் பொருள்கள் என்பதால், உள்ளீட்டு கோப்பிற்கான பாதையைப் பெற நீங்கள் ஒரு கோப்பு" +" பொருளில் பாதை புலத்தைக் குறிப்பிட வேண்டும்; மேலே உள்ள எடுத்துக்காட்டில் தார் கோப்பிற்கான " +"பாதையை குறிப்பிட நீங்கள் `$ (உள்ளீடுகள். tarfile.path)` எழுதுவீர்கள்." + +#: ../../src/topics/parameter-references.md:59 +#: cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "அளவுரு குறிப்புகள் எங்கே அனுமதிக்கப்படுகின்றன?" + +#: ../../src/topics/parameter-references.md:61 +#: 6d3fb423e6c4434697cd113fb27e28ad +msgid "You can only use parameter references in certain fields. These are:" +msgstr "" +"நீங்கள் சில துறைகளில் அளவுரு குறிப்புகளை மட்டுமே பயன்படுத்த முடியும். அவை:" + +#: ../../src/topics/parameter-references.md:63 +#: 7647e0229a924f988cf02b7812a55c06 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" +"[`கட்டளை லைன் டூல்`] (http://www.commonwl.org/v1.0/commandlinetool." +"html#commandlinetool) இலிருந்து)" + +#: ../../src/topics/parameter-references.md:69 +#: 9d663249666045618a0d3acddb85a9a9 +msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" +"[CommandInputParameter] (http://www.commonwl.org/v1.0/commandlinetool." +"html#commandinputarameter) இலிருந்து)" + +#: ../../src/topics/parameter-references.md:72 +#: 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" +"[`InputBinding`] (http://www.commonwl.org/v1.0/commandlinetool." +"html#commandlineBinding) இலிருந்து)" + +#: ../../src/topics/parameter-references.md:74 +#: dbf6153cd02542a6a01c172803122b7f +msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" +"[CommandOutputputParamater] (http://www.commonwl.org/v1.0/commandlinetool." +"html#commandoutputparameter) இலிருந்து)" + +#: ../../src/topics/parameter-references.md:77 +#: b6250cf6fa8a4a0c94b33302e0decca5 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" +"[CommandOutPutPunding] (http://www.commonwl.org/v1.0/commandlinetool." +"html#commandoutputpinting) இலிருந்து)" + +#: ../../src/topics/parameter-references.md:81 +#: fa6ca3bbc6784380a03a950a6f49a180 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" +msgstr "" +"இருந்து [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1" +".0/Workflow.html#WorkflowOutputParameter)" + +#: ../../src/topics/parameter-references.md:85 +#: b92b516e537a4773ad67b4af586e7a25 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" +"[Workflowstepinput] (http://www.commonwl.org/v1.0/workflow.html#" +"workflowstepinput இலிருந்து)" + +#: ../../src/topics/parameter-references.md:89 +#: 467a701228504d06b971b79a59c69064 +msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" +msgstr "" +"இருந்து [InputParameter](http://www.commonwl.org/v1.0/Workflow." +"html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl." +"org/v1.0/Workflow.html#ExpressionToolOutputParameter)" + +#: ../../src/topics/parameter-references.md:92 +#: 2634f989eb304009a8568d70ed42786c +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" +"[`ResourceRecequirement`] இலிருந்து (http://www.commonwl.org/v1.0/" +"commandlinetool.html#resourcerequirement)" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" +"[`Siturtworkdirrequirement`] (http://www.commonwl.org/v1.0/commandlinetool." +"html#initialworkdirrequirement இலிருந்து)" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "[dirent] (http://www.commonwl.org/v1.0/commandlinetool.html#dirent இல்)" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" +"[சுற்றுச்சூழல் டெஃப்] (http://www.commonwl.org/v1.0/commandlinetool.html#" +"enveronmentdef இலிருந்து)" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "தேவைகள் மற்றும் குறிப்புகள்" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "மென்பொருள் தேவைகளைக் குறிப்பிடுகிறது" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 574d93d1d592458a985f259519c036cb +msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." +msgstr "" +"பெரும்பாலும், ஒரு மென்பொருளின் குறிப்பிட்ட பதிப்பிற்கு கருவி விளக்கங்கள் எழுதப்படும். உங்கள்" +" விளக்கங்களைப் பயன்படுத்துவதை மற்றவர்களுக்கு எளிதாக்குவதற்கு, `குறிப்புகள்` பிரிவில்` " +"சாப்ட்வேர் ரெக்யூமென்ட்` புலத்தை சேர்க்கலாம். விளக்கம் ஒரு கருவியின் எந்த பதிப்பில் " +"எழுதப்பட்டது என்பது குறித்த குழப்பத்தைத் தவிர்க்க இது உதவக்கூடும்." + +#: ../../src/topics/specifying-software-requirements.md:13 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" +"இந்த எடுத்துக்காட்டில், விவரிக்கப்படும் மென்பொருள் தேவை இன்டர்ரோச்கான் பதிப்பு 5.21-60 ஆகும்." + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 02e40154eac74ecc98d0447d03475b44 +msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." +msgstr "" +"உங்கள் சி.டபிள்யூ.எல் ரன்னரைப் பொறுத்து, தேவையான மென்பொருள் நிறுவப்பட்டுள்ளதா என்பதைச் " +"சரிபார்க்க இந்த குறிப்புகள் பயன்படுத்தப்படலாம் மற்றும் வேலை இயங்குவதற்கு முன்பு கிடைக்கிறது" +". குறிப்பு செயல்படுத்தலுடன் இந்த காசோலைகளை இயக்க, [சார்பு தீர்வுகள் உள்ளமைவு] " +"[சார்புநிலைகள்] ஐப் பயன்படுத்தவும்." + +#: ../../src/topics/specifying-software-requirements.md:29 +#: 8cb1c5d9b1a54c40924099494eb766c6 +msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." +msgstr "" +"ஒரு பதிப்பு எண், கருவிக்கான தனித்துவமான வள அடையாளங்காட்டி (URI) ஒரு [RRID] [RRID] " +"வடிவத்தில் கொடுக்கப்பட்டுள்ளது. RRIDS உடனான வளங்களை [Scicrunch] [Scicrunch] " +"பதிவேட்டில் பார்க்கலாம், இது விஞ்ஞான வளங்களைக் கண்டறிதல், கண்காணித்தல் மற்றும் " +"குறிப்பிடுவதற்கான ஒரு போர்ட்டலை வழங்குகிறது. நீங்கள் ஒரு கருவியை `சாப்ட்வேர் " +"ரெகுரிகேமென்ட்` எனக் குறிப்பிட விரும்பினால், ச்கைசஞ்ச் மீது கருவியைத் தேடுங்கள் மற்றும் " +"பதிவேட்டில் ஒதுக்கப்பட்டுள்ள RRID ஐப் பயன்படுத்தவும். . உங்கள் தேவை விளக்கத்தின் " +"`விவரக்குறிப்புகள்` புலத்தில் உள்ள கருவியைக் ([அடையாளங்காட்டிகள்.ஆர்ச்] [அடையாளங்காட்டிகள்] " +"வழியாக) குறிப்பிட இந்த RRID ஐப் பயன்படுத்தலாம். பிற நல்ல தேர்வுகள், விருப்பத்தின் " +"வரிசையில், முக்கிய கருவி மேற்கோளுக்கான DOI மற்றும் கருவிக்கு முகவரி ஐ சேர்க்க வேண்டும்." + +#: ../../src/topics/staging-input-files.md:1 +#: b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "உள்ளீட்டு கோப்புகளை நடத்துதல்" + +#: ../../src/topics/staging-input-files.md:3 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 +msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." +msgstr "" +"பொதுவாக, உள்ளீட்டு கோப்புகள் வெளியீட்டு கோப்பகத்திலிருந்து தனித்தனியாக வாசிப்பு மட்டும் " +"கோப்பகத்தில் அமைந்துள்ளன. அதே கோப்பகத்தில் உள்ளீட்டு கோப்போடு அதன் வெளியீட்டு கோப்புகளை எழுத " +"அடிப்படை கருவி எதிர்பார்க்கிறது என்றால் இது சிக்கல்களை ஏற்படுத்துகிறது. வெளியீட்டு " +"கோப்பகத்தில் உள்ளீட்டு கோப்புகளை நிலைநிறுத்த நீங்கள் `SiturtWorkWorkDirRequirement` ஐப் " +"பயன்படுத்துகிறீர்கள். இந்த எடுத்துக்காட்டில், உள்ளீட்டுக் கோப்பின் அடிப்படை பெயரை அதன் முன்னணி " +"அடைவு பாதையில் இருந்து பிரித்தெடுக்க சாவாச்கிரிப்ட் வெளிப்பாட்டைப் பயன்படுத்துகிறோம்." + +#: ../../src/topics/staging-input-files.md:9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "`linkfile.cwl`" + +#: ../../src/topics/troubleshooting.md:1 +#: 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "சரிசெய்தல்" + +#: ../../src/topics/troubleshooting.md:3 +#: fbe0c65b444441f785d0054176d036a6 +msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." +msgstr "" +"இந்த பிரிவில் சி.டபிள்யூ.எல் செயல்படுத்துவதில் சிக்கல் இருக்கும்போது சரிசெய்ய வழிகளைக் " +"காண்பீர்கள். நாங்கள் இங்கே `cwltool` இல் கவனம் செலுத்துகிறோம், ஆனால் இந்த நுட்பங்களில் சில பி" +"ற CWL ஓட்டப்பந்தய வீரர்களுக்கு பொருந்தும்." + +#: ../../src/topics/troubleshooting.md:6 +#: 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "`கேசெடிர்` உடன்` cwltool` ஐ இயக்கவும்" + +#: ../../src/topics/troubleshooting.md:8 +#: 9a710602e00c4934ae3a3b471aa68458 +msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." +msgstr "" +"இடைநிலை கோப்புகளை கேச் செய்ய `cwltool` என்று சொல்ல ஒரு பணிப்பாய்வுகளை இயக்கும் போது " +"நீங்கள்`--cachedir` விருப்பத்தைப் பயன்படுத்தலாம் (உள்ளீடு அல்லது வெளியீட்டு கோப்புகள் அல்ல, " +"ஆனால் உங்கள் பணிப்பாய்வு இயங்கும் போது உருவாக்கப்பட்டது). இயல்பாக, இந்த கோப்புகள் ஒரு " +"தற்காலிக கோப்பகத்தில் உருவாக்கப்படுகின்றன, ஆனால் அவற்றை ஒரு தனி கோப்பகத்திற்கு எழுதுவது " +"அவற்றை அணுகுவதை எளிதாக்குகிறது." + +#: ../../src/topics/troubleshooting.md:14 +#: 21b5be7270a14f0987240c81d1ec879b +msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." +msgstr "" +"பின்வரும் எடுத்துக்காட்டில் `சரிசெய்தல்-wf1.cwl` எங்களுக்கு இரண்டு படிகள் உள்ளன,` step_a` " +"மற்றும் `step_b`. பணிப்பாய்வு `எதிரொலி\" அலோ வேர்ல்ட் \"| க்கு சமம் ரெவ்`, இது \"அலோ " +"வேர்ல்ட்\" என்ற செய்தியை அச்சிடும், அதாவது \"டி.எல்ரோ ஓலே\". இருப்பினும், இரண்டாவது படி" +", `Step_b`, ** ஒரு எழுத்துப்பிழை ** உள்ளது, அங்கு` ரெவ்` கட்டளையை இயக்குவதற்கு பதிலா" +"க, அது தோல்வியுற்ற `ரெவ்.வி` ஐ இயக்க முயற்சிக்கிறது." + +#: ../../src/topics/troubleshooting.md:20 +#: 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "`சரிசெய்தல்-wf1.cwl`" + +#: ../../src/topics/troubleshooting.md:27 +#: cfe9d8241fe84bd5b74042a5625d933f +msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" +msgstr "" +"இந்த பணிப்பாய்வுகளை `/tmp/cachedir/` உடன் `--cachedir` மதிப்பு (` cwltool` இது " +"ஏற்கனவே இல்லையென்றால் உங்களுக்காக கோப்பகத்தை உருவாக்கும்):" + +#: ../../src/topics/troubleshooting.md:35 +#: 764d933cc4da446abd8dd8f913f05dac +msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" +msgstr "" +"`STEP_B` இல்லாத` ரெவ்.வி` கட்டளையை இயக்கத் தவறியதால் பணிப்பாய்வு `நிரந்தர வால்` நிலையில்" +" உள்ளது. `STEP_A` வெற்றிகரமாக செயல்படுத்தப்பட்டது மற்றும் அதன் வெளியீடு உங்கள்` கேசெடிர்` " +"இடத்தில் தற்காலிகமாக சேமிக்கப்பட்டுள்ளது. உருவாக்கப்பட்ட இடைநிலை கோப்புகளை நீங்கள் ஆய்வு " +"செய்யலாம்:" + +#: ../../src/topics/troubleshooting.md:44 +#: c93efc6d4e004859981ee7f5fa28ed03 +msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." +msgstr "" +"ஒவ்வொரு பணிப்பாய்வு படி ஒரு தனித்துவமான ஐடியைப் பெற்றுள்ளது (ஒரு ஆச் போல தோற்றமளிக்கும் " +"நீண்ட மதிப்பு). `$ {HASH} .ச்டேட்டச்` கோப்புகள் பணிப்பாய்வுகளால் செயல்படுத்தப்படும் ஒவ்வொரு " +"அடியின் நிலையையும் காண்பிக்கும். `STEP_A` வெளியீட்டு கோப்பு` stdout.txt` மேலே உள்ள " +"கட்டளையின் வெளியீட்டில் தெரியும்." + +#: ../../src/topics/troubleshooting.md:48 +#: 546601da44cb49bd9611b1c85807fd90 +msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." +msgstr "" +"இப்போது எழுத்துப்பிழையை சரிசெய்யவும், எனவே `step_b` செயல்படுத்துகிறது` rev` (அதாவது " +"`revv` ஆல்` rev` ஆல் `step_b`). எழுத்துப்பிழையை சரிசெய்த பிறகு, முந்தைய நேரத்தின் அதே" +" வாதங்களுடன் `cwltool` ஐ இயக்கும்போது, இப்போது` cwltool` வெளியீட்டில் `Step_a` க்கான " +"முன்-தற்காலிக வெளியீடுகள் பற்றிய தகவல்கள் உள்ளன, மேலும்` step_b`. `STEP_B` இன் நிலை " +"இப்போது வெற்றிபெறுகிறது என்பதையும் நினைவில் கொள்க." + +#: ../../src/topics/troubleshooting.md:59 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 +msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." +msgstr "" +"இந்த எடுத்துக்காட்டில், பணிப்பாய்வு படி `STEP_A` இது தற்காலிக சேமிப்பு செய்யப்பட்டதால் " +"மீண்டும் மதிப்பீடு செய்யப்படவில்லை, மேலும் அதன் சாவுஒறுப்பு அல்லது வெளியீட்டில் எந்த மாற்றமும் " +"இல்லை. மேலும், நாங்கள் இயங்கக்கூடிய பெயரை சரிசெய்த பிறகு `Step_b` ஐ மறு மதிப்பீடு செய்" +"ய வேண்டியிருந்தபோது` cwltool` அடையாளம் காண முடிந்தது. இந்த நுட்பம் உங்கள் சி.டபிள்யூ.எல்" +" ஆவணங்களை சரிசெய்ய பயனுள்ளதாக இருக்கும், மேலும் `cwltool` ஐ தேவையில்லாமல் மறு மதிப்பீடு" +" செய்வதைத் தடுப்பதற்கான ஒரு வழியாகும்." + +#: ../../src/topics/using-containers.md:1 +#: eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "கொள்கலன்களைப் பயன்படுத்துதல்" + +#: ../../src/topics/using-containers.md:3 +#: 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "டோக்கருக்குள் இயங்கும் கருவிகள்" + +#: ../../src/topics/using-containers.md:5 +#: e07f33d01b804663a25ffb08aad74821 +msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." +msgstr "" +"[டோக்கர்] [டோக்கர்] கொள்கலன்கள் மென்பொருள் நிறுவலை எளிதாக்குகின்றன, மென்பொருள் மற்றும் அதன் " +"சார்புகளுக்கு முழுமையான அறியப்பட்ட-நல்ல இயக்க நேரத்தை வழங்குவதன் மூலம். இருப்பினும், " +"கொள்கலன்கள் புரவலன் அமைப்பிலிருந்து வேண்டுமென்றே தனிமைப்படுத்தப்படுகின்றன, எனவே ஒரு " +"கப்பல்துறை கொள்கலனுக்குள் ஒரு கருவியை இயக்குவதற்கு கொள்கலனுக்குள் உள்ளீட்டுக் கோப்புகள் " +"கிடைப்பதை உறுதிசெய்ய கூடுதல் வேலை உள்ளது மற்றும் வெளியீட்டு கோப்புகளை கொள்கலனில் இருந்து " +"மீட்டெடுக்க முடியும். ஒரு சி.டபிள்யூ.எல் ரன்னர் இந்த வேலையை தானாகவே செய்ய முடியும், இது " +"உங்கள் மென்பொருள் நிர்வாகத்தை எளிமைப்படுத்த டோக்கரைப் பயன்படுத்த அனுமதிக்கிறது, அதே " +"நேரத்தில் கப்பல்துறை கொள்கலன்களைத் தொடங்குவதற்கும் நிர்வகிப்பதற்கும் சிக்கலைத் தவிர்க்கிறது." + +#: ../../src/topics/using-containers.md:15 +#: 7a644506619a4f08958ec7d4540cd557 +msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." +msgstr "" +"சி.டபிள்யூ.எல் ரன்னரின் பொறுப்புகளில் ஒன்று, உள்ளீட்டு கோப்புகளின் பாதைகளை கொள்கலனுக்குள் " +"தோன்றும் இடத்தை பிரதிபலிக்கும் வகையில் சரிசெய்வது." + +#: ../../src/topics/using-containers.md:18 +#: b5195b7d8eaa419fb2b90cb33a57783a +msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." +msgstr "" +"இந்த எடுத்துக்காட்டு ஒரு கப்பல்துறை கொள்கலனுக்குள் ஒரு எளிய Node.js ச்கிரிப்டை " +"இயக்குகிறது, பின்னர் அது \"அலோ வேர்ல்ட்\" ஐ நிலையான வெளியீட்டிற்கு அச்சிடும்." + +#: ../../src/topics/using-containers.md:21 +#: 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "`Docker.cwl`" + +#: ../../src/topics/using-containers.md:27 +#: 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "`docker-job.yml`" + +#: ../../src/topics/using-containers.md:33 +#: 2713594c937d4c528fc8d04d9e9819ed +msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." +msgstr "" +"இதை இயக்குவதற்கு முன், அதை உடைத்து சில பிட்கள் என்ன செய்கின்றன என்பதைப் பார்ப்போம். இவற்றில் " +"பெரும்பாலானவை முந்தைய பிரிவுகளில் விளக்கப்பட்டுள்ளன, உண்மையில் புதிய ஒரே பகுதி `டோக்கர் " +"ரெக்கமென்ட்` பிரிவு." + +#: ../../src/topics/using-containers.md:44 +#: cf94c1424fc2413c85647fd1ee73d951 +msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." +msgstr "" +"`பேச் கமாண்ட்: நோட்` சி.டபிள்யூ.எல். ஐ சாவாச்கிரிப்ட் கோப்புகளுக்கான முனைய JS இயக்க " +"நேரத்தைப் பயன்படுத்தி இந்த கட்டளையை இயக்குவோம் என்று கூறுகிறது. நாம் விரும்பும் கொள்கலனை " +"எவ்வாறு கண்டுபிடிப்பது என்பதற்கான சில `குறிப்புகளை 'குறிப்பிட வேண்டும். இந்த விசயத்தில், " +"கப்பல்துறை கொள்கலனுக்கான எங்கள் தேவைகளை `டோக்கர் ரெக்குவிரெமென்ட்ச்` இல் பட்டியலிடுகிறோம். " +"`டோக்கர்புல்:` அளவுரு நீங்கள் ஒரு `டோக்கர் புல்` கட்டளைக்கு அனுப்பும் அதே மதிப்பை எடுக்கும். " +"அதாவது, கொள்கலன் படத்தின் பெயர் (நீங்கள் குறிச்சொல்லைக் கூட குறிப்பிடலாம், இது இனப்பெருக்க " +"ஆராய்ச்சிக்கு கொள்கலன்களைப் பயன்படுத்தும் போது சிறந்த நடைமுறைகளுக்கு நல்ல யோசனையாகும்). இந்" +"த விசயத்தில் `முனை: ச்லிம்` என்ற கொள்கலனைப் பயன்படுத்தினோம்." + +#: ../../src/topics/using-containers.md:52 +#: dc0452107c604e29bdf32bb289fe5db8 +msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" +msgstr "" +"\"Hello.js\" என்ற பெயரில் ஒரு சாவாச்கிரிப்ட் கோப்பை உருவாக்கி, கட்டளை வரியில் கருவி " +"விளக்கத்தையும் உள்ளீட்டு பொருளையும் வழங்கும் `cwltool` ஐ அழைக்கவும்:" + +#: ../../src/topics/using-containers.md:55 +#: 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "`அலோ.சேச்`" + +#: ../../src/topics/using-containers.md:69 +#: 483181f498fc4d968b5fe6ef427709f7 +msgid "Notice the CWL runner has constructed a Docker command line to run the script." +msgstr "" +"ச்கிரிப்டை இயக்க சி.டபிள்யூ.எல் ரன்னர் ஒரு கப்பல்துறை கட்டளை வரியை உருவாக்கியுள்ளது " +"என்பதைக் கவனியுங்கள்." + +#: ../../src/topics/using-containers.md:72 +#: 7487485d6aa4458089a4b4bdf107ea64 +msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." +msgstr "" +"இந்த எடுத்துக்காட்டில், `அலோ.செச்` ச்கிரிப்டுக்கான பாதை கொள்கலனுக்கு வெளியே`/ஓம்/மீ/சி." +"டபிள்யூ.எல்/பயனர்_சியூட்/அலோ.சே.எச். , `முனை` கட்டளையின் அழைப்பில் பிரதிபலிக்கிறது." + +#: ../../src/topics/workflows.md:1 +#: 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "பணிப்பாய்வு" + +#: ../../src/topics/workflows.md:3 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 +msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." +msgstr "" +"பணிப்பாய்வு என்பது ஒரு சி.டபிள்யூ.எல் செயலாக்க அலகு ஆகும், இது கட்டளை-வரி கருவிகள், " +"வெளிப்பாடு கருவிகள் அல்லது பணிப்பாய்வுகளை (துணை வேலை பாய்ச்சல்கள்) படிகளாக " +"செயல்படுத்துகிறது. இது CWL ஆவணத்தில் `உள்ளீடுகள்`,` வெளியீடுகள்` மற்றும் `படிகள்` " +"வரையறுக்கப்பட வேண்டும்." + +#: ../../src/topics/workflows.md:13 +#: f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "சி.டபிள்யூ.எல் பணிப்பாய்வு." + +#: ../../src/topics/workflows.md:41 +#: 5870ac44e4c24b8daf5f06c49f95ce04 +msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." +msgstr "" +"சி.டபிள்யூ.எல் ஆவணம் `எக்கோ-பெர்பெச்.க்விஎல்` கட்டளை-வரி கருவியை இயக்கும் ஒரு பணிப்பாய்வை " +"வரையறுக்கிறது, மேலும் முந்தைய எடுத்துக்காட்டுகளில் காட்டப்பட்ட வெளிப்பாடு கருவி." + +#: ../../src/topics/workflows.md:51 +#: a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "`Echo-wpercase.cwl`" + +#: ../../src/topics/workflows.md:81 +#: 93188ed43ee949cc98b3ea679ce14feb +msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" +msgstr "" +"ஒரு கட்டளை-வரி கருவி அல்லது வெளிப்பாடு கருவி பணிப்பாய்வு போன்ற அதே CWL ஆவணத்தில் " +"நேரடியாக எழுதப்படலாம். எடுத்துக்காட்டாக, `echo-wirpercase.cwl` பணிப்பாய்வுகளை ஒற்றை " +"கோப்பாக மீண்டும் எழுதலாம்:" + +#: ../../src/topics/workflows.md:91 +#: 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "`எக்கோ-பெர்பெச்-சிங்கிள்-ஃபைல்-சி.டபிள்யூ.எல்" + +#: ../../src/topics/workflows.md:150 +#: 1cc17ad26e9c474b895ba5cd20c8b66a +msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." +msgstr "" +"தனித்தனி கோப்புகளை வைத்திருப்பது மட்டுப்படுத்தல் மற்றும் குறியீடு அமைப்புக்கு உதவுகிறது. " +"ஆனால் அபிவிருத்திக்காக ஒரே கோப்பில் எல்லாவற்றையும் எழுதுவது உதவியாக இருக்கும். இந்த பயனர்" +" வழிகாட்டியின் பிற பிரிவுகளில் மேலும் விவாதிக்கப்பட்ட பல கோப்புகளை ஒரே கோப்பாக (எ.கா. " +"`CWLTOOL - -PACK`) இணைக்க வேறு வழிகள் உள்ளன." + +#: ../../src/topics/workflows.md:160 +#: 24aca0bea4d94e3593b844cf0586cffe +msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." +msgstr "" +"ஒரு துணை வேலை பாய்ச்சல்களுக்கு நீங்கள் `subworkflowfeatureerequirement` தேவையை இயக்க " +"வேண்டும். இந்த பயனர் வழிகாட்டியின் மற்றொரு பிரிவில் இது இன்னும் விரிவாக உள்ளது." + +#: ../../src/topics/workflows.md:165 +#: 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "பணிப்பாய்வு எழுதுதல்" + +#: ../../src/topics/workflows.md:167 +#: 9c56528acd5f49deb139e034dfbfac7c +msgid "This workflow extracts a java source file from a tar file and then compiles it." +msgstr "" +"இந்த பணிப்பாய்வு ஒரு தார் கோப்பிலிருந்து சாவா மூல கோப்பைப் பிரித்தெடுத்து பின்னர் " +"தொகுக்கிறது." + +#: ../../src/topics/workflows.md:170 +#: 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "`1 வது-வொர்க்ஃப்ளோ.சிடபிள்யூஎல்`" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "1 வது-வொர்க்ஃப்ளோ.ச்விஎல் காட்சிப்படுத்தல்" + +#: ../../src/topics/workflows.md:180 +#: a2dd833fdca4443181648e41051a5232 +msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" +msgstr ". workflow/1st-workflow.cwl)]] 1 வது-வொர்க்ஃப்ளோ.ச்விஎல்)" + +#: ../../src/topics/workflows.md:183 +#: 7e40cc9f9e1341c195e843c009575b94 +msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" +msgstr "" +"ஒரு ரன்னின் உள்ளீட்டை விவரிக்க ஒரு தனி கோப்பில் ஒரு YAML அல்லது சாதொபொகு பொருளைப் " +"பயன்படுத்தவும்:" + +#: ../../src/topics/workflows.md:185 +#: 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "`1 வது-வொர்க்ஃப்ளோ-JOB.YML`" + +#: ../../src/topics/workflows.md:191 +#: 6fcf8ad3d1bd49afa4a105622437bd59 +msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." +msgstr "" +"அடுத்து, ஒரு மாதிரி சாவா கோப்பை உருவாக்கி, கட்டளை-வரி கருவியுடன் பயன்படுத்த தார் " +"கோப்பில் சேர்க்கவும்." + +#: ../../src/topics/workflows.md:205 +#: 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "இங்கே என்ன நடக்கிறது? அதை உடைப்போம்:" + +#: ../../src/topics/workflows.md:212 +#: def35d6021394def80a53ae49a2cdbde +msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." +msgstr "" +"`Cwlversion` புலம் ஆவணத்தால் பயன்படுத்தப்படும் CWL விவரக்குறிப்பின் பதிப்பைக் குறிக்கிறது" +". `வகுப்பு` புலம் இந்த ஆவணம் ஒரு பணிப்பாய்வுகளை விவரிக்கிறது என்பதைக் குறிக்கிறது." + +#: ../../src/topics/workflows.md:221 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 +msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." +msgstr "" +"`உள்ளீடுகள்` பிரிவு பணிப்பாய்வுகளின் உள்ளீடுகளை விவரிக்கிறது. ஒவ்வொரு அளவுருவும் ஒரு " +"அடையாளங்காட்டி மற்றும் தரவு வகையைக் கொண்ட உள்ளீட்டு அளவுருக்களின் பட்டியல் இது. இந்த " +"அளவுருக்களை குறிப்பிட்ட பணிப்பாய்வு படிகளுக்கான உள்ளீட்டிற்கான ஆதாரங்களாகப் பயன்படுத்தலாம்." + +#: ../../src/topics/workflows.md:233 +#: c84d4450bc6a475dbf34e0b22cea9130 +msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." +msgstr "" +"`வெளியீடுகள்` பிரிவு பணிப்பாய்வுகளின் வெளியீடுகளை விவரிக்கிறது. ஒவ்வொரு அளவுருவும் ஒரு" +" அடையாளங்காட்டி மற்றும் தரவு வகையைக் கொண்ட வெளியீட்டு அளவுருக்களின் பட்டியல் இது. " +"`OutputSource`` தொகுக்கப்பட்ட` படியின் `கிளாச்ஃபைல்` ஐ பணிப்பாய்வு வெளியீட்டு " +"அளவுருவுக்கு` தொகுக்கப்பட்ட_ கிளாச்` உடன் இணைக்கிறது." + +#: ../../src/topics/workflows.md:248 +#: cca9665f6daa44b49233baf34ab9fcc7 +msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." +msgstr "" +"`படிகள்` பிரிவு பணிப்பாய்வுகளின் உண்மையான படிகளை விவரிக்கிறது. இந்த எடுத்துக்காட்டில், " +"முதல் படி ஒரு தார் கோப்பிலிருந்து ஒரு கோப்பைப் பிரித்தெடுக்கிறது, இரண்டாவது படி சாவா " +"கம்பைலரைப் பயன்படுத்தி முதல் படியிலிருந்து கோப்பை தொகுக்கிறது. பணிப்பாய்வு படிகள் அவை " +"பட்டியலிடப்பட்ட வரிசையில் அவசியமில்லை, அதற்கு பதிலாக ஆர்டர் படிகளுக்கு இடையிலான " +"சார்புகளால் தீர்மானிக்கப்படுகிறது (`மூலத்தை` பயன்படுத்தி). கூடுதலாக, ஒருவருக்கொருவர் " +"சார்ந்து இல்லாத பணிப்பாய்வு படிகள் இணையாக இயங்கக்கூடும்." + +#: ../../src/topics/workflows.md:256 +#: 547edbf5fa424b8286cc21674ff159b0 +msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." +msgstr "" +"முதல் படி, `அன்டார்`` tar-param.cwl` ஐ இயக்குகிறது (முன்னர் [அளவுரு குறிப்புகள்] " +"(அளவுரு-குறிப்புகள். எம்.டி) இல் விவரிக்கப்பட்டுள்ளது). இந்த கருவி இரண்டு உள்ளீட்டு " +"அளவுருக்களைக் கொண்டுள்ளது, `டார்ஃபைல்` மற்றும்` எக்ச்ட்ராக்ட்ஃபைல்` மற்றும் ஒரு வெளியீட்டு " +"அளவுரு `பிரித்தெடுக்கப்பட்ட_பைல்`." + +#: ../../src/topics/workflows.md:261 +#: 7ca248888b9d484cb544cd76ba538662 +msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." +msgstr "" +"பணிப்பாய்வு படியின் `` இன்` பிரிவு இந்த இரண்டு உள்ளீட்டு அளவுருக்களையும் பணிப்பாய்வு " +"உள்ளீடுகளுடன் இணைக்கிறது, `டார்பால்` மற்றும்` பெயர்_ஓஎஃப்_ஃபைல்_டோ_எக்டிகல்` `மூலத்தை` " +"பயன்படுத்துகிறது. இதன் பொருள், பணிப்பாய்வு படி செயல்படுத்தப்படும்போது, `டார்பால்` மற்றும்` " +"NAME_OF_FILE_TO_Extract` ஆகியவற்றுக்கு ஒதுக்கப்பட்ட மதிப்புகள் கருவியை இயக்க " +"`டார்ஃபைல்` மற்றும்` எக்ச்ட்ராக்ட்ஃபைல்` ஆகியவற்றிற்கு பயன்படுத்தப்படும்." + +#: ../../src/topics/workflows.md:267 +#: ae6b240718104380b08db5552d7355ea +msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." +msgstr "" +"பணிப்பாய்வு படியின் `அவுட்` பிரிவு கருவியிலிருந்து எதிர்பார்க்கப்படும் வெளியீட்டு " +"அளவுருக்களை பட்டியலிடுகிறது." + +#: ../../src/topics/workflows.md:278 +#: e5a8b7f84be64020b191099f3fad30ed +msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." +msgstr "" +"இரண்டாவது படி `தொகுத்தல் '` அன்டார்/பிரித்தெடுக்கப்பட்ட_பீல்` ஐப் பயன்படுத்தி உள்ளீட்டு " +"அளவுருவை `SRC` இன் வெளியீட்டு அளவுருவுடன் இணைப்பதன் மூலம் முதல் படியின் முடிவுகளைப் " +"பொறுத்தது. இது `வாதங்கள். CWL` ஐ இயக்குகிறது (முன்னர் [கூடுதல் வாதங்கள் மற்றும் " +"அளவுருக்கள்] (கூடுதல்-ஆவணம் மற்றும் அளவுருக்கள். எம்.டி) இல் விவரிக்கப்பட்டுள்ளது). இந்த படி" +" `கிளாச்ஃபைல்` இன் வெளியீடு மேலே விவரிக்கப்பட்ட பணிப்பாய்வுக்கான` வெளியீடுகள்` பிரிவுடன் " +"இணைக்கப்பட்டுள்ளது." + +#: ../../src/topics/workflows.md:285 +#: f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "உள்ளமைக்கப்பட்ட பணிப்பாய்வு" + +#: ../../src/topics/workflows.md:287 +#: 12a06d8358534102b202965d4258c18e +msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" +"பணிப்பாய்வு என்பது ஒரு பெரிய செயல்பாடுகளைச் செய்ய பல கருவிகளை இணைப்பதற்கான வழிகள். ஒரு" +" பணிப்பாய்வு ஒரு கருவியாக இருப்பதையும் நாம் நினைக்கலாம்; ஒரு சி.டபிள்யூ.எல் பணிப்பாய்வு " +"மற்றொரு சி.டபிள்யூ.எல் பணிப்பாய்வுகளின் ஒரு படியாகப் பயன்படுத்தப்படலாம், பணிப்பாய்வு " +"இயந்திரம் `சப்ச்வொர்க்ஃப்ளோஃபீட்டர்ரெக்யூமென்ட்` ஆதரித்தால்:" + +#: ../../src/topics/workflows.md:297 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 +msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" +msgstr "" +"எங்கள் `1 வது-வொர்க்ஃப்ளோ.க்விஎல்` ஐ உள்ளமைக்கப்பட்ட பணிப்பாய்வுகளாகப் பயன்படுத்தும் ஒரு " +"எடுத்துக்காட்டு பணிப்பாய்வு இங்கே:" + +#: ../../src/topics/workflows.md:300 +#: 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "`NestestWorkflows.cwl`" + +#: ../../src/topics/workflows.md:309 +#: b7f93705e5b8416696be01850072e8c0 +msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." +msgstr "" +"இந்த இரண்டு-படி பணிப்பாய்வு `கிரியேட்-டார்` படியுடன் தொடங்குகிறது, இது ஆரஞ்சில்` " +"தொகுத்தல்` படியுடன் இணைக்கப்பட்டுள்ளது; `தொகுத்தல்` என்பது மற்றொரு பணிப்பாய்வு, " +"வலதுபுறத்தில் வரைபடமாக்கப்படுகிறது. ஊதா நிறத்தில் `\" அலோ.சாவா \"` " +"`Name_of_file_to_extract` என வழங்கப்படுவதைக் காண்கிறோம்." + +#: ../../src/topics/workflows.md:314 +#: e87045829b344089ab59dc27063ddd7a +msgid "\"Visualization \"Visualization" +msgstr "" +" " + +#: ../../src/topics/workflows.md:322 +#: 42ef2f145b824d69b63abc1da175c216 +msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." +msgstr "" +"ஒரு சி.டபிள்யூ.எல் `பணிப்பாய்வு` ஒரு` கட்டமாக 'ஒரு `கட்டமாக' போலவே, அதன் சி.டபிள்யூ." +"எல் கோப்பு` ரன்` உடன் சேர்க்கப்பட்டுள்ளது. பணிப்பாய்வு உள்ளீடுகள் (`தர்பால்` மற்றும்` " +"name_of_file_to_extract`) மற்றும் வெளியீடுகள் (`தொகுக்கப்பட்ட_ கிளாச்`) பின்னர் " +"படிநிலையின் உள்ளீடு/வெளியீடுகளாக மாறலாம்." + +#: ../../src/topics/workflows.md:336 +#: c61cedf543664d388183e04b3939cc39 +msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." +msgstr "" +"எங்கள் `1 வது-வொர்க்ஃப்ளோ.க்விஎல்` பணிப்பாய்வு உள்ளீடுகளுடன் அளவுருவாக்கப்பட்டது, எனவே அதை " +"இயக்கும் போது தார் கோப்பு மற்றும்`*.சாவா` கோப்பு பெயர் ஆகியவற்றைக் குறிக்க வேலை கோப்பை " +"வழங்க வேண்டியிருந்தது. இது பொதுவாக சிறந்த நடைமுறையாகும், ஏனெனில் இது பல பெற்றோர் " +"பணிப்பாய்வுகளில் அல்லது ஒரே பணிப்பாய்வுகளுக்குள் பல படிகளில் கூட மீண்டும் பயன்படுத்தப்படலாம்." + +#: ../../src/topics/workflows.md:341 +#: 9e39e3f1501c4fcaab3e8962e090f6be +msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." +msgstr "" +"இங்கே நாம் `இயல்புநிலை:` ஆர்ட்-குறியீடு `\" அலோ.சாவா \"` `பெயர்_எஃப்_ஃபைல்_எக்டேக்சன்` " +"உள்ளீட்டைப் பயன்படுத்துகிறோம், இருப்பினும் எங்கள் பணிப்பாய்வுக்கு` தர்பால்` இல் ஒரு தார் கோப்பு " +"தேவைப்படுகிறது, அதை `படைப்பு-தார் படிநிலையில் நாங்கள் ஆயத்தம் செய்வோம் . இந்த கட்டத்தில், `" +"1 வது-வொர்க்ஃப்ளோ.ச்விஎல்` ஐ மறுசீரமைப்பது நல்ல யோசனையாகும், மேலும் குறிப்பிட்ட " +"உள்ளீடு/வெளியீட்டு பெயர்களைக் கொண்டிருப்பது, ஏனெனில் அவை ஒரு கருவியாக அதன் பயன்பாட்டில் " +"தோன்றும்." + +#: ../../src/topics/workflows.md:347 +#: 03e2f767c4da461982fc3c0f3ba94762 +msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." +msgstr "" +"குறைவான பொதுவான அணுகுமுறையைச் செய்யவும், வேலை கோப்பில் வெளிப்புற சார்புகளைத் " +"தவிர்க்கவும் முடியும். எனவே இந்த பணிப்பாய்வுகளில், முன்னர் குறிப்பிடப்பட்ட `தொடக்கப்பொர்க் " +"டிஐஆர்ரெக்விரெமென்ட்` தேவையைப் பயன்படுத்தி, ஒரு தார் கோப்பில் சேர்ப்பதற்கு முன், கடின " +"குறியிடப்பட்ட` அலோ.சாவா` கோப்பை உருவாக்கலாம்." + +#: ../../src/topics/workflows.md:366 +#: 3bea5822b8694e2aa32c446e1c54a045 +msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" +msgstr "" +"இந்த விசயத்தில் எங்கள் படி அளவுருவாக்கப்படுவதை விட `அலோ.சாவா` என்று கருதலாம், எனவே " +"ஆர்ட்கோட் செய்யப்பட்ட மதிப்புகள்` அலோ.டார்` மற்றும் `அலோ.சாவா` ஆகியவற்றை ஒரு` பேச்கோமாண்ட்` " +"இல் பயன்படுத்தலாம், இதன் விளைவாக `வெளியீடுகள்`:" + +#: ../../src/topics/workflows.md:383 +#: 426023bd6e3a471cbb30dbda3d6f9e57 +msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." +msgstr "" +"`தார் -கிரேட்` கருவியை ஒரு தனி கோப்பில் நாங்கள் பிரிக்கவில்லை என்பதை நீங்கள் கவனித்தீர்களா, " +"மாறாக சி.டபிள்யூ.எல் பணிப்பாய்வு கோப்பில் அதை உட்பொதித்தீர்களா? இது பொதுவாக சிறந்த " +"நடைமுறை அல்ல, ஏனெனில் கருவியை மீண்டும் பயன்படுத்த முடியாது. இந்த விசயத்தில் அதைச் " +"செய்வதற்கான காரணம் என்னவென்றால், கட்டளை வரி கோப்பு பெயர்களால் கடின குறியிடப்பட்டிருப்பதால்" +", இந்த பணிப்பாய்வுக்குள் மட்டுமே அர்த்தமுள்ளதாக இருக்கும்." + +#: ../../src/topics/workflows.md:389 +#: 0d498cd4caf54c15891ca1afe58e2727 +msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." +msgstr "" +"இந்த எடுத்துக்காட்டில் நாங்கள் ஒரு தார் கோப்பை வெளியே தயாரிக்க வேண்டியிருந்தது, ஆனால் எங்கள்" +" உள் பணிப்பாய்வு அதை உள்ளீட்டாக எடுக்க வடிவமைக்கப்பட்டதால் மட்டுமே. உட்புற பணிப்பாய்வுகளின் " +"சிறந்த மறுசீரமைப்பு என்பது சாவா கோப்புகளின் பட்டியலை தொகுக்க வேண்டும், இது மற்ற " +"பணிப்பாய்வுகளில் ஒரு கருவி படியாக அதன் பயன்பாட்டை எளிதாக்கும்." + +#: ../../src/topics/workflows.md:394 +#: b2d75045e02741b4850f5ff1243f7858 +msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." +msgstr "" +"உயர் மட்ட செயல்பாட்டு மற்றும் மறுபயன்பாட்டு பணிப்பாய்வு அலகுகளை உருவாக்குவதற்கு " +"உள்ளமைக்கப்பட்ட பணிப்பாய்வுகள் ஒரு சக்திவாய்ந்த அம்சமாக இருக்கலாம் - ஆனால் ஒரு சி.டபிள்யூ.எல்" +" கருவி விளக்கத்தை உருவாக்குவதைப் போலவே, பல பணிப்பாய்வுகளில் அதன் பயன்பாட்டினை மேம்படுத்த " +"கவனமாக இருக்க வேண்டும்." + +#: ../../src/topics/workflows.md:398 +#: cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "சிதறல் படிகள்" + +#: ../../src/topics/workflows.md:400 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 +msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." +msgstr "" +"இப்போது பணிப்பாய்வுகளை எழுதுவது எப்படி என்று எங்களுக்குத் தெரியும், " +"`சிதறல்ஃபீட்டர்ரெக்யூமென்ட்` ஐப் பயன்படுத்தத் தொடங்கலாம். உள்ளீடுகளின் பட்டியலில் ஒரு கருவி " +"அல்லது பணிப்பாய்வுகளை பல முறை இயக்க விரும்புகிறீர்கள் என்று இந்த நற்பொருத்தம் ரன்னரிடம் " +"கூறுகிறது. பணிப்பாய்வு பின்னர் உள்ளீட்டை (களை) ஒரு வரிசையாக எடுத்து, வரிசையின் ஒவ்வொரு " +"உறுப்பிலும் குறிப்பிட்ட படி (களை) ஒரு உள்ளீடு போல இயக்கும். பல கட்டளைகளை அல்லது உள்ளீட்டு " +"YAML கோப்புகளை உருவாக்காமல் பல உள்ளீடுகளில் ஒரே பணிப்பாய்வுகளை இயக்க இது உங்களை " +"அனுமதிக்கிறது." + +#: ../../src/topics/workflows.md:411 +#: 5fa79c62049a447c8328ebf9db54ebf4 +msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" +msgstr "" +"ஒரு புதிய பயனர் சிதறலைப் பயன்படுத்த விரும்புவதற்கான பொதுவான காரணம் வெவ்வேறு " +"மாதிரிகளில் ஒரே பகுப்பாய்வைச் செய்வதாகும். எங்கள் முதல் உதாரணத்தை (`hello_world.cwl`) " +"அழைக்கும் எளிய பணிப்பாய்வுகளுடன் ஆரம்பிக்கலாம் மற்றும் பணிப்பாய்வுக்கு உள்ளீடாக சரங்களின் " +"வரிசையை எடுத்துக்கொள்வோம்:" + +#: ../../src/topics/workflows.md:415 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "`சிதறல்-வொர்க்ஃப்ளோ.சிடபிள்யூஎல்`" + +#: ../../src/topics/workflows.md:421 +#: 3a67d77a2e7b4c0bb61cc3585ceae942 +msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" +msgstr "" +"`SPATTERFEATUREREQUIREMENT` உட்பட` தேவைகள்` பிரிவைத் தவிர, இங்கே என்ன நடக்கிறது?" + +#: ../../src/topics/workflows.md:429 +#: f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" +"முதலாவதாக, இங்குள்ள முக்கிய பணிப்பாய்வு நிலை உள்ளீட்டிற்கு சரங்களின் வரிசை தேவை என்பதைக் " +"கவனியுங்கள்." + +#: ../../src/topics/workflows.md:441 +#: d947c54933d64aad90df392a1cedd63f +msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." +msgstr "" +"`சிதறல்` எனப்படும்` எதிரொலி` படியில் ஒரு புதிய புலத்தை இங்கே சேர்த்துள்ளோம். இந்த " +"குறிப்பிட்ட படிக்கு இந்த உள்ளீட்டை சிதறடிக்க விரும்புகிறோம் என்று இந்த புலம் ரன்னரிடம் " +"கூறுகிறது. சிதறிக்குப் பிறகு பட்டியலிடப்பட்ட உள்ளீட்டுப் பெயர் படிநிலையின் உள்ளீட்டில் " +"ஒன்றாகும், பணிப்பாய்வு நிலை உள்ளீடு அல்ல என்பதை நினைவில் கொள்க." + +#: ../../src/topics/workflows.md:445 +#: 651d35997332404186aa6d5711da4a3d +msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" +msgstr "" +"எங்கள் முதல் சிதறலுக்கு, அது அவ்வளவு எளிது! எங்கள் கருவி எந்த வெளியீடுகளையும் " +"சேகரிக்கவில்லை என்பதால், நாங்கள் இன்னும் `வெளியீடுகளைப் பயன்படுத்துகிறோம்: []` எங்கள் " +"பணிப்பாய்வுகளில், ஆனால் உங்கள் பணிப்பாய்வுகளின் இறுதி வெளியீடு இப்போது சேகரிக்க பல " +"வெளியீடுகள் இருக்கும் என்று நீங்கள் எதிர்பார்க்கிறீர்கள் என்றால், அதை ஒரு வரிசைக்கு புதுப்பிக்க " +"மறக்காதீர்கள் தட்டச்சு செய்க!" + +#: ../../src/topics/workflows.md:450 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "பின்வரும் உள்ளீட்டு கோப்பைப் பயன்படுத்துதல்:" + +#: ../../src/topics/workflows.md:452 +#: 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "`சிதறல்-job.yml`" + +#: ../../src/topics/workflows.md:458 +#: b662c1a5a4424c8d8350a806356acc61 +msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" +msgstr "" +"ஒரு நினைவூட்டலாக, [`Hello_world.cwl`] (../ அறிமுகம்/விரைவு-தொடக்க. கட்டளை வரியில் " +"`cwltool சிதறல்-வொர்க்ஃப்ளோ." + +#: ../../src/topics/workflows.md:466 +#: 04d6babfd87343d7a5f13867ea02b65f +msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" +msgstr "" +"எங்கள் `Message_Array` இன் ஒவ்வொரு உறுப்பிலும் பணிப்பாய்வு அழைப்புகள் பல முறை " +"எதிரொலிப்பதை நீங்கள் காணலாம். சரி, ஒரு பணிப்பாய்வுகளில் இரண்டு படிகளில் சிதற விரும்பினால்" +" எப்படி?" + +#: ../../src/topics/workflows.md:469 +#: 2eaacf1a90204a2b9bd621344560f2a1 +msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" +msgstr "" +"மேலே உள்ளதைப் போல ஒரு எளிய எதிரொலியைச் செய்வோம், ஆனால் `வெளியீடுகளுக்கு பதிலாக " +"பின்வரும் வரிகளைச் சேர்ப்பதன் மூலம்` stdout` ஐப் பிடிப்போம்: [] `" + +#: ../../src/topics/workflows.md:472 +#: 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "`அலோ_போர்ட்_டோ_ச்டூட்.ச்விஎல்`" + +#: ../../src/topics/workflows.md:480 +#: 4a94e5f7e1bc4d628702140e4e51d6d3 +msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" +msgstr "" +"ஒவ்வொரு கோப்பிலும் உள்ள எழுத்துக்களை எண்ண `wc` ஐப் பயன்படுத்தும் இரண்டாவது படியைச் " +"சேர்க்கவும். கீழே உள்ள கருவியைக் காண்க:" + +#: ../../src/topics/workflows.md:483 +#: e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "`wc-tool.cwl`" + +#: ../../src/topics/workflows.md:489 +#: e3a7182f00f440b8b5461da91194a64b +msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" +msgstr "" +"இப்போது, சிதறலை எவ்வாறு இணைப்பது? சிதறல் புலம் ஒவ்வொரு அடியிலும் உள்ளது என்பதை நினைவில்" +" கொள்ளுங்கள்:" + +#: ../../src/topics/workflows.md:491 +#: 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "`சிதறல்-இரண்டு-படி. cwl`" + +#: ../../src/topics/workflows.md:497 +#: b5338f39e8c74ff28e139da68089a742 +msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." +msgstr "" +"இங்கே நாம் ஒவ்வொரு அடியிலும் சிதறல் புலத்தை வைத்திருக்கிறோம். இந்த எடுத்துக்காட்டு விரைவா" +"க இயங்குவதால் இது நல்லது, ஆனால் நீங்கள் மிகவும் சிக்கலான பணிப்பாய்வுக்காக பல மாதிரிகளை " +"இயக்குகிறீர்கள் என்றால், நீங்கள் ஒரு மாற்றீட்டைக் கருத்தில் கொள்ள விரும்பலாம். இங்கே நாம் ஒவ்வொரு " +"அடியிலும் சுயாதீனமாக சிதறலை இயக்குகிறோம், ஆனால் இரண்டாவது படி அனைத்து மொழிகளையும் " +"நிறைவு செய்யும் முதல் படியைப் பொறுத்தது அல்ல என்பதால், நாங்கள் சிதறல் செயல்பாட்டை " +"திறமையாகப் பயன்படுத்தவில்லை. இரண்டாவது படி ஒரு வரிசையை முதல் படியிலிருந்து உள்ளீடாக " +"எதிர்பார்க்கிறது, எனவே ஒரு படி ஒன்றில் உள்ள அனைத்தும் எதையும் செய்வதற்கு முன் அது " +"முடிவடையும் வரை காத்திருக்கும். `எக்கோ அலோ வேர்ல்ட்!` செய்ய 1 மணித்துளி ஆகும் என்று " +"பாசாங்கு செய்யுங்கள், `wc -c` வெளியீட்டில் 3 நிமிடங்கள் ஆகும், மேலும்` எதிரொலி ஆலோ வெல்ட்" +"! `செய்ய 5 நிமிடங்கள் ஆகும், மேலும் அந்த வெளியீட்டில்` wc` 3 நிமிடங்கள் ஆகும். `எக்கோ அலோ " +"வேர்ல்ட்!` 4 நிமிடங்களில் முடிக்க முடியும் என்றாலும், அது உண்மையில் 8 நிமிடங்களில் " +"முடிவடையும், ஏனெனில் முதல் படி `எக்கோ ஆலோ வெல்ட்!` இல் காத்திருக்க வேண்டும். இது எவ்வாறு " +"சரியாக அளவிடப்படாது என்பதை நீங்கள் காணலாம்." + +#: ../../src/topics/workflows.md:509 +#: f6d92156d67c4a339bcfd194cff897df +msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" +msgstr "" +"சரி, எனவே மற்ற மாதிரிகளிலிருந்து சுயாதீனமாக தொடரக்கூடிய படிகளில் நாம் எவ்வாறு " +"சிதறடிப்பது? [உள்ளமைக்கப்பட்ட பணிப்பாய்வுகளிலிருந்து] (#உள்ளமைக்கப்பட்ட-வேலை பாய்ச்சல்கள்) " +"நினைவில் கொள்ளுங்கள், ஒரு முழு பணிப்பாய்வுகளையும் மற்றொரு பணிப்பாய்வுகளில் ஒரு படி செய்ய " +"முடியும் என்பதை நினைவில் கொள்க! எங்கள் இரண்டு-படி பணிப்பாய்வுகளை ஒற்றை படி அடைப்பகுதிக்கு" +" மாற்றவும்:" + +#: ../../src/topics/workflows.md:513 +#: 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "`சிதறல்-நெச்டட்-வொர்க்ஃப்ளோ.ச்விஎல்`" + +#: ../../src/topics/workflows.md:519 +#: d80ab383eec9402faba997b548fe42eb +msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." +msgstr "" +"இப்போது சிதறல் ஒரு படியில் செயல்படுகிறது, ஆனால் அந்த படி இரண்டு படிகளைக் கொண்டுள்ளது, " +"எனவே ஒவ்வொரு அடியும் இணையாக செய்யப்படுகிறது." + +#: ../../src/topics/workflows.md:522 +#: f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "நிபந்தனை பணிப்பாய்வு" + +#: ../../src/topics/workflows.md:524 +#: 49217c02f58c43ff9ec00f10da8d4e84 +msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." +msgstr "" +"இந்த பணிப்பாய்வு ஒரு நிபந்தனை படி உள்ளது மற்றும் உள்ளீட்டின் அடிப்படையில் " +"செயல்படுத்தப்படுகிறது. நிரலின் தொடக்கத்தில் அல்லது முந்தைய படிகளால் கொடுக்கப்பட்ட உள்ளீட்டு " +"அளவுருக்களின் அடிப்படையில் கூடுதல் படிகளைத் தவிர்க்க இது பணிப்பாய்வுகளை அனுமதிக்கிறது." + +#: ../../src/topics/workflows.md:527 +#: 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "`நிபந்தனை-வொர்க்ஃப்ளோ.சிடபிள்யூஎல்`" + +#: ../../src/topics/workflows.md:566 +#: 8dbd56473f8c40c0bb12a48be06117e3 +msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." +msgstr "" +"நீங்கள் கவனிக்கும் முதல் சேதி என்னவென்றால், இந்த பணிப்பாய்வு பதிப்பு 1.2 அல்லது அதற்கு மேற்பட்" +"ட சி.டபிள்யூ.எல் தரத்திற்கு மட்டுமே இணக்கமானது." + +#: ../../src/topics/workflows.md:573 +#: 78d7f3ede2c746d482042adef050b2c4 +msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." +msgstr "" +"பணிப்பாய்வுகளின் முதல் படி (Step1) இரண்டு உள்ளீட்டு பண்புகளைக் கொண்டுள்ளது மற்றும் " +"நிபந்தனைகள் நிறைவு செய்யப்படும்போது FOO.CWL ஐ இயக்கும். புதிய சொத்து `எப்போது` நிபந்தனை" +" சரிபார்ப்பு நடைபெறுகிறது. இந்த வழக்கில் பணிப்பாய்வுகளிலிருந்து `in1` ஒரு மதிப்பு` <1`" +" இந்த படி செயல்படுத்தப்படும்." + +#: ../../src/topics/workflows.md:587 +#: cbbf93c70fe04ba7932ba25758ddc611 +msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." +msgstr "" +"பின்வரும் கட்டளையைப் பயன்படுத்தி `cwltool cond-wf-003.1.cwl --val 0` மதிப்பு முதல் " +"நிபந்தனை படியைக் கடந்து, எனவே செயல்படுத்தப்படும் மற்றும்` செய்தி [படி 1] தொடக்க` மூலம் " +"பதிவில் காட்டப்படுகிறது, அதேசமயம் இரண்டாவது படி `தகவல் [STEP STEP2] மூலம் " +"சுட்டிக்காட்டப்பட்டபடி தவிர்க்கப்படுகிறது." + +#: ../../src/topics/workflows.md:607 +#: cfa1c1fde4454df283f87cc54a9c59ec +msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." +msgstr "" +"3 இன் மதிப்பு வழங்கப்படும் போது முதல் நிபந்தனை படி செயல்படுத்தப்படாது, ஆனால் இரண்டாவது " +"படி `cwltool cond-wf-003.1.cwl --val 3`." + +#: ../../src/topics/workflows.md:627 +#: 1a8be2950cbb475bbb2617e005f0fac9 +msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." +msgstr "" +"`--Val 2` ஐப் பயன்படுத்தும் போது எந்த நிபந்தனைகளும் நிறைவு செய்யப்படாவிட்டால், பணிப்பாய்வு" +" ஒரு நிரந்தர படத்தை உயர்த்தும்." + +#: ../../src/topics/yaml-guide.md:1 +#: 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "யாம் வழிகாட்டி" + +#: ../../src/topics/yaml-guide.md:6 +#: 5d83c56102e141cc978500f678dd0c1c +msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." +msgstr "" +"[YAML] [YAML] என்பது ஒரு கோப்பு வடிவமாகும், இது கணினிகள் மற்றும் மனிதர்களால் " +"படிக்கக்கூடியதாக வடிவமைக்கப்பட்டுள்ளது. இந்த வழிகாட்டி CWL விளக்கங்கள் மற்றும் உள்ளீட்டு " +"அளவுரு கோப்புகளை எழுதும்போது பொருத்தமான YAML இன் அம்சங்களை அறிமுகப்படுத்துகிறது." + +#: ../../src/topics/yaml-guide.md:13 +#: c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" +"நீங்கள் ஏற்கனவே YAML உடன் வசதியாக இருந்தால் இந்த பகுதியைத் தவிர்க்கலாம்." + +#: ../../src/topics/yaml-guide.md:16 +#: fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "உள்ளடக்கங்கள்" + +#: ../../src/topics/yaml-guide.md:18 +#: 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "[முக்கிய மதிப்பு சோடிகள்] (#விசை மதிப்பு-சோடிகள்)" + +#: ../../src/topics/yaml-guide.md:19 +#: b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "[கருத்துரைகள்] (#கருத்துகள்)" + +#: ../../src/topics/yaml-guide.md:20 +#: b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "[வரைபடங்கள்] (#வரைபடங்கள்)" + +#: ../../src/topics/yaml-guide.md:21 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "[வரிசைகள்] (#வரிசைகள்)" + +#: ../../src/topics/yaml-guide.md:22 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "[JSON ச்டைல்] (#JSON- பாணி)" + +#: ../../src/topics/yaml-guide.md:24 +#: 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "முக்கிய மதிப்பு சோடிகள்" + +#: ../../src/topics/yaml-guide.md:26 +#: cda73485875d4c8e9464679a20558616 +msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" +msgstr "" +"அடிப்படையில், YAML இல் எழுதப்பட்ட ஒரு கோப்பு _கே-மதிப்பு சோடிகளின்_ தொகுப்பைக் " +"கொண்டுள்ளது. ஒவ்வொரு சோடியும் `விசை: மதிப்பு` என எழுதப்பட்டுள்ளன, அங்கு`: `க்குப் பிறகு " +"இடைவெளி தேவைப்படுகிறது. சி.டபிள்யூ.எல் கோப்புகளில் உள்ள முக்கிய பெயர்கள் வைட்ச்பேசைக் " +"கொண்டிருக்கக்கூடாது - [_CAMELCASE _] [ஒட்டக கேச்] CWL விவரக்குறிப்பில் சிறப்பு அர்த்தமுள்" +"ள பல சொல் முக்கிய பெயர்களுக்கு பயன்படுத்தப்படுகிறது மற்றும் இல்லையெனில் அடிக்கோடிட்டுக் " +"காட்டப்பட்ட முக்கிய பெயர்கள். உதாரணமாக:" + +#: ../../src/topics/yaml-guide.md:42 +#: 98cae24919b74c088a5d89706aec581b +msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." +msgstr "" +"மேலே உள்ள YAML நான்கு விசைகளை வரையறுக்கிறது - `First_name`,` கடைசி_பெயர்`, " +"`வயது_இயர்கள்`, மற்றும்` வீடு` - அவற்றின் நான்கு அந்தந்த மதிப்புகளுடன். மதிப்புகள் எழுத்து " +"சரங்கள், எண் (முழு எண், மிதக்கும் புள்ளி, அல்லது அறிவியல் பிரதிநிதித்துவம்), பூலியன் " +"(`உண்மை` அல்லது` தவறு`) அல்லது மிகவும் சிக்கலான உள்ளமைக்கப்பட்ட வகைகளாக இருக்கலாம் (கீழே " +"காண்க)." + +#: ../../src/topics/yaml-guide.md:51 +#: b4b0940b4b5743c09637b36b964202d0 +msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." +msgstr "" +"மதிப்புகள் மேற்கோள் மதிப்பெண்களில் மூடப்பட்டிருக்கலாம், ஆனால் இது அவை விளக்கப்படும் விதத்தை " +"மாற்றக்கூடும் என்பதை அறிந்து கொள்ளுங்கள். அதாவது `\" 1234 \"` ஒரு எழுத்து சரமாக " +"கருதப்படும், அதே நேரத்தில் `1234` ஒரு முழு எண்ணாக கருதப்படும். இந்த வேறுபாடு " +"முக்கியமானது, எடுத்துக்காட்டாக ஒரு கட்டளைக்கு அளவுருக்களை விவரிக்கும் போது: சி.டபிள்யூ." +"எல் இல் `பேச் கமாண்டின் 'அனைத்து பகுதிகளும் சரங்களாக இருக்க வேண்டும், நீங்கள் ஒரு கட்டளைக்கு " +"ஒரு நிலையான எண் மதிப்பைக் குறிப்பிட விரும்பினால், அந்த எண் மதிப்பை நீங்கள் போர்த்திக் " +"கொள்ளுங்கள் என்பதை உறுதிப்படுத்திக் கொள்ளுங்கள் மேற்கோள்கள்: `பேச் கமாண்ட்: [எதிரொலி,\" 42 \"" +"]`." + +#: ../../src/topics/yaml-guide.md:61 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "கருத்துகள்" + +#: ../../src/topics/yaml-guide.md:63 +#: 9ca3554d771d45998e88aaede525b227 +msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" +msgstr "" +"உங்கள் CWL மற்றும் அளவுரு கோப்புகளில் கருத்துகளைச் சேர்க்க `#` பயன்படுத்தலாம். ` #` என்ற " +"வலதுபுறத்தில் உள்ள எந்த எழுத்துக்களும் YAML ஐ விளக்கும் நிரலால் புறக்கணிக்கப்படும். " +"உதாரணமாக:" + +#: ../../src/topics/yaml-guide.md:76 +#: 3fca839cede94cfd8e4f605c73ba699d +msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" +msgstr "" +"கருத்துக்கு முன் வரியில் ஏதேனும் இருந்தால், `#` க்கு முன் குறைந்தது ஒரு இடத்தையாவது சேர்க்" +"க மறக்காதீர்கள்!" + +#: ../../src/topics/yaml-guide.md:79 +#: da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "வரைபடங்கள்" + +#: ../../src/topics/yaml-guide.md:81 +#: 3ded0f125249485c921994b6e6b93ac9 +msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" +msgstr "" +"சி.டபிள்யூ.எல் உடன் ஒரு கருவி அல்லது பணிப்பாய்வுகளை விவரிக்கும் போது, பொதுவாக மிகவும் " +"சிக்கலான, உள்ளமைக்கப்பட்ட பிரதிநிதித்துவங்களை உருவாக்குவது தேவை. _MAPS_ என " +"குறிப்பிடப்படுகிறது, இந்த படிநிலை கட்டமைப்புகள் எந்தவொரு விசையின் மதிப்பாக கூடுதல் " +"விசை-மதிப்பு சோடிகளை வழங்குவதன் மூலம் YAML இல் விவரிக்கப்பட்டுள்ளன. இந்த சோடிகள் (சில " +"நேரங்களில் \"குழந்தைகள்\" என்று குறிப்பிடப்படுகின்றன) அவர்கள் சேர்ந்த விசையின் கீழ் (\"ப" +"ெற்றோர்\") புதிய வரிகளில் எழுதப்பட்டுள்ளன, மேலும் அவை இரண்டு இடங்களுடன் உள்தள்ளப்பட வேண்டும்" +" (⇥TAB எழுத்துக்கள் அனுமதிக்கப்படவில்லை). உதாரணமாக:" + +#: ../../src/topics/yaml-guide.md:104 +#: 53ece35d309a4c8d99f1efb2122a7092 +msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." +msgstr "" +"மேலே உள்ள YAML சிக்கலான உள்ளமைக்கப்பட்ட பொருள் விளக்கங்களை ஒப்பீட்டளவில் விரைவாக " +"உருவாக்குவது எப்படி என்பதை விளக்குகிறது. `உள்ளீடுகள்` வரைபடத்தில்` எடுத்துக்காட்டு_ஃப்ளாக்`" +" ஒரு ஒற்றை விசையைக் கொண்டுள்ளது, இதில் இரண்டு விசைகள் உள்ளன, `வகை` மற்றும்` உள்ளீட்டு " +"பைண்டிங்`, இந்த குழந்தைகளில் ஒருவரான `உள்ளீடு பைண்டிங்` மேலும் இரண்டு முக்கிய மதிப்பு " +"சோடிகளைக் கொண்டுள்ளது (` நிலை` நிலை` மற்றும் `முன்னொட்டு`). ஒற்றை விசைக்கு பல " +"மதிப்புகள்/முக்கிய மதிப்பு சோடிகளை வழங்குவது பற்றிய கூடுதல் தகவலுக்கு கீழே உள்ள " +"[வரிசைகள்] (#வரிசைகள்) பகுதியைக் காண்க. மேலே உள்ள யாம்லுடன் ஒப்பிடுகையில், அது " +"விவரிக்கும் `உள்ளீடுகள்` பொருளின் வரைகலை பிரதிநிதித்துவம் இங்கே." + +#: ../../src/topics/yaml-guide.md:127 +#: d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "வரிசைகள்" + +#: ../../src/topics/yaml-guide.md:129 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 +msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" +msgstr "" +"சில சூழ்நிலைகளில், ஒரு விசைக்கு பல மதிப்புகள் அல்லது பொருள்களை வழங்குவது தேவை. மேலே " +"உள்ள [வரைபடங்கள்] (#வரைபடங்கள்) பிரிவில் நாம் ஏற்கனவே பார்த்தது போல, ஒன்றுக்கு மேற்பட்ட " +"முக்கிய மதிப்பு சோடியை ஒரு விசையில் வரைபடமாக்கலாம். இருப்பினும், ஒவ்வொரு மதிப்புக்கும் " +"ஒரு தனித்துவமான விசையை வழங்காமல் ஒரு விசையின் பல மதிப்புகளை வரையறுக்கவும் முடியும். " +"_Array_ உடன் இதை நாம் அடையலாம், அங்கு ஒவ்வொரு மதிப்பும் அதன் சொந்த வரியில் " +"வரையறுக்கப்பட்டு `-` ஆல் வரையறுக்கப்படுகிறது. உதாரணமாக:" + +#: ../../src/topics/yaml-guide.md:146 +#: fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "வரைபடங்கள் மற்றும் வரிசைகளை இணைக்கும் மிகவும் சிக்கலான எடுத்துக்காட்டு:" + +#: ../../src/topics/yaml-guide.md:167 +#: 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "சாதொபொகு நடை" + +#: ../../src/topics/yaml-guide.md:169 +#: 87bafb845c714b109874f6137b84462d +msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" +msgstr "" +"YAML [சாவாச்கிரிப்ட் பொருள் குறியீடு (JSON)] [JSON] ஐ அடிப்படையாகக் கொண்டது. சொந்த " +"சாதொபொகு தொடரியல் பயன்படுத்தி YAML இல் வரைபடங்கள் மற்றும் வரிசைகளை வரையறுக்கலாம். " +"உதாரணமாக:" + +#: ../../src/topics/yaml-guide.md:177 +#: 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "மற்றும்:" + +#: ../../src/topics/yaml-guide.md:184 +#: fcd05b1ef31a4046946a2399c7fc5575 +msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." +msgstr "" +"ஒரு புலம் வேண்டுமென்றே காலியாக இருக்கும் (`[]` போன்றவை வெற்று வரிசைக்கு) எங்கே என்பதைக் " +"குறிக்க பூர்வீக சாதொபொகு பயனுள்ளதாக இருக்கும், அதேபோல் மதிப்புகள் ஒரே வரியில் " +"அமைந்திருப்பதற்கு அதிக அர்த்தமுள்ள இடம் (எடுத்துக்காட்டாக, எப்போது செல் கட்டளையில் விருப்பக் " +"கொடிகள் மற்றும் அவற்றின் மதிப்புகளை வழங்குதல்). இருப்பினும், மேலே உள்ள இரண்டாவது " +"எடுத்துக்காட்டு காண்பித்தபடி, இது ஒரு YAML கோப்பின் வாசிப்புத்திறனை கடுமையாக பாதிக்கும்" +", மேலும் அவை குறைவாகவே பயன்படுத்தப்பட வேண்டும்." + +#: ../../src/topics/yaml-guide.md:194 +#: f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "குறிப்பு" + +#: ../../src/topics/yaml-guide.md:196 +#: 859368c1f25c4a4aad57abfd046c63f5 +msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." +msgstr "" +"இந்த வழிகாட்டியை நாங்கள் எழுதியபோது [Y MINES] [YAML-Y- Mins] குறிப்பு எங்களுக்கு " +"மிகவும் உதவியாக இருந்தது, இருப்பினும் இது CWL இல் செல்லுபடியாகாத அம்சங்களையும் " +"உள்ளடக்கியது." + +#: ../../src/tutorials.md:1 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "பயிற்சிகள்" + +#: ../../src/tutorials.md:5 +#: 5d92464923c245818c070fbef102be89 +msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." +msgstr "" +"இது சி.டபிள்யூ.எல் சமூகத்தால் வழங்கப்பட்ட பயிற்சிகளின் பட்டியல். பட்டியலில் மற்றொரு " +"டுடோரியலைச் சேர்க்க விரும்பினால் பட்டியலில் உள்ள `திருத்து` இணைப்பைப் பயன்படுத்தவும்." + +#: ../../src/tutorials.md:7 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "தொடக்க பயிற்சிகள்" + +#: ../../src/tutorials.md:9 +#: 13d7e2e92e96432787c712cf6a595424 +msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" +msgstr "" +"[Introduction பெறுநர் Workflows with Common Workflow மொழி: க்கு " +"Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" + +#: ../../src/tutorials.md:11 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "மேம்பட்ட பயிற்சிகள்" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "பயோ இன்ஃபர்மேடிக்ச் பயிற்சிகள்" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" From 9212da479a21010d6bf616002bc2dde23745a055 Mon Sep 17 00:00:00 2001 From: Julian Lopez Gordillo Date: Tue, 12 Aug 2025 12:26:20 +0200 Subject: [PATCH 172/179] Translated using Weblate (Spanish) Currently translated at 12.5% (75 of 599 strings) Co-authored-by: Julian Lopez Gordillo Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/es/ Translation: Common Workflow Language/CWL User Guide --- locales/es/LC_MESSAGES/user_guide.po | 31 ++++++++++++++++++++-------- 1 file changed, 22 insertions(+), 9 deletions(-) diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index 00d7f57d..c38edf76 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,9 +9,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2024-07-10 21:09+0000\n" -"Last-Translator: Benjamin Esteban González Morales \n" +"PO-Revision-Date: 2024-12-18 17:00+0000\n" +"Last-Translator: Julian Lopez Gordillo \n" "Language-Team: Spanish \n" "Language: es\n" @@ -19,7 +18,7 @@ msgstr "" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=2; plural=n != 1;\n" -"X-Generator: Weblate 5.7-dev\n" +"X-Generator: Weblate 5.9.2-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -501,6 +500,8 @@ msgid "" "What should I do when I get CWL Parameter Reference error due to hyphen " "in an input identifier?" msgstr "" +"¿Qué debo hacer cuando obtengo un error de Referencia de Parámetro CWL " +"debido a un guión en un identificador de entrada?" #: ../../src/faq.md:375 e39b65947b294b20a444f18d780246f4 msgid "If `cwltool --validate` returns valid" @@ -511,9 +512,8 @@ msgid "But executing it causes an error like:" msgstr "Pero ejecutarlo causa un error como:" #: ../../src/faq.md:396 2b96665acac449758b852bbe7600e007 -#, fuzzy msgid "The file is here" -msgstr "El documento está aquí" +msgstr "El archivo está aquí" #: ../../src/faq.md:410 f59751d2f0014e59af7879a748062cec msgid "Problem caused by `-` (hyphen character)." @@ -533,7 +533,7 @@ msgstr "" #: ../../src/faq.md:442 fc407a9e8d8c4b699d9cd14b369343b5 msgid "How do I use CWL and cwltool with Singularity?" -msgstr "" +msgstr "¿Cómo uso CWL y cwltool con Singularity?" #: ../../src/faq.md:445 239f5f81cef042b08fb8015c36b3ecad msgid "" @@ -543,9 +543,13 @@ msgid "" "Directly specifying a Singularity format container is not part of the CWL" " standards." msgstr "" +"Los estándares CWL se han construido en base a contenedores en formato " +"Docker (opcionales). El ejecutor de referencia y otras implementaciones de " +"CWL soportan ejecutar dichos contenedores en formato Docker usando el motor " +"de Singularity. Especificar directamente un contenedor en formato " +"Singularity no es parte de los estándares CWL." #: ../../src/faq.md:450 61641314d82b43e982e54c64c73232c5 -#, fuzzy msgid "How do I debug the JavaScript in my CWL tool?" msgstr "¿Como corrijo (debug) el Javascript en mi herramienta CLW?" @@ -562,20 +566,25 @@ msgstr "" #: ../../src/index.md:1 1c9fb72b83c9467a9672943fb47ffe32 msgid "Common Workflow Language User Guide" -msgstr "" +msgstr "Guía de Usuario del Common Workflow Language" #: ../../src/index.md:3 aaa44578e27345e682ab44686b4da159 +#, fuzzy msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" +"Esta guía te presentará cómo escribir workflows (procesos de trabajo) usando " +"los estándares abiertos [Common Workflow Language](https://www.commonwl.org/)" +" (CWL). Esta guía describe la última especificación {{ cwl_version }}." #: ../../src/index.md:7 0adfc2adb0c74372b25d197dd3a73b8b msgid "Contributions and Feedback are Welcome!" msgstr "¡Aceptamos feedback y contribuciones!" #: ../../src/index.md:9 96c8dca812f1415db7c5c006b0c0e022 +#, fuzzy msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -583,6 +592,10 @@ msgid "" "Request by clicking the \"Edit this page\" button at the right sidebar of" " each page." msgstr "" +"Si encuentras que falta algo en esta guía, o si te gustaría proporcionar " +"otros comentarios, abre un Issue en el [repositorio de esta guía][repo]. " +"También puedes sugerir cambios directamente en un Pull Request al clicar el " +"botón \"Editar esta página\" situado en la columna derecha de cada página." #: ../../src/index.md:16 35c50bb5c3a345b4a4ae66b2df065376 msgid "Navigating the User Guide" From a6591b2d236190e72f988842268c62077291ec4b Mon Sep 17 00:00:00 2001 From: Michael Crusoe Date: Tue, 12 Aug 2025 12:26:20 +0200 Subject: [PATCH 173/179] Translated using Weblate (Tamil) Currently translated at 100.0% (598 of 598 strings) Co-authored-by: Michael Crusoe Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ta/ Translation: Common Workflow Language/CWL User Guide --- locales/ta/LC_MESSAGES/user_guide.po | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/locales/ta/LC_MESSAGES/user_guide.po b/locales/ta/LC_MESSAGES/user_guide.po index c1aa9a0b..7bab0d42 100644 --- a/locales/ta/LC_MESSAGES/user_guide.po +++ b/locales/ta/LC_MESSAGES/user_guide.po @@ -8,8 +8,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2024-12-17 12:00+0000\n" -"Last-Translator: தமிழ்நேரம் \n" +"PO-Revision-Date: 2024-12-20 20:00+0000\n" +"Last-Translator: Michael Crusoe \n" "Language-Team: Tamil \n" "Language: ta\n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=2; plural=n != 1;\n" -"X-Generator: Weblate 5.9\n" +"X-Generator: Weblate 5.10-dev\n" #: ../../LICENSE.md:2 #: 4e203044f0464fd5a3256430391dde12 @@ -328,7 +328,7 @@ msgstr "" #: ../../src/faq.md:247 #: a854006054ce4ffe94bbfa73bdbecbf2 msgid "" -msgstr " " +msgstr "" #: ../../src/faq.md:248 #: f80eb714e9df417fbba555b5dd5f4d8c @@ -346,7 +346,7 @@ msgstr "" #: ../../src/faq.md:267 #: ad1c26711ccd4efd8fdb25f9293d33fd msgid "" -msgstr " " +msgstr "" #: ../../src/faq.md:268 #: 49e2095b51f84f609f5d4bc088ad9745 From c33c180b484c52ea56657b2e0c8441cecb672727 Mon Sep 17 00:00:00 2001 From: gfbdrgng Date: Tue, 12 Aug 2025 12:26:20 +0200 Subject: [PATCH 174/179] Translated using Weblate (Russian) Currently translated at 85.4% (511 of 598 strings) Translated using Weblate (Russian) Currently translated at 100.0% (2 of 2 strings) Co-authored-by: gfbdrgng Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-sphinx/ru/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ru/ Translation: Common Workflow Language/CWL User Guide Translation: Common Workflow Language/CWL User Guide: Sphinx --- locales/ru/LC_MESSAGES/sphinx.po | 14 ++-- locales/ru/LC_MESSAGES/user_guide.po | 100 ++++++++++++++++++++++----- 2 files changed, 91 insertions(+), 23 deletions(-) diff --git a/locales/ru/LC_MESSAGES/sphinx.po b/locales/ru/LC_MESSAGES/sphinx.po index 13426aa9..b486cfd9 100644 --- a/locales/ru/LC_MESSAGES/sphinx.po +++ b/locales/ru/LC_MESSAGES/sphinx.po @@ -8,20 +8,24 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" -"Last-Translator: Automatically generated\n" -"Language-Team: none\n" +"PO-Revision-Date: 2025-01-06 04:09+0000\n" +"Last-Translator: gfbdrgng \n" +"Language-Team: Russian \n" "Language: ru\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=3; plural=n%10==1 && n%100!=11 ? 0 : n%10>=2 && " +"n%10<=4 && (n%100<10 || n%100>=20) ? 1 : 2;\n" +"X-Generator: Weblate 5.10-dev\n" #: ../../src/_templates/sidebar-nav-bs.html:1 #: d65b012160e9455eb4d2628279fffc42 msgid "Main navigation" -msgstr "" +msgstr "Основная навигация" #: ../../src/_templates/sidebar-nav-bs.html:3 #: 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" -msgstr "" +msgstr "Раздел Навигация" diff --git a/locales/ru/LC_MESSAGES/user_guide.po b/locales/ru/LC_MESSAGES/user_guide.po index a5098347..efb77e9e 100644 --- a/locales/ru/LC_MESSAGES/user_guide.po +++ b/locales/ru/LC_MESSAGES/user_guide.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2025-01-06 04:00+0000\n" +"PO-Revision-Date: 2025-01-07 06:07+0000\n" "Last-Translator: gfbdrgng \n" "Language-Team: Russian \n" @@ -4275,149 +4275,213 @@ msgstr "[Комментарии](#comments)" #: ../../src/topics/yaml-guide.md:20 #: b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" -msgstr "" +msgstr "[Карты](#maps)" #: ../../src/topics/yaml-guide.md:21 #: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" -msgstr "" +msgstr "[Массивы](#arrays)" #: ../../src/topics/yaml-guide.md:22 #: 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" -msgstr "" +msgstr "[Стиль JSON](#json-style)" #: ../../src/topics/yaml-guide.md:24 #: 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" -msgstr "" +msgstr "Пары ключ-значение" #: ../../src/topics/yaml-guide.md:26 #: cda73485875d4c8e9464679a20558616 msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" msgstr "" +"По сути, файл, написанный на языке YAML, состоит из набора пар _ключ-" +"значение_. Каждая пара записывается как `ключ: значение`, где пробелы после " +"`:` обязательны. Имена ключей в файлах CWL не должны содержать пробельных " +"символов - [_camelCase_][camelCase] используется для многословных имен " +"ключей, которые имеют особое значение в спецификации CWL, и подчеркивания в " +"других именах ключей. Например:" #: ../../src/topics/yaml-guide.md:42 #: 98cae24919b74c088a5d89706aec581b msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" +"В приведенном выше YAML определены четыре ключа - `first_name`, `last_name`, " +"`age_years` и `home` - и четыре соответствующих им значения. Значения могут " +"быть символьными строками, числовыми (целое число, число с плавающей точкой " +"или научное представление), булевыми (`true` или `false`) или более сложными " +"вложенными типами (см. ниже)." #: ../../src/topics/yaml-guide.md:51 #: b4b0940b4b5743c09637b36b964202d0 msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" +"Значения могут быть заключены в кавычки, но имейте в виду, что это может " +"изменить способ их интерпретации, например, `\"1234\"` будет рассматриваться " +"как символьная строка, а `1234` будет рассматриваться как целое число. Это " +"различие может быть важным, например, при описании параметров команды: в CWL " +"все части `baseCommand` должны быть строками, поэтому, если вы хотите " +"указать фиксированное числовое значение для команды, убедитесь, что вы " +"обернули это числовое значение в кавычки: `baseCommand: [echo, \"42\"]`." #: ../../src/topics/yaml-guide.md:61 #: dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" -msgstr "" +msgstr "Комментарии" #: ../../src/topics/yaml-guide.md:63 #: 9ca3554d771d45998e88aaede525b227 msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" msgstr "" +"Вы можете использовать `#` для добавления комментариев к файлам CWL и " +"параметрам. Любые символы справа от `#` будут игнорироваться программой, " +"интерпретирующей YAML. Например:" #: ../../src/topics/yaml-guide.md:76 #: 3fca839cede94cfd8e4f605c73ba699d msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" msgstr "" +"Если в строке перед комментарием что-то есть, не забудьте добавить хотя бы " +"один пробел перед `#`!" #: ../../src/topics/yaml-guide.md:79 #: da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" -msgstr "" +msgstr "Карты" #: ../../src/topics/yaml-guide.md:81 #: 3ded0f125249485c921994b6e6b93ac9 msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" msgstr "" +"При описании инструмента или рабочего процесса с помощью CWL обычно " +"необходимо создавать более сложные, вложенные представления. Эти " +"иерархические структуры, называемые _картой_, описываются в YAML путем " +"предоставления дополнительных пар ключ-значение в качестве значения любого " +"ключа. Эти пары (иногда называемые \"дочерними\") записываются на новых " +"строках под ключом, к которому они относятся (\"родительским\"), и должны " +"быть отступлены двумя пробелами (символы ⇥tab не допускаются). Например:" #: ../../src/topics/yaml-guide.md:104 #: 53ece35d309a4c8d99f1efb2122a7092 msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." msgstr "" +"Приведенный выше YAML иллюстрирует, как можно относительно быстро создавать " +"сложные вложенные описания объектов. Карта `inputs` содержит один ключ, " +"`example_flag`, который сам содержит два ключа, `type` и `inputBinding`, а " +"один из этих дочерних элементов, `inputBinding`, содержит еще две пары ключ-" +"значение (`position` и `prefix`). Дополнительную информацию о предоставлении " +"нескольких значений/пар ключ-значение для одного ключа см. в разделе [Arrays]" +"(#arrays) ниже. Для сравнения с приведенным выше примером YAML здесь " +"показано графическое представление объекта `inputs`, который он описывает." #: ../../src/topics/yaml-guide.md:127 #: d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" -msgstr "" +msgstr "Массивы" #: ../../src/topics/yaml-guide.md:129 #: 7fc0bdf2489a44f2a29e71b86f7c0055 msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" msgstr "" +"В некоторых случаях необходимо предоставить несколько значений или объектов " +"для одного ключа. Как мы уже видели в разделе [Maps](#maps) выше, более " +"одной пары ключ-значение может быть сопоставлено одному ключу. Однако можно " +"также определить несколько значений для ключа без необходимости " +"предоставлять уникальный ключ для каждого значения. Этого можно добиться с " +"помощью _массива_, где каждое значение задается в отдельной строке и " +"предваряется символом `-`. Например:" #: ../../src/topics/yaml-guide.md:146 #: fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" -msgstr "" +msgstr "и более сложный пример, сочетающий карты и массивы:" #: ../../src/topics/yaml-guide.md:167 #: 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" -msgstr "" +msgstr "JSON Стиль" #: ../../src/topics/yaml-guide.md:169 #: 87bafb845c714b109874f6137b84462d msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" msgstr "" +"YAML основан на [JavaScript Object Notation (JSON)][json]. Карты и массивы " +"также могут быть определены в YAML с использованием собственного синтаксиса " +"JSON. Например:" #: ../../src/topics/yaml-guide.md:177 #: 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" -msgstr "" +msgstr "и:" #: ../../src/topics/yaml-guide.md:184 #: fcd05b1ef31a4046946a2399c7fc5575 msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." msgstr "" +"Родной JSON может быть полезен для указания полей, которые намеренно " +"оставлены пустыми (например, `[]` для пустого массива), а также в тех " +"случаях, когда значения имеет смысл располагать в одной строке (например, " +"при указании флагов опций и их значений в команде оболочки). Однако, как " +"видно из второго примера, это может сильно ухудшить читаемость YAML-файла, " +"поэтому использовать его следует осторожно." #: ../../src/topics/yaml-guide.md:194 #: f4b8fc8236044fada420def13a02813d msgid "Reference" -msgstr "" +msgstr "Ссылка" #: ../../src/topics/yaml-guide.md:196 #: 859368c1f25c4a4aad57abfd046c63f5 msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." msgstr "" +"Ссылка [Learn YAML in Y Minutes][yaml-y-mins] была очень полезна для нас при " +"написании этого руководства, хотя в ней также рассматриваются функции, " +"которые не применимы в CWL." #: ../../src/tutorials.md:1 #: 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" -msgstr "" +msgstr "Учебники" #: ../../src/tutorials.md:5 #: 5d92464923c245818c070fbef102be89 msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." msgstr "" +"Это список учебников, предоставленных сообществом CWL. Если вы хотите " +"добавить в список еще один учебник, воспользуйтесь ссылкой `Редактировать " +"эту страницу` в меню." #: ../../src/tutorials.md:7 #: 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" -msgstr "" +msgstr "Учебники для начинающих" #: ../../src/tutorials.md:9 #: 13d7e2e92e96432787c712cf6a595424 msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" +"[Введение в рабочие процессы с помощью Common Workflow Language: Для " +"авторов.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" #: ../../src/tutorials.md:11 #: 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" -msgstr "" +msgstr "Продвинутые учебники" #: ../../src/tutorials.md:13 #: 3cbf1f69a5514fd3bee90e68b201190f +#, fuzzy msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "" +msgstr "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" #: ../../src/tutorials.md:15 #: 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" -msgstr "" +msgstr "Учебники по биоинформатике" #: ../../src/tutorials.md:17 #: a67c7e0eaf4e4d27b3e5db303333a088 +#, fuzzy msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "" +msgstr "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" From 62b53abacd0715a15e14e9871da244196fd90712 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E0=AE=A4=E0=AE=AE=E0=AE=BF=E0=AE=B4=E0=AF=8D=E0=AE=A8?= =?UTF-8?q?=E0=AF=87=E0=AE=B0=E0=AE=AE=E0=AF=8D?= Date: Tue, 12 Aug 2025 12:26:21 +0200 Subject: [PATCH 175/179] Translated using Weblate (Tamil) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Currently translated at 100.0% (598 of 598 strings) Translated using Weblate (Tamil) Currently translated at 100.0% (598 of 598 strings) Co-authored-by: தமிழ்நேரம் Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ta/ Translation: Common Workflow Language/CWL User Guide --- locales/ta/LC_MESSAGES/user_guide.po | 90 ++++++++++++++-------------- 1 file changed, 45 insertions(+), 45 deletions(-) diff --git a/locales/ta/LC_MESSAGES/user_guide.po b/locales/ta/LC_MESSAGES/user_guide.po index 7bab0d42..5c649d68 100644 --- a/locales/ta/LC_MESSAGES/user_guide.po +++ b/locales/ta/LC_MESSAGES/user_guide.po @@ -8,8 +8,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2024-12-20 20:00+0000\n" -"Last-Translator: Michael Crusoe \n" +"PO-Revision-Date: 2025-07-14 17:01+0000\n" +"Last-Translator: தமிழ்நேரம் \n" "Language-Team: Tamil \n" "Language: ta\n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=2; plural=n != 1;\n" -"X-Generator: Weblate 5.10-dev\n" +"X-Generator: Weblate 5.13-dev\n" #: ../../LICENSE.md:2 #: 4e203044f0464fd5a3256430391dde12 @@ -110,8 +110,8 @@ msgstr "மென்பொருள்" msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "வேறுவிதமாகக் குறிப்பிடப்பட்ட இடத்தைத் தவிர, பொதுவான பணிப்பாய்வு மொழி திட்டத்தால் வழங்கப்பட்" -"ட எடுத்துக்காட்டு நிரல்கள் மற்றும் பிற மென்பொருள் [OSI] [OSI]-அங்கீகரிக்கப்பட்ட [அப்பாச்சி " -"2.0 உரிமம்] [அப்பாச்சி -2.0-உரிமம்] இன் கீழ் கிடைக்கின்றன." +"ட எடுத்துக்காட்டு நிரல்கள் மற்றும் பிற மென்பொருள் [ஓஎச்ஐ][osi]-அங்கீகரிக்கப்பட்ட " +"[அப்பாச்சி 2.0 உரிமம்] [apache-2.0-license] இன் கீழ் கிடைக்கின்றன." #: ../../LICENSE.md:51 #: 0f68eafafaef4b54accba7e13bfaa702 @@ -250,7 +250,7 @@ msgstr "சி.டபிள்யூ.எல் இல், எல்லாவற #: c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -"விருப்ப உள்ளீடுகளுக்கு `சுய அடிப்படையிலான உள்ளீட்டு பிணைப்புகளை அமைத்தல்" +"விருப்ப உள்ளீடுகளுக்கு `தன்`-அடிப்படையிலான உள்ளீட்டு பிணைப்புகளை அமைத்தல்" #: ../../src/faq.md:140 #: 2c38cc58cbb340bc935a5f00e96ba95c @@ -525,8 +525,8 @@ msgstr "பயனர் வழிகாட்டியை வழிநடத் #: ed74c9a4b623464480e2c184668fcec0 msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." msgstr "" -"நீங்கள் ஒரு தொடக்க பயனராக இருந்தால் [அறிமுகம்] (/அறிமுகம்/INDEX.MD) பிரிவில் தொடங்கலாம்" -". மேம்பட்ட பயனர்களுக்கு [தலைப்புகள்] (/தலைப்புகள்/குறியீட்டு." +"நீங்கள் ஒரு தொடக்க பயனராக இருந்தால் [அறிமுகம்] (/introduction/index.md) பிரிவில் " +"தொடங்கலாம். மேம்பட்ட பயனர்களுக்கு [தலைப்புகள்] (//topics/index.md)குறியீட்டு." #: ../../src/index.md:23 #: cfa67cf5521b414da6f7d34cbed283f7 @@ -576,11 +576,11 @@ msgstr "" #: 3a71b269bd3c49eb913cf69b60373c24 msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." msgstr "" -"விவரக்குறிப்பு பதிப்பில் `. கள் (புள்ளிகள்) பிரிக்கப்பட்ட மூன்று எண்கள் வரை இருக்கலாம். முதல்" -" எண் முக்கிய வெளியீடு ஆகும், இது நீக்கப்பட்ட அம்சங்களை அகற்றுவது போன்ற பின்தங்கிய-இணக்கமான " -"மாற்றங்களுக்கு பயன்படுத்தப்படுகிறது. இரண்டாவது எண் சிறிய வெளியீடு ஆகும், இது புதிய " +"விவரக்குறிப்பு பதிப்பில் `.`கள் (புள்ளிகள்) பிரிக்கப்பட்ட மூன்று எண்கள்வரை இருக்கலாம். முதல் " +"எண் முக்கிய வெளியீடு ஆகும், இது நீக்கப்பட்ட அம்சங்களை அகற்றுவது போன்ற பின்தங்கிய-இணக்கமான " +"மாற்றங்களுக்குப் பயன்படுத்தப்படுகிறது. இரண்டாவது எண் சிறிய வெளியீடு ஆகும், இது புதிய " "நற்பொருத்தங்கள் அல்லது பின்தங்கிய-இணக்கமான சிறிய மாற்றங்களுக்குப் பயன்படுத்தப்படுகிறது. " -"எழுத்துப்பிழைகள் மற்றும் விவரக்குறிப்புக்கான பிற திருத்தங்கள் போன்ற பிழை திருத்தங்களுக்கு " +"எழுத்துப்பிழைகள் மற்றும் விவரக்குறிப்புக்கான பிற திருத்தங்கள் போன்ற பிழை திருத்தங்களுக்குக் " "கடைசி எண் பயன்படுத்தப்படுகிறது." #: ../../src/introduction/basic-concepts.md:33 @@ -1303,7 +1303,7 @@ msgstr "இந்த பயனர் வழிகாட்டியின் அ #: 77e43c7117fd4c52b140f0dd52cc3963 msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -"[List of CWL Implementations](https://www.commonwl.org/implementations)." +"[CWL செயல்படுத்தலின் பட்டியல்](https://www.commonwl.org/implementations)." #: ../../src/introduction/quick-start.md:98 #: 7282abfa7155497ca47c30f9abfb6474 @@ -1323,8 +1323,8 @@ msgstr "" #: 82a7ca3703bc4f0daa18942a1ac8943b msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -"[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia." -"org/wiki/YAML)." +"[YAML.org](http://yaml.org/) மற்றும் [விக்கியில் YAML](https://en.wikipedia.org/" +"wiki/YAML)." #: ../../src/introduction/quick-start.md:101 #: d039a9d6461c44628d4660c00d9ce6ff @@ -1436,17 +1436,17 @@ msgstr "" #: 4dee8504a8e5496081dadc386ab45540 msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." msgstr "" -"ஒரு சி.டபிள்யூ.எல் ஆவணம் (`டோக்கர்ஃபைல்'ச் போன்ற எந்தவொரு வெளிப்புற கூறுகளுடனும் இணைந்து)" -" மென்பொருள் குறியீடு. மென்பொருள் உரிமத்தின் வழக்கமான விதிகள் இந்த ஆவணத்திற்கு பொருந்தும் " -"என்பதை பணிப்பாய்வு உருவாக்குபவர்கள் அறிந்திருக்க வேண்டும். எடுத்துக்காட்டாக, பணிப்பாய்வு " -"பகிரங்கமாக பகிரப்பட்டால், உரிம விதிமுறைகள் தெளிவாக இருக்க வேண்டும், இதனால் எதிர்கால " -"பயனர் எந்த நிலைமைகளை அவர்கள் பணிப்பாய்வுகளை இயக்கலாம், அதை மாற்றலாம் மற்றும்/அல்லது பிற " -"பணிப்பாய்வுகளுடன் இணைக்க முடியும் என்பதைப் புரிந்துகொள்கிறார். இந்த காரணத்திற்காக, ஆவணத்தில்" -" உரிமம் புலத்தை சேர்ப்பதைக் கவனியுங்கள். இந்த வழிகாட்டியின் ஆசிரியர்கள் உங்கள் சொந்தமாக எழு" -"த முயற்சிப்பதை விட முன்பே இருக்கும் உரிமத்தைத் தேர்வுசெய்யும்படி கேட்டுக்கொள்கிறார்கள் " -"(உரிமத்தைத் தேர்ந்தெடுப்பது பற்றி மேலும் அறிய கீழேயுள்ள இணைப்பைக் காண்க), மேலும் எங்கள் " -"பரிந்துரைக்கப்பட்ட நடைமுறை மீண்டும் பயன்படுத்த அனுமதிக்கும் உரிமத்தைத் தேர்ந்தெடுப்பதாகும் " -"யாராலும், எ.கா. [அப்பாச்சி 2.0] [அப்பாச்சி-லிசென்ச்]." +"ஒரு சி.டபிள்யூ.எல் ஆவணம் (`டோக்கர்ஃபைல்`கள் போன்ற எந்தவொரு வெளிப்புற கூறுகளுடனும் " +"இணைந்து) மென்பொருள் குறியீடு. மென்பொருள் உரிமத்தின் வழக்கமான விதிகள் இந்த ஆவணத்திற்கு " +"பொருந்தும் என்பதை பணிப்பாய்வு உருவாக்குபவர்கள் அறிந்திருக்க வேண்டும். எடுத்துக்காட்டாக, " +"பணிப்பாய்வு பகிரங்கமாகப் பகிரப்பட்டால், உரிம விதிமுறைகள் தெளிவாக இருக்க வேண்டும், இதனால் " +"எதிர்கால பயனர் எந்த நிலைமைகளை அவர்கள் பணிப்பாய்வுகளை இயக்கலாம், அதை மாற்றலாம் " +"மற்றும்/அல்லது பிற பணிப்பாய்வுகளுடன் இணைக்க முடியும் என்பதைப் புரிந்துகொள்கிறார். இந்தக் " +"காரணத்திற்காக, ஆவணத்தில் உரிமம் புலத்தைச் சேர்ப்பதைக் கவனியுங்கள். இந்த வழிகாட்டியின் " +"ஆசிரியர்கள் உங்கள் சொந்தமாக எழுத முயற்சிப்பதை விட முன்பே இருக்கும் உரிமத்தைத் " +"தேர்வுசெய்யும்படி கேட்டுக்கொள்கிறார்கள் (உரிமத்தைத் தேர்ந்தெடுப்பது பற்றி மேலும் அறிய கீழேயுள்" +"ள இணைப்பைக் காண்க), மேலும் எங்கள் பரிந்துரைக்கப்பட்ட நடைமுறை மீண்டும் பயன்படுத்த அனுமதிக்கும் " +"உரிமத்தைத் தேர்ந்தெடுப்பதாகும் யாராலும், எ.கா. [அப்பாச்சி 2.0][apache-license]." #: ../../src/topics/best-practices.md:20 #: 674c238b25e240eda05e22e399f2f78f @@ -1484,8 +1484,8 @@ msgstr "" #: ecf2b9c0b1664afe9c4e180610610021 msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." msgstr "" -"சி.டபிள்யூ.எல் கருவி அல்லது பணிப்பாய்வு விளக்கத்தின் ஆசிரியர் (கள்) க்கான [பண்புக்கூறு " -"தகவல்] [உரிமம்-எடுத்துக்காட்டுக்கு] சேர்க்கவும். [ORCID] [ORCID] போன்ற தெளிவற்ற " +"சி.டபிள்யூ.எல் கருவி அல்லது பணிப்பாய்வு விளக்கத்தின் ஆசிரியர் (கள்) க்கான " +"[பண்புக்கூறு தகவல்][license-example] சேர்க்கவும். [ஆர்சிட்][orcid] போன்ற தெளிவற்ற " "அடையாளங்காட்டிகளைப் பயன்படுத்தவும்." #: ../../src/topics/best-practices.md:44 @@ -1499,8 +1499,8 @@ msgstr "" #: f2b14a92374e449d9fb1e8c86ae0dd61 msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -"`Https: //identifiers.org/rrid/rrid: scr_nnnnnn` வடிவத்தில் சார்புகளுக்கான " -"[SCICRUNCH] [SCICRUNCH] அடையாளங்காட்டிகளைச் சேர்க்கவும்." +"`https://identifiers.org/rrid/rrid:scr_nnnnnn` வடிவத்தில் சார்புகளுக்கான " +"[SciCrunch][scicrunch] அடையாளங்காட்டிகளைச் சேர்." #: ../../src/topics/best-practices.md:50 #: 928e3df7ca3e479ca6474a8e72cf36eb @@ -3272,13 +3272,13 @@ msgstr "" #: 8cb1c5d9b1a54c40924099494eb766c6 msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." msgstr "" -"ஒரு பதிப்பு எண், கருவிக்கான தனித்துவமான வள அடையாளங்காட்டி (URI) ஒரு [RRID] [RRID] " -"வடிவத்தில் கொடுக்கப்பட்டுள்ளது. RRIDS உடனான வளங்களை [Scicrunch] [Scicrunch] " +"ஒரு பதிப்பு எண், கருவிக்கான தனித்துவமான வள அடையாளங்காட்டி (URI) ஒரு [ஆர்ஆர்ஐடி][rrid]" +" வடிவத்தில் கொடுக்கப்பட்டுள்ளது. RRIDS உடனான வளங்களை [அறிநொறுக்கு][scicrunch] " "பதிவேட்டில் பார்க்கலாம், இது விஞ்ஞான வளங்களைக் கண்டறிதல், கண்காணித்தல் மற்றும் " "குறிப்பிடுவதற்கான ஒரு போர்ட்டலை வழங்குகிறது. நீங்கள் ஒரு கருவியை `சாப்ட்வேர் " "ரெகுரிகேமென்ட்` எனக் குறிப்பிட விரும்பினால், ச்கைசஞ்ச் மீது கருவியைத் தேடுங்கள் மற்றும் " "பதிவேட்டில் ஒதுக்கப்பட்டுள்ள RRID ஐப் பயன்படுத்தவும். . உங்கள் தேவை விளக்கத்தின் " -"`விவரக்குறிப்புகள்` புலத்தில் உள்ள கருவியைக் ([அடையாளங்காட்டிகள்.ஆர்ச்] [அடையாளங்காட்டிகள்] " +"`விவரக்குறிப்புகள்` புலத்தில் உள்ள கருவியைக் ([அடையாளங்காட்டிகள்.ஆர்ச்][அடையாளங்காட்டிகள்] " "வழியாக) குறிப்பிட இந்த RRID ஐப் பயன்படுத்தலாம். பிற நல்ல தேர்வுகள், விருப்பத்தின் " "வரிசையில், முக்கிய கருவி மேற்கோளுக்கான DOI மற்றும் கருவிக்கு முகவரி ஐ சேர்க்க வேண்டும்." @@ -3406,13 +3406,13 @@ msgstr "டோக்கருக்குள் இயங்கும் கர #: e07f33d01b804663a25ffb08aad74821 msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." msgstr "" -"[டோக்கர்] [டோக்கர்] கொள்கலன்கள் மென்பொருள் நிறுவலை எளிதாக்குகின்றன, மென்பொருள் மற்றும் அதன் " +"[டோக்கர்][docker] கொள்கலன்கள் மென்பொருள் நிறுவலை எளிதாக்குகின்றன, மென்பொருள் மற்றும் அதன் " "சார்புகளுக்கு முழுமையான அறியப்பட்ட-நல்ல இயக்க நேரத்தை வழங்குவதன் மூலம். இருப்பினும், " "கொள்கலன்கள் புரவலன் அமைப்பிலிருந்து வேண்டுமென்றே தனிமைப்படுத்தப்படுகின்றன, எனவே ஒரு " "கப்பல்துறை கொள்கலனுக்குள் ஒரு கருவியை இயக்குவதற்கு கொள்கலனுக்குள் உள்ளீட்டுக் கோப்புகள் " -"கிடைப்பதை உறுதிசெய்ய கூடுதல் வேலை உள்ளது மற்றும் வெளியீட்டு கோப்புகளை கொள்கலனில் இருந்து " -"மீட்டெடுக்க முடியும். ஒரு சி.டபிள்யூ.எல் ரன்னர் இந்த வேலையை தானாகவே செய்ய முடியும், இது " -"உங்கள் மென்பொருள் நிர்வாகத்தை எளிமைப்படுத்த டோக்கரைப் பயன்படுத்த அனுமதிக்கிறது, அதே " +"கிடைப்பதை உறுதிசெய்யக் கூடுதல் வேலை உள்ளது மற்றும் வெளியீட்டு கோப்புகளைக் கொள்கலனிலிருந்து" +" மீட்டெடுக்க முடியும். ஒரு சி.டபிள்யூ.எல் ரன்னர் இந்த வேலையைத் தானாகவே செய்ய முடியும், " +"இது உங்கள் மென்பொருள் நிர்வாகத்தை எளிமைப்படுத்த டோக்கரைப் பயன்படுத்த அனுமதிக்கிறது, அதே " "நேரத்தில் கப்பல்துறை கொள்கலன்களைத் தொடங்குவதற்கும் நிர்வகிப்பதற்கும் சிக்கலைத் தவிர்க்கிறது." #: ../../src/topics/using-containers.md:15 @@ -4023,9 +4023,9 @@ msgstr "யாம் வழிகாட்டி" #: 5d83c56102e141cc978500f678dd0c1c msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." msgstr "" -"[YAML] [YAML] என்பது ஒரு கோப்பு வடிவமாகும், இது கணினிகள் மற்றும் மனிதர்களால் " +"[YAML][yaml] என்பது ஒரு கோப்பு வடிவமாகும், இது கணினிகள் மற்றும் மனிதர்களால் " "படிக்கக்கூடியதாக வடிவமைக்கப்பட்டுள்ளது. இந்த வழிகாட்டி CWL விளக்கங்கள் மற்றும் உள்ளீட்டு " -"அளவுரு கோப்புகளை எழுதும்போது பொருத்தமான YAML இன் அம்சங்களை அறிமுகப்படுத்துகிறது." +"அளவுருக் கோப்புகளை எழுதும்போது பொருத்தமான YAML இன் அம்சங்களை அறிமுகப்படுத்துகிறது." #: ../../src/topics/yaml-guide.md:13 #: c38438fbf9a04e729ec2e3c962435289 @@ -4146,10 +4146,10 @@ msgstr "" "மேலே உள்ள YAML சிக்கலான உள்ளமைக்கப்பட்ட பொருள் விளக்கங்களை ஒப்பீட்டளவில் விரைவாக " "உருவாக்குவது எப்படி என்பதை விளக்குகிறது. `உள்ளீடுகள்` வரைபடத்தில்` எடுத்துக்காட்டு_ஃப்ளாக்`" " ஒரு ஒற்றை விசையைக் கொண்டுள்ளது, இதில் இரண்டு விசைகள் உள்ளன, `வகை` மற்றும்` உள்ளீட்டு " -"பைண்டிங்`, இந்த குழந்தைகளில் ஒருவரான `உள்ளீடு பைண்டிங்` மேலும் இரண்டு முக்கிய மதிப்பு " -"சோடிகளைக் கொண்டுள்ளது (` நிலை` நிலை` மற்றும் `முன்னொட்டு`). ஒற்றை விசைக்கு பல " -"மதிப்புகள்/முக்கிய மதிப்பு சோடிகளை வழங்குவது பற்றிய கூடுதல் தகவலுக்கு கீழே உள்ள " -"[வரிசைகள்] (#வரிசைகள்) பகுதியைக் காண்க. மேலே உள்ள யாம்லுடன் ஒப்பிடுகையில், அது " +"பைண்டிங்`, இந்தக் குழந்தைகளில் ஒருவரான `உள்ளீடு பைண்டிங்` மேலும் இரண்டு முக்கிய மதிப்பு " +"சோடிகளைக் கொண்டுள்ளது (` நிலை` மற்றும் `முன்னொட்டு`). ஒற்றை விசைக்குப் பல " +"மதிப்புகள்/முக்கிய மதிப்பு சோடிகளை வழங்குவது பற்றிய கூடுதல் தகவலுக்குக் கீழே உள்ள " +"[வரிசைகள்](#வரிசைகள்) பகுதியைக் காண்க. மேலே உள்ள யாம்லுடன் ஒப்பிடுகையில், அது " "விவரிக்கும் `உள்ளீடுகள்` பொருளின் வரைகலை பிரதிநிதித்துவம் இங்கே." #: ../../src/topics/yaml-guide.md:127 @@ -4247,7 +4247,7 @@ msgstr "மேம்பட்ட பயிற்சிகள்" #: ../../src/tutorials.md:13 #: 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" -msgstr "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "[CWL இல் தட்டச்சுஉரை](https://github.com/umccr/cwl-ica/wiki/TypeScript)" #: ../../src/tutorials.md:15 #: 68c97a7065634d02956f3f5c1d4eeb9f @@ -4257,4 +4257,4 @@ msgstr "பயோ இன்ஃபர்மேடிக்ச் பயிற் #: ../../src/tutorials.md:17 #: a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" -msgstr "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "[CWL உடன் ஆர்என்ஏவரிசை](https://arvados.github.io/rnaseq-cwl-training/)" From 81829d76767fcc8a35c1ce393d46df8ef6d89412 Mon Sep 17 00:00:00 2001 From: ssantos Date: Tue, 12 Aug 2025 12:26:21 +0200 Subject: [PATCH 176/179] Translated using Weblate (Portuguese (Portugal)) Currently translated at 100.0% (2 of 2 strings) Translated using Weblate (Portuguese (Portugal)) Currently translated at 19.1% (115 of 599 strings) Co-authored-by: ssantos Translate-URL: https://hosted.weblate.org/projects/commonwl/cwl-user-guide-sphinx/pt_PT/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/pt_PT/ Translation: Common Workflow Language/CWL User Guide Translation: Common Workflow Language/CWL User Guide: Sphinx --- locales/pt_PT/LC_MESSAGES/sphinx.po | 6 +++--- locales/pt_PT/LC_MESSAGES/user_guide.po | 22 +++++++++------------- 2 files changed, 12 insertions(+), 16 deletions(-) diff --git a/locales/pt_PT/LC_MESSAGES/sphinx.po b/locales/pt_PT/LC_MESSAGES/sphinx.po index d03d2b21..714c6510 100644 --- a/locales/pt_PT/LC_MESSAGES/sphinx.po +++ b/locales/pt_PT/LC_MESSAGES/sphinx.po @@ -8,7 +8,7 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2024-07-14 10:09+0000\n" +"PO-Revision-Date: 2025-07-29 17:04+0000\n" "Last-Translator: ssantos \n" "Language-Team: Portuguese (Portugal) \n" @@ -17,7 +17,7 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=2; plural=n > 1;\n" -"X-Generator: Weblate 5.7-dev\n" +"X-Generator: Weblate 5.13-dev\n" #: ../../src/_templates/sidebar-nav-bs.html:1 #: d65b012160e9455eb4d2628279fffc42 @@ -27,4 +27,4 @@ msgstr "Navegação principal" #: ../../src/_templates/sidebar-nav-bs.html:3 #: 4b3441eb77f448daa60718b7bfa862db msgid "Section Navigation" -msgstr "" +msgstr "Secção de navegação" diff --git a/locales/pt_PT/LC_MESSAGES/user_guide.po b/locales/pt_PT/LC_MESSAGES/user_guide.po index 82b90eda..210f7e85 100644 --- a/locales/pt_PT/LC_MESSAGES/user_guide.po +++ b/locales/pt_PT/LC_MESSAGES/user_guide.po @@ -9,15 +9,16 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2023-04-03 19:41+0000\n" +"PO-Revision-Date: 2025-07-29 17:04+0000\n" "Last-Translator: ssantos \n" +"Language-Team: Portuguese (Portugal) \n" "Language: pt_PT\n" -"Language-Team: Portuguese (Portugal) " -"\n" -"Plural-Forms: nplurals=2; plural=n > 1;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 5.13-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -178,9 +179,8 @@ msgid "How do I create non \"`File`\" types using `evalFrom`?" msgstr "Usando `evalFrom` para Tipos Diferentes de \"`File`\"" #: ../../src/faq.md:41 8333f51e3f5945fe8963adfc6685bcb1 -#, fuzzy msgid "How do I rename an input file?" -msgstr "Renomear um Arquivo de Entrada" +msgstr "Como posso renomear um ficheiro de entrada?" #: ../../src/faq.md:43 f6b88d9154d049d7807afa9bb0f1ac98 msgid "" @@ -195,9 +195,8 @@ msgstr "" "utilizar os nomes dados por padrão quando estes arquivos foram criados." #: ../../src/faq.md:59 833510f5896b4a6eb5875d25eca5b047 -#, fuzzy msgid "How do I rename an output file?" -msgstr "Renomear um Arquivo de Saída" +msgstr "Como posso renomear um ficheiro de saída?" #: ../../src/faq.md:61 207e2f97d1c44233ae3f109c5a6ec944 msgid "" @@ -215,9 +214,8 @@ msgid "" msgstr "" #: ../../src/faq.md:86 8641f105131b4ac1bca7e0a46756ef79 -#, fuzzy msgid "How do I reference a local script?" -msgstr "Como Fazer Referência a um Script Local" +msgstr "Como faço referência a um script local?" #: ../../src/faq.md:88 d3e43b40d6994b32bc37067ee116418e msgid "There are two ways to reference a local script:" @@ -294,9 +292,8 @@ msgstr "" "solução mais elegante para este problema." #: ../../src/faq.md:165 6c98b7948059411b8e09cf03a552c5ab -#, fuzzy msgid "How can I model a \"one-or-the-other\" parameter?" -msgstr "Modelar um Parâmetro do tipo \"um-ou-o-outro\"" +msgstr "Como posso modelar um parâmetro \"um ou outro\"?" #: ../../src/faq.md:167 d1424da3f43c4519a4c4735f4a720341 msgid "" @@ -4426,4 +4423,3 @@ msgstr "" #~ " only part that is really new " #~ "is the `dockerRequirement` section." #~ msgstr "" - From c2128f4bb14be8c65e476141248261bba191d2fb Mon Sep 17 00:00:00 2001 From: Michael Crusoe Date: Tue, 12 Aug 2025 12:26:21 +0200 Subject: [PATCH 177/179] Translated using Weblate (Tamil) Currently translated at 100.0% (598 of 598 strings) Translated using Weblate (Tamil) Currently translated at 100.0% (598 of 598 strings) Translated using Weblate (Russian) Currently translated at 85.4% (511 of 598 strings) Co-authored-by: Michael Crusoe Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ru/ Translate-URL: https://hosted.weblate.org/projects/commonwl/user-guide/ta/ Translation: Common Workflow Language/CWL User Guide --- locales/ru/LC_MESSAGES/user_guide.po | 10 +- locales/ta/LC_MESSAGES/user_guide.po | 430 ++++++++++++++------------- 2 files changed, 227 insertions(+), 213 deletions(-) diff --git a/locales/ru/LC_MESSAGES/user_guide.po b/locales/ru/LC_MESSAGES/user_guide.po index efb77e9e..bf8abbf2 100644 --- a/locales/ru/LC_MESSAGES/user_guide.po +++ b/locales/ru/LC_MESSAGES/user_guide.po @@ -8,8 +8,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2025-01-07 06:07+0000\n" -"Last-Translator: gfbdrgng \n" +"PO-Revision-Date: 2025-08-12 10:22+0000\n" +"Last-Translator: Michael Crusoe \n" "Language-Team: Russian \n" "Language: ru\n" @@ -18,7 +18,7 @@ msgstr "" "Content-Transfer-Encoding: 8bit\n" "Plural-Forms: nplurals=3; plural=n%10==1 && n%100!=11 ? 0 : n%10>=2 && " "n%10<=4 && (n%100<10 || n%100>=20) ? 1 : 2;\n" -"X-Generator: Weblate 5.10-dev\n" +"X-Generator: Weblate 5.13-dev\n" #: ../../LICENSE.md:2 #: 4e203044f0464fd5a3256430391dde12 @@ -1544,7 +1544,7 @@ msgstr "" #: ecf2b9c0b1664afe9c4e180610610021 msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." msgstr "" -"Включите [информацию об авторстве][пример лицензии] для автора(ов) описания " +"Включите [информацию об авторстве][license-example] для автора(ов) описания " "инструмента CWL или рабочего процесса. Используйте однозначные " "идентификаторы, например [ORCID][orcid]." @@ -1670,7 +1670,7 @@ msgid "Software containers should be made to be conformant to the [\"Recommendat msgstr "" "Контейнеры для программного обеспечения должны соответствовать [" "\"Рекомендациям по упаковке и контейнеризации программного обеспечения для " -"биоинформатики\"][контейнеры] (также полезны для других дисциплин)." +"биоинформатики\"][containers] (также полезны для других дисциплин)." #: ../../src/topics/command-line-tool.md:1 #: 3f4e98f6bfa141feba8c4b120e3d03e8 diff --git a/locales/ta/LC_MESSAGES/user_guide.po b/locales/ta/LC_MESSAGES/user_guide.po index 5c649d68..abce4430 100644 --- a/locales/ta/LC_MESSAGES/user_guide.po +++ b/locales/ta/LC_MESSAGES/user_guide.po @@ -8,8 +8,8 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-01-25 14:33+0100\n" -"PO-Revision-Date: 2025-07-14 17:01+0000\n" -"Last-Translator: தமிழ்நேரம் \n" +"PO-Revision-Date: 2025-08-12 10:26+0000\n" +"Last-Translator: Michael Crusoe \n" "Language-Team: Tamil \n" "Language: ta\n" @@ -147,8 +147,8 @@ msgstr "இந்த பக்கம் நகர்ந்தது" msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." msgstr "" "இந்த பக்கம் காலாவதியானது மற்றும் பழைய பயனர் வழிகாட்டியின் இணைப்புகளைப் பாதுகாக்க இங்கே " -"வைக்கப்பட்டது. பயனர் வழிகாட்டியை உலவ புதிய [உள்ளடக்க அட்டவணை] (Index." -"MD#அட்டவணை-இன்-உள்ளடக்கங்கள்) ஐப் பயன்படுத்தவும்." +"வைக்கப்பட்டது. பயனர் வழிகாட்டியை உலவ புதிய [உள்ளடக்க அட்டவணை](index.md#table-of-" +"contents) ஐப் பயன்படுத்தவும்." #: ../../src/faq.md:1 #: e2ed894d325a4f50a5e2dc69da5531a1 @@ -282,11 +282,10 @@ msgstr "" #: d9e30e11533b4d53a144f5df7041268d msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -"[`மல்டிபிள்இன் பியூட்ஃபீட்டர்ரெக்மென்ட்`] (https://www.commonwl.org/v1.0/workflow." -"html#multifulutfeatureerequirement) உடன் [` linkerge: mergerge: merge_nested`]" -" (https://wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww" -"wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww" -" /Workflow.html#workflowstepinput)" +"[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/" +"Workflow.html#MultipleInputFeatureRequirement) உடன் " +"[`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/" +"Workflow.html#WorkflowStepInput)" #: ../../src/faq.md:194 #: 941077158ec54ae19bfa2e2ad6662da1 @@ -498,7 +497,7 @@ msgstr "பொதுவான பணிப்பாய்வு மொழி ப #: f8d6e4cd54cb42c88182a43171d97bab msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." msgstr "" -"[பொதுவான பணிப்பாய்வு மொழி] (https://www.commonwl.org/) (சி.டபிள்யூ.எல்) திறந்த " +"[பொதுவான பணிப்பாய்வு மொழி](https://www.commonwl.org/) (சி.டபிள்யூ.எல்) திறந்த " "தரங்களைப் பயன்படுத்தி பணிப்பாய்வுகளை எழுதுவதற்கு இந்த வழிகாட்டி உங்களை அறிமுகப்படுத்தும். " "இந்த வழிகாட்டி அண்மைக் கால விவரக்குறிப்பை விவரிக்கிறது {{ cwl_version }}." @@ -512,7 +511,7 @@ msgstr "பங்களிப்புகள் மற்றும் பின msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" "இந்த வழிகாட்டியிலிருந்து ஏதேனும் காணவில்லை என்று நீங்கள் கண்டால், அல்லது பிற கருத்துக்களை " -"வழங்க விரும்பினால், [இந்த வழிகாட்டிக்கான திட்ட களஞ்சியத்தில்] [ரெப்போ] இல் சிக்கலை தாக்கல் " +"வழங்க விரும்பினால், [இந்த வழிகாட்டிக்கான திட்ட களஞ்சியத்தில்][repo] இல் சிக்கலை தாக்கல் " "செய்யுங்கள். ஒவ்வொரு பக்கத்தின் வலது பக்கப்பட்டியில் \"இந்த பக்கத்தைத் திருத்து\" பொத்தானைக் " "சொடுக்கு செய்வதன் மூலம் இழுக்கும் கோரிக்கையில் நேரடியாக மாற்றங்களை நீங்கள் பரிந்துரைக்கலாம்." @@ -525,8 +524,8 @@ msgstr "பயனர் வழிகாட்டியை வழிநடத் #: ed74c9a4b623464480e2c184668fcec0 msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." msgstr "" -"நீங்கள் ஒரு தொடக்க பயனராக இருந்தால் [அறிமுகம்] (/introduction/index.md) பிரிவில் " -"தொடங்கலாம். மேம்பட்ட பயனர்களுக்கு [தலைப்புகள்] (//topics/index.md)குறியீட்டு." +"நீங்கள் ஒரு தொடக்க பயனராக இருந்தால் [அறிமுகம்](/introduction/index.md) பிரிவில் " +"தொடங்கலாம். மேம்பட்ட பயனர்களுக்கு [தலைப்புகள்](/topics/index.md)குறியீட்டு." #: ../../src/index.md:23 #: cfa67cf5521b414da6f7d34cbed283f7 @@ -588,7 +587,7 @@ msgstr "" msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." msgstr "" "விவரக்குறிப்பு பதிப்பிற்கு பயன்படுத்தப்படும் மாதிரி சொற்பொருள் பதிப்பு என்று " -"அழைக்கப்படுகிறது. இதைப் பற்றி [மேலும் அறிக] (#கற்றுக்கொள்ள) இந்த பிரிவின் முடிவைக் காண்க." +"அழைக்கப்படுகிறது. இதைப் பற்றி [மேலும் அறிக](#learn-more) இந்த பிரிவின் முடிவைக் காண்க." #: ../../src/introduction/basic-concepts.md:37 #: b3df1607e9d242d78b22dc44335fbe2d @@ -678,8 +677,8 @@ msgid "Operation is an abstract process that also takes inputs, produces outputs msgstr "" "செயல்பாடு என்பது ஒரு சுருக்க செயல்முறையாகும், இது உள்ளீடுகளை எடுக்கும், வெளியீடுகளை " "உருவாக்குகிறது மற்றும் பணிப்பாய்வுகளில் பயன்படுத்தப்படலாம். ஆனால் இது பொதுவாகப் " -"பயன்படுத்தப்படாத ஒரு சிறப்பு செயல்பாடு. இது இந்த பயனர் வழிகாட்டியின் [செயல்பாட்டு " -"பிரிவு] (../ தலைப்புகள்/செயல்பாடுகள். எம்.டி) இல் விவாதிக்கப்படுகிறது." +"பயன்படுத்தப்படாத ஒரு சிறப்பு செயல்பாடு. இது இந்த பயனர் வழிகாட்டியின் " +"[செயல்பாட்டு பிரிவு](../topics/operations.md) இல் விவாதிக்கப்படுகிறது." #: ../../src/introduction/basic-concepts.md:131 #: 73b0c1ccb18c4b74a2c0fdf9706eca85 @@ -733,8 +732,8 @@ msgstr "" msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" "குறிப்புகள் தேவைகளுக்கு ஒத்தவை, ஆனால் தேவைகள் தேவைப்படும் அம்சங்களை பட்டியலிடுகையில், " -"குறிப்புகள் விருப்ப அம்சங்களை பட்டியலிடுகின்றன. [தேவைகள்] (../ " -"தலைப்புகள்/தேவைகள்-மற்றும்-இன்ட்ச். எம்.டி) பிரிவில் தேவைகள் விரிவாக விளக்கப்பட்டுள்ளன." +"குறிப்புகள் விருப்ப அம்சங்களை பட்டியலிடுகின்றன. [தேவைகள்](../topics/requirements-and-" +"hints.md) பிரிவில் தேவைகள் விரிவாக விளக்கப்பட்டுள்ளன." #: ../../src/introduction/basic-concepts.md:155 #: c4c3315c96714e81b364f8cc003b87e6 @@ -821,8 +820,8 @@ msgstr "Prov-o: prov ontology-" #: c377a7f5dbe645cebbb6c7eccf831a0b msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." msgstr "" -"சி.டபிள்யூ.எல் செயல்பாடுகள் இந்த பயனர் வழிகாட்டியின் [செயல்பாடுகள்] (../ " -"தலைப்புகள்/செயல்பாடுகள். எம்.டி) பிரிவில் உள்ளன." +"சி.டபிள்யூ.எல் செயல்பாடுகள் இந்த பயனர் வழிகாட்டியின் [செயல்பாடுகள்](../topics/" +"operations.md) பிரிவில் உள்ளன." #: ../../src/introduction/index.md:1 #: 1769a0cbf4de4d77879c1f202cd11af9 @@ -864,8 +863,8 @@ msgid "There are many implementations of the CWL standards. Some are complete CW msgstr "" "சி.டபிள்யூ.எல் தரநிலைகளில் பல செயலாக்கங்கள் உள்ளன. சில முழுமையான சி.டபிள்யூ.எல் ஓட்டப்பந்" "தய வீரர்கள், மற்றவர்கள் பணிப்பாய்வு இயந்திரங்களுக்கு செருகுநிரல்கள் அல்லது நீட்டிப்புகளாக " -"இருக்கலாம். [செயலாக்கங்கள்] (அடிப்படை-கருத்துக்கள். எம்.டி#செயலாக்கங்கள்) பிரிவில் எங்களுக்கு" -" சிறந்த விளக்கம் உள்ளது." +"இருக்கலாம். [செயலாக்கங்கள்](basic-concepts.md#implementations) பிரிவில் எங்களுக்கு " +"சிறந்த விளக்கம் உள்ளது." #: ../../src/introduction/prerequisites.md:19 #: cbbcce4c2a96471b8b0ae3593ad59de4 @@ -898,12 +897,12 @@ msgstr "சாளரங்கள்" #: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." msgstr "" -"நீங்கள் விண்டோசைப் பயன்படுத்துகிறீர்கள் என்றால், நீங்கள் [லினக்ச் 2 க்கான சாளரங்கள் துணை அமைப்பு] " +"நீங்கள் விண்டோசைப் பயன்படுத்துகிறீர்கள் என்றால், நீங்கள் [லினக்ச் 2 க்கான சாளரங்கள் துணை அமைப்பு]" "(https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2) ஐ நிறுவ வேண்டும்" -". WSL2 ஐ நிறுவுவது குறித்த விவரங்களுக்கு `cwltool` [ஆவணம்] (https://github.com/" +". WSL2 ஐ நிறுவுவது குறித்த விவரங்களுக்கு `cwltool` [ஆவணம்](https://github.com/" "common-workflow-language/cwltool/blob/readme.rst#ms-mys-windows-users) ஐப் " -"பார்வையிடவும். உங்கள் இயக்க முறைமைக்கு இணைய அணுகல் மற்றும் பைதானின் அண்மைக் கால பதிப்பு (3" -".6+) தேவை." +"பார்வையிடவும். உங்கள் இயக்க முறைமைக்கு இணைய அணுகல் மற்றும் பைதானின் அண்மைக் கால பதிப்பு " +"(3.6+) தேவை." #: ../../src/introduction/prerequisites.md:35 #: 56d78c95daa54135b6aa9b2bfdc34d01 @@ -936,7 +935,7 @@ msgstr "`PIP` மற்றும்` vev` உடன் `cwltool` ஐ நிற #: f7aaafeee230400da056464c853582c2 msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." msgstr "" -"`Cwltool` உடன்` apt` மற்றும் `கான்டா` உடன் நிறுவ பிற வழிகளில்` cwltool` [ஆவணம்] " +"`cwltool` உடன்` apt` மற்றும் `conda` உடன் நிறுவ பிற வழிகளில்` cwltool` [ஆவணம்]" "(https://github.com/common-workflow-language/cwltool#install) ஐப் பார்வையிடவும்." #: ../../src/introduction/prerequisites.md:65 @@ -1146,8 +1145,8 @@ msgstr "" #: 9390b03889de44638141d705e0ef8322 msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." msgstr "" -"[செயலாக்கங்கள்] (அடிப்படை-கருத்துக்கள். எம்.டி#செயலாக்கங்கள்) தலைப்பு அடுத்த பிரிவில், " -"அடிப்படை கருத்துக்கள்." +"[செயலாக்கங்கள்](basic-concepts.md#implementations) தலைப்பு அடுத்த பிரிவில், அடிப்படை" +" கருத்துக்கள்." #: ../../src/introduction/prerequisites.md:199 #: 12042e411482458f8c35a2491f9433e0 @@ -1176,7 +1175,7 @@ msgstr "“அலோ வேர்ல்ட்”" #: cb203354977d42a58112d09357f62565 msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" msgstr "" -"சி.டபிள்யூ.எல் ஆவணங்கள் [YAML] (../ தலைப்புகள்/Index.MD) (மற்றும்/அல்லது JSON) இல் " +"சி.டபிள்யூ.எல் ஆவணங்கள் [YAML](../topics/index.md) (மற்றும்/அல்லது JSON) இல் " "எழுதப்பட்டுள்ளன. கீழேயுள்ள எடுத்துக்காட்டு கருத்துகளுடன் சிறுகுறிப்பு செய்யப்பட்ட ஒரு எளிய " "சி.டபிள்யூ.எல் “அலோ வேர்ல்ட்” பணிப்பாய்வுகளைக் காட்டுகிறது. கருத்துகள் `#` உடன் தொடங்குகின்" "றன என்பதை நினைவில் கொள்க:" @@ -1200,8 +1199,7 @@ msgid "In CWL, there is a distinction between a command-line tool and a workflow msgstr "" "சி.டபிள்யூ.எல் இல், ஒரு கட்டளை-வரி கருவி மற்றும் பணிப்பாய்வு இடையே வேறுபாடு உள்ளது. " "ஆனால் எளிமைக்காக, நாங்கள் இங்கே “பணிப்பாய்வு” என்ற வார்த்தையைப் பயன்படுத்துகிறோம். இதைப் " -"பற்றி [அடிப்படை கருத்துக்கள்] (அடிப்படை-கருத்துக்கள். எம்.டி) பிரிவில் மேலும் அறிந்து " -"கொள்வீர்கள்." +"பற்றி [அடிப்படை கருத்துக்கள்](basic-concepts.md) பிரிவில் மேலும் அறிந்து கொள்வீர்கள்." #: ../../src/introduction/quick-start.md:32 #: 498a43362a4749f3b8b433709d34a1d5 @@ -1226,7 +1224,7 @@ msgstr "`பிப்` உடன்` cwltool` ஐ நிறுவுகிறத msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." msgstr "" "PIP கட்டளையைப் பயன்படுத்தி CWLTool ஐ நிறுவுவது உங்களுக்காக வேலை செய்யாது என்றால், " -"[முன்நிபந்தனைகள்] (முன்நிபந்தனைகள். MD) பிரிவில் `CWLTool` ஐ நிறுவ பிற வழிகள் உள்ளன, " +"[முன்நிபந்தனைகள்](prerequisites.md) பிரிவில் `cwltool` ஐ நிறுவ பிற வழிகள் உள்ளன, " "மேலும் இந்த பயனரின் மீதமுள்ளவற்றை பின்பற்ற பயன்படுத்தப்படும் மென்பொருள் மற்றும் நூலகங்களின் " "விரிவான பட்டியலையும் கொண்டுள்ளது வழிகாட்டி." @@ -1309,8 +1307,8 @@ msgstr "" #: 7282abfa7155497ca47c30f9abfb6474 msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." msgstr "" -"கிதுபில் [`பொதுவான-வேலை-மொழி-மொழி` அமைப்பு] (https://github.com/common-" -"workflow-language)." +"கிதுபில் [`பொதுவான-வேலை-மொழி-மொழி` அமைப்பு](https://github.com/common-workflow-" +"language)." #: ../../src/introduction/quick-start.md:99 #: 176d8d47830f4031bb95dc231ebf1303 @@ -1330,8 +1328,8 @@ msgstr "" #: d039a9d6461c44628d4660c00d9ce6ff msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." msgstr "" -"{{'[CWL விவரக்குறிப்பு பதிப்பு] (https://www.commonwl.org/version)' .replace " -"('பதிப்பு', cwl_version_text)}}." +"{{'[CWL விவரக்குறிப்பு VERSION](https://www.commonwl.org/VERSION)' .replace (" +"'VERSION', cwl_version_text)}}." #: ../../src/introduction/quick-start.md:102 #: fbc3383d9e1c4eaca7931c3cc4f1752b @@ -1345,8 +1343,8 @@ msgstr "" msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." msgstr "" "இந்த பக்கம் காலாவதியானது மற்றும் பழைய பயனர் வழிகாட்டியின் இணைப்புகளைப் பாதுகாக்க இங்கே " -"வைக்கப்பட்டது. இந்த பக்கத்தில் உள்ள தகவல்கள் புதிய பயனர் வழிகாட்டியின் [கேள்விகள்] " -"(/கேள்விகள்) பகுதிக்கு இடம்பெயர்ந்துள்ளன." +"வைக்கப்பட்டது. இந்த பக்கத்தில் உள்ள தகவல்கள் புதிய பயனர் வழிகாட்டியின் [கேள்விகள்](/faq.md) " +"பகுதிக்கு இடம்பெயர்ந்துள்ளன." #: ../../src/topics/additional-arguments-and-parameters.md:1 #: 9c87c76c690948ac8e18088a0fffe679 @@ -1408,9 +1406,10 @@ msgid "This example references a runtime parameter. Runtime parameters provide msgstr "" "இந்த எடுத்துக்காட்டு ஒரு இயக்க நேர அளவுருவைக் குறிக்கிறது. கருவி உண்மையில் " "செயல்படுத்தப்படும்போது இயக்க நேர அளவுருக்கள் வன்பொருள் அல்லது மென்பொருள் சூழல் பற்றிய " -"தகவல்களை வழங்குகின்றன. `$ (Runtime.outdir)` அளவுரு என்பது நியமிக்கப்பட்ட வெளியீட்டு " -"கோப்பகத்திற்கான பாதை. பிற அளவுருக்களில் `$ (runtime.tmpdir)`, `$ (இயக்க நேரம். " -"விவரங்களுக்கு CWL விவரக்குறிப்பின் [இயக்க நேர சூழல்] [இயக்க நேரம்] பகுதியைப் பார்க்கவும்." +"தகவல்களை வழங்குகின்றன. `$(runtime.outdir)` அளவுரு என்பது நியமிக்கப்பட்ட வெளியீட்டு " +"கோப்பகத்திற்கான பாதை. பிற அளவுருக்களில் `$(runtime.tmpdir)`, `$(runtime.ram)`, " +"`$(runtime.cores)`, `$(runtime.outdirSize)`, மற்றும் `$(runtime.tmpdirSize)`. " +"விவரங்களுக்கு CWL விவரக்குறிப்பின் [இயக்க நேர சூழல்] [runtime] பகுதியைப் பார்க்கவும்." #: ../../src/topics/best-practices.md:1 #: 612c4a66c36a43d4ac5d74c1757d6845 @@ -1452,8 +1451,8 @@ msgstr "" #: 674c238b25e240eda05e22e399f2f78f msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." msgstr "" -"முடிந்தால், உரிமம் அதனுடன் தொடர்புடைய [SPDX அடையாளங்காட்டி] [SPDX] உடன் குறிப்பிடப்பட " -"வேண்டும். `Https://spdx.org/licenses/ [spdx-id]` `SPDX-ID` படிவத்தின் முகவரி ஐ " +"முடிந்தால், உரிமம் அதனுடன் தொடர்புடைய [SPDX அடையாளங்காட்டி] [spdx] உடன் குறிப்பிடப்பட " +"வேண்டும். `https://spdx.org/licenses/[SPDX-ID]` `SPDX-ID` படிவத்தின் முகவரி ஐ " "வழங்குவதன் மூலம் உரிமத்திற்கான மேனிலை தரவு புலத்தை உருவாக்குங்கள், அங்கு மேலே இணைக்கப்பட்" "ட அடையாளங்காட்டிகளின் பட்டியலிலிருந்து எடுக்கப்படுகிறது. வழிகாட்டுதலுக்கு கீழே உள்ள " "எடுத்துக்காட்டு துணுக்கைக் காண்க. SPDX அடையாளங்காட்டி இல்லாமல் தரமற்ற உரிமங்களுக்கு, " @@ -1463,22 +1462,23 @@ msgstr "" #: b651f80f47b4442fbf29454a233697fc msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" msgstr "" -"பயனுள்ள வாசிப்பு: \"[விஞ்ஞானி-புரோகிராமருக்கான மென்பொருள் உரிமத்திற்கான விரைவான " -"வழிகாட்டி] [அறிவியல்-உரிமம்]\"" +"பயனுள்ள வாசிப்பு: \"" +"[விஞ்ஞானி-புரோகிராமருக்கான மென்பொருள் உரிமத்திற்கான விரைவான வழிகாட்டி][sci-license]]" +"\"" #: ../../src/topics/best-practices.md:28 #: 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -"எச்பி SPDX அடையாளங்காட்டியுடன் உரிமத்திற்கான மேனிலை தரவு புலத்தின் மாதிரி: _" +"_எச்பி SPDX அடையாளங்காட்டியுடன் உரிமத்திற்கான மேனிலை தரவு புலத்தின் மாதிரி:_" #: ../../src/topics/best-practices.md:37 #: 3a87a0fb2a364e3da5aaa4017e430b19 msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." msgstr "" "சி.டபிள்யூ.எல் விளக்கங்களுக்குள் மெட்டாடேட்டாவை வழங்குவதற்கான கூடுதல் எடுத்துக்காட்டுகளுக்கு" -", [இந்த பயனர் வழிகாட்டியின் மேனிலை தரவு மற்றும் எழுத்தாளர் பிரிவு] (../ " -"தலைப்புகள்/மெட்டாடேட்டா-மற்றும்-அணுகல். எம்.டி) ஐப் பார்க்கவும்." +", [இந்த பயனர் வழிகாட்டியின் மேனிலை தரவு மற்றும் எழுத்தாளர் பிரிவு](../topics/" +"metadata-and-authorship.md) ஐப் பார்க்கவும்." #: ../../src/topics/best-practices.md:40 #: ecf2b9c0b1664afe9c4e180610610021 @@ -1523,13 +1523,14 @@ msgstr "" msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types//" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." msgstr "" "அனைத்து உள்ளீடு மற்றும் வெளியீடு `கோப்பு'க்கு` வடிவமைப்பு` குறிப்பிடப்பட வேண்டும். " -"பயோ-இன்ஃபர்மேடிக்ச் கருவிகள் [எடாம்] [எடாம்-எடுத்துக்காட்டாக] இருந்து வடிவமைப்பு " -"அடையாளங்காட்டிகளைப் பயன்படுத்த வேண்டும். `Iana: உரை/வெற்று`,` iana: உரை/தாவலால் " -"பிரிக்கப்பட்ட-மதிப்புகள்` `$ பெயர்வெளிகளுடன்: {iana:\" https://www.iana.org/" -"assignments/media-types/ \". [முழு ஐஏஎன்ஏ மீடியா வகை பட்டியல்] [ஐஏஎன்ஏ வகைகள்] (மைம்" -" வகைகள் என்றும் அழைக்கப்படுகிறது). பயோஇன்ஃபர்மேடிக்ச் அல்லாத கருவிகளுக்கு, அதே வழியில் " -"பொருத்தமான ஆன்டாலசி/கட்டுப்படுத்தப்பட்ட சொற்களஞ்சியத்தைப் பயன்படுத்தவும் அல்லது உருவாக்கவும். " -"இதைப் பற்றி எங்களுக்குத் தெரியப்படுத்த இந்தப் பக்கத்தைத் திருத்தவும்." +"பயோ-இன்ஃபர்மேடிக்ச் கருவிகள் [EDAM][edam-example]] இருந்து வடிவமைப்பு " +"அடையாளங்காட்டிகளைப் பயன்படுத்த வேண்டும். `iana:text/plain`,`iana:text/tab-separated-" +"values` `$namespaces: { iana: " +"\"https://www.iana.org/assignments/media-types//" }`. " +"[முழு ஐஏஎன்ஏ மீடியா வகை பட்டியல்][iana-types] (மைம் வகைகள் என்றும் அழைக்கப்படுகிறது). " +"பயோஇன்ஃபர்மேடிக்ச் அல்லாத கருவிகளுக்கு, அதே வழியில் பொருத்தமான ஆன்டாலசி/கட்டுப்படுத்தப்பட்" +"ட சொற்களஞ்சியத்தைப் பயன்படுத்தவும் அல்லது உருவாக்கவும். இதைப் பற்றி எங்களுக்குத் தெரியப்படுத்" +"த இந்தப் பக்கத்தைத் திருத்தவும்." #: ../../src/topics/best-practices.md:66 #: 3ef57e6862f240bebcf193a52397af0a @@ -1578,9 +1579,9 @@ msgstr "" msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." msgstr "" "சாத்தியமான நீக்குதல் அல்லது மாற்றுவதற்கு சாவாச்கிரிப்டின் அனைத்து பயன்பாடுகளையும் மதிப்பீடு " -"செய்யுங்கள். ஒரு பொதுவான எடுத்துக்காட்டு: `கோப்பு` பெயர்கள் மற்றும் பாதைகளை " -"கையாளுகிறீர்களா? [`கோப்பு` பண்புகள்] [கோப்பு-முன்மாதிரிகளில்]` பேச்நேம்`, `நமெரூட்`,` " -"நேமெக்ச்ட்` போன்றவற்றில் ஒன்றைப் பயன்படுத்த முடியுமா என்பதைக் கவனியுங்கள்." +"செய்யுங்கள். ஒரு பொதுவான எடுத்துக்காட்டு: `File` பெயர்கள் மற்றும் பாதைகளை கையாளுகிறீர்களா" +"? [`File` பண்புகள்][file-prop] `basename`, `nameroot`,`nameext` போன்றவற்றில் ஒன்றைப்" +" பயன்படுத்த முடியுமா என்பதைக் கவனியுங்கள்." #: ../../src/topics/best-practices.md:90 #: d8e2280a75a74916a1630afaa2fe2ae3 @@ -1603,8 +1604,8 @@ msgstr "" msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." msgstr "" "மென்பொருள் கொள்கலன்கள் [\"பயோ -இன்ஃபர்மேடிக்ச் மென்பொருளை பேக்கேசிங் மற்றும் கொள்கலனுக்கான " -"பரிந்துரைகளுக்கு\" இணக்கமாக இருக்க வேண்டும் [கொள்கலன்கள்] (பிற துறைகளுக்கும் பயனுள்ளதாக " -"இருக்கும்)." +"பரிந்துரைகளுக்கு\"][containers] இணக்கமாக இருக்க வேண்டும் (பிற துறைகளுக்கும் பயனுள்ளதா" +"க இருக்கும்)." #: ../../src/topics/command-line-tool.md:1 #: 3f4e98f6bfa141feba8c4b120e3d03e8 @@ -1643,8 +1644,8 @@ msgstr "`echo.cwl`" msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." msgstr "" "உள்ளீடுகள் மற்றும் வெளியீடுகளை வரையறுக்க மேலே உள்ள எடுத்துக்காட்டு எளிமையான படிவத்தைப் " -"பயன்படுத்துகிறது. [உள்ளீடுகள்] (../ தலைப்புகள்/உள்ளீடுகள். எம்.டி) மற்றும் [வெளியீடுகள்] " -"(../ தலைப்புகள்/வெளியீடுகள்) பிரிவுகளில் நீங்கள் மேலும் அறிந்து கொள்வீர்கள்." +"பயன்படுத்துகிறது. [உள்ளீடுகள்](../topics/inputs.md) மற்றும் [வெளியீடுகள்](../topics/" +"outputs.md) பிரிவுகளில் நீங்கள் மேலும் அறிந்து கொள்வீர்கள்." #: ../../src/topics/command-line-tool.md:68 #: 1849b8f3ae1c4a84ae59a78ffd6b371e @@ -1694,8 +1695,8 @@ msgstr "`criatefile.cwl`" #: cfffc518ba6e4ed1a80762ed6f7d25df msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." msgstr "" -"`$ (உள்ளீடுகள். மெசேச்)` போன்ற எந்த [வெளிப்பாடுகள்] (../ தலைப்புகள்/வெளிப்பாடுகள். இங்கே, " -"`செய்தி` உள்ளீட்டில் மதிப்பை செருகவும்." +"`$(inputs.message)` போன்ற எந்த [வெளிப்பாடுகள்](../topics/expressions.md). இங்கே, " +"`message` உள்ளீட்டில் மதிப்பை செருகவும்." #: ../../src/topics/creating-files-at-runtime.md:20 #: 9454a330b9324744b89448f2694b1b03 @@ -1728,8 +1729,8 @@ msgstr "`Echo-job.yml`" msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." msgstr "" "இதை இயக்குவதற்கு முன், ஒவ்வொரு அடியையும் இன்னும் கொஞ்சம் விரிவாகப் பார்ப்போம். அடிப்படை " -"கட்டளை `பேச் கமாண்ட்: [\" எச்.எச் \",\" எடுத்துக்காட்டு. இது செல்லில் நாம் உருவாக்கும் " -"கோப்பை இயக்கும்." +"கட்டளை `baseCommand: [\"sh\", \"example.sh\"]`என்ற கட்டளையை இயக்கும் `sh " +"example.sh`. இது செல்லில் நாம் உருவாக்கும் கோப்பை இயக்கும்." #: ../../src/topics/creating-files-at-runtime.md:40 #: 70e257091bdb456e8957f90a8fa90e8c @@ -1747,8 +1748,8 @@ msgstr "" #: 1741804e33aa43ce88b4320c11ae5973 msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." msgstr "" -"வடிவமைப்பைப் பற்றி மேலும் அறிய [YAML வழிகாட்டி] (../ தலைப்புகள்/yaml-quide.md#maps) " -"ஐப் பார்க்கவும்." +"வடிவமைப்பைப் பற்றி மேலும் அறிய [YAML வழிகாட்டி](../topics/yaml-guide.md#maps) ஐப் " +"பார்க்கவும்." #: ../../src/topics/creating-files-at-runtime.md:54 #: ../../src/topics/environment-variables.md:18 @@ -1783,8 +1784,8 @@ msgstr "" #: 73e68b3af9cf41338d843c0c40e50cdc msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." msgstr "" -"ஒரு நிலையான பயோம் அட்டவணை கோப்பை HDF5 வடிவமாக மாற்றுவதற்கான [பயோம் மாற்றும் வடிவம்] " -"[பயோம்] கருவியின் CWL விளக்கம் கீழே உள்ள எடுத்துக்காட்டு." +"ஒரு நிலையான பயோம் அட்டவணை கோப்பை HDF5 வடிவமாக மாற்றுவதற்கான [பயோம் மாற்றும் வடிவம்]" +"[biom] கருவியின் CWL விளக்கம் கீழே உள்ள எடுத்துக்காட்டு." #: ../../src/topics/custom-types.md:12 #: ef5f35acb97f4ddfad7b688712f53484 @@ -1845,7 +1846,7 @@ msgstr "" #: 9a97acd430064710bcdf76edbd9f711c msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." msgstr "" -"இந்த சி.டபிள்யூ.எல் விளக்கத்தின் ஆசிரியருக்கு `ரிசோர்ச் ரெக்விரெமென்ட்'ச் ஆகியவை அடங்கும் " +"இந்த சி.டபிள்யூ.எல் விளக்கத்தின் ஆசிரியருக்கு `ResourceRequirement`'ச் ஆகியவை அடங்கும் " "என்பதையும் நினைவில் கொள்க, கருவிக்கு வெற்றிகரமாக இயங்க தேவையான குறைந்தபட்ச ரேம் மற்றும் " "கோரின் எண்ணிக்கையையும், விளக்கம் எழுதப்பட்ட மென்பொருளின் பதிப்பின் விவரங்களையும் " "குறிப்பிடுகிறது என்பதையும் நினைவில் கொள்க மற்றும் பிற பயனுள்ள மேனிலை தரவு. இந்த பயனர் " @@ -1927,10 +1928,10 @@ msgstr "" msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." msgstr "" "சாவாச்கிரிப்ட் வெளிப்பாடுகள் முற்றிலும் தேவைப்படும்போது மட்டுமே பயன்படுத்தப்பட வேண்டும். " -"கோப்பு பெயர்கள், நீட்டிப்புகள், பாதைகள் போன்றவற்றைக் கையாளும் போது, `பேச்இன் பெயர்`,` " -"நமெரூட்`, `நேமெக்ச்ட்` போன்றவற்றைப் போன்ற [` கோப்பு` பண்புகளில்] [கோப்பு-ப்ராப்] ஒன்றைப் " -"பயன்படுத்த முடியுமா என்பதைக் கவனியுங்கள். [சிறந்த நடைமுறைகளின் பட்டியல்] (சிறந்த " -"நடைமுறைகள். எம்.டி) ஐப் பார்க்கவும்." +"கோப்பு பெயர்கள், நீட்டிப்புகள், பாதைகள் போன்றவற்றைக் கையாளும் போது, `basename`,`nameroot`" +", `nameext` போன்றவற்றைப் போன்ற [` கோப்பு` பண்புகளில்][file-prop] ஒன்றைப் பயன்படுத்த " +"முடியுமா என்பதைக் கவனியுங்கள். [சிறந்த நடைமுறைகளின் பட்டியல்](best-practices.md) ஐப் " +"பார்க்கவும்." #: ../../src/topics/expressions.md:16 #: 7fdbfd1c937b4991bf4a2fa26ea310e4 @@ -1941,8 +1942,8 @@ msgstr "`Expression.cwl`" #: efb5fd14988c4e2a8f834ee5369d4102 msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" msgstr "" -"இந்த கருவிக்கு `உள்ளீடுகள் 'தேவையில்லை என்பதால், அதை (கிட்டத்தட்ட) வெற்று வேலை கோப்புடன் " -"இயக்க முடியும்:" +"இந்த கருவிக்கு `inputs`தேவையில்லை என்பதால், அதை (கிட்டத்தட்ட) வெற்று வேலை கோப்புடன் இயக்" +"க முடியும்:" #: ../../src/topics/expressions.md:25 #: e833649b951841c49397796f996d29f3 @@ -1991,15 +1992,15 @@ msgstr "சாவாச்கிரிப்ட் வெளிப்பாட #: cbec9277b5004e50af2728cbda0df740 msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" msgstr "" -"[அளவுரு குறிப்புகள்] (அளவுரு-குறிப்புகள். எம்.டி) போலவே, நீங்கள் சில துறைகளில் மட்டுமே " +"[அளவுரு குறிப்புகள்](parameter-references.md) போலவே, நீங்கள் சில துறைகளில் மட்டுமே " "சாவாச்கிரிப்ட் வெளிப்பாடுகளைப் பயன்படுத்தலாம். அவை:" #: ../../src/topics/expressions.md:66 #: e259f55f8000479bbd8009e25cf0ca6c msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -"[`கட்டளை லைனெட்டூல்`] (https://www.commonwl.org/v1.0/commandlinetool." -"html#commandlinetool) இலிருந்து)" +"[`CommandLineTool`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandLineTool) இலிருந்து" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 @@ -2048,8 +2049,8 @@ msgstr "`ச்டைடர்`" #: 8210b36347a749889450529ecdf4ff0e msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -"[CommandInputParameter] (https://www.commonwl.org/v1.0/commandlinetool." -"html#commandinputarameter) இலிருந்து)" +"[CommandInputParameter](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandInputParameter) இலிருந்து" #: ../../src/topics/expressions.md:73 #: ../../src/topics/expressions.md:78 @@ -2093,22 +2094,22 @@ msgstr "`இரண்டாம் நிலை கோப்புகள்`" #: 23088850ad02459696f6bbd385109aac msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -"[`InputBinding`] (https://www.commonwl.org/v1.0/commandlinetool.html#" -"commandlinebinding இலிருந்து)" +"[`inputBinding`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandLineBinding) இலிருந்து" #: ../../src/topics/expressions.md:77 #: f02257a822ad46ac93c5981531cc85d5 msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -"[CommandOutPutputParamater] (https://www.commonwl.org/v1.0/commandlinetool." -"html#commandoutputparameter) இலிருந்து)" +"[CommandOutputParamater](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandOutputParameter)இலிருந்து" #: ../../src/topics/expressions.md:80 #: 989a1c4aaa1143be9f53b90cd8b6d500 msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -"[CommandOutPutpunding] (https://www.commonwl.org/v1.0/commandlinetool." -"html#commandoutputpinting) இலிருந்து)" +"[CommandOutputBinding](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandOutputBinding) இலிருந்து" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 @@ -2122,7 +2123,7 @@ msgstr "`குளோப்`" #: d555a3d991e344a5a8e1289168d7c6d1 #: 44b3f123c9b04a308c1161b742a7b34b msgid "`outputEval`" -msgstr "`வெளிச்செல்லும்" +msgstr "`outputEval`" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 @@ -2150,15 +2151,17 @@ msgstr "`படிகள்` இலிருந்து" #: 81b4d1f23a3642bfa9bb395b94260cd1 msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -"[Workflowstepinput] (https://www.commonwl.org/v1.0/workflow.html#" -"workflowstepinput இலிருந்து)" +"[WorkflowStepInput](https://www.commonwl.org/v1.0/" +"Workflow.html#WorkflowStepInput) இலிருந்து" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 #: e1cde4aa32c041238ed2596173c6d824 #: 557694f82e314baa9ccafba14d6ff2c9 msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" -msgstr "[வெளிப்பாடு)" +msgstr "" +"[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool) " +"இலிருந்து" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 @@ -2179,8 +2182,8 @@ msgstr "" #: bdb4c68a175047ddbe141ca24960127f msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" -"[`Resourcerequirement`] இலிருந்து (https://www.commonwl.org/v1.0/" -"commandlinetool.html#resourcerequirement)" +"[`ResourceRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#ResourceRequirement) இலிருந்து" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 @@ -2201,7 +2204,7 @@ msgstr "`colorsmax`" #: c07ab08eb75d4528949c56a3d7c12b28 #: 846cd427ae25410eae7c920b237edcb0 msgid "`ramMin`" -msgstr "`ராம்மின் '" +msgstr "`ramMin`" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 @@ -2215,7 +2218,7 @@ msgstr "`rammax`" #: 700c57ccd5e347be86702c83a8af24b3 #: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" -msgstr "`tmpdirmin '" +msgstr "`tmpdirMin`" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 @@ -2242,8 +2245,8 @@ msgstr "`outtirmax`" #: 97b61352363f47cb890e8937c5613fa3 msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" -"[`SiturtWorkDirRequirement`] (https://www.commonwl.org/v1.0/commandlinetool." -"html#initialworkdirrequirement இலிருந்து)" +"[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement) இலிருந்து" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 @@ -2255,8 +2258,7 @@ msgstr "`பட்டியல்`" #: ../../src/topics/expressions.md:106 #: 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "" -"[dirent] (https://www.commonwl.org/v1.0/commandlinetool.html#dirent இல்)" +msgstr "[Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)இல்" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 @@ -2283,8 +2285,8 @@ msgstr "`Envvarrequirement` இலிருந்து" #: 0bc424ef2ca346099f29b937379908a0 msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" -"[சுற்றுச்சூழல் டெஃப்] (https://www.commonwl.org/v1.0/commandlinetool.html#" -"enveronmentdef இலிருந்து)" +"[EnvironmentDef](https://www.commonwl.org/v1.0/" +"CommandLineTool.html#EnvironmentDef) இலிருந்து" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 @@ -2321,10 +2323,11 @@ msgstr "" #: cd74f34b21af4de9be96fd897efc469b msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" -"CWL தரநிலைகள் (https://www.commonwl.org/v1.0/commandlinetool.html#expressions)" -" சி.டபிள்யூ.எல். : //262.ecma-international.org/5.1/). இதன் பொருள் உங்கள் சி.டபிள்யூ" -".எல் ஆவணத்தில் நீங்கள் உள்ளடக்கிய அல்லது எழுதும் எந்த குறியீடும் எக்மாச்கிரிப்ட் 5.1 உடன் " -"இணக்கமாக இருக்க வேண்டும்." +"CWL தரநிலைகள் (பதிப்புகள் 1.0 முதல் 1.2 வரை) CWL வெளிப்பாடுகளில் செல்லுபடியாகும் ஒரே " +"ஜாவாஸ்கிரிப்ட் பதிப்பு [ECMAScript 5.1](https://262.ecma-international.org/5.1/) " +"[என்று](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) " +"கூறுகிறது. சி.டபிள்யூ.எல். இதன் பொருள் உங்கள் சி.டபிள்யூ.எல் ஆவணத்தில் நீங்கள் உள்ளடக்கிய " +"அல்லது எழுதும் எந்த குறியீடும் எக்மாச்கிரிப்ட் 5.1 உடன் இணக்கமாக இருக்க வேண்டும்." #: ../../src/topics/expressions.md:135 #: f12e371f3f1a4b0cb2cff9800352d48c @@ -2404,10 +2407,10 @@ msgstr "`அலோ-வேர்ல்ட்-எக்ச்பிரசன் #: fd4579a3c9844492b314b5c3c1775fc7 msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." msgstr "" -"உள்ளக வட்டில் இருந்து அல்லது தொலைதூர இடத்திலிருந்து ஒரு கோப்பைச் சேர்க்க `$ சேர்க்கவும்` " -"அறிக்கை பயன்படுத்தப்படலாம். இது உறவினர் மற்றும் முழுமையான பாதைகளுடன் செயல்படுகிறது. சி." -"டபிள்யூ.எல் விவரக்குறிப்பிலிருந்து அதைப் பற்றி மேலும் அறிய CWL விவரக்குறிப்பிலிருந்து " -"[`$ incllion அடங்கும்." +"உள்ளக வட்டில் இருந்து அல்லது தொலைதூர இடத்திலிருந்து ஒரு கோப்பைச் சேர்க்க `$include` " +"அறிக்கை பயன்படுத்தப்படலாம். இது உறவினர் மற்றும் முழுமையான பாதைகளுடன் செயல்படுகிறது. " +"சி.டபிள்யூ.எல் விவரக்குறிப்பிலிருந்து அதைப் பற்றி மேலும் அறிய CWL விவரக்குறிப்பிலிருந்து" +" [`$include` அடங்கும்](https://www.commonwl.org/v1.0/SchemaSalad.html#Include)." #: ../../src/topics/file-formats.md:1 #: 3f038e7371f84ed9b4547358dfb55a11 @@ -2573,7 +2576,7 @@ msgstr "" #: ../../src/topics/inputs.md:47 #: 651e032007ea4a119d20c820bb61f86b msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." -msgstr "அடுத்து, கட்டளை வரியில் `டச் திமிங்கலம்." +msgstr "`touch whale.txt `டச் திமிங்கலம்." #: ../../src/topics/inputs.md:53 #: 0b056dde9e87428996e47870b12119da @@ -2641,7 +2644,7 @@ msgstr "" msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." msgstr "" "உள்ளீட்டு கோப்புகள் படிக்க மட்டுமே. உள்ளீட்டு கோப்பை நீங்கள் புதுப்பிக்க விரும்பினால், நீங்கள் " -"[முதலில் அதை வெளியீட்டு கோப்பகத்திற்கு நகலெடுக்க வேண்டும்] (ச்டேசிங்-இன்ட்-ஃபைல்ச்.எம்டி)." +"[முதலில் அதை வெளியீட்டு கோப்பகத்திற்கு நகலெடுக்க வேண்டும்](staging-input-files.md)." #: ../../src/topics/inputs.md:134 #: 74f7a6b8f8f74dc2a970fdd6e63d8f80 @@ -2710,11 +2713,11 @@ msgstr "" #: 874c6f19abbf45d7ab7d30a378c4048d msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." msgstr "" -"உள்ளீடுகளின் வரிசைகள் சதுர அடைப்புக்குறிக்குள் குறிப்பிடப்பட்டுள்ளன `[]` " -"வரிசை-உள்ளீடுகள்-JOB.YML` இல். பல வரிகளிலும் வரிசைகளையும் வெளிப்படுத்தலாம், அங்கு " +"உள்ளீடுகளின் வரிசைகள் சதுர அடைப்புக்குறிக்குள் குறிப்பிடப்பட்டுள்ளன `[]` வரிசை-உள்ளீடுகள" +"்`array-inputs-job.yml` இல். பல வரிகளிலும் வரிசைகளையும் வெளிப்படுத்தலாம், அங்கு " "தொடர்புடைய விசையுடன் வரையறுக்கப்படாத வரிசை மதிப்புகள் ஒரு முன்னணி `-` ஆல் " -"குறிக்கப்படுகின்றன. இது அடுத்த பாடத்தில் நிரூபிக்கப்படும் மற்றும் [YAML வழிகாட்டி] (YAML-" -"Quide.MD#வரிசைகள்) இல் விரிவாக விவாதிக்கப்படுகிறது. வரிசைகளின் வரிசைகள், பதிவுகளின் " +"குறிக்கப்படுகின்றன. இது அடுத்த பாடத்தில் நிரூபிக்கப்படும் மற்றும் [YAML வழிகாட்டி](yaml-" +"guide.md#arrays) இல் விரிவாக விவாதிக்கப்படுகிறது. வரிசைகளின் வரிசைகள், பதிவுகளின் " "வரிசைகள் மற்றும் பிற சிக்கலான வகைகளை நீங்கள் குறிப்பிடலாம்." #: ../../src/topics/inputs.md:191 @@ -2839,12 +2842,12 @@ msgstr "" "சரியான செயலாக்கத்திற்கு அமலாக்க நீட்டிப்புகள் தேவையில்லை (எடுத்துக்காட்டாக, GUI " "விளக்கக்காட்சி தொடர்பான புலங்கள்) மற்றும் கருவி அல்லது பணிப்பாய்வு பற்றிய மேனிலை தரவு " "(எடுத்துக்காட்டாக, மேற்கோள்களில் பயன்படுத்துவதற்கான படைப்புரிமை) எந்தவொரு பொருளிலும் " -"கூடுதல் புலங்களாக வழங்கப்படலாம். [SCAMEAL SALAD EXPLICATION இல் விவரிக்கப்பட்டுள்ளபடி, " -"ஆவணத்தின் `$ பெயர்வெளிகள்` பிரிவில் (எ.கா. EDAM: http://edamontology.org/) " -"பட்டியலிடப்பட்டுள்ள பெயர்வெளி முன்னொட்டை இத்தகைய நீட்டிப்பு புலங்கள் (எ.கா. ] [ச்கீமா-சலாத்]" -". பெயர்வெளி முன்னொட்டை நீங்கள் சேர்த்தவுடன், கீழே காட்டப்பட்டுள்ளபடி ஆவணத்தில் எங்கும் அதை " -"அணுகலாம். இல்லையெனில், ஒருவர் முழு முகவரி களைப் பயன்படுத்த வேண்டும்: `வடிவம்: http: // " -"edamontology.org/format_2572`." +"கூடுதல் புலங்களாக வழங்கப்படலாம். [Schema Salad specification][schema-salad] இல் " +"விவரிக்கப்பட்டுள்ளபடி, ஆவணத்தின் `$ பெயர்வெளிகள்` பிரிவில் (எ.கா. `edam: http://" +"edamontology.org/`) பட்டியலிடப்பட்டுள்ள பெயர்வெளி முன்னொட்டை இத்தகைய நீட்டிப்பு புலங்கள் " +"(எ.கா.`format: edam:format_2572`). பெயர்வெளி முன்னொட்டை நீங்கள் சேர்த்தவுடன், கீழே " +"காட்டப்பட்டுள்ளபடி ஆவணத்தில் எங்கும் அதை அணுகலாம். இல்லையெனில், ஒருவர் முழு முகவரி களைப் " +"பயன்படுத்த வேண்டும்: `format: http://edamontology.org/format_2572`." #: ../../src/topics/metadata-and-authorship.md:13 #: 80af387fe3ff4e2da999903385bd602b @@ -2877,7 +2880,7 @@ msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 #: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" -msgstr "`டிரான்ச்மிட்டர்_எக்ச்." +msgstr "`metadata_example3.cwl`" #: ../../src/topics/operations.md:1 #: 8acf361cf77c4d45ba3f2e344146259f @@ -2986,15 +2989,15 @@ msgstr "கட்டாய வாதங்களை `பேச் கமாண #: 22447a560f6f4317bf67bd7c4336126c msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" msgstr "" -"முந்தைய எடுத்துக்காட்டுகளில், `பேச் கமாண்ட்` ஒரு சரம் மட்டுமே, எந்தவொரு வாதங்களும் சி." -"டபிள்யூ.எல் உள்ளீடுகளாக நிறைவேற்றப்பட்டன. ஒற்றை சரத்திற்கு பதிலாக நாம் _array இன் _array " -"ஐப் பயன்படுத்தலாம். முதல் உறுப்பு இயக்க கட்டளை, மற்றும் அடுத்தடுத்த கூறுகள் கட்டாய கட்டளை " -"வரி வாதங்கள்" +"முந்தைய எடுத்துக்காட்டுகளில், `baseCommand` ஒரு சரம் மட்டுமே, எந்தவொரு வாதங்களும் " +"சி.டபிள்யூ.எல் உள்ளீடுகளாக நிறைவேற்றப்பட்டன. ஒற்றை சரத்திற்கு பதிலாக நாம் _array இன் " +"சரத்திற்கு_ ஐப் பயன்படுத்தலாம். முதல் உறுப்பு இயக்க கட்டளை, மற்றும் அடுத்தடுத்த கூறுகள் கட்டா" +"ய கட்டளை வரி வாதங்கள்" #: ../../src/topics/outputs.md:26 #: f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" -msgstr "'tar.cwl`" +msgstr "`tar.cwl`" #: ../../src/topics/outputs.md:32 #: ad8e1acb251246d2a47c39b20d4e483a @@ -3070,7 +3073,7 @@ msgstr "`array-outputs-job.yml`" #: cc067051f22f433bbece08f60933e002 msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" -"[YAML வழிகாட்டி] (yaml-quide.md#வரிசைகள்) இல் விவரிக்கப்பட்டுள்ளபடி, எதிர்பார்க்கப்படும் " +"[YAML வழிகாட்டி](yaml-guide.md#arrays) இல் விவரிக்கப்பட்டுள்ளபடி, எதிர்பார்க்கப்படும் " "வெளியீடுகளின் வரிசை `array-outputs-job.yml` இல் குறிப்பிடப்பட்டுள்ளது. வரவிருக்கும் " "பல பிரிவுகளில் நிரூபிக்கப்பட்டபடி, வரிசைகளில் உள்ளீடுகளைக் குறிக்க CWL விளக்கங்களில் இந்த " "வடிவத்தைப் பயன்படுத்தலாம்." @@ -3123,7 +3126,8 @@ msgstr "" msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." msgstr "" "சாவாச்கிரிப்ட் தொடரியல் துணைக்குழுவைப் பயன்படுத்தி குறிப்புகள் எழுதப்பட்டுள்ளன. இந்த " -"எடுத்துக்காட்டில், `$ (உள்ளீடுகள்." +"எடுத்துக்காட்டில், `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, மற்றும் " +"`$(inputs['extractfile'])` ஆகியவை சமமானவை." #: ../../src/topics/parameter-references.md:51 #: 8b70a072aa87414c88e89a3e19af0a51 @@ -3154,36 +3158,36 @@ msgstr "" #: 7647e0229a924f988cf02b7812a55c06 msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -"[`கட்டளை லைன் டூல்`] (http://www.commonwl.org/v1.0/commandlinetool." -"html#commandlinetool) இலிருந்து)" +"[`CommandLineTool`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandLineTool) இலிருந்து" #: ../../src/topics/parameter-references.md:69 #: 9d663249666045618a0d3acddb85a9a9 msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -"[CommandInputParameter] (http://www.commonwl.org/v1.0/commandlinetool." -"html#commandinputarameter) இலிருந்து)" +"[CommandInputParameter](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandInputParameter) இலிருந்து" #: ../../src/topics/parameter-references.md:72 #: 5fed4984f6784347b4cbe0630b1dd2c2 msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -"[`InputBinding`] (http://www.commonwl.org/v1.0/commandlinetool." -"html#commandlineBinding) இலிருந்து)" +"[`inputBinding`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandLineBinding) இலிருந்து" #: ../../src/topics/parameter-references.md:74 #: dbf6153cd02542a6a01c172803122b7f msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -"[CommandOutputputParamater] (http://www.commonwl.org/v1.0/commandlinetool." -"html#commandoutputparameter) இலிருந்து)" +"[CommandOutputParamater](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandOutputParameter) இலிருந்து" #: ../../src/topics/parameter-references.md:77 #: b6250cf6fa8a4a0c94b33302e0decca5 msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -"[CommandOutPutPunding] (http://www.commonwl.org/v1.0/commandlinetool." -"html#commandoutputpinting) இலிருந்து)" +"[CommandOutputBinding](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#CommandOutputBinding) இலிருந்து" #: ../../src/topics/parameter-references.md:81 #: fa6ca3bbc6784380a03a950a6f49a180 @@ -3197,8 +3201,8 @@ msgstr "" #: b92b516e537a4773ad67b4af586e7a25 msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -"[Workflowstepinput] (http://www.commonwl.org/v1.0/workflow.html#" -"workflowstepinput இலிருந்து)" +"[WorkflowStepInput](http://www.commonwl.org/v1.0/" +"Workflow.html#WorkflowStepInput) இலிருந்து" #: ../../src/topics/parameter-references.md:89 #: 467a701228504d06b971b79a59c69064 @@ -3212,27 +3216,27 @@ msgstr "" #: 2634f989eb304009a8568d70ed42786c msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" -"[`ResourceRecequirement`] இலிருந்து (http://www.commonwl.org/v1.0/" -"commandlinetool.html#resourcerequirement)" +"[`ResourceRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#ResourceRequirement) இலிருந்து" #: ../../src/topics/parameter-references.md:101 #: 5d8bed66282c408695292ea92a03b2c4 msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" -"[`Siturtworkdirrequirement`] (http://www.commonwl.org/v1.0/commandlinetool." -"html#initialworkdirrequirement இலிருந்து)" +"[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#InitialWorkDirRequirement) இலிருந்து" #: ../../src/topics/parameter-references.md:103 #: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" -msgstr "[dirent] (http://www.commonwl.org/v1.0/commandlinetool.html#dirent இல்)" +msgstr "[Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent) இல்" #: ../../src/topics/parameter-references.md:107 #: 9a6b311ded8d4e43ae635b1b927dbdf2 msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" -"[சுற்றுச்சூழல் டெஃப்] (http://www.commonwl.org/v1.0/commandlinetool.html#" -"enveronmentdef இலிருந்து)" +"[EnvironmentDef](http://www.commonwl.org/v1.0/" +"CommandLineTool.html#EnvironmentDef) இலிருந்து" #: ../../src/topics/requirements-and-hints.md:5 #: aac74f957774479a83aab4c6ff1390ae @@ -3265,22 +3269,22 @@ msgid "Depending on your CWL runner, these hints may be used to check that the r msgstr "" "உங்கள் சி.டபிள்யூ.எல் ரன்னரைப் பொறுத்து, தேவையான மென்பொருள் நிறுவப்பட்டுள்ளதா என்பதைச் " "சரிபார்க்க இந்த குறிப்புகள் பயன்படுத்தப்படலாம் மற்றும் வேலை இயங்குவதற்கு முன்பு கிடைக்கிறது" -". குறிப்பு செயல்படுத்தலுடன் இந்த காசோலைகளை இயக்க, [சார்பு தீர்வுகள் உள்ளமைவு] " -"[சார்புநிலைகள்] ஐப் பயன்படுத்தவும்." +". குறிப்பு செயல்படுத்தலுடன் இந்த காசோலைகளை இயக்க, [சார்பு தீர்வுகள் உள்ளமைவு]" +"[dependencies] ஐப் பயன்படுத்தவும்." #: ../../src/topics/specifying-software-requirements.md:29 #: 8cb1c5d9b1a54c40924099494eb766c6 msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." msgstr "" -"ஒரு பதிப்பு எண், கருவிக்கான தனித்துவமான வள அடையாளங்காட்டி (URI) ஒரு [ஆர்ஆர்ஐடி][rrid]" -" வடிவத்தில் கொடுக்கப்பட்டுள்ளது. RRIDS உடனான வளங்களை [அறிநொறுக்கு][scicrunch] " -"பதிவேட்டில் பார்க்கலாம், இது விஞ்ஞான வளங்களைக் கண்டறிதல், கண்காணித்தல் மற்றும் " -"குறிப்பிடுவதற்கான ஒரு போர்ட்டலை வழங்குகிறது. நீங்கள் ஒரு கருவியை `சாப்ட்வேர் " -"ரெகுரிகேமென்ட்` எனக் குறிப்பிட விரும்பினால், ச்கைசஞ்ச் மீது கருவியைத் தேடுங்கள் மற்றும் " -"பதிவேட்டில் ஒதுக்கப்பட்டுள்ள RRID ஐப் பயன்படுத்தவும். . உங்கள் தேவை விளக்கத்தின் " -"`விவரக்குறிப்புகள்` புலத்தில் உள்ள கருவியைக் ([அடையாளங்காட்டிகள்.ஆர்ச்][அடையாளங்காட்டிகள்] " -"வழியாக) குறிப்பிட இந்த RRID ஐப் பயன்படுத்தலாம். பிற நல்ல தேர்வுகள், விருப்பத்தின் " -"வரிசையில், முக்கிய கருவி மேற்கோளுக்கான DOI மற்றும் கருவிக்கு முகவரி ஐ சேர்க்க வேண்டும்." +"ஒரு பதிப்பு எண், கருவிக்கான தனித்துவமான வள அடையாளங்காட்டி (URI) ஒரு [RRID][rrid] " +"வடிவத்தில் கொடுக்கப்பட்டுள்ளது. RRIDS உடனான வளங்களை [SciCrunch][scicrunch] பதிவேட்டில்" +" பார்க்கலாம், இது விஞ்ஞான வளங்களைக் கண்டறிதல், கண்காணித்தல் மற்றும் குறிப்பிடுவதற்கான ஒரு " +"போர்ட்டலை வழங்குகிறது. நீங்கள் ஒரு கருவியை `SoftwareRequirement` எனக் குறிப்பிட " +"விரும்பினால், ச்கைசஞ்ச் மீது கருவியைத் தேடுங்கள் மற்றும் பதிவேட்டில் ஒதுக்கப்பட்டுள்ள RRID ஐப் " +"பயன்படுத்தவும். உங்கள் தேவை விளக்கத்தின் `specs` புலத்தில் உள்ள கருவியைக் (" +"[அடையாளங்காட்டிகள்.ஆர்ச்][scicrunch-add-tool] வழியாக) குறிப்பிட இந்த RRID ஐப் " +"பயன்படுத்தலாம். பிற நல்ல தேர்வுகள், விருப்பத்தின் வரிசையில், முக்கிய கருவி மேற்கோளுக்கான " +"DOI மற்றும் கருவிக்கு முகவரி ஐ சேர்க்க வேண்டும்." #: ../../src/topics/staging-input-files.md:1 #: b85eb83e05e845d7a179f1b1d74db444 @@ -3528,7 +3532,7 @@ msgstr "" #: ../../src/topics/workflows.md:91 #: 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" -msgstr "`எக்கோ-பெர்பெச்-சிங்கிள்-ஃபைல்-சி.டபிள்யூ.எல்" +msgstr "`echo-uppercase-single-file.cwl`" #: ../../src/topics/workflows.md:150 #: 1cc17ad26e9c474b895ba5cd20c8b66a @@ -3573,7 +3577,14 @@ msgstr "1 வது-வொர்க்ஃப்ளோ.ச்விஎல் க #: ../../src/topics/workflows.md:180 #: a2dd833fdca4443181648e41051a5232 msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" -msgstr ". workflow/1st-workflow.cwl)]] 1 வது-வொர்க்ஃப்ளோ.ச்விஎல்)" +msgstr "" +"[![1st-workflow.cwl காட்சிப்படுத்தல்](https://view.commonwl.org/graph/png/" +"github.com/common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)](https://view.commonwl.org/graph/png/github.com/" +"common-workflow-language/user_guide/blob/" +"a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-" +"workflow.cwl)" #: ../../src/topics/workflows.md:183 #: 7e40cc9f9e1341c195e843c009575b94 @@ -3638,20 +3649,20 @@ msgstr "" #: 547edbf5fa424b8286cc21674ff159b0 msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." msgstr "" -"முதல் படி, `அன்டார்`` tar-param.cwl` ஐ இயக்குகிறது (முன்னர் [அளவுரு குறிப்புகள்] " -"(அளவுரு-குறிப்புகள். எம்.டி) இல் விவரிக்கப்பட்டுள்ளது). இந்த கருவி இரண்டு உள்ளீட்டு " -"அளவுருக்களைக் கொண்டுள்ளது, `டார்ஃபைல்` மற்றும்` எக்ச்ட்ராக்ட்ஃபைல்` மற்றும் ஒரு வெளியீட்டு " -"அளவுரு `பிரித்தெடுக்கப்பட்ட_பைல்`." +"முதல் படி, `untar` `tar-param.cwl` ஐ இயக்குகிறது (முன்னர் [அளவுரு குறிப்புகள்]" +"(parameter-references.md) இல் விவரிக்கப்பட்டுள்ளது). இந்த கருவி இரண்டு உள்ளீட்டு " +"அளவுருக்களைக் கொண்டுள்ளது, `tarfile` மற்றும்`extractfile` மற்றும் ஒரு வெளியீட்டு அளவுரு" +" `extracted_file`." #: ../../src/topics/workflows.md:261 #: 7ca248888b9d484cb544cd76ba538662 msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" -"பணிப்பாய்வு படியின் `` இன்` பிரிவு இந்த இரண்டு உள்ளீட்டு அளவுருக்களையும் பணிப்பாய்வு " -"உள்ளீடுகளுடன் இணைக்கிறது, `டார்பால்` மற்றும்` பெயர்_ஓஎஃப்_ஃபைல்_டோ_எக்டிகல்` `மூலத்தை` " -"பயன்படுத்துகிறது. இதன் பொருள், பணிப்பாய்வு படி செயல்படுத்தப்படும்போது, `டார்பால்` மற்றும்` " -"NAME_OF_FILE_TO_Extract` ஆகியவற்றுக்கு ஒதுக்கப்பட்ட மதிப்புகள் கருவியை இயக்க " -"`டார்ஃபைல்` மற்றும்` எக்ச்ட்ராக்ட்ஃபைல்` ஆகியவற்றிற்கு பயன்படுத்தப்படும்." +"பணிப்பாய்வு படியின் `` in`` பிரிவு இந்த இரண்டு உள்ளீட்டு அளவுருக்களையும் பணிப்பாய்வு " +"உள்ளீடுகளுடன் இணைக்கிறது, `tarball` மற்றும்`name_of_file_to_extract` `source` " +"பயன்படுத்துகிறது. இதன் பொருள், பணிப்பாய்வு படி செயல்படுத்தப்படும்போது, `tarball` " +"மற்றும்`name_of_file_to_extract` ஆகியவற்றுக்கு ஒதுக்கப்பட்ட மதிப்புகள் கருவியை இயக்க " +"`tarfile` மற்றும்`extractfile` ஆகியவற்றிற்கு பயன்படுத்தப்படும்." #: ../../src/topics/workflows.md:267 #: ae6b240718104380b08db5552d7355ea @@ -3664,12 +3675,12 @@ msgstr "" #: e5a8b7f84be64020b191099f3fad30ed msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." msgstr "" -"இரண்டாவது படி `தொகுத்தல் '` அன்டார்/பிரித்தெடுக்கப்பட்ட_பீல்` ஐப் பயன்படுத்தி உள்ளீட்டு " -"அளவுருவை `SRC` இன் வெளியீட்டு அளவுருவுடன் இணைப்பதன் மூலம் முதல் படியின் முடிவுகளைப் " -"பொறுத்தது. இது `வாதங்கள். CWL` ஐ இயக்குகிறது (முன்னர் [கூடுதல் வாதங்கள் மற்றும் " -"அளவுருக்கள்] (கூடுதல்-ஆவணம் மற்றும் அளவுருக்கள். எம்.டி) இல் விவரிக்கப்பட்டுள்ளது). இந்த படி" -" `கிளாச்ஃபைல்` இன் வெளியீடு மேலே விவரிக்கப்பட்ட பணிப்பாய்வுக்கான` வெளியீடுகள்` பிரிவுடன் " -"இணைக்கப்பட்டுள்ளது." +"இரண்டாவது படி `compile `(தொகுத்தல்) `untar/extracted_file` ஐப் பயன்படுத்தி உள்ளீட்டு " +"அளவுருவை `src` இன் வெளியீட்டு அளவுருவுடன் இணைப்பதன் மூலம் முதல் படியின் முடிவுகளைப் " +"பொறுத்தது. இது `arguments.cwl` ஐ இயக்குகிறது (முன்னர் " +"[கூடுதல் வாதங்கள் மற்றும் அளவுருக்கள்](additional-arguments-and-parameters.md) இல் " +"விவரிக்கப்பட்டுள்ளது). இந்த படி `classfile` இன் வெளியீடு மேலே விவரிக்கப்பட்ட " +"பணிப்பாய்வுக்கான `outputs` பிரிவுடன் இணைக்கப்பட்டுள்ளது." #: ../../src/topics/workflows.md:285 #: f0b04849253c4693904512ddd7f9ce84 @@ -3710,14 +3721,16 @@ msgstr "" #: e87045829b344089ab59dc27063ddd7a msgid "\"Visualization \"Visualization" msgstr "" -" " +"nestedworkflows.cwl\">\"nestedworkflows.cwl \"1st-workflow.cwl" #: ../../src/topics/workflows.md:322 #: 42ef2f145b824d69b63abc1da175c216 @@ -3870,8 +3883,9 @@ msgstr "`சிதறல்-job.yml`" #: b662c1a5a4424c8d8350a806356acc61 msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" msgstr "" -"ஒரு நினைவூட்டலாக, [`Hello_world.cwl`] (../ அறிமுகம்/விரைவு-தொடக்க. கட்டளை வரியில் " -"`cwltool சிதறல்-வொர்க்ஃப்ளோ." +"நினைவூட்டலாக, [`hello_world.cwl`](../introduction/quick-start.md) என்பது ஒரு " +"செய்தியில் `echo` என்ற கட்டளையை மட்டுமே அழைக்கிறது. கட்டளை வரியில் `cwltool scatter-" +"workflow.cwl scatter-job.yml` ஐ செயல்படுத்தினால்:" #: ../../src/topics/workflows.md:466 #: 04d6babfd87343d7a5f13867ea02b65f @@ -3940,10 +3954,10 @@ msgstr "" msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" msgstr "" "சரி, எனவே மற்ற மாதிரிகளிலிருந்து சுயாதீனமாக தொடரக்கூடிய படிகளில் நாம் எவ்வாறு " -"சிதறடிப்பது? [உள்ளமைக்கப்பட்ட பணிப்பாய்வுகளிலிருந்து] (#உள்ளமைக்கப்பட்ட-வேலை பாய்ச்சல்கள்) " -"நினைவில் கொள்ளுங்கள், ஒரு முழு பணிப்பாய்வுகளையும் மற்றொரு பணிப்பாய்வுகளில் ஒரு படி செய்ய " -"முடியும் என்பதை நினைவில் கொள்க! எங்கள் இரண்டு-படி பணிப்பாய்வுகளை ஒற்றை படி அடைப்பகுதிக்கு" -" மாற்றவும்:" +"சிதறடிப்பது? [உள்ளமைக்கப்பட்ட பணிப்பாய்வுகளிலிருந்து](#nested-workflows) நினைவில் " +"கொள்ளுங்கள், ஒரு முழு பணிப்பாய்வுகளையும் மற்றொரு பணிப்பாய்வுகளில் ஒரு படி செய்ய முடியும் " +"என்பதை நினைவில் கொள்க! எங்கள் இரண்டு-படி பணிப்பாய்வுகளை ஒற்றை படி அடைப்பகுதிக்கு " +"மாற்றவும்:" #: ../../src/topics/workflows.md:513 #: 1c9e386922324ec8a59306572c19fb8b @@ -4041,27 +4055,27 @@ msgstr "உள்ளடக்கங்கள்" #: ../../src/topics/yaml-guide.md:18 #: 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" -msgstr "[முக்கிய மதிப்பு சோடிகள்] (#விசை மதிப்பு-சோடிகள்)" +msgstr "[முக்கிய மதிப்பு சோடிகள்](#key-value-pairs)" #: ../../src/topics/yaml-guide.md:19 #: b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" -msgstr "[கருத்துரைகள்] (#கருத்துகள்)" +msgstr "[கருத்துரைகள்](#comments)" #: ../../src/topics/yaml-guide.md:20 #: b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" -msgstr "[வரைபடங்கள்] (#வரைபடங்கள்)" +msgstr "[வரைபடங்கள்](#maps)" #: ../../src/topics/yaml-guide.md:21 #: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" -msgstr "[வரிசைகள்] (#வரிசைகள்)" +msgstr "[வரிசைகள்](#arrays)" #: ../../src/topics/yaml-guide.md:22 #: 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" -msgstr "[JSON ச்டைல்] (#JSON- பாணி)" +msgstr "[JSON ச்டைல்](#json-style)" #: ../../src/topics/yaml-guide.md:24 #: 98056c5cfd5640ad9de0679360797cc7 @@ -4075,7 +4089,7 @@ msgstr "" "அடிப்படையில், YAML இல் எழுதப்பட்ட ஒரு கோப்பு _கே-மதிப்பு சோடிகளின்_ தொகுப்பைக் " "கொண்டுள்ளது. ஒவ்வொரு சோடியும் `விசை: மதிப்பு` என எழுதப்பட்டுள்ளன, அங்கு`: `க்குப் பிறகு " "இடைவெளி தேவைப்படுகிறது. சி.டபிள்யூ.எல் கோப்புகளில் உள்ள முக்கிய பெயர்கள் வைட்ச்பேசைக் " -"கொண்டிருக்கக்கூடாது - [_CAMELCASE _] [ஒட்டக கேச்] CWL விவரக்குறிப்பில் சிறப்பு அர்த்தமுள்" +"கொண்டிருக்கக்கூடாது - [[_camelCase_][camelCase] CWL விவரக்குறிப்பில் சிறப்பு அர்த்தமுள்" "ள பல சொல் முக்கிய பெயர்களுக்கு பயன்படுத்தப்படுகிறது மற்றும் இல்லையெனில் அடிக்கோடிட்டுக் " "காட்டப்பட்ட முக்கிய பெயர்கள். உதாரணமாக:" @@ -4144,12 +4158,12 @@ msgstr "" msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." msgstr "" "மேலே உள்ள YAML சிக்கலான உள்ளமைக்கப்பட்ட பொருள் விளக்கங்களை ஒப்பீட்டளவில் விரைவாக " -"உருவாக்குவது எப்படி என்பதை விளக்குகிறது. `உள்ளீடுகள்` வரைபடத்தில்` எடுத்துக்காட்டு_ஃப்ளாக்`" -" ஒரு ஒற்றை விசையைக் கொண்டுள்ளது, இதில் இரண்டு விசைகள் உள்ளன, `வகை` மற்றும்` உள்ளீட்டு " -"பைண்டிங்`, இந்தக் குழந்தைகளில் ஒருவரான `உள்ளீடு பைண்டிங்` மேலும் இரண்டு முக்கிய மதிப்பு " -"சோடிகளைக் கொண்டுள்ளது (` நிலை` மற்றும் `முன்னொட்டு`). ஒற்றை விசைக்குப் பல " -"மதிப்புகள்/முக்கிய மதிப்பு சோடிகளை வழங்குவது பற்றிய கூடுதல் தகவலுக்குக் கீழே உள்ள " -"[வரிசைகள்](#வரிசைகள்) பகுதியைக் காண்க. மேலே உள்ள யாம்லுடன் ஒப்பிடுகையில், அது " +"உருவாக்குவது எப்படி என்பதை விளக்குகிறது. `inputs` வரைபடத்தில்`example_flag` ஒரு " +"ஒற்றை விசையைக் கொண்டுள்ளது, இதில் இரண்டு விசைகள் உள்ளன, `type`(வகை) " +"மற்றும்`inputBinding`(உள்ளீட்டு பைண்டிங்), இந்தக் குழந்தைகளில் ஒருவரான `உள்ளீடு பைண்டிங்` " +"மேலும் இரண்டு முக்கிய மதிப்பு சோடிகளைக் கொண்டுள்ளது (` நிலை` மற்றும் `முன்னொட்டு`). ஒற்றை" +" விசைக்குப் பல மதிப்புகள்/முக்கிய மதிப்பு சோடிகளை வழங்குவது பற்றிய கூடுதல் தகவலுக்குக் " +"கீழே உள்ள [வரிசைகள்](#arrays) பகுதியைக் காண்க. மேலே உள்ள யாம்லுடன் ஒப்பிடுகையில், அது " "விவரிக்கும் `உள்ளீடுகள்` பொருளின் வரைகலை பிரதிநிதித்துவம் இங்கே." #: ../../src/topics/yaml-guide.md:127 @@ -4162,9 +4176,9 @@ msgstr "வரிசைகள்" msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" msgstr "" "சில சூழ்நிலைகளில், ஒரு விசைக்கு பல மதிப்புகள் அல்லது பொருள்களை வழங்குவது தேவை. மேலே " -"உள்ள [வரைபடங்கள்] (#வரைபடங்கள்) பிரிவில் நாம் ஏற்கனவே பார்த்தது போல, ஒன்றுக்கு மேற்பட்ட " -"முக்கிய மதிப்பு சோடியை ஒரு விசையில் வரைபடமாக்கலாம். இருப்பினும், ஒவ்வொரு மதிப்புக்கும் " -"ஒரு தனித்துவமான விசையை வழங்காமல் ஒரு விசையின் பல மதிப்புகளை வரையறுக்கவும் முடியும். " +"உள்ள [வரைபடங்கள்](#maps) பிரிவில் நாம் ஏற்கனவே பார்த்தது போல, ஒன்றுக்கு மேற்பட்ட முக்கிய " +"மதிப்பு சோடியை ஒரு விசையில் வரைபடமாக்கலாம். இருப்பினும், ஒவ்வொரு மதிப்புக்கும் ஒரு " +"தனித்துவமான விசையை வழங்காமல் ஒரு விசையின் பல மதிப்புகளை வரையறுக்கவும் முடியும். " "_Array_ உடன் இதை நாம் அடையலாம், அங்கு ஒவ்வொரு மதிப்பும் அதன் சொந்த வரியில் " "வரையறுக்கப்பட்டு `-` ஆல் வரையறுக்கப்படுகிறது. உதாரணமாக:" @@ -4182,7 +4196,7 @@ msgstr "சாதொபொகு நடை" #: 87bafb845c714b109874f6137b84462d msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" msgstr "" -"YAML [சாவாச்கிரிப்ட் பொருள் குறியீடு (JSON)] [JSON] ஐ அடிப்படையாகக் கொண்டது. சொந்த " +"YAML [சாவாச்கிரிப்ட் பொருள் குறியீடு (JSON)] [json] ஐ அடிப்படையாகக் கொண்டது. சொந்த " "சாதொபொகு தொடரியல் பயன்படுத்தி YAML இல் வரைபடங்கள் மற்றும் வரிசைகளை வரையறுக்கலாம். " "உதாரணமாக:" @@ -4211,7 +4225,7 @@ msgstr "குறிப்பு" #: 859368c1f25c4a4aad57abfd046c63f5 msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." msgstr "" -"இந்த வழிகாட்டியை நாங்கள் எழுதியபோது [Y MINES] [YAML-Y- Mins] குறிப்பு எங்களுக்கு " +"இந்த வழிகாட்டியை நாங்கள் எழுதியபோது [Y MINES][yaml-y-mins] குறிப்பு எங்களுக்கு " "மிகவும் உதவியாக இருந்தது, இருப்பினும் இது CWL இல் செல்லுபடியாகாத அம்சங்களையும் " "உள்ளடக்கியது." From 58475d188a3a2a5aa16c380f6c64989708771b5e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 5 Sep 2025 00:05:02 +0200 Subject: [PATCH 178/179] Bump actions/setup-python from 5 to 6 (#499) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v5...v6) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/ci-tests.yml | 2 +- .github/workflows/gh-pages.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml index 5c992d18..261e3200 100644 --- a/.github/workflows/ci-tests.yml +++ b/.github/workflows/ci-tests.yml @@ -31,7 +31,7 @@ jobs: - uses: actions/checkout@v5 - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: ${{ env.py-semver }} cache: pip diff --git a/.github/workflows/gh-pages.yaml b/.github/workflows/gh-pages.yaml index cb5c4da1..b74cae91 100644 --- a/.github/workflows/gh-pages.yaml +++ b/.github/workflows/gh-pages.yaml @@ -22,7 +22,7 @@ jobs: sudo apt-get install -y graphviz tree - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: '3.9' cache: pip From 6d2bd4ed2225cd52e0e3b7da8f22dee1c6ca091b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 8 Oct 2025 10:51:04 +0200 Subject: [PATCH 179/179] Bump github/codeql-action from 3 to 4 (#500) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3 to 4. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/v3...v4) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: '4' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/codeql.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index a3602998..ad4c5454 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -27,16 +27,16 @@ jobs: uses: actions/checkout@v5 - name: Initialize CodeQL - uses: github/codeql-action/init@v3 + uses: github/codeql-action/init@v4 with: languages: ${{ matrix.language }} queries: +security-and-quality - name: Autobuild - uses: github/codeql-action/autobuild@v3 + uses: github/codeql-action/autobuild@v4 if: ${{ matrix.language == 'javascript' || matrix.language == 'python' }} - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v3 + uses: github/codeql-action/analyze@v4 with: category: "/language:${{ matrix.language }}"